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Is the number of legs in myriapoda determined entirely by the genome?

Is the number of legs in myriapoda determined entirely by the genome?


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Myriapoda (comprising, among others, millipedes and centipedes) can have hundreds of legs (Illacme plenipes having up to 750 legs). Interestingly, the number of legs (or leg pairs) appears to differ not only between myriapod species, but even between individuals of the same species:

Body light cream-colored, thread-like, extremely narrow and long (max. width: ♂ 0.55, ♀ 0.64; max. length: ♂ 28.16, ♀ 40.40). Adult individuals with 84 - 192 segments, and with 318 - 750 legs (VMNH paratype ♀ with 192 segments and 750 legs, more than any other organism known on Earth).

Source: "A redescription of the leggiest animal, the millipede Illacme plenipes, with notes on its natural history and biogeography"

This raises the question: Is the number of legs in myriapoda determined entirely by the genome, or do environmental factors play a role in precisely how many legs eventually develop?

Note: Myriapoda generelly hatch with very few legs, and more legs develop during successive moults. Some examples can be found here.


Three factors that influence the number of legs are:

1) Sex : In some species of myriapoda, the females have been found to have more leg segments than males (reference) eg: Himantarium gabrielis

2) age

Growth is by adding segments and legs with successive molts (anamorphic), and myriapods continue to add additional segments and legs after they have reached sexual maturity (reference).

3) Working of a "segmentation clock" (set of genes) that periodically adds segments (reference).


The dog days of autumn

In the world which we know, among the different and primitive geniuses that preside over the evolution of the several species, there exists not one, excepting that of the dog, that ever gave a thought to the presence of man. Maurice Maeterlinck

Greg Petsko is tied up with teaching, so, by popular demand - actually, he wonders why there never seems to be a demand for more from him- his column will be guest-written this month by his two dogs, the mixed poodle/spaniel Clifford and the chocolate Labrador retriever Mink (Figure 1). They are not strangers to these pages, having written before, to much acclaim. Precisely how they manage to type their text is unclear.

Mink (right) and Clifford proudly display their different coats and wish to remind the Editor that, although they don't work for peanuts, they do work for lamb chops.

Mink: Did you see the paper in the issue of Science for 2 October 2009 (326:150-153) by Cadieu and coworkers? It's entitled Coat variation in the domestic dog is governed by variants in three genes.

Clifford: What's a domestic dog?

Mink: I'm not sure. I think maybe it's the opposite of a foreign dog.

Clifford: Are you a foreign dog? After all, you're from Labrador.

Mink: No, I'm from New England. My ancestors were from Labrador. And yours were from France and England.

Clifford: Does that mean I'm not a domestic dog? I don't want to be a foreign dog! I don't speak French!

Mink: Calm down. We're both domestic dogs, I'm sure. But we're getting off the subject here. Did you see that paper?

Clifford: No, I didn't. Was it written in French?

Mink: Will you forget about French! It was written in scientific English, which means it's not easy for a little puppy to understand, but I'll explain it to you. It's about the genes that control different coats in dogs.

Clifford: You mean like how your coat is dark brown and mine is like wheat?

Mink: No, the genes that govern coat color have been known for quite a while. This paper is about the genes that control coat length, growth pattern, and curl. For example, I have a fur coat that's all one color, and it only grows to a certain length and then it stops. I shed in winter -

Clifford: I'll say you do! I've never seen so much brown fur flying around! Why, the carpet in the family room is covered with little mounds of -

Mink: Yes, yes, I know. I can't help it. But as I was saying, I have solid brown, straight fur while you have patchy off-white and beige curly hair. Your coat would just keep growing forever and curl into huge mats if you didn't get taken to the groomer for -

Clifford: I hate the groomer! Hate them!

Mink: Can we stay focused here? I know you hate the groomer. You make that perfectly plain every time Greg tries to take you there. I haven't seen such a performance of suffering since we watched that television broadcast of King Lear with Greg last spring.

Clifford (sotto voce): Hate them!

Mink: OK, we've established that. But the point I'm trying to make is: look how different our coats are.

Clifford: Mine's better. Except for having to go to the groomer. I hate -

Mink (quickly): I'm glad you like your coat. I think mine is perfectly fine, too. And I don't have to go to the groomer. So there.

Clifford (sullenly): What was your point about the paper?

Mink: Oh, yes. The paper. Well, our coats are so completely different, you would think that there would be many genes that were involved in determining those different properties. But the authors of this paper found that's simply not the case. They carried out what are called genome-wide association studies (which is basically just looking for variations in gene sequence that correlate with changes in some property) of more than 1,000 dogs from 80 domestic breeds to identify genes associated with canine fur phenotypes. They were able to take advantage of both inter- and intrabreed variability.

Clifford: What does that mean?

Mink: I think it means that, although dogs' coats vary a lot from breed to breed, like with you and me, they also vary a bit within breeds. Not all poodles have the same kinds of coat, as any groomer can tell you.

Clifford: I hate the groomer!

Mink: Right. Nothing more about groomers, I promise. Anyway, it's an advantage when you have small variations within a breed, because you can use that to find the small number of genes that most likely account for those variations (they stand out against a background that doesn't vary so much since all the dogs are from the same breed), and then you can pay particular attention to those genes when you look for what controls the much larger variations between breeds. That makes genome-wide association studies in dogs much easier and more rewarding than genome-wide association studies in people, where it's harder to find candidate genes, so you have to look at thousands of individuals and it's very expensive.

Clifford (proudly): Dogs are better than people.

Mink: Of course we are. But as I was saying, Greg has talked about this before. He is convinced that, for association studies in people, it would be smart to use the relatively common mutations that give rise to autosomal recessive diseases and examine the carriers for association with other diseases. For example, people with Gaucher Disease are much more likely to get multiple myeloma, so an obvious thing to do would be to see if Gaucher carriers are overrepresented among myeloma patients. Greg thinks that's what the human genome people ought to be doing if they want to make rapid progress on diseases, because the carrier mutations are known to affect the functions of those proteins, so they're much more likely to do something than the common variants that the gene association studies mostly look at. Greg says those people are barking up the wrong tree.

Clifford: Barking up the wrong tree? Why would anybody bark up the wrong tree?

Clifford: Can we get back to talking about dogs?

Mink: Sorry. As I was saying, with dogs you can get a good idea what genes to look at as well, from variations within a breed. That's how the people in this paper started their project. The team of scientists, which was headed by Elaine Ostrander of the National Institutes of Health -

Clifford: I've heard of her! She's a genome biologist. We like her. She works on genes responsible for cancer susceptibility in people and dogs. Cancer is the number one killer of dogs. We hate cancer! We hate it almost as much as we hate the gr -

Mink (even more quickly): Yes, she is a great benefactor of the canine race. You may remember that, about two years ago, she headed the team that studied height variation in dogs (Science, 316:112-115, 2007). Dogs have the greatest variation in height of any mammalian species. She discovered that the default for dogs is to be tall, like me, but that a mutation in a single gene, insulin-like growth factor 1, could account for the fact that many dogs are quite small, like Chihuahuas, fox terriers, and, well, like you.

Clifford: I'm not small! I just have short legs for my body height.

Mink: Whatever. The point is, it was a big surprise that one gene could account for such big differences.

Clifford: How did they find that gene? I forget.

Mink: Exactly the same way they found the genes in this study. They first looked at variation in height within a breed where it varies a lot: Portuguese water dogs. That allowed them to home in on the likely gene. Then they checked it across breeds.

Clifford: President Barack Obama has a Portuguese water dog named Bo, doesn't he? I wonder why he didn't pick a poodle/spaniel mix.

Mink: Or a chocolate Lab. Well, nobody's perfect. Anyway, that discovery sort of made sense because insulin-like growth factor is one of the genes that controls cell growth and lifespan.

Clifford (musing): I'd like to meet Bo. Do you think President Obama would let him play with us?

Mink: Can we stay on the topic here? This column'll be over soon.

Clifford: OK. Did they use Portuguese water dogs in this new study about coat variation too?

Mink: As a matter of fact, they did. One of their same-breed groups comprised 76 Portuguese water dogs, because it's a breed that varies a lot in hair curl. They looked at three phenotypes, actually: hair curl, hair length, and the presence or absence of what they call 'furnishings' - you know, that little moustache and bushy eyebrows you have.

Clifford (proudly): I am well furnished.

Mink: Of course you are. Well, after they looked at a few same-breed groups, they then examined genetic variation across 903 dogs from 80 different breeds. They found that distinct mutations in just three genes, RSPO2, FGF5, and KRT71, together account for most coat phenotypes in pure-bred dogs in the United States.

Clifford: You mean my coat is controlled by just three genes?

Mink: Maybe not. They only looked at purebreds, and you're a mixture of two breeds.

Clifford: Are you insulting my mother? I'm just as pure as -

Mink: No, not at all. It's just that, er, uh, more sophisticated dogs like you are too complex for simple genetic analysis.

Clifford: That's me, all right. I'm complicated.

Mink: You can say that again. Anyway, RSPO2 largely controls furnishing, which is interesting, because the gene codes for a protein called R-spondin-2, which is a signaling regulator that synergizes with the Wnt pathway to activate β-catenin, and Wnt signaling is required for the establishment of hair follicles in mammals. The mutation doesn't seem to change the protein sequence it probably affects the mRNA level. You know, this same pathway is involved in the development of hair-follicle tumors, or pilomatricomas, which occur most frequently in breeds that have furnishings. Recent studies have shown that a mutation in the EDAR gene, also involved in the Wnt pathway, is responsible for a coarse East-Asian hair type found in humans, and as you know, that hair type has some similarity to canine wirehair.

Clifford: Do you think this pathway controls Greg's hair?

Mink: He's a middle-aged man. What hair?

Clifford: How about the other two phenotypes?

Mink: Curl seems to be determined by the KRT71 gene, which codes for one of the forms of keratin, the major protein component of hair.

Clifford: That makes sense. Does the mutation change the protein sequence?

Mink: Yes, it does. It replaces one amino acid, an arginine, with a tryptophan. But why that leads to curly hair is not obvious. The third gene, FGF5, is involved in hair length.

Clifford: What does that protein do?

Mink: It makes one of the fibroblast growth factors. Makes sense, right?

Clifford: It does. Amazing. And if a dog has all three genes mutated.

Clifford: Like our friend Max in the park. Cool. But why is this important - besides the fact that it refers to dogs, of course?

Mink: Isn't that enough? Well, I guess one other reason is that it explains how so many different sizes, shapes and appearances of dog could have arisen in only about 15,000 years of accidental and deliberate breeding. If combinations of only a few genes can have a big effect on morphology and so forth, it won't take that many generations to produce a large number of possibilities. In fact, it's thought that most of the breeds we see today originated since about 1800, so it really can happen fast. Dog evolution is much faster than evolution of other mammals in the wild.

Clifford: That's because we're a superior species.

Mink: Obviously. After all, who lies around all day and gets fed, while the other species works to support us?

Clifford: Isn't evolution wonderful?

Mink: It is, but in our case, I prefer the term intelligent design.


Background

Quantitative traits affecting morphology, physiology, behavior, disease susceptibility and reproductive fitness are controlled by multiple interacting genes whose effects are conditional on the genetic, sexual and external environments [1]. Advances in medicine, agriculture, and an understanding of adaptive evolution depend on discovering the genes that regulate these complex traits, and determining the genetic and molecular properties of alleles at loci that cause segregating genetic variation in natural populations. Assessing subtle effects of induced mutations on quantitative trait phenotypes in model organisms is a straightforward approach to identify genes regulating complex traits [1–3]. However, the large number of potential mutations to evaluate, the necessity to induce mutations in a common inbred background, and the level of replication required to detect subtle effects [1] all limit the feasibility of systematic whole-genome mutagenesis screens for complex traits in higher eukaryotes. Mapping quantitative trait loci (QTLs) affecting variation in complex traits to broad genomic regions by linkage to polymorphic molecular markers is also straightforward. However, our ability to determine what genes in the QTL regions cause the trait variation is hampered by the large number of recombinants required for high-resolution mapping, and the small and environmentally sensitive effects of QTL alleles [1, 4].

There has been great excitement recently about the utility of whole-genome transcriptional profiling to identify candidate genes regulating complex traits, by assessing changes in gene expression in the background of single mutations affecting the trait [5, 6], between lines selected for different phenotypic values of the trait [7], and in response to environmental stress and aging [8–12]. Transcript abundance is also a quantitative trait for which there is considerable variation between wild-type strains [11, 13–17], and for which expression QTLs (eQTLs) [18] have been mapped [15–17, 19]. Thus, candidate genes affecting variation in quantitative trait phenotypes are those for which the map positions of trait QTL and eQTL coincide [16, 20].

Transcript profiling typically implicates hundreds to thousands of genes in the regulation of quantitative traits and associated with trait variation between strains the majority of these genes are computationally predicted genes that have not been experimentally verified. To what extent do changes in transcript abundance predicate effects of induced mutations and allelic variants between strains on quantitative trait phenotypes? It is encouraging that several studies have confirmed the phenotypic effects of mutations in genes implicated by changes in expression [5–7]. However, limited numbers of genes were tested, and their choice was not unbiased. None of the candidate QTLs nominated by transcriptional profiling has been validated according to the rigorous standards necessary to prove that any candidate gene corresponds to a QTL [1, 4]. To begin to answer this question, we need to compare gene-expression data with genes known to affect the trait from independent mutagenesis and QTL mapping studies. This comparison has not been possible to date because there are only a few complex traits for which the genetic architecture is known at this level of detail, one of which is resistance to starvation stress in Drosophila.

Previously, we used P-element mutagenesis in an isogenic background to identify 383 candidate genes affecting starvation tolerance in D. melanogaster [21]. Further, we mapped QTLs affecting variation in starvation resistance between two isogenic Drosophila strains, Oregon-R (Ore) and 2b [21], followed by complementation tests to mutations to identify twelve candidate genes affecting variation in starvation resistance between these strains [21]. Here, we used Affymetrix Drosophila GeneChips to examine expression profiles of two starvation-resistant and two starvation-sensitive recombinant inbred (RI) lines, as well as parental lines Ore and 2b, under normal and starvation stress conditions. We used a statistically rigorous analysis to identify genes whose expression was altered between the sexes, during starvation stress treatment, between lines, and interactions between these main effects. In the comparison of expression profiling with the P-element mutagenesis performed previously, we found nearly 50% concordance between the effects of 160 P-element mutations on starvation stress resistance and changes in gene expression during starvation - 77 mutations with significant effects also had significant changes in transcript abundance, while 83 mutations did not affect the starvation resistance phenotype, yet had significant changes in transcript level. We identified 153 novel candidate genes for which there was variation in gene expression between the lines and which co-localized with starvation resistance QTLs. However, we did not detect genetic variation in expression for any of the candidate genes identified by complementation tests. Our efforts to associate genetic variation in expression with variation in quantitative trait phenotypes is confounded by the observation of widespread regulation of transcript abundance by unlinked genes, the difficulty in detecting rare transcripts that may be expressed in only a few cell types at a particular period of development, and genetic variation between QTL alleles that is not regulated at the level of transcription.


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† Both authors contributed equally to this work.

Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.4893804.

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

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Results

Neither Minuscule nor Massive, a Remarkably Complete Mite Genome

Being so tiny, approximately 12,000 females were required to produce sufficient high-quality DNA for construction of a shotgun and two mate-pair sequencing libraries (see Materials and Methods). Maximizing genome homozygosity within this population was therefore critical, and was achieved by subjecting the already inbred carbaryl-organophosphate-sulfur resistant laboratory strain to ten additional generations of sibling matings. These efforts enabled an extremely contiguous assembly of 2,211 scaffolds spanning 152 Mb, with a contig N50 of 200.7 kb and a scaffold N50 of almost 900 kb ( table 1 ). Compared with other sequenced arachnids, this genome is nearly twice as large as the compact T. urticae genome, but much smaller than most others: About half the size of the V. destructor assembly (whose genome is estimated to be even larger at 565 Mb Cornman et al. 2010 ) and less than a tenth of the I. scapularis genome ( table 1 ). The dust and scabies mite genomes are estimated to be small like that of T. urticae , but their draft assemblies appear to capture only about half of their total estimated nucleotide content ( Chan et al. 2015 Rider et al. 2015 ). Assessing assembly completeness in terms of expected gene content with 248 Conserved Eukaryotic Genes (CEGs Parra et al. 2007 ) and 2,675 arthropod BUSCOs ( Waterhouse et al. 2013 Simão et al. 2015 ) revealed a remarkably complete M. occidentalis genome assembly, the most complete of any arachnid to date ( table 1 ).

Metaseiulus occidentalis Genome Assembly and Gene Set Statistics Compared with Eight Other Arachnids

. Acari: Parasitiformes . Acari: Acariformes . Araneae . Scorpiones .
SpeciesMetaseiulus occidentalisVarroa destructorIxodes scapularisDermatophagoides farinaeSarcoptes scabieiTetranychus urticaeStegodyphus mimosarumAcanthoscurria geniculataMesobuthus martensii
OrganismWestern orchard predatory miteHoney bee parasitic miteBlack-legged deer tickAmerican house dust miteItch mite (scabies)Two-spotted spider miteAfrican social velvet spiderBrazilian white-knee tarantulaChinese scorpion
AssemblyGCA_000255335.1 GCA_000181155.1 GCA_000208615.1 GCA_000767015.1 GCA_000828355.1 GCA_000239435.1 GCA_000611955.2 GCA_000661875.1 GCA_000484575.1
Assembly methodCelera v.6.1 Celera v.5.2 Celera v.4.0 AllPaths v.39075 Minia v.1.6088 Arachne 20071016 SOAPdenovo v.2 SOAPdenovo v.2 Velvet v.1.1.04
Velvet v.1.1.03 SSPACE
SOAPdenovo v.1.05 Standard v.3.0
Coverage ( × )17.7 5 6 436 174 8 a 70 70 200
Assembly length (Mb)151.7 294.1 1,765.4 53.5 56.3 90.8 2,738.7 7,178.4 925.5
1,128.5 b
No. of Contigs3,993 184,190 570,637 11,600 19,811 2,035 174,164 12,478,692 92,408
18,600 c
Contig N50 (bp)200,706 2,262 2,942 8,538 11,197 212,780 40,146 541 45,228
11.6 kb c 17,272 d 277 d 43,135 b
No. of scaffolds2,211 na 369,492 515 na 640 68,653 na na
Scaffold N50 (bp)896,831 na 76,228 186,342 na 2,993,488 480,636 47,837 d 223,560 b
No. of protein-coding genes 18,338 e 11,432 g 20,486 h 16,376 i 10,473 18,414 a 27,135 73,821 k 32,016 b
11,430 f 10,644 c 18,224 j 27,235 d
% CEGs l 98.0/96.8 67.7/32.3 79.8/41.9 97.6/96.4 98.0/93.5 98.0/95.2 61.7/24.2 32.7/14.9 57.3/24.2
% BUSCOs m (assembly)82.3 [6.4], 8.3, 9.9 15.2 [0.5], 15.4, 69.5 68.9 [2.4], 21.0, 10.1 63.8 [3.5], 7.6, 28.6 62.0 [3.0], 8.4, 29.6 68.8 [5.8], 9.9, 21.3 53.7 [4.0], 27.4, 18.9 13.7 [1.9], 10.6, 75.7 34.4 [4.0], 23.0, 42.7
% BUSCOs m (gene set)82.8 [12.0], 10.6, 6.5 na 69.4 [6.7], 23.4, 7.2 na 54.0 [4.7], 11.4, 34.6 69.3 [11.4], 9.6, 21.0 64.6 [10.5], 17.3, 18.1 na 23.1 [6.7], 16.4, 60.5
. Acari: Parasitiformes . Acari: Acariformes . Araneae . Scorpiones .
SpeciesMetaseiulus occidentalisVarroa destructorIxodes scapularisDermatophagoides farinaeSarcoptes scabieiTetranychus urticaeStegodyphus mimosarumAcanthoscurria geniculataMesobuthus martensii
OrganismWestern orchard predatory miteHoney bee parasitic miteBlack-legged deer tickAmerican house dust miteItch mite (scabies)Two-spotted spider miteAfrican social velvet spiderBrazilian white-knee tarantulaChinese scorpion
AssemblyGCA_000255335.1 GCA_000181155.1 GCA_000208615.1 GCA_000767015.1 GCA_000828355.1 GCA_000239435.1 GCA_000611955.2 GCA_000661875.1 GCA_000484575.1
Assembly methodCelera v.6.1 Celera v.5.2 Celera v.4.0 AllPaths v.39075 Minia v.1.6088 Arachne 20071016 SOAPdenovo v.2 SOAPdenovo v.2 Velvet v.1.1.04
Velvet v.1.1.03 SSPACE
SOAPdenovo v.1.05 Standard v.3.0
Coverage ( × )17.7 5 6 436 174 8 a 70 70 200
Assembly length (Mb)151.7 294.1 1,765.4 53.5 56.3 90.8 2,738.7 7,178.4 925.5
1,128.5 b
No. of Contigs3,993 184,190 570,637 11,600 19,811 2,035 174,164 12,478,692 92,408
18,600 c
Contig N50 (bp)200,706 2,262 2,942 8,538 11,197 212,780 40,146 541 45,228
11.6 kb c 17,272 d 277 d 43,135 b
No. of scaffolds2,211 na 369,492 515 na 640 68,653 na na
Scaffold N50 (bp)896,831 na 76,228 186,342 na 2,993,488 480,636 47,837 d 223,560 b
No. of protein-coding genes 18,338 e 11,432 g 20,486 h 16,376 i 10,473 18,414 a 27,135 73,821 k 32,016 b
11,430 f 10,644 c 18,224 j 27,235 d
% CEGs l 98.0/96.8 67.7/32.3 79.8/41.9 97.6/96.4 98.0/93.5 98.0/95.2 61.7/24.2 32.7/14.9 57.3/24.2
% BUSCOs m (assembly)82.3 [6.4], 8.3, 9.9 15.2 [0.5], 15.4, 69.5 68.9 [2.4], 21.0, 10.1 63.8 [3.5], 7.6, 28.6 62.0 [3.0], 8.4, 29.6 68.8 [5.8], 9.9, 21.3 53.7 [4.0], 27.4, 18.9 13.7 [1.9], 10.6, 75.7 34.4 [4.0], 23.0, 42.7
% BUSCOs m (gene set)82.8 [12.0], 10.6, 6.5 na 69.4 [6.7], 23.4, 7.2 na 54.0 [4.7], 11.4, 34.6 69.3 [11.4], 9.6, 21.0 64.6 [10.5], 17.3, 18.1 na 23.1 [6.7], 16.4, 60.5

Note.—Unless otherwise indicated, values were retrieved from the NCBI.

Identified open-reading frames with significant sequence similarity to database sequences from Cornman et al. (2010 ).

IscaW1.4 gene set from VectorBase ( www.vectorbase.org ).

From Sanggaard et al. (2014 ), transcripts of more than 17 amino acids.

% of 248 CEGMA genes Found/Complete, in the assembly.

% of 2,675 arthropod BUSCOs Complete [Duplicated], Fragmented, Missing, in the assembly or in the gene set.

Metaseiulus occidentalis Genome Assembly and Gene Set Statistics Compared with Eight Other Arachnids

. Acari: Parasitiformes . Acari: Acariformes . Araneae . Scorpiones .
SpeciesMetaseiulus occidentalisVarroa destructorIxodes scapularisDermatophagoides farinaeSarcoptes scabieiTetranychus urticaeStegodyphus mimosarumAcanthoscurria geniculataMesobuthus martensii
OrganismWestern orchard predatory miteHoney bee parasitic miteBlack-legged deer tickAmerican house dust miteItch mite (scabies)Two-spotted spider miteAfrican social velvet spiderBrazilian white-knee tarantulaChinese scorpion
AssemblyGCA_000255335.1 GCA_000181155.1 GCA_000208615.1 GCA_000767015.1 GCA_000828355.1 GCA_000239435.1 GCA_000611955.2 GCA_000661875.1 GCA_000484575.1
Assembly methodCelera v.6.1 Celera v.5.2 Celera v.4.0 AllPaths v.39075 Minia v.1.6088 Arachne 20071016 SOAPdenovo v.2 SOAPdenovo v.2 Velvet v.1.1.04
Velvet v.1.1.03 SSPACE
SOAPdenovo v.1.05 Standard v.3.0
Coverage ( × )17.7 5 6 436 174 8 a 70 70 200
Assembly length (Mb)151.7 294.1 1,765.4 53.5 56.3 90.8 2,738.7 7,178.4 925.5
1,128.5 b
No. of Contigs3,993 184,190 570,637 11,600 19,811 2,035 174,164 12,478,692 92,408
18,600 c
Contig N50 (bp)200,706 2,262 2,942 8,538 11,197 212,780 40,146 541 45,228
11.6 kb c 17,272 d 277 d 43,135 b
No. of scaffolds2,211 na 369,492 515 na 640 68,653 na na
Scaffold N50 (bp)896,831 na 76,228 186,342 na 2,993,488 480,636 47,837 d 223,560 b
No. of protein-coding genes 18,338 e 11,432 g 20,486 h 16,376 i 10,473 18,414 a 27,135 73,821 k 32,016 b
11,430 f 10,644 c 18,224 j 27,235 d
% CEGs l 98.0/96.8 67.7/32.3 79.8/41.9 97.6/96.4 98.0/93.5 98.0/95.2 61.7/24.2 32.7/14.9 57.3/24.2
% BUSCOs m (assembly)82.3 [6.4], 8.3, 9.9 15.2 [0.5], 15.4, 69.5 68.9 [2.4], 21.0, 10.1 63.8 [3.5], 7.6, 28.6 62.0 [3.0], 8.4, 29.6 68.8 [5.8], 9.9, 21.3 53.7 [4.0], 27.4, 18.9 13.7 [1.9], 10.6, 75.7 34.4 [4.0], 23.0, 42.7
% BUSCOs m (gene set)82.8 [12.0], 10.6, 6.5 na 69.4 [6.7], 23.4, 7.2 na 54.0 [4.7], 11.4, 34.6 69.3 [11.4], 9.6, 21.0 64.6 [10.5], 17.3, 18.1 na 23.1 [6.7], 16.4, 60.5
. Acari: Parasitiformes . Acari: Acariformes . Araneae . Scorpiones .
SpeciesMetaseiulus occidentalisVarroa destructorIxodes scapularisDermatophagoides farinaeSarcoptes scabieiTetranychus urticaeStegodyphus mimosarumAcanthoscurria geniculataMesobuthus martensii
OrganismWestern orchard predatory miteHoney bee parasitic miteBlack-legged deer tickAmerican house dust miteItch mite (scabies)Two-spotted spider miteAfrican social velvet spiderBrazilian white-knee tarantulaChinese scorpion
AssemblyGCA_000255335.1 GCA_000181155.1 GCA_000208615.1 GCA_000767015.1 GCA_000828355.1 GCA_000239435.1 GCA_000611955.2 GCA_000661875.1 GCA_000484575.1
Assembly methodCelera v.6.1 Celera v.5.2 Celera v.4.0 AllPaths v.39075 Minia v.1.6088 Arachne 20071016 SOAPdenovo v.2 SOAPdenovo v.2 Velvet v.1.1.04
Velvet v.1.1.03 SSPACE
SOAPdenovo v.1.05 Standard v.3.0
Coverage ( × )17.7 5 6 436 174 8 a 70 70 200
Assembly length (Mb)151.7 294.1 1,765.4 53.5 56.3 90.8 2,738.7 7,178.4 925.5
1,128.5 b
No. of Contigs3,993 184,190 570,637 11,600 19,811 2,035 174,164 12,478,692 92,408
18,600 c
Contig N50 (bp)200,706 2,262 2,942 8,538 11,197 212,780 40,146 541 45,228
11.6 kb c 17,272 d 277 d 43,135 b
No. of scaffolds2,211 na 369,492 515 na 640 68,653 na na
Scaffold N50 (bp)896,831 na 76,228 186,342 na 2,993,488 480,636 47,837 d 223,560 b
No. of protein-coding genes 18,338 e 11,432 g 20,486 h 16,376 i 10,473 18,414 a 27,135 73,821 k 32,016 b
11,430 f 10,644 c 18,224 j 27,235 d
% CEGs l 98.0/96.8 67.7/32.3 79.8/41.9 97.6/96.4 98.0/93.5 98.0/95.2 61.7/24.2 32.7/14.9 57.3/24.2
% BUSCOs m (assembly)82.3 [6.4], 8.3, 9.9 15.2 [0.5], 15.4, 69.5 68.9 [2.4], 21.0, 10.1 63.8 [3.5], 7.6, 28.6 62.0 [3.0], 8.4, 29.6 68.8 [5.8], 9.9, 21.3 53.7 [4.0], 27.4, 18.9 13.7 [1.9], 10.6, 75.7 34.4 [4.0], 23.0, 42.7
% BUSCOs m (gene set)82.8 [12.0], 10.6, 6.5 na 69.4 [6.7], 23.4, 7.2 na 54.0 [4.7], 11.4, 34.6 69.3 [11.4], 9.6, 21.0 64.6 [10.5], 17.3, 18.1 na 23.1 [6.7], 16.4, 60.5

Note.—Unless otherwise indicated, values were retrieved from the NCBI.

Identified open-reading frames with significant sequence similarity to database sequences from Cornman et al. (2010 ).

IscaW1.4 gene set from VectorBase ( www.vectorbase.org ).

From Sanggaard et al. (2014 ), transcripts of more than 17 amino acids.

% of 248 CEGMA genes Found/Complete, in the assembly.

% of 2,675 arthropod BUSCOs Complete [Duplicated], Fragmented, Missing, in the assembly or in the gene set.

Protein-coding genes, pseudogenes, and noncoding RNAs were annotated using the NCBI Eukaryotic Genome Annotation Pipeline (see Materials and Methods and supplementary table S1 , Supplementary Material online ), which identified a total of 18,338 Gnomon protein-coding genes, with a processed subset of 11,430 well-supported RefSeq genes. The gene repertoire is larger than that of many sequenced insects ( Waterhouse 2015 ), but it is similar in size to those of I. scapularis and T. urticae and only about two-thirds those of the spider Stegodyphus mimosarum , and the scorpion Mesobuthus martensii ( table 1 ). Comparative analysis with genes from ten representative arthropod species to estimate numbers of near-universally present orthologs that are potentially missing indicated that the Gnomon gene set is more complete than the gene sets of both I. scapularis and T. urticae ( supplementary fig. S1 , Supplementary Material online ). The predatory mite genome is thus neither as compact as that of the spider mite nor as large as many other arachnids, and represents a remarkably complete assembly and annotation for the study of the currently sparsely sampled Acari.

Paraphyly of the Acari and Orphan Arachnid Genes

Phylogenomics offers opportunities to address conflicting views of the evolutionary relationships among mites and other arachnids ( Pepato et al. 2010 Sharma et al. 2014 ) using genome-wide sequence data, albeit with a limited sample of fully sequenced genomes with good quality gene annotations. The maximum-likelihood species phylogeny estimated from the concatenated protein sequence alignments of single-copy orthologs (see Materials and Methods) confidently pairs the two Parasitiformes M. occidentalis and I. scapularis ( fig. 1 A). However, placement of the African social velvet spider Ste. mimosarum as a sister group to these Parasitiformes with the acariform two-spotted spider mite T. urticae as the outgroup results in the paraphyly of the Acari. Complementary phylogenomic analyses with subsets of the species from figure 1 A and with orthologs from the less complete gene sets (see table 1 ) of the M. martensii scorpion and the S. scabiei mite further support these observed relationships ( supplementary fig. S2 , Supplementary Material online ). Depending on the species set and the alignment trimming stringency, these analyses employed some 100 to more than 1,000 single-copy orthologs to build superalignments of between about 55,000 and almost 250,000 amino acids, all resulting in phylogenies with 100% bootstrap support ( supplementary material , Supplementary Material online ). The relationships are in agreement with recent phylogenomic analyses that also found spiders (Araneae) and ticks to be sister groups ( Sanggaard et al. 2014 ). The molecular phylogeny also highlights the ancient divergence of the two Parasitiformes and their last common ancestor with T. urticae , conservatively estimated to be some 320–360 and 370–420 Ma, respectively ( Jeyaprakash and Hoy 2009 ).

Species phylogeny and orthology profiles. ( A ) The molecular species phylogeny built from aligned protein sequences of single-copy orthologs and rooted with the cnidarian Hydra vulgaris highlights the ancient divergence of the two Parasitiformes, the fast rate of gene-sequence evolution in Metaseiulus occidentalis , and supports the paraphyly of the Acari. All nodes showed 100% bootstrap support. Branch lengths in substitutions per site (s.s.). Inset: Female (♀) M. occidentalis are about 500 microns long, about twice the size of males (♂). ( B ) Homology assessments across 173 metazoan species from OrthoDB identify ancient orthologs for more than half of M. occidentalis genes (blue fractions: Orthologs in >90% or >70% of metazoans, or in any nonarthropod metazoan) and a small fraction with only arthropod orthologs (red), but about a quarter remain “orphaned” with no clear orthology, reflecting the sparse sampling and ancient divergences within the arachnids. Homology cutoff: e value < 1e-3. Species: Predatory mite Metaseiulus occidentalis Mocc deer tick Ixodes scapularis Isca velvet spider Stegodyphus mimosarum Smim spider mite Tetranychus urticae Turt fruit fly Drosophila melanogaster Dmel flour beetle Tribolium castaneum body louse Pediculus humanus water flea Daphnia pulex owl limpet Lottia gigantea polychaete worm Capitella teleta zebrafish Danio rerio human Homo sapiens Hsap .

Species phylogeny and orthology profiles. ( A ) The molecular species phylogeny built from aligned protein sequences of single-copy orthologs and rooted with the cnidarian Hydra vulgaris highlights the ancient divergence of the two Parasitiformes, the fast rate of gene-sequence evolution in Metaseiulus occidentalis , and supports the paraphyly of the Acari. All nodes showed 100% bootstrap support. Branch lengths in substitutions per site (s.s.). Inset: Female (♀) M. occidentalis are about 500 microns long, about twice the size of males (♂). ( B ) Homology assessments across 173 metazoan species from OrthoDB identify ancient orthologs for more than half of M. occidentalis genes (blue fractions: Orthologs in >90% or >70% of metazoans, or in any nonarthropod metazoan) and a small fraction with only arthropod orthologs (red), but about a quarter remain “orphaned” with no clear orthology, reflecting the sparse sampling and ancient divergences within the arachnids. Homology cutoff: e value < 1e-3. Species: Predatory mite Metaseiulus occidentalis Mocc deer tick Ixodes scapularis Isca velvet spider Stegodyphus mimosarum Smim spider mite Tetranychus urticae Turt fruit fly Drosophila melanogaster Dmel flour beetle Tribolium castaneum body louse Pediculus humanus water flea Daphnia pulex owl limpet Lottia gigantea polychaete worm Capitella teleta zebrafish Danio rerio human Homo sapiens Hsap .

Rooted with the cnidarian Hydra vulgaris (= H. magnipapillata ), the molecular species phylogeny shows the variable rates of gene sequence evolution, particularly among the fast-evolving arthropods, and highlights the fastest rates in the two mites and Drosophila melanogaster ( fig. 1 A). These conserved orthologs show that amino acid substitutions per site between M. occidentalis and I. scapularis are more than three times more numerous than between Danio rerio and Homo sapiens , underscoring the large evolutionary distance between these two Parasitiformes. Assessing homology and orthology with 172 other metazoan species (see Materials and Methods) identified ancient orthology for approximately 35% of the M. occidentalis Gnomon gene set ( fig. 1 B). Others are less well maintained across the metazoans (∼36%), or have orthologs only in other arthropods (∼4%). This leaves about a quarter of this mite’s genes with no clear orthology most of these have homologs in other metazoans, but a small fraction remains with no detectable homology. Other arachnids exhibit similarly high proportions of genes that lack clear orthology ( fig. 1 B), reflecting the sparse sampling and ancient divergences within this lineage, as previously noted for a tick transcriptome ( Gibson et al. 2013 ), and in contrast to the dipterans and primates, represented by D. melanogaster and H. sapiens , which are well-sampled with many closely related species.

Dynamic Gene Architecture Evolution in a Genome Rich in Helitrons

Examining gene architectures of ancient universal orthologs to identify shared and unique intron positions (see Materials and Methods) revealed dramatic intron losses from M. occidentalis genes accompanied by striking numbers of intron gains ( fig. 2 ). The vast majority of these losses and gains occurred since the last common ancestor with ticks, and only D. melanogaster , known for substantial intron losses ( Csuros et al. 2011 ), exhibits more total losses across the phylogeny. At the same time, these mite genes exhibit the most numerous intron gains, exceeding even those of Daphnia pulex , previously noted for extensive intron accumulation ( Li et al. 2009 ). The combination of extensive intron losses with numerous gains leaves this predatory mite with an unusually large proportion of unique, lineage-specific introns ( fig. 2 ). This contrasts the intron-rich gene architectures of the tick, which are more similar to those of a metazoan ancestor than to other arthropods ( Gulia-Nuss et al. 2015 ). The representative vertebrates, fish and human, have the most introns that are shared with any other species, that is, introns that have been stably maintained since the last common metazoan ancestor. Comparing gained versus lost intron sites in M. occidentalis genes revealed an approximately 50:25:25% 0–1–2 phase distribution for both—a ratio observed across many eukaryotes ( Csuros et al. 2011 ) (phase 0: Between codons phases 1 and 2: After first or second nucleotide in a codon, respectively). However, small but significant biases showed more losses occurred from phase 0 sites ( P = 2.0 × 10 − 07 ) and more gains occurred at phase 1 sites ( P = 1.3 × 10 − 06 ), with losses tending to occur more frequently toward the ends of genes (last ten th , P = 1.8 × 10 − 04 second last ten th , P = 5.1 × 10 − 05 ) ( supplementary fig. S3 , Supplementary Material online ). Comparing the lengths of introns unique to M. occidentalis with those that are shared with at least two other species revealed that unique introns are generally shorter (mean 143, 257 bp and median 116, 122 bp unique, shared, respectively P = 6.3 × 10 − 04 ). Across the examined phylogeny, the relative stability of vertebrate gene architectures contrasts the dynamic changes in intron content throughout the evolution of the arthropods, which appear especially dramatic in M. occidentalis genes that have about half the intron content of I. scapularis and almost double that of T. urticae ( fig. 2 ).

Dynamic Metaseiulus occidentalis intron evolution. Comparing orthologous intron positions in extant species to infer gain and loss events since their last common ancestors reveals dramatic changes in intron content throughout the evolution of arthropods, in contrast to the relative stability of vertebrate gene architectures. Metaseiulus occidentalis has by far the largest proportion of unique introns, driven by the combination of extensive losses and numerous gains. For each species, the three stacked bars show the following: (top bar) shows introns in this species, colored according to the “Introns Present” legend from those found in orthologs from all ten examined species (black) to only two species (gray), or unique (pink) or inferred (almond) to this species (middle bar, labeled +) shows introns gained in this species color-coded to match the nodes in the adjacent phylogeny where the gains occurred, with gains since the most recent node (extant) shown in bright green (bottom bar, labeled −) shows lost introns in this species color-coded to match the nodes in the adjacent phylogeny where the losses occurred, with losses since the most recent node (extant) shown in bright red. Introns present in all species are found in the nine organisms labeled on the dendrogram as well as the cnidarian Hydra vulgaris (the outgroup for this analysis). Species: A subset from figure 1. Ancestral nodes on dendrogram: P, Parasitiformes A, Arachnida R, Arthropoda H, Holometabola I, Insecta M, Mandibulata V, Vertebrata. Relative number of introns: Counts normalized by the inferred number of introns in the last common ancestor.

Dynamic Metaseiulus occidentalis intron evolution. Comparing orthologous intron positions in extant species to infer gain and loss events since their last common ancestors reveals dramatic changes in intron content throughout the evolution of arthropods, in contrast to the relative stability of vertebrate gene architectures. Metaseiulus occidentalis has by far the largest proportion of unique introns, driven by the combination of extensive losses and numerous gains. For each species, the three stacked bars show the following: (top bar) shows introns in this species, colored according to the “Introns Present” legend from those found in orthologs from all ten examined species (black) to only two species (gray), or unique (pink) or inferred (almond) to this species (middle bar, labeled +) shows introns gained in this species color-coded to match the nodes in the adjacent phylogeny where the gains occurred, with gains since the most recent node (extant) shown in bright green (bottom bar, labeled −) shows lost introns in this species color-coded to match the nodes in the adjacent phylogeny where the losses occurred, with losses since the most recent node (extant) shown in bright red. Introns present in all species are found in the nine organisms labeled on the dendrogram as well as the cnidarian Hydra vulgaris (the outgroup for this analysis). Species: A subset from figure 1. Ancestral nodes on dendrogram: P, Parasitiformes A, Arachnida R, Arthropoda H, Holometabola I, Insecta M, Mandibulata V, Vertebrata. Relative number of introns: Counts normalized by the inferred number of introns in the last common ancestor.

Despite many studies exploring intron gain/loss mechanisms, they remain poorly understood and, while losses can occur by reverse transcriptase-mediated processes and genomic deletions, gain mechanisms remain elusive but may be facilitated by processes including intron transpositions and transposon insertions ( Yenerall et al. 2011 Yenerall and Zhou 2012 ). Analysis of the TE content of the M. occidentalis genome revealed a comparable total fraction of TEs (6.8%) to that of the D. melanogaster euchromatic genome (6.6%) ( supplementary figs. S4 and S5 and Supplementary Data , Supplementary Material online ). However, although the fruit fly genome is dominated by long terminal repeat (LTR) elements, this genome contains much greater proportions of both cut-and-paste DNA transposons and Helitrons (rolling-circle transposons). In contrast, LTR elements are the most abundant TE in the compact T. urticae genome ( Grbić et al. 2011 ) and Mariner -type DNA transposons are the most common in V. destructor ( Cornman et al. 2010 ). Helitron activity can capture gene fragments and may generate chimeric transcripts or alter gene architectures ( Thomas and Pritham 2015 ), thereby contributing to genomic innovations such as alternative transcripts expressed in maize ( Barbaglia et al. 2012 ) or possible gains or losses of gene features as described in bats ( Thomas et al. 2014 ). Compared with other representative arthropods, this genome harbors the greatest proportion of Helitrons ( supplementary fig. S5 , Supplementary Material online ), suggesting a possible link between elevated rolling-circle transposon activity and dynamic gene architecture evolution in this phytoseiid mite.

Detecting, Disabling, and Digesting Prey

This obligatory predator has no eyes, yet it is able to detect and distinguish between prey species using various sensory receptors to identify silk and chemical cues deposited by spider mites and other prey. The ability to then subdue active prey species and to conduct preoral digestion is critical to this mite’s feeding behavior investigating genes and gene families likely to be involved in these biological traits therefore offers the best clues to understanding its success.

Chemosensation

Like most arthropods, M. occidentalis obtains considerable information about its environment through chemical cues. Noninsect arthropods employ two major gene families for chemosensation, the gustatory receptors (GRs) ( Robertson et al. 2003 ) and the ionotropic receptors (IRs) ( Rytz et al. 2013 ). The insects, however, possess a third family of chemoreceptors, the odorant receptors (ORs), which is likely to have evolved in ancient insects from the GRs ( Missbach et al. 2014 ). Accordingly, like those of other noninsect arthropods including the crustacean Da. pulex ( Peñalva-Arana et al. 2009 ), the myriapod Strigamia maritima ( Chipman et al. 2014 ), and the spider mite ( Grbić et al. 2011 ), the M. occidentalis genome does not harbor any ORs. Instead, it must rely on the 64 GR (six of which appear to be pseudogenes) and 65 IR genes encoded in its genome (see Materials and Methods and supplementary fig. S6 and Supplementary Data , Supplementary Material online ) for processing the chemical signals from other individuals, for example, male–female signals, as well as from potential prey. The identified GRs are highly divergent from insect GRs of known function, such as the sugar, fructose, carbon dioxide, and bitter taste receptors assignment of specific functions therefore requires further experimental evidence beyond the clues from homology. Interestingly, although arthropod GRs generally have about five introns, the majority (50/64) of this mite’s GRs form a large clade of intronless genes, spread across the genome, some as singletons but most in small tandem arrays, suggesting multiple duplications of an intronless ancestral gene. Although functional studies are required to explore their specific biological roles, the IRs form two groups comparable to the “conserved” and “divergent” IRs involved in smell and taste, respectively, in D. melanogaster ( Rytz et al. 2013 ). Like the GRs, the mite genome encodes a group of intronless IRs however, three IR genes that cluster with this group appear to have independently acquired novel introns. In the second large group most genes have five to eight introns, generally fewer than most insect IRs, but one has only a single intron and another has 14. Thus, gene architecture evolution of these divergent groups of chemoreceptors mirrors the dynamism observed from the analysis of introns from near-universal single-copy orthologs, and although sequence divergence prevents detailed functional inferences, the identified GR and IR gene repertoires suggest a comprehensive chemosensory capacity of this predatory mite.

Light Perception

Although spiders are well-known for their many eyes, this phytoseiid has no apparent eyes or ocelli and thus cannot rely on even weak visual cues for prey detection. Nevertheless, diapause induced by shortening daylengths suggests that this mite is capable of perceiving and responding to light ( Hoy 1975 ). Searches for genes involved in early eye development and retinal differentiation (see Materials and Methods) identified homologs of known regulators ( supplementary table S4 , Supplementary Material online ), including twin of eyeless but not eyeless , the D. melanogaster Pax6 -like genes that regulate ocular development ( Shaham et al. 2012 ). Homology searches for canonical genes of the phototransduction cascade (see Materials and Methods) identified all four key components: Photoreceptors, trimeric G-proteins, phospholipases, and transient receptor potential channels ( supplementary table S5 , Supplementary Material online ). However, the two putative photoreceptors both appear to be visual pigment-like peropsins rather than true visual opsins, unlike in spiders that have both opsins and peropsins, which, in the wandering spider Cupiennius salei show different expression patterns in primary and secondary eyes ( Eriksson et al. 2013 ). In addition to mite diapause behaviors, examining oviposition times revealed synchronized periodicity ( supplementary fig. S7 , Supplementary Material online ) that provides further support for the ability to perceive light. This is despite the apparent absence of several key components of the circadian rhythm system—no orthologs of Cycle , Period , or Cryptochrome genes were found ( supplementary table S6 , Supplementary Material online ). In contrast, I. scapularis and T. urticae have orthologs of both Period and Cryptochrome , and although Cycle appears to be missing from the tick, it is present in the spider mite. Thus, despite having no eyes this mite seems to possess key eye developmental genes, as well as all the major molecular components necessary for light perception, and it exhibits behaviors that indicate light-induced responses.

Paralysis and Preoral Digestion

Observations of M. occidentalis feeding confirm the use of preoral digestion common to most predaceous arthropods and reveal symptoms of paralysis in spider mite prey suggesting they immobilize their quarry ( Flechtmann and McMurtry 1992 ). Homology searches with digestive peptidases and some 800 salivary peptides from spiders and other venomous arthropods (see Materials and Methods) identified genes with putative roles in this predator’s feeding ( supplementary tables S7 and S8 , Supplementary Material online ). Two neurotoxin-like genes were identified with matches to agatoxins from funnel-web spiders, which block calcium channels causing paralysis in insects ( Wang et al. 2001 ). A single sphingomyelinase D -like gene matched those from recluse and assassin spiders, which cause lesions in mammals and are potent insecticidal toxins ( Zobel-Thropp et al. 2012 ), compared with at least five in T. urticae , three in Ste. mimosarum and four in I. scapularis . Many toxins are short peptides that appear to have emerged independently in different lineages or diverged rapidly it is thus not surprising that homology searches revealed few confident matches. In contrast, proteolytic digestive enzymes are more easily recognizable, for example, InterPro protein domain annotations identified 124 M. occidentalis trypsin-like cysteine/serine peptidases however, this is substantially fewer than in the spider mite and tick genomes ( supplementary table S9 , Supplementary Material online ). Specifically, this predator has only one C13 legumain cysteine peptidase and at least 23 confidently identified C1A cathepsins whereas the spider mite has 19 and 57, respectively ( supplementary table S10 , Supplementary Material online ). Interestingly, all the M. occidentalis C1A peptidases belong to the subfamily of cathepsin L-like proteins, with no cathepsin B-like peptidases, unlike in T. urticae , which has at least 17 ( supplementary fig. S8 , Supplementary Material online ). It is possible that such variations in the repertoires of encoded proteases may reflect the different diets and feeding behaviors of these two distantly related mites.

Sex Determination and Development of a Parahaploid Mite with Completely Atomized Hox Genes

Also known as pseudoarrhenotoky or paternal genome elimination, parahaploidy is a rare genetic system found in some mites, beetles, mealybugs, and scale insects ( Sánchez 2014 ). An improved understanding of this embryonic process could help control programs by biasing predatory mite production toward females, which consume more prey than males. The adults exhibit the reduced body-plan segmentation characteristic of mites and ticks, which in acariform mites has been linked to changes in Hox gene expression ( Barnett and Thomas 2013 ) or Hox gene loss ( Grbić et al. 2011 ). As a distantly related mite with similarly reduced segmentation, characterizing M. occidentalis Hox genes offers clues to understanding their roles in body-plan development.

Parahaploidy and Epigenetics

Paternally derived chromosomes are heterochromatinized and eliminated in M. occidentalis embryos that develop into haploid adult males ( Nelson-Rees et al. 1980 ) through a process that allows the mother to control the sex ratios of her offspring ( Nagelkerke and Sabelis 1998 ). As little is known about the molecular players in this unusual genetic system, the identification of candidate genes involved in sex determination focused on searches both for canonical components of signaling cascades as well as on genes involved in epigenetic DNA modifications that precede chromosome elimination in similar systems (see Materials and Methods). Studies in insects have revealed substantial variations in the components of sex-determination systems and their regulatory circuits ( Gempe and Beye 2011 ), so it is not surprising that several elements of the D. melanogaster system appear to be missing from M. occidentalis ( supplementary tables S11–S14 , Supplementary Material online ). Nevertheless, orthologs of the key upstream splicing factor Sex lethal and at least one of its targets, transformer-2 , are present, as well as the downstream target transcription factor doublesex ( Pomerantz et al. 2014 ). Although the transformer-2 ortholog did not exhibit any sex-biased gene expression in M. occidentalis , two doublesex -like genes displayed male-biased expression, but without any evidence of alternative splicing ( Pomerantz and Hoy 2015a ). Although such signals may be involved in controlling sex determination, the process of heterochromatinization itself is likely governed by sex-specific epigenetic marks, as revealed by studies of the parahaploid mealybug Planococcus citri ( Bongiorni et al. 2009 ). DNA methylation is associated with processes such as genomic imprinting and X chromosome inactivation, but searches for DNA methytransferases ( Dnmts ) in the M. occidentalis genome revealed only the widely conserved Dnmt2 gene and no Dnmt1 or Dnmt3 homologs ( supplementary fig. S9 , Supplementary Material online ). Dnmt2 in fact functions primarily as a tRNA methytransferase, and species with only Dnmt2 are therefore unlikely to be able to rely on DNA methylation for epigenetic regulation ( Raddatz et al. 2013 ). In contrast, the repertoires of histone deacetylases and their cofactors are similar to those of other arthropods ( supplementary table S15 , Supplementary Material online ), suggesting that this epigenetic regulatory system is fully functional. These comparisons point to candidate genes that can now be targeted for detailed characterizations however, it seems that DNA methylation may not hold the key to unlocking the secrets underlying the unusual system of sex determination in this parahaploid mite.

Completely Atomized Hox Genes

Regardless of their sex, embryonic development leads to the adult form with only two body segments, the gnathosoma fused with flexible cuticle to the idiosoma. This reduced segmentation of mites and ticks is dramatically different from the body plans of insects, crustaceans, and myriapods, and is presumably achieved through segmental fusions during early development. Segment identities and development along the anteroposterior axis are determined by the expression patterns of Hox genes, a widely conserved subset of homeobox-containing transcription factors typically found physically clustered within genomes ( Duboule 2007 ). Of the ten Hox genes present in the arthropod ancestor, searching the M. occidentalis genome (see Materials and Methods) identified orthologs for all except Hox3/zerknüllt/zen and no gene duplications ( fig. 3 ), unlike in the scorpion M. martensii where the complete Hox gene cluster appears to have been duplicated ( Di et al. 2015 ). The zen gene is also missing from the spider mite, but it is present in I. scapularis and has been identified in an oribatid mite ( Telford and Thomas 1998 ) and other chelicerates. Most strikingly, M. occidentalis Hox genes are completely atomized with each gene on a different scaffold, unlike in other examined arthropods where they are generally found to be collinear with no or few intervening genes ( fig. 3 ). They are located on scaffolds ranging in size from 220 kb with 43 genes to 3,231 kb with 413 genes ( supplementary fig. S10 and Supplementary Data , Supplementary Material online ), supporting the conclusion that their atomization is not an artefact of genome assembly fragmentation. Hox genes generally form canonical “organized” clusters but some may be described as “split,” “disorganized,” or “atomized” ( Duboule 2007 ) however, complete Hox gene atomization such as in the tunicate sea squirt Oikopleura dioica ( Seo et al. 2004 ) or the cephalopod Octopus bimaculoides ( Albertin et al. 2015 ), and now for the first time in any arthropod, appears to be a rare occurrence indeed.

Complete atomization of Metaseiulus occidentalis Hox genes. In stark contrast to M. occidentalis , the genomic organization of ten Hox genes from two other arachnids and representative species from seven arthropod lineages shows their generally well-maintained collinearity with no or few intervening genes. This complete atomization of Hox genes is the first reported for any arthropod and highlights the turbulent and dynamic evolutionary history of this predatory mite’s genome. Hox gene orthologs in each species are depicted as color-matched ellipses with dotted ellipses indicating putatively missing genes. Connecting black lines show their scaffold or chromosome collinearity with the number of intervening or neighboring genes indicated by boxes of different heights and colors: Thin gray boxes for 1, 2, or 3–5 intervening or neighboring genes thicker brown boxes for 6–10 or 11–20 genes thicker purple boxes for 21–30, 31–50, 51–100, or 101–200 genes and the thickest bright pink boxes for more than 200 genes. Hox genes: lab , labial pb , proboscipedia zen , zerknüllt Dfd , Deformed Scr , Sex combs reduced ftz , fushi tarazu Antp , Antennapedia Ubx , Ultrabithorax AdbA , abdominal A AbdB , Abdominal B and labeled in D. melanogaster , 1 , zerknüllt 2 , zerknüllt-related and b , bicoid . Species: A subset from figure 1, plus the centipede Strigamia maritima the honeybee Apis mellifera and the monarch butterfly Danaus plexippus .

Complete atomization of Metaseiulus occidentalis Hox genes. In stark contrast to M. occidentalis , the genomic organization of ten Hox genes from two other arachnids and representative species from seven arthropod lineages shows their generally well-maintained collinearity with no or few intervening genes. This complete atomization of Hox genes is the first reported for any arthropod and highlights the turbulent and dynamic evolutionary history of this predatory mite’s genome. Hox gene orthologs in each species are depicted as color-matched ellipses with dotted ellipses indicating putatively missing genes. Connecting black lines show their scaffold or chromosome collinearity with the number of intervening or neighboring genes indicated by boxes of different heights and colors: Thin gray boxes for 1, 2, or 3–5 intervening or neighboring genes thicker brown boxes for 6–10 or 11–20 genes thicker purple boxes for 21–30, 31–50, 51–100, or 101–200 genes and the thickest bright pink boxes for more than 200 genes. Hox genes: lab , labial pb , proboscipedia zen , zerknüllt Dfd , Deformed Scr , Sex combs reduced ftz , fushi tarazu Antp , Antennapedia Ubx , Ultrabithorax AdbA , abdominal A AbdB , Abdominal B and labeled in D. melanogaster , 1 , zerknüllt 2 , zerknüllt-related and b , bicoid . Species: A subset from figure 1, plus the centipede Strigamia maritima the honeybee Apis mellifera and the monarch butterfly Danaus plexippus .

Immunity without Imd , and RNAi with Duplicated Dicers

In the wild, M. occidentalis is found in low-density populations (less than 0.1/leaf) where diseases appear uncommon. In contrast, infections with microsporidia and other pathogens occur in dense colonies and can seriously impede rearing for mass production in biological control programs ( Bjørnson 2008 ). Understanding this mite’s immune-defense capacities, including the RNAi system, is necessary to improve productivity at mass-rearing facilities.

The Immune Repertoire

Classical arthropod immune responses include phagocytosis, melanization, and the production of antimicrobial peptides in response to signals induced by pathogen recognition, and have been characterized principally with studies in insects ( Buchon et al. 2014 Barribeau et al. 2015 ). Surveying the M. occidentalis genome (see Materials and Methods) identified homologs of key immune-related genes including recognition proteins and signaling pathway members ( supplementary table S17 , Supplementary Material online ). Only a single gene encoding a peptidoglycan recognition protein (PGRP) was identified T. urticae also has only one PGRP, whereas I. scapularis has at least four, and none of these Acari appears to have any Gram-negative bacteria-binding proteins (GNBPs). Other recognition-related genes include those encoding a fibrinogen-related protein, at least two thioester-containing proteins and four phagocytosis-related Dscam-like proteins counts of which are generally lower than in other chelicerates ( Palmer and Jiggins 2015 ). The Toll pathway appears largely intact: A single toll-activating spaetzle gene and six toll-like receptor genes the signal transducers Myd88 and Pelle (but no Tube -like gene, which is also absent from I. scapularis and T. urticae [ Palmer and Jiggins 2015 ]) the nuclear factor-κB (NF-κB) transcription factor dorsal and its inhibitor cactus , are all present. In contrast, neither Imd nor the NF-κB transcription factor of the Imd pathway, relish , could be identified, and the absence of additional pathway members further suggests that canonical Imd signaling does not occur. Although homologs of the JAK/STAT pathway receptor domeless and transcription factor Stat92E were identified, no clear homolog of the janus kinase hopscotch was found. Finally, like I. scapularis ( Smith and Pal 2014 ), this predatory mite lacks genes related to the melanization (phenoloxidase) pathway.

RNAi Pathways

Orally delivered double-stranded RNAs (dsRNAs) induce robust, prolonged, and systemic gene knockdowns in M. occidentalis ( Wu and Hoy 2014a, , 2014b Pomerantz and Hoy 2015b Wu and Hoy 2015 ). Candidate genes likely involved in facilitating these responses were identified (see Materials and Methods) with searches for homologs of genes of the RNAi or microRNA (miRNA) pathways as well as dsRNA uptake and transport processes ( supplementary tables S18 and S19 , Supplementary Material online ). Most genes implicated in dsRNA uptake and transport were identified, including clathrin heavy chain which, when knocked down, severely impaired RNAi responses ( Wu and Hoy 2014a ), suggesting this mite uses a receptor-mediated endocytosis pathway for dsRNA uptake. The identification of at least three RNA-dependent RNA polymerase (RDRP) genes, which are also found in other arachnids and Str. maritima but not in other arthropods, suggests RDRP-based dsRNA amplification may occur. The presence of both Dicer-1 and Dicer-2 homologs suggests that, like Drosophila , distinct dicer proteins are used for processing miRNAs and small interfering RNAs (siRNAs). However, although homologs of the miRNA precursor processors Drosha and Pasha , as well as Dicer-1 ’s partner for miRNA processing, Loquacious , were all identified, Dicer-2 ’s partner, R2D2 , appears to be absent. Most strikingly, the M. occidentalis genome encodes at least five distinct full-length copies of Dicer-2 , located on four different scaffolds, with three to seven introns each ( fig. 4 ). These divergent gene copies vary in sequence identity from 66% to 31% (amino acids) and 66–43% (nucleotides). Four of these Dicer-2 genes matched transcripts from a multi-life-stage RNA-seq transcriptome ( Hoy et al. 2013 ) ( supplementary table S20 , Supplementary Material online ), providing support for their functional relevance. Such duplications of Dicer-2 genes appear to be rare events: A single duplication was found in Da. pulex ( Mukherjee et al. 2013 Palmer and Jiggins 2015 ), and surveying more than 80 arthropod species identified no other confidently distinct and full-length gene duplications. Comparing their gene architectures reveals the paucity of introns in M. occidentalis Dicers , especially when compared with the intron-rich genes of I. scapularis and Apis mellifera , and their uniqueness—with only a single confidently aligned intron position that is shared with D. melanogaster Dicer-2 ( fig. 4 ). Such multiple duplications of a normally single-copy gene were also noted for the gene encoding the muscle myosin heavy chain protein, which also showed very different intron–exon architectures, as well as mutually exclusive spliced exons ( Kollmar and Hatje 2014 ). The multiple duplications of Dicer-2 genes highlight how the dynamic evolutionary history of this genome has led to the creation and maintenance of several gene copies, which exhibit dramatic changes in their intron content.

The expanded set of Metaseiulus occidentalis Dicer-2 genes. The phylogeny of Dicer-1 and Dicer-2 genes from four distantly related arthropods (left) with five distinct copies of Dicer-2 from M. occidentalis showing the locations of shared and unique intron positions along the length of the multiple protein sequence alignment (right). Dashed vertical lines mark the positions of unambiguous shared intron positions along the length of the alignment, which are colored according to the number of genes in which they are found (5 pink, 4 purple, 3 green, 2 blue). Confidently identified unique intron positions are shown in yellow, and ambiguous (poorly aligned regions) intron positions are shown in almond. Dramatic gains and losses of introns in M. occidentalis genes have left only a single intron position in three Dicer-2 genes that is shared with any other DicersDicer-2 from Drosophila melanogaster . Examining these gene structures highlights the paucity of introns in M. occidentalis genes, especially compared with the intron-rich orthologs from Ixodes scapularis and Apis mellifera . Dicer-1 and Dicer-2 genes in the phylogeny are color-matched by species, and the only node with less than 100% bootstrap support is labeled “75.” The positions of Dicer protein domains are indicated (top) as well as the relative quality of the alignment (bottom). Dashed lines for I. scapularis Dicer-2 denote missing sequence information due to gaps in the genome assembly. DIM, dicer dimerization domain PAZ, domain named after Piwi, Argonaut and Zwille proteins.

The expanded set of Metaseiulus occidentalis Dicer-2 genes. The phylogeny of Dicer-1 and Dicer-2 genes from four distantly related arthropods (left) with five distinct copies of Dicer-2 from M. occidentalis showing the locations of shared and unique intron positions along the length of the multiple protein sequence alignment (right). Dashed vertical lines mark the positions of unambiguous shared intron positions along the length of the alignment, which are colored according to the number of genes in which they are found (5 pink, 4 purple, 3 green, 2 blue). Confidently identified unique intron positions are shown in yellow, and ambiguous (poorly aligned regions) intron positions are shown in almond. Dramatic gains and losses of introns in M. occidentalis genes have left only a single intron position in three Dicer-2 genes that is shared with any other DicersDicer-2 from Drosophila melanogaster . Examining these gene structures highlights the paucity of introns in M. occidentalis genes, especially compared with the intron-rich orthologs from Ixodes scapularis and Apis mellifera . Dicer-1 and Dicer-2 genes in the phylogeny are color-matched by species, and the only node with less than 100% bootstrap support is labeled “75.” The positions of Dicer protein domains are indicated (top) as well as the relative quality of the alignment (bottom). Dashed lines for I. scapularis Dicer-2 denote missing sequence information due to gaps in the genome assembly. DIM, dicer dimerization domain PAZ, domain named after Piwi, Argonaut and Zwille proteins.


Contents

Wild horses were known since prehistory from central Asia to Europe, with domestic horses and other equids being distributed more widely in the Old World, but no horses or equids of any type were found in the New World when European explorers reached the Americas. When the Spanish colonists brought domestic horses from Europe, beginning in 1493, escaped horses quickly established large feral herds. In the 1760s, the early naturalist Buffon suggested this was an indication of inferiority of the New World fauna, but later reconsidered this idea. [3] William Clark's 1807 expedition to Big Bone Lick found "leg and foot bones of the Horses", which were included with other fossils sent to Thomas Jefferson and evaluated by the anatomist Caspar Wistar, but neither commented on the significance of this find. [4]

The first Old World equid fossil was found in the gypsum quarries in Montmartre, Paris, in the 1820s. The tooth was sent to the Paris Conservatory, where it was identified by Georges Cuvier, who identified it as a browsing equine related to the tapir. [5] His sketch of the entire animal matched later skeletons found at the site. [6]

During the Beagle survey expedition, the young naturalist Charles Darwin had remarkable success with fossil hunting in Patagonia. On 10 October 1833, at Santa Fe, Argentina, he was "filled with astonishment" when he found a horse's tooth in the same stratum as fossil giant armadillos, and wondered if it might have been washed down from a later layer, but concluded this was "not very probable". [7] After the expedition returned in 1836, the anatomist Richard Owen confirmed the tooth was from an extinct species, which he subsequently named Equus curvidens, and remarked, "This evidence of the former existence of a genus, which, as regards South America, had become extinct, and has a second time been introduced into that Continent, is not one of the least interesting fruits of Mr. Darwin's palæontological discoveries." [4] [8]

In 1848, a study On the fossil horses of America by Joseph Leidy systematically examined Pleistocene horse fossils from various collections, including that of the Academy of Natural Sciences, and concluded at least two ancient horse species had existed in North America: Equus curvidens and another, which he named Equus americanus. A decade later, however, he found the latter name had already been taken and renamed it Equus complicatus. [3] In the same year, he visited Europe and was introduced by Owen to Darwin. [9]

The original sequence of species believed to have evolved into the horse was based on fossils discovered in North America in 1879 by paleontologist Othniel Charles Marsh. The sequence, from Eohippus to the modern horse (Equus), was popularized by Thomas Huxley and became one of the most widely known examples of a clear evolutionary progression. The horse's evolutionary lineage became a common feature of biology textbooks, and the sequence of transitional fossils was assembled by the American Museum of Natural History into an exhibit that emphasized the gradual, "straight-line" evolution of the horse.

Since then, as the number of equid fossils has increased, the actual evolutionary progression from Eohippus to Equus has been discovered to be much more complex and multibranched than was initially supposed. The straight, direct progression from the former to the latter has been replaced by a more elaborate model with numerous branches in different directions, of which the modern horse is only one of many. George Gaylord Simpson in 1951 [10] first recognized that the modern horse was not the "goal" of the entire lineage of equids, [11] but is simply the only genus of the many horse lineages to survive.

Detailed fossil information on the distribution and rate of change of new equid species has also revealed that the progression between species was not as smooth and consistent as was once believed. Although some transitions, such as that of Dinohippus to Equus, were indeed gradual progressions, a number of others, such as that of Epihippus to Mesohippus, were relatively abrupt in geologic time, taking place over only a few million years. Both anagenesis (gradual change in an entire population's gene frequency) and cladogenesis (a population "splitting" into two distinct evolutionary branches) occurred, and many species coexisted with "ancestor" species at various times. The change in equids' traits was also not always a "straight line" from Eohippus to Equus: some traits reversed themselves at various points in the evolution of new equid species, such as size and the presence of facial fossae, and only in retrospect can certain evolutionary trends be recognized. [12]

Phenacodontidae Edit

Phenacodontidae is the most recent family in the order Condylarthra believed to be the ancestral to the odd-toed ungulates. [ citation needed ] It contains the genera Almogaver, Copecion, Ectocion, Eodesmatodon, Meniscotherium, Ordathspidotherium, Phenacodus and Pleuraspidotherium. The family lived from the Early Paleocene to the Middle Eocene in Europe and were about the size of a sheep, with tails making slightly less than half of the length of their bodies and unlike their ancestors, good running skills for eluding predators. [ citation needed ]

Eohippus Edit

Eohippus appeared in the Ypresian (early Eocene), about 52 mya (million years ago). It was an animal approximately the size of a fox (250–450 mm in height), with a relatively short head and neck and a springy, arched back. It had 44 low-crowned teeth, in the typical arrangement of an omnivorous, browsing mammal: three incisors, one canine, four premolars, and three molars on each side of the jaw. Its molars were uneven, dull, and bumpy, and used primarily for grinding foliage. The cusps of the molars were slightly connected in low crests. Eohippus browsed on soft foliage and fruit, probably scampering between thickets in the mode of a modern muntjac. It had a small brain, and possessed especially small frontal lobes. [12]

Its limbs were long relative to its body, already showing the beginnings of adaptations for running. However, all of the major leg bones were unfused, leaving the legs flexible and rotatable. Its wrist and hock joints were low to the ground. The forelimbs had developed five toes, of which four were equipped with small proto-hooves the large fifth "toe-thumb" was off the ground. The hind limbs had small hooves on three out of the five toes, while the vestigial first and fifth toes did not touch the ground. Its feet were padded, much like a dog's, but with the small hooves in place of claws. [13]

For a span of about 20 million years, Eohippus thrived with few significant evolutionary changes. [12] The most significant change was in the teeth, which began to adapt to its changing diet, as these early Equidae shifted from a mixed diet of fruits and foliage to one focused increasingly on browsing foods. During the Eocene, an Eohippus species (most likely Eohippus angustidens) branched out into various new types of Equidae. Thousands of complete, fossilized skeletons of these animals have been found in the Eocene layers of North American strata, mainly in the Wind River basin in Wyoming. Similar fossils have also been discovered in Europe, such as Propalaeotherium (which is not considered ancestral to the modern horse). [14]

Orohippus Edit

Approximately 50 million years ago, in the early-to-middle Eocene, Eohippus smoothly transitioned into Orohippus through a gradual series of changes. [14] Although its name means "mountain horse", Orohippus was not a true horse and did not live in the mountains. It resembled Eohippus in size, but had a slimmer body, an elongated head, slimmer forelimbs, and longer hind legs, all of which are characteristics of a good jumper. Although Orohippus was still pad-footed, the vestigial outer toes of Eohippus were not present in Orohippus there were four toes on each fore leg, and three on each hind leg.

The most dramatic change between Eohippus and Orohippus was in the teeth: the first of the premolar teeth was dwarfed, the last premolar shifted in shape and function into a molar, and the crests on the teeth became more pronounced. Both of these factors gave the teeth of Orohippus greater grinding ability, suggesting Orohippus ate tougher plant material.

Epihippus Edit

In the mid-Eocene, about 47 million years ago, Epihippus, a genus which continued the evolutionary trend of increasingly efficient grinding teeth, evolved from Orohippus. Epihippus had five grinding, low-crowned cheek teeth with well-formed crests. A late species of Epihippus, sometimes referred to as Duchesnehippus intermedius, had teeth similar to Oligocene equids, although slightly less developed. Whether Duchesnehippus was a subgenus of Epihippus or a distinct genus is disputed. [15] Epihippus was only 2 feet tall. [15]

Mesohippus Edit

In the late Eocene and the early stages of the Oligocene epoch (32–24 mya), the climate of North America became drier, and the earliest grasses began to evolve. The forests were yielding to flatlands, [ citation needed ] home to grasses and various kinds of brush. In a few areas, these plains were covered in sand, [ citation needed ] creating the type of environment resembling the present-day prairies.

In response to the changing environment, the then-living species of Equidae also began to change. In the late Eocene, they began developing tougher teeth and becoming slightly larger and leggier, allowing for faster running speeds in open areas, and thus for evading predators in nonwooded areas [ citation needed ] . About 40 mya, Mesohippus ("middle horse") suddenly developed in response to strong new selective pressures to adapt, beginning with the species Mesohippus celer and soon followed by Mesohippus westoni.

In the early Oligocene, Mesohippus was one of the more widespread mammals in North America. It walked on three toes on each of its front and hind feet (the first and fifth toes remained, but were small and not used in walking). The third toe was stronger than the outer ones, and thus more weighted the fourth front toe was diminished to a vestigial nub. Judging by its longer and slimmer limbs, Mesohippus was an agile animal.

Mesohippus was slightly larger than Epihippus, about 610 mm (24 in) at the shoulder. Its back was less arched, and its face, snout, and neck were somewhat longer. It had significantly larger cerebral hemispheres, and had a small, shallow depression on its skull called a fossa, which in modern horses is quite detailed. The fossa serves as a useful marker for identifying an equine fossil's species. Mesohippus had six grinding "cheek teeth", with a single premolar in front—a trait all descendant Equidae would retain. Mesohippus also had the sharp tooth crests of Epihippus, improving its ability to grind down tough vegetation.

Miohippus Edit

Around 36 million years ago, soon after the development of Mesohippus, Miohippus ("lesser horse") emerged, the earliest species being Miohippus assiniboiensis. As with Mesohippus, the appearance of Miohippus was relatively abrupt, though a few transitional fossils linking the two genera have been found. Mesohippus was once believed to have anagenetically evolved into Miohippus by a gradual series of progressions, but new evidence has shown its evolution was cladogenetic: a Miohippus population split off from the main genus Mesohippus, coexisted with Mesohippus for around four million years, and then over time came to replace Mesohippus. [16]

Miohippus was significantly larger than its predecessors, and its ankle joints had subtly changed. Its facial fossa was larger and deeper, and it also began to show a variable extra crest in its upper cheek teeth, a trait that became a characteristic feature of equine teeth.

Miohippus ushered in a major new period of diversification in Equidae. [17]

Kalobatippus Edit

The forest-suited form was Kalobatippus (or Miohippus intermedius, depending on whether it was a new genus or species), whose second and fourth front toes were long, well-suited to travel on the soft forest floors. Kalobatippus probably gave rise to Anchitherium, which travelled to Asia via the Bering Strait land bridge, and from there to Europe. [18] In both North America and Eurasia, larger-bodied genera evolved from Anchitherium: Sinohippus in Eurasia and Hypohippus and Megahippus in North America. [19] Hypohippus became extinct by the late Miocene. [20]

Parahippus Edit

The Miohippus population that remained on the steppes is believed to be ancestral to Parahippus, a North American animal about the size of a small pony, with a prolonged skull and a facial structure resembling the horses of today. Its third toe was stronger and larger, and carried the main weight of the body. Its four premolars resembled the molar teeth the first were small and almost nonexistent. The incisor teeth, like those of its predecessors, had a crown (like human incisors) however, the top incisors had a trace of a shallow crease marking the beginning of the core/cup.

Merychippus Edit

In the middle of the Miocene epoch, the grazer Merychippus flourished. [21] It had wider molars than its predecessors, which are believed to have been used for crunching the hard grasses of the steppes. The hind legs, which were relatively short, had side toes equipped with small hooves, but they probably only touched the ground when running. [17] Merychippus radiated into at least 19 additional grassland species.

Hipparion Edit

Three lineages within Equidae are believed to be descended from the numerous varieties of Merychippus: Hipparion, Protohippus and Pliohippus. The most different from Merychippus was Hipparion, mainly in the structure of tooth enamel: in comparison with other Equidae, the inside, or tongue side, had a completely isolated parapet. A complete and well-preserved skeleton of the North American Hipparion shows an animal the size of a small pony. They were very slim, rather like antelopes, and were adapted to life on dry prairies. On its slim legs, Hipparion had three toes equipped with small hooves, but the side toes did not touch the ground.

In North America, Hipparion and its relatives (Cormohipparion, Nannippus, Neohipparion, and Pseudhipparion), proliferated into many kinds of equids, at least one of which managed to migrate to Asia and Europe during the Miocene epoch. [22] (European Hipparion differs from American Hipparion in its smaller body size – the best-known discovery of these fossils was near Athens.)

Pliohippus Edit

Pliohippus arose from Callippus in the middle Miocene, around 12 mya. It was very similar in appearance to Equus, though it had two long extra toes on both sides of the hoof, externally barely visible as callused stubs. The long and slim limbs of Pliohippus reveal a quick-footed steppe animal.

Until recently, Pliohippus was believed to be the ancestor of present-day horses because of its many anatomical similarities. However, though Pliohippus was clearly a close relative of Equus, its skull had deep facial fossae, whereas Equus had no fossae at all. Additionally, its teeth were strongly curved, unlike the very straight teeth of modern horses. Consequently, it is unlikely to be the ancestor of the modern horse instead, it is a likely candidate for the ancestor of Astrohippus. [23]

Dinohippus Edit

Dinohippus was the most common species of Equidae in North America during the late Pliocene. It was originally thought to be monodactyl, but a 1981 fossil find in Nebraska shows some were tridactyl.

Plesippus Edit

Plesippus is often considered an intermediate stage between Dinohippus and the extant genus, Equus.

The famous fossils found near Hagerman, Idaho were originally thought to be a part of the genus Plesippus. Hagerman Fossil Beds (Idaho) is a Pliocene site, dating to about 3.5 mya. The fossilized remains were originally called Plesippus shoshonensis, but further study by paleontologists determined the fossils represented the oldest remains of the genus Equus. [24] Their estimated average weight was 425 kg, roughly the size of an Arabian horse.

At the end of the Pliocene, the climate in North America began to cool significantly and most of the animals were forced to move south. One population of Plesippus moved across the Bering land bridge into Eurasia around 2.5 mya. [25]

Equus Edit

The genus Equus, which includes all extant equines, is believed to have evolved from Dinohippus, via the intermediate form Plesippus. One of the oldest species is Equus simplicidens, described as zebra-like with a donkey-shaped head. The oldest fossil to date is

3.5 million years old from Idaho, USA. The genus appears to have spread quickly into the Old World, with the similarly aged Equus livenzovensis documented from western Europe and Russia. [26]

Molecular phylogenies indicate the most recent common ancestor of all modern equids (members of the genus Equus) lived

5.6 (3.9–7.8) mya. Direct paleogenomic sequencing of a 700,000-year-old middle Pleistocene horse metapodial bone from Canada implies a more recent 4.07 Myr before present date for the most recent common ancestor (MRCA) within the range of 4.0 to 4.5 Myr BP. [27] The oldest divergencies are the Asian hemiones (subgenus E. (Asinus), including the kulan, onager, and kiang), followed by the African zebras (subgenera E. (Dolichohippus), and E. (Hippotigris)). All other modern forms including the domesticated horse (and many fossil Pliocene and Pleistocene forms) belong to the subgenus E. (Equus) which diverged

4.8 (3.2–6.5) million years ago. [28]

Pleistocene horse fossils have been assigned to a multitude of species, with over 50 species of equines described from the Pleistocene of North America alone, although the taxonomic validity of most of these has been called into question. [29] Recent genetic work on fossils has found evidence for only three genetically divergent equid lineages in Pleistocene North and South America. [28] These results suggest all North American fossils of caballine-type horses (which also include the domesticated horse and Przewalski's horse of Europe and Asia), as well as South American fossils traditionally placed in the subgenus E. (Amerhippus) [30] belong to the same species: E. ferus. Remains attributed to a variety of species and lumped as New World stilt-legged horses (including H. francisci, E. tau, E. quinni and potentially North American Pleistocene fossils previously attributed to E. cf. hemiones, and E. (Asinus) cf. kiang) probably all belong to a second species endemic to North America, which despite a superficial resemblance to species in the subgenus E. (Asinus) (and hence occasionally referred to as North American ass) is closely related to E. ferus. [28] Surprisingly, the third species, endemic to South America and traditionally referred to as Hippidion, originally believed to be descended from Pliohippus, was shown to be a third species in the genus Equus, closely related to the New World stilt-legged horse. [28] The temporal and regional variation in body size and morphological features within each lineage indicates extraordinary intraspecific plasticity. Such environment-driven adaptative changes would explain why the taxonomic diversity of Pleistocene equids has been overestimated on morphoanatomical grounds. [30]

According to these results, it appears the genus Equus evolved from a Dinohippus-like ancestor

4–7 mya. It rapidly spread into the Old World and there diversified into the various species of asses and zebras. A North American lineage of the subgenus E. (Equus) evolved into the New World stilt-legged horse (NWSLH). Subsequently, populations of this species entered South America as part of the Great American Interchange shortly after the formation of the Isthmus of Panama, and evolved into the form currently referred to as Hippidion

2.5 million years ago. Hippidion is thus only distantly related to the morphologically similar Pliohippus, which presumably became extinct during the Miocene. Both the NWSLH and Hippidium show adaptations to dry, barren ground, whereas the shortened legs of Hippidion may have been a response to sloped terrain. [30] In contrast, the geographic origin of the closely related modern E. ferus is not resolved. However, genetic results on extant and fossil material of Pleistocene age indicate two clades, potentially subspecies, one of which had a holarctic distribution spanning from Europe through Asia and across North America and would become the founding stock of the modern domesticated horse. [31] [32] The other population appears to have been restricted to North America. However, one or more North American populations of E. ferus entered South America

1.0–1.5 million years ago, leading to the forms currently known as E. (Amerhippus), which represent an extinct geographic variant or race of E. ferus.

Genome sequencing Edit

Early sequencing studies of DNA revealed several genetic characteristics of Przewalski's horse that differ from what is seen in modern domestic horses, indicating neither is ancestor of the other, and supporting the status of Przewalski horses as a remnant wild population not derived from domestic horses. [33] The evolutionary divergence of the two populations was estimated to have occurred about 45,000 YBP, [34] [35] while the archaeological record places the first horse domestication about 5,500 YBP by the ancient central-Asian Botai culture. [34] [36] The two lineages thus split well before domestication, probably due to climate, topography, or other environmental changes. [34]

Several subsequent DNA studies produced partially contradictory results. A 2009 molecular analysis using ancient DNA recovered from archaeological sites placed Przewalski's horse in the middle of the domesticated horses, [37] but a 2011 mitochondrial DNA analysis suggested that Przewalski's and modern domestic horses diverged some 160,000 years ago. [38] An analysis based on whole genome sequencing and calibration with DNA from old horse bones gave a divergence date of 38–72 thousand years ago. [39]

In June 2013, a group of researchers announced that they had sequenced the DNA of a 560–780 thousand year old horse, using material extracted from a leg bone found buried in permafrost in Canada's Yukon territory. [40] Before this publication, the oldest nuclear genome that had been successfully sequenced was dated at 110–130 thousand years ago. For comparison, the researchers also sequenced the genomes of a 43,000-year-old Pleistocene horse, a Przewalski's horse, five modern horse breeds, and a donkey. [41] Analysis of differences between these genomes indicated that the last common ancestor of modern horses, donkeys, and zebras existed 4 to 4.5 million years ago. [40] The results also indicated that Przewalski's horse diverged from other modern types of horse about 43,000 years ago, and had never in its evolutionary history been domesticated. [27]

A new analysis in 2018 involved genomic sequencing of ancient DNA from mid-fourth-millennium B.C.E. Botai domestic horses, as well as domestic horses from more recent archaeological sites, and comparison of these genomes with those of modern domestic and Przewalski's horses. The study revealed that Przewalski's horses not only belong to the same genetic lineage as those from the Botai culture, but were the feral descendants of these ancient domestic animals, rather than representing a surviving population of never-domesticated horses. [42] The Botai horses were found to have made only negligible genetic contribution to any of the other ancient or modern domestic horses studied, which must then have arisen from an independent domestication involving a different wild horse population. [42]

The karyotype of Przewalski's horse differs from that of the domestic horse by an extra chromosome pair because of the fission of domestic horse chromosome 5 to produce the Przewalski's horse chromosomes 23 and 24. In comparison, the chromosomal differences between domestic horses and zebras include numerous translocations, fusions, inversions and centromere repositioning. [43] This gives Przewalski's horse the highest diploid chromosome number among all equine species. They can interbreed with the domestic horse and produce fertile offspring (65 chromosomes). [44]

Pleistocene extinctions Edit

Digs in western Canada have unearthed clear evidence horses existed in North America until about 12,000 years ago. [45] However, all Equidae in North America ultimately became extinct. The causes of this extinction (simultaneous with the extinctions of a variety of other American megafauna) have been a matter of debate. Given the suddenness of the event and because these mammals had been flourishing for millions of years previously, something quite unusual must have happened. The first main hypothesis attributes extinction to climate change. For example, in Alaska, beginning approximately 12,500 years ago, the grasses characteristic of a steppe ecosystem gave way to shrub tundra, which was covered with unpalatable plants. [46] [47] The other hypothesis suggests extinction was linked to overexploitation by newly arrived humans of naive prey that were not habituated to their hunting methods. The extinctions were roughly simultaneous with the end of the most recent glacial advance and the appearance of the big game-hunting Clovis culture. [48] [49] Several studies have indicated humans probably arrived in Alaska at the same time or shortly before the local extinction of horses. [49] [50] [51] Additionally, it has been proposed that the steppe-tundra vegetation transition in Beringia may have been a consequence, rather than a cause, of the extinction of megafaunal grazers. [52]

In Eurasia, horse fossils began occurring frequently again in archaeological sites in Kazakhstan and the southern Ukraine about 6,000 years ago. [31] From then on, domesticated horses, as well as the knowledge of capturing, taming, and rearing horses, probably spread relatively quickly, with wild mares from several wild populations being incorporated en route. [32] [53]

Return to the Americas Edit

Horses only returned to the Americas with Christopher Columbus in 1493. These were Iberian horses first brought to Hispaniola and later to Panama, Mexico, Brazil, Peru, Argentina, and, in 1538, Florida. [54] The first horses to return to the main continent were 16 specifically identified [ clarification needed ] horses brought by Hernán Cortés. Subsequent explorers, such as Coronado and De Soto, brought ever-larger numbers, some from Spain and others from breeding establishments set up by the Spanish in the Caribbean. Later, as Spanish missions were founded on the mainland, horses would eventually be lost or stolen, and proliferated into large herds of feral horses that became known as mustangs. [55]

The indigenous peoples of the Americas did not have a specific word for horses, and came to refer to them in various languages as a type of dog or deer (in one case, "elk-dog", in other cases "big dog" or "seven dogs", referring to the weight each animal could pull). [56]

Toes Edit

The ancestors of the horse came to walk only on the end of the third toe and both side (second and fourth) "toes". Skeletal remnants show obvious wear on the back of both sides of metacarpal and metatarsal bones, commonly called the "splint bones". They are the remnants of the second and the fourth toes. Modern horses retain the splint bones they are often believed to be useless attachments, but they in fact play an important role in supporting the carpal joints (front knees) and even the tarsal joints (hocks).

A 2018 study has found remnants of the remaining digits in the horse's hoof, suggesting a retention of all five digits (albeit in a "hourglass" arrangement where metacarpals/tarsals are present proximally and phalanges distally). [57]

Teeth Edit

Throughout the phylogenetic development, the teeth of the horse underwent significant changes. The type of the original omnivorous teeth with short, "bumpy" molars, with which the prime members of the evolutionary line distinguished themselves, gradually changed into the teeth common to herbivorous mammals. They became long (as much as 100 mm), roughly cubical molars equipped with flat grinding surfaces. In conjunction with the teeth, during the horse's evolution, the elongation of the facial part of the skull is apparent, and can also be observed in the backward-set eyeholes. In addition, the relatively short neck of the equine ancestors became longer, with equal elongation of the legs. Finally, the size of the body grew as well. [ citation needed ]

Coat color Edit

The ancestral coat color of E. ferus was possibly a uniform dun, consistent with modern populations of Przewalski's horses. Pre-domestication variants including black and spotted have been inferred from cave wall paintings and confirmed by genomic analysis. [58] Domestication may have also led to more varieties of coat colors. [59]


Acknowledgements

We thank Masaaki Kimura and Yasunori Hagino for assistance with the collection and identification of myriapod samples. We also thank Katsumi Miyazaki for collecting the chelicerate, Ammothella biunguiculata and the Oda Laboratory at JT Biohistory Research Hall (BRH) for providing the arachnid, Parasteatoda tepidariorum. We are also grateful to Takashi Miyata and all of the members of the Su Laboratory at BRH for their helpful comments. This work was supported in part by a grant from JSPS KAKENHI (No. 24570121).


MITES

      (Trombiculidae)
      • common chigger, Trombicula alfreddugesi (Oudemans)
        • Trombicula splendens Ewing
        • Trombicula lipovskyana (Wolfenbarger)
        • Trombicula belkini Gould
        • Trombicula batatas (L.)

        Mites (order Acarina) are very small arthropods, with head and thorax fused into a cephalothorax. They have sucking mouthparts, no antennae, and those of interest as household pests have 4 pairs of legs as adults. Although most of these species have only 3 pairs of legs in the first (larval) stage after hatching from the egg, they gain a fourth pair in the second (nymphal) stage. The life cycle generally consists of the egg, larval stage, one or more nymphal instars or stages, and an adult stage. The life cycle usually requires only 2 or 3 weeks, and results in rapid increase and huge populations of mites under favorable conditions. A thorough discussion on the morphology and development of the free-living mites, on their role as parasites of animals and plants, and as vectors of disease, may be found in Mites, or the Acari by T. E. Hughes (1959).

        Chiggers (Trombiculidae)

        Chiggers or "red bugs," called "harvest mites" in Europe, are.the larvae of mites belonging to the suborder Trombidiformes, which are worldwide in distribution. There are over 200 families of mites, but the family to which chiggers belong (Trombiculidae) contains about 10% of all mite species (Sasa, 1961). Some species attack humans and cause a dermatitis (trombidiosis). The red welts and severe itching do not appear until several hours or even a day after exposure therefore, it is difficult to know exactly when or where the infestation occurred. Several chiggers transmit a rickettsial disease called "scrub typhus" or "tsutsugamushi disease" in the Orient and various areas of the Pacific.

        Description. The members of the suborder Trombidiformes are characterized by the respiratory system, when present, opening in the region of the gnathosoma, the portion of the body bearing the mouth and its appendages. Chiggers are very small, 150 to 300 microns (0.15 to 0.3 mm) long when unengorged, and are red to pale yellow or white, depending on the species. Like all mite larvae, they have 6 legs. They are parasitic, but later stages are free-living, 8-legged mites. Only the larvae are harmful and only they are correctly referred to as "chiggers." The adults are bright red, hairy, or granular (Michener, 1946 Wharton and Fuller, 1952 Baker et al., 1956). The various stages of the trombiculid mites in general are adequately represented by figure 309 , which shows an unengorged and engorged larva, a nymph, and an adult of Trombicula batatas (L.).

        Common chigger, Trombicula alfreddugesi (Oudemans)

        In the Western Hemisphere, this is the most common and widespread species, ranging from Canada to South America and the West Indies. Trombicula alfreddugesi parasitizes many species of mammals, birds, reptiles, and amphibians, as well as man. On humans, chiggers tend to congregate in areas constricted by clothing, such as ankles, crotch, waistline, and armpits. It is unfortunate that when chiggers attach to humans they are not noticed for some time, for they are easily removed. According to Baker et al. (1956):
        Itching is usually noted 3 to 6 hours after the chiggers have attached, and may persist for as long as 2 weeks. Part of the irritation is thought to be an allergic response to the salivary secretions of the mite. A papule forms at the site of attachment which may develop into a vesicle. Scratching usually removes the offending mite but, if repeated often enough, may result in an infection.

        In some regions, this mite is a.pest of chickens and turkeys, affecting the younger birds most seriously. When heavily parasitized, the birds become droopy, refuse to feed, and may eventually die from starvation and exhaustion (Baker et al., 1956). A much more important chigger pest of chickens and turkeys, however, is Neoschongastia americana (Hirst), which ranges across the southern United States from California to Georgia, but does not attack man (Kunz et al., 1969).

        Description. Chigger larvae are 0.15 to 0.25 mm long before engorgement, and are red to reddish orange, rarely white. Their mouthparts include 2 pairs of grasping palps provided with forked claws. The nymphs are much more hirsute than the larvae. The body is constricted behind the second pair of legs, giving them and the adults the characteristic shape of trombiculid mites shown in figure 309 . The adults are much larger than the nymphs, and are even more hirsute. They are 0.9 to 1.1 mm long, and brilliant red (Jenkins, 1949 Baker et al., 1956).

        Life Cycle. The spherical eggs, approximately 0.1 to 0.2 mm in diameter, are usually laid in the soil. The larva crawls about on the surface of the soil until it finds a suitable vertebrate host. It attaches to the host by means of its chelicerae and sucks blood, but as a rule does not burrow under the skin. Engorgement usually takes about 3 days. The larva then drops, enters the soil, and changes, via the nymphochrysalis, to the nymphal stage. The nymphs probably feed on the eggs and young instars of small arthropods. The adult emerges from a dorsal split in the imagochrysalis and nymphal cuticle (Baker et al., 1956).

        The life cycle may require 2 to 12 months or longer, depending on the temperature. There may be 1 to 3 generations per year in temperate climatic zones, but reproduction may be continuous throughout the year in warmer regions, with as many as 6 generations. Females kept at suitable temperatures and supplied with water and food were observed to live more than a year and to produce larvae throughout that period. The time when chiggers are active varies from 2 months in Minnesota and Massachusetts to the entire year in southern Florida. Chiggers are most abundant during rainy spells in the area from Kansas to Texas, and may disappear during hot, dry weather (Jenkins, 1948).

        Trombicula splendens Ewing is a related species in the eastern United States. It prefers moister habitats, such as swamps and rotten logs or stumps. It is one of the most common causes of trombidiosis in the southeastern states.

        Trombicula lipovskyana (Wolfenbarger) may be found in similar places in Tennessee, Kansas, Oklahoma, and Arkansas.

        Trombicula belkini Gould is widely distributed in California, and has also been collected in Utah. Reptiles seem to be its favored hosts, but it also infests rodents and ground birds. It sometimes annoys humans and their pets (CEIR, 1960). This species is closely related to T. alfreddugesi, but the larvae lack nude, whiplike setae on the tarsus of leg II (Baker et al., 1956 Gould, 1956).

        Trombicula batatas (L.) ( figure 309 ) is common in Central and South America, the state of Puebla, Mexico, and has been reported from the southeastern United States (Michener, 1946 Jenkins, 1948). It has been collected on humans and many domestic and wild animals. One 12-year-old boy had 138 attached larvae (Michener, 1946). It has been reported to attack humans in the San Joaquin Valley of California (Doetschman and Furman, 1949).

        Gould (1956) published an extensive monographic study of the larval trombiculid mites of California.

        Favored Habitats. Chiggers are most abundant in areas that support thickets or scrub-type vegetation and where the ground is undisturbed, supporting many rabbits, other rodents, and various small host animals. They are generally eliminated automatically by habitat destruction in areas that are heavily populated or intensively farmed. In new urban subdivisions, however, chiggers may persist in lawns for several years. To determine the exact area of chigger infestation, a piece of black cardboard can be placed edgewise on the ground where an infestation is suspected. If chiggers are present, the tiny yellow or pink larvae will crawl rapidly over the cardboard and accumulate on the upper edge. Chiggers can also be easily detected on black, polished shoes (USDA, 1963). Jenkins (1948) suggested the possibility that chiggers might be of value in decreasing mosquito populations. The adults were often abundant in depressions in the ground which had become temporary pools containing Aedes and Psorophora larvae in the spring. Mosquito eggs laid in such depressions probably were serving as food for Trombicula adults.

        Repellents. In areas where chiggers are known to be a problem, the avoidance of their favored habitats is, of course, a way of minimizing infestation. Protective clothing and repellents are recommended as already described for protection against mosquitoes and ticks. If infested, a thorough soapy bath as soon as possible is a highly effective treatment. Repeat the lathering and rinsing several times. Most of the chiggers, attached or unattached, will be killed.

        Among the best repellents for chiggers are those containing diethyl toluamide (OFF), ethyl hexanediol (6-12), and dimethyl phthalate, applied to the skin and clothing around the ankles, waist, and armpits. To apply dusting sulfur to skin and clothing is an old but effective method of preventing chiggers. Repellents should be applied particularly to the legs, ankles, cuffs, waist, and sleeves. Some relief from itching can be obtained by applying a solution of 5% benzocaine, 2% methyl salicylate, 0.5% salicylic acid, 73% ethyl alcohol, and 19.5% water. This can be prepared by a druggist. It may be applied to each welt with a piece of cotton. Each treatment gives relief for an hour or more (USDA, 1963).

        Control. Good control of chiggers in the field can be obtained for 1 or 2 months with toxaphene at 2 lb (0.91 kg) or lindane at 0.25 lb (0.11 kg) of actual toxicant per acre, preferably as emulsions. The amount of water used as a carrier of such quantities depends, of course, on the type of spray equipment available. A given quantity of insecticide can be used with either a large or small quantity of water, as long as the toxicant is thoroughly and uniformly distributed. The following quantities (stated as emulsifiable concentrates) of 4 insecticides that are effective against chiggers as well as insects have been recommended (Anonymous, 1970d).

        Insecticide and formulation For 1,000 sq ft (93 sq m) For 1 acre (0.405 ha)
        Chlordane 45% 10 tsp (50 cc) 3 pt (1,440 cc)
        Toxaphene 60% 7 tsp (35 cc) 2 pt (960 cc)
        Diazinon 25% 0.5 pt (240 cc) 2.50 gal (9.50 1)
        Malathion 57% 0.5 pt (240 cc) 2.50 gal (9.50 1)

        A convenient way to treat 1,000 sq ft (93 sq m) of lawn would be to mix any one of the formulations shown in the table with 3 gal (11 L) of water, but if weeds or tall grass were present, the same quantities of insecticide could be more effectively applied in 6 gal (22 L) of water. To spray an acre (0.405 ha), at least 25 gal (95 L) of water are required. Malathion treatments may need to be repeated because malathion is nonpersistent. There are also dust formulations of these insecticides that can be used effectively for chigger control. (Consult appropriate authorities about pesticides currently authorized.)

        Straw itch mite, Pyemotes ventricosus (Newport) (Pyemotidae)

        This extremely small mite, almost invisible to the unaided eye, is primarily a parasite of certain insects, including 3 moths, 10 beetles, 4 wasps and bees, a bug, a fly, and a termite. Some of these host insects infest straw, wheat, stored food products, straw mattresses, and wood, and are therefore found in the home. The straw itch mite has also been called "grain itch," "hay itch," and "straw mattress" mite. Humans can become infested, with resulting dermatitis, by coming in contact with materials such as straw, hay, grasses, grains, and even beans, peas, cottonseed, tobacco, and broomcorn that have been infested with insect larvae upon which the mites feed. These mites also attack horses, cattle, and possibly other mammals (Goldberger and Schamberg, 1909 Baker et al., 1956 A. M. Hughes, 1961 Fine and Scott, 1963, 1965 Scott and Fine, 1963, 1964, 1967 Butler, 1972).

        Description. The female is an almost microscopically small,. elongate mite ( figure 310 ), 0.22 mm long and white to yellow in color. When gravid, she becomes greatly distended behind the fourth pair of legs, and attains a length of up to 2 mm. Her abdomen shows traces of lateral segmentation, and she has clublike hair between the first and second pairs of legs. The male is only 0.16 mm long, but is wider than the female.

        Life Cycle. This mite has a strange and unusual biology. The males wander continuously over the distended body of the pregnant female, feeding on it parasitically. The large eggs hatch, and 206 to 300 mites develop to adulthood within the female's enlarged abdomen. They are extruded at the rate of about 50 per day. Only some 3% are males, but they emerge first and remain clustered around the genital opening. With the aid of their hind legs, they drag the females through the opening, even though they can emerge unassisted, and copulation takes place immediately. The females then search for hosts. Only 6 to 10 days are required from the time of fertilization to the hatching of eggs. The mites are active during the warmer months of the year at 80 °F (27 °C) or above (Baker et al., 1956 Scott and Fine, 1963).

        Distribution of Bites. The bites of straw itch mites are characteristically distributed almost exclusively on clothed portions of the body, although they occur rarely on other areas, with the exceptions of the palms, soles, and mucous membranes. There is no tendency for the mites to be grouped, although this sometimes occurs fortuitously. A person may feel a prickling sensation at the time of the bite, but otherwise no immediate reaction seems to occur. The period between the time of the bite and the delayed reaction has been variously reported as 10 to 16, 16, 27, and 17 to 28 hours (Fine and Scott, 1965).

        Straw Itch Mite Dermatitis. A considerable number of epidemics of dermatitis have been traced to infestation by Pyemotes ventricosus. Since many such outbreaks have not been recorded or correctly diagnosed, it is likely that this ailment is more common than is generally realized. Straw itch mite dermatitis is usually associated with sleeping on straw mattresses, harvesting grain, or otherwise handling or coming in contact with grain, straw, hay or other substances such as those just mentioned. The possibility of infestation is particularly strong if there are large numbers of the mites' host insects present, such as the Angoumois grain moth (Sitotroga cerealella) and the wheat jointworm (Harmolita tritici). The host insect need not necessarily be a species associated with hay or grain. For example, cases of straw itch mite dermatitis have been associated with severe infestations of furniture beetles (Anobium punctatum) in the floor joists of houses. The recurrence of such cases during the same season for 3 successive years led investigators to conclude that the mites migrated in search of new hosts as the adult beetles emerged and left the wood. The mites apparently were not able to penetrate the thick exoskeletons of the beetles when the latter were in the pupal and adult stages, and therefore they left and sought new hosts. In one house, the mites were controlled by treating the floors with 2% deodorized malathion emulsion (Fine and Scott, 1963, 1965 Scott and Fine, 1963).

        Treatment and Prevention. The treatment of symptoms is not the solution to the problem. Either a person must avoid infested areas, or the mites and their host insects must be eliminated.

        Tropical rat mite, Ornithonyssus bacoti (Hirst) (Macronyssidae)

        The tropical rat mite commonly occurs on rats throughout the world, particularly in tropical and subtropical regions, but also in some temperate areas. It is an ectoparasite of rats, and attacks people living in rat-infested buildings. Its bite may cause irritation and sometimes painful dermatitis. It is an important pest of laboratory animals, particularly rats, mice, and hamsters, sometimes deteriorating their health or even causing death by exsanguination (Baker et al., 1956).

        When rats occur in a house, their fecal pellets may be found in the attic, and can often be seen from the crawl hole. When rats are killed, the mites leave their bodies and may travel great distances, particularly along the heating pipes in the walls, for when they are not engorged with blood they are very active. When searching for mite infestations, a flashlight should be used and warm areas such as those near hot-water and steam pipes should be examined with particular care.

        Description. The tropical rat mite is gray to pale yellowish gray, changing to red or black when engorged with blood ( figure 311 , inset). The females vary in length from about 1.15 mm when unfed to 1.41 mm when engorged. The males are about two-thirds as long as the females. A useful taxonomic character is the single dorsal plate, which is relatively narrow and does not cover the entire dorsal surface, even in specimens that have not fed. The dorsal plate bears pairs of long setae, more numerous on the anterior half and in most specimens with only 6 or 7 pairs on the posterior half (Skaliy and Hayes, 1949 Baker et al., 1956).

        Life Cycle. After the adult female engorges, her first eggs may be laid within 2 days at ordinary temperatures (68 to 72 °F 20 to 22 °C). They are deposited on debris in rat nests and burrows, but apparently not on the rats themselves. They hatch in about 36 hours. The larvae do not feed, and within a day they molt to enter the first nymphal stage, the protonymph. The protonymphs attach to a host and obtain a blood meal before dropping off and molting to become deutonymphs. In this stage they do not feed, but in 24 to 36 hours molt to become adult males or females. They mate and engorge within 3 days. Unfertilized females reproduce parthenogenetically. Four or 5 blood meals are required for the completion of the entire life cycle. The life of an adult female was found to average 61.9 days the number of eggs laid, 98.8 and the life cycle from egg to egg, 10 to 12 days (Sheimire and Dove, 1931 Bertram et al., 1946 Baker et al., 1956).

        Tropical Rat Mite Dermatitis. When the mites are abundant, they may be found anywhere in the house, and both nymphs and adults may attack people. Their bites produce irritation, and sometimes a painful dermatitis will continue for 2 or 3 days, leaving red spots on the infested areas ( figure 311 ). Scratching may result in secondary infections.

        Within some households certain individuals are affected while others are not. Sometimes, much time and money will be spent on ineffective medication and it is usually difficult for the infested person to obtain a correct diagnosis. This acariasis cannot be distinguished from flea bites, and is sometimes misidentified as scabies.

        Control. The complete control of rats would, of course, eventually result in the elimination of tropical rat mites from infested premises. However, rat control often proves to be difficult, and "ratproofing" an attic may also be difficult and very expensive. It should also be borne in mind that trapping or otherwise killing rats may increase the attacks on the inhabitants of the house for a time because of the suddenly increased number of mites that leave the bodies of the dead rats. Unfed protonymphs have been observed to survive for as long a period as 43 days without food (Sudd, 1952).

        Acaricides that depend on toxic action lose their toxicity too rapidly, particularly in the high summer temperatures of an attic. Reinfestation may then occur. HCN gas fumigation has been used successfully, but it is expensive and leaves no residue.

        The successful results of a fluorinated silica aerogel dust, blown into attics for the prevention of drywood termites (Incisitermes minor) suggested a similar use of this material for the control of the tropical rat mite (Ebeling, 1960). In 5 infested houses and 1 2-story apartment house, in each of which 1 or more inhabitants had been attacked by rat mites for prolonged periods, the silica aerogel Dri-die 67 was blown into the attic at the rate of 1 lb to 1,000 sq ft (0.45 kg to 93 sq m) of attic area. For 4 of the houses, the dust was also blown into the crawl space under the house at the same rate (for floor space) as that for the attic area. An electric duster with a 1-gal (4-L) hopper was used to apply the dust. In the attic, the dust was applied entirely from the crawl hole, and under the house, from 1 or 2 crawl holes or a larger number of foundation vents. Since in all cases the mites were already distributed throughout the dwelling, some dust was applied with a small bellows hand duster under mattresses, on the spring supports of beds, along the edges and in the 4 corners of bed frames, into the junctures of seats and back or arm rests and under the pillows of sofas and lounges, under furniture and other out-of-the way places, and in a few spots along the floor boards and ceiling moldings.

        The decision to make use of Dri-die 67 dust was made in an effort to bring about the immediate cessation of mite attacks. Principal reliance was placed on the dusting of the attic for longterm control.

        Rat mites may live as long as 63 days with no food (Scott, 1949), so those not coming into contact with the dust may continue to infest the inhabitants of a house. In all the buildings treated, severe infestations had been experienced up to the date of treatment, but ceased immediately afterward, and were never resumed except in 1 house where the housewife received a few more bites after treatment. In this instance, she applied more dust behind the electric outlet plates and various other areas that had not been covered the first time. Control was soon obtained, and no reinfestation occurred. Conventional liquid acaricides could have been applied in the living spaces of the treated houses, for people usually try to avoid leaving an unsightly residue. However, dusting is appropriate in attics, wall voids, and other inconspicuous areas. The dusting should be done before rat control is attempted, so that mites leaving the bodies of dead rats will contact the dust and will not be able to reach the living space and infest its occupants.

        House mouse mite, Liponyssoides sanguineus (Hirst) (= Allodermanyssus) (Macronyssidae)

        This mite occurs in northern Africa, Asia, Europe, and the United States. Although the house mouse (Mus musculus) is its preferred host, it will also feed on rats and other rodents. The house mouse mite attacks man, and causes a dermatitis in about the same way as does the tropical rat mite.

        Importantly, there is also considerable circumstantial evidence that it can transmit rickettsial pox, caused by Rickettsia akari (Baker et al., 1956).

        Description. Unengorged mites are 0.65 to 0.75 mm long, and engorged females may reach a length of 1 mm or more. Their color may range from red to blackish, depending on how recently blood meals have been taken they cause the mites to appear black. This species has 2 dorsal plates on the adult female, but even on unengorged specimens, the plates do not cover the entire dorsal surface. The anterior plate on the dorsum is 10 times larger than the posterior plate, and bears several pairs of setae, whereas the posterior plate bears only 1 pair. The chelicerae are long and whiplike (Baker et al., 1956).

        Life Cycle. As with most macronyssid mites, there is an egg, larva, protonymph, deutonymph, and adult stage. Unlike the tropical rat mite, both protonymph and deutonymph require blood meals.

        The life cycle occupies 17 to 23 days, and unfed females have been observed to live as long as 51 days. The adult mite leaves its host after feeding, and may be found crawling about in mouse nests, runways, or on the walls and ceilings of infested buildings (Baker et al., 1956).

        Control. Control measures are the same as for the tropical rat mite.

        Northern fowl mite, Ornithonyssus sylviarum (Canestrini and Fanzago) (Macronyssidae)

        This species ( figure 312 ) is an ectoparasite of domestic fowls and many wild birds, but in the absence of bird hosts it will sometimes attack humans, causing an itch. It is similar to the tropical rat mite in appearance and life cycle. It can become a household pest when birds build nests under eaves of a house or in the attic. For control, these nests should be removed. Otherwise, treatment is the same as that recommended for control of the tropical rat mite.

        Chicken mite, Dermanyssus gallinae (De Geer) (Dermanyssidae)

        This cosmopolitan species is a pest of poultry and wild birds. Poultry roosts or bird nests can be sources of home infestations, and the human occupants can also be infested. The bite of this mite causes painful skin irritation. Unfed adult mites are about 0.75 mm long and nearly white ( figure312 ). After a blood meal, they may become 1 mm long and bright red. The female oviposits in crevices or under debris in chickenhouses or bird nests. Under favorable conditions, the entire life cycle may require only 7 days. The adults can survive without blood meals for 4 or 5 months (Baker et al., 1956). Chicken mites have been controlled by spraying the chickenhouse with l% malathion or by dusting infested litter with 2%, malathion dust at the rate of 1 lb to 20 sq ft (0.45 kg to 1.85 sq m) (Furman et al., 1955).

        Human itch mite, Sarcoptes scabiei var. hominis (Hering) (Sarcoptidae)

        Different varieties of Sarcoptes scabiei (De Geer) are believed to be specific for different mammals, including man and a large variety of domestic and wild animals, but are transferable from one host to another. The variety specific to man is generally referred to as the "itch" or "scab" mite, and acariasis caused by it is sometimes called "scabies." People are most likely to become infested when living in continually crowded quarters, such as slums or jails, or during periods of major calamities that result in prolonged overcrowding.

        The human itch mite has a legitimate claim to fame in the history of biology. The original description of the life cycle and habits of this mite and the proof that it was the cause of scabies were accomplished by the Italian pharmacist Diacinto Cestoni and the relatively obscure young physician Giovan Cosino Bonomo. This was in the seventeenth century, when endo- and ectoparasites were usually considered to be produced by spontaneous generation. The observations made by Cestoni and Bonomo became generally known through a letter written by Bonomo to Francesco Redi (1626-1697), an experimental entomologist best known as a debunker of the "spontaneous generation" myth. The letter was reproduced in facsimile by Lane (1928). It has been described as "the birth certificate of parasitology" (Sadun, 1969).

        Buxton (1921a) made a detailed study of the external anatomy of the equine itch mite, Sarcoptes scabiei var. equi (Gerlach, 1857). A subsequent study of the anatomy of the human itch mite, Sarcoptes scabiei De Geer, 1778, var. hominis (Hering, 1880), revealed certain minute differences in scales and spines, but these differences were not constant and measurements overlapped. Buxton (1921 b) concluded that it was convenient to regard the 2 forms as varieties, but that this was more justifiable on physiological than on morphological grounds. For practical purposes, Buxton's (1921a) drawings and descriptions of the variety equi serve for the variety hominis. Heilesen (1946) made a detailed study of the anatomy of all stages of hominis, as well as an investigation of the biology of the species scabiei.

        Description. Itch mites ( figure 313 ) are broadly oval, somewhat hemispherical, and so small that even the adults are barely visible to the unaided eye. Adult females are 0.33 to 0.45 mm long, and the males, 0.20 to 0.24 mm. The mites are a translucent, dirty-white color, with the more highly chitinized portions brownish. The integument is finely striate over most of its surface. In living specimens, the body is seen to be divided into 2 regions by a fold in the integument the posterior portion bears the last 2 pairs of the 4 pairs of very short legs. The last 2 pairs of legs do not extend as far as the margins of the body. The anterior 2 pairs of legs on females and all but the third pair on males are provided with delicate, stalked, terminal suction pads. In the females the posterior 2 pairs of legs, and in the males the third pair, terminate in bristles. The adults lack eyes and many special respiratory organs. Characteristic spines and bristles on the dorsal surface aid in identifying the species. The spines are directed backward, and may serve to anchor the mite in position when it is digging burrows in the skin (Munro, 1919 Buxton, 1941b Hand, 1946 Heilesen, 1946).

        Life Cycle. Both sexes and all stages of the itch mite tend to burrow into the skin immediately when placed on it, but the nymphs and males make only small, temporary holes, and move about frequently. The largest and longest burrows are made by the egg-laying female. The female always burrows in folds of the skin, preferring the deeper furrows and cracks. She can be induced to enter when a fine scratch has been made with a needle in the surface of the skin. She may also place herself in the acute angle between a sloping hair and the surface of the skin to gain support for initiating the burrowing (Heilesen, 1946). The winding burrow may reach a length of 5 to 15 mm. It is excavated in the deeper part of the horny epidermal layer, rarely as far as the granular layers (Buxton, 1941b Heilesen, 1946).

        Munro (1919) believed that, if undisturbed, the female would lay all her eggs in 1 burrow ( figure 313 ). A second mating does not take place she dies in the burrow. It appears from the observations of various authors that the adult life of the mite is from 2 to as many as 6 weeks. It is difficult to determine the number of eggs laid by a female in her lifetime, but it is usually estimated to be between 40 and 50. Munro also observed that the period between the beginning of burrow formation and the finding of the first larva varied from 71 to 78 hours. He also found that 9 eggs removed from burrows and kept at 29 °to 30 °C (about 85 °F) hatched in 68 to 80 (average 74) hours. He gave the following numbers of days for the duration of the various life stages of the female: egg, 2.5 to 3.5 larva, 1.5 to 3 first nymph, 1.5 to 2.5 and second nymph, 2 to 4. He concluded that the life cycle required from 9 to 15 days. The numbers of days for the various life stages of the female, as determined by Heilesen (1946), were as follows: egg, 3 to 4 larva, 3 first nymph, 3 to 4 second nymph, 3 to 4 and from copulation to oviposition, 2 a total of 14 to 17 days. The developmental period for the male was only 9 to 11 days. The male has only 1 nymphal stage, whereas 2 are recognized in the female. In the second nymphal stage, the female can be fertilized by the male, even though the orifice (tocoptome) by which the eggs are laid has not yet been formed (Warburton, 1920).

        Means of Transmission. The ease of transmission of body lice via infested clothing and bedding has led many people to assume that itch mites could be transmitted in the same way. An important difference, however, is that body lice live on their host's clothes and contact his body only to feed, whereas itch mites spend most of their lives beneath the host's skin. In experiments with 63 male volunteers, in none of 31 men were itch mites transferred via blankets previously used by infested men, and in only 2 cases out of 32 were mites transmitted when uninfested men used underclothing immediately after it had been used by infested men (Mellanby, 1941). Merely putting clothing away for 2 or 3 days at ordinary room temperature should be sufficient to rid it of mites. Two persons in a bed gave the greatest opportunity for the spread of itch mites. However, transmission is also possible through "dancing, flirtation, and ordinary intimate contact between members of a family" (Heilesen, 1946).

        Body Regions Infested. Munro (1919) observed the burrowing procedures of egg-bearing females. The suckers of a female's anterior pair of legs were fixed onto the skin, and she propped her body up with the bristles on her posterior pair, assuming an almost perpendicular position. With her chelate mouthparts she commenced to cut the skin and bore in, becoming completely concealed in as little as 2.5 minutes. (This was a much shorter period than the one recorded by Heilesen, who found that 6 adult females burrowed into his skin in 15 to 40 minutes.) She ceased burrowing at a low temperature or when the body of her host was cold, and recommenced with a slight rise in temperature or warming of the body. Munro was able to activate burrowing of female mites in his wrist by passing from a cold room to a warm one, and was able to regulate the rate of burrowing by alternately warming and cooling an infested wrist over a radiator or other source of heat. He observed that under normal conditions, the burrowing period corresponded more or less to the time spent in bed. He stated:
        The parts of the body selected by the ovigerous female are the interdigital spaces the wrists and the ulnar margins of the wrists the elbows and the anterior folds of the axillae the penis, scrotum, and buttocks the back of the knee and the ankles and toes. In young children, the egg burrows may occur on any part of the body, and in women, the undersides of the breasts are very commonly selected.

        Localization of Infestation. In an examination of 886 soldiers, 9,978 adult female mites were found and removed, an average of slightly over 11 per patient. About 52%, had fewer than 6 mites and only 3.9% had more than 50. One patient had 511. The percentages of mites found in the various areas of the body were: hands and wrists, 63.1 elbows (extensor aspect), 10.9 feet and ankles, 9.2 penis and scrotum, 8.4 buttocks, 4.0 axillae, 2.4 and in the remaining regions of the body, a total of 2 (Johnson and Mellanby, 1942). In another investigation, among 119 women the percentages of mites in various body areas were as follows: hands and wrists (excluding palms), 74.3% palms of hands, 7.5% (none were found on the palms of men) elbows, 5.8 feet and ankles, 8.8 buttocks, 1.1 and in all other areas, 2.5. Among 18 children, itch mites were found to be more uniformly spread over many parts of the body, As indicated by Munro (1919), with many mites on their ankles and feet (Hartley and Mellanby, 1944).

        Active stages of mites confined in cells on parts of the body other than the foregoing will burrow into these parts, but if the cells are removed, they will leave them for the nearest sites usually selected. When Munro confined female mites on his forearm, they always burrowed into his skin enough for concealment, but left these burrows and were recovered on the wrist in from 20 minutes to 2.5 hours.

        Symptoms of Infestation. Whereas in animals large numbers of mites give rise to "sarcoptic mange," in humans relatively small numbers of mites can cause unpleasant symptoms, and the disease is known as "scabies." At a certain stage, the irritation may become so severe that the patient becomes frantic and suffers from lack of sleep. If the infestation is long continued, or if a later infestation occurs, an allergic reaction develops, with intense itching and a redness, or rash of follicular papules over much of the body. The rash may develop on areas such as around the armpits, the wrists, the waist, inside the thighs, and backs of the calves, but these areas do not necessarily coincide with those of mite infestation. The rash may occur over much of the body, even though only a few mites may be present in restricted locations between the fingers (Pratt, 1963). In an investigation of 55 volunteers who had not been infested with itch mites before, Mellanby (1944) observed that during the first month of itch mite infestation, there were few or no symptoms and no erythema. Infested persons might even be unaware that mites were burrowing into their skin.

        Symptoms began to be evident in about a month, and in about 6 weeks the irritation was sufficiently severe to cause some loss of sleep. Then the itching grew progressively worse, and after 100 days it was practically continuous and almost unbearable. However, when secondary infections and impetigo developed, the mite population decreased, and was sometimes completely eliminated. (If secondary infections are neglected, they may themselves require prolonged medical treatment.) When volunteers already infested were treated and then reinfested, intense local irritation was felt within 24 hours, and a patch of erythema surrounded each mite. This apparently caused an adverse environment for the mites, for in another 2 days most of them had disappeared, some scratched out by the patient and others leaving the burrow. Relatively few mites reached maturity when compared with the original infestation.

        Medical Treatment. It is important to diagnose scabies correctly, for neither the irritation nor the liability to skin diseases can cease until the mites have been eliminated. Look for the burrow of a female in such places as between the knuckles and in folds of the wrist and elbow, and then gently prick the burrow open. Toward the end of the burrow, the mite can usually be distinguished as a dull-white spot. Remove it with a needle. A bath before treatment is desirable for hygienic reasons. Thorough treatment is essential, and is best done by a physician or a reliable nurse or orderly. Treatment consists of application of ointments or liquid preparations. Ramsay (1969) prescribed either 25% benzyl benzoate emulsions, Kwell® (1 % lindane) cream or lotion, or Eurax® cream or lotion. The latter contains 10% of crotamiton (N-ethyl-o-crotonotoluide). Ramsay recommended that these preparations be applied in the evening after the patient had taken a warm bath, and that the application be left in place until the next evening, when the treatment would be repeated. All areas of the skin below the neck should be treated, including body folds, palms, and soles. A cleansing bath should be taken 48 hours after the second application. Some tingling of the skin is to be expected after treatment, and it may last as long as 10 to 14 days. Calamine lotion or emulsion may be applied to alleviate this condition. Instructions on the package in which the medication is sold should always be read and followed carefully. Secondary infections may require the skills of a medical doctor or dermatologist. If the treatment is satisfactory and reinfestation occurs, an effort should be made to find untreated persons with whom the patient may have had contact.

        Canine mange mite, Sarcoptes scabiei var. canis Gerlach, on Dogs and Humans

        Sarcoptes scabiei on domestic animals has generally been referred to as a sarcoptic mange mite, and the symptom as "mange" or "scabies." The mite causes a self-limiting but very uncomfortable eruption if the secondary host is human. Man is particularly vulnerable to infestation by the variety of mange mite that infests the dog, probably because of his closer association with that animal than with others.

        Description. This broadly oval mite is very small about the size of the human itch mite. As in the human itch mite, in both sexes the anterior 2 pairs of legs and, in the male, also the fourth pair, have delicate, terminal, stalked suction pads. In the females, the posterior 2 pairs of legs, and in the males the third pair, end in bristles. Characteristic spines and bristles on the dorsal surface aid in identifying the species.

        Life Cycle. The female lays her eggs in burrows she makes in the skin. They hatch in 3 to 5 days, and a complete life cycle requires 8 to 17 days (Smith and Claypoole, 1967).

        Symptoms on Dogs. The eruption begins with small, white or erythematous (reddish, inflamed) papules, initially appearing, in the groin and "armpit" areas and on the periphery of the ears. The papules may become so numerous that they appear to be contiguous, especially on the relatively hairless portions of the body. Crusts form, composed of dried exudates of serum and blood. The skin becomes lichenous, scaly, and corrugated in appearance. The eruption spreads, but is usually most severe on the ears, head, abdomen, and in groin and "armpit" areas. Hair is lost, or can be easily pulled out in patches. The remaining hair becomes dull and lusterless, and the animal develops a characteristic "mousey" odor. Intense generalized itching accompanies the eruption, and if untreated, the animal may become emaciated and even die of exhaustion from the itching and extensive chronic inflammatory reaction, often with a secondary infection. Canine scabies occurs most commonly in undernourished puppies, particularly if they are suffering from internal parasites (Smith and Claypoole, 1967).

        Symptoms on Humans. A rash develops on some persons after only brief contact with an infested dog, but the most severe cases develop in those with prolonged close contact. The eruption is most often in the form of pimples, but may be characterized by blisters and inflammation. There is frequently a sloughing away of the skin. Lesions are most common on the forearms, lower region of the chest, and on the abdomen and thighs, but may be generalized. The distribution of symptoms usually differs from that of human scabies, in that the finger webs and the genitalia are usually not affected, but both these areas may be involved if the infestation is severe. The face is not affected except in children. In view of the facts that (1) the sarcoptic mite can live for 4 to 5 weeks, (2) in no cases have symptoms lasted longer than this, and (3) burrows have not been found in human skin it appears that Sarcoptes scabiei var. canis does not reproduce on human skin, but this could be definitely proved only by prolonged observation on heavily infested human volunteers - an unlikely development (Smith and Claypoole, 1967).

        Control of Mange on Dogs. In mange or scabies control on dogs, advantage has been taken of the fact that male mites do not do any significant boring into the skin, and may be controlled by continuous exposure to toxic vapors. In one experiment, a dichlorvos resin strip (NO-Pest Strip¨) was placed in the bedding inside the doghouse of a beagle, 3 x 1.5 x 2 ft (90 x 45 x 60 cm) in area. Within 2 weeks, the dog's skin, which had been red on the lower half of the body and on the legs from a severe case of sarcoptic mange, lost its redness, and new hair began to appear. The strip was moved to one side of the doghouse, and the dog's condition continued to improve he recovered completely in 6 weeks. Whereas mites were taken from all skin scrapings before treatment, none were taken 6 weeks later. The dog had chewed the edges of the dichlorvos strip, but no ill effect was noted (Whitney, 1969).

        The specialist who conducted this experiment had used dichlorvos resin strips for several years to protect dogs and cats from flies and mosquitoes, and had observed no sarcoptic mange or fleas on 60 beagles and 36 cats that had been kept in kennels and a cat room where the strips had been used.

        Treatment for Scabies or Mange. Both dogs and humans have been effectively treated with "gamma benzene hexachloride cream." Humans were cured with 1 application. The patient should avoid further close contact with the pet until it is cured (Smith and Claypoole, 1967). The old NBIN lotion for a combination treatment for lice and scabies (Eddy, 1946) is still available under the name of Topocide, but may be procured by prescription only.

        Figure Legends

        Figure 303 . Cat flea, Ctenocephalides felis. A, adult B, larvae C, eggs D, larva in cocoon E, pupa in cocoon.

        Figure 304 . The pajaroello, Ornithodoros coriaceus.

        Figure 305 . External morphological features of hard ticks (Ixodidae). A, ventral aspect of capitulum B, dorsal aspect of female C, ventral aspect of male D, leg. (From Pratt and Littig, 1962.)

        Figure 306 . American dog tick, Dermacentor variabilis. A, dorsal aspect of larva B, nymph C, adult male D, adult unengorged female. (From Smith et al., 1946.)

        Figure 307 . Engorged female of the American dog tick, Dermacentor variabilis. (From Smith et al., 1946.)

        Figure 308 . Brown dog tick, Rhipicephalus sanguineus

        Figure 309 . A chigger mite, Trombicula batatas. A, unengorged larva B, engorged larva C, nymph D, ventral view of preadult E, adult. (From Michener, 1946.)

        Figure 310 , Straw itch mite, Pyemotes ventricosus. From left, male female gravid female. (From Fine.and Scott, 1963.)

        Figure 311 . Back and neck of a woman, showing maculae caused by bites of the tropical rat mite, Ornithonyssus bacoti. Inset: Engorged mite. (From Ebeling, 1960.)

        Figure 312 . Northern fowl mite, Ornithonyssus sylviarum (left), and chicken mite, Dermanyssus gallinae.


        Detailed new genome for maize shows the plant has deep resources for continued adaptation

        A new, much more detailed reference genome for maize, or corn, as it is called in the U.S., will be published in Nature. In its accounting of the sequence of DNA letters in the plant's 10 chromosomes, the new version helps us understand as never before why maize, and not some other plant, is today the most productive and widely grown crop in the world.

        Among many other things, the new sequence reveals that maize individuals are much, much less alike at the level of the genome than people are.

        "Our new genome for maize shows how incredibly flexible this plant is, a characteristic that directly follows from the way its genome is organized," says Doreen Ware, Ph.D., of Cold Spring Harbor Laboratory (CSHL) and the U.S. Department of Agriculture, who led scientists at seven academic institutions and several genome technology companies in the project.

        This flexibility not only helps explain why maize has been so successful since its adaptation by agriculturalists thousands of years ago, but also bodes well for its ability to grow in new places as Earth's climate changes, and for increasing the plant's productivity and environmental sustainability in the U.S. and abroad.

        The maize genome is large, but its size is not really what is responsible for what scientists call the plant's "phenotypic plasticity," i.e., the potential range in its ability to adapt. In trying to determine what possibilities are available to a plant when adapting to new or changing conditions, it is just as much the context in which genes are activated -- or silenced -- as the identity of the genes themselves that determines what the total set of genes enables a plant to do, Ware explains.

        It is precisely this context of gene activity -- variations in way the plant's genes are regulated in different individuals across the species -- that the new genome is bringing to light. By assembling a highly accurate and very detailed reference genome for an important maize line called B73, and then comparing it with genome maps for maize individuals from two other lines (W22 and Ki11), grown in different climates, the sequencing team arrived at an astonishing realization.

        "Maize individuals are much, much less alike at the level of the genome than people are, for one thing," Ware says. The genome maps of two people will each match the reference human genome at around 98% of genome positions. Humans are virtually identical, in genome terms. "But we've found that two maize individuals -- from the W22 and Ki11 lines -- each align with our new reference genome for B73 maize only 35%, on average. Their genome organization is incredibly different!"

        This difference between maize individuals is a reflection "not only of changes in the sequence of the genes themselves, but also where and when genes are expressed, and at what levels," explains Yinping Jiao, Ph.D., a postdoctoral researcher in the Ware lab and first author of the paper announcing the new genome.

        It is possible to home in on these variabilities in gene expression in unprecedented detail in the new reference genome sequence. The first reference genome for maize, completed in 2009, was a major milestone, but owing to now outdated technology, it yielded a final genome "text" more akin to a speed-reading version than one fit for close reading, says Ware.

        The 2009 sequence tended to miss two things. So-called first-generation sequencing technology could not solve the great number of repetitive sequences in the maize genome, and tended to miss a significant number of spaces between genes. Because so many tiny pieces had to be stitched together to form a whole, it was particularly hard to accurately capture the many places in maize where DNA letters form long repeating sequences. Repeat sequences are especially important in maize, owing to the particular way its genome evolved over millions of years.

        The new sequence makes use of what biologists call long-read sequencing, which, as the name suggests, assembles a complete genome from many fewer pieces -- about 3,000 as opposed to the over 100,000 smaller pieces it took to build the 2009 reference genome. The new technology is also much cheaper the just completed effort cost around $150,000, compared with more than $35 million for its predecessor.

        Long-read technology, by giving scientists a granular view of the space between genes in maize, sheds revealing light on how those genes are regulated, since regulatory elements are often physically situated in regions just up- or downstream from genes.

        Help for breeders

        "Because of its amazing phenotypic plasticity," concludes Ware, "so many more combinations are available to this plant. What does this mean to breeding? It means we have a very large variation in the regulatory component of most of the plant's genes. They have lots of adaptability beyond what we see them doing now. That has huge implications for growing maize as the population increases and climate undergoes major change in the period immediately ahead of us."

        The new genome's resolution of spaces between genes -- "intergenic" regions -- also makes it possible to read detailed histories from the "texts" of genomes from different maize individuals. "We want to understand how the maize genome evolved," Ware says, "to be able to look at the genome in an individual and have it tell us a story. Why does the expression of a given gene change, and under what circumstances?"

        Consider, for instance, the impact of transposons -- bits of DNA that jump around in genomes. This can now be assessed with specificity not previously possible. Transposons, which are present in all genomes, were first seen and described in maize in the 1940s by CSHL Nobel laureate Barbara McClintock.

        The new reference genome helps scientists understand how the history and structure of the maize genome has been determined by the action of transposons more than in most plants. When they "jump" into a position within a gene, the gene can be compromised entirely. Other times, whether a transposon has hopped into a position just before or after a gene can determine when and how much it is expressed.

        While the phenomenon of "jumping genes" has been understood for decades, its impact in different individuals in various maize lines provides precisely the kind of information that can help explain the plant's evolutionary success.

        The plant's genomic plasticity is also a boon to breeders. "Diversity in maize is the resource base for breeding," says Jiao. "It's the key to making better maize, and more of it, in the future."


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