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How to recognise the type of allele by pedigree analysis diagrams?

How to recognise the type of allele by pedigree analysis diagrams?



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It was said that this interference pattern is due to dominant allele. I fail to see that.
In general how to recognise the type of allele by pedigree analysis diagrams?


This question is a bit broad. You have to understand a lot of concepts to figure out the nature of the allele. I'll just point out some basics:

  1. If an allele is dominant it should affect both males and females equally (not X-linked)
  2. If one of the parents shows the trait (while other does not) then at least one offspring should show the trait (basic Mendelian segregation)
  3. If both parents show the trait and one of the offspring does not then it means that the parents are heterozygous and the allele is dominant.

Advances in the identification and analysis of allele-specific expression

Allele-specific expression (ASE) is essential for normal development and many cellular processes but, if impaired, can result in disease. ASE is a feature of organisms with genomes consisting of more than one set of homologous chromosomes. The higher the number of chromosome sets (ploidy) per cell, the higher the potential complexity of ASE. Humans, for instance, are diploid (except germ cells, which are haploid), resulting in multiple possible expression states in time and space for each set of alleles. ASE is invoked and modulated by both genetic and epigenetic changes, affecting the underlying DNA sequence or chromatin of each allele, respectively. Although numerous methods have been developed to assay ASE, they usually require RNA to be available and are dependent upon genetic polymorphisms (such as single nucleotide polymorphisms (SNPs)) to differentiate between allelic transcripts. The rapid convergence to second-generation sequencing as the method of choice to examine genomic, epigenomic and transcriptomic data enables an integrated and more general approach to define and predict ASE, independent of SNPs. This 'Omni-Seq' approach has the potential to advance our understanding of the biology and pathophysiology of ASE-mediated processes by elucidating subtle combinatorial effects, leading to the accurate delineation of sub-phenotypes with consequential benefit for improved insight into disease etiology.


Study Questions

1. What are some of the modes of inheritance that are consistent with this pedigree?

2. In this pedigree in question 1, the mode of inheritance cannot be determined unamibguously.What are some examples of data (e.g. from other generations) that, if added to the pedigree would help determine the mode of inheritance?

3. For each of the following pedigrees, name the most likely mode of inheritance (AR=autosomal recessive, AD=autosomal dominant, XR=X-linked recessive, XD=X-linked dominant).(These pedigrees were obtained from various external sources).

4. The following pedigree represents a rare, autosomal recessive disease. What are the genotypes of the individuals who are indicated by letters?

5. If individual #1 in the following pedigree is a heterozygote for a rare, AR disease, what is the probability that individual #7 will be affected by the disease? Assume that #2 and the spouses of #3 and #4 are not carriers.

6. You are studying a population in which the frequency of individuals with a recessive homozygous genotype is 1%. Assuming the population is in Hardy-Weinberg equilibrium, calculate:

a) The frequency of the recessive allele.

b) The frequency of dominant allele.

c) The frequency of the heterozygous phenotype.

d) The frequency of the homozygous dominant phenotype.

7. Determine whether the following population is in Hardy-Weinberg equilibrium.

8. Out of 1200 individuals examined, 432 are homozygous dominant (AA)for a particular gene. What numbers of individuals of the other two genotypic classes (Aa, aa) would be expected if the population is in Hardy-Weinberg equilibrium?

9. Propose an explanation for the deviation between the genotypic frequencies calculated in question 8 and those observed in the table in question 7.


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3. Results

(i) Genetic diversity

Figure 1 shows a scatter plot of the gene diversity versus the drift diversities of the birth cohorts. The figure suggests that gene diversity is identical with drift diversity, if squared deviations are used. It is not difficult to show that both notions of genetic diversity are indeed identical, that is,

for any age cohort j. Thus, drift diversities generalize gene diversity. A proof can be found in the Appendix. There it is also shown that the drift diversity DD2(j) would coincide with gene diversity even if another initial frequency is used in definition (2). Figure 1 shows a strong monotone dependency also for d=1. Therefore, further investigations may be based on the notion that is mathematically most tractable.

Fig. 1. Comparison of genetic diversities.

Figure 2 visualizes the development of the gene diversity GD(P t) of the population throughout the entire Kromfohrländer breeding history by using a continuous timescale. The diversity remained almost constant until recognition of the breed in 1955 because most dogs born before recognition had the same parents. Recognition was followed by a sudden drop of gene diversity. Since 1970, the gene diversity was almost constant, except for a small but sustained decline after 1990. However, more important than the gene diversity of the population is the potential gene diversity PD(t) of the population, given by the dashed line in Fig. 2. The strong rise of the potential gene diversity in 1959 was due to an additional founder. It can be seen that nowadays no substantial improvement of gene diversity can be achieved by optimal contributions of the breeding animals. The upper bound BD(t) of Lacy (dotted line) heavily overestimates the scope for improvement since it does not account for the effects of mixing rare and common alleles and it accounts for genetic drift only via the number of different alleles.

Fig. 2. Gene diversity and potential gene diversity of the population.

Fig. 3. Gene diversity and potential gene diversity of the birth cohorts.

Figure 3 shows the development of the gene diversity GD(B t) of the birth cohorts. It can be seen that the small but sustained decrease, that was detected in Figure 2, took place in 1990. The increase of potential diversity PD(t) in 1968 and 1969 resulted from an increased number of birth. The upper bound PD(t) did not increase in 1968 and 1969 since it does not depend on the size of the birth cohorts.

(ii) Distribution of allele frequencies

The distribution of the frequency of a rare neutral allele in the current population depends on the founder from whom the allele originates. The founders of the Kromfohrländer are Peter, Fiffi and Elfe. Their relative contributions to the current population are 0·41, 0·41 and 0·18. The distribution of the frequency of a rare neutral allele that originates from a particular founder is shown in Fig. 4. An allele is eliminated with a probability of round about 50%, no matter from whom the allele originates. The probability of fixation is 0·4% and it is negligible if the allele originates from Elfe. But alleles that originate from Peter or Fiffi have large frequencies with high probability, if not undergone selection until now.

Fig. 4. Distributions of allele frequencies.

(iii) Mating system

Figure 5 shows a scatter plot of the inbreeding coefficients versus the dates of birth for all dogs in the database. The inbreeding coefficients are based on all generations back to the formation of the stud book, which accounts for the high values. Inbreeding coefficients increased until 1985. After that, the mean inbreeding coefficient decreased slightly and the variation of inbreeding coefficients decreased substantially. Nowadays, there exist no dogs with inbreeding coefficients larger than 0·6.

Fig. 5. Development of inbreeding coefficients.

In order to identify the prevalent mating system at a given time, the expectation of the mean frequency of homozygous carriers of a rare neutral allele within the population is compared with its expectation in HWE. The expectations Hom(P t) of the mean frequency of homozygous carriers are given by the continuous line in Fig. 6, whereas the dashed line shows their expectations HomHW(P t) in the case of HWE. Recall that the population consists of all individuals up to an age of 9 years, so that effects of changes in population management can be seen only with a delay. The loss of genetic diversity and the small number of founders account for the increase of homozygous carriers from 1955 to 1965. It is not due to line breeding since the expected frequencies were below their expectations in HWE, which suggests that outbreeding occurred. This outbreeding was due to the additional founder Elfe who had his first litter in 1960. Around 1985, line breeding or inbreeding was the dominating breeding system, since the expected frequencies were larger than their expectations in HWE. But thereafter, it shifted in the direction of outbreeding. Note that the mean fraction of homozygous carriers could be diminished only very little by the shift in the direction of outbreeding.

Fig. 6. Mean frequency of homozygous carriers of a rare neutral allele.

Dogs with inbreeding coefficients larger than 0·6 that were born between 1970 and 1990 were clustered by means of their pedigrees in order to identify the different lines of the Kromfohrländer breed. But only one dog from each litter was included. Closely related individuals belong to the same branch of the clustering tree shown in Fig. 7. It can be seen that there existed three different lines. The first group consists mainly of German smooth coated dogs, the second group consists mainly of German rough-coated dogs and the third group consists of Finnish dogs.

Fig. 7. The lines of the Kromfohrländer.

Table 1 shows the founders and all dogs whose contribution to one of the lines or to the current population is at least 35%. It can be seen that the first line is founded by Alan and Betta vom Weddern. The second group is linebred to Axel van de Poort van Drenthe (contribution 72% to Line 2), and the third line is founded by the Finnish dog Pallas av Ros-Loge (contribution 66% to Line 3). The relatively small contribution of Alan and Pallas to the current population indicate that the Alan-Line (Line 1) and the Pallas-Line (Line 3) are more historical, whereas the current population is dominated by descendants of the Axel-Line (Line 2).

Table 1. Genetic contributions

(iv) Bottlenecks

Two decreases of genetic diversity were detected in Fig. 3. A major decrease is observed between 1955 and 1965 and a minor decrease was in 1990. The Kromfohrländer population was very small for several years after recognition of the breed and several dogs were used extensively for breeding (see Fig. 8 and Table 1). This caused the dramatic loss of genetic diversity between 1955 and 1965, shown in Figs 2 and 3.

Fig. 8. Development of population size.

Axel's contributions to the birth cohorts increased substantially in 1990, which is considered to be the reason for the second decrease. Since a subdivision of the population was suggested by our cluster analysis, relative population sizes and contributions of Axel to birth cohorts were calculated separately for the Finnish subpopulation, for the non-Finnish rough-coated kennels, and for the non-Finnish smooth-coated kennels. A kennel is considered as a smooth-coated kennel, if more litter parents were smooth coated than rough coated. Figure 9 shows that the increased influence of Axel results from a breakdown of the Finnish population, an expansion of the German rough-coated subpopulation, and an export of German dogs to Finland. The reasons were determined by questionnaire from breeders.

The lines were established in the 1970s by mating very closely related individuals (see Table 1). In the 1980s, no German breeder exported dogs to Finland because of strict quarantine legislation. Thus, Finnish breeders could not breed to less related dogs. But problems (e.g. cataract) accumulated due to the fixation of deleterious alleles and breeders did not find enough offspring for breeding. As a consequence, no Finnish breeder had a litter in 1990. After Finland relaxed the strict quarantine legislation in 1988, dogs from the Axel-Line were exported to Finland and had their first litters in 1991. They were mated to the dogs that remained and could re-establish the breed in Finland. Apart from that, the unequal ancestor contributions in the current birth cohorts indicate little gene flow among subpopulations.

(v) Necessary amount of purging due to bottlenecks

We consider three rare, neutral and independent alleles from different genes, one from each founder. Figure 10 shows the scatter plot of the probability of an individual to be not affected by one of these alleles versus the inbreeding coefficient. The probabilities are estimated from 20 000 repetitions by computer simulation for the Kromfohrländer. The function P(F x, 1) from eqn (5) approximates these probabilities very well, if all alleles are recessive. But if the three alleles are dominant, then the dependency is the opposite. Although there exist dominant alleles with incomplete penetrance that cause heritable diseases, e.g. osteosarcoma in Scottish deerhounds (Phillips et al., Reference Phillips, Stephenson, Hauck and Dillberger 2007), the majority of such diseases is caused by recessive alleles. If all deleterious alleles are recessive and if alleles with largest deleteriousness have priority, then the fraction that should be purged is given by eqn (6). Inbreeding coefficients of the Kromfohrländer increased from about F before≔0·25 due to bottlenecks until they reached about F after≔0·5, and thus, the correctness probability from before the bottleneck would be recovered by purging 50% of the deleterious alleles. But note that a better recommendation could, in principle, be derived from disease records. In addition, less purging would be necessary if deleterious alleles with highest frequencies have priority or if some disease alleles are dominant.

Fig. 10. Probability to be not affected.


Diagrams in Anthropology: Lines and Interactions

“Diagramming is the procedure of abstraction when it is not concerned with reducing the world to an aggregate of objects but, quite the opposite, when it is attending to their genesis… extracting the relational-qualitative arc of one occasion of experience and systematically depositing it in the world for the next occasion to find… the activity of formation appearing stilled” (Massumi 2011: 14, 99).

The ongoing use of diagrams in anthropology has its roots in the emergence of the discipline itself. Ever since the work of Malinowski and a number of notable predecessors, diagrams (along with maps) have become a customary feature of ethnographic monographs – with some more standardised and familiar than others. A two-dimensional, often schematic, arrangement of lines drawn to show the organisation, appearance, arrangement, mechanisms or interactions within an area or action of analysis, the diagram has appeared in many different forms.This introductory review focuses first on two particular kinds: those used to convey information regarding kinship, and those depicting different forms of exchange.

Critiques and Challenges

Compared with other practices that rely on the visualisation of ideas and data, and which also operate within an interdisciplinary context, diagrams in anthropology have received less critical scrutiny than, for example, cartography and visual research methods. Photography and film – within Visual Anthropology – have become established forms of both presentation, and of method. They also provide objects of analysis in and of themselves. Interrogating the pitfalls and potential of their display via digital media has led to the development of ‘hypermedia anthropology’ (Pink 2006: xi) – enabling novel combinations of the visual, aural and textual. For some, this counteracts a previous rejection of the ‘visual, sensory and applied’ that coincided with social and cultural anthropology establishing itself as ‘a scientific discipline’ – a rejection of the ‘subjectivity of photography and film’ in favour of adopting ‘visual metaphors such as diagrams, grids and maps to synthesise and objectify knowledge’ (Pink 2006: 8 Grimshaw 2001: 67).Framed this way, diagrams lack the sensory transmission that multimedia forms of presentation seek, in part, to address.

Another critique questions the ‘decontextualisinglinearity’ (Ingold 2000: 140) of diagrams. In this light, the kinship diagram, for example, is seen as a chart that ‘can be taken in at a glance’ and ‘scanned indifferently from any point in any direction’, thus presenting ‘the complete network of kinship relations over several generations… as a totality present in simultaneity’ (Bourdieu 1977: 38, at Ingold 2007: 111). For Ingold, such a ‘snapshot’ resembles ‘the sterile austerity of an electrical circuit board’ – a schematic devoid of human inspiration – even adopting the technical convention of drawing a ‘hump’ where unconnected lines cross one another, echoing the circuit drawing of electrical engineers (Barnes 1967: 122 Ingold 2007: 111).

(Leach 1961, at Ingold 2007 112: Kinship Diagram as Circuit Board): “The lines of the kinship chart join up, they connect, but they are not lifelines or even storylines. It seems that what modern thought has done to place – fixing it to spatial locations – it has also done to people, wrapping their lives into temporal moments” (Ingold 2007: 3).

However, given their innate reliance on the visualisation of data, diagrams also appear to have much to offer the development of forms of ethnographic presentation that challenge, or augment, an exclusive reliance on text. Relationships between the two vary greatly, and critical approaches to cartography raise questions that are equally applicable to diagrams. For example, the idea that they conceal as much as, if not far more than, they reveal, and that any sense of accuracy comes at the cost of minimising complexities inherent in the lives and locales of research. Recognising that maps, as representations, are necessarily selective (Turnbull 2000: 101) leads many, among them Monmonier (1991), to emphasise how all maps ‘tell lies’.

This is not simply because the quest for an ‘accurate’ or ‘precise and comprehensive’ representation of reality raises impossible questions regarding what counts as ‘detail’ and ‘information’ on one hand and what constitutes the infinite, remaining ‘particulars’ on the other, but is because in the cartographic world, all is ‘still and silent’ – as opposed to the world of our experience that is ‘suspended in movement’ (Ingold 2000: 242). Crucially, for the types of diagram under consideration here, this cartographic or diagrammatic world threatens to conceptualise social relations as static social facts rather than as ‘dynamic phenomena,’ offering a particularly empty conception of social life (Kertcher 2006) and envisaging these relations without space to query how they persist or diminish over time (Suitor et al 1997). As we shall see, however, questions around how diagrams are used in anthropology are as numerous as the forms they adopt. Maps of places can be used for guiding and informing our interaction with the world. Diagrams of human relations of different kinds tend not to share such an explicit purpose, however. The role of an exchange diagram, for example – what we might decide it is for – depends very much on the ethnographic material that accompanies it, and which generated it in the first place. In what follows, I present various examples drawn from the anthropological to begin exploring some of these issues and relations.

Bourdieu questioned the origins and meanings of familiar ‘graphic representations of kinship,’ recommending a ‘social history of the genealogical tool’ (Bourdieu 1977: 38, 207) – a task which Mary Bouquet addresses by highlighting affinities between ‘European iconographical tradition’ in ’sacred, secular and scientific family trees’ and the ‘conceptual field’ around the anthropological kinship diagram (Bouquet 1996: 45, 59). As elsewhere, these traditions and influences are seen as coalescing and finding form within the work of W. H. R. Rivers and his visualisation of kinship in the genealogical diagram (ibid.).

(Rivers 1910: 1 – The Genealogical Method (Kurka’s genealogical diagram)

Rivers is usually credited with developing the ‘genealogical method’ within anthropological inquiry. In his words, this was to involve the means of both ‘obtaining information’ and of ‘demonstrating the truth of this information.’ In this, diagrams were seen as crucial devices in the presentation of ‘facts,’ and as a way to ‘guarantee the accuracy and completeness [of those facts]’ (Rivers 1910: 11). This was a ‘staunchly positivistic approach’ (Stocking 1992: 34) and explicitly sought to establish the emergent discipline of ethnology ‘on a level with other sciences’ by ‘demonstrating the facts of social organisation’ in such a way as to ‘carry conviction to the reader with as much definiteness as is possible in any biological science’ (Rivers 1910: 12). Visual representations thus became ‘an argument for the credibility of the scientists’ inferences’ (Gifford-Gonzalez 1993: 26, at Bouquet 1996: 45). Kinship diagrams were not his invention, however: Morgan’s ‘diagrams of consanguinity’ in his Systems of Consanguinity and Affinity of the Human Family (1871) were also based on historical models of the ‘family tree.’

(Left) One of Morgan’s (1871) ‘diagrams of consanguinity’.
(Right) This ‘Dance Diagram’ by Charles Seligman (1910: 156 – WHR Rivers’ colleague and part of the Torres Strait Expedition) prefigures the symbols used today in kinship diagrams with circles in outline (women) or shaded (men), to distinguish between people of different genders.

Rivers argued that the systematic presentation of genealogical ‘facts’ offered a way to get ‘beneath the skin’ of human beings to the relations that people were born into and developed throughout their lifetime, admiring how once people had been identified in a genealogical diagram they ‘became real personages… although I had never seen them’ (Rivers 1968: 105, at Bouquet 1996: 45). This reflects both the ‘concrete method’ of questioning in order to learn personal names and terms ‘known by informants,’ and also the weight given to the ‘abstract system of relations underlying those names’ – an abstract order that was itself ‘reconcretized (visualized)’ in the ‘genealogical diagram’ (Bouquet 1996: 45). Rivers’ diagrams led to the conventionalisation of inverting the ‘tree’ of family trees, placing ‘its roots at the top’ (Bouquet 1995: 42–3 1996), and thus erasing “the image of the tree as a living, growing entity, branching out along its many boughs and shoots, and [replacing] it with an abstract, dendritic geometry of points and lines, in which every point represents a person, and every line a genealogical connection” (Ingold 2000: 135).

This inversion had lasting effects.The stories that ‘people tell about themselves’ and ‘the information gleaned from them by systematic forensic inquiry’ (Bouquet 1993: 140) that Rivers described continued to influence the ‘systematic collection of genealogical data’ – methods that in 1967 Barnes acknowledged could ‘scarcely be improved’ (Barnes 1967: 106, at Ingold 2007: 110). Bouquet also suggests that visualising kinship in the genealogical diagram reflects “the limits of a specific ideological consciousness, [marking] the conceptual points beyond which that consciousness cannot go, and between which it is condemned to oscillate (Jameson, in Clifford 1988: 223)” (Bouquet 1996: 44). Their presence persists (Bouquet 1996: 44) and genealogical diagrams are established as images for use “on the edge of the text” (Stoller 1994: 96) – each (diagram and text) expanding on the explanatory reach of the other.

Diagram as Method and Delivery

To recognise this is to emphasise how “the diagram is a possibility of fact – it is not the fact itself” (Deleuze 2004: 110). That is, genealogical diagrams are ‘contemporary models for social relations’ (Barnard & Good 1984: 9), portraying the inter-relationships of ‘real or imaginary individuals’ (ibid. p.8). The significance of these diagrams is not established until ‘the nature of those relationships between the individuals portrayed is clarified’ (Bouquet 1996: 45). Malinowski recognised the visual clout and direct efficacy of the reduction of data within visual forms, whilst at the same time elaborating on the kinds of details and observations that are necessary in establishing the relationships portrayed – how to flesh out the bones of the genealogical diagram: “The method of reducing information, if possible, into charts or synoptic tables ought to be extended to the study of practically all aspects of native life. All types of economic transactions may be studied by following up connected, actual cases, and putting them into a synoptic chart. Also, systems of magic, connected series of ceremonies, types of legal acts… a table ought to be drawn up of all the gifts and presents customary in a given society, a table including the sociological, ceremonial, and economic definition of every item… Besides this, of course, the genealogical census of every community, studied more in detail, extensive maps, plans and diagrams, illustrating ownership in garden land, hunting and fishing privileges, etc., serve as the more fundamental documents of ethnographic research” (Malinowski 1922: 11).

(Left) Malinowski’s use of diagrams extended to documenting canoe types and construction (1922: 83/top 85/bottom). (Right) He also used diagrams in his linguistic work (here from 1948: 261), on the ‘phatic’ (or performative) use of language (Gellner 1998: 148).

Malinowski, along with Radcliffe-Brown, Evans-Pritchard, and Fortes (among others) sought to understand the ‘basis for the orderly functioning’ of small-scale, effectively state-less societies, and kinship was seen as ‘constituting the basis and structure for social continuity’ in these settings (Carsten 2004: 10). Latter work was dominated by ‘avowedly ahistorical studies of African unilineal kinship systems,’ treating the lineage as bounded units, and developing a ‘complex typology’ to describe the functioning of these systems, involving ‘maximal’ and ‘minimal’ ‘lineages’ and ‘sublineages’ (Carsten 2004: 11).

Evans-Pritchard adapted the visual metaphor of the tree to account for such notions of scale in the inter-relationships between Nuer clans and lineages. He also made attempts to represent Nuer descriptions and depictions of these inter-relationships.

Evans-Pritchard’s (1940) diagrammatic lineage trees of the Jinaca (196/l) and Gaatgankiir (197/r).

In these attempts, Evans-Pritchard explicitly states that it was only the analyst (or ‘we’) who insisted on this visual metaphor, highlighting something of its limitations and biases: “[the Nuer] do not present [lineages] the way we figure them as a series of bifurcations of descent, as a tree of descent, or as a series of triangles of ascent, but as a number of lines running at angles from a common point… they see [the system] as actual relations between groups of kinsmen within local communities rather than as a tree of descent, for the persons after whom the lineages are called do not all proceed from a single individual” (Evans-Pritchard 1940: 202).

(Left) Evans-Pritchard’s (1940: 201) outline of a Nuer system of lineage, compared with (Right) “how the Nuer themselves figure a lineage system” (1940: 202).

During this era of kinship studies in Britain, ‘largely preoccupied with the analysis of descent groups’ (Carsten 2004: 12), such projects in France followed a route influenced by Lévi-Strauss’s The Elementary Structures of Kinship with an emphasis instead on social rules, the generation of exchange, and marriage (ibid.). The once-raging debates between adherents of “alliance” or “descent” theories do not need to be repeated here. For current purposes, I focus on how the established symbolic formulae of kinship diagrams have been adapted for use in different ethnographic works, and how the diagram has been modified to focus analytical attention on different aspects of social life. Kinship diagrams do not always fit the static model they imply: it’s not always the intention for ‘each triangle and circle [to represent] one real man or woman’ since they may be used ‘to be used to represent fictive genealogies of imaginary persons’ (Barnard & Good 1984:7). Even when the correlation between diagram symbols and living individuals is more direct, kinship diagrams have been diversely adapted, and ‘constructed so as to bring out certain structural features’ that the work seeks to draw attention to (Bouquet 1996: 60).

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Relationality and Decentering

The different variations on kinship diagrams above share in common a recognisable linearity. Reflections on these conventions question their impact on reinforcing particular notions of relationality, and subsequent effects on ideas around alterity and the individual. In the above examples, the passage of time (in people’s lives) has a directional, generational thrust that can be depicted (across the page) accordingly. For Ingold, this trend reinforces anthropological habits of insisting that ‘the way people in modern Western societies comprehend the passage of history, generations and time’ is ‘essentially linear,’ which casts anything that is not immediately recognisable in an opposing category: “alterity, we are told, is non-linear” (Ingold 2007: 3) – and this, in turn, equates ‘the march of progress’ with the ‘increasing domination of an unruly – and therefore non-linear – nature” (Ingold 2007: 155).

Sahlins, meanwhile, suggests that “the partible ‘dividual’ has become a regular figure of kinship studies as well as a widely distributed icon of the pre-modern subject,” perhaps as a result of anthropologists “staring too long at ego-centred, cum egocentric, kinship diagrams” (Sahlins 2011: 13). As such, we have learned to make the mistake of “rendering the relationships of kinship as the attributes of singular persons” (ibid.). Not only this, but also considering ‘kin persons’ as the only kind of persons who are ‘multiple, divisible, and relationally constructed’ leads to a tendency to overlook the fact that more familiar terms are also relational, among them ‘employees’, ‘clients’, ‘teammates’, ‘classmates ‘, guests’, ‘customers’ and ‘aliens’: “When aspects of the same person, variously salient in different social contexts, they are instances of partibility. But they are not instances of ‘dividuality,’ since they do not entail the incorporation of others in the one person” (Sahlins 2011: 13).

Clockwise from bottom left: social structure and marriage rules within Aranda kinship (Lévi-Strauss 1972 [1966]: 83) Ambryan kinship systems (Lévi-Strauss 1969, fig. 5), cited by Gell 1998: 91 (Upper right) Figure 24 – Relationships and Contexts (Rose 2000: 222) (Lower right) Figure 9 – Yarralin marriage practices and identities cross-cutting moieties and social categories (Rose 2000: 77).

In her description of the Yarralin people’s world view, Rose (2000: 221) describes individuals as shaped by their own personal ‘angle of perception,’ the angle of their matrilineal identity, and their ‘various country angles which tie them into other species and to the workings of the world” (ibid.). The diagram drawn to reflect this resembles Deleuze and Guattari’s ‘rhizome’ (Deleuze and Guattari 1988: 18): “a dense and tangled cluster of interlaced threads or filaments, [where] any point in which can be connected to any other” (Ingold 2000: 134). As we have seen, the tree has become one of the ‘most potent images in the intellectual history of the Western world,’ not only used in diagrammatical form to represent ‘hierarchies of control and schemes of taxonomic division’ but also, and above all, ‘chains of genealogicalconnection’ (ibid.). The rhizome model, by contrast, looks beyond the ‘static and linear, arborescent and dendritic imagery of the genealogical model’ to begin thinking ‘about persons, relationships and land’ in a world in movement, “wherein every part or region enfolds, in its growth, its relations with all the others” (ibid.): “a continually ravelling and unravellingrelational manifold” (Ingold 2000: 140).

Rose’s description of relationships and contexts – based on Yarralin ideas about wisdom, difference and interconnection – includes the influence of (physical and relational) positioning on perception, in a strikingly ‘rhizomatic’ account: “an angle of perception is a boundary, and boundaries are both necessary and arbitrary. Necessity lies in the fact that there are no relationships unless there are parts, and without relationships there is only uniformity and chaos. Arbitrariness lies in the fact that since all parts are ultimately interconnected, the particular boundary drawn at a given point is only one of many possible boundaries. Each line in Figure 24 is both and boundary and a relationship. Each node (A, B, C, etc) is both a context and an angle of vision, another centre… One particular human angle defines our world as it is because it is we who are looking. Perception distorts, but wisdom lies in knowing that distortion is not understanding” (Rose 2000: 222).

Such developments and reflections take us beyond the more recognisable examples of kinship diagrams, especially those focused on lineages and descent. As mentioned above, Lévi-Strauss’s work on kinship shifted focus to the importance of marriage, and of exchange more generally, in ‘establishing and maintaining relations between groups, rather than just individuals’ (Carsten 2004: 14). In this, he developed models for ‘elaborate, long-term exchange[s] involving the transfer of goods, services, and people that cemented relations between groups’ (Carsten 2004: 14) – making extensive use of diagrams.

(Left) Lévi-Strauss (1969: 64) draws on Firth (1936) to highlight the ‘astonishing complexity of matrimonial exchanges in Tikopia’ (Solomon Islands), cementing relations between specific groups of ‘in-laws’ and binding each lineage (or kinship group) in ‘a system of directional exchanges’.
(Lower right) Lévi-Strauss (1969: 35) focuses on the ceremonial distribution of meat in Burma, emphasising the role played by kinship systems in determining the kinds and quantities of meat received by different individuals, and the subsequent effects that generosity expended in such feasts have on future marriage arrangements.
(Upper right) Robinson (in the volume Marriage in Tribal Societies, ed. Meyer Fortes 1962: 129) specifies not only the kinds of foodstuffs (re)distributed as marriage gifts and the order of consent and expectation between specific members of the bride and groom’s families, but also the temporal order of the transfers, spread over a number of days around the ceremony itself (1962: 130).

There is a tension at the heart of anthropological diagrams of exchange concerning attempts to represent movement (spatiotemporal change) and the effects of time passing. Holbraad (2012: 101) asks why a line is ‘appropriate for representing a trajectory [of change]’ and how the inherent continuity of trajectories relates to the ‘momentum’ of movements and action. Is demarcating, visualising and representing the ‘continuity of plotted trajectories’ not a ‘very faint way of expressing momentum’ (ibid.)? He adds that ‘tota simul representations on paper’ have to be ‘economical’ since ‘they do not move in themselves, and hence they cannot really have a momentum,’ but argues that this economy ‘comes at a price’: “For the point about momentum is not only that it renders motion both continuous and directional, but also that it does so as a matter of necessity: momentum describes the inner compulsion of motion. The best way to understand this, I think, is cinematic: imagine panning away from the bird‘s-eye perspective of diagrams, and placing the “camera” at the helm of a moving trajectory, cockpit-style” (Holbraad 2012: 101).

With kinship diagrams, their linearity directed the passage of time and the segregation (or interaction) of generations. Attempts to visualise and represent exchange, however, emphasise the ‘movement’ of transfer – relying on directional arrows to depict action and change, often across both time and space. As the following examples illustrate, on the more abstract level of economic theory, diagrams are apt devices for illustrating modes and relations of trade and transfer – operating at different scales in order to reflect different ‘flows’ (Appadurai 1996) of goods, labour, capital, value, commodities, people and technologies.

(Left) Gudeman (2001: 6) diagrams the neoclassical economy, in the style of work that deals explicitly with ‘Economics,’ eg. (Right) Harvey (2003: 10) outlining the ‘paths of capital circulation’ (in capitalist society).

Building on diagrams of neoclassical economy (see above), Gudeman (2001: 7) draws the Economy as a complex of ‘practices and relationships’ that are ‘constituted within the two realms of market and community’ and the four ‘value domains’ he terms ‘the base, social relationships, trade, and accumulation’ (Gudeman 2001: 5). In this diagram (below, left), he emphasises the difference between established contemporary theories of value relativism through individual preference and its influence on demand and supply, and his own that proposes a world of ‘inconsistent, or incommensurate, domains of value that are locally specified’ – ‘culture’ is thus “made and re­made through contingent categories, such as home and work, body and the other, weekdays and weekends, beauty and efficiency, or friend­ship and love. Different value arenas make up economy” (Gudeman 2001: 6-7).

(Left) Gudeman 2001: ‘market’, ‘community’ and ‘value domains’. (Right) Gudeman & Rivera (1990: 119, used here by Mayer 2002: 22) delineates the flow of expenditures and leftovers within a specific (if unidentified) site – the house (more on ‘Sites’ of exchange, below).

The economic diagram format suits cases where the directional flow of abstract goods or entities is depicted in transfer or exchange with similarly abstract (or, rather, generalized) actors. Gregory’s work on gift economies makes extensive use of such diagrams: at the initial level, distinguishing between the single, quantitative exchange relation ‘established between objects’ in commodity transfer, and gift exchange that ‘consists of two transactions [where] the transactors become mutually indebted to each other – the exchange relation is established between the transactors rather than the objects’ (Gregory 1982: 46). The gist of these differences is summarized in two, simple figures (3.1/2, below).

(Upper left) Gregory on Commodity exchange and Gift exchange (1982: 46).
(Bottom left) The standard conception of ‘the general relations of production, consumption, distribution and exchange’ within the broader economy is represented diagrammatically by placing production (represented by firms) in opposition to consumption (represented by households), in a relation mediated by exchange (the product market) and distribution: ‘households supply labour and demand consumption goods firms demand labour and supply consumption goods’ (Gregory 1982: 103).
(Right) The échange a trois central to Mauss’s work on The Gift as developed by Sahlins (1972: 159), emphasising the role of ‘the second donee in the parable’ (Damren 2002: 86), and using a particular case (4.1) to elaborate on the consequences for our understanding of gift exchange more broadly (4.2). In the former, “the mauri that holds the increase-power (hau) is placed in the forest by the priests (tohunga) the mauri causes game birds to abound accordingly, some of the captured birds should be ceremoniously returned to the priests who placed the mauri the consumption of these birds by the priests in effect restores the fertility (hau) of the forest (hence the name of the ceremony, whangai hau, ‘nourishing hau’” (Sahlins 1972: 158). Thus, “the meaning of hau one disengages from the exchange of taonga is as secular as the exchange itself. If the second gift is the hau of the first, then the hau of a good is its yield, just as the hau of a forest is its productiveness… if the point is neither spiritual nor reciprocity as such, if it is rather that one man’s gift should not be another man’s capital, and therefore the fruits of a gift ought to be passed back to the original holder, then the introduction of a third party is necessary. It is necessary precisely to show a turnover: the gift has had issue the recipient has used it to advantage” (Sahlins 1972: 160).

(Left) The Temporal the Dimension of Exchange: Gregory (1982: 48) responds directly to the question of temporality in exchange: “simple commodity exchange established a relation of equality between heterogeneous things at a given point in time while gift exchange establishes a relation of equality between homogenous things at different points in time” (Gregory 1982: 47). The earlier diagram is tabulated to illustrate this: “A and B exchange x and y. This is simultaneous exchange but it can be split up into two parts that can be thought of as occurring at two different points in time. If this pair of temporally separated transactions is reproduced at a further two points in time, but in the reverse direction, the temporal outcomes of the debts thereby created will differ depending on whether the debt was of the commodity or the gift variety” (Gregory 1982: 47).
(Right) Roads of Gift-debt:the circulation of gifts of different ‘rank’ and ‘velocity’ create ‘roads of gift-debt’ that ‘bind people together in complicated webs of gift-debt’ Gregory (1982: 57-9). The two diagrams show the ‘minor roads’ of exchange that formed the outward and return sequences of exchange, respectively, and emphasise the importance of timing: in both sequences C was a major injunction, whose gifts depended on the prior receipt of goods and gifts from others, which in turn were dependent on the prior return of offerings from still other parties (Gregory 1982: 59).

Sites of Exchange

Another broad category of anthropological exchange diagrams attends less to abstract principles or temporality and instead focuses on the specific locales, or sites, of exchange interactions. As such they more closely resemble maps/plans, but often also contain or suggest particular forms of movement and/or interaction.

(Left) Gell’s (1999: 122) plan of the Dhorai market, and (Right) how people in the market are ‘put in their place’ in symmetrical and competitive (as opposed to hierarchical) relations: in the outer zones relations are ‘territorial and segmentary,’ with traders and associates from a given locality all expected to be seated together (Gell 1999: 127).

Gell’s account of the Dhorai market (in Madhya Pradesh, central India) pictures the market as a wheel: different groups of traders are able to sit and transact business in particular areas according to social rank, and the goods they trade in are also ranked, from the most prized (more central) to the less valuable (more peripheral) (Gell 1999: 121).

(Left) Duranti (1994: 50) publishes a page of fieldnote sketches later refined for print (Right) where the organisation of spatial relations exerts a critical influence on the political prestige of participants during a meeting held to distribute kava, and the sequential serving of drinks makes and remakes social hierarchies (Duranti 1994: 70).

(Left) Sequences of affinal payments made for a canoe by individual recipients: each payee makes his gift directly to the canoe’s builder (Munn 1986: 133).
(Right) This diagram (Gurven et al 2004: 33) models relationships of interaction, viz. the path model of foraging and sharing partnerships, specifying sites in relation to ‘forest days’ and time spent away from home.

(Left) Gell (1999: 64) and an ‘impossible figure’ to reflect the symbolic practices of marriage and affinity, dependent on ‘cross/sex unmediated and same/sex mediated ‘readings’ of gendered exchanges’ – at the root of conflict between alliance theory and feminist critiques (ibid.). This model derives from the fact that ‘any Melanesian marriage is both collective and individual’ unlike what might be a more familiar stipulation that ‘relations are either between individuals (interpersonal/private) or between collectivities (corporate/public)’ (Gell 1999: 63). Since individual and society are not opposed, the ‘relationship between marriage (the union between specific spouses) and alliance (affinal alliance linking collectivities such as clans) can be understood in terms of fractal magnification/minimization’: an approximate, but not exact, analogy between ‘spouse-to-spouse relations and affinal-group to affinal-group relations’ (ibid.)
(Right) Another ‘Strathernogram’ from Gell (1999: 72) detailing the specific working and feeding relations that constitute and support the dala: a matrilineal sub-clan described as the ‘enduring, self-reproducing, building-blocks of Trobriand society’ (1999: 70).

Malinowski’s (1922: 63) famous map of the Kula ring – an extensive form of exchange carried out across a wide range of islands that form a ‘closed circuit’: “in the direction of the hands of a clock… long necklaces of red shell, called soulava… in the opposite direction… bracelets of white shell called mwali… Each of these articles, as it travels in its own direction on the closed circuit, meets on its way articles of the other class, and is constantly being exchanged for them” (1922: 64). We are told that ‘every movement of the Kula articles’ is ‘fixed and regulated,’ that no one ‘ever keeps any of the articles for any length of time in his possession,’ and that transactions lead to ‘permanent and lifelong’ connections – none of which is visualized around the text (Malinowski 1922: 62). Others (two examples follow) have subsequently revisited the Kula ring.

Malinowski’s (1922: 63) famous map of the Kula ring.

Hage’s (1977) “undirected graph of the Kula Ring”.

Hage (1977: 29) describes his diagram as “an undirected graph of the Kula Ring” – it follows Malinowski’s descriptions and plots 18 points (each representing a Kula community) at their ‘approximate relative locations’: “Each point is enclosed by a broken line roughly indicating the territorial extent of the Kula community as an island, a part of an island or a group of islands as in Map V in Argonauts of the Western Pacific. The unbroken lines represent trading relations between these communities” (ibid.) – adopting this form to highlight how trade links may be of any physical distance but ‘may not pass through the territory of another Kula community’ (Hage 1977: 30).

(Left) Damon’s (2002: 108) map of locations within and around the Kula ring adopts cartographic norms and scales, and focuses on the names of locations (as part of a paper focusing on the production of ‘fame’ within the system’s exchanges).
(Right) An earlier map (from Herskovits’ landmark Economic Anthropology 1952: 200) tracing historical trade routes for various commodities exchanged across the Australian continent, with trade connections extending to the ‘Torres Strait islands and Western Papua’.

‘Baruya trading partners’ (Godelier & Jablonko 1998).

Godelier and Jablonk’s (1998) diagram (above) combines elements of each category outlined above: flows sites sequences (interactions) routes. The Baruya had trade links with 12 other tribes whose territories are located from 1/2 day’s walk to more than 3 days’ walk away’ – journeys were made to exchange ‘bark cloth, bows and arrows, stone adzes or steel axes, feathers, shells, dogs, and pigs’ (ibid.). This account queries standard notions of the operations within cashless economies: “With such a diversity of goods being exchanged, it might be difficult to find just the partner who had on hand the item one wanted. The problem does not arise, however, because salt bars, like currency, can be exchanged for all kinds of subsistence goods (e.g., bark cloth, stone adzes, arrows) and all kinds of luxury goods (e.g. feathers, shells). Salt bars crisscross all these distinctions. There is a known and accepted rate of exchange of salt bars for any given type of item with each other tribe. The partners in this exchange system are not trading in order to make profit, but rather in order to fulfill their needs as individuals and as members of their society. Nobody hoards salt bars, and nobody withholds goods in order to create an artificial scarcity to force a rise in price. This trading system requires regular, permanent, face-to-face relationships with people with whom one will continue to deal for many years. Everyone knows the accepted rates of exchange” (Godelier & Jablonko 1998).

Directionality and Irreversibility

Questioning and expanding on the diverse use of diagrams in anthropology parallels broader concerns within the discipline as a whole – not least how we understand attempts to create ‘a moving picture of a world that doesn’t stand still’ (Clifford 1997). Bourdieu (1990) challenged the structuralist analysis of gift exchange and the idea of ‘some abstracted and synchronic “law of reciprocity,”’ highlighting instead ‘the political judgement of the agents involved as regards the timing of the giving of the initial gift and then of the counter gift’ (Jedrej 2010: 692). This is to question structural analyses that ‘deal with a synchronic virtual reality’ and tends to ‘privilege spatial relations and their analogues in such forms as synoptic tables, diagrams (structures) and figures,’ and is instead to deal with ‘practice,’ which ‘necessarily unfolds in time and has all the properties which synchronic structures cannot take into account, such as directionality and irreversibility’ (ibid.). There are works – such as those on the concept of landscape – that explore and articulate the intersections of time, space and practice (Jedrej 2010: 692). As the above examples suggest, those same intersections urge further examination and exploration through the use of diagrams in anthropology.


Comparative Medical Genetics

A Linkage Analysis

Linkage analysis is based on the same principle of recombination used for genetic linkage mapping. However, unlike a genetic marker, the genotype of the disease locus is not known. Therefore, it is important to know the mode of inheritance of the disorder. Pedigree analysis or experimental breeding can help to identify how a disease is inherited. Single gene diseases are usually easier to evaluate and are commonly classified into Mendelian inheritance patterns as described earlier: autosomal recessive, autosomal dominant, and X-linked inheritance. More complex inheritance patterns are due to the involvement of two or more genes (polygenic) necessary to cause disease, variable penetrance, variable expressivity, and influences from the environment.

Once a mode of inheritance is established, the underlying genotype at the disease locus is inferred and analyzed for linkage with all genetic markers that were tested, which is mostly done with the help of computer programs. If a marker is located close to the disease locus, the result will show no or a very small recombination fraction between the marker and the disease locus. Based on this recombination fraction, a numeric value, called the LOD score, is calculated. This value expresses the likelihood that the result is due to linkage between the tested marker and the disease locus rather than by chance. For example, if the LOD score has a value of 3, this indicates that obtained results are a thousand times (10 3 ) more likely due to linkage between the tested marker and disease than by chance. In most cases, an LOD score ≥3 is statistically significant. Once linkage is established to a marker, the chromosomal region surrounding the marker can be analyzed for potential candidate genes (positional candidate gene approach). Frequently, more markers will have to be analyzed in that area to confirm and further narrow the genome region of interest.

B Association Study

Genotyping data from hundreds of markers analyzed in groups of affected and unaffected animals can be evaluated for differences in allele frequencies in the two groups, thus demonstrating association between a genetic marker and the disease phenotype. If the marker and the disease locus are located close to each other, both loci will be inherited together, through several generations, and recombination between the two will be rare. Consequently, specific alleles of the marker and the disease locus will mostly be found together within the group of affected animals, which means they are associated (they are said to be in linkage disequilibrium). Therefore, an association study compares the frequency of marker alleles within the two groups, and an increased occurrence of a specific marker allele in the group of affected animals indicates that this marker is located at or close to the disease gene.

C Positional Candidate Gene Approach

A major goal of a genome-wide linkage analysis is to find the gene or genes responsible for the development of the disease or phenotype that was used for the study. The markers found to be linked allow the assignment of the disease locus to a chromosomal area, and the more markers that are tested, the narrower the region will become. A small region is desirable to minimize the number of possible candidate genes that needs to be analyzed for mutations. Because the approximate location of the candidate gene is known, this method is called the positional candidate gene approach. Genes coding for products with a known function that could be involved in the development of the disease will be considered first for analysis.


How to recognise the type of allele by pedigree analysis diagrams? - Biology

Section I Question 16 - 2002 HSC

Discuss a statement about prevention as a modern method of disease control.

Student Responses (3)

Question 16-18

Section I Question 16-18 - 2001 HSC

16. Validity of survey about genetically modified food. 17. Relationship between a structural feature and the function of an artery. 18. Products extracted from donated blood and reason for development of artificial blood.

Student Responses (3)

Question 17

Section I Question 17 - 2002 HSC

(a) Draw an outline diagram of a transverse section of a plant root. (b) Describe a current theory about the movement of materials through phloem tissue in plants.

Student Responses (3)

Question 18

Section I Question 18 - 2002 HSC

Describe improvements to the design of an investigation into the relationship between smoking and lung cancer.

Student Responses (3)

Question 19

Section I Question 19 - 2002 HSC

Explain how a process of water treatment reduces the risk of infection from pathogens in drinking water extracted from a lake.

Student Responses (3)

Question 19-21

Section I Question 19-21 - 2001 HSC

19. Procedure followed in a first-hand investion, including safe work practices. 20. Table showing responses of an ectothermic and an endothermic animal to temperature changes. 21. Contribution of two scientists from a list to the understanding of the chromosomal nature of inheritance.

Student Responses (3)

Question 20

Section I Question 20 - 2002 HSC

Outline how mitosis and cell differentiation assist in the maintenance of health.

Student Responses (3)

Question 21

Section I Question 21 - 2010 HSC

Complete a table showing results of breeding experiments by Mendel and Morgan.

Student Responses (3)

Question 21

Section I Question 21 - 2002 HSC

Describe a first-hand investigation used to estimate the size of red blood cells on a prepared microscope slide.

Student Responses (3)

Question 22

Section I Question 22 - 2010 HSC

(a) Draw a graph to represent data recorded in a table. (b) Explain the impact of human processes on biodiversity.

Student Responses (3)

Question 22

Section I Question 22 - 2002 HSC

Construct a table that lists the possible genotypes and the expected frequency of each genotype that could be produced when three pairs of chromosomes divide by random segregation.

Student Responses (1)

Question 23

Section I Question 23 - 2002 HSC

(a, b) Identify an area in a nephron where filtration and reabsorption occur. (c) Discuss the importance of hormone replacement therapy for people who cannot secrete aldosterone.

Student Responses (1)

Question 24

Section I Question 24 - 2010 HSC

Design an experiment testing how opening a window affects the blood oxygen saturation of people in a room.

Student Responses (3)

Question 24

Section I Question 24 - 2002 HSC

Assess the potential impact on genetic diversity of using disease-free tissue from existing plants to clone banana plants.

Student Responses (2)

Question 25

Section I Question 25 - 2010 HSC

(a) Justify equipment or resources used in a first-hand investigation of a longitudinal section of xylem tissue. (b) Draw a diagram to represent a longitudinal section of xylem tissue and label one characteristic feature.

Student Responses (3)

Question 25

Section I Question 25 - 2002 HSC

(a) Define the concept of punctuated equilibrium in evolution. (b) Explain how punctuated equilibrium differs from the process proposed by Darwin.

Student Responses (3)

Question 25-28

Section I Question 25-28 - 2001 HSC

25. Possible future effects of the widespread use of antibiotics on the spread of disease. 26. Reason for taking immune suppressing drugs following an organ transplant and consequence for patients. 27. Assessment of a statement's validity using graphical data. 28. Impact of scientific understanding and technology on developments in reproductive technologies.

Student Responses (3)

Question 26

Section I Question 26 - 2002 HSC

Describe a first-hand investigation to verify the effects of pH on the colour of hydrangea flowers.

Student Responses (1)

Question 27

Section I Question 27 - 2002 HSC

Evaluate the contributions made by Pasteur and Koch to our present understanding of the causes and possible prevention of infectious diseases.

Student Responses (1)

Question 28

Section II Question 28 - 2010 HSC

(a) Assess the effectiveness of a given model to explain the cause of organ transplant rejection. (b) Outline the role of two types of T lymphocytes in organ rejection.

Student Responses (3)

Question 28

Section II Question 28 - 2002 HSC

(a) Organ of Corti wavelength, frequency and pitch of a sound structures used by animals to produce sound. (b) Features of the cerebrum, cerebellum and medulla oblongta regions of the brain involved in speech. (c) Graph of data and statement of relationship between variables human eye's ability to focus on objects at different distances. (d) Structures and processes in the retina that transform light into electrochemical signals.

Student Responses (1)

Question 29

Section II Question 29 - 2010 HSC

(a) Using source material provided, identify responses of plants to temperature change. (b) Evaluate relevance and reliability of each source of information.

Student Responses (3)

Question 29

Section II Question 29 - 2001 HSC

(a) Location and function of structures in the eye. (b) Collection and assessment of information on structures used by animals to produce sound. (c) Describe use of technology to overcome effects of cataracts. (d) Justify the procedure and conclusions of an investigation into the process of accommodation. (e) Evaluate the appropriateness of devices that assist people with hearing impairment.

Student Responses (3)

Question 30

Section II Question 30 - 2010 HSC

Using information provided and other relevant knowledge, demonstrate how the practice of biology led to the validation of current theories of evolution.

Student Responses (2)

Question 31

Section II Question 31 - 2010 HSC

(a) Contruct a table identifying structures used by insects, fish and mammals to detect vibrations. (b) Draw diagrams illustrating vocal folds for high and low pitched notes. (c) Explain the effect of location in the retina on the stucture of cones. Outline the role of rhodopsin in rods. (d) Explain causes for lack of action potentials in part of a mammal's brain. Outline how this condition could change behaviour. (e) Evaluate how understanding of the ear and eye has led to development of 3D images and surround sound systems.

Student Responses (3)

Question 32

Section II Question 32 - 2001 HSC

(a) Mammalian characteristics. Skeletal differences between Homo sapiens and Australopithecus afarensis. (b) Explain how to gather radiometric data to date fossilised material and assess the information for relevance and reliability. (c) Analyse the evolutionary significance of polymorphism in humans. (d) Outline and justify the conclusions of an analysis of similarities and differences between groups of primates. (e) Justify predictions of factors affecting future human evolution.

Student Responses (3)

Question 33

Section II Question 33 - 2010 HSC

(a) Construct a table identifying effects of mutations. (b) Draw diagrams to show similarities and differences between chromosomes in the diploid cell and a haploid cell resulting from meiosis. (c) Predict ratios of phenotypes from a pedigree for linked and non-linked genes. (d) Explain how data can be collected to identify relative position of linked genes. Reasons why human genome project could not be achieved using linkage maps. (e) Evaluate how understanding of gene cloning and gene cascades has led to new applications for technologies.

Component: Blueprint of Life

Student Responses (3)

Question 19-21

Section I Question 19-21 - 2001 HSC

19. Procedure followed in a first-hand investion, including safe work practices. 20. Table showing responses of an ectothermic and an endothermic animal to temperature changes. 21. Contribution of two scientists from a list to the understanding of the chromosomal nature of inheritance.

Student Responses (3)

Question 21

Section I Question 21 - 2010 HSC

Complete a table showing results of breeding experiments by Mendel and Morgan.

Student Responses (3)

Question 22

Section I Question 22 - 2002 HSC

Construct a table that lists the possible genotypes and the expected frequency of each genotype that could be produced when three pairs of chromosomes divide by random segregation.

Student Responses (3)

Question 22-24

Section I Question 22-24 - 2001 HSC

22a. Effect of cloning on the genetic diversity of a species. 22b. Evolutionary effects of a disease entering an endangered population with some cloned individuals. 23. Explanation of historical practices to increase immunity against smallpox. 24. Relationship between a cause and a symptom of a non-infectious disease.

Student Responses (2)

Question 23

Section I Question 23 - 2010 HSC

(a) Explain using an example why hybridisation within a species is carried out. (b) Use an example of a named transgenic species to discuss the social and environmental impact of hybridisation.

Student Responses (3)

Question 24

Section I Question 24 - 2002 HSC

Assess the potential impact on genetic diversity of using disease-free tissue from existing plants to clone banana plants.

Student Responses (3)

Question 25

Section I Question 25 - 2002 HSC

(a) Define the concept of punctuated equilibrium in evolution. (b) Explain how punctuated equilibrium differs from the process proposed by Darwin.

Student Responses (3)

Question 25-28

Section I Question 25-28 - 2001 HSC

25. Possible future effects of the widespread use of antibiotics on the spread of disease. 26. Reason for taking immune suppressing drugs following an organ transplant and consequence for patients. 27. Assessment of a statement's validity using graphical data. 28. Impact of scientific understanding and technology on developments in reproductive technologies.

Student Responses (3)

Question 26

Section I Question 26 - 2002 HSC

Describe a first-hand investigation to verify the effects of pH on the colour of hydrangea flowers.

Student Responses (3)

Question 30

Section II Question 30 - 2010 HSC

Using information provided and other relevant knowledge, demonstrate how the practice of biology led to the validation of current theories of evolution.

Component: Maintaining a Balance

Student Responses (3)

Question 16-18

Section I Question 16-18 - 2001 HSC

16. Validity of survey about genetically modified food. 17. Relationship between a structural feature and the function of an artery. 18. Products extracted from donated blood and reason for development of artificial blood.

Student Responses (3)

Question 17

Section I Question 17 - 2002 HSC

(a) Draw an outline diagram of a transverse section of a plant root. (b) Describe a current theory about the movement of materials through phloem tissue in plants.

Student Responses (3)

Question 19-21

Section I Question 19-21 - 2001 HSC

19. Procedure followed in a first-hand investion, including safe work practices. 20. Table showing responses of an ectothermic and an endothermic animal to temperature changes. 21. Contribution of two scientists from a list to the understanding of the chromosomal nature of inheritance.

Student Responses (3)

Question 21

Section I Question 21 - 2002 HSC

Describe a first-hand investigation used to estimate the size of red blood cells on a prepared microscope slide.

Student Responses (1)

Question 23

Section I Question 23 - 2002 HSC

(a, b) Identify an area in a nephron where filtration and reabsorption occur. (c) Discuss the importance of hormone replacement therapy for people who cannot secrete aldosterone.

Student Responses (1)

Question 24

Section I Question 24 - 2010 HSC

Design an experiment testing how opening a window affects the blood oxygen saturation of people in a room.

Student Responses (2)

Question 25

Section I Question 25 - 2010 HSC

(a) Justify equipment or resources used in a first-hand investigation of a longitudinal section of xylem tissue. (b) Draw a diagram to represent a longitudinal section of xylem tissue and label one characteristic feature.

Student Responses (1)

Question 29

Section II Question 29 - 2010 HSC

(a) Using source material provided, identify responses of plants to temperature change. (b) Evaluate relevance and reliability of each source of information.

Component: Option - Communication

Student Responses (3)

Question 28

Section II Question 28 - 2002 HSC

(a) Organ of Corti wavelength, frequency and pitch of a sound structures used by animals to produce sound. (b) Features of the cerebrum, cerebellum and medulla oblongta regions of the brain involved in speech. (c) Graph of data and statement of relationship between variables human eye's ability to focus on objects at different distances. (d) Structures and processes in the retina that transform light into electrochemical signals.

Student Responses (3)

Question 29

Section II Question 29 - 2001 HSC

(a) Location and function of structures in the eye. (b) Collection and assessment of information on structures used by animals to produce sound. (c) Describe use of technology to overcome effects of cataracts. (d) Justify the procedure and conclusions of an investigation into the process of accommodation. (e) Evaluate the appropriateness of devices that assist people with hearing impairment.

Student Responses (2)

Question 31

Section II Question 31 - 2010 HSC

(a) Contruct a table identifying structures used by insects, fish and mammals to detect vibrations. (b) Draw diagrams illustrating vocal folds for high and low pitched notes. (c) Explain the effect of location in the retina on the stucture of cones. Outline the role of rhodopsin in rods. (d) Explain causes for lack of action potentials in part of a mammal's brain. Outline how this condition could change behaviour. (e) Evaluate how understanding of the ear and eye has led to development of 3D images and surround sound systems.

Component: Option - Genetics: The Code Broken?

Student Responses (3)

Question 33

Section II Question 33 - 2010 HSC

(a) Construct a table identifying effects of mutations. (b) Draw diagrams to show similarities and differences between chromosomes in the diploid cell and a haploid cell resulting from meiosis. (c) Predict ratios of phenotypes from a pedigree for linked and non-linked genes. (d) Explain how data can be collected to identify relative position of linked genes. Reasons why human genome project could not be achieved using linkage maps. (e) Evaluate how understanding of gene cloning and gene cascades has led to new applications for technologies.

Component: Option - The Human Story

Student Responses (3)

Question 32

Section II Question 32 - 2001 HSC

(a) Mammalian characteristics. Skeletal differences between Homo sapiens and Australopithecus afarensis. (b) Explain how to gather radiometric data to date fossilised material and assess the information for relevance and reliability. (c) Analyse the evolutionary significance of polymorphism in humans. (d) Outline and justify the conclusions of an analysis of similarities and differences between groups of primates. (e) Justify predictions of factors affecting future human evolution.

Component: The Search for Better Health

Student Responses (3)

Question 16

Section I Question 16 - 2002 HSC

Discuss a statement about prevention as a modern method of disease control.

Student Responses (3)

Question 18

Section I Question 18 - 2002 HSC

Describe improvements to the design of an investigation into the relationship between smoking and lung cancer.

Student Responses (3)

Question 19

Section I Question 19 - 2002 HSC

Explain how a process of water treatment reduces the risk of infection from pathogens in drinking water extracted from a lake.

Student Responses (3)

Question 20

Section I Question 20 - 2002 HSC

Outline how mitosis and cell differentiation assist in the maintenance of health.

Student Responses (3)

Question 22

Section I Question 22 - 2010 HSC

(a) Draw a graph to represent data recorded in a table. (b) Explain the impact of human processes on biodiversity.

Student Responses (3)

Question 22-24

Section I Question 22-24 - 2001 HSC

22a. Effect of cloning on the genetic diversity of a species. 22b. Evolutionary effects of a disease entering an endangered population with some cloned individuals. 23. Explanation of historical practices to increase immunity against smallpox. 24. Relationship between a cause and a symptom of a non-infectious disease.

Student Responses (3)

Question 25-28

Section I Question 25-28 - 2001 HSC

25. Possible future effects of the widespread use of antibiotics on the spread of disease. 26. Reason for taking immune suppressing drugs following an organ transplant and consequence for patients. 27. Assessment of a statement's validity using graphical data. 28. Impact of scientific understanding and technology on developments in reproductive technologies.

Student Responses (1)

Question 27

Section I Question 27 - 2010 HSC

(a) Outline examples of effective quarantine regulations. (b) Explain why this method is effective for one example.

Student Responses (1)

Question 27

Section I Question 27 - 2002 HSC

Evaluate the contributions made by Pasteur and Koch to our present understanding of the causes and possible prevention of infectious diseases.

Student Responses (1)

Question 28

Section II Question 28 - 2010 HSC

(a) Assess the effectiveness of a given model to explain the cause of organ transplant rejection. (b) Outline the role of two types of T lymphocytes in organ rejection.


Introduction

DNA polymorphisms such as short tandem repeats (STRs) occur frequently in the human genome and serve as interesting tools providing numerous applications in interdisciplinary research. STR typing is very useful for population and evolutionary genetics, human genetics (e.g., stem cell transplantation), pathology and forensic sciences [1,2,3,4]. Male specific Y-chromosome STRs (Y-STRs) provide additional applications as it enables the direct separation of male DNA in mixed samples without female DNA interference, useful in for example fetal gender or male lineage determination and forensic sexual assault cases [3, 5]. Furthermore, Y-STRs enable the identification of genealogical patrilineages as the majority of the Y-chromosome lacks recombination driving its inheritance from father to son in a relative conserved manner [4]. These Y-STR patrilineages are particularly useful for population and evolutionary genetics, kinship analysis (e.g., family history and paternity testing) and forensic familial searching. The latter defines a forensic identification method based on Y-STRs to characterize patrilineages in order to identify close or distant male relatives of the unknown perpetrator using the DNA collected at the crime scene [6]. Discrimination of these familial lineages is possible through the presence of Y-STR variants, due to a meiotic change (replication slippage) in DNA sequence in one of the lineages.

Y-haplotype comparison from direct father-son couples reveals Y-STR changes, which made it possible to estimate individual Y-STR mutation rates [7]. Another calculation method called the ‘genealogical pair approach’ is based on paternally related male namesakes (men sharing the same surname) in deep-rooted pedigrees separated by a number of generations [8]. This approach enables the deduction of individual Y-STR mutation rates from a large number of meiosis with a minimal set of DNA samples [9]. Both autosomal and Y-STR mutation rates have been observed to be correlated with paternal allele transfer, the age of the father and the allele length [7, 9, 10]. High microsatellite variation makes autosomal STR typing less relevant for extended kinship analysis as the difference in number of shared alleles with (un)related individuals fades away over generations [11].

For distant paternal kinship analysis, it is important to identify all Y-STR variants and to have knowledge of exact individual Y-STR mutation rates in order to correctly estimate the time to their most recent common ancestor (tMRCA). To date, various Y-STR markers have been characterized with their mutation rate ranging between 10 −4 and 10 −2 per generation (mpg) [7, 9, 12, 13]. The latter group (>10 −2 mpg) defines the rapidly mutating (RM) Y-STRs and is useful to discriminate close paternally related males [14]. The inclusion of RM Y-STRs in modern Y-STR profiling kits increases the discriminatory power and the weight-of-evidence for a Y-haplotype match [15].

Y-STR typing is still widely performed through fragment analysis by capillary electrophoresis (CE), which characterizes the number of repeats through size separation [6]. CE technology improvements (e.g., novel fluorescent dyes, 5-dyes and 6-dyes) and new PCR-based STR assays increased the throughput and postponed the need for the more laborious and expensive methodology of next generation sequencing [16]. Fragment size allele frequencies are valuable in for example the prediction of useful objectives in forensic medicine and in the observation of the chimeric status after stem cell transplantation [1]. However, when CE genotyping is used to analyze the Y-haplotypes of genealogical pairs, there is a possibility that certain Y-STR variations at sequence level will not be detected, referring to hidden variants. It is for example impossible to distinguish a loss of a tetrameric repeat with a deletion of 4 bp located in the flanking region without sequence analysis [17, 18]. Additionally, sequencing analysis of Y-STRs containing a compound or complex repeat motif (interrupted repeat structures with variable lengths and sequences) can reveal more information concerning the location of the insertion/deletion and therefore increase the observable allelic variation [19, 20].

As Y-STR alleles are rarely sequenced, the question if this lack excludes potential useful information causing false positive mistakes, remains rather unanswered. An interesting example of hidden STR variations with a possible high impact on kinship analysis are the so called parallel modifications (PM). PM are two (or more) independent DNA sequence slippages during meiotic division resulting into alleles with an identical number of repeats in different lineages of a genealogic tree. The phenomenon of independently originated equal changes has already been observed and described on an evolutionary scale, called homoplasy or convergent evolution [21]. On an evolutionary scale, it is already known that different Y-SNP haplogroups can have high Y-haplotype resemblance due to recurrent and independent parallel Y-STR changes, causing difficulties in Y-haplogroup age estimations [22] and in studying population genetic patterns [23]. The detection of PM at a genealogical level in deep-rooting family pedigrees could expand our knowledge of homoplasy to a genealogical time scale. Through sequencing technology, the increased information of allelic variation could eventually reveal a previously hidden PM. If not, at least two unique Y-STR changes remain invisible between two relatives and tMRCA underestimations of biological kinships could be made.

This study arises from previously obtained genealogical pairs collected to investigate the extra pair paternity (EPP rates and differences in Y-STR mutation rates between Y-haplogroups [8, 9]. Here, we discuss the observation of multiple parallel modification events at a genealogical level in extended family pedigrees including multiple genealogical pairs. Furthermore, we indicate the importance and the added value of detailed sequencing analysis useful for population genetics, genetic genealogy and familial searching.


Examiners report

Well prepared candidates could state &lsquoplateau phase and exponential growth or log phase&rsquo. A surprising number reversed the answers, probably due to carelessness.

There were many convoluted answers without substance. Most gained the marks by stating that fossils can be compared with living organisms with an example.

Most managed to give a reasonable explanation of genotype and phenotype.

Many missed the word 'chromosomes' in the stem. The knowledge of naked v proteins or circular v linear was expected from the core. Using the data it was expected that the candidates could state that the human chromosomes were much bigger (divide by 46) or that there were many more base pairs as there was about 3 X 10 3 difference.

Considering that everyone on the IB diploma course studies maths at some level, a surprising number left (iii) blank or gave answers that did not make sense.

A pleasing number were able to state that all 4 blood groups were possible in (i), and most had a reasonable attempt at explaining codominance in part (ii).

A pleasing number were able to state that all 4 blood groups were possible in (i), and most had a reasonable attempt at explaining codominance in part (ii).


Watch the video: Stammbaumanalyse (August 2022).