Saturday, May 27, 2006

The genetics of the human brain

The Jewels of Our Genome: The Search for the Genomic Changes Underlying the Evolutionarily Unique Capacities of the Human Brain
James M. Sikela

PLoS Genetics, 2006, v. 2:646-655

Abstract: The recent publication of the initial sequence and analysis of the chimp genome allows us, for the first time, to compare our genome with that of our closest living evolutionary relative. With more primate genome sequences being pursued, and with other genome-wide, cross-species comparative techniques emerging, we are entering an era in which we will be able to carry out genomic comparisons of unprecedented scope and detail. These studies should yield a bounty of new insights about the genes and genomic features that are unique to our species as well as those that are unique to other primate lineages, and may begin to causally link some of these to lineage-specific phenotypic characteristics. The most intriguing potential of these new approaches will be in the area of evolutionary neurogenomics and in the possibility that the key human lineage–specific (HLS) genomic changes that underlie the evolution of the human brain will be identified. Such new knowledge should provide fresh insights into neuronal development and higher cognitive function and dysfunction, and may possibly uncover biological mechanisms for information storage, analysis, and retrieval never previously seen.

Wednesday, May 24, 2006

IHEP (International Human Epigenome Project)

a news feature in Nature, about this project looking at the "epigenetic code":

Methylation and other alterations to DNA can significantly alter gene activity, causing inter-individual variation and sometimes disease, notably cancers. Such changes are 'epigenetic', and the term 'epigenome' refers to all the heritable biological factors other than DNA sequence that influence gene expression. Proposals for a large-scale Human Epigenome Project, modelled on the Human Genome Project, have provoked heated debate. Can this multimillion-dollar project be justified?

News FeatureEpigenetics: Unfinished symphony

To correctly 'play' the DNA score in our genome, cells must read another notation that overlays it — the epigenetic code. A global effort to decode it is now in the making, reports Jane Qiu.

-- more on this when I finish reading it.

Tuesday, May 23, 2006

Population subdivision in Indian subcastes

Genetic diversity within a caste population of India as measured by Y-chromosome haplogroups and haplotypes: Subcastes of the Golla of Andhra Pradesh

R. J. Mitchell, B. M. Reddy, D. Campo, T. Infantino, M. Kaps, M.H. Crawford

AJPA: July, 2006, 130:385-393

The extent of population subdivision based on 15 Y-chromosome polymorphisms was studied in seven subcastes of the Golla (Karnam, Pokanati, Erra, Doddi, Punugu, Puja, and Kurava), who inhabit the Chittoor district of southern Andhra Pradesh, India. These Golla subcastes are traditionally pastoralists, culturally homogeneous and endogamous. DNA samples from 146 Golla males were scored for seven unique event polymorphisms (UEPs) and eight microsatellites, permitting allocation of each into haplogroups and haplotypes, respectively. Genetic diversity (D) was high (range, 0.9048-0.9921), and most of the genetic variance (>91%) was explained by intrapopulation differences. Median-joining network analysis of microsatellite haplotypes demonstrated an absence of any structure according to subcaste affiliation. Superimposition of UEPs on this phylogeny, however, did create some distinct clusters, indicating congruence between haplotype and haplogroup phylogenies. Our results suggest many male ancestors for the Golla as well as for each of the subcastes. Genetic distances among the seven subcastes, based on autosomal markers (short tandem repeats and human leukocyte antigens) as well as those on the chromosome Y, indicate that the Kurava may not be a true subcaste of the Golla. Although this finding is based on a very small Kurava sample, it is in accordance with ethnohistorical accounts related by community elders. The Punugu was the first to hive off the main Golla group, and the most recently separated subcastes (Karnam, Erra, Doddi, and Pokanati) fissioned from the Puja. This phylogeny receives support from the analysis of autosomal microsatellites as well as HLA loci in the same samples. In particular, there is a significant correlation (r = 0.8569; P = 0.0097) between Y-chromosome- and autosomal STR-based distances.

some notes:
- concordance between population subdivision based on Y-chromosome analysis and population subdivision based on perceptions of elders is mixed.
- some controversy as to when the Indian caste system originated
- this population practices consanguineous marriage and village endogamy (so, no male or female biased dispersion, I guess?)
-TMRCA of these Y-chromosomes is 34, 370, lending some support to the hypothesis that the caste system originated earlier than some think.

Sunday, May 21, 2006

Do men hunt to provision or to show off?

A new paper in Current Anthropology:

Prestige or Provisioning? A Test of Foraging Goals among the Hadza
Brian Wood

Current Anthropology, 47:383-387

Tests of hypotheses
concerning the foraging goals of Hadza men and women using an interview involving a hypothetical instance of foraging group formation show that most Hadza men and all Hadza women prefer to join foraging groups that ensure the greatest household provisioning advantages. Men with dependent offspring are no more likely to choose a strategy beneficial for household provisioning than men without dependent offspring. These results suggest that most Hadza men agree with women's camp preferences and value family provisioning more than broadcasting signals of their hunting ability when deciding with whom to live.

Some have argued that the predominant motivation for male hunting (especially of large game) is to aquire benefits of prestige. This paper fails to support this hypothesis as it shows that Hadza men prefer to join a camp with a lot of good hunters rather than join a group of poor hunters (where they might have higher prestige, themselves). This is similar to the question of whether to join a team of very good players (not so much individual prestige) or join a team of mediocre players (more individual prestige). I think than in this and the hunting case, mens' responses will differ based on their own hunting ability and will also be partly based on the fact that a really good hunter/player can't be good when he isn't surrounded by other equally good players/hunters. I am not sure to what degree teamwork is an important part of Hadza hunting.
final thoughts:
- two hypotheses examined in this paper are not mutually exclusive.
- prestige seems to be more of a byproduct than a primary motivator for male hunting, and is probably dependent on marital status/age/number of dependent offspring (as shown in the Ache, but not here).

Friday, May 19, 2006

Need for an evolutionary perspective in medicine

This is a short editorial from a few months back in Science by:

R. Nesse, S. Stearns & G. Omenn
Medicine Needs Evolution
Science, v. 311:1071

Areas of particular interest:
-anatomical anomalies
-metabolic syndromes
-persistence of genes that cause certain diseases
-when is it safe to block cough, fever, diarrhea etc...?

The authors call for an incorporation of evolutionary theory in medical licensing exams, "ensure evolutionary expertise in agencies that fund biomedical research", and incorporate evol. theory into all curriculums.

...and this more recent very short letter by Joseph McInerney (Science 312:998) discusses the insights gained from "evolution theory's recognition of individual variation within populations of organisms."
He also briefly mentions the "recently announced Genes and Environment Initiative at NIH, which will investigate the interaction of genetic and environmental variations in common diseases."

Thursday, May 18, 2006

Consumer Ethology

An interesting piece from PCMag (via TAMU Anthropology in the News) on how major corporations spend billions (yes, billions) on ethnographic research. This can involve looking at differences within and between cultures, between sexes, and across different age groups.

Wednesday, May 17, 2006

Nuclear DNA recovered from Neanderthal

John Hawks has a post on a report that Paabo et al. have been able to sequence parts of the Y-chromosome in Neanderthal remains found in a cave in Croatia. I wonder how much of the genome they will be able to amplify. What are the major questions that they might attempt to answer?
-admixture with moderns
-time since divergence (looks like 315,000 years ago, according to their analysis)
-Neanderthal genetic diversity (from the 10 or so individuals that they hope to eventually look at)
-a multitute of polymorphisms that are of interest in humans - what do they look like in Neanderthals? etc...

Tuesday, May 16, 2006

More on mutations in humans

From a paper in Nature in 1999 (397:344-347), by the same authors as the paper below on fitness effects of mutations:

High genomic deleterious mutation rates in hominids
Adam Eyre-Walker, Peter D. Keightley

It has been suggested that humans may suffer a high genomic deleterious mutation rate,. Here we test this hypothesis by applying a variant of a molecular approach to estimate the deleterious mutation rate in hominids from the level of selective constraint in DNA sequences. Under conservative assumptions, we estimate that an average of 4.2 amino-acid-altering mutations per diploid per generation have occurred in the human lineage since humans separated from chimpanzees. Of these mutations, we estimate that at least 38% have been eliminated by natural selection, indicating that there have been more than 1.6 new deleterious mutations per diploid genome per generation. Thus, the deleterious mutation rate specific to protein-coding sequences alone is close to the upper limit tolerable by a species such as humans that has a low reproductive rate, indicating that the effects of deleterious mutations may have combined synergistically. Furthermore, the level of selective constraint in hominid protein-coding sequences is atypically low. A large number of slightly deleterious mutations may therefore have become fixed in hominid lineages.

Fitness effects of mutations in humans

I'm not at all familiar with the methods in this paper, but the conclusion sounds interesting, namely that "it will be difficult to locate the majority of mutations involved in genetic disease unless the disease is completely un-associated with fitness, or some of the mutations have been subject to positive selection."

The Distribution of Fitness Effects of New Deleterious Amino Acid Mutations in Humans

Adam Eyre-Walker, Meg Woolfit, Ted Phelps

Genetics, March 17, 2006, Epub ahead of print.

The distribution of fitness effects of new mutations is a fundamental parameter in genetics. Here we present a new method by which the distribution can be estimated. The method is fairly robust to changes in population size and admixture, and it can be corrected for any residual effects if a model of the demography is available . We apply the method to extensively sampled single nucleotide polymorphism data from humans and estimate the distribution of fitness effects for amino acid changing mutations. We show that a gamma distribution with a shape parameter of 0.23 provides a good fit to the data and we estimate that more than 50% of mutations are likely to have mild effects, such that they reduce fitness by between 1/1000 and 1/10. We also infer that fewer than 15% of new mutations are likely to have strongly deleterious effects. We estimate that on average a non-synonymous mutation reduces fitness by ~4.3% and that the average strength of selection acting against a non-synonymous polymorphism is ~9 x 10-5. We argue that the relaxation of natural selection due to modern medicine and reduced variance in family size is not likely to lead to a rapid decline in genetic quality, but that it will be very difficult to locate most of the genes involved in complex genetic diseases.

The advantages of publishing in open access journals

In the new issue of PLoS Biology (open access). I had trouble getting the end of the abstact for some reason so you might just want to click on the link (there is more below, after the abstract):

Citation Advantages of Open Access Articles
Gunther Eysenbach
PLoS Biology, v.4, May 2006, p.692-698

"Open access (OA) to the research literature has the potential to accelerate recognition and dissemination of research findings, but its actual effects are controversial. This was a longitudinal bibliometric analysis of a cohort of OA and non-OA articles published between June 8, 2004, and December 20, 2004, in the same journal (PNAS: Proceedings of the National Academy of Sciences). Article characteristics were extracted, and citation data were compared between the two groups at three different points in time: at "quasi-baseline" (December 2004, 0-6 mo after publication), in April 2005 (4-10 mo after publication), and in October 2005 (10-16 mo after publication). Potentially confounding variables, including number of authors, authors' lifetime publication count and impact, submission track, country of corresponding author, funding organization, and discipline, were adjusted for in logistic and linear multiple regression models. A total of 1,492 original research articles were analyzed: 212 (14.2% of all articles) were OA articles paid by the author, and 1,280 (85.8%) were non-OA articles. In April 2005 (mean 206 d after publication), 627 (49.0%) of the non-OA articles versus 78 (36.8%) of the OA articles were not cited (relative risk = 1.3 [95% Confidence Interval: 1.1-1.6]; p = 0.001). 6 mo later (mean 288 d after publication), non-OA articles were still more likely to be uncited (non-OA: 172 [13.6%], OA: 11 [5.2%]; relative risk = 2.6 [1.4-4.7]; p<0.001).the sd =" 2.5]" sd =" 2.0];" z =" 3.123;" p =" 0.002;" sd =" 10.4]" sd =" 4.9];" z =" 4.058;" ratio =" 2.1">

I find it surprising that there would be a significant increase in citations from papers in an open-access journal, since it is very probable that people who would be citing papers would already have access through their research institution.
The authors seem to have included a substantial number of controls, and also briefly examined self-archived journals, such as those that are on an author's website or can be obtained through Google or other internet site.

The authors briefly discuss in the conclusion below how more papers/journals might become open access:

"OA journals and hybrid journals like PNAS, as well as traditional publishers like Blackwell Publishing (“Online Open”), Oxford University Press (“Oxford Open”), and Springer (“Springer Open Choice”) are now offering authors an immediate OA option if the author pays a fee. Researchers, publishers, and policymakers confronted with the question of whether or not to invest in OA publishing have reason to believe that OA accelerates scientific advancement and knowledge translation of research into practice. While more work remains to be done to evaluate citation patterns over longer periods of time and in different fields and journals, this study provides evidence and new arguments for scientists and granting agencies to invest money into article processing fees to cover the costs of OA publishing. It also provides an incentive for publishers seeking to increase their impact factor to offer an OA option.

The findings indirectly also support policies of granting agencies which made (or consider to make) OA publishing (be it only through self-archiving) mandatory for grantees, as it illustrates the advantage of openess in the dissemination of knowledge. However, this study suggests that publishing papers as OA articles on the journal site facilitates knowledge dissemination to a greater degree than self-archiving, presumably because few scientists search the Internet or Google for articles if they have encountered an access problem on the journal Web site."

Friday, May 12, 2006

Increasing sexual dimorphism in skin color away from the equator.

Dienekes had a post on this paper in AJPA...plenty of good comments too.

The authors failed to support the hypothesis that as you move away from the equator, sexual dimorphism in skin color should increase. This hypothesis is based on the effect of sexual selection for lighter females and darker males.
In one of his comments, Dienekes raises an interesting question which is whether genes involved in skin pigmentation are sex-linked. Sexual dimorphism in skin color (that is found in many populations) might be sex-linked indirectly through effects of hormones, not the effects of skin color genes, per se, perhaps?

one more interesting thing: Apparently, according to the authors, the vitamin D hypothesis for lighter skin is not so convinving due to "a lack of paleopathological evidence of rickets , and the abundant dietary adaptations of humans living in such areas to acquire the component."

By the way, Jared Diamond (The Third Chimp) and Henry Harpending, I believe, have discussed the importance of sexual selection for skin color, since there are areas in the world that are not exposed to very much sun (new Guinea , for example), where skin color is dark. There are other examples that escape me right now.

Wednesday, May 10, 2006

ENCODE project, genome complexity

An interesting post by JP at Gene Expression on the ENCODE project and the scary complexity of the genome.

Tuesday, May 09, 2006

Affymetrix GeneChip 100K SNPs

Here's a paper from PLoS comparing the set of SNPs in the Affymetrix Gene Chip to the HapMap and Perlegen set of SNPs.

Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set
Dan L. Nicolae, Xiaoquan Wen, Benjamin F. Voight, Nancy J. Cox
PLoS Genetics 2(5):e67

The paper mentions that the HapMap SNPs were ascertained in Utah Europeans and Yoruba Nigerians. It doesn't say in what populations the SNPs for the Affymetrix 100k set were acsertained.
The authors mention the need to take into account LD between SNPs to reduce redundancy.

A major finding is that the SNPs in the Affymetrix set are undersampled from coding regions and pversampled from areas outside genes, compared to the Perlegen and HapMap SNPs, although the difference is not all that great..see this table.

..also they find, not surprisingly, more LD in European than Africans.

Abstract: Improvements in technology have made it possible to conduct genome-wide association mapping at costs within reach of academic investigators, and experiments are currently being conducted with a variety of high-throughput platforms. To provide an appropriate context for interpreting results of such studies, we summarize here results of an investigation of one of the first of these technologies to be publicly available, the Affymetrix GeneChip Human Mapping 100K set of single nucleotide polymorphisms (SNPs). In a systematic analysis of the pattern and distribution of SNPs in the Mapping 100K set, we find that SNPs in this set are undersampled from coding regions (both nonsynonymous and synonymous) and oversampled from regions outside genes, relative to SNPs in the overall HapMap database. In addition, we utilize a novel multilocus linkage disequilibrium (LD) coefficient based on information content (analogous to the information content scores commonly used for linkage mapping) that is equivalent to the familiar measure r2 in the special case of two loci. Using this approach, we are able to summarize for any subset of markers, such as the Affymetrix Mapping 100K set, the information available for association mapping in that subset, relative to the information available in the full set of markers included in the HapMap, and highlight circumstances in which this multilocus measure of LD provides substantial additional insight about the haplotype structure in a region over pairwise measures of LD.

On the promise of bioinformatics and evolutionary biology

Great post at John Hawks' Weblog on prostate cancer risk alleles, population differences, bio-informatics and evolutionary biology.

Saturday, May 06, 2006

"Multilevel selection"

It's funny how we abandon words like sociobiology or group selection, as if we are ashamed of them...Anyway, here's a link to "Group Selection" in Wikipedia. They mention that group selection is making a comeback, but Sober & Wilson and others (I suppose) prefer to call it "multilevel selection theory".

Admixture --- BMI, and blood pressure

In this paper, authors look at a population of 3207 African Americans and 1506 Hispanics (Mexican Americans from Starr County, Texas). They used Structure and 284 autosomal microsatellites in their IA analyses. They find median NA ancestry in Hispanics to be 35%. Their results are somewhat surprising in that they find a postive correlation between Caucasian admixture and BMI.

Racial admixture and its impact on BMI and blood pressure in African and Mexican Americans

Hua Tang, Eric Jorgenson, Maya Gadde, Sharon L. R. Kardia, D. C. Rao, Xiaofeng Zhu, Nicholas J. Schork, Craig L. Hanis, Neil Risch

Human Genetics: Published Online, 05 May 2006

Abstract: Admixed populations such as African Americans and Hispanic Americans present both challenges and opportunities in genetic epidemiologic research. Because of variation in admixture levels among individuals, case-control association studies may be subject to stratification bias. On the other hand, admixed populations also present special opportunities both for examining the role of genetic and environmental factors for observed racial/ethnic differences, and for possibly mapping alleles that contribute to such differences. Here we examined the distribution and relationship of individual admixture (IA) estimates with BMI and three measures of blood pressure in two admixed populations in the NHLBI Family Blood Pressure Program (FBPP): African Americans and Mexican Americans. For the African Americans, we observed modest but significant differences in average African IA among four recruitment sites. We observed a slight excess of African IA among hypertensives compared to normotensives, and a positive (non-significant) regression of African IA on blood pressure in untreated participants. Within Mexican Americans, we found no difference in average IA between hypertensives and normotensives, but a positive (marginally significant) regression of African IA on diastolic blood pressure. We also observed a significant positive regression of Caucasian IA (and negative regression of Native American IA) on BMI. Our results are suggestive of genetic differences between Africans and non-Africans that influence blood pressure, but such effects are likely to be modest compared to environmental ones. Excess obesity among Native Americans compared to whites is not consistent with a simple genetic explanation.

Friday, May 05, 2006

Green Beard (armpit effect, SRPM) growing

Post from Science Blog on greed beard "altruism" in lizards.

Self Recognition, color signals, and cycles of greenbeard mutualism and altruism
Barry Sinervo, Alexis Chaine, Jean Clobert, Ryan Calsbeek, Lisa Hazard, Lesley Lancaster, Andrew G. McAdam, Suzanne Alonzo, Gwynne Corrigan, and Michael E. Hochberg

PNAS: Published online May 1, 2006

Abstract: Altruism presents a challenge to evolutionary theory because selection should favor selfish over caring strategies. Greenbeard altruism resolves this paradox by allowing cooperators to identify individuals carrying similar alleles producing a form of genic selection. In side-blotched lizards, genetically similar but unrelated blue male morphs settle on adjacent territories and cooperate. Here we show that payoffs of cooperation depend on asymmetric costs of orange neighbors. One blue male experiences low fitness and buffers his unrelated partner from aggressive orange males despite the potential benefits of defection. We show that recognition behavior is highly heritable in nature, and we map genetic factors underlying color and self-recognition behavior of genetic similarity in both sexes. Recognition and cooperation arise from genome-wide factors based on our mapping study of the location of genes responsible for self-recognition behavior, recognition of blue color, and the color locus. Our results provide an example of greenbeard interactions in a vertebrate that are typified by cycles of greenbeard mutualism interspersed with phases of transient true altruism. Such cycles provide a mechanism encouraging the origin and stability of true altruism.

... and another recent paper in Nature that invokes green beard type marker recognition:

Mikhail Burtsev and Peter Turchin: 'Evolution of cooperative strategies from first principles', Nature, vol. 440, 20 April 2006, 1041-1044.

Abctract:One of the greatest challenges in the modern biological and social sciences is to understand the evolution of cooperative behaviour. General outlines of the answer to this puzzle are currently emerging as a result of developments in the theories of kin selection, reciprocity, multilevel selection and cultural group selection. The main conceptual tool used in probing the logical coherence of proposed explanations has been game theory, including both analytical models and agent-based simulations. The game-theoretic approach yields clear-cut results but assumes, as a rule, a simple structure of payoffs and a small set of possible strategies. Here we propose a more stringent test of the theory by developing a computer model with a considerably extended spectrum of possible strategies. In our model, agents are endowed with a limited set of receptors, a set of elementary actions and a neural net in between. Behavioural strategies are not predetermined; instead, the process of evolution constructs and reconstructs them from elementary actions. Two new strategies of cooperative attack and defence emerge in simulations, as well as the well-known dove, hawk and bourgeois strategies. Our results indicate that cooperative strategies can evolve even under such minimalist assumptions, provided that agents are capable of perceiving heritable external markers of other agents.

...commented on at:
John Hawks
Gene Expression

Thursday, May 04, 2006

Admixture Dynamics of Hispanics of Antioquia (Colombia)

Admixture dynamics in Hispanics: A shift in the nuclear genetic ancestry of a South American population isolate

Gabriel Bedoya, Patricia Montoya, Jenny Garcia, Ivan Soto, Stephane Bourgeois, Luis Carvajal, Damian Labuda, Victor Alvarez, Jorge Ospina, Philip W. Hedrick, Andres Ruiz-Linares

PNAS: published online April 28, 2006

Although it is well established that Hispanics generally have a mixed Native American, African, and European ancestry, the dynamics of admixture at the foundation of Hispanic populations is heterogeneous and poorly documented. Genetic analyses are potentially very informative for probing the early demographic history of these populations. Here we evaluate the genetic structure and admixture dynamics of a province in northwest Colombia (Antioquia), which prior analyses indicate was founded mostly by Spanish men and native women. We examined surname, Y chromosome, and mtDNA diversity in a geographically structured sample of the region and obtained admixture estimates with highly informative autosomal and X chromosome markers. We found evidence of reduced surname diversity and support for the introduction of several common surnames by single founders, consistent with the isolation of Antioquia after the colonial period. Y chromosome and mtDNA data indicate little population substructure among founder Antioquian municipalities. Interestingly, despite a nearly complete Native American mtDNA background, Antioquia has a markedly predominant European ancestry at the autosomal and X chromosome level, which suggests that, after foundation, continuing admixture with Spanish men (but not with native women) increased the European nuclear ancestry of Antioquia. This scenario is consistent with historical information and with results from population genetics theory.

some interesting lines:
"Because, in populations such as Antioquia, Spanish ancestry has historically been associated with higher social status and probably with greater reproductive success, it is possible that cultural selection also impacted the current genetic makeup of these populations."

, and:
"...continuous gene flow implies higher levels of {LD} than admixture followed by isolation, resulting in a variable density of markers required for mapping in populations with different admixture dynamics."

Wednesday, May 03, 2006

Ageing as an adaptation to stabilize population dynamics

This is a paper found through Science Blog -- see link here.
It is a paper in Evolutionary Ecology Research (March 2006), by Joshua Mitteldorf.

Chaotic Popluation dynamics and the evolution of ageing

Problem: "Genetic and demographic studies suggest that ageing is an adaptive genetic program, but population genetic analysis indicates that the benefit of ageing to the group is too slow and too diffuse to offset its individual cost."
Premise: "Demographic homeostasis is a major target of natural selection at the group level, with a strength that can compete with the imperative to higher individual reproductive value."

The author invokes a group selection type mechanism in enforcing the selective advantage of ageing. He uses computer simulation to show how this might work.
I'm not quite sure what to think of this. I'm afraid that I'm partly biased to dismiss it simply because it was published in a somewhat obscure journal. He claims among other things that current theories of aging are not well supported.

Here's a link to the Wikepedia entry on senescence. It goes through the evolutionary theories of aging and provides some links.

Tuesday, May 02, 2006

Clusters, clines, and geographic dispersion

This paper appeared in PLoS last December. It uses the CEPH panel of 1050 or so individuals from around the world. It looks at about 1000 markers (mostly microsatellites, and some I/D), and uses STRUCTURE to look at the effect of number of loci, sample size, number of clusters and geographic dispersion of the sample on clustering of individuals. Surprisingly, geographic dispersion does not have an effect on clustering.

Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure
Noah Rosenberg, Saurabh Mahajan, Sohini Ramachandran, Chengfeng Zhao, Jonathan K. Pritchard, Marcus W. Feldman
PLoS Genetics December 2005; 1: 660-671

Abstract: Previously, we observed that without using prior information about individual sampling locations, a clustering algorithm applied to multilocus genotypes from worldwide human populations produced genetic clusters largely coincident with major geographic regions. It has been argued, however, that the degree of clustering is diminished by use of samples with greater uniformity in geographic distribution, and that the clusters we identified were a consequence of uneven sampling along genetic clines. Expanding our earlier dataset from 377 to 993 markers, we systematically examine the influence of several study design variables—sample size, number of loci, number of clusters, assumptions about correlations in allele frequencies across populations, and the geographic dispersion of the sample—on the “clusteredness” of individuals. With all other variables held constant, geographic dispersion is seen to have comparatively little effect on the degree of clustering. Examination of the relationship between genetic and geographic distance supports a view in which the clusters arise not as an artifact of the sampling scheme, but from small discontinuous jumps in genetic distance for most population pairs on opposite sides of geographic barriers, in comparison with genetic distance for pairs on the same side. Thus, analysis of the 993-locus dataset corroborates our earlier results: if enough markers are used with a sufficiently large worldwide sample, individuals can be partitioned into genetic clusters that match major geographic subdivisions of the globe, with some individuals from intermediate geographic locations having mixed membership in the clusters that correspond to neighboring regions.
Locations of visitors to this page