"Male Homosexual Preference" and social stratification

I don't necessarily buy positive selection for genes predisposing to male homosexuality in stratified societies via pleiotropic effects in females. But I could easily believe that evolutionary mismatch leads to higher levels of homosexuality in denser (though population density is apparently not a significant predictor in their analysis) and/or more stratified societies, and that sexually antagonistic selection plays some role in slowing down selection against homosexuality.

Male Homosexual Preference: Where, When, Why? (PLoS ONE):

Male homosexual preference (MHP) has long been of interest to scholars studying the evolution of human sexuality. Indeed, MHP is partially heritable, induces a reproductive cost and is common. MHP has thus been considered a Darwinian paradox. Several questions arise when MHP is considered in an evolutionary context. At what point did MHP appear in the human evolutionary history? Is MHP present in all human groups? How has MHP evolved, given that MHP is a reproductively costly trait? These questions were addressed here, using data from the anthropological and archaeological literature. Our detailed analysis of the available data challenges the common view of MHP being a “virtually universal” trait present in humans since prehistory. The conditions under which it is possible to affirm that MHP was present in past societies are discussed. Furthermore, using anthropological reports, the presence or absence of MHP was documented for 107 societies, allowing us to conclude that evidence of the absence of MHP is available for some societies. A recent evolutionary hypothesis has argued that social stratification together with hypergyny (the hypergyny hypothesis) are necessary conditions for the evolution of MHP. Here, the link between the level of stratification and the probability of observing MHP was tested using an unprecedented large dataset. Furthermore, the test was performed for the first time by controlling for the phylogenetic non-independence between societies. A positive relationship was observed between the level of social stratification and the probability of observing MHP, supporting the hypergyny hypothesis. [. . .]

Minor sub-Saharan and substantial Levantine admixture in Southern Europe

According to "The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape", something like a third of Southern Italian and Tuscan genetic ancestry appears to derive from the Levant in Roman times:

Moorjani et al [S?], who use a method based on allele frequency comparisons, and not haplotypes (ROLLOFF), found evidence for sub-Saharan African admixture in Sardinia 71±28 generations ago, at a proportion of 3%. These are the same Sardinians included in our analysis. In the largest Sardinian (sardi13) cluster in our analysis we infer West African admixture 66 (53-82) generations ago at a proportion of 2%.

S5.2 Continuous low level African admixture in the Mediterranean and Anatolia

We infer West African admixture across broad date ranges, but at low admixture proportions (admixture α < 0.07; Figs. 2 and S3) in several Mediterranean groups, consistent with a long term movement be- tween sub-Saharan Africa and southern Europe [S?,S?]. Specific West African admixture dating to the Arabic conquest of the Mediterranean [S?] is seen in Spanish (spani27: 1042 (740-1201CE)), Southern Italian and Sicilian (sicil30: 1105 (882-1250CE)), and Basque (basqu24: 886 (283-1162CE)) clusters. Earlier African admixture at low admixture proportion is inferred in the Cypriots (cypri12: 427(107- 734CE)), and a Sardinian cluster (sardi13: 36 (458BCE-430CE); α = 0.02). This latter event is con- sistent with the occurrence of A3b2-M13 (0.6%) and E1a-M44 (0.4%) African Y chromosome lineages in Sardinia [S?]. and the dating is more compatible with documented exchanges between the island and Mauretania Cesariensis in Roman times (2 nd century BCE to 2 nd century CE) than later displacements of northern-African males to Sardinia at the time of the Vandals rule (5 th century CE) [S?]. [. . .]

S5.3 A key role for the Levant in the genetic history of the Mediterranean

Early admixture involving source groups most similar to contemporary populations from in and around the Levant (which we define as the World Region containing individuals from Syria, Palestine, Lebanon, Jordan, Saudi, Yemen and Egypt) is seen at high proportions in several clusters from Italy dating to the first half of the first millennium CE, from Southern Italy (itali8: 295CE (72BCE-604CE); α = 0.34), Tuscany (tsi23: 400CE(30BCE-686); α = 0.29), and Sardinia, as well as in a large cluster from Armenia at an early date (armen27: 363BCE(1085BCE-383CE)). [. . .] these events loosely coincide with the formation of the pan-Mediterranean Roman Empire [S?], which may also have allowed increased gene flow from east to west Mediterranean. [. . .] We infer more recent Levant admixture in the French (frenc24: 728(424-1011CE)) and in a complex multiway event in a Spanish cluster (spani9: 668 (286-876CE)). The dates and sources of admixture in these cases are consistent with movements of Middle Eastern and North African individuals during the Islamic Conquest of Spain [S?], and suggest a legacy of this key moment in southern European history in the genomes of French as well as Spanish populations.

Autosomal DNA from Atapuerca pre- or proto-Neanderthals

DNA from Neandertal relative may shake up human family tree

The Sima people, who lived before Neandertals, were thought to have emerged in Europe. Yet their teeth, jaws, and large nasal cavities were among the traits that closely resembled those of Neandertals, according to a team led by paleontologist Juan-Luis Arsuaga of the Complutense University of Madrid. As a result, his team classified the fossils as members of Homo heidelbergensis, a species that lived about 600,000 to 250,000 years ago in Europe, Africa, and Asia. Many researchers have thought H. heidelbergensis gave rise to Neandertals and perhaps also to our species, H. sapiens, in the past 400,000 years or so. [. . .]

After 2 years of intense effort, paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology has finally sequenced enough nuclear DNA from fossils of a tooth and a leg bone from the pit to solve the mystery. [. . .] They scanned this DNA for unique markers found only in Neandertals or Denisovans or modern humans, and found that the two Sima fossils shared far more alleles—different nucleotides at the same address in the genome—with Neandertals than Denisovans or modern humans. “Indeed, the Sima de los Huesos specimens are early Neandertals or related to early Neandertals,” suggesting that the split of Denisovans and Neandertals should be moved back in time, Meyer reported at the meeting. [. . .]

“It resolves one controversy—that they’re in the Neandertal clade,” says paleoanthropologist Chris Stringer of the Natural History Museum in London. “But it’s not all good news: From my point of view, it pushes back the origin of H. sapiens from the Neandertals and Denisovans.” The possibility that humans were a distinct group so early shakes up the human family tree, promising to lead to new debate about when and where the branches belong.

Darren Curnoe points out:

What are the broader implications of the research for understanding the evolution of living humans?

First, the finding pushes the age of the shared human-Neanderthal ancestor well beyond 400,000 years ago, suggesting our species, H. sapiens, might also be at least this old.

Also, with the Atapuerca group living in Europe, it’s even possible that our species evolved in this or an adjacent region of Eurasia, and later migrated back into Africa.

And being close to the common ancestor, the Atapuerca fossils give us real insights into what it must have looked like and the ancestral body form of our own species.

The fossils from Europe, Asia and Africa from around this time are physically very diverse, with some researchers thinking they represent multiple species, only one of which could be the ancestor of living humans.

Question is, which one?

This new research suggests the European branch is closest among them all and deserves much more attention in this regard.

In contrast, we don’t know, and will doubtless ever know, whether Homo naledi had anything to do with the evolution of living humans, least of all whether its brain, mind or behaviour were anything like our own.

ASHG 2015: growth rate estimates from whole Y chromosome sequences

Estimation of growth rates for populations and haplogroups using full Y chromosome sequences.

F. L. Mendez; G. D. Poznik; C. D. Bustamante; 1000 Genomes Project Consortium

Department of Genetics, Stanford University, Stanford, CA.

Evolutionary processes affecting a population influence gene genealogies across the genome. Coalescent theory provides the mathematical framework to connect realized genealogies to the underlying evolutionary processes. However, in most cases, information about the genealogies is obtained only indirectly through the observation of genetic variation. Therefore, in general, very limited information about any individual locus is available. As the longest non-recombining portion of the human genome, the Y chromosome accumulates mutations relatively quickly. When large amounts of sequence are used, the Y chromosome provides an unparalleled ability to resolve the structure and coalescence times of its genealogy. Because patterns of variation in the Y chromosome are only influenced by processes affecting men, they can be used to study both demographic and social phenomena. The 1000 Genomes Project includes whole Y-chromosome data from more than 1000 men and has an extensive representation of most lineages that have experienced recent massive expansions in size. Though the dynamics of population growth have likely changed over time, we are more interested in the growth rates at the times of these rapid expansions than on an average effect. To study this, we have developed a new method that takes advantage of the temporal resolution provided by Y-chromosome data and of historical data, while accounting for the uncertainties associated with the coalescent and mutational processes. We estimate the growth rates for several branches of the Y-chromosome tree, including those in Europe, sub-Saharan Africa and South Asia. We estimate that several lineages within the European R1b, sub-Saharan African E1b, and South Asian R1a haplogroups experienced growth rates of at least 20-60% per generation at the onset of their massive expansions, some 3-5 thousand years ago. These high growth rates are comparable to those experienced by human populations during the 20th century. However, we find that most observed genealogies are unlikely to be the result of whole population expansion or of natural selection.

ASHG 2015: Population differentiation analysis of 54,734 European Americans

Population differentiation analysis of 54,734 European Americans reveals independent evolution of ADH1Bgene in Europe and East Asia.

K. J. Galinsky1,2 ; G. Bhatia2,3 ; P. Loh2,3 ; S. Georgiev4 ; S. Mukherjee5 ; N. J. Patterson2 ; A. L. Price1,2,3

Population differentiation is a widely used approach to detect the action of natural selection. Existing methods search for unusual differentiation in allele frequencies across discrete populations, e.g. using FST. Loci that are unusually differentiated with respect to the genome-wide FST or with respect to a null distribution of F­ST are reported as signals of selection. These approaches are particularly powerful for closely related populations with large sample sizes.However, population genetic data often is not naturally partitioned into discrete populations. We developed a test for selection that uses SNP loadings from principal components analysis (PCA). For a given PC reflecting geographic ancestry, under the null hypothesis of no selection, the square of the SNP loadings, rescaled by a scaling factor derived from the eigenvalue of the PC, follows a chi-square (1 d.o.f.) distribution. This statistic is able to infer selection with genome-wide significance, a key consideration in genome scans for selection. We confirmed via simulations that this statistic has correct null calibration under a wide range of demographies and is well-powered to detect selection at large sample sizes.We applied the method to a cohort of 54,734 European Americans genotyped on genome-wide arrays. PCs were inferred using our FastPCA software (running time: 57 minutes). The top 4 PCs corresponded to clines of Irish, Eastern European, Northern European, Southeast European and Ashkenazi Jewish ancestry, validated via PCA projection of samples of known ancestry. We detected genome-wide significant signals of selection at 4 known selected loci (LCT, HLA, OCA2 and IRF4) and 3 novel loci: ADH1B, IGFBP3 and IGH. 2 of the 3 novel loci could not be detected using discrete-population tests (or other existing tests). The ADH1B gene is associated with alcoholism (via the same coding SNP rs1229984 producing a signal in our selection scan) and has been shown to be under recent selection in East Asians (via a haplotype-based test for recent selection); we show here that it is a rare example of independent evolution on two continents. The IGFBP3 gene and IGH locus have been implicated in breast cancer and multiple sclerosis, respectively. Our results show that application of our PC-based selection statistic to large data sets can infer novel, genome-wide significant signals of selection at loci linked to disease traits.

ASHG 2015: The lingering load of archaic admixture in modern human populations

The lingering load of archaic admixture in modern human populations.

K. Harris1,2 ; R. Nielsen2,3

1) Stanford University, Stanford, CA; 2) University of California Berkeley, Berkeley, CA; 3) Center for Bioinformatics, University of Copenhagen, Copenhagen, Denmark.

Founder effects and bottlenecks can damage fitness by letting deleterious alleles drift to high frequencies. This almost certainly imposed a burden on Neanderthals and Denisovans, archaic hominid populations whose genetic diversity was less than a quarter of the level seen in humans today. A more controversial question is whether the out-of-Africa bottleneck created differences in genetic load between modern human populations. Some previous studies concluded that this bottleneck saddled non-Africans with potentially damaging genetic variants that could affect disease incidence across the globe today (e.g. Lohmueller, et al. 2009; Fu, et al. 2014), while other studies have concluded that there is little difference in genetic load between Africans and non-Africans (e.g. Simons, et al. 2014; Do, et al. 2015). Although previous studies have devoted considerable attention to simulating the accumulation of deleterious mutations during the out-of-Africa bottleneck, none to our knowledge have incorporated the fitness effects of introgression from Neanderthals into non-Africans. We present simulations showing that archaic introgression may have had a greater fitness effect than the out-of-Africa bottleneck itself, saddling non-Africans with weakly deleterious alleles that accumulated as nearly neutral variants in Neanderthals. Assuming that the exome experiences deleterious mutations with additive fitness effects drawn from a previously inferred gamma distribution, we predict that the fitness of the average Neanderthal was about 50% lower than the fitness of the average human, implying the existence of strong selection against early Neanderthal-human hybrids. This is a direct consequence of mutation accumulation during a period of low Neanderthal population size that is thought to have lasted ten times longer than the out-of-Africa bottleneck (Pruefer, et al. 2014). Although our model predicts some transmission of deleterious Neanderthal variation to present-day non-Africans, it also predicts that many Neanderthal alleles have been purged away, depleting conserved genomic regions of Neanderthal ancestry as observed empirically by Sankararaman, et al. (2014). Our results imply that the deficit of Neanderthal DNA from functional genomic regions can be explained without the action of epistatic reproductive incompatibilities between human and Neanderthal alleles.

ASHG 2015: The genetic structure of the Saudi Arabian population

The genetic structure of the Saudi Arabian population.

H. Al-Saud1 ; SM. Wakil1 ; BF. Meyer1 ; M. Falchi2 ; N. Dzimiri1

1) Genetics Department, King Faisal Hospital and Research Centre, Riyadh, Saudi Arabia; 2) Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom.

Saudi Arabia is the largest Gulf Cooperation Council (GCC) country. Its population consists of different tribes that originated in the northern, western, eastern, middle and south regions of Saudi Arabia, respectively. Due to political and cultural reasons, there has historically been very limited admixture between different tribes. People from the different Saudi tribes then migrated from Saudi Arabia, contributing to foundation of the populations now inhabiting other Gulf countries. Few population genetics research projects have been conducted on this highly consanguineous population that has been shown to have one of the highest prevalence in the world of recessive disorders and common metabolic diseases, especially diabetes. It is therefore important to identify the genetic substructures of the Saudi population, both to help in tracing the migratory genetic flows that contributed to other Gulf populations, and to permit designing of efficient genetic studies aimed at the identification of risk factors underlying common and rare diseases in the GCC countries. We carried out the largest population genetic study in Saudi Arabia to date, by genotyping 2,150 Saudi nationals sampled from different regions of Saudi Arabia using Axiom GWH-96 Array (Affymetrix) arrays. Model-based and model-free clustering were applied to these data, including in our analyses data on eight populations (encompassing Europe, America, Oceana, East Asia, Central South Asia, Middle East, Africa and Qatari populations) from the Human Genetic Diversity Project (HGDP) data set. We identified clear clustering of the Saudi samples into different subgroups, with some tribes showing similarity with both Central East Asian (Kalash Pakistan, Balochi Pakistan, Sindhi Pakistan, Makrani Pakistan and Brahui Pakistan subpopulations) European (Orkney Islands Europe, Russian Europe and Russian Caucasus subpopulations) and Qatari populations, while other tribes appear to show specificity of background.These data strongly support the presence of genetic stratification within the Saudi population, and suggest the presence of subgroups that are characterized by a unique genetic background different from other Arabian populations. Our findings constitute a valuable resource for the investigation of both general and population-specific genetic risk variants associated with different disorders in this population.

ASHG 2015: Reconstructing genetic history of Siberian and Northeastern European populations

Reconstructing genetic history of Siberian and Northeastern European populations.

E. Wong1 ; A. Khrunin2 ; L. Nichols2 ; D. Pushkarev3 ; D. Khokhrin2 ; D. Verbenko2 ; O. Evgradov4 ; J. Knowles4 ; J. Novembre5; S. Limborska2 ; A. Valouev1

Siberia and Western Russia are home to some of the least studied ethnic groups in the world, and their genetic history holds keys to understanding peopling of the world. We present whole-genome sequencing data from 28 individuals belonging to 14 distinct indigenous populations from that region. We used these datasets together with an additional 32 modern-day and 15 ancient human genomes to build and compare autosomal, Y-DNA and mtDNA trees and delineate genetic history. Our analyses uncover complex migratory processes that shaped the genetic landscapes in Asia and Europe. Admixture events between ancient Siberian groups resulted in distinct ancestries of nowadays Western and Eastern Siberians. Western Siberians share genetic affinity with modern Europeans. Both can trace their ancestry to the lineage of a 24,000-year-old Siberian Mal’ta boy. For Eastern Siberians, they have much weaker genetic affinity with Europeans and their ancestor separated from East Asians much later (approximately 10,000 years ago). Major migration wave from Eastern Siberians into Western Siberian groups occurred approximately 7,000 years ago, and it extended into Northeastern Europe. This is based on the admixtures we observed between Siberians and lineages represented by the 5,000-year-old hunter-gatherer Ire8 from Pitted Ware Culture excavated in Sweden, the 2,900-year-old Iron age Hungarian IR1 from the Mezocsat Culture, and modern-day northeastern Europeans. Our whole-genome data based on a broad sample of populations in Siberia and Western Russia provides new insights at a high-resolution into the genetic history of Eurasians.

Population genetic differentiation of height and body mass index across Europe

From Visscher and colleagues:

Population genetic differentiation of height and body mass index across Europe

Across-nation differences in the mean values for complex traits are common1, 2, 3, 4, 5, 6, 7, 8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58).

ASHG 2015: ancient Anatolians similar to European Neolithic farmers and distinct from modern Near Easterners

Genome-wide data on 34 ancient Anatolians identifies the founding population of the European Neolithic.

I. Lazaridis1,2 ; D. Fernandes3 ; N. Rohland1,2 ; S. Mallick1,2,4 ; K. Stewardson1,4 ; S. Alpaslan5 ; N. Patterson2 ; R. Pinhasi*3 ; D. Reich*1,2,4

1) Department of Genetics, Harvard Medical School, Boston, MA USA; 2) Broad Institute of MIT and Harvard, Cambridge, MA USA; 3) Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland; 4) Howard Hughes Medical Institute, Harvard Medical School, Boston, MA USA; 5) Independent physical anthropologist, Netherlands.

It has hitherto been difficult to obtain genome-wide data from the Near East. By targeting the inner ear region of the petrous bone for extraction [Pinhasi et al., PLoS One 2015] and using a genome-wide capture technology [Haak et al., Nature, 2015] we achieved unprecedented success in obtaining genome-wide data on more than 1.2 million single nucleotide polymorphism targets from 34 Neolithic individuals from Northwestern Anatolia (~6,300 years BCE), including 18 at greater than 1× coverage. Our analysis reveals a homogeneous population that is genetically a plausible source for the first farmers of Europe in the sense of (i) having a high frequency of Y-chromosome haplogroup G2a, and (ii) low Fst distances from early farmers of Germany (0.004 ± 0.0004) and Spain (0.014 ± 0.0009). Model-free principal components and model-based admixture analyses confirm a strong genetic relationship between Anatolian and European farmers. We model early European farmers as mixtures of Neolithic Anatolians and Mesolithic European hunter-gatherers, revealing very limited admixture with indigenous hunter-gatherers during the initial spread of Neolithic farmers into Europe. Our results therefore provide an overwhelming support to the migration of Near Eastern/Anatolian farmers into southeast and Central Europe around 7,000-6,500 BCE [Ammerman & Cavalli Sforza, 1984, Pinhasi et al., PLoS Biology, 2005]. Our results also show differences between early Anatolians and all present-day populations from the Near East, Anatolia, and Caucasus, showing that the early Anatolian farmers, just as their European relatives, were later demographically replaced to a substantial degree.

ASHG 2015: Moorish admixture in Spain

Fine scale population structure of Spain and the genetic impact of historical invasions and migrations.

C. Bycroft1 ; C. Fernandez-Rozadilla1,2 ; A. Carracedo2 ; C. Ruiz-Ponte2 ; I. Quintela-García3 ; P. Donnelly1,4 ; S. Myers1,4

As well as being linguistically and culturally diverse, the Iberian Peninsula is unusual among European regions in that its demographic history includes a prolonged and large-scale occupation by people of predominately north-west African origin. Therefore, the Iberian Peninsula provides a unique opportunity for studying fine-scale population structure and admixture, and to test cutting-edge methods of detecting complex or subtle population genetic patterns.Previous studies using Y-chromosome, mtDNA as well as autosomal data have detected limited genetic structure in Iberia. However, powerful new methods and larger datasets mean it has recently become possible to detect and characterise genetic differentiation at a sub-national level. We performed the largest and most comprehensive study of Spanish population structure to date by analysing a dataset of ~1,400 Spanish individuals typed at ~700,000 SNPs. Using the fineSTRUCTURE method we detected striking and rich patterns of population differentiation within Spain, at scales down to tens of kilometres. Strikingly, the major axis of genetic differentiation in Spain runs from west to east, while conversely there is remarkable genetic similarity in the north-south direction.To infer details of historical population movements into Spain, we analysed Spain alongside a sample of ~6,000 individuals from Europe, North Africa, and sub-Saharan Africa. Across Spanish groups, we identify varying genetic contributions from north-west African ancestral populations, at times that all fall within the period of Islamic occupation. We also identify Basque-like admixture within Spanish groups to the south of the Basque-speaking region, implying southerly gene flow from this region. This analysis has revealed details of the strengths and weaknesses of different approaches to investigating population genetic history, as well as providing important new insights into the complex genetic history of Spain.

ASHG 2015: Historical mating patterns in the U.S.

Historical mating patterns in the U.S. revealed through admixture and IBD patterns from genome-wide data from over 800,000 individuals.

J. M. Granka1 ; Y. Wang1 ; E. Han1 ; J. K. Byrnes1 ; A. Kermany1 ; R. E. Curtis2 ; P. Carbonetto1 ; K. Noto1 ; M. J. Barber1 ; N. M. Myres2 ; C. A. Ball1 ; K. G. Chahine2

1) AncestryDNA, San Francisco, CA; 2) AncestryDNA, Provo, UT.

Within a diverse population like the United States, many individuals are admixed, with ancestry from many worldwide regions. Non-random mating and migration can result in non-random combinations of ancestries within ad­­­mixed individuals (i.e., certain sets of ancestries may be common, and others may be rare); such dynamics can also affect patterns of identity-by-descent (IBD) among admixed and non-admixed individuals. To shed insight into historical mating and migration, we study genome-wide genotype data of over 800,000 AncestryDNA customers, as well as a subset of over 400,000 born in the US. First, we use a supervised algorithm to estimate individuals’ genetic admixture proportions across 26 global regions. We measure correlations between the estimated ancestries, and find certain sets of ancestries to frequently co-occur in individuals’ estimates. Such relationships may reflect historical events; e.g., the association between ancestry from the Americas and the Iberian Peninsula could reflect Colonial Era admixture. In addition to historical mating patterns, however, the admixture inference procedure and the delineation of global regions could also impact such correlations. To disentangle whether these trends could reflect mating patterns and preferences, we examine associations between the estimated ancestries of the parents of over 10,000 trios. Observed correlations agree with many of those identified within individuals, and potentially reflect more recent historical trends. Thirdly, we extend our study to IBD patterns in an inferred IBD network among genotyped individuals. Sub-clusters of the IBD network, which can often be annotated by ethnicity or historical US migration, are often inter-connected by bridging IBD connections; we highlight several connected sub-clusters in light of findings from genetic ancestry. Finally, we corroborate findings from these three analyses, as well as their potential timescales, by examining over 500,000 AncestryDNA customer pedigrees. Associations of country-level birth locations between pairs of couples support many of the non-random associations of ethnicities and IBD connections identified using genetic data. Many of the associations we observe reflect historical phenomena, and while not conclusive about their cause, suggest that many individuals with admixed ancestry, including those in the US, have present-day genetic signatures reflecting the migration and subsequent non-random mating of their ancestors.

Ancient genomes from Iberia

Both papers are freely accessible.

A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures (pdf; supplementary material)

The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: an initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK tradition, which followed the Danube River into Central Europe. While genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400 year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter-gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques (pdf; supplementary material)

The consequences of the Neolithic transition in Europe—one of the most important cultural changes in human prehistory—is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter–gatherers. The proportion of hunter–gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

Group Size and Social Interaction: a Canada-US Comparison of Interracial Marriage

Group Size and Social Interaction: a Canada-US Comparison of Interracial Marriage (pdf)

Abstract: While black-white intermarriage is uncommon in the United States, blacks in Canada are just as likely to marry whites as to marry blacks. Asians, in contrast, are more likely to marry whites in the US than in Canada. We test the claim that high rates of interracial marriage are indicative of high levels of social integration against Peter Blau's "macrostructural" thesis that relative group size is the key to explaining differences in intermarriage rates across marriage markets. Using micro-data drawn from the American Community Survey and the Canadian Census, we demonstrate that the relative size of racial groups accounts for over two-thirds of the US-Canada difference in black-white unions and largely explains the cross-country difference in Asian-white unions. Under broadly similar social and economic conditions, a large enough difference in relative group size can become the predominant determinant of group differences in the prevalence of interracial unions.