Dating the age of admixture via wavelet transform analysis of genome-wide data

Reconstructing the population history of European Romani from genome-wide data

The Romani, the largest European minority group with approximately 11 million people, constitute a mosaic of languages, religions, and lifestyles while sharing a distinct social heritage. Linguistic and genetic studies have located the Romani origins in the Indian subcontinent. However, a genome-wide perspective on Romani origins and population substructure, as well as a detailed reconstruction of their demographic history, has yet to be provided. Our analyses based on genome-wide data from 13 Romani groups collected across Europe suggest that the Romani diaspora constitutes a single initial founder population that originated in north/northwestern India ~1.5 thousand years ago (kya). Our results further indicate that after a rapid migration with moderate gene flow from the Near or Middle East, the European spread of the Romani people was via the Balkans starting ~0.9 kya. The strong population substructure and high levels of homozygosity we found in the European Romani are in line with genetic isolation as well as differential gene flow in time and space with non-Romani Europeans. Overall, our genome-wide study sheds new light on the origins and demographic history of European Romani.

The date of interbreeding between Neandertals and modern humans

Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

One of the key discoveries from the analysis of the Neandertal genome is that Neandertals share more genetic variants with non-Africans than with Africans. This observation is consistent with two hypotheses: interbreeding between Neandertals and modern humans after modern humans emerged out of Africa or population structure in the ancestors of Neandertals and modern humans. These hypotheses make different predictions about the date of last gene exchange between the ancestors of Neandertals and modern non-Africans. We estimate this date by measuring the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

Human population admixture in Asia

Genetic admixture in human, the result of inter-marriage among people from different well-differentiated populations, has been extensively studied in the New World, where European colonization brought contact between peoples of Europe, Africa, and Asia and the Amerindian populations. In Asia, genetic admixing has been also prevalent among previously separated human populations. However, studies on admixed populations in Asia have been largely underrepresented in similar efforts in the New World. Here, I will provide an overview of population genomic studies that have been published to date on human admixture in Asia, focusing on population structure and population history.

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5-10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4-5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

Genomic data reveal a complex making of humans

In the last few years, two paradigms underlying human evolution have crumbled. Modern humans have not totally replaced previous hominins without any admixture, and the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level. Here we review current evidence about archaic admixture and lack of strong selective sweeps in humans. We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.

Principal components analysis of population admixture

With the availability of high-density genotype information, principal components analysis (PCA) is now routinely used to detect and quantify the genetic structure of populations in both population genetics and genetic epidemiology. An important issue is how to make appropriate and correct inferences about population relationships from the results of PCA, especially when admixed individuals are included in the analysis. We extend our recently developed theoretical formulation of PCA to allow for admixed populations. Because the sampled individuals are treated as features, our generalized formulation of PCA directly relates the pattern of the scatter plot of the top eigenvectors to the admixture proportions and parameters reflecting the population relationships, and thus can provide valuable guidance on how to properly interpret the results of PCA in practice. Using our formulation, we theoretically justify the diagnostic of two-way admixture. More importantly, our theoretical investigations based on the proposed formulation yield a diagnostic of multi-way admixture. For instance, we found that admixed individuals with three parental populations are distributed inside the triangle formed by their parental populations and divide the triangle into three smaller triangles whose areas have the same proportions in the big triangle as the corresponding admixture proportions. We tested and illustrated these findings using simulated data and data from HapMap III and the Human Genome Diversity Project.

The impact of recent events on human genetic diversity

The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.

Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion

Although the Austronesian expansion had a major impact on the languages of Island Southeast Asia, controversy still exists over the genetic impact of this expansion. The coexistence of both Asian and Papuan genetic ancestry in Eastern Indonesia provides a unique opportunity to address this issue. Here, we estimate recombination breakpoints in admixed genomes based on genome-wide SNP data and date the genetic admixture between populations of Asian vs. Papuan ancestry in Eastern Indonesia. Analyses of two genome-wide datasets indicate an eastward progression of the Asian admixture signal in Eastern Indonesia beginning about 4,000-3,000 y ago, which is in excellent agreement with inferences based on Austronesian languages. The average rate of spread of Asian genes in Eastern Indonesia was about 0.9 km/y. Our results indicate that the Austronesian expansion had a strong genetic as well as linguistic impact on Island Southeast Asia, and they significantly advance our understanding of the biological origins of human populations in the Asia-Pacific region.

Learning about human population history from ancient and modern genomes

Genome-wide data, both from SNP arrays and from complete genome sequencing, are becoming increasingly abundant and are now even available from extinct hominins. These data are providing new insights into population history; in particular, when combined with model-based analytical approaches, genome-wide data allow direct testing of hypotheses about population history. For example, genome-wide data from both contemporary populations and extinct hominins strongly support a single dispersal of modern humans from Africa, followed by two archaic admixture events: one with Neanderthals somewhere outside Africa and a second with Denisovans that (so far) has only been detected in New Guinea. These new developments promise to reveal new stories about human population history, without having to resort to storytelling.

New approaches to disease mapping in admixed populations

Admixed populations such as African Americans and Hispanic Americans are often medically underserved and bear a disproportionately high burden of disease. Owing to the diversity of their genomes, these populations have both advantages and disadvantages for genetic studies of complex phenotypes. Advances in statistical methodologies that can infer genetic contributions from ancestral populations may yield new insights into the aetiology of disease and may contribute to the applicability of genomic medicine to these admixed population groups.