The Behavior of Admixed Populations in Neighbor-Joining Inference of Population Trees

Kopelman, Naama M.; Stone, Lewi; Gascuel, Olivier; Rosenberg, Noah A.

doi:10.1142/9789814447973_0027

Cited by 19 publications

(21 citation statements)

References 32 publications

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“…As expected, African populations exhibited the greatest diversity (Pool et al 2012) and clustered at the base of the tree while European populations clustered at the tip. North American and Australian populations generally clustered between African and European populations (Figure 2), a pattern that supports the model (Kopelman et al 2013) that both North American and Australian populations result from secondary contact of European and African ones.…”

Section: Resultssupporting

confidence: 81%

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Bergland

Tobler

González

et al. 2014

Preprint

130

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Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this hybridization event likely contributed to genome-wide patterns of parallel clinal variation between continents. The pervasive effects of admixture mean that differentiation at only several hundred loci can be attributed to the operation of spatially varying selection using an F ST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation in D. melanogaster and provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as temperate endemics.

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Section: Resultssupporting

confidence: 81%

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Bergland

Tobler

González

et al. 2014

Preprint

130

View full text Add to dashboard Cite

show abstract

“…As expected from the analyses of population genetic similarity and prior neighborjoining analysis of admixed populations (Kopelman et al 2013), the Q3 (African) and African Americans do not form large clusters, but rather appear as multiple individual branches close to the indigenous African populations, most similar to their African admixture source (Fig. 6E,F).…”

Section: Wwwgenomeorgsupporting

confidence: 69%

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

et al. 2016

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An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out-of-Africa migrations that occurred between 125,000 and 60,000 yr ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups, and these genomes showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out-of-Africa bottleneck but before the major Neanderthal admixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, although the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out-of-Africa migrations.

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“…Considering all comparisons between East Asian populations and Middle Eastern, European, and Central and South Asian populations, mean pairwise F ST is 0.091 (SD = 0.024, 504 pairs). The African American and Mexican American populations cluster at intermediate distances between the European cluster and most African and Central American populations, respectively, reflecting the expectation of intermediate placement for admixed groups [9], [36]–[39]. Note that due to differences in their dimensionality reduction approaches, the MDS and neighbor-joining analyses are not always in agreement: for example, the Seri and Pima from northwestern Mexico cluster together on the MDS plot, whereas they have a relatively high F ST value (0.094), as shown by the long branches separating these populations on the neighbor-joining tree.…”

Section: Resultsmentioning

confidence: 79%

Patterns of Admixture and Population Structure in Native Populations of Northwest North America

et al. 2014

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The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

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The Behavior of Admixed Populations in Neighbor-Joining Inference of Population Trees

Cited by 19 publications

References 32 publications

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

Patterns of Admixture and Population Structure in Native Populations of Northwest North America

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