Bayesian inference of admixture graphs on Native American and Arctic populations

Nielsen, Sandro; Vaughn, Andrew H.; Leppälä, Kalle; Landis, Michael J.; Mailund, Thomas; Nielsen, Rasmus

doi:10.1371/journal.pgen.1010410

Cited by 17 publications

(29 citation statements)

References 28 publications

(42 reference statements)

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“…Except for certain cases where Anzick-1 is one source , all other models were rejected, and consequently, we found no evidence of PPE admixture into present-day PNW populations, at least based on our dataset ( Tables S3 and S4 ). We note that it was recently suggested that Saqqaq may not serve as the best proxy for gene flow into the NNA because the PPE source that contributed ancestry to some North American groups may have been more closely related to the Koryak than to the Paleo-Inuit 88 ; however, our results are consistent when the Koryak and Chukchi peoples are used a source.…”

Section: Resultscontrasting

confidence: 49%

A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska

Aqil¹,

Gill²,

Gökçümen³

et al. 2023

iScience

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Section: Resultscontrasting

confidence: 49%

A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska

Aqil¹,

Gill²,

Gökçümen³

et al. 2023

iScience

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“…To further support our ABC-RF models, we performed an admixture graph estimate using AdmixtureBayes ( Nielsen et al 2023 ). AdmixtureBayes is a Bayesian approach that uses a reversible jump Markov Chain Monte Carlo (MCMC) to find a best-fitting graph that describes the ancestry of the analyzed populations, not requiring a priori information (i.e., a tree topology) on populations splits or the number of admixture events.…”

Section: Methodsmentioning

confidence: 99%

Tracing Eastern Wolf Origins From Whole-Genome Data in Context of Extensive Hybridization

Vilaça

Donaldson

Benazzo

et al. 2023

Molecular Biology and Evolution

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Southeastern Canada is inhabited by an amalgam of hybridizing wolf-like canids, raising fundamental questions regarding their taxonomy, origins, and timing of hybridization events. Eastern wolves (Canis lycaon), specifically, have been the subject of significant controversy, being viewed as either a distinct taxonomic entity of conservation concern or a recent hybrid of coyotes (C. latrans) and grey wolves (C. lupus). Mitochondrial DNA analyses show some evidence of eastern wolves being North American evolved canids. In contrast, nuclear genome studies indicate eastern wolves are best described as a hybrid entity, but with unclear timing of hybridization events. To test hypotheses related to these competing findings we sequenced whole genomes of 25 individuals, representative of extant Canadian wolf-like canid types of known origin and levels of contemporary hybridization. Here we present data describing eastern wolves as a distinct taxonomic entity that evolved separately from grey wolves for the past ∼67,000 years with an admixture event with coyotes ∼37,000 years ago. We show that Great Lakes wolves originated as a product of admixture between grey wolves and eastern wolves after the last glaciation (∼8,000 years ago) while eastern coyotes originated as a product of admixture between “western” coyotes and eastern wolves during the last century. Eastern wolf nuclear genomes appear shaped by historical and contemporary gene flow with grey wolves and coyotes, yet evolutionary uniqueness remains among eastern wolves currently inhabiting a restricted range in southeastern Canada.

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“…To further explore the ancestry of samples, we obtained an admixture graph estimate using AdmixtureBayes (Nielsen et al, 2023).…”

Section: Species Tree and Divergence Times Estimation With Snp Datamentioning

confidence: 99%

Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary

Dalapicolla,

Weir,

Vilaça

et al. 2024

Ecology and Evolution

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The “Amazon tipping point” is a global change scenario resulting in replacement of upland terra‐firme forests by large‐scale “savannization” of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra‐firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole‐genomes of an Amazonian endemic organism (Scale‐backed antbirds – Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon–Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80–60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical “tipping point” conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.

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Bayesian inference of admixture graphs on Native American and Arctic populations

Cited by 17 publications

References 28 publications

A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska

A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska

Tracing Eastern Wolf Origins From Whole-Genome Data in Context of Extensive Hybridization

Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary

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