Population history of Berthelot's pipit: colonization, gene flow and morphological divergence in Macaronesia

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

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Denisovan ancestry and population history of early East Asians

10.1101/2020.06.03.131995 ◽

2020 ◽

Cited By ~ 1

Author(s):

Diyendo Massilani ◽

Laurits Skov ◽

Mateja Hajdinjak ◽

Byambaa Gunchinsuren ◽

Damdinsuren Tseveendorj ◽

...

Keyword(s):

Gene Flow ◽

Human Population ◽

Modern Human ◽

Population History ◽

East Asians ◽

Aboriginal Australians ◽

North East ◽

History Of ◽

Female Member ◽

Admixture Event

AbstractWe present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in North East Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

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Gene flow from multiple sources maintains high genetic diversity and stable population history of Common MoorhenGallinula chloropusin China

Ibis ◽

10.1111/ibi.12579 ◽

2018 ◽

Vol 160 (4) ◽

pp. 855-869 ◽

Cited By ~ 4

Author(s):

Luzhang Ruan ◽

Wei Xu ◽

Yuqing Han ◽

Chaoying Zhu ◽

Bicai Guan ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Population History ◽

Stable Population ◽

Multiple Sources ◽

High Genetic Diversity ◽

History Of

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Denisovan ancestry and population history of early East Asians

Science ◽

10.1126/science.abc1166 ◽

2020 ◽

Vol 370 (6516) ◽

pp. 579-583

Author(s):

Diyendo Massilani ◽

Laurits Skov ◽

Mateja Hajdinjak ◽

Byambaa Gunchinsuren ◽

Damdinsuren Tseveendorj ◽

...

Keyword(s):

Gene Flow ◽

Human Population ◽

Modern Human ◽

Population History ◽

East Asians ◽

Aboriginal Australians ◽

History Of ◽

East And West ◽

Female Member ◽

Admixture Event

We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in northeastern Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

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Phylogeography, postglacial gene flow, and population history of North American Northern Goshawks (Accipiter gentilis)

The Auk ◽

10.1525/auk.2013.12120 ◽

2013 ◽

Vol 130 (2) ◽

pp. 342-354 ◽

Cited By ~ 7

Author(s):

Shelley Bayard de Volo ◽

Richard T. Reynolds ◽

Sarah A. Sonsthagen ◽

Sandra L. Talbot ◽

Michael F. Antolin

Keyword(s):

Gene Flow ◽

North American ◽

Population History ◽

Accipiter Gentilis ◽

History Of ◽

Northern Goshawks

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Genetic structure and sex-biased gene flow in the history of southern African populations

10.1101/237297 ◽

2017 ◽

Cited By ~ 1

Author(s):

Vladimir Bajić ◽

Chiara Barbieri ◽

Alexander Hübner ◽

Tom Güldemann ◽

Christfried Naumann ◽

...

Keyword(s):

Gene Flow ◽

Y Chromosome ◽

Southern Africa ◽

Social Dynamics ◽

Population History ◽

Eastern Africa ◽

The Social ◽

African Populations ◽

History Of ◽

Over Time

ABSTRACTObjectivesWe investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y-chromosome haplogroup E1b1b was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex-biased gene flow in southern Africa.Material and MethodsWe analyzed previously published complete mtDNA genome sequences and ~900 kb of NRY sequences from 23 populations from Namibia, Botswana and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y-linked STR loci for samples assigned to haplogroup E1b1b.ResultsOur results support an eastern African origin for Y-chromosome haplogroup E1b1b; however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting a more complex origin for pastoralism in this region. We confirm that the Bantu expansion had a notable genetic impact in southern Africa, and that in this region it was probably a rapid, male-dominated expansion. Furthermore, we find a significant increase in the intensity of sex-biased gene flow from north to south, which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.ConclusionsOur study shows that the population history of southern Africa has been very complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex-biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

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Introgression makes waves in inferred histories of effective population size

10.1101/121483 ◽

2017 ◽

Author(s):

John Hawks

Keyword(s):

Gene Flow ◽

Population Size ◽

Effective Population Size ◽

Population History ◽

Human Populations ◽

Effective Population ◽

History Of ◽

Or Gene ◽

Time Of Origin ◽

Past Population

AbstractHuman populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have large effects on the inference of effective population size.

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The population history of the Xibe in northern China: A comparison of autosomal, mtDNA and Y-chromosomal analyses of migration and gene flow

Forensic Science International Genetics ◽

10.1016/j.fsigen.2007.01.015 ◽

2007 ◽

Vol 1 (2) ◽

pp. 115-119 ◽

Cited By ~ 7

Author(s):

Gareth T. Powell ◽

Huanming Yang ◽

Chris Tyler-Smith ◽

Yali Xue

Keyword(s):

Gene Flow ◽

Northern China ◽

Population History ◽

History Of

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Episodes of gene flow and selection during the evolutionary history of domesticated barley

BMC Genomics ◽

10.1186/s12864-021-07511-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Peter Civáň ◽

Konstantina Drosou ◽

David Armisen-Gimenez ◽

Wandrille Duchemin ◽

Jérôme Salse ◽

...

Keyword(s):

Gene Flow ◽

Genetic Interaction ◽

Seedling Emergence ◽

Genetic Selection ◽

Pathogen Resistance ◽

Population History ◽

Founding Population ◽

Fertile Crescent ◽

History Of ◽

Cultivated Barley

Abstract Background Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is ‘non-brittleness’ of the rachis (the stem of the inflorescence), which facilitates harvesting of the crop. Other phenotypic differences appear to result from facultative or regional selective pressures. The population structure resulting from these regional events has been interpreted as evidence for multiple domestications or a mosaic ancestry involving genetic interaction between multiple wild or proto-domesticated lineages. However, each of the three mutations that confer non-brittleness originated in the western Fertile Crescent, arguing against multiregional origins for the crop. Results We examined exome data for 310 wild, cultivated and hybrid/feral barley accessions and showed that cultivated barley is structured into six genetically-defined groups that display admixture, resulting at least in part from two or more significant passages of gene flow with distinct wild populations. The six groups are descended from a single founding population that emerged in the western Fertile Crescent. Only a few loci were universally targeted by selection, the identity of these suggesting that changes in seedling emergence and pathogen resistance could represent crucial domestication switches. Subsequent selection operated on a regional basis and strongly contributed to differentiation of the genetic groups. Conclusions Identification of genetically-defined groups provides clarity to our understanding of the population history of cultivated barley. Inference of population splits and mixtures together with analysis of selection sweeps indicate descent from a single founding population, which emerged in the western Fertile Crescent. This founding population underwent relatively little genetic selection, those changes that did occur affecting traits involved in seedling emergence and pathogen resistance, indicating that these phenotypes should be considered as ‘domestication traits’. During its expansion out of the western Fertile Crescent, the crop underwent regional episodes of gene flow and selection, giving rise to a modern genetic signature that has been interpreted as evidence for multiple domestications, but which we show can be rationalized with a single origin.

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Genetic diversity and biogeographic history inform future conservation management strategies for the rare sunset frog (Spicospina flammocaerulea)

Australian Journal of Zoology ◽

10.1071/zo11005 ◽

2011 ◽

Vol 59 (2) ◽

pp. 63 ◽

Cited By ~ 3

Author(s):

D. L. Edwards ◽

J. D. Roberts

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Western Australia ◽

Agricultural Landscape ◽

Management Strategies ◽

Population History ◽

Conservation Strategy ◽

Management Options ◽

Biogeographic History ◽

History Of

Outlining the distribution of genetic variation, patterns of gene flow and clarifying the biogeographic processes underlying population history are critical components of a comprehensive conservation strategy for endangered or vulnerable species. We provide this information for the vulnerable sunset frog (Spicospina flammocaerulea) using a comprehensive genetic dataset (ND2) with samples from 17 of 22 geographic localities where this species has been found. From genetic, biogeographic and coalescent-based analyses, we document the existing genetic variation, likely movement patterns and explore the biogeographic history of S. flammocaerulea. While catchment-based genetic variation is well documented in other high-rainfall taxa in south-western Australia, a much more complex scenario including dispersal across ridge lines between catchments better explains the distribution of genetic variation and observed patterns of gene flow in S. flammocaerulea. The population history of S. flammocaerulea is strongly indicative of recent population contraction and expansion, which may be related to late Pleistocene climate fluctuations. This suggests that this species can adapt or move in response to fluctuating climates provided suitable habitats or expansion areas are available. However, like many other endemic taxa with limited geographic ranges in south-western Australia, the potential to shift distributions is hampered by being land-locked within an agricultural landscape, limiting management options in the face of climate change.

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