scholarly journals Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

2018 ◽  
Author(s):  
Leonardo Arias ◽  
Roland Schröder ◽  
Alexander Hübner ◽  
Guillermo Barreto ◽  
Mark Stoneking ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Native American ◽  
Cultural Practices ◽  
Demographic History ◽  
Population History ◽  
Human Populations ◽  
Effective Population ◽  
Trade Networks ◽  
Males And Females ◽  
The Impact

ABSTRACTHuman populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language.We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

scholarly journals Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

2019 ◽  
Author(s):  
Quentin Rougemont ◽  
Jean-Sébastien Moore ◽  
Thibault Leroy ◽  
Eric Normandeau ◽  
Eric B. Rondeau ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Demographic History ◽  
Glacial Refugium ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Geographical Patterns ◽  
Genome Wide Data

AbstractA thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

scholarly journals The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives

2016 ◽  
Author(s):  
Yuval B. Simons ◽  
Guy Sella
Keyword(s):  
Demographic History ◽  
Population History ◽  
Human Populations ◽  
Data Sets ◽  
Loss Of Function ◽  
Mutation Load ◽  
Synonymous Mutations ◽  
Show Evidence ◽  
Out Of Africa ◽  
The Impact

AbstractOver the past decade, there has been both great interest and confusion about whether recent demographic events—notably the Out-of-Africa-bottleneck and recent population growth—have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.

scholarly journals Fine-scale population structure and demographic history of British Pakistanis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Elena Arciero ◽  
Sufyan A. Dogra ◽  
Daniel S. Malawsky ◽  
Massimo Mezzavilla ◽  
Theofanis Tsismentzoglou ◽  
...  
Keyword(s):  
Population Structure ◽  
Disease Risk ◽  
Demographic History ◽  
Population History ◽  
Genomic Diversity ◽  
Fine Scale ◽  
Effective Population ◽  
Scale Population ◽  
The Impact ◽  
British Pakistanis

AbstractPrevious genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genotype chip data from 2,200 British Pakistanis. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low recent effective population sizes (Ne), with some showing a decrease 15‒20 generations ago that has resulted in extensive identity-by-descent sharing and homozygosity, increasing the risk of recessive disorders. Our results from two orthogonal methods (one using machine learning and the other coalescent-based) suggest that the detailed reporting of parental relatedness for mothers in the cohort under-represents the true levels of consanguinity. These results demonstrate the impact of cultural practices on population structure and genomic diversity in Pakistanis, and have important implications for medical genetic studies.

scholarly journals Historical climate change and megafaunal extinctions linked to genetic diversity declines in shorebirds

2021 ◽  
Author(s):  
Hui Zhen Tan ◽  
Justin J.F.J. Jansen ◽  
Gary A. Allport ◽  
Kritika M Garg ◽  
Balaji Chattopadhyay ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Late Quaternary ◽  
Extinction Risk ◽  
Breeding Habitat ◽  
Human Populations ◽  
Mass Extinctions ◽  
Effective Population ◽  
Extant Species ◽  
The Impact

The impact of accelerated climate change on extinction risk is not well-characterised despite its increasing relevance. Comparative genomics of extinct versus extant species might be useful in elucidating broad trends in faunal endangerment. We investigated fluctuations in genetic diversity and extinction timing in our genomic dataset of nine species of particularly vulnerable migratory shorebirds (Numenius), including two species widely thought to be extinct. Most species faced generally sharp declines in effective population sizes, a proxy for genetic diversity, soon after the Last Glacial Maximum. During this time, a warming climate supported forest expansions at the expense of open habitats, exacerbated by human-induced mass extinctions of megafauna only a few thousand years prior, resulting in unprecedented reductions in shorebird breeding habitat. Species breeding in temperate regions, where they widely overlap with human populations, have been most strongly affected. Late Quaternary events can exert long-lasting effects on some species' susceptibility to extinction. Genomic inquiry is crucial in informing conservation actions in the fight against ongoing biodiversity loss.

scholarly journals Models of archaic admixture and recent history from two-locus statistics

2018 ◽  
Author(s):  
Aaron P. Ragsdale ◽  
Simon Gravel
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Evolutionary Biology ◽  
Demographic History ◽  
Population History ◽  
Human Populations ◽  
Evolutionary Models ◽  
Human History ◽  
Wide Range ◽  
Archaic Admixture

AbstractWe learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4-8% genetic ancestry to individuals in world-wide populations.Author SummaryThroughout human history, populations have expanded and contracted, split and merged, and ex-changed migrants. Because these events affected genetic diversity, we can learn about human history by comparing predictions from evolutionary models to genetic data. Here, we show how to rapidly compute such predictions for a wide range of diversity measures within and across populations under complex demographic scenarios. While widely used models of human history accurately predict common measures of diversity, we show that they strongly underestimate the co-occurence of low frequency mutations within human populations in Asia, Europe, and Africa. Models allowing for archaic admixture, the relatively recent mixing of human populations with deeply diverged human lineages, resolve this discrepancy. We use such models to infer demographic models that include both recent and ancient features of human history. We recover the well-characterized admixture of Neanderthals in Eurasian populations, as well as admixture from an as-yet unknown diverged human population within Africa, further suggesting that admixture with deeply diverged lineages occurred multiple times in human history. By simultaneously testing model predictions for a broad range of diversity statistics, we can assess the robustness of common evolutionary models, identify missing historical events, and build more informed models of human demography.

scholarly journals Fine-scale population structure and demographic history of British Pakistanis

2020 ◽  
Author(s):  
Elena Arciero ◽  
Sufyan A. Dogra ◽  
Massimo Mezzavilla ◽  
Theofanis Tsismentzoglou ◽  
Qin Qin Huang ◽  
...  
Keyword(s):  
Population Structure ◽  
Disease Risk ◽  
Demographic History ◽  
Population History ◽  
Genomic Diversity ◽  
Fine Scale ◽  
Effective Population ◽  
Scale Population ◽  
The Impact ◽  
British Pakistanis

AbstractPrevious genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genetic and questionnaire data from >4,000 British Pakistani individuals, mostly with roots in Azad Kashmir and Punjab. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low effective population sizes (Ne) over the last 50 generations, with some showing a decrease in Ne 15-20 generations ago that has resulted in extensive identity-by-descent sharing and increased homozygosity. Using new theory, we show that the footprint of regions of homozygosity in the two largest subgroups is about twice that expected naively based on the self-reported consanguinity rates and the inferred historical Ne trajectory. These results demonstrate the impact of the cultural practices of endogamy and consanguinity on population structure and genomic diversity in British Pakistanis, and have important implications for medical genetic studies.

scholarly journals Differences in local population history at the finest level: the case of the Estonian population

2020 ◽  
Vol 28 (11) ◽  
pp. 1580-1591 ◽  
Author(s):  
Vasili Pankratov ◽  
Francesco Montinaro ◽  
Alena Kushniarevich ◽  
Georgi Hudjashov ◽  
Flora Jay ◽  
...  
Keyword(s):  
Natural Selection ◽  
Genetic Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Local Population ◽  
Population History ◽  
Human Populations ◽  
Effective Population ◽  
The Impact ◽  
Estonian Population

Abstract Several recent studies detected fine-scale genetic structure in human populations. Hence, groups conventionally treated as single populations harbour significant variation in terms of allele frequencies and patterns of haplotype sharing. It has been shown that these findings should be considered when performing studies of genetic associations and natural selection, especially when dealing with polygenic phenotypes. However, there is little understanding of the practical effects of such genetic structure on demography reconstructions and selection scans when focusing on recent population history. Here we tested the impact of population structure on such inferences using high-coverage (~30×) genome sequences of 2305 Estonians. We show that different regions of Estonia differ in both effective population size dynamics and signatures of natural selection. By analyzing identity-by-descent segments we also reveal that some Estonian regions exhibit evidence of a bottleneck 10–15 generations ago reflecting sequential episodes of wars, plague and famine, although this signal is virtually undetected when treating Estonia as a single population. Besides that, we provide a framework for relating effective population size estimated from genetic data to actual census size and validate it on the Estonian population. This approach may be widely used both to cross-check estimates based on historical sources as well as to get insight into times and/or regions with no other information available. Our results suggest that the history of human populations within the last few millennia can be highly region specific and cannot be properly studied without taking local genetic structure into account.

scholarly journals Runs of Homozygosity in sub-Saharan African populations provide insights into a complex demographic and health history

2018 ◽  
Author(s):  
Francisco C. Ceballos ◽  
Scott Hazelhurst ◽  
Michele Ramsay
Keyword(s):  
Cultural Practices ◽  
Demographic History ◽  
Population History ◽  
Runs Of Homozygosity ◽  
Protein Coding ◽  
Heterogeneous Distribution ◽  
Health History ◽  
Multiple Protein ◽  
Sub Saharan ◽  
The Impact

AbstractThe study of runs of homozygosity (ROH), contiguous regions in the genome where an individual is homozygous across all sites, can shed light on the demographic history and cultural practices. We present a fine-scale ROH analysis of 1679 individuals from 28 sub-Saharan African (SSA) populations along with 1384 individuals from 17 world-wide populations. Using high-density SNP coverage, we could accurately obtain ROH as low as 300Kb using PLINK software. The analyses showed a heterogeneous distribution of autozygosity across SSA, revealing a complex demographic history. They highlight differences between African groups and can differentiate between the impact of consanguineous practices (e.g. among the Somali) and endogamy (e.g. among several Khoe-San groups1). The genomic distribution of ROH was analysed through the identification of ROH islands and regions of heterozygosity (RHZ). These homozygosity cold and hotspots harbour multiple protein coding genes. Studying ROH therefore not only sheds light on population history, but can also be used to study genetic variation related to the health of extant populations.

scholarly journals Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Emmanuel A. Lozada-Soto ◽  
Christian Maltecca ◽  
Duc Lu ◽  
Stephen Miller ◽  
John B. Cole ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Inbreeding Depression ◽  
Growth Traits ◽  
Effective Population ◽  
Angus Cattle ◽  
Genomic Inbreeding ◽  
Chromosome Segments ◽  
The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

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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