scholarly journals The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

2018 ◽  
Author(s):  
Sandra Oliveira ◽  
Alexander Hübner ◽  
Anne-Maria Fehn ◽  
Teresa Aço ◽  
Fernanda Lages ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sequence Data ◽  
Population History ◽  
Female Population ◽  
Bantu Languages ◽  
Mtdna Sequence ◽  
Population Sizes ◽  
Group Variation ◽  
History Of ◽  
Previous Demonstration

AbstractSouthwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx’a, Khoe-Kwadi and Bantu languages. Although present-day Bantu-speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been though to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the non-recombining Y chromosome (NRY) from 170 individuals with previously reported mitochondrial genomes (mtDNA), to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun) and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu NRY lineages among Bantu-speaking groups, except for small amounts of “Khoisan” introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for NRY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.

Population history of the plateau pika endemic to the Qinghai-Tibetan Plateau based on mtDNA sequence data

2009 ◽  
Vol 279 (4) ◽  
pp. 396-403 ◽  
Author(s):  
H. X. Ci ◽  
G. H. Lin ◽  
Z. Y. Cai ◽  
L. Z. Tang ◽  
J. P. Su ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Sequence Data ◽  
Population History ◽  
Plateau Pika ◽  
Mtdna Sequence ◽  
History Of

scholarly journals Recurrent hybridization underlies the evolution of novelty in Gentiana (Gentianaceae) in the Qinghai-Tibetan Plateau

AoB Plants ◽  
2020 ◽  
Author(s):  
Peng-Cheng Fu ◽  
Alex D Twyford ◽  
Shan-Shan Sun ◽  
Hong-Yu Wang ◽  
Ming-Ze Xia ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Source Area ◽  
Nuclear Data ◽  
Population History ◽  
Plastid Genomes ◽  
Key Factor ◽  
History Of ◽  
Postglacial Expansion

Abstract The Qinghai-Tibetan Plateau (QTP) and adjacent areas are centers of diversity for several alpine groups. Although the QTP acted as a source area for diversification of the alpine genus Gentiana, the evolutionary process underlying diversity in this genus, especially the formation of narrow endemics, is still poorly understood. Hybridization has been proposed as a driver of plant endemism in the QTP but few cases have been documented with genetic data. Here, we describe a new endemic species in Gentiana section Cruciata as G. hoae sp. nov., and explore its evolutionary history with complete plastid genomes and nuclear ribosomal ITS sequence data. Genetic divergence within G. hoae approximately 3 million years ago was followed by postglacial expansion on the QTP, suggesting Pleistocene glaciations as a key factor shaping the population history of G. hoae. Furthermore, a mismatch between plastid and nuclear data suggest that G. hoae participated in historical hybridization, while population sequencing show this species continues to hybridize with the co-occurring congener G. straminea in three locations. Our results indicate that hybridization may be a common process in the evolution of Gentiana and may be widespread among recently diverged taxa of the QTP.

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

2017 ◽  
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.

Canonical analysis of facial variation

1972 ◽  
Vol 4 (2) ◽  
pp. 175-185 ◽  
Author(s):  
D. R. Brothwell ◽  
M. J. R. Healy ◽  
R. G. Harvey
Keyword(s):  
Recent Work ◽  
Exploratory Study ◽  
Point Of View ◽  
Population History ◽  
Canonical Analysis ◽  
The People ◽  
New Thinking ◽  
The Face ◽  
Group Variation ◽  
History Of

Although the face is one of the most variable parts of the human physique, there is little recent work on this region. Consequently, there is a need for an appraisal of the variation, new thinking as regards the methodology of recording and analysis, and further thought as to the possible applications of such methods. The present exploratory study uses information derived from standardized photographs, to try to elucidate the affinities—and thus the population history—of the people of Tristan da Cunha and the Ainu of Japan. The methods used have also permitted a consideration of within-group variation from the point of view of family differences and varying degrees of admixture. The potential biosocial as well as anthropological value of this type of investigation is discussed.

scholarly journals Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand

2017 ◽  
Author(s):  
Yeşerin Yıldırım ◽  
Marti J. Anderson ◽  
Selina Patel ◽  
Craig D. Millar ◽  
Paul B. Rainey
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Haplotype Network ◽  
Founding Population ◽  
Mtdna Sequence ◽  
Expansion Time ◽  
History Of

AbstractPleurobranchaea maculatais a rarely studied species of the Heterobranchia found throughout the south and western Pacific – and recently recorded in Argentina – whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history ofP. maculatapopulations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and theCOIandCytBregions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence from Argentinian sea slugs did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.

scholarly journals Estimation of coalescence probabilities and population divergence times from SNP data

Heredity ◽  
2021 ◽  
Author(s):  
Kristy Mualim ◽  
Christoph Theunert ◽  
Montgomery Slatkin
Keyword(s):  
Demographic History ◽  
Population History ◽  
Divergence Times ◽  
Population Divergence ◽  
High Coverage ◽  
Snp Data ◽  
Population Sizes ◽  
History Of ◽  
Relationship Of ◽  
The Relationship

AbstractWe present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.

Reconstructing the population history of Nicaragua by means of mtDNA, Y-chromosome STRs, and autosomal STR markers

2010 ◽  
Vol 143 (4) ◽  
pp. 591-600 ◽  
Author(s):  
Carolina Nuñez ◽  
Miriam Baeta ◽  
Cecilia Sosa ◽  
Yolanda Casalod ◽  
Jianye Ge ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Population History ◽  
Str Markers ◽  
Autosomal Str ◽  
History Of

scholarly journals The comparative genomics and complex population history ofPapiobaboons

2019 ◽  
Vol 5 (1) ◽  
pp. eaau6947 ◽  
Author(s):  
Jeffrey Rogers ◽  
Muthuswamy Raveendran ◽  
R. Alan Harris ◽  
Thomas Mailund ◽  
Kalle Leppälä ◽  
...  
Keyword(s):  
Sequence Data ◽  
Population History ◽  
Whole Genome Sequence ◽  
Evolutionary Divergence ◽  
Papio Anubis ◽  
Phenotypic Differences ◽  
Extant Species ◽  
Complex Population ◽  
In The Wild ◽  
History Of

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genusPapio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation ofPapiobaboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

scholarly journals Inference of Historical Population-Size Changes with Allele-Frequency Data

2019 ◽  
Vol 10 (1) ◽  
pp. 211-223 ◽  
Author(s):  
Michael Lynch ◽  
Bernhard Haubold ◽  
Peter Pfaffelhuber ◽  
Takahiro Maruki
Keyword(s):  
Population Size ◽  
Probability Distributions ◽  
Daphnia Pulex ◽  
Population History ◽  
Effective Population ◽  
Size Change ◽  
Conceptual Approach ◽  
Population Genomic ◽  
Population Sizes ◽  
History Of

With up to millions of nearly neutral polymorphisms now being routinely sampled in population-genomic surveys, it is possible to estimate the site-frequency spectrum of such sites with high precision. Each frequency class reflects a mixture of potentially unique demographic histories, which can be revealed using theory for the probability distributions of the starting and ending points of branch segments over all possible coalescence trees. Such distributions are completely independent of past population history, which only influences the segment lengths, providing the basis for estimating average population sizes separating tree-wide coalescence events. The history of population-size change experienced by a sample of polymorphisms can then be dissected in a model-flexible fashion, and extension of this theory allows estimation of the mean and full distribution of long-term effective population sizes and ages of alleles of specific frequencies. Here, we outline the basic theory underlying the conceptual approach, develop and test an efficient statistical procedure for parameter estimation, and apply this to multiple population-genomic datasets for the microcrustacean Daphnia pulex.

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