scholarly journals Refining the Y chromosome phylogeny with southern African sequences

2015 ◽  
Author(s):  
Chiara Barbieri ◽  
Alexander Hübner ◽  
Enrico Macholdt ◽  
Shengyu Ni ◽  
Sebastian Lippold ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Large Scale ◽  
Sequence Data ◽  
Population Expansion ◽  
Branch Length ◽  
Paternal Age ◽  
Effective Population ◽  
Chromosome Sequence ◽  
Human Y Chromosome ◽  
Major Haplogroups

The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We find new branches within haplogroups A2 and A3b1 and suggest that the prehistory of haplogroup B2a is more complex than previously suspected; this haplogroup is likely to have existed in Khoisan groups before the arrival of Bantu-speakers, who brought additional B2a lineages to southern Africa. Furthermore, we estimate older dates than obtained previously for both the A2-T node within the human Y chromosome phylogeny and for some individual haplogroups. Finally, there is pronounced variation in branch length between major haplogroups; haplogroups associated with Bantu-speakers have significantly longer branches. This likely reflects a combination of biases in the SNP calling process and demographic factors, such as an older average paternal age (hence a higher mutation rate), a higher effective population size, and/or a stronger effect of population expansion for Bantu-speakers than for Khoisan groups.

scholarly journals Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent

2015 ◽  
Vol 7 (7) ◽  
pp. 1940-1950 ◽  
Author(s):  
Beniamino Trombetta ◽  
Eugenia D’Atanasio ◽  
Andrea Massaia ◽  
Marco Ippoliti ◽  
Alfredo Coppa ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Large Scale ◽  
African Continent ◽  
Human Y Chromosome

scholarly journals Human Population Structure and Its Effects on Sampling Y Chromosome Sequence Variation

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1495-1509
Author(s):  
Michael F Hammer ◽  
Felisa Blackmer ◽  
Dan Garrigan ◽  
Michael W Nachman ◽  
Jason A Wilder
Keyword(s):  
Population Structure ◽  
Y Chromosome ◽  
Rare Variants ◽  
Population Expansion ◽  
Significant Negative Correlation ◽  
Coalescent Simulations ◽  
Chromosome Sequence ◽  
Sequencing Studies ◽  
Pooled Samples ◽  
Globally Distributed

Abstract The excess of rare variants in global sequencing studies of the nonrecombining portion of the Y chromosome (NRY) has been interpreted as evidence for the effects of human demographic expansion. However, many NRY polymorphisms are geographically localized and the effect of different geographical sampling on patterns of NRY variation is unknown. We use two sampling designs to detect population structure and its effects on patterns of human NRY polymorphism. First, we sequence 26.5 kb of noncoding Y chromosome DNA from 92 globally distributed males representing 35 populations. We find that the number of polymorphisms with singleton variants is positively correlated with the number of populations sampled and that there is a significant negative correlation of Tajima’s D (TD) and Fu and Li’s D (FD) statistics with the number of pooled populations. We then sequence the same region in a total of 73 males sampled from 3 distinct populations and find that TD and FD values for the 3 pooled and individual population samples were much less negative than those in the aforementioned global sample. Coalescent simulations show that a simple splitting model of population structure, with no changes in population size, is sufficient to produce the negative values of TD seen in our pooled samples. These empirical and simulation results suggest that observed levels of NRY population structure may lead to an upward bias in the number of singleton variants in global surveys and call into question inferences of population expansion based on global sampling strategies.

Evidence of recent population expansion in the field cricket Teleogryllus commodus

2010 ◽  
Vol 58 (1) ◽  
pp. 33 ◽  
Author(s):  
Kylie M. Cairns ◽  
Jonci N. Wolff ◽  
Robert C. Brooks ◽  
J. William O. Ballard
Keyword(s):  
Genetic Variation ◽  
Large Scale ◽  
Elongation Factor ◽  
Population Expansion ◽  
Field Cricket ◽  
Molecular Variation ◽  
Effective Population ◽  
Recent Population Expansion ◽  
Teleogryllus Commodus ◽  
European Farming

The patterns of intraspecific genetic variation can be driven by large-scale environmental events or smaller-scale phenomena such as land clearing. In Australia, European farming techniques have altered the landscape by increasing the amount of arable farmland. We hypothesised that this increase in farmland would result in a concomitant increase in the effective population size of the black field cricket (Teleogryllus commodus). To test our hypothesis, we investigated genetic variation in 1350 bp of mitochondrial mtDNA and in two nuclear encoded loci, hexokinase and elongation factor 1-α, from 20 crickets collected at Smiths Lake, New South Wales. Molecular variation in T. commodus was characterised by an over-representation of singleton mutations (negative Tajima’s D and Fu and Li’s D) in all loci studied. Further, HKA tests do not suggest that selection is acting on any one gene. Combined, these data support the hypothesis that population expansion is the force driving molecular variation in T. commodus. If an increase in agricultural habitats is the cause of population expansion in T. commodus we hypothesise greater genetic subdivision in natural than farmland habitats. An alternative possibility is that the effective geographical range of the species has increased but the density at a given site remains unchanged.

scholarly journals mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates

2019 ◽  
Author(s):  
Eleanor F. Miller ◽  
Rhys E. Green ◽  
Andrew Balmford ◽  
Robert Beyer ◽  
Marius Somveille ◽  
...  
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Habitat Type ◽  
Potential Range ◽  
Last Deglaciation ◽  
Effective Population ◽  
Distribution Models ◽  
Terrestrial Habitats ◽  
Population Sizes ◽  
The Last Glacial

AbstractDuring the Quaternary, large climate oscillations had profound impacts on the distribution, demography and diversity of species globally. Birds offer a special opportunity for studying these impacts because surveys of geographical distributions, publicly-available genetic sequence data, and the existence of species with adaptations to life in structurally different habitats, permit large-scale comparative analyses. We use Bayesian Skyline Plot (BSP) analysis of mitochondrial DNA to reconstruct profiles depicting how effective population size (Ne) may have changed over time, focussing on variation in the effect of the last deglaciation among 102 Holarctic species. Only 3 species showed a decline in Ne since the Last Glacial Maximum (LGM) and 7 showed no sizeable change, whilst 92 profiles revealed an increase in Ne. Using bioclimatic Species Distribution Models (SDMs), we also estimated changes in species potential range extent since the LGM. Whilst most modelled ranges also increased, we found no correlation across species between the magnitude of change in range size and change in Ne. The lack of correlation between SDM and BSP reconstructions could not be reconciled even when range shifts were considered. We suggest the lack of agreement between these measures might be linked to changes in population densities which can be independent of range changes. We caution that interpreting either SDM or BSPs independently is problematic and potentially misleading. Additionally, we found that Ne of wetland species tended to increase later than species from terrestrial habitats, possibly reflecting a delayed increase in the extent of this habitat type after the LGM.

scholarly journals Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences

2020 ◽  
Vol 12 (7) ◽  
pp. 1031-1039 ◽  
Author(s):  
Thijessen Naidoo ◽  
Jingzi Xu ◽  
Mário Vicente ◽  
Helena Malmström ◽  
Himla Soodyall ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sequence Data ◽  
Demographic History ◽  
Data Sets ◽  
High Coverage ◽  
Hunter Gatherers ◽  
Data Set ◽  
Chromosome Sequence ◽  
Shared Ancestry ◽  
Chromosome Variant

Abstract Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.

scholarly journals De novo genome assembly of the marine teleost, Bluefin Trevally (Caranx melampygus)

2021 ◽  
Author(s):  
Brandon D Pickett ◽  
Jessica R Glass ◽  
Perry G Ridge ◽  
John S K Kauwe
Keyword(s):  
Genome Assembly ◽  
Large Scale ◽  
De Novo ◽  
Demographic History ◽  
Population Expansion ◽  
Marine Teleost ◽  
Population Demography ◽  
Population Declines ◽  
Effective Population ◽  
De Novo Genome Assembly

Abstract The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely-prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai‘i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Most research to-date has been performed in Hawai‘i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range. Genomic resources allow for expanded research on stock status, genetic diversity, and population demography. We present a high-quality, 711Mbp nuclear genome assembly of a Hawaiian bluefin trevally from noisy long-reads with a contig NG50 of 1.2Mbp and longest contig length of 8.9Mbp. As measured by single-copy orthologs, the assembly was 95% complete, and the genome is comprised of 16.9% repetitive elements. The assembly was annotated with 33.1K protein-coding genes, 71.4% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual. This is the first whole-genome assembly published for the carangoid genus Caranx. Using this assembled genome, a multiple sequentially Markovian coalescent model was implemented to assess population demography. Estimates of effective population size suggest population expansion has occurred since the Late Pleistocene. This genome will be a valuable resource for comparative phylogenomic studies of carangoid fishes and will help elucidate demographic history and delineate stock structure for bluefin trevally populations throughout the Indo-Pacific.

scholarly journals Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia

2018 ◽  
Vol 115 (13) ◽  
pp. 3428-3433 ◽  
Author(s):  
Cristina Valdiosera ◽  
Torsten Günther ◽  
Juan Carlos Vera-Rodríguez ◽  
Irene Ureña ◽  
Eneko Iriarte ◽  
...  
Keyword(s):  
Bronze Age ◽  
Large Scale ◽  
Sequence Data ◽  
Isotope Analysis ◽  
Population Expansion ◽  
European Population ◽  
Climatic Conditions ◽  
The North ◽  
The Impact ◽  
The Bronze Age

Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500–3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

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