scholarly journals Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens

2020 ◽  
Vol 37 (10) ◽  
pp. 2944-2954 ◽  
Author(s):  
Carina M Schlebusch ◽  
Per Sjödin ◽  
Gwenna Breton ◽  
Torsten Günther ◽  
Thijessen Naidoo ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Extreme Values ◽  
Homo Sapiens ◽  
Population Divergence ◽  
Effective Population ◽  
Genome Wide ◽  
Novel Variants ◽  
Paleoclimate Records ◽  
Unique Variation

Abstract The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.

scholarly journals Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

2019 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

scholarly journals Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 577
Author(s):  
Huiwen Zhan ◽  
Saixian Zhang ◽  
Kaili Zhang ◽  
Xia Peng ◽  
Shengsong Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Average Length ◽  
The Other ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genomic Regions

Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.

scholarly journals Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0124157 ◽  
Author(s):  
Silvia Teresa Rodríguez-Ramilo ◽  
Jesús Fernández ◽  
Miguel Angel Toro ◽  
Delfino Hernández ◽  
Beatriz Villanueva
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Effective Population ◽  
Genome Wide ◽  
Holstein Population

scholarly journals Evaluating the use of ABBA-BABA statistics to locate introgressed loci

2013 ◽  
Author(s):  
Simon H. Martin ◽  
John W. Davey ◽  
Chris D. Jiggins
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Ancestral Population ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Data ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson?s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f̂d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f̂d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f̂d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

scholarly journals Runs of homozygosity in killer whale genomes provide a global record of demographic histories

2021 ◽  
Author(s):  
Andy Foote ◽  
Rebecca Hooper ◽  
Alana Alexander ◽  
Robin Baird ◽  
Charles Baker ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Killer Whale ◽  
Demographic History ◽  
Population History ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
High Background ◽  
Genome Wide ◽  
Conservation Concern

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global dataset of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstruct demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We find a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations and populations of known conservation concern, including a Scottish population, for which 37.8% of the autosomes comprised of ROH >1.5 Mb in length.

Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds

2016 ◽  
Vol 48 (1) ◽  
pp. 85-89 ◽  
Author(s):  
P. Sudrajad ◽  
D. W. Seo ◽  
T. J. Choi ◽  
B. H. Park ◽  
S. H. Roh ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Effective Population ◽  
Korean Cattle ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Genome Wide Linkage Disequilibrium

Genome-wide SNPs reveal low effective population size within confined management units of the highly vagile Galapagos shark (Carcharhinus galapagensis)

2017 ◽  
Vol 18 (5) ◽  
pp. 1151-1163 ◽  
Author(s):  
Diana A. Pazmiño ◽  
Gregory E. Maes ◽  
Colin A. Simpfendorfer ◽  
Pelayo Salinas-de-León ◽  
Lynne van Herwerden
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Effective Population ◽  
Management Units ◽  
Genome Wide
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