scholarly journals Genome-Wide Evidence for Efficient Positive and Purifying Selection in Capsella grandiflora, a Plant Species with a Large Effective Population Size

2010 ◽  
Vol 27 (8) ◽  
pp. 1813-1821 ◽  
Author(s):  
T. Slotte ◽  
J. P. Foxe ◽  
K. M. Hazzouri ◽  
S. I. Wright
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Plant Species ◽  
Purifying Selection ◽  
Effective Population ◽  
Large Effective Population Size ◽  
Genome Wide

scholarly journals Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1089
Author(s):  
Andreia J. Amaral ◽  
Ana L. Pavão ◽  
Luis T. Gama
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Wide Association Study ◽  
Cattle Breed ◽  
Production Traits ◽  
Effective Population ◽  
Age At First Calving ◽  
Large Effective Population Size ◽  
Genomic Inbreeding ◽  
Genomic Regions

Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction.

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 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 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 Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees

2020 ◽  
Author(s):  
Arthur Weyna ◽  
Jonathan Romiguier
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Ecosystem Engineer ◽  
Relative Rate ◽  
Population Decline ◽  
Purifying Selection ◽  
Life History Strategies ◽  
Effective Population ◽  
Social Bees ◽  
Pollinator Species

ABSTRACTWith one of the highest number of parasite, eusocial and pollinator species among all insect orders, Hymenoptera features a great diversity of specific lifestyles. At the population genetic level, such life-history strategies are expected to decrease effective population size and efficiency of purifying selection. In this study, we tested this hypothesis by estimating the relative rate of non-synonymous substitution in 169 species to investigate the variation in natural selection efficiency throughout the hymenopteran tree of life. We found no effect of parasitism or body size, but show that relaxed selection is associated with eusociality, suggesting that the division of reproductive labour decreases effective population size in ants, bees and wasps. Unexpectedly, the effect of eusociality is marginal compared to a striking and widespread relaxation of selection in both social and non social bees, which indicates that these keystone pollinator species generally feature low effective population sizes. This widespread pattern suggests specific constraints in pollinating bees potentially linked to limited resource and high parental investment. The particularly high load of deleterious mutations we report in the genome of these crucial ecosystem engineer species also raises new concerns about their ongoing population decline.

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