scholarly journals Detecting a Local Signature of Genetic Hitchhiking Along a Recombining Chromosome

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 765-777 ◽  
Author(s):  
Yuseob Kim ◽  
Wolfgang Stephan
Keyword(s):  
Genetic Variation ◽  
Dna Polymorphism ◽  
Nucleotide Diversity ◽  
Sequence Data ◽  
Directional Selection ◽  
Genetic Hitchhiking ◽  
Dna Sequence Data ◽  
Local Reduction ◽  
Polymorphism Data ◽  
Ancestral Recombination Graphs

Abstract The theory of genetic hitchhiking predicts that the level of genetic variation is greatly reduced at the site of strong directional selection and increases as the recombinational distance from the site of selection increases. This characteristic pattern can be used to detect recent directional selection on the basis of DNA polymorphism data. However, the large variance of nucleotide diversity in samples of moderate size imposes difficulties in detecting such patterns. We investigated the patterns of genetic variation along a recombining chromosome by constructing ancestral recombination graphs that are modified to incorporate the effect of genetic hitchhiking. A statistical method is proposed to test the significance of a local reduction of variation and a skew of the frequency spectrum caused by a hitchhiking event. This method also allows us to estimate the strength and the location of directional selection from DNA sequence data.

scholarly journals Disentangling selection on genetically correlated polygenic traits using whole-genome genealogies

2020 ◽  
Author(s):  
Aaron J. Stern ◽  
Leo Speidel ◽  
Noah A. Zaitlen ◽  
Rasmus Nielsen
Keyword(s):  
Dna Sequence ◽  
Population Genetic ◽  
Sequence Data ◽  
Directional Selection ◽  
Likelihood Method ◽  
Correlated Response ◽  
Correlated Traits ◽  
Dna Sequence Data ◽  
Polygenic Traits ◽  
Polygenic Trait

AbstractWe present a full-likelihood method to estimate and quantify polygenic adaptation from contemporary DNA sequence data. The method combines population genetic DNA sequence data and GWAS summary statistics from up to thousands of nucleotide sites in a joint likelihood function to estimate the strength of transient directional selection acting on a polygenic trait. Through population genetic simulations of polygenic trait architectures and GWAS, we show that the method substantially improves power over current methods. We examine the robustness of the method under uncorrected GWAS stratification, uncertainty and ascertainment bias in the GWAS estimates of SNP effects, uncertainty in the identification of causal SNPs, allelic heterogeneity, negative selection, and low GWAS sample size. The method can quantify selection acting on correlated traits, fully controlling for pleiotropy even among traits with strong genetic correlation (|rg| = 80%; c.f. schizophrenia and bipolar disorder) while retaining high power to attribute selection to the causal trait. We apply the method to study 56 human polygenic traits for signs of recent adaptation. We find signals of directional selection on pigmentation (tanning, sunburn, hair, P=5.5e-15, 1.1e-11, 2.2e-6, respectively), life history traits (age at first birth, EduYears, P=2.5e-4, 2.6e-4, respectively), glycated hemoglobin (HbA1c, P=1.2e-3), bone mineral density (P=1.1e-3), and neuroticism (P=5.5e-3). We also conduct joint testing of 137 pairs of genetically correlated traits. We find evidence of widespread correlated response acting on these traits (2.6-fold enrichment over the null expectation, P=1.5e-7). We find that for several traits previously reported as adaptive, such as educational attainment and hair color, a significant proportion of the signal of selection on these traits can be attributed to correlated response, vs direct selection (P=2.9e-6, 1.7e-4, respectively). Lastly, our joint test uncovers antagonistic selection that has acted to increase type 2 diabetes (T2D) risk and decrease HbA1c (P=1.5e-5).

Genetic Variation and Evolution of the Alpine Bamboos (Poaceae: Bambusoideae) using DNA Sequence Data

2001 ◽  
Vol 114 (3) ◽  
pp. 315-322 ◽  
Author(s):  
Zhen-Hua Guo ◽  
Yong-Yan Chen ◽  
De-Zhu Li ◽  
Jun-Bo Yang
Keyword(s):  
Genetic Variation ◽  
Dna Sequence ◽  
Sequence Data ◽  
Dna Sequence Data

scholarly journals Genetic diversity and chromosome complement of Galictis cuja (Molina, 1782) (Carnivora: Mustelidae) with comments about its role as parasite hosts

2020 ◽  
Vol 15 (3) ◽  
pp. 717-726
Author(s):  
Julia Bontempo ◽  
Cecília Bueno ◽  
Paulo Sérgio D'Andrea ◽  
Cibele Rodrigues Bonvicino
Keyword(s):  
Genetic Diversity ◽  
Atlantic Forest ◽  
Nucleotide Diversity ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Chromosome Complement ◽  
Dna Sequence Data ◽  
Haplotypic Diversity ◽  
Distrito Federal ◽  
Zoonotic Parasites

The distribution of Galictis cuja encompasses several countries of South America, including Brazil, where it inhabits the Atlantic Forest, part of Caatinga and part of Cerrado biomes. Herein we analyzed G. cuja specimens from localities in the Brazilian states of Rio de Janeiro, Minas Gerais, and Bahia, and the Distrito Federal, mainly roadkilled animals. The genetic diversity was estimated based on DNA sequence data of the mitochondrial gene cytochrome b (mt-cyb). Analysis of mt-cyb identified high haplotypic diversity, albeit with low nucleotide diversity, suggesting that this population is in expansion and confirming the presence of gene flow. The karyotypes of two Galictis cuja specimens were described as 2n = 38 and FNa = 66. Our data showed that G. cuja is frequent in the investigated areas of Atlantic Forest biome, being a common roadkill mammal. Our data suggest that G. cuja may play a role as a spreader of zoonotic parasites.

scholarly journals Phylogeny and Biogeography of the Amazona Ochrocephala (Aves: Psittacidae) Complex

The Auk ◽  
2004 ◽  
Vol 121 (2) ◽  
pp. 318-332
Author(s):  
Jessica R. Eberhard ◽  
Elredge Bermingham
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Genetic Variation ◽  
South America ◽  
Dna Sequence ◽  
Species Complex ◽  
Sequence Data ◽  
Land Bridge ◽  
Dna Sequence Data ◽  
Middle America

Abstract We present a phylogenetic analysis of relationships among members of the Amazona ochrocephala species complex of parrots, a broadly distributed group in Middle and South America that has been a “taxonomic headache.” Mitochondrial DNA sequence data are used to infer phylogenetic relationships among most of the named subspecies in the complex. Sequence-based phylogenies show that Middle American subspecies included in the analysis are reciprocally monophyletic, but subspecies described for South America do not reflect patterns of genetic variation. Samples from the lower Amazon cluster with samples collected in western Amazonia—not with samples from Colombia and Venezuela, as was predicted by subspecies classification. All subspecies of the complex are more closely related to one another than to other Amazona species, and division of the complex into three species (A. ochrocephala, A. auropalliata, and A. oratrix) is not supported by our data. Divergence-date estimates suggest that these parrots arrived in Middle America after the Panama land-bridge formed, and then expanded and diversified rapidly. As in Middle America, diversification of the group in South America occurred during the Pleistocene, possibly driven by changes in distribution of forest habitat.

Biodiversity at the molecular genetic level: experiences from disparate macroorganisms

1994 ◽  
Vol 345 (1311) ◽  
pp. 59-64 ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Sequence Data ◽  
Molecular Genetic ◽  
Dna Sequence Data ◽  
Genetic Level ◽  
Management Policies ◽  
Term Maintenance

Genetic variation is the basis of adaptive flexibility in populations and is the ultimate evolutionary basis of much species and community-level diversity. Accordingly, the preservation and maintenance of genetic diversity has a high priority in many conservation programmes. This paper discusses how genetic diversity is measured at the molecular level, including some newer measures made possible with restriction site or DNA sequence data as well as the development of a phylogenetic approach to assessing the significance of genetic variation within a species. These measures of genetic diversity are then used to re-examine the validity of the 50/500 rule of conservation biology; a rule that states that populations should have no fewer than 50 individuals for short-term maintenance of genetic variation and no fewer than 500 individuals for long-term maintenance. Both the 50 and 500 parts of this rule are found to be invalid and frequently misleading. Instead of invoking ‘universal’ rules, conservation biologists should recognize the role of biodiversity in management policies. Not all species are the same, and we need more research and a willingness to try novel approaches rather than naively apply a ‘rule’ that has no demonstrable generality.

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