scholarly journals Genomic and demographic processes differentially influence genetic variation across the X chromosome

2021 ◽  
Author(s):  
Daniel J. Cotter ◽  
Timothy H. Webster ◽  
Melissa A. Wilson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
X Chromosome ◽  
Global Scale ◽  
Careful Consideration ◽  
Human Populations ◽  
Evolutionary Forces ◽  
Ideal System ◽  
Demographic Patterns

AbstractMutation, recombination, selection, and demography affect genetic variation across the genome. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. The X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these processes, notably the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. Here we investigate diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. We find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1 and highest on the non-recombining X chromosome, with the XTR falling in between, suggesting that the XTR (usually included in the non-recombining X) may need to be considered separately in future studies. We also observed strong population-specific effects on genetic diversity; not only does genetic variation differ on the X and autosomes among populations, but the effects of linked selection on the X relative to autosomes have been shaped by population-specific history. The substantial variation in patterns of variation across these regions provides insight into the unique evolutionary history contained within the X chromosome.Significance StatementDemography and selection affect the X chromosome differently from non-sex chromosomes. However, the X chromosome can be subdivided into multiple distinct regions that facilitate even more fine-scaled assessment of these processes. Here we study regions of the human X chromosome in 26 populations to find evidence that recombination may be mutagenic in humans and that the X-transposed region may undergo recombination. Further we observe that the effects of selection and demography act differently on the X chromosome relative to the autosomes across human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.

scholarly journals Genetic Diversity and Evolutionary Relationships of Chinese Pepper Based on nrDNA Markers

Forests ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 543
Author(s):  
Shijing Feng ◽  
Jinshuang Niu ◽  
Zhenshan Liu ◽  
Lu Tian ◽  
Xiangyuan Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic System ◽  
Haplotype Network ◽  
Evolutionary Relationships ◽  
Genetic Profile ◽  
Coding Region ◽  
Demographic Trends ◽  
Evolutionary Forces ◽  
High Level

Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.

scholarly journals Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Christelle Vangenot ◽  
José Manuel Nunes ◽  
Gaby M. Doxiadis ◽  
Estella S. Poloni ◽  
Ronald E. Bontrop ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Molecular Diversity ◽  
Selective Sweep ◽  
Balancing Selection ◽  
Substantial Effect ◽  
Human Populations ◽  
Large Set ◽  
Large Populations ◽  
Population Sizes

Abstract Background Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations’ survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. Results Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. Conclusions We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations – like that ascribed to a viral epidemic – exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans’ peopling history. We thus propose a model where chimpanzees’ MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.

scholarly journals Genetic variation and population structure in China summer maize germplasm

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guoping Shu ◽  
Gangqiang Cao ◽  
Niannian Li ◽  
Aifang Wang ◽  
Fang Wei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Germplasm Collection ◽  
Genotyping By Sequencing ◽  
Inbred Lines ◽  
Summer Maize ◽  
Heterotic Groups ◽  
Breeding Germplasm

AbstractMaize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.

Already at the bottom? Demographic declines are unlikely further to undermine genetic diversity of a large Arctic ungulate: muskox, Ovibos moschatus (Artiodactyla: Bovidae)

2019 ◽  
Vol 129 (2) ◽  
pp. 459-469
Author(s):  
Erin Prewer ◽  
Susan Kutz ◽  
Lisa Marie Leclerc ◽  
Christopher J Kyle
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Allelic Richness ◽  
Evolutionary Potential ◽  
Ovibos Moschatus ◽  
Low Genetic Diversity ◽  
Expected Heterozygosity ◽  
Large Populations ◽  
Victoria Island ◽  
Demographic Patterns

Abstract Low genetic diversity is associated with low fitness and evolutionary potential, yet the demographic and life-history traits of some species contribute to low genetic diversity, without empirical evidence of negative impacts on fitness. Modelling past and future trajectories of genetic diversity under different demographic scenarios can provide insight into how genetic variation might impact population fitness. The muskox is an Arctic species that has undergone multiple population bottlenecks and, although populations have rebounded repeatedly, two large populations have recently declined by > 50%. It is unclear how these demographic patterns influence muskox genetic diversity and fitness. We compared the genetic diversity of Canadian muskox populations undergoing opposing population trends. Genotyping 84 mainland and 244 Victoria Island individuals at ten microsatellite loci revealed low genetic variation (Victoria Island, mean allelic richness 1.66, expected heterozygosity 0.16; mainland, mean allelic richness 2.58, expected heterozygosity 0.41), with no evidence of further reductions in diversity subsequent to recent demographic declines. Bayesian modelling showed that a 1900s bottleneck contributed to the lack of diversity in contemporary populations, and forward-in-time simulations suggested little effect on genetic diversity over the next 100 years. Muskoxen might have reached a genetic diversity minimum, and additional research will be needed to determine their capacity to adapt to rapid changes in selective pressures in a rapidly changing Arctic.

scholarly journals Nucleotide Variability atG6pdand the Signature of Malarial Selection in Humans

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1849-1861 ◽  
Author(s):  
Matthew A Saunders ◽  
Michael F Hammer ◽  
Michael W Nachman
Keyword(s):  
Linkage Disequilibrium ◽  
X Chromosome ◽  
G6pd Deficiency ◽  
Human Populations ◽  
Nucleotide Variability ◽  
Signature Of Selection ◽  
History Of ◽  
Glucose 6 Phosphate Dehydrogenase ◽  
The Impact

AbstractGlucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzymopathy in humans. Deficiency alleles for this X-linked disorder are geographically correlated with historical patterns of malaria, and the most common deficiency allele in Africa (G6PD A-) has been shown to confer some resistance to malaria in both hemizygous males and heterozygous females. We studied DNA sequence variation in 5.1 kb of G6pd from 47 individuals representing a worldwide sample to examine the impact of selection on patterns of human nucleotide diversity and to infer the evolutionary history of the G6PD A-allele. We also sequenced 3.7 kb of a neighboring locus, L1cam, from the same set of individuals to study the effect of selection on patterns of linkage disequilibrium. Despite strong clinical evidence for malarial selection maintaining G6PD deficiency alleles in human populations, the overall level of nucleotide heterozygosity at G6pd is typical of other genes on the X chromosome. However, the signature of selection is evident in the absence of genetic variation among A-alleles from different parts of Africa and in the unusually high levels of linkage disequilibrium over a considerable distance of the X chromosome. In spite of a long-term association between Plasmodium falciparum and the ancestors of modern humans, patterns of nucleotide variability and linkage disequilibrium suggest that the A-allele arose in Africa only within the last 10,000 years and spread due to selection.

scholarly journals A comparison of worldwide phonemic and genetic variation in human populations

2015 ◽  
Vol 112 (5) ◽  
pp. 1265-1272 ◽  
Author(s):  
Nicole Creanza ◽  
Merritt Ruhlen ◽  
Trevor J. Pemberton ◽  
Noah A. Rosenberg ◽  
Marcus W. Feldman ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Demographic History ◽  
Horizontal Transmission ◽  
Geographic Distance ◽  
Global Scale ◽  
Human Populations ◽  
Isolated Populations ◽  
Human Dispersal ◽  
Genetic Sampling ◽  
Serial Founder Effect

Worldwide patterns of genetic variation are driven by human demographic history. Here, we test whether this demographic history has left similar signatures on phonemes—sound units that distinguish meaning between words in languages—to those it has left on genes. We analyze, jointly and in parallel, phoneme inventories from 2,082 worldwide languages and microsatellite polymorphisms from 246 worldwide populations. On a global scale, both genetic distance and phonemic distance between populations are significantly correlated with geographic distance. Geographically close language pairs share significantly more phonemes than distant language pairs, whether or not the languages are closely related. The regional geographic axes of greatest phonemic differentiation correspond to axes of genetic differentiation, suggesting that there is a relationship between human dispersal and linguistic variation. However, the geographic distribution of phoneme inventory sizes does not follow the predictions of a serial founder effect during human expansion out of Africa. Furthermore, although geographically isolated populations lose genetic diversity via genetic drift, phonemes are not subject to drift in the same way: within a given geographic radius, languages that are relatively isolated exhibit more variance in number of phonemes than languages with many neighbors. This finding suggests that relatively isolated languages are more susceptible to phonemic change than languages with many neighbors. Within a language family, phoneme evolution along genetic, geographic, or cognate-based linguistic trees predicts similar ancestral phoneme states to those predicted from ancient sources. More genetic sampling could further elucidate the relative roles of vertical and horizontal transmission in phoneme evolution.

scholarly journals Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Babu Valliyodan ◽  
Anne V. Brown ◽  
Juexin Wang ◽  
Gunvant Patil ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Glycine Max ◽  
Linkage Disequilibrium ◽  
Genetic Structure ◽  
Glycine Soja ◽  
Geographic Location ◽  
High Similarity ◽  
Genetic Diversity And Structure ◽  
Selection Of

AbstractWe report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.

scholarly journals Models of archaic admixture and recent history from two-locus statistics

2018 ◽  
Author(s):  
Aaron P. Ragsdale ◽  
Simon Gravel
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Evolutionary Biology ◽  
Demographic History ◽  
Population History ◽  
Human Populations ◽  
Evolutionary Models ◽  
Human History ◽  
Wide Range ◽  
Archaic Admixture

AbstractWe learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4-8% genetic ancestry to individuals in world-wide populations.Author SummaryThroughout human history, populations have expanded and contracted, split and merged, and ex-changed migrants. Because these events affected genetic diversity, we can learn about human history by comparing predictions from evolutionary models to genetic data. Here, we show how to rapidly compute such predictions for a wide range of diversity measures within and across populations under complex demographic scenarios. While widely used models of human history accurately predict common measures of diversity, we show that they strongly underestimate the co-occurence of low frequency mutations within human populations in Asia, Europe, and Africa. Models allowing for archaic admixture, the relatively recent mixing of human populations with deeply diverged human lineages, resolve this discrepancy. We use such models to infer demographic models that include both recent and ancient features of human history. We recover the well-characterized admixture of Neanderthals in Eurasian populations, as well as admixture from an as-yet unknown diverged human population within Africa, further suggesting that admixture with deeply diverged lineages occurred multiple times in human history. By simultaneously testing model predictions for a broad range of diversity statistics, we can assess the robustness of common evolutionary models, identify missing historical events, and build more informed models of human demography.

scholarly journals Evolutionary Dynamics of Oropouche Virus in South America

2019 ◽  
Vol 94 (5) ◽  
Author(s):  
Bernardo Gutierrez ◽  
Emma L. Wise ◽  
Steven T. Pullan ◽  
Christopher H. Logue ◽  
Thomas A. Bowden ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
South America ◽  
Amazon Basin ◽  
Evolutionary Dynamics ◽  
Yellow Fever Virus ◽  
Surface Proteins ◽  
Human Populations ◽  
Evolutionary Processes ◽  
Public Health Burden ◽  
Evolutionary Forces

ABSTRACT The Amazon basin is home to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the genus Orthobunyavirus, family Peribunyaviridae, that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the OROV genome remain poorly understood. Here, we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genome sequences obtained from patients in Ecuador, representing the first set of genomes from this country. Our results show differing evolutionary processes on the three segments that comprise the viral genome. We infer differing times of the most recent common ancestors of the genome segments and propose that this can be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, as well as codons that evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of OROV through a combined phylogenetic and structural approach. IMPORTANCE The emergence and reemergence of pathogens such as Zika virus, chikungunya virus, and yellow fever virus have drawn attention toward other cocirculating arboviruses in South America. Oropouche virus (OROV) is a poorly studied pathogen responsible for over a dozen outbreaks since the early 1960s and represents a public health burden to countries such as Brazil, Panama, and Peru. OROV is likely underreported since its symptomatology can be easily confounded with other febrile illnesses (e.g., dengue fever and leptospirosis) and point-of-care testing for the virus is still uncommon. With limited data, there is a need to optimize the information currently available. Analysis of OROV genomes can help us understand how the virus circulates in nature and can reveal the evolutionary forces that shape the genetic diversity of the virus, which has implications for molecular diagnostics and the design of potential vaccines.

scholarly journals Using Genome-Wide SNP Discovery and Genotyping to Reveal the Main Source of Population Differentiation inNothofagus dombeyi(Mirb.) Oerst. in Chile

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Rodrigo Hasbún ◽  
Jorge González ◽  
Carolina Iturra ◽  
Glenda Fuentes ◽  
Diego Alarcón ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Woody Species ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Diversity Studies ◽  
Nothofagus Dombeyi

Within a woody plant species, environmental heterogeneity has the potential to influence the distribution of genetic variation among populations through several evolutionary processes. In some species, a relationship between environmental characteristics and the distribution of genotypes can be detected, showing the importance of natural selection as the main source of differentiation.Nothofagus dombeyi(Mirb.) Oerst. (Nothofagaceae) is an endemic tree species occurring both in Chile and in Argentina temperate forests. Postglacial history has been studied with chloroplast DNA and evolutionary forces shaping genetic variation patterns have been analysed with isozymes but fine-scale genetic diversity studies are needed. The study of demographic and selection histories inNothofagus dombeyirequires more informative markers such as single nucleotide polymorphisms (SNP). Genotyping-by-Sequencing tools now allow studying thousands of SNP markers at reasonable prices in nonmodel species. We investigated more than 10 K SNP loci for signatures of local adaptation and showed that interrogation of genomic resources can identify shifts in genetic diversity and putative adaptive signals in this nonmodel woody species.

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