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1.
Acta amaz ; 50(3): 232-238, jul. - set. 2020.
Artigo em Inglês | LILACS | ID: biblio-1118836

RESUMO

The genus Bryconcomprises fish species of significant socioeconomic and biological importance in Brazil. Despite that, the genetic knowledge about these species is scarce, especially regardingBrycon falcatus. Thus, the objective of this study was to evaluate the transferability of heterologous microsatellite primers inB. falcatus for the first time. Heterologous primers obtained from B. opalinus, B. hilarii, B. insignis, B. orbignyanus, B. amazonicus, Prochilodus argenteus, Prochilodus lineatus, Piaractus mesopotamicus, and Colossoma macropomum were evaluated. The primers that showed the best amplification patterns were applied to a sample of 22 individuals and the genetic parameters were calculated. Nine primers displayed satisfactory cross-amplification withB. falcatus: BoM5 (Brycon opalinus); Bh8, Bh13 and Bh16 (B. hilarii); Borg59 (B. orbignyanus); Bag22 (B. amazonicus); Par12 and Par80 (P. argenteus), and Cm1A8 (C. macropomum). The genetic parameters (number of alleles, effective alleles, allele richness, and expected and observed heterozygosity) and the polymorphic information content (PIC) confirmed the viability of these primers for population genetics analyses. Our study demonstrates the potential of transferability of microsatellite markers from related species and even different genera to B. falcatus, providing usefull tools for future population genetic studies in this species. (AU)


Assuntos
Variação Genética , Repetições de Microssatélites , Parâmetros/classificação , Genética Populacional
2.
PLoS Comput Biol ; 16(8): e1008065, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32797037

RESUMO

Inference of admixture proportions is a classical statistical problem in population genetics. Standard methods implicitly assume that both parents of an individual have the same admixture fraction. However, this is rarely the case in real data. In this paper we show that the distribution of admixture tract lengths in a genome contains information about the admixture proportions of the ancestors of an individual. We develop a Hidden Markov Model (HMM) framework for estimating the admixture proportions of the immediate ancestors of an individual, i.e. a type of decomposition of an individual's admixture proportions into further subsets of ancestral proportions in the ancestors. Based on a genealogical model for admixture tracts, we develop an efficient algorithm for computing the sampling probability of the genome from a single individual, as a function of the admixture proportions of the ancestors of this individual. This allows us to perform probabilistic inference of admixture proportions of ancestors only using the genome of an extant individual. We perform extensive simulations to quantify the error in the estimation of ancestral admixture proportions under various conditions. To illustrate the utility of the method, we apply it to real genetic data.


Assuntos
Genética Populacional/métodos , Avós , Pais , Linhagem , Bases de Dados Genéticas , Humanos , Funções Verossimilhança , Cadeias de Markov
3.
Proc Biol Sci ; 287(1932): 20201459, 2020 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-32752983

RESUMO

Hybridization events are not uncommon in marine environments where physical barriers are attenuated. Studies of coral reef taxa have suggested that hybridization predominantly occurs between parapatric species distributed along biogeographic suture zones. By contrast, little is known about the extent of sympatric hybridization on coral reefs, despite the large amount of biogeographic overlap shared by many coral reef species. Here, we investigate if the propensity for hybridization along suture zones represents a general phenomenon among coral reef fishes, by focusing on the marine angelfishes (family Pomacanthidae). Although hybridization has been reported for this family, it has not been thoroughly surveyed, with more recent hybridization studies focusing instead on closely related species from a population genetics perspective. We provide a comprehensive survey of hybridization among the Pomacanthidae, characterize the upper limits of genetic divergences between hybridizing species and investigate the occurrence of sympatric hybridization within this group. We report the occurrence of hybridization involving 42 species (48% of the family) from all but one genus of the Pomacanthidae. Our results indicate that the marine angelfishes are among the groups of coral reef fishes with the highest incidences of hybridization, not only between sympatric species, but also between deeply divergent lineages.


Assuntos
Peixes/fisiologia , Hibridização Genética , Simpatria , Animais , Recifes de Corais , Fluxo Gênico , Genética Populacional
4.
BMC Med ; 18(1): 216, 2020 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-32664879

RESUMO

BACKGROUND: Coronavirus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has now been confirmed worldwide. Yet, COVID-19 is strangely and tragically selective. Morbidity and mortality due to COVID19 rise dramatically with age and co-existing health conditions, including cancer and cardiovascular diseases. Human genetic factors may contribute to the extremely high transmissibility of SARS-CoV-2 and to the relentlessly progressive disease observed in a small but significant proportion of infected individuals, but these factors are largely unknown. MAIN BODY: In this study, we investigated genetic susceptibility to COVID-19 by examining DNA polymorphisms in ACE2 and TMPRSS2 (two key host factors of SARS-CoV-2) from ~ 81,000 human genomes. We found unique genetic susceptibility across different populations in ACE2 and TMPRSS2. Specifically, ACE2 polymorphisms were found to be associated with cardiovascular and pulmonary conditions by altering the angiotensinogen-ACE2 interactions, such as p.Arg514Gly in the African/African-American population. Unique but prevalent polymorphisms (including p.Val160Met (rs12329760), an expression quantitative trait locus (eQTL)) in TMPRSS2, offer potential explanations for differential genetic susceptibility to COVID-19 as well as for risk factors, including those with cancer and the high-risk group of male patients. We further discussed that polymorphisms in ACE2 or TMPRSS2 could guide effective treatments (i.e., hydroxychloroquine and camostat) for COVID-19. CONCLUSION: This study suggested that ACE2 or TMPRSS2 DNA polymorphisms were likely associated with genetic susceptibility of COVID-19, which calls for a human genetics initiative for fighting the COVID-19 pandemic.


Assuntos
Infecções por Coronavirus/genética , Predisposição Genética para Doença , Peptidil Dipeptidase A/genética , Pneumonia Viral/genética , Serina Endopeptidases/genética , Grupo com Ancestrais do Continente Africano , Betacoronavirus , Infecções por Coronavirus/etnologia , Genética Populacional , Humanos , Masculino , Pandemias , Pneumonia Viral/etnologia , Polimorfismo Genético , Locos de Características Quantitativas , Fatores de Risco
5.
Science ; 369(6501): 249-250, 2020 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-32675359
6.
Science ; 369(6501)2020 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-32675347

RESUMO

Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.


Assuntos
Adaptação Fisiológica/genética , Antozoários/genética , Genoma , Animais , Recifes de Corais , Genética Populacional , Estudo de Associação Genômica Ampla , Genômica
7.
Biochem Biophys Res Commun ; 529(2): 263-269, 2020 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-32703421

RESUMO

The World Health Organization recently announced that pandemic status has been achieved for coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Exponential increases in patient numbers have been reported around the world, along with proportional increases in the number of COVID-19-related deaths. The SARS-CoV-2 infection rate in a population is expected to be influenced by social practices, availability of vaccines or prophylactics, and the prevalence of susceptibility genes in the population. Previous work revealed that cellular uptake of SARS-CoV-2 requires Angiotensin Converting Enzyme 2 (ACE-2) and a cellular protease. The spike (S) protein on SARS-CoV-2 binds ACE-2, which functions as an entry receptor. Following receptor binding, transmembrane protease serine 2 (encoded by TMPRSS2) primes the S protein to allow cellular uptake. Therefore, individual expression of TMPRSS2 may be a crucial determinant of SARS-CoV-2 infection susceptibility. Here, we utilized multiple large genome databases, including the GTEx portal, SNP nexus, and Ensembl genome project, to identify gene expression profiles for TMPRSS2 and its important expression quantitative trait loci. Our results show that four variants (rs464397, rs469390, rs2070788 and rs383510) affect expression of TMPRSS2 in lung tissue. The allele frequency of each variant was then assessed in regional populations, including African, American, European, and three Asian cohorts (China, Japan and Taiwan). Interestingly, our data shows that TMPRSS2-upregulating variants are at higher frequencies in European and American populations than in the Asian populations, which implies that these populations might be relatively susceptible to SARS-CoV-2 infection.


Assuntos
Betacoronavirus/metabolismo , Regulação da Expressão Gênica/genética , Internacionalidade , Pulmão/metabolismo , Receptores Virais/genética , Serina Endopeptidases/genética , Ásia/etnologia , Estudos de Coortes , Europa (Continente)/etnologia , Frequência do Gene , Genética Populacional , Mapeamento Geográfico , Humanos , Especificidade de Órgãos/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas/genética , Estados Unidos/etnologia , Regulação para Cima/genética
9.
PLoS One ; 15(7): e0235288, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32614920

RESUMO

The American crocodile (Crocodylus acutus) is a widely distributed species across coastal and brackish areas of the Neotropical region of the Americas and the Greater Antilles. Available information on patterns of genetic differentiation in C. acutus shows a complex structuring influenced by interspecific interactions (mainly hybridization) and anthropogenic actions (mostly historical hunting, recent poaching, habitat loss and fragmentation, and unintentional translocation of individuals). In this study, we used data on mitochondrial DNA control region and 11 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus in South America, North America, Central America and the Greater Antilles. We used traditional genetic differentiation indices, Bayesian clustering and multivariate methods to create a more comprehensive picture of the genetic relationships within the species across its range. Analyses of mtDNA and microsatellite loci show evidence of a strong population genetic structure in the American crocodile, with unique populations in each sampling locality. Our results support previous findings showing large degrees of genetic differentiation between the continental and the Greater Antillean C. acutus. We report three new haplotypes unique to Venezuela, which are considerably less distant from the Central and North American haplotypes than to the Greater Antillean ones. Our findings reveal genetic population differentiation between Cuban and Jamaican C. acutus and offer the first evidence of strong genetic differentiation among the populations of Greater Antillean C. acutus.


Assuntos
Jacarés e Crocodilos/genética , Animais , Região do Caribe , América Central , DNA Mitocondrial/genética , Variação Genética , Genética Populacional , Haplótipos , Repetições de Microssatélites , Mitocôndrias/genética , América do Norte , América do Sul
10.
Nat Commun ; 11(1): 3403, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32636372

RESUMO

Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.


Assuntos
Variação Genética , Genética Populacional , Aves Canoras/genética , Animais , Inversão Cromossômica , Deleção de Genes , Genoma , Variação Estrutural do Genoma , Genótipo , Filogenia , Polimorfismo de Nucleotídeo Único , Retroelementos , Análise de Sequência de DNA
11.
PLoS Genet ; 16(7): e1008922, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32667917

RESUMO

A challenge in medical genomics is to identify variants and genes associated with severe genetic disorders. Based on the premise that severe, early-onset disorders often result in a reduction of evolutionary fitness, several statistical methods have been developed to predict pathogenic variants or constrained genes based on the signatures of negative selection in human populations. However, we currently lack a statistical framework to jointly predict deleterious variants and constrained genes from both variant-level features and gene-level selective constraints. Here we present such a unified approach, UNEECON, based on deep learning and population genetics. UNEECON treats the contributions of variant-level features and gene-level constraints as a variant-level fixed effect and a gene-level random effect, respectively. The sum of the fixed and random effects is then combined with an evolutionary model to infer the strength of negative selection at both variant and gene levels. Compared with previously published methods, UNEECON shows improved performance in predicting missense variants and protein-coding genes associated with autosomal dominant disorders, and feature importance analysis suggests that both gene-level selective constraints and variant-level predictors are important for accurate variant prioritization. Furthermore, based on UNEECON, we observe a low correlation between gene-level intolerance to missense mutations and that to loss-of-function mutations, which can be partially explained by the prevalence of disordered protein regions that are highly tolerant to missense mutations. Finally, we show that genes intolerant to both missense and loss-of-function mutations play key roles in the central nervous system and the autism spectrum disorders. Overall, UNEECON is a promising framework for both variant and gene prioritization.


Assuntos
Aptidão Genética/genética , Genoma Humano/genética , Mutação de Sentido Incorreto/genética , Seleção Genética , Aprendizado Profundo , Feminino , Aptidão Genética/fisiologia , Genética Populacional , Genômica/métodos , Humanos , Mutação com Perda de Função/genética , Masculino
12.
PLoS One ; 15(7): e0233808, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32673320

RESUMO

Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.


Assuntos
Grupo com Ancestrais do Continente Africano/genética , Grupo com Ancestrais do Continente Europeu/genética , Genoma Humano , Índios Sul-Americanos/genética , Casamento , Linhagem , Grupo com Ancestrais do Continente Africano/etnologia , Argentina , Colonialismo , DNA/genética , Escravização , Grupo com Ancestrais do Continente Europeu/etnologia , Marcadores Genéticos , Variação Genética , Genética Populacional , Genótipo , Migração Humana , Humanos , Índios Sul-Americanos/etnologia , Modelos Genéticos
13.
Proc Biol Sci ; 287(1931): 20201206, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-32693716

RESUMO

The grey wolf (Canis lupus) is one of the most widely distributed mammals in which a variety of distinct populations have been described. However, given their currently fragmented distribution and recent history of human-induced population decline, little is known about the events that led to their differentiation. Based on the analysis of whole canid genomes, we examined the divergence times between Southern European wolf populations and their ancient demographic history. We found that all present-day Eurasian wolves share a common ancestor ca 36 000 years ago, supporting the hypothesis that all extant wolves derive from a single population that subsequently expanded after the Last Glacial Maximum. We also estimated that the currently isolated European populations of the Iberian Peninsula, Italy and the Dinarics-Balkans diverged very closely in time, ca 10 500 years ago, and maintained negligible gene flow ever since. This indicates that the current genetic and morphological distinctiveness of Iberian and Italian wolves can be attributed to their isolation dating back to the end of the Pleistocene, predating the recent human-induced extinction of wolves in Central Europe by several millennia.


Assuntos
Genética Populacional , Lobos/genética , Animais , Europa (Continente) , Fluxo Gênico , Genoma
14.
PLoS Comput Biol ; 16(7): e1008010, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32628660

RESUMO

Antibiotic-resistant infections are a growing threat to human health, but basic features of the eco-evolutionary dynamics remain unexplained. Most prominently, there is no clear mechanism for the long-term coexistence of both drug-sensitive and resistant strains at intermediate levels, a ubiquitous pattern seen in surveillance data. Here we show that accounting for structured or spatially-heterogeneous host populations and variability in antibiotic consumption can lead to persistent coexistence over a wide range of treatment coverages, drug efficacies, costs of resistance, and mixing patterns. Moreover, this mechanism can explain other puzzling spatiotemporal features of drug-resistance epidemiology that have received less attention, such as large differences in the prevalence of resistance between geographical regions with similar antibiotic consumption or that neighbor one another. We find that the same amount of antibiotic use can lead to very different levels of resistance depending on how treatment is distributed in a transmission network. We also identify parameter regimes in which population structure alone cannot support coexistence, suggesting the need for other mechanisms to explain the epidemiology of antibiotic resistance. Our analysis identifies key features of host population structure that can be used to assess resistance risk and highlights the need to include spatial or demographic heterogeneity in models to guide resistance management.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Genética Populacional , Infecções Estreptocócicas/microbiologia , Algoritmos , Evolução Molecular , Geografia , Humanos , Modelos Teóricos , Prevalência , Análise de Regressão , Risco , Espanha/epidemiologia , Infecções Estreptocócicas/epidemiologia , Streptococcus pneumoniae/efeitos dos fármacos , Streptococcus pneumoniae/genética
15.
Bull Tokyo Dent Coll ; 61(2): 83-94, 2020 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-32522936

RESUMO

Population flow between Southeast Asian countries and Japan continues to gather pace. Accordingly, the number of foreigners involved in incidents in Japan has markedly increased, which means that forensic dentistry is now increasingly being faced with the need to analyze DNA from persons of non-Japanese extraction. The DNA test currently used for personal identification mainly utilizes short tandem repeats (STRs) on autosomal chromosomes and the Y-chromosome. This test was developed for use in personal identification, not for distinguishing among races; nonetheless, the standard method for personal identification is often used because the procedure has been established. To determine the degree to which racial differences can be distinguished by standard DNA analysis, 23 STRs located on the Y chromosome were investigated in 218 Malay and 426 Japanese males. The frequencies of each STR were calculated in the two populations. The difference in the power of discrimination between the Malay and Japanese populations ranged from a minimum of 0.01 to a maximum of 0.27; the difference in polymorphic information content ranged from 0.01 (minimum) to 0.23 (maximum). No major differences were noted in the polymorphisms in these two Mongoloid populations, but the distributions of the 17 STRs differed significantly. Short tandem repeat types demonstrating a likelihood of racial differences were identified in 14 of the STRs. Race-specific STR types were identified in 10 STRs. These results suggest that the likelihood of Malay or Japanese genetic background can be judged based on Y-chromosome STR test results.


Assuntos
Cromossomos Humanos Y , Genética Populacional , Haplótipos , Humanos , Japão , Malásia , Masculino
16.
Ying Yong Sheng Tai Xue Bao ; 31(2): 634-642, 2020 Feb.
Artigo em Chinês | MEDLINE | ID: mdl-32476358

RESUMO

A total of 64 haplotypes were obtained from the complete Cytochrome b gene (Cyt b) of 77 Sorex isodon collected from three populations (Daxing'anling, Xiaoxing'anling, and Changbai Mountains) in Northeast China. The haplotype diversity was 0.9920 and the nucleotide diversity was 0.0105, indicating high genetic diversity. The genetic diversity of Changbai Mountains population was significantly higher than that of Daxing'anling and Xiaoxing'anling populations. The F-statistics, the number of migrants per generation and the genetic distance results showed that the genetic distances among the populations and among the sampling sites were generally consistent with geographical distance. Analysis of molecular variance showed that the differentiation among populations, among sampling sites, and within sampling site accounted for 33.4%, 10.2% and 56.4% of total variation, respectively. The analysis of population history showed that S. isodon in Northeast China experienced no population expansion. The reported complete sequence of Cyt b gene of S. isodon (GenBank) of Europe and other parts of Asia was downloaded to examine the genetic structure of S. isodon. The phylogenetic tree was divided into two large branches. One branch consisted mainly of Daxing'anling and Xiaoxing'anling samples. The other branch was departed into two sub-branches. Median-joining network analysis showed that there were three lineages: one lineage mainly consisted of haplotypes from Daxing'anling and Xiaoxing'anling, and also four haplotypes of Changbai Mountains, while the other lineage included a few haplotypes of three populations in Northeast China, and those from Baikal Lake, Russia and Finland. The last lineage was entirely composed of haplotypes from Changbai Mountains. The results of genetic diversity, phylogenetic tree and median-joining network all suggested that the Changbai Mountains was the refuge for S. isodon during last glacial.


Assuntos
Isodon , Ásia , China , DNA Mitocondrial , Europa (Continente) , Estruturas Genéticas , Variação Genética , Genética Populacional , Haplótipos , Filogenia , Filogeografia
17.
Leg Med (Tokyo) ; 46: 101726, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32526672

RESUMO

China harbors 56 ethnic groups and Han is the largest population. It is informative and useful to explore the available population genetic characteristics of Chinese Han population from Fujian Province, Southeast China. In our study, we explored the genetic characteristics of 20 autosomal Short tandem repeat (STR) loci in 1555 unrelated Chinese Han individuals from Zhangzhou City, Southeastern China using the SureID® 21G Human STR Identification Kit. Moreover, phylogenetic analysis was performed between the Zhangzhou Han population and other relevant populations based on the shared autosomal STR genotyping. The neighbor-joining tree and multidimensional scaling analysis were analyzed based on the Nei's standard genetic distance. We found 262 alleles among 1555 unrelated individuals and the corresponding allele frequencies ranged from 0.5521 to 0.0003. The combined power of discrimination and exclusion of the 20 autosomal STR loci were 0.99999999999999999999999943 and 0.999999996166537, respectively. Population comparison revealed that the Zhangzhou Han population were lining up together with the southern Han populations in China while showed significant differences from other China populations. Our results found that the 20 autosomal STR loci in Zhangzhou Han population are meaningful for forensic medicine and human genetic. The genetics characteristic of Zhangzhou Han population is similar with the southern Han population in China.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Medicina Legal , Loci Gênicos/genética , Genética Populacional/métodos , Repetições de Microssatélites/genética , China , Humanos , Polimorfismo Genético
18.
PLoS Genet ; 16(6): e1008867, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32555579

RESUMO

Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method-VolcanoFinder-to detect recent events of adaptive introgression using polymorphism data from the recipient species only. VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity. Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder.


Assuntos
Introgressão Genética , Genética Populacional/métodos , Genoma Humano/genética , Modelos Genéticos , Polimorfismo Genético , África ao Sul do Saara , Grupo com Ancestrais do Continente Africano/genética , Alelos , Antígenos/genética , Simulação por Computador , Europa (Continente) , Grupo com Ancestrais do Continente Europeu/genética , Evolução Molecular , Haplótipos , Humanos , Proteínas de Filamentos Intermediários/genética , Receptores da Tireotropina/genética , Proteínas S100/genética , Seleção Genética , Software
19.
Sci Total Environ ; 740: 140046, 2020 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-32563876

RESUMO

Genetic diversity is expected to erode in disturbed habitats through strong selection, local extinctions, and recolonization associated with genetic bottlenecks and restricted gene flow. Despite this general prediction and over three decades of population genetics studies, our understanding of the long-term effect of environmental disturbance on local and regional genetic diversity remains limited. We conducted a population genetic survey of the microcrustacean Daphnia across a landscape subject to anthropogenic stressors from a century of industrial mining. At the local scale we found moderate genetic diversity (i.e., low clonal diversity), characteristic of habitat-specific selective sweeps and local extinctions, but high diversity and strong genetic structure at the regional scale despite the shared watershed of many lakes and exceptional dispersal ability of daphniids. Many habitats experienced changes in species assemblages, with the obligate asexual Daphnia pulex lineages-known only to inhabit ponds-dominating disrupted urban lakes. This habitat transition (pond to lake) was likely facilitated by the disruption of ecological barriers maintaining the genomic separation of these young species. Thus, disrupted habitats can exhibit complex and unexpected genetic patterns of local extinctions and recolonizations, followed by habitat transitions, hybridization and potential speciation events that are difficult to predict and should not be underestimated.


Assuntos
Genética Populacional , Hibridização Genética , Animais , Ecossistema , Fluxo Gênico , Variação Genética
20.
Proc Biol Sci ; 287(1928): 20200318, 2020 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-32486973

RESUMO

Metapopulation theory assumes a balance between local decays/extinctions and local growth/new colonisations. Here we investigate whether recent population declines across part of the UK harbour seal range represent normal metapopulation dynamics or are indicative of perturbations potentially threatening the metapopulation viability, using 20 years of population trends, location tracking data (n = 380), and UK-wide, multi-generational population genetic data (n = 269). First, we use microsatellite data to show that two genetic groups previously identified are distinct metapopulations: northern and southern. Then, we characterize the northern metapopulation dynamics in two different periods, before and after the start of regional declines (pre-/peri-perturbation). We identify source-sink dynamics across the northern metapopulation, with two putative source populations apparently supporting three likely sink populations, and a recent metapopulation-wide disruption of migration coincident with the perturbation. The northern metapopulation appears to be in decay, highlighting that changes in local populations can lead to radical alterations in the overall metapopulation's persistence and dynamics.


Assuntos
Phoca , Dinâmica Populacional , Animais , Ecossistema , Genética Populacional , Repetições de Microssatélites
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