Effects of Colonization, Geography and Environment on Genetic Divergence in the Intermediate Leaf-Nosed Bat, Hipposideros larvatus

Determining the evolutionary history and population drivers, such as past large-scale climatic oscillations, stochastic processes and ecological adaptations, represents one of the aims of evolutionary biology. Hipposideros larvatus is a common bat species in Southern China, including Hainan Island. We examined genetic variation in H. larvatus using mitochondrial DNA and nuclear microsatellites. We found a population structure on both markers with a geographic pattern that corresponds well with the structure on mainland China and Hainan Island. To understand the contributions of geography, the environment and colonization history to the observed population structure, we tested isolation by distance (IBD), isolation by adaptation (IBA) and isolation by colonization (IBC) using serial Mantel tests and RDA analysis. The results showed significant impacts of IBD, IBA and IBC on neutral genetic variation, suggesting that genetic variation in H. larvatus is greatly affected by neutral processes, environmental adaptation and colonization history. This study enriches our understanding of the complex evolutionary forces that shape the distribution of genetic variation in bats.

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Comparative population genetic structure of two Ixodidae ticks (Ixodes ovatus and Haemaphysalis flava) in Niigata Prefecture, Japan

10.1101/862904 ◽

2019 ◽

Author(s):

Maria Angenica Fulo Regilme ◽

Megumi Sato ◽

Tsutomu Tamura ◽

Reiko Arai ◽

Marcello Otake Sato ◽

...

Keyword(s):

Genetic Structure ◽

Large Scale ◽

Southern China ◽

Isolation By Distance ◽

Mantel Test ◽

Rrna Gene ◽

Data Set ◽

Genetic Groups ◽

Niigata Prefecture ◽

Haemaphysalis Flava

AbstractIxodid tick species such as Ixodes ovatus and Haemaphysalis flava are important vector of tick-borne diseases in Japan. In this study, we used genetic structure at two mitochondrial loci (cox1, 16S rRNA gene) to infer gene flow patterns of I. ovatus and H. flava from Niigata Prefecture, Japan. Samples were collected in 29 (I. ovatus) and 17 (H. flava) sampling locations across Niigata Prefecture (12,584.18 km2). For I. ovatus, pairwise FST and analysis of molecular variance (AMOVA) analyses of cox1 sequences indicated significant among-population differentiation. This was in contrast to H. flava, for which there were few cases of low significant pairwise differentiation. A Mantel test revealed isolation by distance and there was positive spatial autocorrelation of haplotypes in I. ovatus cox1 and 16S sequences, but non-significant results were observed in H. flava in both markers. We found three genetic groups (China 1, China 2 and Japan) in the cox1 I. ovatus tree. Newly sampled I. ovatus grouped together with a published I. ovatus sequence from northern Japan and were distinct from two other I. ovatus groups that were reported from southern China. The three genetic groups in our data set suggest the potential for cryptic species among the groups. While many factors can potentially account for the observed differences in genetic structure between the two species, including population persistence and large-scale patterns of range expansion, the differences in the mobility of hosts of tick immature stages (small mammals in I. ovatus; birds in H. flava) is possibly driving the observed patterns.

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Birds are islands for parasites

Biology Letters ◽

10.1098/rsbl.2014.0255 ◽

2014 ◽

Vol 10 (8) ◽

pp. 20140255 ◽

Cited By ~ 25

Author(s):

Jennifer A. H. Koop ◽

Karen E. DeMatteo ◽

Patricia G. Parker ◽

Noah K. Whiteman

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Evolutionary Biology ◽

Isolation By Distance ◽

Spatial Scales ◽

Island Populations ◽

Louse Species ◽

Parasite Populations

Understanding the mechanisms driving the extraordinary diversification of parasites is a major challenge in evolutionary biology. Co-speciation, one proposed mechanism that could contribute to this diversity is hypothesized to result from allopatric co-divergence of host–parasite populations. We found that island populations of the Galápagos hawk ( Buteo galapagoensis ) and a parasitic feather louse species ( Degeeriella regalis ) exhibit patterns of co-divergence across variable temporal and spatial scales. Hawks and lice showed nearly identical population genetic structure across the Galápagos Islands. Hawk population genetic structure is explained by isolation by distance among islands. Louse population structure is best explained by hawk population structure, rather than isolation by distance per se , suggesting that lice tightly track the recent population histories of their hosts. Among hawk individuals, louse populations were also highly structured, suggesting that hosts serve as islands for parasites from an evolutionary perspective. Altogether, we found that host and parasite populations may have responded in the same manner to geographical isolation across spatial scales. Allopatric co-divergence is likely one important mechanism driving the diversification of parasites.

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Isonymy and population structure of Irish isolates during the 1890s

Journal of Biosocial Science ◽

10.1017/s002193200001405x ◽

1982 ◽

Vol 14 (2) ◽

pp. 241-247 ◽

Cited By ~ 14

Author(s):

John H. Relethford

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Isolation By Distance ◽

Breeding Population ◽

Isolated Populations ◽

Estimated Parameters ◽

Distance Model ◽

Local Breeding ◽

And Migration ◽

Close Fit

SummaryThe estimation of genetic similarity from correspondence of surnames (isonymy) allows investigation of historical population structure. This study uses surname data from seven isolates located along the west coast of Ireland during the 1890s to assess geographic and historic influences on population structure. Observed genetic variation among populations shows a close fit with the expected isolation by distance model, with estimated parameters of isolation and migration being similar to those obtained in other studies of isolated populations. Local genetic variation appears to be due primarily to the size of the local breeding population, with deviations being explained in terms of recent emigration.

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Population structure in two geographically sympatric and congeneric ectoparasites (Cimex adjunctus and Cimex lectularius) in the North American Great Lakes region

Canadian Journal of Zoology ◽

10.1139/cjz-2017-0014 ◽

2017 ◽

Vol 95 (12) ◽

pp. 901-907 ◽

Cited By ~ 2

Author(s):

Benoit Talbot ◽

Maarten J. Vonhof ◽

Hugh G. Broders ◽

M. Brock Fenton ◽

Nusha Keyghobadi

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Geographic Area ◽

Abundant Species ◽

Cimex Lectularius ◽

Genetic Structuring ◽

The North ◽

Genetic Clusters

Subdivided populations can be described by different models of population structure that reflect population organization, dynamics, and connectivity. We used genetic data to investigate population structure in two geographically sympatric, congeneric species of generalist ectoparasites of warm-blooded animals. We characterized the spatial genetic structure of the eastern bat bug (Cimex adjunctus Barber, 1939), an understudied and fairly abundant species, using microsatellite markers at a spatial scale representing contemporary dispersal of the species. We found seven genetic clusters, global [Formula: see text] of 0.2, 33% of genetic variation among sites, and nonsignificant isolation-by-distance. We compared these results with the common bed bug (Cimex lectularius L., 1758), a closely related but conversely well-known species, in the same geographic area. We found stronger genetic structuring in C. lectularius than in C. adjunctus, with 11 genetic clusters, [Formula: see text] of 0.7, 57% of genetic variation among sites, and significant but weak isolation-by-distance (R2 = 0.09). These results suggest that while both species can be described as having classic metapopulation structure, C. adjunctus leans more towards a patchy population and C. lectularius leans more towards a nonequilibrium metapopulation. The difference in population structure between these species may be attributable to differences in movement potential and extinction–colonization dynamics.

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Visualizing spatial population structure with estimated effective migration surfaces

10.1101/011809 ◽

2014 ◽

Cited By ~ 5

Author(s):

Desislava Petkova ◽

John Novembre ◽

Matthew Stephens

Keyword(s):

Population Structure ◽

Gene Flow ◽

Genetic Similarity ◽

Large Scale ◽

Genetic Model ◽

Isolation By Distance ◽

Genetic Data ◽

Migration Rates ◽

Spatial Population ◽

Spatial Population Structure

Genetic data often exhibit patterns that are broadly consistent with "isolation by distance" - a phenomenon where genetic similarity tends to decay with geographic distance. In a heterogeneous habitat, decay may occur more quickly in some regions than others: for example, barriers to gene flow can accelerate the genetic differentiation between groups located close in space. We use the concept of "effective migration" to model the relationship between genetics and geography: in this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to quantify and visualize variation in effective migration across the habitat, which can be used to identify potential barriers to gene flow, from geographically indexed large-scale genetic data. Our approach uses a population genetic model to relate underlying migration rates to expected pairwise genetic dissimilarities, and estimates migration rates by matching these expectations to the observed dissimilarities. We illustrate the potential and limitations of our method using simulations and data from elephant, human, and Arabidopsis thaliana populations. The resulting visualizations highlight important features of the spatial population structure that are difficult to discern using existing methods for summarizing genetic variation such as principal components analysis.

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Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus

Royal Society Open Science ◽

10.1098/rsos.171532 ◽

2018 ◽

Vol 5 (5) ◽

pp. 171532 ◽

Cited By ~ 1

Author(s):

Joaquin C. B. Nunez ◽

Leann M. Biancani ◽

Patrick A. Flight ◽

Diane E. Nacci ◽

David M. Rand ◽

...

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Fundulus Heteroclitus ◽

Isolation By Distance ◽

Spatial Scales ◽

Purifying Selection ◽

Spatial Distance ◽

Estuarine Fish ◽

Synonymous Mutations ◽

Microsatellite Analyses

Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in N e and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade.

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Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow, and fine-scale population structure in northern Dolly Varden (Salvelinus malma malma) in Canada

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2015-0016 ◽

2015 ◽

Vol 72 (10) ◽

pp. 1477-1493 ◽

Cited By ~ 17

Author(s):

Les N. Harris ◽

Robert Bajno ◽

Colin P. Gallagher ◽

Itsuro Koizumi ◽

Lucy K. Johnson ◽

...

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Life History ◽

Gene Flow ◽

Isolation By Distance ◽

Dolly Varden ◽

Salvelinus Malma ◽

Dolly Varden Salvelinus Malma ◽

Northern Dolly Varden ◽

Population Demographic

The northern Dolly Varden (Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in northern Dolly Varden from the western Canadian Arctic to resolve landscape and life-history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls, with stream-resident forms intermediate between the two. Anadromous and isolated populations were genetically divergent from each other, while no genetic differentiation was detectable between sympatric anadromous and stream-resident forms. Population structure was stable over 25 years, hierarchically organized, and conformed to an isolation-by-distance pattern, but stream-isolated forms often deviated from these patterns. Gene flow occurred primarily among Yukon North Slope populations and between sympatric anadromous and resident forms. These results were sex-dependent to some extent, but were influenced more by reproductive status and life history. Our study provides novel insights into the life history, population demographic, and habitat variables that shape the distribution of genetic variation and population structure in Arctic fluvial habitats while providing a spatial context for management and conservation.

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Genetic Diversity and Population Structure of a Threatened African Tree Species,Milicia excelsa,Using Nuclear Microsatellites DNA Markers

International Journal of Forestry Research ◽

10.1155/2009/210179 ◽

2009 ◽

Vol 2009 ◽

pp. 1-8 ◽

Cited By ~ 4

Author(s):

Christine Ouinsavi ◽

Nestor Sokpon ◽

Damase P. Khasa

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Isolation By Distance ◽

In Situ Conservation ◽

Agroforestry Systems ◽

Microsatellites Dna ◽

Geographical Distances ◽

Hardy Weinberg Equilibrium ◽

Milicia Excelsa

To accurately estimate the genetic diversity and population structure for improved conservation planning ofMilicia excelsatree, 212 individuals from twelve population samples covering the species' range in Benin were surveyed at seven specific microsatellite DNA loci. All loci were variable, with the mean number of alleles per locus ranging from 5.86 to 7.69. Considerable genetic variability was detected for all populations at the seven loci (AR=4.60;HE=0.811). Moderate but statistically significant genetic differentiation was found among populations considering bothFST(0.112) andRST(0.342). All of the populations showed heterozygosity deficits in test of Hardy-Weinberg Equilibrium and significantly positiveFISvalues due to inbreeding occurring in the species. PairwiseFSTvalues were positively and significantly correlated with geographical distances (r=0.432;P=.007, Mantel's test) indicating that populations are differentiated by “isolation by distance.” Bayesian analysis of population structure showed division of the genetic variation into four clusters revealing the existence of heterogeneity in population genetic structure. Altogether, these results indicate that genetic variation inMilicia excelsais geographically structured. Information gained from this study also emphasized the need for in situ conservation of the relict populations and establishment of gene flow corridors through agroforestry systems for interconnecting these remnant populations.

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Demographic modeling informs functional connectivity and management interventions in Graham’s beardtongue

Conservation Genetics ◽

10.1007/s10592-021-01392-9 ◽

2021 ◽

Author(s):

Matthew R. Jones ◽

Daniel E. Winkler ◽

Rob Massatti

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Functional Connectivity ◽

Isolation By Distance ◽

Management Practice ◽

Demographic History ◽

Principal Component ◽

Management Options ◽

Demographic Modeling ◽

Management Interventions

AbstractFunctional connectivity (i.e., the movement of individuals across a landscape) is essential for the maintenance of genetic variation and persistence of rare species. However, illuminating the processes influencing functional connectivity and ultimately translating this knowledge into management practice remains a fundamental challenge. Here, we combine various population structure analyses with pairwise, population-specific demographic modeling to investigate historical functional connectivity in Graham’s beardtongue (Penstemon grahamii), a rare plant narrowly distributed across a dryland region of the western US. While principal component and population structure analyses indicated an isolation-by-distance pattern of differentiation across the species’ range, spatial inferences of effective migration exposed an abrupt shift in population ancestry near the range center. To understand these seemingly conflicting patterns, we tested various models of historical gene flow and found evidence for recent admixture (~ 3400 generations ago) between populations near the range center. This historical perspective reconciles population structure patterns and suggests management efforts should focus on maintaining connectivity between these previously isolated lineages to promote the ongoing transfer of genetic variation. Beyond providing species-specific knowledge to inform management options, our study highlights how understanding demographic history may be critical to guide conservation efforts when interpreting population genetic patterns and inferring functional connectivity.

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Scalable probabilistic PCA for large-scale genetic variation data

10.1101/729202 ◽

2019 ◽

Cited By ~ 4

Author(s):

Aman Agrawal ◽

Alec M. Chiu ◽

Minh Le ◽

Eran Halperin ◽

Sriram Sankararaman

Keyword(s):

Principal Component Analysis ◽

Population Structure ◽

Genetic Variation ◽

Principal Components ◽

Large Scale ◽

Principal Component ◽

Uk Biobank ◽

Genome Wide ◽

Variation Data ◽

The Uk

AbstractPrincipal component analysis (PCA) is a key tool for understanding population structure and controlling for population stratification in genome-wide association studies (GWAS). With the advent of large-scale datasets of genetic variation, there is a need for methods that can compute principal components (PCs) with scalable computational and memory requirements. We present ProPCA, a highly scalable method based on a probabilistic generative model, which computes the top PCs on genetic variation data efficiently. We applied ProPCA to compute the top five PCs on genotype data from the UK Biobank, consisting of 488,363 individuals and 146,671 SNPs, in less than thirty minutes. Leveraging the population structure inferred by ProPCA within the White British individuals in the UK Biobank, we scanned for SNPs that are not well-explained by the PCs to identify several novel genome-wide signals of recent putative selection including missense mutations in RPGRIP1L and TLR4.Author SummaryPrincipal component analysis is a commonly used technique for understanding population structure and genetic variation. With the advent of large-scale datasets that contain the genetic information of hundreds of thousands of individuals, there is a need for methods that can compute principal components (PCs) with scalable computational and memory requirements. In this study, we present ProPCA, a highly scalable statistical method to compute genetic PCs efficiently. We systematically evaluate the accuracy and robustness of our method on large-scale simulated data and apply it to the UK Biobank. Leveraging the population structure inferred by ProPCA within the White British individuals in the UK Biobank, we identify several novel signals of putative recent selection.

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