Inferring continuous and discrete population genetic structure across space

AbstractA classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the “clines versus clusters” problem in modeling population genetic variation. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.Author summaryOne of the first steps in the analysis of genetic data, and a principal mission of biology, is to describe and categorize natural variation. A continuous pattern of differentiation (isolation by distance), where individuals found closer together in space are, on average, more genetically similar than individuals sampled farther apart, can confound attempts to categorize natural variation into groups. This is because current statistical methods for assigning individuals to discrete clusters cannot accommodate spatial patterns, and so are forced to use clusters to describe what is in fact continuous variation. As isolation by distance is common in nature, this is a substantial shortcoming of existing methods. In this study, we introduce a new statistical method for categorizing natural genetic variation - one that describes variation as a combination of continuous and discrete patterns. We demonstrate that this method works well and can capture patterns in population genomic data without resorting to splitting populations where they can be described by continuous patterns of variation.

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Genetic Relationships of Cory's Shearwater: Parentage, Mating Assortment, and Geographic Differentiation Revealed by DNA Fingerprinting

The Auk ◽

10.1093/auk/117.3.651 ◽

2000 ◽

Vol 117 (3) ◽

pp. 651-662 ◽

Cited By ~ 1

Author(s):

Corinne Rabouam ◽

Vincent Bretagnolle ◽

Yves Bigot ◽

Georges Periquet

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Dna Fingerprinting ◽

Genetic Relatedness ◽

Isolation By Distance ◽

Genetic Relationships ◽

Cory’S Shearwater ◽

Genetic Structure Of Populations ◽

The Social ◽

Calonectris Diomedea

Abstract We used DNA fingerprinting to assess genetic structure of populations in Cory's Shearwater (Calonectris diomedea). We analyzed mates and parent-offspring relationships, as well as the amount and distribution of genetic variation within and among populations, from the level of subcolony to subspecies. We found no evidence of extrapair fertilization, confirming that the genetic breeding system matches the social system that has been observed in the species. Mates were closely related, and the level of genetic relatedness within populations was within the range usually found in inbred populations. In contrast to previous studies based on allozymes and mtDNA polymorphism, DNA fingerprinting using microsatellites revealed consistent levels of genetic differentiation among populations. However, analyzing the two subspecies separately revealed that the pattern of genetic variation among populations did not support the model of isolation by distance. Natal dispersal, as well as historic and/or demographic events, probably contributed to shape the genetic structure of populations in the species.

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Population genetic structure of European wildcats inhabiting the area between the Dinaric Alps and the Scardo-Pindic mountains

10.21203/rs.3.rs-443648/v1 ◽

2021 ◽

Author(s):

Felicita Urzi ◽

Nikica Šprem ◽

Hubert Potočnik ◽

Magda Sindičić ◽

Dean Konjević ◽

...

Keyword(s):

Genetic Variation ◽

Population Genetic ◽

Allelic Richness ◽

Isolation By Distance ◽

Domestic Cats ◽

Genetic Purity ◽

Eastern Group ◽

Two Samples ◽

European Wildcat ◽

Genetic Clusters

Abstract Habitat fragmentation and loss have contributed significantly to the demographic decline of European wildcat populations and hybridization with domestic cats poses a threat to the loss of genetic purity of the species. In this study we used microsatellite markers to analyse genetic variation and structure of the wildcat populations from the area between the Dinaric Alps and the Scardo-Pindic mountains in Slovenia, Croatia, Serbia and North Macedonia. We also investigated hybridisation between populations of wildcats and domestic cats in the area. One hundred and thirteen samples from free-leaving European wildcats and thirty-two samples from domestic cats were analysed. Allelic richness across populations ranged from 3.61 to 3.98. The observed Ho values ranged between 0.57 and 0.71. The global FST value for the four populations was 0.080 (95% CI 0.056–0.109) and differed significantly from zero (P < 0.001). The highest FST value was observed between the populations North Macedonia and Slovenia and the lowest between Slovenia and Croatia. We also found a signal for the existence of isolation by distance between populations. Our results showed that wildcats are divided in two genetic clusters largely consistent with a geographic division into a genetically diverse northern group (Slovenia, Croatia) and genetically eroded south-eastern group (Serbia, N. Macedonia). Hybridisation rate between wildcats and domestic cats varied between 13% and 52% across the regions.

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A spectral theory for Wright’s inbreeding coefficients and related quantities

PLoS Genetics ◽

10.1371/journal.pgen.1009665 ◽

2021 ◽

Vol 17 (7) ◽

pp. e1009665

Author(s):

Olivier François ◽

Clément Gain

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Population Genetic ◽

Principal Component ◽

Large Data ◽

Population Subdivision ◽

Adaptive Genetic Variation ◽

Genomic Locus ◽

Inbreeding Coefficients ◽

Definition Of

Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

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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 genetic structure of the Gulf of St. Lawrence aster, Symphyotrichum laurentianum (Asteraceae), a threatened coastal endemic

Botany ◽

10.1139/b09-068 ◽

2009 ◽

Vol 87 (11) ◽

pp. 1089-1095 ◽

Cited By ~ 5

Author(s):

Stephen B. Heard ◽

Linley K. Jesson ◽

Kirby Tulk

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Threatened Species ◽

Population Genetic Structure ◽

Population Genetic ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Population Decline ◽

Allelic Diversity ◽

Magdalen Islands

The Gulf of St. Lawrence aster ( Symphyotrichum laurentianum (Fernald) G.L. Nesom) is an endemic annual of saline habitats in the southern Gulf of St. Lawrence. It is listed as a threatened species, and has recently experienced population declines in much of its range. We used 11 allozyme markers to assay population genetic variation in six wild populations of S. laurentianum from the Magdalen Islands, Quebec (QC), the only remaining wild population from Prince Edward Island National Park (PEI), and a greenhouse population founded in 1999 with seed collected from PEI. Symphyotrichum laurentianum harbours moderate genetic diversity (Ps = 0.36, As = 1.54), with only modest spatial genetic structure (pairwise FST < 0.15) and no significant isolation by distance. The PEI population had greatly reduced allelic diversity compared with the populations from the Magdalen Islands, which likely act as a reservoir of genetic variation in S. laurentianum. Recent loss of alleles during population decline in PEI is suggested by the retention of greater allelic diversity in the greenhouse population. Estimates of breeding structure suggest small but nonzero rates of outcross pollination (FIS = 0.73, 95% CI = 0.48–0.97; outcrossing rate ∼16%). Population genetic structure in S. laurentianum can inform those forming and carrying out conservation and recovery plans for this threatened species.

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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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Speciation in Stickleback Facilitated by Admixture – Where is the Evidence?

10.20944/preprints202005.0428.v1 ◽

2020 ◽

Author(s):

Daniel Berner

Keyword(s):

Genetic Variation ◽

Central Europe ◽

Population Genetic ◽

Population structure and dispersal across small and large spatial scales in a direct developing marine isopod

10.1101/2020.03.01.971333 ◽

2020 ◽

Author(s):

William S. Pearman ◽

Sarah J. Wells ◽

Olin K. Silander ◽

Nikki E. Freed ◽

James Dale

Keyword(s):

Population Structure ◽

Gene Flow ◽

Population Genetic ◽

Isolation By Distance ◽

Spatial Scales ◽

Population Connectivity ◽

Clear Pattern ◽

Small Spatial Scale ◽

Cook Strait ◽

Genetic Break

AbstractMarine organisms generally exhibit one of two developmental modes: biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, in contrast to our relatively good understanding of dispersal and population connectivity for biphasic species, comparatively little is known about direct developers. In this study, we use a panel of 8,020 SNPs to investigate population structure and gene flow for a direct developing species, the New Zealand endemic marine isopod Isocladus armatus. On a small spatial scale (20 kms), gene flow between locations is extremely high and suggests an island model of migration. However, over larger spatial scales (600km), populations exhibit a clear pattern of isolation-by-distance. Because our sampling range is intersected by two well-known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. Our results indicate that I. armatus exhibits significant migration across these barriers, and suggests that ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we do find evidence of a north-south population genetic break occurring between Māhia and Wellington, two locations where there are no obvious biogeographic barriers between them. We conclude that developmental life history largely predicts dispersal in intertidal marine isopods. However, localised biogeographic processes can disrupt this expectation.

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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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