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

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.

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

PLoS Genetics ◽  
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.

Isonymy and population structure of Irish isolates during the 1890s

1982 ◽  
Vol 14 (2) ◽  
pp. 241-247 ◽  
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.

scholarly journals Species-Wide Genetic Variation and Demographic History ofDrosophila sechellia, a Species Lacking Population Structure

Genetics ◽  
2009 ◽  
Vol 182 (4) ◽  
pp. 1197-1206 ◽  
Author(s):  
Delphine Legrand ◽  
Maud I. Tenaillon ◽  
Pat Matyot ◽  
Justin Gerlach ◽  
Daniel Lachaise ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Demographic History

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

2017 ◽  
Vol 95 (12) ◽  
pp. 901-907 ◽  
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.

scholarly journals Genetic and morphometric divergence in the Garnet-Throated Hummingbird Lamprolaima rhami (Aves: Trochilidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5733 ◽  
Author(s):  
Luz E. Zamudio-Beltrán ◽  
Blanca E. Hernández-Baños
Keyword(s):  
Genetic Variation ◽  
El Salvador ◽  
Species Delimitation ◽  
Biological Diversity ◽  
Environmental Changes ◽  
Isolation By Distance ◽  
Demographic History ◽  
Cloud Forests ◽  
Divergence Time Estimates ◽  
Geographic Structure

Cloud forests are one of the most endangered ecosystems in the Americas, as well as one of the richest in biological diversity in the world. The species inhabiting these forests are susceptible to environmental changes and characterized by high levels of geographic structure. The Garnet-Throated Hummingbird, Lamprolaima rhami, mainly inhabits cloud forests, but can also be found in other habitats. This species has a highly restricted distribution in Mesoamerica, and five disjunct regions have been delimited within the current geographic distribution of the species from Mexico to Honduras. According to variation in size and color, three subspecies have been described: L. r. rhami restricted to the Mexican highlands and Guatemala, L. r. occidentalis distributed in Guerrero (Mexico), and L. r. saturatior, distributed in the highlands from Honduras and El Salvador. We analyzed the levels of geographic structure in L. rhami and its taxonomic implications. We used mitochondrial and nuclear DNA to analyze genetic variation, demographic history, divergence times, reconstructed a multilocus phylogeny, and performed a species delimitation analyses. We also evaluated morphological variation in 208 specimens. We found high levels of genetic differentiation in three groups, and significant variation in morphological traits corresponding with the disjunct geographic populations. L. rhami presents population stability with the highest genetic variation explained by differences between populations. Divergence time estimates suggest that L. rhami split from its sister group around 10.55 million years ago, and the diversification of the complex was dated ca. 0.207 Mya. The hypotheses tested in the species delimitation analyses validated three independent lineages corresponding to three disjunct populations. This study provides evidence of genetic and/or morphometric differentiation between populations in the L. rhami complex where four separate evolutionary lineages are supported: (1) populations from the Sierra Madre Oriental and the highlands of Oaxaca (rhami), (2) populations from the highlands of Guerrero (occidentalis), (3) populations from the highlands of Chiapas and Guatemala (this is a non-previously proposed potential taxon: tacanensis), and (4) populations from the highlands of Honduras and El Salvador (saturatior). The main promoters of the geographic structure found in the L. rhami complex are likely the Isthmus of Tehuantepec as a geographic barrier, isolation by distance resulting from habitat fragmentation, and climatic conditions during the Pleistocene.

scholarly journals Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis (Rodentia, Supramyomorpha, Cricetidae) in a geographical and environmental context

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9517 ◽  
Author(s):  
Lourdes Valdez ◽  
Marcial Quiroga-Carmona ◽  
Guillermo D’Elía
Keyword(s):  
Genetic Variation ◽  
Isolation By Distance ◽  
Demographic History ◽  
Mitochondrial Gene ◽  
General Pattern ◽  
Mediterranean Ecosystem ◽  
Gene Genealogy ◽  
Quaternary Climate ◽  
Mitochondrial Cytochrome B ◽  
Isolation By Environment

Quaternary climate and associated vegetational changes affected the fauna of the Chilean Mediterranean ecosystem. Here we studied the genetic variation of the long-haired mouse, Abrothrix longipilis, a sigmodontine rodent endemic to this area. Within an environmentally explicit context, we examined the geographic distribution of the genetic diversity and demographic history of the species based on sequences of the mitochondrial Cytochrome-b gene of 50 individuals from 13 localities and a large panel of single nucleotide polymorphisms of 17 individuals from 6 localities. The gene genealogy of A. longipilis revealed three intraspecific lineages that are allopatric and latitudinally segregated (northern, central, and southern lineages) with an estimated crown age for the whole species clade of 552.3 kyr B.P. A principal component analysis based on 336,596 SNP loci is in line with the information given by the the mitochondrial gene genealogy. Along its complete distributional range, A. longipilis showed patterns of isolation by distance and also isolation by environment. The general pattern of historical demography showed stability for most intraspecific lineages of A. longipilis. Northern and central lineages showed signals of historical demographic stability, while the southern lineage showed contrasting signals. In agreement with this, the niche models performed showed that in the northern range of A. longipilis, areas of high suitability for this species increased towards the present time; areas of central range would have remained relatively stable, while southern areas would have experienced more change through time. In summary, our study shows three distinct allopatric lineages of A. longipilis, each showing slightly different demographic history.

scholarly journals Isolation-By-Distance-and-Time in a stepping-stone model

2015 ◽  
Author(s):  
Nicolas Duforet-Frebourg ◽  
Montgomery Slatkin
Keyword(s):  
Principal Component Analysis ◽  
Population Genetics ◽  
Population Structure ◽  
Isolation By Distance ◽  
Principal Component ◽  
Joint Effect ◽  
Stepping Stone ◽  
Ancient Times ◽  
The Impact ◽  
Stepping Stone Model

With the great advances in ancient DNA extraction, population genetics data are now made of geographically separated individuals from both present and ancient times. However, population genetics theory about the joint effect of space and time has not been thoroughly studied. Based on the classical stepping--stone model, we develop the theory of Isolation by Distance and Time. We derive the correlation of allele frequencies between demes in the case where ancient samples are present in the data, and investigate the impact of edge effects with forward-in-time simulations. We also derive results about coalescent times in circular/toroidal models. As one of the most common way to investigate population structure is to apply principal component analysis, we evaluate the impact of this theory on plots of principal components. Our results demonstrate that time between samples is a non-negligible factor that requires new attention in population genetics.

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

2018 ◽  
Vol 5 (5) ◽  
pp. 171532 ◽  
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.

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

2015 ◽  
Vol 72 (10) ◽  
pp. 1477-1493 ◽  
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.

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

2009 ◽  
Vol 2009 ◽  
pp. 1-8 ◽  
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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