scholarly journals Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11498
Author(s):  
Imogene A. Cancellare ◽  
Elizabeth M. Kierepka ◽  
Jan Janecka ◽  
Byron Weckworth ◽  
Richard T. Kazmaier ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Gene Flow ◽  
Spatial Scale ◽  
Behavioral Plasticity ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Lynx Rufus ◽  
Multiscale Approach ◽  
Ecological Processes

Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

scholarly journals A genomic assessment of population structure and gene flow in an aquatic salamander identifies the roles of spatial scale, barriers, and river architecture

2018 ◽  
Vol 63 (5) ◽  
pp. 407-419 ◽  
Author(s):  
Mason O. Murphy ◽  
Kara S. Jones ◽  
Steven J. Price ◽  
David W. Weisrock
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Spatial Scale

scholarly journals Isolation by resistance across a complex coral reef seascape

2015 ◽  
Vol 282 (1812) ◽  
pp. 20151217 ◽  
Author(s):  
Luke Thomas ◽  
W. Jason Kennington ◽  
Michael Stat ◽  
Shaun P. Wilkinson ◽  
Johnathan T. Kool ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Divergence ◽  
Larval Dispersal ◽  
Population Genetic ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Genetic Data ◽  
Genetic Structure Of Populations ◽  
Seascape Genetics

A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance surface to predict the spatial genetic structure of populations and explain deviations from the widely applied isolation-by-distance model. The majority of seascape approaches to date have been applied to linear coastal systems or at large spatial scales (more than 250 km), with very few applied to complex systems at regional spatial scales (less than 100 km). Here, we apply a seascape genetics approach to a peripheral population of the broadcast-spawning coral Acropora spicifera across the Houtman Abrolhos Islands, a high-latitude complex coral reef system off the central coast of Western Australia. We coupled population genetic data from a panel of microsatellite DNA markers with a biophysical dispersal model to test whether oceanographic processes could explain patterns of genetic divergence. We identified significant variation in allele frequencies over distances of less than 10 km, with significant differentiation occurring between adjacent sites but not between the most geographically distant ones. Recruitment probabilities between sites based on simulated larval dispersal were projected into a measure of resistance to connectivity that was significantly correlated with patterns of genetic divergence, demonstrating that patterns of spatial genetic structure are a function of restrictions to gene flow imposed by oceanographic currents. This study advances our understanding of the role of larval dispersal on the fine-scale genetic structure of coral populations across a complex island system and applies a methodological framework that can be tailored to suit a variety of marine organisms with a range of life-history characteristics.

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 Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2020 ◽  
Author(s):  
Kelly Brie Klingler ◽  
Joshua P Jahner ◽  
Thomas L Parchman ◽  
Chris Ray ◽  
Mary Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background: Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results: Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (𝜋=0.0006–0.0009; 𝜃W=0.0005–0.0007) relative to populations in California (𝜋=0.0014–0.0019; 𝜃W=0.0011–0.0017) and the Rocky Mountains (𝜋=0.0025–0.0027; 𝜃W=0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D=0.240-0.811), consistent with recent contraction in population sizes range-wide. Conclusions: Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

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

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.

scholarly journals Spatial Genetic Structure of the Insect-Vectored Conifer Pathogen Leptographium wageneri Suggests Long Distance Gene Flow Among Douglas-fir Plantations in Western Oregon

2021 ◽  
Vol 4 ◽  
Author(s):  
Patrick I. Bennett ◽  
Javier F. Tabima ◽  
Anna L. Leon ◽  
John Browning ◽  
Michael J. Wingfield ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Bark Beetles ◽  
Population Genomics ◽  
Spatial Genetic Structure ◽  
Douglas Fir ◽  
Insect Vector ◽  
Long Distance ◽  
Tree Disease ◽  
Genetic Clustering

Many fungi in the Ophiostomatales are vectored by bark beetles that introduce these fungi directly into their tree hosts. Most of these fungal associates have little effect on their hosts, but some can cause serious diseases. One such fungus, Leptographium wageneri, causes an economically and ecologically important tree disease known as black stain root disease (BSRD). For this study, 159 full genome sequences of L. wageneri were analyzed using a population genomics approach to investigate the epidemiology, dispersal capabilities, and reproductive biology of this fungus. Analyses were performed with SNP haplotypes from 155 isolates of L. wageneri var. pseudotsugae collected in 16 Douglas-fir stands in Oregon and 4 isolates of L. wageneri var. wageneri collected in pinyon pine stands in southern California. These two host-specific varieties appear to be evolutionarily divergent, likely due a combination of factors such as host differentiation and geographic isolation. We analyzed gene flow and population structure within and among Douglas-fir plantations in western Oregon to infer the relative importance of local vs. long distance dispersal in structuring populations of L. wageneri var. pseudotsugae. Long-distance gene flow has occurred between Douglas-fir plantations, contributing to diversity and population structure within stands, and likely reflecting the behavior of an important insect vector. Genetic clustering analyses revealed the presence of unique local clusters within stands and plantations in addition to those common among multiple stands or plantations. Although populations of L. wageneri var. pseudotsugae are primarily asexual, two mating types were present in many stands, suggesting that recombination is at least possible and may contribute to genetic diversity.

scholarly journals Spatial Genetic Structure Within Two Contrasting Stands of Scots Pine (Pinus sylvestris L.)

2008 ◽  
Vol 57 (1-6) ◽  
pp. 193-202 ◽  
Author(s):  
I. J. Chybicki ◽  
A. Dzialuk ◽  
M. Trojankiewicz ◽  
M. Slawski ◽  
J. Burczyk
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Pinus Sylvestris ◽  
Scots Pine ◽  
Spatial Genetic Structure ◽  
Nuclear Markers ◽  
Genetic Pool ◽  
Establishment History ◽  
Two Populations

AbstractWhen considering neutral nuclear markers, genetic differentiation of Scots pine (Pinus sylvestris L.) populations is known to be low. The homogeneity arises particularly as an effect of common ancestry in a recent evolutionary history as well as an extensive gene flow, especially through pollen. However, within populations several other forces may shape the spatial distribution of genetic variation, including establishment history, environmental and silvicultural selection. These local forces are known to produce non-random spatial patterns of genetic variation, however little is known on fine-scale spatial genetic structure of Scots pine. In this study, two stands of this species with different establishment histories, selected within one larger population located in northern Poland were genotyped and analysed for genetic variation and within-stand spatial genetic structure. Results revealed no differences in genetic variation, although stands are separated about 60 km, suggesting that the two populations share a common genetic pool. The spatial genetic structure in both stands was found to be slightly different and was attributed to differences in the mode of populations’ establishments. Finally, results confirmed that gene flow in Scots pine is extensive, causing genetic homogeneity within a single population.

scholarly journals Going with the flow: analysis of population structure reveals high gene flow shaping invasion pattern and inducing range expansion of Mikania micrantha in Asia

2020 ◽  
Vol 125 (7) ◽  
pp. 1113-1126
Author(s):  
Achyut Kumar Banerjee ◽  
Zhuangwei Hou ◽  
Yuting Lin ◽  
Wentao Lan ◽  
Fengxiao Tan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Distance ◽  
Range Expansion ◽  
Mikania Micrantha ◽  
High Gene Flow ◽  
Genetic Pattern ◽  
High Gene

Abstract Background and Aims Mikania micrantha, a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region. Methods We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations. Key Results We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces. Conclusions These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species.

Analysis of the spatial genetic structure of Passiflora incarnata in recently disturbed sites

2005 ◽  
Vol 83 (4) ◽  
pp. 420-426 ◽  
Author(s):  
Rebecca T Tague ◽  
Stephanie A Foré
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Multilocus Genotype ◽  
Long Distance ◽  
Short Life Span ◽  
Successional Species ◽  
Passiflora Incarnata ◽  
Coefficient Of Coancestry

In early successional species, short life span and frequent spatial relocation may affect the distribution of genetic variation but the pattern may be altered by reproductive patterns. Passiflora incarnata L. (Passifloraceae), an early successional vine found throughout the southeastern United States, reproduces sexually and asexually through clonal sprouts. We examined the genetic structure of P. incarnata in recently disturbed habitats at three spatial scales: within a patch, among patches separated by 250 m, and between sites separated by 10 km. Genetic variation may be clumped at the scale of neighboring plants if stem resprouting is significant. In each patch, eleven arbitrarily selected plants and their four nearest neighbors were mapped and leaf samples were collected for genetic analysis. The multilocus genotype of each individual for seven polymorphic allozymes was determined. Potential clones were determined by estimating the probability of a second occurrence of each genotype and a multilocus coefficient of coancestry. Data indicated P. incarnata was reproducing primarily sexually. Most of the genetic variation was within a patch with little variation among patches. These data suggest that the genetic structure of this colonizing species was determined by founder effects interacting with long distance pollen movement.Key words: allozymes, passionflower, spatial, genetic structure, early colonizer, Passiflora incarnata.

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