scholarly journals Genetic divergence correlates with the contemporary landscape in populations of Slimy Salamander (Plethodon glutinosus) species complex across the lower Piedmont and Coastal Plain of the southeastern United States

2018 ◽  
Vol 96 (11) ◽  
pp. 1244-1254 ◽  
Author(s):  
Walter H. Smith ◽  
Jessica A. Wooten ◽  
Carlos D. Camp ◽  
Dirk J. Stevenson ◽  
John B. Jensen ◽  
...  
Keyword(s):  
South Carolina ◽  
Genetic Distance ◽  
Principal Components ◽  
Coastal Plain ◽  
Genetic Divergence ◽  
Species Complex ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Plethodon Glutinosus ◽  
Isolation By Environment

A primary goal of landscape genetics is to elucidate factors associated with genetic structure among populations. Among the important patterns identified have been isolation by distance (IBD), isolation by barrier (IBB), and isolation by environment (IBE). We tested hypotheses relating each of these possible patterns to genetic divergence in the Slimy Salamander (Plethodon glutinosus (Green, 1818)) species complex across the lower Piedmont and Coastal Plain of Georgia, USA, and adjacent areas of South Carolina, USA. We sequenced 2148 total bp, including three regions of the mitochondrial genome and a nuclear intron, and related genetic distance to GIS-derived surrogate variables representing possible IBD (geographic distance), IBE (principal components of 19 climate variables, watershed, and normalized difference vegetation index (NDVI)), and IBB (streams of fourth order and higher). Multiple matrix regression with randomization analysis indicated significant relationships between genetic distance and two principal components of climate, as well as NDVI. These results support roles for environment (IBE) in helping to drive genetic divergence in this group of salamanders. The absence of a significant influence of IBD and IBB was surprising. It is possible that the signal effects of geographic distance and barriers on genetic divergence may have been erased by more recent responses to the environment.

scholarly journals Genetic structure is stronger across human-impacted habitats than among islands in the coralPorites lobata

2019 ◽  
Author(s):  
Kaho H. Tisthammer ◽  
Zac H. Forsman ◽  
Robert J. Toonen ◽  
Robert H. Richmond
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
High Stress ◽  
Disruptive Selection ◽  
Single Location ◽  
Isolation By Environment ◽  
Genetic Patterns ◽  
Significant Genetic Structure ◽  
Contrasting Habitats

ABSTRACTWe examined genetic structure in the lobe coralPorites lobataamong pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oʻahu and Maui, Hawai‘i. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVAFST= 0.04 ∼ 0.19,P< 0.001), but no significant isolation by distance between islands. In contrast, a third site with a less impacted nearshore site showed no significant structure. Strikingly, corals from the two impacted nearshore sites on different islands over 100km apart with similar environmentally stressful conditions were genetically closer (FST∼ 0, P = 0.733) than those within a single location less than 2 km apart (FST= 0.041∼0.079, P < 0.01). Our results suggest that ecological boundaries appear to play a strong role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow may be explained by disruptive selection across contrasting habitats.

scholarly journals Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations

2019 ◽  
Vol 125 (1) ◽  
pp. 105-117 ◽  
Author(s):  
Yixuan Kou ◽  
Li Zhang ◽  
Dengmei Fan ◽  
Shanmei Cheng ◽  
Dezhu Li ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genetic Divergence ◽  
Evolutionary History ◽  
Isolation By Distance ◽  
Demographic History ◽  
East China ◽  
Population Divergence ◽  
Isolation By Environment ◽  
Late Neogene ◽  
History Of

Abstract Background and Aims Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae). Methods DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD). Key Results Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD. Conclusions These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora.

scholarly journals Landscape genetics and species delimitation in the Andean palm rocket frog, Rheobates spp

2020 ◽  
Author(s):  
Gabrielle Genty ◽  
Carlos E. Guarnizo ◽  
Juan P. Ramírez ◽  
Lucas Barrientos ◽  
Andrew J. Crawford
Keyword(s):  
Genetic Divergence ◽  
Species Delimitation ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Nuclear Genes ◽  
Genetic Lineages ◽  
Local Environments ◽  
Isolation By Environment ◽  
Bayesian Species Delimitation ◽  
Landscape Genetic

AbstractThe complex topography of the species-rich northern Andes creates heterogeneous environmental landscapes that are hypothesized to have promoted population fragmentation and diversification by vicariance, gradients and/or the adaptation of species. Previous phylogenetic work on the Palm Rocket Frog (Anura: Aromobatidae: Rheobates spp.), endemic to mid-elevation forests of Colombia, suggested valleys were important in promoting divergence between lineages. In this study, we use a spatially, multi-locus population genetic approach of two mitochondrial and four nuclear genes from 25 samples representing the complete geographic range of the genus to delimit species and test for landscape effects on genetic divergence within Rheobates. We tested three landscape genetic models: isolation by distance, isolation by resistance, and isolation by environment. Bayesian species delimitation (BPP) and a Poisson Tree Process (PTP) model both recovered five highly divergent genetic lineages within Rheobates, rather than the three inferred in a previous study. We found that an isolation by environment provided the only variable significantly correlated with genetic distances for both mitochondrial and nuclear genes, suggesting that local adaptation may have a role driving the genetic divergence within this genus of frogs. Thus, genetic divergence in Rheobates may be driven by the local environments where these frogs live, even more so that by the environmental characteristics of the intervening regions among populations (i.e., geographic barriers).

scholarly journals Genetic Divergence of Two Sitobion avenae Biotypes on Barley and Wheat in China

Insects ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 117
Author(s):  
Da Wang ◽  
Xiaoqin Shi ◽  
Deguang Liu ◽  
Yujing Yang ◽  
Zheming Shang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Host Plant ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
Critical Role ◽  
Geographic Distance ◽  
Sitobion Avenae ◽  
Insect Populations

Host plant affinity and geographic distance can play critical roles in the genetic divergence of insect herbivores and evolution of insect biotypes, but their relative importance in the divergence of insect populations is still poorly understood. We used microsatellite markers to test the effects of host plant species and geographic distance on divergence of two biotypes of the English grain aphid, Sitobion avenae (Fabricius). We found that clones of S. avenae from western provinces (i.e., Xinjiang, Gansu, Qinghai and Shaanxi) had significantly higher genetic diversity than those from eastern provinces (i.e., Anhui, Henan, Hubei, Zhejiang and Jiangsu), suggesting their differentiation between both areas. Based on genetic diversity and distance estimates, biotype 1 clones of eastern provinces showed high genetic divergence from those of western provinces in many cases. Western clones of S. avenae also showed higher genetic divergence among themselves than eastern clones. The Mantel test identified a significant isolation-by-distance (IBD) effect among different geographic populations of S. avenae, providing additional evidence for a critical role of geography in the genetic structure of both S. avenae biotypes. Genetic differentiation (i.e., FST) between the two biotypes was low in all provinces except Shaanxi. Surprisingly, in our analyses of molecular variance, non-significant genetic differentiation between both biotypes or between barley and wheat clones of S. avenae was identified, showing little contribution of host-plant associated differentiation to the divergence of both biotypes in this aphid. Thus, it is highly likely that the divergence of the two S. avenae biotypes involved more geographic isolation and selection of some form than host plant affinity. Our study can provide insights into understanding of genetic structure of insect populations and the divergence of insect biotypes.

Path analysis of collective properties and habitat relationships of fish assemblages in coastal plain streams

1995 ◽  
Vol 52 (1) ◽  
pp. 23-33 ◽  
Author(s):  
Andrew L. Sheldon ◽  
Gary K. Meffe
Keyword(s):  
South Carolina ◽  
Path Analysis ◽  
Principal Components ◽  
Coastal Plain ◽  
Fish Assemblages ◽  
Path Model ◽  
Directional Model ◽  
Predictive Variables ◽  
Site Density ◽  
Mean Size

Collective properties of fish assemblages at 44 sites in low-gradient streams (orders 1–3) on the upper coastal plain of South Carolina, U.S.A., were highly variable among sites: richness, 2–17 species per site; density, 0.2–9.5 individuals∙m−2; mean individual mass, 0.4–22.2 g per individual; and biomass, 0.1–42.1 g∙m−2. Principal components analysis reduced 15 habitat parameters to four interpretable components that were used as orthogonal predictive variables in path analysis. Path analysis, with a directional model containing intermediate steps and multiple dependent variables, was used as an alternative to multiple regression. Two principal components, associated with velocity (and its covariates) and depth (and its covariates), were the primary correlates of biomass (R2 = 49%), richness (44%), mean size (36%), and density (20%), with cover variables contributing relatively little to any R2 value. Velocity effects were negative and depth effects positive for all collective properties. Habitat effects on biomass were mediated by effects on individual fish size rather than numbers. Correlations of collective properties at sites sampled in 2 years were similar to those from the single year, habitat-based path model, implying that the path model was adequate and inclusive, and accurately reflected collective properties of these communities.

scholarly journals Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8550 ◽  
Author(s):  
Kaho H. Tisthammer ◽  
Zac H. Forsman ◽  
Robert J. Toonen ◽  
Robert H. Richmond
Keyword(s):  
Genetic Structure ◽  
Human Impacts ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
High Stress ◽  
Single Location ◽  
Isolation By Environment ◽  
Porites Lobata ◽  
Significant Genetic Structure ◽  
Contrasting Habitats

We examined genetic structure in the lobe coral Porites lobata among pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oahu and Maui, Hawaii. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVA FST = 0.04∼0.19, P < 0.001), but no significant isolation by distance between islands. Strikingly, corals from the two nearshore sites with higher levels of environmental stressors on different islands over 100 km apart with similar environmentally stressful conditions were genetically closer (FST = 0.0, P = 0.73) than those within a single location less than 2 km apart (FST = 0.04∼0.08, P < 0.01). In contrast, a third site with a less impacted nearshore site (i.e., less pronounced environmental gradient) showed no significant structure from the offshore comparison. Our results show much stronger support for environment than distance separating these populations. Our finding suggests that ecological boundaries from human impacts may play a role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow might be explained by selective pressure across contrasting habitats.

Redescription and circumscription of the Acuminate Crayfish, Cambarus acuminatus Faxon, 1884 (Decapoda: Cambaridae)

Zootaxa ◽  
2019 ◽  
Vol 4560 (1) ◽  
pp. 40
Author(s):  
BRONWYN W. WILLIAMS ◽  
EMMY M. DELEKTA ◽  
ZACHARY J. LOUGHMAN
Keyword(s):  
South Carolina ◽  
Coastal Plain ◽  
Species Complex ◽  
Type Material ◽  
C Complex ◽  
Central South

Cambarus acuminatus was described by Walter Faxon in 1884 from three specimens collected from the Saluda River in northwestern South Carolina, USA. Cambarus acuminatus sensu lato has since been acknowledged to comprise a species complex. This complex, also known as Cambarus sp. C, spans a range across much of the Piedmont Plateau and Coastal Plain from central South Carolina north to Maryland and southeastern Pennsylvania. A primary impediment to a much-needed thorough taxonomic assessment and revision of C. sp. C is the absence of taxonomically useful type material of C. acuminatus coupled with the lack of a detailed description of the species. Here we provide a redescription of C. acuminatus based on modern standards for astacoidean crayfishes in the genus Cambarus and emend the circumscription of the species, thereby laying the groundwork necessary for future taxonomic and phylogenetic work within, and involving, the C. sp. C complex. 

scholarly journals First genome-wide analysis of an endangered lichen reveals isolation by distance and strong population structure

2017 ◽  
Author(s):  
Jessica L. Allen ◽  
Sean K. McKenzie ◽  
Robin S. Sleith ◽  
S. Elizabeth Alter
Keyword(s):  
Genetic Diversity ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Distribution Models ◽  
Extrinsic Factors ◽  
Biogeographic Patterns ◽  
Ecological Requirements ◽  
Genome Wide ◽  
Isolation By Environment

AbstractLichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes driving diversification and genetic differentiation in these lineages. Though few studies have examined population genetic patterns in lichens, their geographic distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, while their reproductive structures are observable, the lack of information about recombination mechanisms and rates can make inferences about reproductive strategies difficult. Here we investigate the population genomics ofCetradonia linearis, an endangered lichen narrowly endemic to the southern Appalachians of eastern North America, to test the relative contributions of environmental factors and geographic distance in shaping genetic structure, and to gain insights into the demography and reproductive biology of range restricted fungi. Analysis of genome-wide SNP data indicated strong evidence for both low rates of recombination and for strong isolation by distance, but did not support isolation by environment. Hindcast species distribution models and the spatial distribution of genetic diversity also suggested thatC. linearishad a larger range during the last glacial maximum, especially in the southern portion of its current extent, consistent with previous findings in other southern Appalachian taxa. These results contribute to our understanding of intrinsic and extrinsic factors shaping genetic diversity and biogeographic patterns inC. linearis, and more broadly, in rare and endangered fungi.

scholarly journals Theoretical Analysis of Principal Components in an Umbrella Model of Intraspecific Evolution

2021 ◽  
Author(s):  
Maxime Estavoyer ◽  
Olivier Francois
Keyword(s):  
Principal Components ◽  
Rare Variants ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Principal Component ◽  
Ancestral Population ◽  
Alternative Theory ◽  
Multilocus Genotype ◽  
Coalescent Simulations ◽  
Largest Eigenvalues

Principal component analysis (PCA) is one of the most frequently-used approach to describe population structure from multilocus genotype data. Regarding geographic range expansions of modern humans, interpretations of PCA have, however, been questioned, as there is uncertainty about the wave-like patterns that have been observed in principal components. It has indeed been argued that wave-like patterns are mathematical artifacts that arise generally when PCA is applied to data in which genetic differentiation increases with geographic distance. Here, we present an alternative theory for the observation of wave-like patterns in PCA. We study a coalescent model -- the umbrella model -- for the diffusion of genetic variants. The model is based on a hierarchy of splits from an ancestral population without any particular geographical structure. In the umbrella model, splits occur almost continuously in time, giving birth to small daughter populations at a regular pace. Our results provide detailed mathematical descriptions of eigenvalues and eigenvectors for the PCA of sampled genomic sequences under the model. Removing variants uniquely represented in the sample, the PCA eigenvectors are defined as cosine functions of increasing periodicity, reproducing wave-like patterns observed in equilibrium isolation-by-distance models. Including rare variants in the analysis, the eigenvectors corresponding to the largest eigenvalues exhibit complex wave shapes. The accuracy of our predictions is further investigated with coalescent simulations. Our analysis supports the hypothesis that highly structured wave-like patterns could arise from genetic drift only, and may not always be artificial outcomes of spatially structured data. Genomic data related to the peopling of the Americas are reanalyzed in the light of our new theory.

scholarly journals Life in the desert: habitat spatial complexity, gene flow, and functional connectivity in Ivesia webberi

2021 ◽  
Author(s):  
Israel Borokini ◽  
Kelly Klingler ◽  
Mary Peacock
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Functional Connectivity ◽  
Genetic Distance ◽  
Isolation By Distance ◽  
Species Range ◽  
Peripheral Populations ◽  
Pairwise Genetic Distance ◽  
Isolation By Environment

Habitat protection, by itself, is not sufficient to conserve range-restricted species with disjunct populations. Indeed, it becomes critical to characterize gene flow among the populations and factors that influence functional connectivity in order to design effective conservation programs for such species. In this study, we genotyped 314 individuals of Ivesia webberi, a United States federally threatened Great Basin Desert perennial forb using six microsatellite loci, to estimate genetic diversity and population genetic structure, as well as rates and direction of gene flow among 16 extant I. webberi populations. We assessed the effects of Euclidean distance, landscape features, and ecological dissimilarity on the genetic structure of the sampled populations, while also testing for a relationship between I. webberi genetic diversity and diversity in the vegetative communities. The results show low levels of genetic diversity overall (He = 0.200–0.441; Ho = 0.192–0.605) and high genetic differentiation among populations. Genetic diversity was structured along a geographic gradient, congruent with patterns of isolation by distance. Populations near the species’ range core have relatively high genetic diversity, supporting a central-marginal pattern, while peripheral populations have lower genetic diversity, significantly higher genetic distances, higher relatedness, and evidence of genetic bottlenecks. Genotype cluster admixture results support a predominant west to east gene flow pattern for populations near the species’ range center, as well as smaller genotype clusters with a narrow north to south distribution and little admixture, suggesting that dispersal direction and distance vary on the landscape. Pairwise genetic distance strongly correlates with actual evapotranspiration and precipitation, indicating a role for isolation by environment, which the observed phenological mismatches among the populations also support. The significant correlation between pairwise genetic distance and dissimilarity in the soil seed bank suggest that annual regeneration of the floristic communities contributes to the maintenance of genetic diversity in I. webberi.

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