scholarly journals Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana)

2018 ◽  
Vol 9 ◽  
Author(s):  
Kai-Ming Shih ◽  
Chung-Te Chang ◽  
Jeng-Der Chung ◽  
Yu-Chung Chiang ◽  
Shih-Ying Hwang
Keyword(s):  
Genetic Divergence ◽  
Isolation By Distance ◽  
Adaptive Genetic Divergence

scholarly journals Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

2000 ◽  
Vol 23 (4) ◽  
pp. 739-743 ◽  
Author(s):  
Mariana Pires de Campos Telles ◽  
José Alexandre Felizola Diniz-Filho
Keyword(s):  
Stochastic Process ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Small Sample ◽  
Group Method ◽  
Gene Frequencies ◽  
Exponential Relationship ◽  
Local Populations ◽  
Pair Group

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.

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 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 Detection of Genetic Variation in Wild Populations of Three Allium Species Using Amplified Fragment Length Polymorphisms

HortScience ◽  
2008 ◽  
Vol 43 (3) ◽  
pp. 637-643 ◽  
Author(s):  
Nathan C. Phillips ◽  
Steven R. Larson ◽  
Daniel T. Drost
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Fragment Length ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
The United States ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Geographical Regions ◽  
Collection Sites

Three wild onion species native to the intermountain west in the United States—Allium acuminatum, A. brandegei, and A. passeyi—show horticultural potential, but little is known about patterns of genetic diversity among localized populations and geographical regions. We examined amplified fragment length polymorphisms (AFLP) within and among five Allium acuminatum, four A. brandegei, and three A. passeyi collection sites in Utah. These three congeners with contrasting abundance and distribution patterns provide an opportunity to investigate the role of geographic distance, altitude, and rarity in patterns of genetic divergence. The collection sites were selected along an altitudinal gradient to reflect ecogeographic variation. Individual plants from each of the 12 sites were genotyped using six AFLP primer combinations detecting DNA variation within and among all three species. Genetic differences between species were high enough to render comparisons among species impractical, so each species was analyzed separately for differences between populations and variability within populations. Similarity coefficients were significantly greater within collection sites versus among collection sites indicating divergence between populations. Within-population genetic diversity was not correlated with elevation for any of the three species. Analysis of molecular variance revealed that 66% (A. acuminatum), 83% (A. passeyi), and 64% (A. brandegei) of observed variation is found within populations. Genetic divergence among populations (ФST) was higher in the widely distributed species, suggesting that interpopulation gene flow may be negatively correlated with range size. Allium acuminatum and A. brandegei individuals cluster into groups corresponding strictly to collection sites based on neighbor-joining analysis of the total number of DNA polymorphisms between individual plants. Allium passeyi populations, however, had less overall genetic variation between populations. Genetic isolation by distance appeared responsible for much of the variability among populations, although there was one notable exception showing significant differences between two geographically close populations in A. acuminatum.

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