Genetic structure of a montane perennial plant: the influence of landscape and flowering phenology

Arabidopsis lyrata ssp. lyrata is widespread but edaphically restricted, which suggests that the dispersal ability and level of genetic exchange among populations might be limited. We assessed levels of genetic diversity and population differentiation within and among six A. lyrata ssp. lyrata populations from along the eastern seaboard of the United States by examining variation at nine microsatellite loci among 233 individuals. These data were also evaluated to assess any relationship between geographic and genetic distance and correlation of genetic diversity with population size. Measures of genetic diversity across all 9 microsatellite loci were high in most populations. Genetic diversity, as measured by number of alleles, was generally higher in the Maryland and New York populations, as compared with the southern most sampled populations in Virginia. Genetic differentiation among regions was highly significant and large (FST = 0.47). This was supported by several analyses, suggesting that there is little gene flow among the regions sampled. There was a strong positive correlation between geographic and genetic distance, which is indicative of the pattern of isolation-by-distance. Population size correlated with the number of alleles within populations, supporting population genetic theory that larger populations harbor greater genetic diversity. Wright's FST and genetic structure analysis also provided evidence of genetic partitioning at small (<100 m) geographic distances between two areas sampled within one locality. These results indicate that the largest proportion of variation was explained by within population differences and may have implications for the conservation of this widespread but fragmented taxon.

Management of game species requires an understanding not just of population abundance, but also the structure of and connections between populations. Like other large-bodied carnivores, the cougar (Puma concolor) exhibits density –dependent dispersal and is capable of long-distance movement; in the absence of barriers to movement, these traits should lead to high connectivity between individuals and a lack of genetic differentiation across areas of continuous habitat. Previous research has suggested that cougar movement may be influenced by landscape variables such as forest cover, elevation, human population density, and highways. I assessed the population structure of cougars (Puma concolor) in Washington and southern British Columbia by examining patterns of genetic variation in 17 microsatellite loci, and the contribution of landscape variables to this genetic variation. I evaluated population structure using genetic clustering algorithms and spatial principal components analysis. I quantified the effect of distance on genetic variation by calculating the correlation between the genetic distance and geographic distance between every pair of individuals, as well as the spatial autocorrelation of genetic distances. To compare the observed pattern of genetic differentiation with that which would arise solely from isolation by distance, I simulated allele frequencies across the study area where the cost to movement between individuals was proportional to the distance between them. I also evaluated the support for evidence of male-biased dispersal in allele frequencies. Bayesian clustering analyses identified four populations in the study area, corresponding to the Olympic Peninsula, Cascade Mountains, northeastern Washington and Blue Mountains; these clusters were supported by patterns of genetic differentiation revealed with spatial PCA. v Although I found a significant relationship between the geographic and genetic distance between individuals, simulated allele frequencies displayed no meaningful spatial pattern of differentiation, suggesting that male dispersal would be adequate within the scale of the study area to prevent genetic isolation from occurring if the only factor to affect dispersal was geographic distance. While cougars are capable of long-distance dispersal movements, dispersal in heterogeneous landscapes may be mediated by the resistance of the landscape to movement. I derived resistance surfaces for forest canopy cover, elevation, human population density and highways based on GIS data and estimated the landscape resistance between pairs of individuals using circuit theory. I quantified the effect of the resistance to movement due to each landscape factor on genetic distance using multiple regression on distance matrices and boosted regression tree analysis. Both models indicated that only forest canopy cover and the geographic distance between individuals had an effect on genetic distance, with forest cover exhibiting the greatest relative influence. The boundaries between the genetic clusters I found largely corresponded with breaks in forest cover, showing agreement between population structure and landscape variable selection. The greater relative influence of forest cover may also explain why a significant relationship was found between geographic and genetic distance, yet geographic distance alone could not explain the observed pattern of allele frequencies. While cougars inhabit unforested areas in other parts of their range, forested corridors appear to be important for maintaining population connectivity in the northwest.

Eighty-six almond accessions of diverse geographic origin, ranging from Central Asia to the USA, were genotyped in 15 simple sequence repeat (SSR) loci to compare genetic diversity parameters, characterize genetic differentiation, and examine factors responsible for the maintenance of genetic diversity and population structure in almond. The mean allele number was 18.86 alleles per locus. All but one primer demonstrated polymorphic information content higher than 0.7. Almond genotypes clustered according to their pedigree and geographic origin. STRUCTURE analysis determined nine genetically distinct subgroups within the studied genotypes including the Kyrgyz, Akdamar, Bademli, Hungarian, Monor, Italian, Moroccan, and Californian accessions and wild species and an admixed group. An AMOVA analysis confirmed that considerable genetic variation occurred within populations (71.30%), and genetic variation among populations was also significant (28.70%). The mean values of the fixation index (FST) varied between 0.38 and 0.55, indicating marked genetic differentiation among the populations. The among-population genetic differentiation based on allele sizes (RST) was significantly higher than that based on allele identities (FST) between the most groups, suggesting that stepwise mutations have also contributed to genetic differentiation. A Mantel test and a neighbor-joining tree showed no significant correlation between the geographic distance and the genetic distance (Rxy = 0.173, P = 0.226) and indicated that geographic distance among the assessed populations has little influence on their genetic differentiation (Rxy = 0.248, P = 0.194). Our data show drift, mutations, and massive gene exchange between several wild species and cultivated P. dulcis as crucial components of genetic differentiation. Slight losses of genetic diversity are attributable to geographic isolation, human selection and not to the relatively recent occurrence of self-compatibility. There was no indication of a major decrease in genetic variability in almond germplasm from Asia to Europe. The present results reveal that almond domestication avoided the occurrence of a genetic bottleneck although its risk is present in many subpopulations.

Formerly common plant species are expected to be particularly susceptible to recent habitat fragmentation. We studied the population genetics of 19 recently fragmented Saxifraga granulata populations (max. distance 61 km) in Luxembourg and neighboring Germany using RAPD markers and a common garden experiment. We assessed (1) the relationships between plant fitness, quantitative genetic variation, molecular genetic variation, and population size; and (2) the relative importance of genetic drift and selection in shaping genetic variation. Molecular genetic diversity was high but did not correlate with population size, habitat conditions, or plant performance. Genetic differentiation was low (F ST=0.079 ± 0.135), and there was no isolation by distance. Longevity, clonality, and the long-lived seed bank of S.granulata may have prevented strong genetic erosion and genetic differentiation among populations. However, genetic distinctness increased with decreasing genetic diversity indicating that random genetic drift occurred in the studied populations. Quantitative and molecular genetic variations were correlated, and their differentiation (Q ST vs. F ST) among S.granulata populations was similar, suggesting that mainly random processes have shaped the quantitative genetic differentiation among populations. However, pairwise quantitative genetic distances increased with geographic and climatic distances, even when adjusted for molecular genetic distances, indicating diversifying selection. Our results indicate that long-lived clonal species may be buffered at least temporarily against the negative effects of fragmentation. The relationship between quantitative genetic and geographic distance may be a more sensitive indicator of selection than Q ST-F ST differences.

AimThe coqui frog (Eleutherodactylus coqui) was introduced to the Hawai'ian archipelago in the late 1980s and became established as a widespread species on Hawai'i Island over a short timespan, suggesting that humans are facilitating their movement. To determine the importance of human facilitation, we assessed dispersal patterns and genetic structure of coqui populations using microsatellite data.LocationHawai'i Island.MethodsWe obtained genotype data using seven microsatellites from coqui specimens collected from 25 populations on Hawai'i Island. The dispersal mechanism was examined using a Mantel test in GenAlEx and a genetic distance tree analysis in Phylip. Allelic diversity, measures of equilibrium, and genetic structure were analysed in GenAlEx and Arlequin. The correlation between genetic distance and geographical distance was used to distinguish between diffusion dispersal (positive correlation) and jump dispersal (zero or negative correlation).ResultsThe Mantel test for isolation by distance found no significant correlation between genetic and geographical distance (r2 = 0.002, P = 0.4401). The genetic distance tree topology is consistent with this result and exhibited a pattern expected if population establishment occurred through jump dispersal. Migration rates were high (NM = 4.228), inbreeding was high, genetic differentiation between populations was low, and significant genetic structure was detected among populations (4% of total variation, P &lt; 0.002).Main conclusionsGenetic distance is not correlated with geographical distance, suggesting that humans are important facilitators of coqui dispersal. Migration rate was high, indicating that the rapid expansion of coquies on Hawai'i Island was human‐facilitated, while high levels of inbreeding and significant genetic structure suggest low post‐establishment dispersal. If this is the case, early detection of coqui populations will be crucial for management due to their propensity to be spread through human‐facilitated jump dispersal, followed by slow rates of diffusion dispersal from these newly established populations.

Among the animal species first introduced in Brazil during the country's discovery, horses (Equus caballus) stand out because of their evolutionary history and relationship with humans. Among the Brazilian horse breeds, the Pantaneiro draws attention due to its adaptative traits. Blood samples of 116 Pantaneiro horses were divided into six populations based on their sampling location, aiming to identify the existence of genetic structure and quantify genetic diversity within and between them. Populations were compared to elucidate genetic variability and differentiation better and assess the impact of Pantanal's natural geographic barriers on gene flow between populations. Data from the GGP Equine BeadChip (Geneseek-Neogen, 65.157 SNPs) was used to assess basic diversity parameters, genetic distance (FST), principal component analysis (PCA), and population structure (ADMIXTURE) for the sampled animals. Mantel test was also performed to investigate the correlation between the populations' genetic and geographic distances. Results showed high genetic variability in all populations, with elevated levels of admixture in their structure. High levels of admixture make it challenging to establish a racial pattern and, consequently, populations within the breed, being that only one of the populations differentiated itself from the others. No significant correlations between genetic and geographic distances were observed, indicating that environmental barriers did not hinder gene flow between populations, and neither farmers' selection practices might have change breed genetic composition significantly. Low genetic distance and similar heterozygosity values were observed among populations, suggesting strong genetic proximity and low differentiation. Thereby, the Pantaneiro breed does not exhibit genetic subpopulations and could be considered, for conservation purposes, a single big population in the Panatnal region. This study will support sampling strategies for National genebank.

AimThe effects of geographic and environmental variables on patterns of genetic and phenotypic differentiation have been thoroughly studied. Ecological speciation involves reproductive isolation due to divergent natural selection that can result in a positive correlation between genetic divergence and adaptive phenotypic divergence (isolation by adaptation, IBA). If the phenotypic target of selection is unknown or not easily measured, environmental variation can be used as a proxy, expecting positive correlation between genetic and environmental distances, independent of geographic distances (isolation by environment, IBE). The null model is that the amount of gene flow between populations decreases as the geographic distance between them increases, and genetic divergence is due simply to the neutral effects of genetic drift (isolation by distance, IBD). However, since phenotypic differentiation in natural populations may be autocorrelated with geographic distance, it is often difficult to distinguish IBA from the neutral expectation of IBD. In this work, we test hypotheses of IBA, IBE, and IBD in the Red‐crowned Ant tanager (Habia rubica).LocationMesoamerica (Mexico—Central America) and South America.TaxonHabia rubica (Aves: Cardinalidae).MethodsWe compiled genetic data, coloration, and morphometric data from specimens from collections in Mexico and the United States. We used the Multiple Matrix Regression with Randomization (MMRR) approach to evaluate the influence of geographic and environmental distances on genetic and phenotypic differentiation of H. rubica at both phylogroup and population levels.ResultsOur results provide strong evidence that geographic distance is the main driver of genetic variation in H. rubica. We did not find evidence that climate variation is driving population differentiation in this species across a widespread geographic region.Main conclusionsOur data point to geographic isolation as the main factor structuring genetic variation within populations of H. rubica and suggest that climate is not playing a major role in genetic differentiation within this species.

Aedes aegypti is the main vector of dengue virus in the tropics and subtropics. Prevention of dengue depends on vector control due to the vaccine is still in development, understanding the survival of the species can be determined by tracking the genetic variations among individuals and determine the genetic structure of Aedes aegypti population. The purpose of this study was to analyze genetic variation and genetic structure of populations of Ae. aegypti in four dengue-endemic region in Sumatra Barat. All collected sample was performed DNA extraction to obtain DNA genomic of Ae. aegypti. DNA was amplified by using microsatellite primers resulted from previous study. Homozygous and heterozygous alleles were detected by using PAGE. Genetic variation and genetic differentiation were high in four dengue-endemic regions in West Sumatra. He scores ranged from 0.7886 to 08,404, I score were 1.5215 to 1.7263, FST score was 0.1205, and Nm was 1.8240. Genetic variation and gene flow of Ae. aegypti among populations, so that is easy for mosquito to adapt. There were two groups of Ae. aegypti resulted based on UPGMA analysis, and there was no correlation between genetic distance and geographical distance. Genetic variation of Ae. aegypti in some endemic areas of dengue fever in West Sumatra was high with moderate genetic differentiation. There were two groups of population based on genetic structure. There was no correlation between genetic distance and geographic distance

Proportioning Whole-Genome Single-Nucleotide–Polymorphism Diversity for the Identification of Geographic Population Structure and Genetic Ancestry

ABSTRACTVenezuelan savannas are exposed to land‐use changes and biological invasions which compromise their persistence and function. The native C4 grass Trachypogon plumosus is the most important component of the savannas under diverse combinations of climate and soils, suggesting substantial interpopulation variation. We examined quantitative traits and isozyme variation of nine populations of this grass and related these estimates to geographical and environmental features of sampled locations. Isozyme diversity estimates were based on 10 polymorphic enzyme systems whereas 21 quantitative traits, from field and controlled growth conditions, were evaluated. Distance matrices for quantitative traits, isozyme, geographical and environmental data were subjected to clustering analysis. Correspondence between quantitative trait distance and genetic distance, and their association to geographical and environmental distances were analysed with Mantel tests. All quantitative traits differed significantly among populations. The average QST calculated for eight quantitative traits measured in the greenhouse was 0.157. Isozyme diversity differed significantly among populations. About 28% of total isozyme variation occurred among populations. Significant positive associations were detected between environmental, quantitative field traits, and geographical distance as well as between the later and genetic distances. Genetic distances did not correspond significantly with quantitative traits nor did environmental distances. Ecologically meaningful associations were detected between field quantitative traits, environmental, and geographical data using cluster analysis. Our results support the hypothesis that processes of the neutral type are mainly responsible for the variation patterns observed in T. plumosus populations in Venezuelan savannas. Variation observed for quantitative traits among populations seems to be due to the effect of environmental conditions on phenotypically plastic traits, and not the result of directional selection favouring different phenotypes in different populations.

BackgroundPrunus tomentosa Thunb, a fruit tree native to China, is an important and excellent plant material. It exhibits high adaptability to almost all soil types and climatic conditions. The germplasm resources are found in the six geographical regions of China, covering a vast expanse, and comprise a variety of ecological types. However, little is known about genetic diversity and population structure, with its abundant genetic information. Nuclear simple sequence repeat markers, with biparentally inherited characteristics, is powerful for evaluating the genetic diversity of population. Therefore, this research assessed the genetic diversity and population structure of P. tomentosa by collecting extensive samples. The finding will contribute to not only proposing scientific conservation strategies of P. tomentosa but also developing the germplasm to breed novel cherry cultivar.ResultsA total of 822 germplasms from 40 populations were used for assessing. The indicators of genetic diversity showed high values, including observable heterozygosity (0.546), expected heterozygosity (0.819), Shannon’s information index (I = 1.951), polymorphism information content (0.799). The populations displaying the greatest diversity—Gan-XlM, Shaan-HM, and Gan-ZhC. In addition, extensive genetic differentiation was detected. The genetic differentiation coefficient (FST) values calculated from heterozygosity and analysis of molecular variance were greater than 0.15. Gene flow was relatively stable (number of migrants [Nm] = 1.065). Mantel test analysis showed that there was a significant correlation (R2 = 0.065, P < 0.05) between the genetic distance and the geographical distance of the populations. Integrated cluster, structure, and principal component analysis indicated that the 40 populations were clustered into a Northwest Group and a Northeast Group. However, the Chuan-Aba, Xin-TKS, and Xin-ALR populations were clearly differentiated.ConclusionsThe P. tomentosa populations showed high or moderate polymorphism. The genetic differentiation within each population was higher than that between populations. There was a significant correlation between the genetic distance and the geographical distance. Based on genetic diversity and population differentiation levers, the most diverse populations—Gan-XlM, Shaan-HS, and Gan-PL from Gansu and Shaanxi provinces, should first be protected and applied to the innovation of cherry germplasm, followed by significantly differentiated populations, including Chuan-Aba, Ning-HlM, and Gan-PL.

Ziziphus jujuba (jujube) of buckthorn family (Rhamnaceae) is an important medicinal crop plant cultivated in different provinces of Iran. It has also wild populations in some geographical areas. We carried out population genetic study on 8 populations of cultivated versus wild jujuba by using ISSR molecular markers to produce data on population genetic structure, gene flow, and genetic variability in the studied populations. We also aimed to investigate genetic differentiation between wild and cultivated plants and identify the potential gene pools of this medicinal plant species. The studied populations had a moderate genetic variability and were grouped in two major groups by PCoA plot. AMOVA revealed significant genetic difference among these cultivars. Mantel test showed significant correlation between genetic distance and geographical distance in the studied populations. PCoA analysis showed genetic differentiation between wild and cultivated plants within each province. STRUCTURE analysis identified two potential gene pools for jujube cultivars. Data obtained may be used in genetic conservation and future breeding programs of this medicinal plant species in the country.

Brycon henni is a native species in Magdalena's River basin, and because of its cultural and economic importance, is strongly overexploited. This study aimed to describe the genetic variability and population structure of this species from Nare and Guatapé rivers basins. A total of 195 individuals were collected and DNA extractions were obtained from muscle and blood tissue. Fourteen primers were evaluated with the RAPD technique, being four of them polymorphic, and produced 66 different fragments (63% polymorphism). Besides, using the molecular variance (AMOVA) analysis, the population structure was described for all sites (phi(ST) = 0.297, phi(ST) = 0.163; Nare and Guatapé river basins, respectively), and suggested the importance of the migratory behaviour of the species in the genetic differentiation. Genetic distances among sampled sites showed that most of the genetic differentiation occurred between sites Guatapé and El Cardal with respect to the others. A Mantel Test demonstrated a correlation between genetic and geographic distances (r = 0.431 both of the basins evaluated; r = 0.377, Nare river middle basin), and suggested isolation by distance. The outcomes obtained in this study have valuable implications in species conservation and the genetic variability of natural populations of B. henni, and should be complemented with morphological analyses.

BackgroundUnderstanding genetic diversity of wild plant germplasm and the relationships between ecogeographic and genetic characteristics may provide insights for better utilizing and conserving genetic resources. Elymus tangutorum (Nevski) Hand.-Mazz, a cool-season hexaploid perennial, is an important pasture bunchgrass species used for forages and grassland restoration in Qinghai-Tibet Plateau and northwest China. In this study, 27 E. tangutorum accessions from diverse origins of western China were evaluated using AFLP markers in an effort to delve into the genetic relationships among them. The effects of eco-environmental factors and geographical isolation on the genetic diversity and population structure were also elucidated.ResultsOn account of 554 polymorphic fragments amplified with 14 primer combinations, the mean values of some marker parameters including polymorphic information content, resolving power and marker index were 0.2504, 14.10 and 23.07, respectively, validating the high efficiency and reliability of the markers selected. Genetic dissimilarity index values among accessions ranged from 0.1024 to 0.7137 with a mean of 0.2773. STRUCTURE, UPGMA clustering and PCoA analyses showed that all accessions could be divided into the three main clusters; however, this results do not exactly coincide with geographic groups. We found medium differentiation (FST = 0.162) between Qinghai-Tibet Plateau (QTP) and Xinjiang (XJC), and high differentiation (FST = 0.188) among three Bayesian subgroups. A significant correlation (r = 0.312) between genetic and geographical distance was observed by Mantel test in the species level, while the weak correlation was detected between genetic and environmental distance for all accessions and most of geographical groups. In addition, a significant ecological influence of average annual precipitation on genetic distance was revealed in XJC group and the Bayesian subgroup A.ConclusionThis study indicates that AFLP technique are a useful tool to measure genetic diversity in E. tangutorum, showing that geographical and environmental factors (especially precipitation) together, play a crucial role in genetic differentiation patterns. These findings underline the importance of local adaptation in shaping patterns of genetic variability and population structure in E. tangutorum germplasm collected in Western China.

Investigation of genetic and morphological variation in the sago palm (Metroxylon sagu; Arecaceae) in Papua New Guinea.