Fine-Scale Spatial Genetic Structure of Remnant Populations of Abies religiosa, in a Temperate Forest in Central Mexico
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Genetic structure of a population can be molded by the resistance of the landscape or the distance between populations that function as barriers to gene flow. We analyzed the population genetic structure of Abies religiosa on a fine spatial scale and examined isolation models by resistance and distance. We collected vegetative tissue from populations located at the altitudinal extremes of the distribution range of the species on three slopes of La Malinche National Park (LMNP) (South, North, and East) in central Mexico. Genomic DNA was obtained using the CTAB 2X method, and eight microsatellite chloroplast loci were amplified. The genetic structure was identified based on an Analysis of Molecular Variance, a Discriminant Analysis of Principal Components with cross-validation and a spatial Principal Component Analysis using the Gabriel-type connectivity network. The isolation hypotheses were evaluated by constructing partial Mantel tests using Reciprocal Causal Modeling and Maximum Likelihood Population Effects models. A genetic structure of isolation by resistance to elevation was identified, and two genetic groups were recognized: one including populations of the South slope and the other comprising populations of the North and East slopes. We detected in Abies religiosa populations of the LMNP an isolation by resistance to elevation that determines the genetic structure, and the greatest genetic exchange between groups of populations located at higher altitudes. It is suggested to promote the connectivity between slopes through assisted migration and immediately halt land-use changes, as part of the actions to preserve genetic diversity in the LMPN. This study contributes to the knowledge of the spatial genetic structure of species at risk in the Mexican temperate forest for their conservation.Keywords:
Isolation by distance
Mantel test
Geographical distance
Genetic distance
Isolation by distance
Geographical distance
Genetic distance
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We investigated the genetic structure of 16 populations (from five geographical groups) of clouded salamander (Hynobius nebulosus) in northern Kyushu, Japan, by analyzing the sequence of the mitochondrial DNA control region. A total of 24 haplotypes were found in 199 individuals of the salamander. In the analysis of genetic diversity of the populations, an isolated small population sustained in an urban area had a low level of genetic diversity. This is considered to be due to both the less suitable nature of the habitat and a recent artificial barrier to gene flow. In the analysis of genetic differentiation (FST) among 16 populations, significant differences were detected in 76.7% of all possible population pairs. Analysis of molecular variance (AMOVA) showed that most of the genetic variation was attributed to individual differences within populations, but a significant genetic difference among groups was also detected. This fine-scale genetic differentiation would be formed through genetic isolation (or gene flow) by geographic distance, because strong correlations between genetic FST/(1-FST) and geographic distances were detected. In 10 northern populations from two adjacent groups that were separated by a small lowland river there is a significant positive correlation between geographic and genetic distance, but there tends to be a larger genetic distance between the inter-group populations than the distance within groups. These results suggest that even a small lowland river, if combined with past rising of sea level by transgression, might be a landscape barrier to gene flow of this species.
Genetic distance
Isolation by distance
Geographical distance
mtDNA control region
Genetic Variability
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Abstract Aim The coqui frog ( E leutherodactylus coqui ) was introduced to the H awai'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. Location Hawai'i Island. Methods We 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). Results The Mantel test for isolation by distance found no significant correlation between genetic and geographical distance ( r 2 = 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 ( N M = 4.228), inbreeding was high, genetic differentiation between populations was low, and significant genetic structure was detected among populations (4% of total variation, P < 0.002). Main conclusions Genetic 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.
Mantel test
Isolation by distance
Geographical distance
Genetic distance
Inbreeding avoidance
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The isolation-by-distance model predicts that genetic similarity between populations will decrease exponentially as the geographic distance between them increases, because of the limiting effect of geographic distance on rates of gene flow. Many studies of human populations have applied the isolation-by-distance model to genetic variation between local populations in a limited geographic area, but few have done so on a global level, and these few used different models and analytical methods. I assess genetic variation between human populations across the world using data on red blood cell polymorphisms, microsatellite DNA markers, and craniometric traits. The isolation-by-distance model provides an excellent fit to average levels of genetic similarity within geographic distance classes for all three data sets, and the rate of distance decay is the same in all three. These results suggest that a common pattern of global gene flow mediated by geographic distance is detectable in diverse genetic and morphological data. An alternative explanation is that the correspondence between genetic similarity and geographic distance reflects the history of dispersal of the human species out of Africa.
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Geographical distance
Genetic distance
Similarity (geometry)
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Distance measures
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In many species genes move over limited distances, such that genetic differences among populations or individuals are expected to increase as a function of geographical distance. In other species, however, genes may move any distance over a single generation time, such that no increase of genetic differences is expected to occur with distance. Patterns of gene dispersal have been assessed typically using this theoretical property. In this study, this classical approach based on a Mantel test was compared to a new method using individual assignment to reveal contrasts in dispersal patterns between 15 populations of brook charr Salvelinus fontinalis and 10 populations of Atlantic salmon Salmo salar sampled in eastern Canada, where both species co-occur naturally. Based on the Mantel test, we found evidence for neither an increase of genetic differences with distance in either species nor a significant contrast between them. The individual-based method, in contrast, revealed that individual assignment in both species was non random, being significantly biased toward geographically proximate locations. Furthermore, brook charr were on average assigned to a closer river than were salmon, according to a priori expectations based on the dispersal behaviour of the two species. We thus propose that individual assignment methods might be a promising and more powerful alternative to Mantel tests when isolation by distance cannot be postulated a priori.
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Mantel test
Isolation by distance
Genetic distance
Metapopulation
Geographical distance
Genetic divergence
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In this study we aimed to examine the effects of both Nei’s genetic distance and Bray Curtis distance versus geographical distance for Mantel test on chicken diversity data. Many researchers used Nei’s genetic distance which measure that genetic differences arise due to mutations and genetic drift but some researchers used Bray Curtis distance which used to quantify the compositional dissimilarity between two different locations. We used molecular data from 28 microsatellite loci with the sample size of 364 local chicken from 45 locations and Euclidean distance of this locations using Google Earth v.4. Mantel test results suggest that relationship between genetic differentiations and geographic distance between populations using Bray Curtis distance could be substituted for Nei’s genetic distance with great reliability on chicken diversity data.
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Genetic distance
Geographical distance
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Distance measures
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Landscape complexity provides opportunities for local adaptation and creates population genetic structure at limited geographic scales. We determined if fine-scale genetic structure was evident in a population of ringtails (Bassariscus astutus) inhabiting the Guadalupe Mountains, a small, isolated, and ecologically diverse mountain range in the southwest United States. We hypothesized that ringtails would exhibit either a genetic pattern of isolation by distance (IBD), because their small body size would most likely limit dispersal distances, or a pattern of isolation by resistance (IBR), because the topographical complexity of the mountain range would result in complex dispersal patterns. To investigate for the presence of fine-scale genetic structure in this population, we genotyped 153 ringtails at 15 microsatellite loci and described genetic structure using 2 Bayesian clustering techniques. Six genetic clusters were identified revealing complex spatial genetic structure within a localized geographic area. We used partial Mantel tests to test for a correlation between genetic distance and geographic distance or resistance distance but found no evidence for a genetic pattern related to IBD or IBR. We subsequently tested for an association between genetic structure and isolation by environment (IBE) using a discriminant function analysis and classified a high proportion of individuals (> 91%) to their observed genetic cluster based exclusively on landscape features. We also used a nonparametric, multivariate analysis of variance to further explore the role of land-cover type and found that plant association explained 26% of the genetic variation. These results suggest that IBE influences the genetic structure of ringtails at local geographic scales, a finding that deserves consideration in conservation planning.
Isolation by distance
Mantel test
Geographical distance
Genetic distance
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Isolation by distance
Genetic distance
Geographical distance
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