Landscape Genetics of the Yellow-Bellied Toad (Bombina variegata) in the Northern Weser Hills of Germany

Anthropogenic influences such as deforestation, increased infrastructure, and general urbanization has led to a continuous loss in biodiversity. Amphibians are especially affected by these landscape changes. This study focuses on the population genetics of the endangered yellow-bellied toad (Bombina variegata) in the northern Weser Hills of Germany. Additionally, a landscape genetic analysis was conducted to evaluate the impact of eight different landscape elements on the genetic connectivity of the subpopulations in this area. Multiple individuals from 15 study sites were genotyped using 10 highly polymorphic species-specific microsatellites. Four genetic clusters were detected, with only two of them having considerable genetic exchange. The average genetic differentiation between populations was moderate (global FST = 0.1). The analyzed landscape elements showed significant correlations with the migration rates and genetic distances between populations. Overall, anthropogenic structures had the greatest negative impact on gene flow, whereas wetlands, grasslands, and forests imposed minimal barriers in the landscape. The most remarkable finding was the positive impact of the underpasses of the motorway A2. This element seems to be the reason why some study sites on either site of the A2 showed little genetic distance even though their habitat has been separated by a strong dispersal barrier.

Effect of the Landscape on Functional and Spatial Connectivity in Magnolia Cubensis (Magnoliaceae) in Two Mountain Massifs of Cuba

Landscape features impact gene flow and the spatial patterns of genetic variation between populations of a species. Because many Magnoliaceae species occur in fragmented and highly disturbed landscapes, the family is an excellent model for landscape genetic studies. This research focuses on the subspecies and localities of Magnolia cubensis and aims to: (1) compare the genetic diversity, (2) search for genetic patterns, (3) describe the functional connectivity and (4) access the structural connectivity of the landscape. This study employs 21 microsatellite markers on two subspecies, complemented with landscape characteristics of the Guamuhaya and Sierra Maestra massifs in Cuba. Magnolia cubensis subsp. acunae does not have a well-defined spatial genetic pattern: there is no evidence of isolation by distance or spatial autocorrelation and the little genetic differentiation between the two localities does not reflect the characteristics of the landscape that separates them or the cost values to cross it. Magnolia cubensis subsp. cubensis presents evidence of isolation by distance and the autocorrelation analyses indicate that the approximate scale of the genetic neighborhood is between 35 and 40 km. There is a marked genetic structure with probability values that indicate the existence of three genetic groups. Large genetic differentiation was only found between Gran Piedra and the other localities, which reflects low gene flow. Our results support the recognition of these subspecies at the species level. We define one evolutionary significant unit in Magnolia cubensis subsp. acunae and two evolutionary significant units in Magnolia cubensis subsp. cubensis. These results must be combined with ecological, social and distribution data, in order to obtain a more accurate and realistic perspective of the conservation management strategies for these taxa.

Visualizing the cultural landscape gene of traditional settlements in China: a semiotic perspective

China has a deep traditional culture and a very long history, and is very rich in traditional settlements (designated as “Famous Historic-Cultural Villages/Towns”, “China Traditional Villages” by China Government). To help people develop the traditional settlements to achieve the great goal of Chinese National Rejuvenation, Chinese scholar put forward the Cultural Landscape Gene Theory of Traditional Settlements (CLGTS) in 2003. Since then, CLGTS has been employed to solve the issues of Chinese traditional settlements, such as the identification and regionalization of cultural genes in traditional settlements, and the understanding of architectural features. Although CLGTS has made great strides in many fields, there is still a lack of scientific findings in exploring the symbol mechanism from a perspective of semiotics. To explore this, we first examine the core features of CLGTS through a dialectic perspective. We analyze two features of CLGTS in depth. First, CLGTS is the dialectic combination of macro settlement image and micro cultural factors of traditional settlements, material appearance and inherent traditional cultural implications, overall features and local self-renewal mechanisms, qualitative and quantitative methods, superiority of cultural factors and rich cultural connotation. Second, CLGTS is famous for its nonlinearity, self-organization, and self-iteration due to various spatial shape and complex structures. Based on the above, we present the concept of a CLGTS Symbolization Method. Then, we further elaborate the key features, classification methods, and corresponding representation methods of CLGTS symbols. Finally, by using Visual C#.net program language, we develop a prototype system of the Traditional Landscape Genetic Symbol Database (TLGSD) to create and manage CLGTS symbols. Test results show that TLGSD can meet the needs of constructing a CLGTS symbol database for a given region. This study is of great significance to explore and contribute to the CLGTS Symbolization Method.

Landscape Genetic Connectivity and Evidence for Recombination in the North American Population of the White-Nose Syndrome Pathogen, Pseudogymnoascus destructans

White-Nose Syndrome is an ongoing fungal epizootic caused by epidermal infections of the fungus, Pseudogymnoascus destructans (P. destructans), affecting hibernating bat species in North America. Emerging early in 2006 in New York State, infections of P. destructans have spread to 38 US States and seven Canadian Provinces. Since then, clonal isolates of P. destructans have accumulated genotypic and phenotypic variations in North America. Using microsatellite and single nucleotide polymorphism markers, we investigated the population structure and genetic relationships among P. destructans isolates from diverse regions in North America to understand its pattern of spread, and to test hypotheses about factors that contribute to transmission. We found limited support for genetic isolation of P. destructans populations by geographic distance, and instead identified evidence for gene flow among geographic regions. Interestingly, allelic association tests revealed evidence for recombination in the North American P. destructans population. Our landscape genetic analyses revealed that the population structure of P. destructans in North America was significantly influenced by anthropogenic impacts on the landscape. Our results have important implications for understanding the mechanism(s) of P. destructans spread.

Using empirical datasets to quantify uncertainty in inferences of landscape genetic resistance due to variation of individual-based genetic distance metrics

Estimates of gene flow are commonly based on inferences of landscape resistance in ecological and evolutionary research and they frequently inform decision-making processes in conservation management. It is therefore imperative that inferences of a landscape factors relevance and its resistance are robust across approaches and reflect real-world gene flow instead of methodological artefacts. Here, we tested the impact of 160 different individual-based pairwise genetic metrics on consistency of landscape genetic inferences.We used three empirical datasets that adopted individual-based sampling schemes and varied in scale (35-25,000 km2) and total number of samples (184-790) and comprise the wild boar, Sus scrofa, the red fox, Vulpes vulpes and the common wall lizard, Podarcis muralis. We made use of a machine-learning algorithm implemented in ResistanceGA to optimally fit resistances of landscape factors to genetic distance metrics and ranked their importance. Employed for nine landscape factors this resulted in 4,320 unique combinations of dataset, landscape factor and genetic distance metric, which provides the basis for quantifying uncertainty in inferences of landscape resistance.Our results demonstrate that there are clear differences in Akaike information criteria (AICc)-based model support and marginal R2-based model fit between different genetic distance metrics. Metrics based on between 1-10 axes of eigenvector-based multivariate analyses (Factorial correspondence analysis, FCA; Principal component analysis, PCA) outperformed more widely used metrics, including the proportion of shared alleles (DPS), with AICc and marginal R2 values often an order of magnitude greater in the former. Across datasets, inferences of the directionality of a landscape factors influence on gene flow, e.g. facilitating or impeding it, changed across different genetic distance metrics. The directionality of the inferred resistance was largely consistent when considering metrics based on between 1-10 FCA/PCA axes.Inferences of landscape genetic resistance need to be corroborated using calculations of multiple individual-based pairwise genetic distance metrics. Our results call for the adoption of eigenvector-based quantifications of pairwise genetic distances. Specifically, a preliminary step of analysis should be incorporated, which explores model ranks across genetic distance metrics derived from FCA and PCA, and, contrary to findings of a simulation study, we demonstrate that it suffices to quantify these distances spanning the first ten axes only.

High dispersal capacity of Culicoides obsoletus (Diptera: Ceratopogonidae), vector of bluetongue and Schmallenberg viruses, revealed by landscape genetic analyses

Background In the last two decades, recurrent epizootics of bluetongue virus and Schmallenberg virus have been reported in the western Palearctic region. These viruses affect domestic cattle, sheep, goats and wild ruminants and are transmitted by native hematophagous midges of the genus Culicoides (Diptera: Ceratopogonidae). Culicoides dispersal is known to be stratified, i.e. due to a combination of dispersal processes occurring actively at short distances and passively or semi-actively at long distances, allowing individuals to jump hundreds of kilometers. Methods Here, we aim to identify the environmental factors that promote or limit gene flow of Culicoides obsoletus, an abundant and widespread vector species in Europe, using an innovative framework integrating spatial, population genetics and statistical approaches. A total of 348 individuals were sampled in 46 sites in France and were genotyped using 13 newly designed microsatellite markers. Results We found low genetic differentiation and a weak population structure for C. obsoletus across the country. Using three complementary inter-individual genetic distances, we did not detect any significant isolation by distance, but did detect significant anisotropic isolation by distance on a north-south axis. We employed a multiple regression on distance matrices approach to investigate the correlation between genetic and environmental distances. Among all the environmental factors that were tested, only cattle density seems to have an impact on C. obsoletus gene flow. Conclusions The high dispersal capacity of C. obsoletus over land found in the present study calls for a re-evaluation of the impact of Culicoides on virus dispersal, and highlights the urgent need to better integrate molecular, spatial and statistical information to guide vector-borne disease control.

Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics

Comparisons of microsatellite and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, calling into the question the continued utility of microsatellites in population and landscape genetics. Yet highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated analyses previously done using microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source populations to the remaining sink populations. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.