Comparison of Bayesian Clustering and Edge Detection Methods for Inferring Boundaries in Landscape Genetics

Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods’ effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance

Variation and genetic structure of Serratula lycopifolia populations (Vill.) Kern. (Asteraceae) in Poland and adjacent regions

AFLPs were used to analyze the genetic variability of Serratula lycopifolia, one of the rarest plant species in Central and Western Europe, in six populations from the Wyżyna Małopolska upland (Poland), White Carpathian Mts (Slovakia and Czech Republic) and Podolian Upland (Ukraine). The results of polymorphism, PCoA and neighbor-net analyzes showed similar and relatively low genetic variation and high genetic similarity of individuals within each Polish population but there were differences between those populations. The population from Slovakia also showed comparatively high intrapopulation homogeneity and evident genetic separation from the other studied populations. Intrapopulation genetic variation was higher in the Czech and Ukrainian populations. However, AMOVA analyses revealed no significant differentiation at population and regional levels. The estimated low genetic diversity in the populations from Poland and Slovakia may be due to genetic processes such as genetic drift and inbreeding in local populations resulting from their low abundance, and does not seem characteristic of the species as a whole. These genetic analyzes make it clear that the Polish and Slovakian populations need support programmes to maintain their genetic variation. Measures should focus on increasing the number of individuals in the populations and on protecting their habitat

Epidemiology and Evolution of Fungal Pathogens in Plants and Animals

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Boraginaceae Varronia rupicola (Urb.) Brtton : biogeography, systematic placement and conservation genetics of a threatened species endemic to the Caribbean

In the Caribbean region, Varronia rupicola (Boraginaceae) is a medium to large, woody shrub endemic to the Puerto Rican Bank where it is threatened with extinction due to its limited area of occupancy, small populations and on-going threats. The greatest of these is currently loss of suitable habitat through development and degradation. These are caused by human activities that are expected to continue and possibly worsen. The species is also threatened by sea level rise and drought as well as natural disasters, particularly hurricanes and tsunamis. Combined, the effects of anthropogenic and climate change induced threats could push the species to extinction over the coming century. Through interrogation of the findings of cyto-, phylo- and population genetic as well as biogeographical research, it is clear that V. rupicola is a distinct species that is endemic to the islands of Puerto Rico, Vieques and Anegada where five populations were detected. The species has lost genetic diversity in the wild through a reduction in population size with allelic diversity proportional to the size of the population. The five populations were found to have lower than expected levels of heterozygosity as well as significant genetic differentiation and inbreeding. Varronia rupicola plants were found in an extremely limited area of intact habitat (<90 km2) overlying substrates that cover <200 km2 across the three islands. Protected areas contain less than a third (<30 km2) of the remaining intact habitat that supports the species and established ex-situ collections capture less than half of the private alleles found in the wild. An integrated approach to the species conservation is needed to maximise genetic diversity and potentiality allow adaptation of V. rupicola to environmental change and new threats

Population genetics and structure of the Sumatran tiger

The two key determinants of population persistence in fragmented landscapes are population size and connectivity. Populations with high levels of genetic variation and large population size are expected to have a lower risk of extinction. Similarly, populations with high rates of connectivity are expected to persist long-term. For many elusive landscape species it is difficult to obtain direct estimates of these parameters, but genetic sampling can offer powerful indirect assessments. Whilst these techniques have been applied to the study of many wide-ranging carnivores, this study represents the first example in the Sumatran tiger (Panthera tigris sumatrae). Extensive field surveys were conducted to collect faecal samples from several Tiger Conservation Landscapes and protected areas on Sumatra. Samples were then processed according to optimised protocols to obtain reliable results. In order to quantify extinction risk I first estimated genetic variation and effective population size using microsatellite loci. I also determined relative levels of connectivity using estimates of differentiation (FST), gene flow and genetic clustering. Results indicate that Sumatran tigers have high levels of genetic variation and that their effective population size is within the expected range. There is very little population structure and there is no obvious evidence for barriers to dispersal. The Batang Hari/Kerinci Seblat ecosystem emerged as a potential source population and in contrast there was some evidence of isolation affecting the population of Way Kambas NP in the extreme south of the island. Overall, despite high levels of human land cover conversion over the past 20-30 years, few genetic changes have been expressed in the Sumatran tiger. The immediate threat to tigers is not the loss of genetic diversity, but the rapidly declining area of suitable habitat in which they can survive

Comment on 'On the inference of spatial structure from population genetics data'.

International audienc

Boraginaceae Varronia rupicola (Urb.) Brtton : biogeography, systematic placement and conservation genetics of a threatened species endemic to the Caribbean

In the Caribbean region, Varronia rupicola (Boraginaceae) is a medium to large, woody shrub endemic to the Puerto Rican Bank where it is threatened with extinction due to its limited area of occupancy, small populations and on-going threats. The greatest of these is currently loss of suitable habitat through development and degradation. These are caused by human activities that are expected to continue and possibly worsen. The species is also threatened by sea level rise and drought as well as natural disasters, particularly hurricanes and tsunamis. Combined, the effects of anthropogenic and climate change induced threats could push the species to extinction over the coming century. Through interrogation of the findings of cyto-, phylo- and population genetic as well as biogeographical research, it is clear that V. rupicola is a distinct species that is endemic to the islands of Puerto Rico, Vieques and Anegada where five populations were detected. The species has lost genetic diversity in the wild through a reduction in population size with allelic diversity proportional to the size of the population. The five populations were found to have lower than expected levels of heterozygosity as well as significant genetic differentiation and inbreeding. Varronia rupicola plants were found in an extremely limited area of intact habitat (<90 km2) overlying substrates that cover <200 km2 across the three islands. Protected areas contain less than a third (<30 km2) of the remaining intact habitat that supports the species and established ex-situ collections capture less than half of the private alleles found in the wild. An integrated approach to the species conservation is needed to maximise genetic diversity and potentiality allow adaptation of V. rupicola to environmental change and new threats