Population genetic structure of mahogany (Swietenia macrophylla King, Meliaceae) across the Brazilian Amazon, based on variation at microsatellite loci: implications for conservation

Mahogany (Swietenia macrophylla, Meliaceae) is the most valuable and intensively exploited Neotropical tree. No information is available regarding the genetic structure of mahogany in South America, yet the region harbours most of the unlogged populations of this prized hardwood. Here we report on the genetic diversity within and the differentiation among seven natural populations separated by up to 2100 km along the southern arc of the Brazilian Amazon basin. We analysed the variation at eight microsatellite loci for 194 adult individuals. All loci were highly variable, with the number of alleles per locus ranging from 13 to 27 (mean = 18.4). High levels of genetic diversity were found for all populations at the eight loci (mean HE = 0.781, range 0.754-0.812). We found moderate but statistically significant genetic differentiation among populations considering both estimators of FST and RST, theta = 0.097 and rho = 0.147, respectively. Estimates of theta and rho were significantly greater than zero for all pairwise population comparisons. Pairwise rho-values were positively and significantly correlated with geographical distance under the isolation-by-distance model. Furthermore, four of the populations exhibited a significant inbreeding coefficient. The finding of local differentiation among Amazonian mahogany populations underscores the need for in situ conservation of multiple populations of S. macrophylla across its distribution in the Brazilian Amazon. In addition, the occurrence of microgeographical genetic differentiation at a local scale indicates the importance of maintaining populations in their diverse habitats, especially in areas with mosaics of topography and soil.     

bottlesim: a bottleneck simulation program for long‐lived species with overlapping generations

Population bottlenecks reduce genetic diversity and thus cause great concern in conservation biology. Previous theoretical studies often assume discrete generations in projecting declines in genetic diversity caused by bottlenecks. This assumption creates complexities when applying the models to long‐lived species with overlapping generations. bottlesim is a program for simulating bottlenecks to estimate the impact on genetic diversity; the novelties include an overlapping‐generation model, a wide range of reproductive systems, and flexible population size settings. With these features, bottlesim will be a useful tool for estimating the genetic consequences of bottlenecks, evaluating conservation plans, and performing power analysis.     

Hierarchical partitioning of ant diversity: implications for conservation of biogeographical diversity in arid and semi‐arid areas

Aim The scale of observation is important in detecting the spatial variation of biological assemblages, which should be taken into consideration for an appropriate plan of biogeographical conservation. We investigated whether (1) World Wildlife Fund’s ecoregion units are the appropriate scale for conserving ant diversity in Iran, (2) each ecoregion represents a distinct ant community composition and (3) patterns of diversity partitioning differ among four ecoregions. Location Iran, a sampling transect along four arid and semi‐arid ecoregions. Methods We applied hierarchical partitioning to data collected from a nested sampling design including four hierarchical levels: ‘local’, ‘landscape’, ‘ecoregional’ and ‘whole‐region’. Observed alpha and beta diversity components were compared with values of null distributions. Hierarchical cluster analysis was applied to evaluate similarity of ant species composition among ecoregions. Results Partitioning of whole‐region species richness showed that 85% of the species richness was generated by beta diversity among ecoregions and landscapes. The highest value of diversity was generated by beta diversity among ecoregions. Unlike whole‐region partitioning, separate partitioning within each ecoregion revealed that beta component among localities contributed to species richness of each ecoregion. Ecoregions showed different patterns of diversity partitioning. The alpha component contributed largely to the total diversity of two ecoregions, but for two other ecoregions, beta component contributed more than alpha component. Cluster analysis identified four discrete ant species compositions; however, it split landscapes of one ecoregion into two distinct groups. Main conclusions Whole‐region diversity partitioning indicates that ecoregions represent the appropriate scale for conserving ant diversity and that each ecoregion has a distinct ant fauna. However, different conservation strategies should be considered for different ecoregions owing to the differing scales of variation within them. Boundaries of ecoregions remain a subject for further studies. The influence of climate change on ecoregional boundaries should be considered and should be predicted with respect to future conservation maps.     

Determinants of fine‐scale homogenization and differentiation of native freshwater fish faunas in a Mediterranean Basin: implications for conservation

Aim Increasing threats to freshwater biodiversity are rapidly changing the distinctiveness of regional species pools and local assemblages. Biotic homogenization/differentiation processes are threatening the integrity and persistence of native biodiversity patterns at a range of spatial scales and pose a challenge for effective conservation planning. Here, we evaluate the extent and determinants of fine‐scale alteration in native freshwater fish assemblages among stream reaches throughout a large river basin and consider the implications of these changes for the long‐term conservation of native fishes. Location Guadiana River basin (South‐Western Iberian Peninsula). Methods We quantified the magnitude of change in compositional similarity between observed and reference assemblages and its potential effect on natural patterns of compositional distinctiveness. Reference assemblages were defined as the native species expected to occur naturally (in absence of anthropogenic alterations) and were reconstructed using a multivariate adaptive regression splines predictive model. We also evaluated the role of habitat degradation and introduced species as determinants of biotic homogenization/differentiation. Results We found a significant trend towards homogenization for native fish assemblages. Changes in native fish distributions led to the loss of distinctiveness patterns along natural environmental gradients. Introduced species were the most important factor explaining the homogenization process. Homogenization of native assemblages was stronger in areas close to reservoirs and in lowland reaches where introduced species were more abundant. Main conclusions The implementation of efficient conservation for the maintenance of native fish diversity is seriously threatened by the homogenization processes. The identification of priority areas for conservation is hindered by the fact that the most diverse communities are vanishing, which would require the selection of broader areas to adequately protect all the species. Given the principal role that introduced species play in the homogenization process and their relation with reservoirs, special attention must be paid to mitigating or preventing these threats.     

On the verge of extinction: genetics of the critically endangered Iberian plant species, Borderea chouardii (Dioscoreaceae) and implications for conservation management

Borderea chouardii is a relictual and dioecious, strictly sexually reproducing, long-living geophyte of the Dioscoreaceae family. Previous biological and demographic studies have indicated the existence of a uniformly distributed panmictic population of this taxon at the southernmost Spanish pre-Pyrenean mountain ranges where it occurs in rather inaccessible crevices of a single limestone cliff. However, individuals of B. chouardii are spatially subdivided into two subpopulations located, respectively, on the upper and lower parts of the cliff, and vertically separated 150 m. Because of its extreme rarity, B. chouardii was the first Iberian taxon to have a specific conservation plan and has been included in several red lists under the category of critically endangered (CR). However, no previous attempts have been conducted to analyse the fine scale evolutionary mechanisms involved in its present microspatial distribution. Genetic diversity and population structure have been investigated through the analysis of neutral hypervariable markers such as simple sequence repeats (SSRs) and randomly amplified polymorphic DNAs (RAPDs) to unravel the impact of life history traits in the differentiation of the two subpopulations. Both types of molecular markers were unequivocal in distinguishing two genetically distinct groups of individuals corresponding to their spatial separation. However, SSRs detected a higher level of subpopulation differentiation (F(ST) = 0.35, R(ST) = 0.32) than RAPDs (F(ST) = 0.21). SSR data indicated significant deviation from random dispersal of genes and genotypes between the two groups, suggesting that mating occurs mainly among individuals within subpopulations, thus, favouring the divergence between the two groups. This microevolutionary differentiation scenario might have been caused by a coupled effect of past genetic drift and reproductive isolation, as a result of strong glacial age bottlenecks and inefficient dispersal system of pollen and seeds, respectively. The identification of such genetic structure in this narrow endemic prompts a modification of the management strategies of its single extant population.     

Genetic Diversity of a Tropical Tree Species,Shorea leprosula Miq. (Dipterocarpaceae), in Malaysia: Implications for Conservation of Genetic Resources and Tree Improvement1

Genetic diversity and population genetic structure of Shorea leprosula was investigated using seven natural populations distributed throughout Peninsular Malaysia and one natural population from Borneo. The mean population and species level genetic diversity were exceptionally high (H_e= 0.369 ± 0.025 and 0.406 ± 0.070, respectively). Heterozygosity varied among populations, ranging from 0.326 to 0.400, with the highest values found in the populations from central Peninsular Malaysia. Correlations among ecological factors (longitude, latitude, and annual rainfall) were not significant (P > 0.05), indicating that these ecological variables were not responsible for the observed genetic differences among populations. The Bangi adult population exhibited a higher level of observed heterozygosity but lower fixation indices in comparison to its seedling population. All other seedling populations also showed positive fixation indices (f), indicating a general excess of homozygotes. This also may suggest selection against homozygotes between the seedling and adult stages. A low level of population differentiation was detected (G_ST= 0.117 with the Lambir population and GST= 0.085 without the Lambir population). Furthermore, gene flow (N_m) between populations was not significantly correlated with geographical distances for the populations within Peninsular Malaysia. Cluster analysis also did not reflect geographical proximity and gave little insight into the genetic relatedness of the populations. This may indicate that the populations sampled are part of a continuous population with fragmentation having occurred in the recent past.     

Morphological and genetic differentiation in populations of the dispersal‐limited coco de mer (Lodoicea maldivica): implications for management and conservation

Aims Developing plant conservation strategies requires knowledge of ecological and genetic processes underlying population dynamics. We aimed to quantify morphological and genetic differentiation among remnant populations of the iconic coco‐de‐mer palm Lodoicea maldivica. We hypothesized that limited gene flow among widely spaced populations would result in high genetic variation and large phenotypic differences among populations. Location Islands of Praslin and Curieuse (CU), Seychelles, Indian Ocean. Methods We conducted an extensive population survey and recorded morphological parameters for 447 Lodoicea in the main populations at Vallée de Mai (VM) and Fond Ferdinand (FF) on Praslin, and on CU. We collected leaf material from 180 trees in these populations for DNA genotyping using amplified fragment length polymorphisms. Results A total of 16,766 Lodoicea trees were recorded in the three populations (72.6% of Lodoicea on both islands). Lodoicea trees at VM and FF showed similar morphology, but differed in most parameters from those at CU, which were shorter, grew more slowly and produced fewer seeds. Mean overall genetic diversity was 0.337, and percentage of polymorphic loci was 91.1. Genetic diversity of the CU population was lower than that at VM and FF. There was weak genetic differentiation between CU and Praslin populations, but 99% of all genetic diversity was within populations. Main conclusions Trees on CU differed in growth and morphology from those of the two Praslin populations. These phenotypic differences, however, were not mirrored in the genetic structure of the populations. All populations were relatively genetically diverse with remarkably little differentiation among populations. This suggests that the capacity of Lodoicea to dominate across a range of habitats may be because of high phenotypic plasticity. High genetic connectivity may be maintained through long‐distance wind pollination. Given the uncertainty about the extent of underlying adaptive variation, we recommend that restoration projects avoid transferring seeds between island populations.