Population genetic structure and conservation implications of Ceriops decandra in Malay Peninsula and North Australia

Comprehensive information of mangrove genetic resources is requisite for developing strategies for their effective conservation and sustainable use. Genetic diversity within and among populations of a widespread viviparous mangrove Ceriops decandra was determined using inter-simple sequence repeat (ISSR). Ten natural populations were collected from Malay Peninsula and North Australia. At the species level, high genetic variation was detected (P = 72%, H_E = 0.253, and I = 0.379). The estimate of G_ST was 0.882, indicating a high level of genetic differentiation among populations. When populations were grouped according to geographic regions, i.e., East Malaya, West Malaya, Southmost Malaya, and North Australia, AMOVA suggested that most of the total variation (87%) was accounted for by differentiation between regions, with only 4% accounting for variation among populations within regions, and a further 9% partitioned among individuals within a population. A UPGMA dendrogram based on genetic distance revealed a deep split between populations from the eastern Indian Ocean and all others from the western Pacific Ocean, which may result from the historical lowering of sea level at these regions during the recent Pleistocene glaciations. An understanding of the genetic structure of C. decandra provides insight for the conservation and management of this species.     

Population genetic structure of rock ptarmigan in the 'sky islands' of French Pyrenees: implications for conservation

Expected consequences of global warming include habitat reduction in many cool climate species. Rock ptarmigan is a Holarctic grouse that inhabits arctic and alpine tundra. In Europe, the Pyrenean ptarmigan inhabits the southern edge of the species' range and since the last glacial maximum its habitat has been severely fragmented and is restricted to high-alpine zones or 'sky islands'. A recent study of rock ptarmigan population genetic in Europe found that the Pyrenean ptarmigan had very low genetic diversity compared with that found in the Alps and Scandinavia. Habitat fragmentation and reduced genetic diversity raises concerns about the viability of ptarmigan populations in the Pyrenees. However, information on population structuring and gene flow across the Pyrenees, which is essential for designing a sound management plan, is absent. In this study, we use seven microsatellites and mitochondrial control region sequences to investigate genetic variation and differentiation among five localities across the Pyrenees. Our analyses reveal the presence of genetic differentiation among all five localities and a significant isolation-by-distance effect that is likely the result of short dispersal distances and high natal and breeding philopatry of Pyrenean ptarmigan coupled with severe habitat fragmentation. Furthermore, analysis of molecular variance, principal component analysis and Bayesian analysis of genetic structuring identified the greatest amount of differentiation between the eastern and main parts of the Pyrenean chain separated by the Sègre Valley. Our data also show that the Canigou massif may host an isolated population and requires special conservation attention. We propose a management plan which includes the translocation of birds. If a sky island structure affects genetic divergence in rock ptarmigan, it may also affect the genetic structure of other sky island species having low dispersal abilities.     

Phylogeography and spatial genetic structure of the Southern torrent salamander: implications for conservation and management

The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.     

Inbreeding and genetic structure in the endangered Sorraia horse breed: implications for its conservation and management

The Sorraia horse is a closed breed with reduced effective population size and considered in critical maintained risk status. The breed exists in 2 main breeding populations, one in Portugal and one in Germany, with a smaller population size. A set of 22 microsatellite loci was used to examine genetic diversity and structure of the Sorraia horse breed and to compare individual inbreeding coefficient F, estimated from pedigree data, with individual heterozygosity and mean d(2). The Sorraia horse shows lower levels of microsatellite diversity when compared with other horse breeds. Due to management strategies, there are clear differences in the genetic structure of the 2 main Sorraia horse populations. Individual heterozygosity was shown to be a good estimator, used together with or as an alternative to inbreeding coefficient, in predicting fitness and evaluating the inbreeding level of the Sorraia horse. The information gathered in this study, combined with information available from previous studies, offers an important and wide information base for the future development of an effective breeding management of the Sorraia horse in order to preserve this endangered breed.     

Population genetic structure of the endangered Eastern Bristlebird, Dasyornis brachypterus; implications for conservation

For species that are habitat specialists or sedentary, population fragmentation may lead to genetic divergence between populations and reduced genetic diversity within populations, with frequent inbreeding. Hundreds of kilometres separate three geographical regions in which small populations of the endangered Eastern Bristlebird, Dasyornis brachypterus, a small, ground-dwelling passerine that occurs in fire-prone bushland in eastern Australia, are currently found. Here, we use mitochondrial and microsatellite DNA markers to: (i) assess the sub-specific taxonomy designated to northern range-edge, and central and southern range-edge D. brachypterus, respectively, and (ii) assess levels of standing genetic variation and the degree of genetic subdivision of remnant populations. The phylogenetic relationship among mtDNA haplotypes and their spatial distribution did not support the recognised subspecies boundaries. Populations in different regions were highly genetically differentiated, but in addition, the two largest, neighboring populations (located within the central region and separated by ~50 km) were moderately differentiated, and thus are likely closed to migration (microsatellites, F _ST = 0.06; mtDNA, F _ST = 0.12, ?? _ST = 0.08). Birds within these two populations were genotypically diverse and apparently randomly mating. A long-term plan for the conservation of D. brachypterus??s genetic diversity should consider individual populations as separate management units. Moreover, managers should avoid actively mixing birds from different populations or regions, to conserve the genetic integrity of local populations and avoid outbreeding depression, should further translocations be used as a recovery tool for this species.     

Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implications for management and conservation

We investigated 25 natural populations of Chamaecyparis obtusa using 51 cleaved amplified polymorphic sequence (CAPS) markers, which were developed using information on sequence-tagged sites (STS) in Cryptomeria japonica. Most CAPS markers have codominant expression patterns, and are suitable for population studies because of their robustness and convenience. We estimated various genetic diversity parameters, including average heterozygosity (H(e)) and allelic richness and found that the more peripheral populations tended to have lower genetic diversity than central populations, in agreement with a previous theoretical study. The overall genetic differentiation between populations was low, but statistically significant (G(ST)=0.039), and similar to the level reported in a previous allozyme study. We attempted to detect non-neutral loci associated with local adaptation to clarify the relationship between the fixation index (F(ST)) and H(e) values for each locus and found seven candidates non-neutral loci. Phylogenetic tree analysis of the populations and Bayesian clustering analysis revealed a pattern of gradually increasing isolation of populations with increasing geographical distance. Three populations had a high degree of linkage disequilibrium, which we attribute to severe bottlenecks due to human disturbance or competition with other species during their migration from refugia after the most recent glaciation. We concluded that the small populations in western Japan and in Kanto district are more important, from a conservation perspective, than the populations in central Japan, due to their genetic divergence, relatively small sizes and restricted areas.     

Social and genetic population structure of free-ranging cheetah in Botswana: implications for conservation

Once widely distributed throughout Africa, cheetahs (Acinonyx jubatus) occur today within fragmented populations and are listed as vulnerable by the IUCN. Botswana currently hosts the second largest cheetah population throughout the species’ range. This study initiated a molecular genetic survey of wild Botswana cheetah populations. It focused on the relatedness within presumed social groups using 14 microsatellite markers and revealed a higher proportion of unrelated male coalitions than was expected. Based on the unrelated cheetahs only, the estimation of the genetic variation corresponded with results from recent studies on different African populations. The analysis of unrelated individuals indicated limited genetic differentiation between cheetahs from different regions of Botswana. This suggests that the Botswana cheetah population might represent a unique panmictic population as long as sufficient levels of gene flow are maintained within the distribution range. This baseline information will now be incorporated to develop management strategies and set priorities for cheetah conservation in Botswana.     

Population genetic structure of the endangered crayfish Austropotamobius pallipes in France based on microsatellite variation: biogeographical inferences and conservation implications

1. One important goal in conservation biology is to characterise evolutionary lineages within endangered species before management decisions are taken. Here, we assess population differentiation in the freshwater crayfish Austropotamobius pallipes, an endangered species endemic to western Europe and provide valuable information for the conservation of French populations. 2. Analysis of five microsatellite loci in 44 populations revealed very different within population levels of genetic diversity (0.000 < H₀ < 0.564). Two groups, corresponding to northern and southern French populations, showed a high degree of genetic differentiation in both allele frequencies and allele sizes. Comparison of these results with previous studies of A. pallipes strongly suggests that the divergence between northern and southern populations could have occurred during the last glaciation period of the Pleistocene from one Atlantic and one Mediterranean refuge. 3. Evidence for genetic admixture between these two lineages was revealed by correspondence analyses in southern populations, probably as the result of artificial translocations. 4. French populations appeared significantly differentiated among the different river drainages and were highly structured within rivers. The impact of population size, population bottlenecks and founder events on the population genetic differentiation are discussed. 5. Based on these results, we propose the designation of two evolutionarily significant units for A. pallipes in France. Our data also support the maintenance of separate demographic management strategies for crayfish inhabiting different river systems. However, genetic analyses will have to be combined with demographic and ecological data for sustainable conservation programmes.     

Strong population genetic structure and its implications for the conservation and management of the endangered Itasenpara bitterling

To infer the population genetic structure and genetic diversity of Itasenpara bitterling (Acheilognathus longipinnis), a cyprinid species endemic to Japan and distributed in only three specific regions, we investigated mitochondrial DNA variation. The distribution of the haplotypes among the three regions showed distinct geographic structure, and no common haplotypes were observed among regions. Analysis of molecular variance revealed a significant proportion of the genetic variance was partitioned among regions (93.1 %, P < 0.001), and pairwise estimates of D_A and Φ_ST between regions also revealed strong population structure. Given the strong genetic structure and low genetic diversity within regions, we strongly suggest that each region should be treated as a separate unit in any conservation program and any inter-regional translocations should be avoided.     

Noninvasive genotyping and Mendelian analysis of microsatellites in African savannah elephants

We obtained fresh dung samples from 202 (133 mother-offspring pairs) savannah elephants (Loxodonta africana) in Samburu, Kenya, and genotyped them at 20 microsatellite loci to assess genotyping success and errors. A total of 98.6% consensus genotypes was successfully obtained, with allelic dropout and false allele rates at 1.6% (n = 46) and 0.9% (n = 37) of heterozygous and total consensus genotypes, respectively, and an overall genotyping error rate of 2.5% based on repeat typing. Mendelian analysis revealed consistent inheritance in all but 38 allelic pairs from mother-offspring, giving an average mismatch error rate of 2.06%, a possible result of null alleles, mutations, genotyping errors, or inaccuracy in maternity assignment. We detected no evidence for large allele dropout, stuttering, or scoring error in the dataset and significant Hardy-Weinberg deviations at only two loci due to heterozygosity deficiency. Across loci, null allele frequencies were low (range: 0.000-0.042) and below the 0.20 threshold that would significantly bias individual-based studies. The high genotyping success and low errors observed in this study demonstrate reliability of the method employed and underscore the application of simple pedigrees in noninvasive studies. Since none of the sires were included in this study, the error rates presented are just estimates.     

Population genetic structure of and inbreeding in an insular cattle breed, the Jersey, and its implications for genetic resource management

The Jersey is a ubiquitous and successful breed of cattle that originates from the UK Channel Island of Jersey. While the breed has been exported extensively, no imports have taken place to the island since 1789, leading to a concern regarding possible losses of genetic diversity and increased inbreeding. We have conducted the first large-scale genetic analysis of the Jersey cattle using only samples from the island. A total of 223 cattle from all parishes except one were genotyped for 12 microsatellite loci. The average number of alleles per locus and expected heterozygosity were found to be comparatively high (n(A)=4, H(e)=0.64) with respect to that observed in a number of continental breeds. Only breeds that have been upgraded and are therefore the result of admixture are clearly more variable than the Jersey. We also found a significant but limited amount of genetic differentiation between parishes (F(st)=0.013), or even between farms (F(st)=0.035) despite an apparent lack of movement. This is confirmed by the application of two recent statistical methods. A Bayesian partition analysis shows that the most probable value of K, the number of possible hidden partitions, is 1 (P approximately 0.98). K=2 has a much lower probability (P approximately 0.02) while other values are essentially zero. Similarly, we were able to show that there was no support for departure from panmixia other than due to population structure, and thus that there is sufficient background gene flow across the island to overcome local drift. Overall, it appears that the current level of genetic diversity and its distribution within the island means it is unnecessary to import unrelated genetic material to the island for management purposes.     

Population genetic structure, local adaptation, and conservation genetics of Kandelia obovata

Topographic changes during the Pleistocene glacial/interglacial cycles affected the distribution of coastline mangroves and influenced their population genetic structure. The submergence of the continental shelf off southeast China during the postglacial age caused coastline expansions and resulted in the colonization of mangroves. Here, we performed multilocus genome scans using amplified fragment-length polymorphisms to explore the effects of topography and natural selection in structuring Kandelia obovata populations. Long-term isolation by the Taiwan Strait since the end of the last glacial maximum, which obstructed gene flow, differentiated the Taiwanese and Chinese populations. Founders that colonized from both outlets of the Taiwan Strait were sourced from the northern South China Sea and the Ryukyus, thereby creating a melting pot in the Taiwan Strait. Inner-strait currents played roles as vectors for propagule dispersal among populations. Upon examination of the allele-frequency distributions of outlier loci, most negative outliers reflected the widespread polymorphisms shared by common ancestors. Furthermore, significant differentiation in the genetic components of positive outliers between this and other populations and the negative correlation with geographic distance suggested the presence of geography- or latitude-independent population divergence. Restored populations were compared with their sources and revealed biased sampling of nursery seedlings, which caused within-population substructures and reduced effective population sizes. This study indicated that multiple factors affect the population structure of the mangroves off southeast China.     

Microsatellite markers unravel the population genetic structure of the Azorean Leontodon: implications in conservation

The genus Leontodon L. (Asteraceae) comprises approximately 50 species with a natural distribution area covering North America, Europe, northern Africa, and western Asia. Two of these species are endemic to the Azores Archipelago: Leontodon filii and Leontodon rigens. Although both species were targeted with several taxonomic revisions, so far no studies into their genetic diversity have been carried out. In this research, the population genetic structure and diversity of both taxa were assessed using five newly developed SSR markers. Four hundred and thirty-seven individuals collected throughout the archipelago were included in the study. A total of 98 alleles (25–12 per locus, average = 19.6) and an overall excess of homozygotes (multilocus F _is = 0.37, range 0.16–0.53) were found for L. rigens populations. For L. filii, 52 alleles in total (8–13 per locus, average = 10.4) were found, overall near the HW equilibrium (multilocus F _is = 0.07, range ?0.25 to 0.57). The two species showed an equivalent proportion of rare alleles (L. rigens 80.6 %; L. filii 76.9 %). Both a Principal Coordinate Analysis and a Bayesian analysis proposed the existence of two well-defined groups, but pooled L. filii populations from Faial Island with L. rigens populations. The largest proportion of genetic variability was found within populations (L. rigens 72.6%; L. filii 78.9 %). The highest values of gene flow were obtained for L. filii within the central group of islands. Our results update the current distribution given for the Azorean Leontodon taxa, clearly indicating that conservation measures should be applied to several populations. The results also reveal that a revision of the Azorean Leontodon should be carried out to clarify species delimitation.     

Population genetic structure and long-distance dispersal among seabird populations: implications for colony persistence

Dramatic local population decline brought about by anthropogenic-driven change is an increasingly common threat to biodiversity. Seabird life history traits make them particularly vulnerable to such change; therefore, understanding population connectivity and dispersal dynamics is vital for successful management. Our study used a 357-base pair mitochondrial control region locus sequenced for 103 individuals and 18 nuclear microsatellite loci genotyped for 245 individuals to investigate population structure in the Atlantic and Pacific populations of the pelagic seabird, Leach's storm-petrel Oceanodroma leucorhoa leucorhoa. This species is under intense predation pressure at one regionally important colony on St Kilda, Scotland, where a disparity between population decline and predation rates hints at immigration from other large colonies. AMOVA, F(ST), Φ(ST) and Bayesian cluster analyses revealed no genetic structure among Atlantic colonies (Global Φ(ST) = -0.02 P > 0.05, Global F(ST) = 0.003, P > 0.05, STRUCTURE K = 1), consistent with either contemporary gene flow or strong historical association within the ocean basin. The Pacific and Atlantic populations are genetically distinct (Global Φ(ST) = 0.32 P < 0.0001, Global F(ST) = 0.04, P < 0.0001, STRUCTURE K = 2), but evidence for interocean exchange was found with individual exclusion/assignment and population coalescent analyses. These findings highlight the importance of conserving multiple colonies at a number of different sites and suggest that management of this seabird may be best viewed at an oceanic scale. Moreover, our study provides an illustration of how long-distance movement may ameliorate the potentially deleterious impacts of localized environmental change, although direct measures of dispersal are still required to better understand this process.