Elucidating the multiple genetic lineages and population genetic structure of the brooding coral <Emphasis Type="Italic">Seriatopora</Emphasis> (Scleractinia: Pocilloporidae) in the Ryukyu Archipelago

The elucidation of species diversity and connectivity is essential for conserving coral reef communities and for understanding the characteristics of coral populations. To assess the species diversity, intraspecific genetic diversity, and genetic differentiation among populations of the brooding coral Seriatopora spp., we conducted phylogenetic and population genetic analyses using a mitochondrial DNA control region and microsatellites at ten sites in the Ryukyu Archipelago, Japan. At least three genetic lineages of Seriatopora (Seriatopora-A, -B, and -C) were detected in our specimens. We collected colonies morphologically similar to Seriatopora hystrix, but these may have included multiple, genetically distinct species. Although sexual reproduction maintains the populations of all the genetic lineages, Seriatopora-A and Seriatopora-C had lower genetic diversity than Seriatopora-B. We detected significant genetic differentiation in Seriatopora-B among the three populations as follows: pairwise F _ST = 0.064–0.116 (all P = 0.001), pairwise G′′_ST = 0.107–0.209 (all P = 0.001). Additionally, only one migrant from an unsampled population was genetically identified within Seriatopora-B. Because the peak of the settlement of Seriatopora larvae is within 1 d and almost all larvae are settled within 5 d of spawning, our observations may be related to low dispersal ability. Populations of Seriatopora in the Ryukyu Archipelago will probably not recover unless there is substantial new recruitment from distant populations.     

Genetic population structure and low genetic diversity in the over-exploited sea cucumber <Emphasis Type="Italic">Holothuria edulis</Emphasis> Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island

Understanding genetic connectivity is fundamental for ecosystem-based management of marine resources. Here we investigate the metapopulation structure of the edible sea cucumber Holothuria edulis Lesson, 1830 across Okinawa Island, Japan. This species is of economic and ecological importance and is distributed from the Red Sea to Hawai‘i. We examined sequence variation in fragments of mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S), and nuclear histone (H3) at six locations across Okinawa Island. We found higher haplotype diversity for mtDNA (COI: Hd = 0.69 and 16S: Hd = 0.67) and higher heterozygosity of nDNA (H3: H _E = 0.39) in populations from the west coast of Okinawa compared to individuals from populations on the east coast (COI: Hd = 0.40; 16S: Hd = 0.21; H3: H _E = 0.14). Overall population structure was significant (AMOVA results for COI: Φ _ST = 0.49, P < 0.0001; 16S: Φ _ST = 0.34, P < 0.0001; H3: Φ _ST = 0.12, P < 0.0001). One population in the east, Uruma, showed elevated pairwise Φ _ST values in comparisons with all other sites and a marked reduction of genetic diversity (COI: Hd = 0.25 and 16S: Hd = 0.24), possibly as a consequence of a shift to a more dominant asexual reproduction mode. Recent reports have indicated that coastal development in this area influences many marine organisms, and ecosystem degradation in this location could cause the observed decrease of genetic diversity and isolation of H. edulis in Uruma. Our study should provide valuable data to help with the urgently needed management of sea cucumber populations in Okinawa, and indicates particular attention needs to be paid to vulnerable locations.     

Population genetic analyses of the endangered alpine <Emphasis Type="Italic">Sinadoxa corydalifolia</Emphasis> (Adoxaceae) provide insights into future conservation

With increasing temperature and anthropogenic activity, endangered alpine species in the high altitudes of the Qinghai-Tibet Plateau face high risk of extinction; however, they have received little attention in the past. In this study, we used 12 nuclear and nine chloroplast microsatellites (simple sequence repeats, SSR) to assess genetic diversity within and among the only two populations of the highly endangered alpine species Sinadoxa corydalifolia (Adoxaceae). We identified only one individual exhibiting clonal reproduction across all 160 extant plants. The levels of genetic variability were estimated to be very low, with the allele number N_a = 3.2 and the expected heterozygosity H_e = 0.368. The genetic differentiation is extremely high between the two regional populations (F_ST = 0.214), with a limited rate of gene flow in the recent past. In addition, numerous endemic alleles were found for each subpopulation within each population. Our analyses suggest that it is critical not only to conserve all surviving individuals of the two populations in situ but also to mediate gene flow artificially between subpopulations within each population in this endangered species.     

Rangewide genetic analysis of Lesser Prairie-Chicken reveals population structure,range expansion,and possible introgression

The distribution of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) has been markedly reduced due to loss and fragmentation of habitat. Portions of the historical range, however, have been recolonized and even expanded due to planting of conservation reserve program (CRP) fields that provide favorable vegetation structure for Lesser Prairie-Chickens. The source population(s) feeding the range expansion is unknown, yet has resulted in overlap between Lesser and Greater Prairie-Chickens (T. cupido) increasing the potential for hybridization. Our objectives were to characterize connectivity and genetic diversity among populations, identify source population(s) of recent range expansion, and examine hybridization with the Greater Prairie-Chicken. We analyzed 640 samples from across the range using 13 microsatellites. We identified three to four populations corresponding largely to ecoregions. The Shinnery Oak Prairie and Sand Sagebrush Prairie represented genetically distinct populations (F _ST > 0.034 and F _ST > 0.023 respectively). The Shortgrass/CRP Mosaic and Mixed Grass ecoregions appeared admixed (F _ST = 0.009). Genetic diversity was similar among ecoregions and N _e ranged from 142 (95 % CI 99–236) for the Shortgrass/CRP Mosaic to 296 (95 % CI 233–396) in the Mixed Grass Prairie. No recent migration was detected among ecoregions, except asymmetric dispersal from both the Mixed Grass Prairie and to a lesser extent the Sand Sagebrush Prairie north into adjacent Shortgrass/CRP Mosaic (m = 0.207, 95 % CI 0.116–0.298, m = 0.097, 95 % CI 0.010–0.183, respectively). Indices investigating potential hybridization in the Shortgrass/CRP Mosaic revealed that six of the 13 individuals with hybrid phenotypes were significantly admixed suggesting hybridization. Continued monitoring of diversity within and among ecoregions is warranted as are actions promoting genetic connectivity and range expansion.     

Conservation genetics of the annual hemiparasitic plant <Emphasis Type="Italic">Melampyrum sylvaticum</Emphasis> (Orobanchaceae) in the UK and Scandinavia

Melampyrum sylvaticum is an endangered annual hemiparasitic plant that is found in only 19 small and isolated populations in the United Kingdom (UK). To evaluate the genetic consequences of this patchy distribution we compared levels of diversity, inbreeding and differentiation from ten populations from the UK with eight relatively large populations from Sweden and Norway where the species is more continuously distributed. We demonstrate that in both the UK and Scandinavia, the species is highly inbreeding (global F _IS = 0.899). Levels of population differentiation were high (F’_ST = 0.892) and significantly higher amongst UK populations (F’_ST = 0.949) than Scandinavian populations (F’_ST = 0.762; P < 0.01). The isolated populations in the UK have, on average, lower genetic diversity (allelic richness, proportion of loci that are polymorphic, gene diversity) than Scandinavian populations, and this diversity difference is associated with the smaller census size and population area of UK populations. From a conservation perspective, the naturally inbreeding nature of the species may buffer the species against immediate effects of inbreeding depression, but the markedly lower levels of genetic diversity in UK populations may represent a genetic constraint to evolutionary change. In addition, the high levels of population differentiation suggest that gene flow among populations will not be effective at replenishing lost variation. We thus recommend supporting in situ conservation management with ex situ populations and human-mediated seed dispersal among selected populations in the UK.     

Demographic history and population genetic structure of <Emphasis Type="Italic">Hagenia abyssinica</Emphasis> (Rosaceae), a tropical tree endemic to the Ethiopian highlands and eastern African mountains

The distribution of genetic diversity among natural populations is significantly shaped by geographical and environmental heterogeneity. The key objectives of this study were to outline the population genetic structure and to investigate the effects of historical and current factors in shaping the population structure of an endemic tropical tree, Hagenia abyssinica. We used 11 polymorphic microsatellites to estimate genetic variability and evaluate gene flow among natural populations of H. abyssinica. Further, we employed ecological niche modeling approaches, to analyze the demographic history and map potential distributions of H. abyssinica during the Last Glacial Maximum and the present. Significant levels of genetic diversity (H _O = 0.477, H _E = 0.439) were observed among the sampled locations. High coefficient of genetic differentiation (F _ST = 0.32) and considerable genetic variation within the sampled locations (68.01%) were detected. Our results indicated the existence of three genetic groups with limited gene exchange and revealed positive correlations (r = 0.425, P < 0.05) between genetic diversity and geo-graphic distance. The ecological niche modeling (ENM) results support the existence of three distribution zones during the Last Glacial Maximum (LGM), with high probability of occurrence (0.8–1.0), and indicated slight distribution disturbances during and after the LGM. The fundamental patterns of genetic diversity and population structuring of H. abyssinica result from a combination of both environmental and geographical factors, including long-term isolation by distance and characteristic life history of this species. Our ENM results identified three zones that could have served as glacial refugia for this species and lay a foundation for further studies, outlining demographic histories and population structures of Afromontane species.     

Genetic Differentiation of Colombian Populations of <Emphasis Type="Italic">Anopheles darlingi</Emphasis> Root (Diptera: Culicidae)

Anopheles darlingi Root is a primary vector of malaria in the neotropic region, a species not just highly anthropophilic but very efficient in transmitting Plasmodium species and considered the most important vector in the Amazon region. The main goal of this study was to determine the genetic structure of the A. darlingi populations using microsatellites (STR) in western and eastern regions of Colombia. DNA extraction was done with the cited protocol of band using the Genomic Prep? cell and tissue isolation commercial kits. We used the STR reported by Conn et al (Mol Ecol Notes 1: 223-225, 2001). The analysis with STR proved there was a high genetic diversity and significant alterations of the Hardy-Weinberg equilibrium. The greatest genetic diversity was recorded in Mitu (Vaupes) (Na = 14, Ho = 0.520). The lowest was in Pueblo Nuevo (Cordoba) (Na = 12, Ho = 0.457). The eastern region and the Mitu (Vaupes) populations presented the highest number of primer alleles (Ap = 30; Ap = 13; Ap = 9), with variations between 0.010 and 0.097. The AMOVA revealed that the whole population underwent moderate genetic differentiation (F _ST = 0.063, p < 0.05). The same differentiation was noticed (0.06 < F _ST > 0.06, p < 0.05) with five of the six populations included in this job, and there was a low differentiation in the Las Margaritas (Santander) area (F _ST = 0.02s3, p < 0.05). Our results suggest a slight positive correlation, which does not show a statistical significance between the geographic and genetic distances, probably suggesting that the moderate genetic differentiation found between pairs of populations does not need to be explained for the hypothesis of separation by distance.     

Genetic assessment of <Emphasis Type="Italic">Abies koreana</Emphasis> (Pinaceae), the endangered Korean fir,and conservation implications

To establish a management plan for endangered and rare species, genetic assessment must first be conducted. The genetic characteristics of plant species are affected by demographic history, reproductive strategy, and distributional range as well as anthropological effects. Abies koreana E. H. Wilson (Pinaceae), Korean fir, is endemic to Korea and found only in sub-alpine areas of the southern Korean Peninsula and Jejudo Island. This species has been designated as critically endangered by the International Union for Conservation of Nature due to a continuous decline in its range and population fragmentation. We genotyped 176 individuals from seven natural populations and two afforested populations on the Korean Peninsula using 19 microsatellite loci. STRUCTURE analysis revealed two genetic clusters in natural populations (F _st  = 0.040 and R _st  = 0.040) despite low differentiation. We did not detect a significant reduction in genetic diversity or the signature of a genetic bottleneck despite population fragmentation and small population size. We deduced that this species exhibits a metapopulation structure, with the population on Jirisan Mountain acting as a source of genetic diversity for other local small populations on the Korean Peninsula, through contemporary asymmetric gene flow. However, the majority of afforested individuals on the Korean Peninsula originated from a different gene cluster. Thus, we recommend a conservation strategy that maintains two genetically unique clusters.     

Unspecific histological and hematological alterations in anadromous and resident <Emphasis Type="Italic">Salvelinus malma</Emphasis> induced by volcanogenic pollution

Knowledge of larval dispersal and connectivity in coral reef species is crucial for understanding population dynamics, resilience, and evolution of species. Here, we use ten microsatellites and one mitochondrial marker (cytochrome b) to investigate the genetic population structure, genetic diversity, and historical demography of the powder-blue tang Acanthurus leucosternon across more than 1000 km of the scarcely studied Eastern African region. The global AMOVA results based on microsatellites reveal a low but significant F _ST value (F _ST = 0.00252 P < 0.001; D _EST = 0.025 P = 0.0018) for the 336 specimens sampled at ten sample sites, while no significant differentiation could be found in the mitochondrial cytochrome b dataset. On the other hand, pairwise F _ST, PCOA, and hierarchical analysis failed to identify any genetic breaks among the Eastern African populations, supporting the hypothesis of genetic homogeneity. The observed genetic homogeneity among Eastern African sample sites can be explained by the lengthy post-larval stage of A. leucosternon, which can potentiate long-distance dispersal. Tests of neutrality and mismatch distribution signal a population expansion during the mid-Pleistocene period.     

Using genetic monitoring to inform best practice in a captive breeding programme: inbreeding and potential genetic rescue in the freshwater pearl mussel <Emphasis Type="Italic">Margaritifera margaritifera</Emphasis>

Freshwater pearl mussel (Margaritifera margaritifera) populations are declining in Northern Ireland to the extent that a captive breeding programme was established on the Upper Ballinderry river in 1998. Previous genetic analysis of the hatchery broodstock and their first cohort of offspring showed significant levels of inbreeding (F _IS  = 0.166). The broodstock, which currently numbers ca. 90 individuals, was supplemented with new individual mussels, whilst in 2013, a previously unknown population was discovered on the Lower Ballinderry river. The aim of the present study was to determine whether the rotation of the broodstock has led to a decrease in the levels of inbreeding in the second cohort of juveniles, and to determine whether the new population found in the Lower Ballinderry was genetically distinct from the captive bred population and populations from the Upper Ballinderry, which represent the source of the hatchery broodstock. Genotyping using eight microsatellite markers indicated that levels of inbreeding in the second cohort of captive-bred mussels were high, (F _IS  = 0.629), and were comparable to those sampled from the original cohort and the hatchery broodstock (F _IS  = 0.527 and 0.636 respectively). Bayesian analysis of population structure indicated that the newly discovered Lower Ballinderry population was genetically distinct from the broodstock and its source populations on the Upper Ballinderry. The observed differentiation was primarily due to differences in allele frequencies, and was most likely a result of genetic drift. The occurrence of ten alleles, albeit at low frequency, in the Lower Ballinderry population, including four private alleles, suggests that this new population could be incorporated into the broodstock with the aim of decreasing levels of inbreeding in the future.     

Genetic consequences of anthropogenic disturbances and population fragmentation in <Emphasis Type="Italic">Acacia senegal</Emphasis>

Acacia senegal is endemic to dry forest and woodland ecosystems of Sub-Saharan Africa and provides both ecological and socio-economic benefits. However, these ecosystems are threatened by escalating human disturbances and fragmentation. To investigate the human impacts on genetic diversity and structure of A. senegal, we studied genetic variability and differentiation of 330 individual trees from 11 natural A. senegal populations, grouped into lightly and heavily disturbed, using 12 polymorphic nuclear microsatellite markers. Gene diversity (H _E ) ranged from H _E = 0.570 to H _E = 0.632. Significant differences (P < 0.05) between the levels of disturbances are reported for mean gene diversity, number of alleles and allelic richness with lightly disturbed populations showing higher values. Overall, the indirect estimates of average outcrossing rates ranged from 0.794 (Kiserian) to 0.999 (Kampi ya Moto) with a mean of 0.997 suggesting a predominantly outcrossing species. There was no significant relationship (P > 0.05) detected between genetic and geographic distances, showing lack of isolation by distance. Analysis of population structure using unweighted pair group method with arithmetic mean and Bayesian model suggests presence of three gene pools as most probable, although most individuals showed mixed ancestry. The diversity and genetic structure reported in this study revealed negative impacts of human disturbance on A. senegal within this ecosystem. We recommend in-situ conservation strategies to safeguard the woodland ecosystem from further deforestation.     

Phylogeography of endangered <Emphasis Type="Italic">Dendrobium moniliforme</Emphasis> in East Asia based on mitochondrial DNA sequence variations

Belonging to the genus Dendrobium of Orchidaceae, Dendrobium moniliforme is an endangered species with disjunct distribution in East Asia, possessing significant medicinal value. To investigate its phylogeography, this study compared sequences of two mitochondrial DNA (mtDNA) fragments (nad 1/b-c and nad 7/2-3) from 143 samples of 18 natural populations of D. moniliforme almost covering the entire range of the Sino-Japanese Floristic Region (SJFR) of East Asia. As a result, a total of 30 mtDNA haplotypes were identified in these populations which revealed high levels of haplotype diversity (H _d  = 0.8733) and total genetic diversity (H _T  = 0.8886). Additionally, G _ST value being significantly lower (0.451) than N _ST value (0.722) (P < 0.05) indicated the presence of strong phylogeographic structure in these populations, and the network of mtDNA haplotypes showed that all haplotypes were divided into two clades (A and B). Haplotype overlap was observed among several D. moniliforme population groups in mainland China, suggesting the occurrence of ongoing and/or historical gene flow among them. No common haplotypes were shared by D. moniliforme populations from mainland China and the CKJ Islands (representing Taiwan [China], South Korea, and Japan collectively), pointing to their allopatric evolution in the two regions. Moreover, mismatch distribution analysis and neutral test of mtDNA data rejected the population expansion model. According to the mtDNA-based results, we infer that multiple refugia for D. moniliforme existed in the SJFR of East Asia during the Quaternary glacial period.     

Genetic diversity and reproductive traits in triploid and tetraploid populations of <Emphasis Type="Italic">Gladiolus tenuis</Emphasis> (Iridaceae)

Most perennial herbaceous plants are able to reproduce vegetatively as well as sexually. Sometimes, such plants may lose the capacity for sexual reproduction. We have studied the case of sterility in triploid populations (2n = 3x = 45) of Gladiolus tenuis M.Bieb. in a considerable part of its area of distribution. Initially, we recorded the presence of a large clone of G. tenuis to the east of the Volga River, as a result of isozyme analysis. We also used AFLP fingerprinting to genotype 55 samples from 10 populations of G. tenuis and one population of the closely related G. imbricutus L. This analysis revealed an extremely low genetic diversity in sterile triploid populations of G. tenuis and a rather high genetic diversity in fertile tetraploid populations (2n = 4x = 60) over most of the area of this species. Genetic distances between fertile and sterile populations of G. tenuis were similar to those between different species of gladioli. It appears that a single sterile genotype has spread vegetatively over 800 km, propagating by daughter corms. The study of the reproductive features of G. tenuis suggests that the cause of sterility may be self-incompatibility between individuals of the clone.     

Genetic diversity and structure of <Emphasis Type="Italic">Capparis spinosa</Emphasis> L. in Iran as revealed by ISSR markers

Capparis spinosa L. (caper bush) is an economically and ecologically important perennial shrub that grows across different regions of Iran. In this study, the genetic diversity and population structure of Iranian genepool of C. spinosa is evaluated using Inter Simple Sequence Repeat (ISSR) markers. Using 10 ISSR primers, 387 DNA fragments (bands) were amplified from the genomic DNA of 92 individuals belonging to twenty-one populations of C. spinosa, of which 378 (97.7%) were polymorphic. High level of genetic diversity (percentage of polymorphic loci = 98.2%, h = 0.1382, I = 0.243), high genetic differentiation (G_st = 0.5234) and low gene flow (Nm = 0.4553) among populations were observed. Caper bush populations were divided into 4 groups in the dendrogram, PCoA plot and Bayesian clustering results, mostly corresponded to their geographic regions. The results showed that there are value in sampling Iranian caper bush populations to look for valuable alleles for use in plant breeding programs.     

Negligence in the Atlantic forest,northern Brazil: a case study of an endangered orchid

Currently, many Brazilian orchids are threatened with extinction resulting from habitat loss and intense harvesting pressure stemming from their value as ornamental plants. Therefore, the genetic diversity in remaining populations is fundamental to the survival of these species in natural environments. In order to inform conservation strategies, this study evaluated the genetic diversity and structure of Cattleya granulosa populations. The sample consisted of 151 individuals from 12 populations in the Atlantic Forest, northeastern Brazil, evaluated using 91 ISSR markers. Genetic variability was assessed through molecular variance, diversity indexes, clusters of genotypes through Bayesian analysis, and tests for genetic bottlenecks. From all polymorphic loci, genetic diversity (H_E) varied between 0.210 and 0.321 and the Shannon index ranged from 0.323 and 0.472. Significant genetic differentiation between populations (Φ_ST = 0.391; P < 0.0001) resulted in the division of the populations into five groups based on the log-likelihood Bayesian analysis. We found significant positive correlation between geographical and genetic distances between populations (r = 0.794; P = 0.017), indicating isolation by distance. Patterns of allelic diversity within populations suggest the occurrence of bottlenecks in most C. granulosa populations (n = 8). Therefore, in order to maintain the genetic diversity of the species, the conservation of spatially distant groups is necessary.     

Genetic diversity and population structure of <Emphasis Type="Italic">Melia azedarach</Emphasis> in North-Western Plains of India

Key message

Genetic structure among M. azedarach populations was detected and two subpopulations were present among them. A significant ‘isolation by distance’ was found in M. azedarach population in North-Western Plains of India.

Abstract

Melia azedarach is an important forest tree with pharmaceutical, insecticidal, pesticidal, and commercial significance. It is a good reforestation tree because of its fast growth and drought hardy nature. Genetic variation in a species allows itself to adapt, evolve and respond to environmental stress. It provides the basis for survival of a species and critically influences its evolutionary potential. Assessment of genetic diversity is necessary for improvement and conservation of a species. For this, microsatellite markers are of particular interest given the attributes like co-dominance, reproducibility, hyper variability and abundance throughout the genome. In the present study, we analyzed the genetic diversity and population structure of M. azedarach, an ecologically imperative species growing in the North-Western Plains of India. We developed 43 microsatellite markers, of which 20 were subsequently employed for analysis of diversity and population structure among 33 populations encompassing 318 genotypes representing North-Western Plains of India. A moderate level of diversity (Na = 5.1, Ho = 0.506, He = 0.712, I = 1.386) was assessed. The highest value of ΔK estimated using STRUCTURE indicated 2 subpopulations (K = 2). AMOVA exhibited 73 % variation within populations and 12 % variation was found among regions. Significant positive correlation between geographical and genetic distance was found (Rxy = 0.365, P = 0.010). The present study lays a foundation on a better understanding of genetic dynamics of the species and reveals its diversity and population structure in North-Western Plains of India.

     

De novo development and characterization of polymorphic microsatellite markers in a schilbid catfish, <Emphasis Type="Italic">Silonia silondia</Emphasis> (Hamilton, 1822) and their validation for population genetic studies

The stock characterization of wild populations of Silonia silondia is important for its scientific management. At present, the information on genetic parameters of S. silondia is very limited. The species-specific microsatellite markers were developed in current study. The validated markers were used to genotype individuals from four distant rivers. To develop de novo microsatellite loci, an enriched genomic library was constructed for S. silondia using affinity–capture approach. The markers were validated for utility in population genetics. A total number of 76 individuals from four natural riverine populations were used to generate data for population analysis. The screening of isolated repeat sequences yielded eleven novel polymorphic microsatellite loci. The microsatellite loci exhibited high level of polymorphism, with 6–24 alleles per locus and the PIC value ranged from 0.604 to 0.927. The observed (Ho) and expected (He) heterozygosities ranged from 0.081 to 0.84 and 0.66 to 0.938, respectively. The AMOVA analysis indicated significant genetic differentiation among riverine populations (overall F_ST = 0.075; P < 0.0001) with maximum variation (92.5 %) within populations. Cross-priming assessment revealed successful amplification (35–38 %) of heterologous loci in four related species viz. Clupisoma garua, C. taakree, Ailia coila and Eutropiichthys vacha. The results demonstrated that these de novo polymorphic microsatellite loci are promising for population genetic variation and diversity studies in S. silondia. Cross-priming results indicated that these primers can help to get polymorphic microsatellite loci in the related catfish species of family Schilbidae.     

Rangewide population differentiation and population substructure in <Emphasis Type="Italic">Quercus rubra</Emphasis> L.

Genetic diversity and differentiation in Quercus rubra remains undescribed for most of the native range. Using 10 highly informative gSSR markers, we genotyped 23 populations (980 trees), from across the native range, at local and rangewide spatial scales. We used a hierarchical Bayesian method to generate population-specific F _st estimates. The posterior probabilities of 3 spatial and 19 climate factors revealed that latitude and precipitation in the warmest quarter were the only plausible models for population-specific F _st estimates. Population-specific F _st estimates increased as a linear function of population latitude (R ² = 0.745, p < 0.0001), the expected effect of postglacial range expansion. Measures of shared ancestry (pairwise local differentiation) among populations sampled at fine spatial scales within locations also increased with the latitude of the location (R ² = 0.495, p = 0.014), suggesting an influence on differentiation that could not be attributed to postglacial range expansion. As precipitation in the warmest quarter drives radial growth rate in this species, we propose that growth rate influences generation time, which determines the time required to re-establish migration-drift equilibrium among local regenerating stands. Population substructure analysis detected four groups, only one of which was geographically coherent. Most other populations were moderately admixed. Sampling designs that include both fine and coarse spatial scales can begin to disentangle the effect of past range expansions from the effect of recent disturbances. Accounting for population substructure in this species will require additional studies involving functional genes, interspecific interactions, and species distribution modeling.     

Population genetic diversity and geographical differentiation of MHC class II DAB genes in the vulnerable Chinese egret (<Emphasis Type="Italic">Egretta eulophotes</Emphasis>)

Major histocompatibility complex (MHC) genes are excellent markers for the study of adaptive genetic variation occurring over different geographical scales. The Chinese egret (Egretta eulophotes) is a vulnerable ardeid species with an estimated global population of 2600–3400 individuals. In this study, we sampled 172 individuals of this egret (approximately 6 % of the global population) from five natural populations that span the entire distribution range of this species in China. We examined their population genetic diversity and geographical differentiation at three MHC class II DAB genes by identifying eight exon 2 alleles at Egeu-DAB1, eight at Egeu-DAB2 and four at Egeu-DAB3. Allelic distributions at each of these three Egeu-DAB loci varied substantially within the five populations, while levels of genetic diversity varied slightly among the populations. Analysis of molecular variance showed low but significant genetic differentiation among five populations at all three Egeu-DAB loci (haplotype-based ?_ST: 0.029, 0.020 and 0.042; and distance-based ?_ST: 0.036, 0.027 and 0.043, respectively; all P < 0.01). The Mantel test suggested that this significant population genetic differentiation was likely due to an isolation-by-distance pattern of MHC evolution. However, the phylogenetic analyses and the Bayesian clustering analysis based on the three Egeu-DAB loci indicated that there was little geographical structuring of the genetic differentiation among five populations. These results provide fundamental population information for the conservation genetics of the vulnerable Chinese egret.