Phylogeography and population genetic structure of double-crested cormorants (Phalacrocorax auritus)

We examined the genetic structure of double-crested cormorants (Phalacrocorax auritus) across their range in the United States and Canada. Sequences of the mitochondrial control region were analyzed for 248 cormorants from 23 breeding sites. Variation was also examined at eight microsatellite loci for 409 cormorants from the same sites. The mitochondrial and microsatellite data provided strong evidence that the Alaskan subspecies (P. a. cincinnatus) is genetically divergent from other populations in North America (net sequence divergence = 5.85 %; Φ_ST for mitochondrial control region = 0.708; F_ST for microsatellite loci = 0.052). Historical records, contemporary population estimates, and field observations are consistent with recognition of the Alaskan subspecies as distinct and potentially of conservation interest. Our data also indicated the presence of another divergent lineage, associated with the southwestern portion of the species range, as evidenced by highly unique haplotypes sampled in southern California. In contrast, there was little support for recognition of subspecies within the conterminous U.S. and Canada. Rather than genetically distinct regions corresponding to the putative subspecies [P. a. albociliatus (Pacific), P. a. auritus (Interior and North Atlantic), and P. a. floridanus (Southeast)], we observed a distribution of genetic variation consistent with a pattern of isolation by distance. This pattern implies that genetic differences across the range are due to geographic distance, rather than discrete subspecific breaks. Although three of the four traditional subspecies were not genetically distinct, possible demographic separation, habitat differences, and documented declines at some colonies within the regions, suggests that the Pacific and possibly North Atlantic portions of the breeding range may warrant differential consideration from the Interior and Southeast breeding regions.     

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.     

Genetic diversity of the African poplar (<Emphasis Type="Italic">Populus ilicifolia</Emphasis>) populations in Kenya

We evaluated the genetic diversity of the African poplar (Populus ilicifolia) populations found in Kenya compared with reference samples of five poplar species from North America and one species introduced in Kenya from India (KEFRI-Kenya). Amplified fragment length polymorphism (AFLP) was used with the objective of providing important information for breeding and in situ/ex situ conservation of this species. Samples collected from three locations along the species’ natural range (Athi, Ewaso Nyiro, and Tana rivers) were compared with four samples of locally planted Populus deltoides stand introduced from India and ten reference samples from North America. Six AFLP primer combinations produced 521 clear bands for analysis. The percentage polymorphic loci were lowest in Tana (20.4 %) and highest in Athi (40.6 %). The average heterozygosity across the studied populations was between 0.07 and 0.3. AMOVA revealed more genetic variation partitioning within population (87 %; P?<?0.01) than among populations (13 %; P?<?0.01) suggesting significant genetic variation between populations. Further, UPGMA delineation showed two clusters of the Tana, Athi, and Ewaso Nyiro populations clustered together compared to the North America and India/KEFRI reference samples. Moreover, the study showed that the Athi population is more diverse than those of Tana and Ewaso Nyiro and may be important for conservation, domestication, and improvement studies. The genetic differentiation (F _ST ?=?0.134) among Kenyan P. ilicifolia populations suggests limited possibility of gene flow between these populations.     

Higher immunocompetence is associated with higher genetic diversity in feral honey bee colonies (<Emphasis Type="Italic">Apis mellifera</Emphasis>)

Honey bees are the most important managed pollinators as they provide key ecosystem services for crop production worldwide. Recent losses of honey bee colonies in North America and Europe have demonstrated a need to develop strategies to improve their health and conserve their populations. Previously, we showed that feral honey bees—colonies that live in the wild without human assistance—exhibit higher levels of immunocompetence than managed colonies in North Carolina (USA). In a first attempt to investigate the underlying mechanisms of this difference in immune response, here we characterize the genetic composition of feral and managed honey bees using microsatellite markers. Our results reveal significant but small genetic differentiation between feral and managed honey bee colonies (?_CT = 0.047, P?=?0.03) indicating admixture between these two groups. Higher genetic diversity was correlated with higher immune response in feral (P _MANOVA = 0.011) but not managed bees, despite the fact that the latter group showed significantly higher average genetic diversity (P _ANCOVA < 0.001). These findings suggest that genetic diversity is positively associated with immunocompetence in feral honey bee colonies, and that the benefits of genetic diversity are obscured in managed bees, perhaps as a result of artificial selection. We hypothesize that high genetic variability provides the raw material upon which natural selection acts and generates adaptive genotypes in unmanaged populations. Feral populations could be useful sources of genetic variation to use in breeding programs that aim to improve honey bee health.     

Pronounced differences in genetic structure despite overall ecological similarity for two Ambystoma salamanders in the same landscape

Studies linking genetic structure in amphibian species with ecological characteristics have focused on large differences in dispersal capabilities. Here, we test whether two species with similar dispersal potential but subtle differences in other ecological characteristics also exhibit strong differences in genetic structure in the same landscape. We examined eight microsatellites in marbled salamanders (Ambystoma opacum) from 29 seasonal ponds and spotted salamanders (Ambystoma maculatum) from 19 seasonal ponds in a single geographic region in west-central Massachusetts. Despite overall similarity in ecological characteristics of spotted and marbled salamanders, we observed clear differences in the genetic structure of these two species. For marbled salamanders, we observed strong overall genetic differentiation (F _ST = 0.091, F′ _ST = 0.375), three population-level clusters of populations (K = 3), a strong pattern of isolation by distance (r = 0.58), and marked variation in family-level structure (from 1 to 23 full-sibling families per site). For spotted salamanders, overall genetic differentiation was weaker (F _ST = 0.025, F′ _ST = 0.102), there was no evidence of population-level clustering (K = 1), the pattern of isolation by distance (r = 0.17) was much weaker compared to marbled salamanders, and there was less variation in family-level structure (from 10 to 36 full-sibling families per site). We suspect that a combination of breeding site fidelity, effective population size, and generation interval is responsible for these marked differences. Our results suggest that marbled salamanders, compared to spotted salamanders, are more sensitive to fragmentation from various land-use activities and would be less likely to recolonize extirpated sites on an ecologically and conservation-relevant time frame.     

Population stock structure of leatherback turtles (Dermochelys coriacea) in the Atlantic revealed using mtDNA and microsatellite markers

This study presents a comprehensive genetic analysis of stock structure for leatherback turtles (Dermochelys coriacea), combining 17 microsatellite loci and 763 bp of the mtDNA control region. Recently discovered eastern Atlantic nesting populations of this critically endangered species were absent in a previous survey that found little ocean-wide mtDNA variation. We added rookeries in West Africa and Brazil and generated longer sequences for previously analyzed samples. A total of 1,417 individuals were sampled from nine nesting sites in the Atlantic and SW Indian Ocean. We detected additional mtDNA variation with the longer sequences, identifying ten polymorphic sites that resolved a total of ten haplotypes, including three new variants of haplotypes previously described by shorter sequences. Population differentiation was substantial between all but two adjacent rookery pairs, and F _ST values ranged from 0.034 to 0.676 and 0.004 to 0.205 for mtDNA and microsatellite data respectively, suggesting that male-mediated gene flow is not as widespread as previously assumed. We detected weak (F _ST = 0.008 and 0.006) but significant differentiation with microsatellites between the two population pairs that were indistinguishable with mtDNA data. POWSIM analysis showed that our mtDNA marker had very low statistical power to detect weak structure (F _ST < 0.005), while our microsatellite marker array had high power. We conclude that the weak differentiation detected with microsatellites reflects a fine scale level of demographic independence that warrants recognition, and that all nine of the nesting colonies should be considered as demographically independent populations for conservation. Our findings illustrate the importance of evaluating the power of specific genetic markers to detect structure in order to correctly identify the appropriate population units to conserve.     

Population structure and cryptic speciation in bonnethead sharks Sphyrna tiburo in the south‐eastern U.S.A. and Caribbean

Population structure and lineage diversification within a small, non‐dispersive hammerhead shark species, the bonnethead shark Sphyrna tiburo, was assessed. Sphyrna tiburo is currently described as one continuously distributed species along the Atlantic continental margins of North, Central and South America, but recent genetic analysis of an insular population (Trinidad) suggests the possibility of cryptic speciation. To address this issue S. tiburo were sampled at six sites along c. 6200 km of continuous, continental coastline and from one island location (Grand Bahama) across a discontinuity in their distribution (the Straits of Florida), in order to test if they constitute a single lineage over this distribution. A total of 1030 bp of the mitochondrial control region (CR) was obtained for 239 S. tiburo, revealing 73 distinct haplotypes, high nucleotide diversity (0·01089) and a pair of highly divergent lineages estimated to have separated 3·61–5·62 million years ago. Mitochondrial cytochrome oxidase I and nuclear internal transcribed spacer loci show the same pattern. Divergence is similar within S. tiburo to that observed between established elasmobranch sister species, providing further evidence of cryptic speciation. A global AMOVA based on CR confirms that genetic diversity is primarily partitioned among populations (Φ_ST = 0·828, P < 0·001) because the divergent lineages are almost perfectly segregated between Belize and North America–The Bahamas. An AMOVA consisting solely of the North American and Bahamian samples is also significantly different from zero (Φ_ST = 0·088, P < 0·001) and pairwise F_ST is significantly different between all sites. These findings suggest that S. tiburo comprises a species complex and supports previous research indicating fine population structure, which has implications for fisheries management and biodiversity conservation.     

Assessing the impact of stocking northern-origin hatchery brook trout on the genetics of wild populations in North Carolina

The release of hatchery-origin fish into streams with endemics can degrade the genetics of wild populations if interbreeding occurs. Starting in the 1800s, brook trout descendent from wild populations in the northeastern United States were stocked from hatcheries into streams across broad areas of North America to create and enhance fishery resources. Across the southeastern United States, many millions of hatchery-origin brook trout have been released into hundreds of streams, but the extent of introgression with native populations is not well resolved despite large phylogeographic distances between these groups. We used three assessment approaches based on 12 microsatellite loci to examine the extent of hatchery introgression in 406 wild brook trout populations in North Carolina. We found high levels of differentiation among most collections (mean F′_ST = 0.718), and among most wild collections and hatchery strains (mean F′_ST = 0.732). Our assessment of hatchery introgression was consistent across the three metrics, and indicated that most wild populations have not been strongly influenced by supplemental stocking. However, a small proportion of wild populations in North Carolina appear to have been strongly influenced by stocked conspecifics, or in some cases, may have been founded entirely by hatchery lineages. In addition, we found significant differences in the apparent extent of hatchery introgression among major watersheds, with the Savannah River being the most strongly impacted. Conversely, populations in the Pee Dee River watershed showed little to no evidence of hatchery introgression. Our study represents the first large-scale effort to quantify the extent of hatchery introgression across brook trout populations in the southern Appalachians using highly polymorphic microsatellite markers.     

Host-parasite relationship between colonial terns and bacteria is modified by a mutualism with a plant with antibacterial defenses

Predator–prey and host-parasite interactions and mutualisms are common and may have profound effects on ecosystems. Here we analyze the parasitic and mutualistic associations between three groups of organisms: the plant Artemisia maritima, bacteria, and a colonial seabird (the sandwich tern Sterna sandvicensis) that breeds in dense colonies covered in feces produced by both adults and chicks. A disproportionately large fraction of colonies of the sandwich tern in Denmark were located in patches covered by A. maritima. This association was specific for the densely colonial sandwich tern, but was not present for four other sympatric species of terns that breed in much less dense colonies. A. maritima reduced the abundance of pathogenic Staphylococcus on chicken eggshells in a field experiment. Recruitment by sandwich terns breeding in patches of A. maritima was 18 % higher than for sandwich terns breeding in the absence of A. maritima. A. maritima benefitted from the association with sandwich terns due to the supply of nutrients from feces and uneaten food lost by young. These findings are consistent with sandwich terns exploiting the association with A. maritima and its antimicrobial properties to improve their reproductive success, while sandwich terns and A. maritima are involved in a mutualistic interaction.     

Estimating migratory connectivity of birds when re‐encounter probabilities are heterogeneous

Understanding the biology and conducting effective conservation of migratory species requires an understanding of migratory connectivity – the geographic linkages of populations between stages of the annual cycle. Unfortunately, for most species, we are lacking such information. The North American Bird Banding Laboratory (BBL) houses an extensive database of marking, recaptures and recoveries, and such data could provide migratory connectivity information for many species. To date, however, few species have been analyzed for migratory connectivity largely because heterogeneous re‐encounter probabilities make interpretation problematic. We accounted for regional variation in re‐encounter probabilities by borrowing information across species and by using effort covariates on recapture and recovery probabilities in a multistate capture–recapture and recovery model. The effort covariates were derived from recaptures and recoveries of species within the same regions. We estimated the migratory connectivity for three tern species breeding in North America and over‐wintering in the tropics, common (Sterna hirundo), roseate (Sterna dougallii), and Caspian terns (Hydroprogne caspia). For western breeding terns, model‐derived estimates of migratory connectivity differed considerably from those derived directly from the proportions of re‐encounters. Conversely, for eastern breeding terns, estimates were merely refined by the inclusion of re‐encounter probabilities. In general, eastern breeding terns were strongly connected to eastern South America, and western breeding terns were strongly linked to the more western parts of the nonbreeding range under both models. Through simulation, we found this approach is likely useful for many species in the BBL database, although precision improved with higher re‐encounter probabilities and stronger migratory connectivity. We describe an approach to deal with the inherent biases in BBL banding and re‐encounter data to demonstrate that this large dataset is a valuable source of information about the migratory connectivity of the birds of North America.     

Barn owls (<Emphasis Type="Italic">Tyto alba</Emphasis>) in western North America: phylogeographic structure,connectivity, and genetic diversity

The barn owl (Tyto alba) is a non-migratory species widely distributed across much of North America in areas with extensive old-field and grassland habitat and without extensive winter snow cover. We investigated the genetic diversity and phylogeographic patterns of barn owl populations in western North America, ranging from British Columbia (BC) to southern California, and one eastern population from Pennsylvania. We also determined the genetic distinctiveness of a population off the coast of southern California, Santa Barbara Island, as management plans to control the local owl population are being considered to decrease predation rate on the now threatened Scripps’s Murrelet (Synthliboramphus scrippsi). Using 8 polymorphic microsatellite markers (N = 126) and ND2 mitochondrial sequences (N = 37), we found little to no genetic structure among all sampled regions, with the exception of Santa Barbara Island. The BC mainland population, despite its northwestern geographically peripheral location and ongoing habitat degradation, is not genetically depauperate. However, individuals from Vancouver Island, likewise a peripheral population in BC, exhibited the lowest genetic diversity of all sampled locations. The low global F_ST value (0.028) estimated from our study suggests that old-field agricultural habitats are well connected in North America. Since the BC population has declined by about 50 % within the last three decades, it is vital to focus on preserving the remaining barn owl habitats in BC to allow successful establishment from neighbouring populations. Additionally, our microsatellite data revealed that the population on Santa Barbara Island showed genetic divergence from its continental counterpart. Mitochondrial data, however, demonstrated that this island population is not a monophyletic lineage containing unique haplotypes, and hence cannot be designated as an Evolutionarily Significant Unit.     

Population genetic structure of wild daffodils (Narcissus pseudonarcissus L.) at different spatial scales

We studied the population genetic and clonal structure of the endangered long-lived perennial plant Narcissus pseudonarcissus using random amplified polymorphic markers. Estimates for mean gene diversity within 15 populations of N. pseudonarcissus of three neighbouring geographical regions were high in comparison to other long-lived perennials (H _eN = 0.33). The genetic diversity of the two smallest populations (<200 plants) was significantly reduced, indicating loss of genetic variability due to drift. The analysis of the population genetic structure revealed a significant genetic differentiation both between regions (Φ_ST = 0.06) and between populations within regions (Φ_ST = 0.20). However, there was incomplete correspondence between geographical regions and the population genetic structure. In order to preserve the overall genetic variation in wild populations of N. pseudonarcissus, management measures should thus aim to protect many populations in each region. The spatial genetic structure within populations of N. pseudonarcissus was in agreement with an isolation by distance model indicating limited gene flow due to pollinator behaviour and restricted seed dispersal. The very restricted spatial extent of clonal growth (<5 cm) and the high level of clonal diversity indicate that clonal growth in N. pseudonarcissus is not an important mode of propagation and that management measures should favour sexual reproduction in order to avoid further reductions in the size and number of populations.     

Conservation genetics of snowy plovers (<Emphasis Type="Italic">Charadrius alexandrinus</Emphasis>) in the Western Hemisphere: population genetic structure and delineation of subspecies

We examined the genetic structure of snowy plovers (Charadrius alexandrinus) in North America, the Caribbean, and the west coast of South America to quantify variation within and among breeding areas and to test the validity of three previously recognized subspecies. Sequences (676 bp) from domains I and II of the mitochondrial control region were analyzed for 166 snowy plovers from 20 breeding areas. Variation was also examined at 10 microsatellite loci for 144 snowy plovers from 14 breeding areas. The mtDNA and microsatellite data provided strong evidence that the Puerto Rican breeding group is genetically divergent from sites in the continental U.S. (net sequence divergence = 0.38%; F _ST for microsatellites = 0.190). Our data also revealed high levels of differentiation between sites from South America and North America (net sequence divergence = 0.81%; F _ST for microsatellites = 0.253). In contrast, there was little genetic structure among breeding sites within the continental U.S. Our results suggest that snowy plovers in Florida should be considered part of C. a. nivosus (rather than part of C. a. tenuirostris, where they are currently placed), whereas snowy plovers from Puerto Rico should be considered part of C. a. tenuirostris. Snowy plovers in South America should remain a separate subspecies (C. a. occidentalis). Although U.S. Pacific and Gulf Coast breeding areas were not genetically distinct from other continental U.S. sites, demographic isolation, unique coastal habitats, and recent population declines suggest they warrant special concern.     

Use of aerial imagery to assess habitat suitability and predict site occupancy for a declining wetland-dependent bird

Remote sensing is a valuable tool for wetland habitat quantification, monitoring and assessment. Here we show that habitat assessment via aerial image inspection is useful in predicting wetland site occupancy by black terns (Chlidonias niger), an imperiled and declining species throughout much of North America. We used Google Earth^® images and National Wetlands Inventory maps to rank 390 candidate wetlands throughout Wisconsin (USA) according to their apparent suitability as nesting habitat for black terns and quantified habitat features associated with the suitability rankings. We then conducted ground-based suitability assessments and point counts of terns at most wetlands from May to July 2010. Pre-survey assessment resulted in 123 wetlands classified as suitable, 81 as marginal, and 186 as unsuitable. Wetlands ranked as suitable were more likely to be in the hemi-marsh stage, part of a wetland complex and relatively undisturbed. Black terns were present at 47 % of the wetlands considered suitable but only 11 % of the sites considered marginal or unsuitable. Of the 42 sites where nesting was confirmed, 79 % were at wetlands classified as suitable; no nesting was recorded in any wetlands deemed unsuitable. We found strong concordance in wetland suitability rankings between the two assessment methods (remote sensing, site surveys). We propose that remote sensing is an efficient and inexpensive way to predict site occupancy by wetland birds, such as black terns, that prefer a specific kind of habitat discernible from aerial imagery. This method may be particularly useful in areas, such as the Prairie Pothole region of North America, where ground surveys of all wetlands are not feasible.     

Population structure of North Atlantic and North Pacific sei whales (<Emphasis Type="Italic">Balaenoptera borealis</Emphasis>) inferred from mitochondrial control region DNA sequences and microsatellite genotypes

Currently, three stocks of sei whales (Balaenoptera borealis) are defined in the North Atlantic; the Nova Scotian, Iceland-Denmark Strait and Eastern North Atlantic stocks, which are mainly based upon historical catch and sighting data. We analyzed mitochondrial control region DNA (mtDNA) sequences and genotypes from 7 to 11 microsatellite loci in 87 samples from three sites in the North Atlantic; Iceland, the Gulf of Maine and the Azores, and compared against the North Pacific using 489 previously published samples. No statistically significant deviations from homogeneity were detected among the North Atlantic samples at mtDNA or microsatellite loci. The genealogy estimated from the mtDNA sequences revealed a clear division of the haplotypes into a North Atlantic and a North Pacific clade, with the exception of one haplotype detected in a single sample from the Azores, which was included in the North Pacific clade. Significant genetic divergence between the North Atlantic and North Pacific Oceans was detected (mtDNA Φ_ST?=?0.72, microsatellite Weir and Cockerham’s ? = 0.20; p?<?0.001). The coalescent-based estimate of the population divergence time between the North Atlantic and North Pacific populations from the sequence variation among the mtDNA sequences was at 163,000 years ago. However, the inference was limited by an absence of samples from the Southern Hemisphere and uncertainty regarding mutation rates and generation times. The estimates of inter-oceanic migration rates were low (Nm at 0.007 into the North Pacific and at 0.248 in the opposite direction). Although estimates of genetic divergence among the current North Atlantic stocks were low and consistent with the extensive range of movement observed in satellite tagged sei whales, the high uncertainty of the genetic divergence estimates precludes rejection of multiple stocks in the North Atlantic.     

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.     

Genetic structure of the Korean black scraper Thamnaconus modestus inferred from microsatellite marker analysis

The Korean black scraper, Thamnaconus modestus, is one of the most economically important maricultural fish species in Korea. However, the annual catch of this fish has been continuously declining over the past several decades. In this study, the genetic diversity and relationships among four wild populations and two hatchery stocks of Korean black scraper were assessed based on 16 microsatellite (MS) markers. A total of 319 different alleles were detected over all loci with an average of 19.94 alleles per locus. The hatchery stocks [mean number of alleles (N _A) = 12, allelic richness (A _R) = 12, expected heterozygosity (He) = 0.834] showed a slight reduction (P > 0.05) in genetic variability in comparison with wild populations (mean N _A = 13.86, A _R = 12.35, He = 0.844), suggesting a sufficient level of genetic variation in the hatchery populations. Similarly low levels of inbreeding and significant Hardy–Weinberg equilibrium deviations were detected in both wild and hatchery populations. The genetic subdivision among all six populations was low but significant (overall F _ST = 0.008, P < 0.01). Pairwise F _ST, a phylogenetic tree, and multidimensional scaling analysis suggested the existence of three geographically structured populations based on different sea basin origins, although the isolation-by-distance model was rejected. This result was corroborated by an analysis of molecular variance. This genetic differentiation may result from the co-effects of various factors, such as historical dispersal, local environment and ocean currents. These three geographical groups can be considered as independent management units. Our results show that MS markers may be suitable not only for the genetic monitoring of hatchery stocks but also for revealing the population structure of Korean black scraper populations. These results will provide critical information for breeding programs, the management of cultured stocks and the conservation of this species.     

Does the Platanthera dilatata (Orchidaceae) complex contain cryptic species or continuously variable populations?

Floral phenotypic traits are expected to reflect evolutionary changes and are used as a reliable basis for species delimitation. However, when traits overlap among populations of newly emerging species, this confounds identification of evolutionarily distinct lineages and reduces taxonomic stability. In this study, we quantified variation in ten floral traits and plastid DNA sequences across 26 populations of Platanthera dilatata (Orchidaceae) in North America to determine geographic structure among populations and to evaluate support for three varieties recognized in the current taxonomy. k-means clustering analysis, in the absence of a priori designation of groups, indicated two morphologically distinct groups. Spur length was the most distinctive character between groups. The group containing larger flowers with longer spurs corresponds to the var. leucostachys and most samples in this group are from western North America. The vars. albiflora and dilatata could not be distinguished within the second group, which exhibited flowers with short to intermediate spurs and include samples from eastern and western North America. Morphological variation in P. dilatata may reflect pollinator-mediated selection, particularly in spur length, which is known to vary in association with pollinators across Platanthera. Significant genetic divergence was observed between the two groups (F _ST = 0.15; P ≤ 0.001), but we did not find corresponding phylogenetic structure, which may reflect recent divergence and retention of ancestral polymorphisms. Based on these results, we suggest preserving the current intraspecific taxonomy until further studies determine the origin of floral variation and the extent of gene flow between morphologically divergent populations.     

Genetic diversity and structure of an endemic and critically endangered stream river salamander (Caudata: Ambystoma leorae) in Mexico

Small or isolated populations are highly susceptible to stochastic events. They are prone and vulnerable to random demographic or environmental fluctuations that could lead to extinction due to the loss of alleles through genetic drift and increased inbreeding. We studied Ambystoma leorae an endemic and critically threatened species. We analyzed the genetic diversity and structure, effective population size, presence of bottlenecks and inbreeding coefficient of 96 individuals based on nine microsatellite loci. We found high levels of genetic diversity expressed as heterozygosity (H_o = 0.804, H_e = 0.613, H_e* = 0.626 and H_Nei = 0.622). The population presents few alleles (4–9 per locus) and genotypes (3–14 per locus) compared with other mole salamanders species. We identified three genetically differentiated subpopulations with a significant level of genetic structure (F_ST = 0.021, R_ST = 0.044 y D_est = 0.010, 95 % CI). We also detected a reduction signal in population size and evidence of a genetic bottleneck (M = 0.367). The effective population size is small (Ne = 45.2), but similar to another mole salamanders with restricted distributions or with recently fragmented habitat. The inbreeding coefficient levels detected are low (F_IS = ?0.619–0.102) as is gene flow. Despite, high levels of genetic diversity A. leorae is critically endangered because it is a small isolated population.     

Genetic differentiation between clone collections and natural populations of European black poplar (<Emphasis Type="Italic">Populus nigra</Emphasis> L.) in turkey

The European black poplar (Populus nigra L.) is an ecologically and economically important tree species for Turkey. The important and major genetic resources of species for future breeding and ex situ conservation purposes have been archived in a clone bank in Ankara by selecting clones from natural populations and old plantations throughout Turkey. There is no study to date assessing genetic composition these materials. Two-hundred-thirty-three P. nigra clones from six geographic region of Turkey (clone collection populations), and 32 trees from two natural populations (Tunceli and Melet) were genotyped by using 12 nuclear microsatellite DNA markers. There were nine clones which duplicated in various frequencies. The analysis carried out with removal of the duplicated clones revealed a moderately high genetic diversity in studied populations. The observed heterozygosities ranged from 0.59 in Tunceli natural to 0.69 in Central Anatolia clone collection populations. In general, there was excess of heterozygosity in the studied populations. Populations composed of clone collections were significantly differentiated from natural populations (F _ST = 0.17), while there was little differentiation among those populations in the clone collection (F _ST = 0.03). Two distantly located natural populations with small sizes also differed from each other (F _ST = 0.17). Genetic structure analysis revealed two distinct groups (clone collection vs natural populations) with very high membership values (>92%). Clone collection populations had high level of admixture while natural populations had homogenous genetic structure. The presence of large number of clonal duplication, reduced genetic differentiation, and high level of admixture in clone collection populations indicate that genetic resources of European black poplar were highly degraded through genetic erosion and pollution caused by intensive cultural practices and extensive dispersal of clonal materials. To understand genetic diversity and its structural pattern thoroughly in the six clone collection populations, a further study with extensive and systematic sampling of European black poplar populations in major river ecosystems in Turkey will be useful.