Environmental variables,habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the F _ST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species.     

Population Genetic Structuring in Opisthorchis viverrini over Various Spatial Scales in Thailand and Lao PDR

Khon Kaen Province in northeast Thailand is known as a hot spot for opisthorchiasis in Southeast Asia. Preliminary allozyme and mitochondrial DNA haplotype data from within one endemic district in this Province (Ban Phai), indicated substantial genetic variability within Opisthorchis viverrini. Here, we used microsatellite DNA analyses to examine the genetic diversity and population structure of O. viverrini from four geographically close localities in Khon Kaen Province. Genotyping based on 12 microsatellite loci yielded a mean number of alleles per locus that ranged from 2.83 to 3.7 with an expected heterozygosity in Hardy–Weinberg equilibrium of 0.44–0.56. Assessment of population structure by pairwise F_ST analysis showed inter-population differentiation (P<0.05) which indicates population substructuring between these localities. Unique alleles were found in three of four localities with the highest number observed per locality being three. Our results highlight the existence of genetic diversity and population substructuring in O. viverrini over a small spatial scale which is similar to that found at a larger scale. This provides the basis for the investigation of the role of parasite genetic diversity and differentiation in transmission dynamics and control of O. viverrini.     

High genetic structure of the Cozumel Harvest mice,a critically endangered island endemic: conservation implications

We assessed the genetic structure and diversity of Reithrodontomys spectabilis, a critically endangered, endemic rodent from Cozumel Island, México. A total of 90 individuals were trapped from September 2001 to January 2005. Microsatellite data analysis revealed high genetic diversity values: a total of 113 alleles (average 12.5 per locus), H _o  = 0.78, H _e  = 0.80. These high values can be related to Cozumel’s size (478 km²) and extensive native vegetation cover, factors that could be promoting a suitable population size, high heterozygosity and the persistence of rare alleles in the species, as well as some long-term movement of individuals between sampling localities. A strong genetic structure was also observed, with at least four genetic groups, associated with a pattern of isolation by distance. We found a strong allelic and genetic differentiation shown between localities, with negligible recent gene flow and low inbreeding coefficients. The species life history and ecological characteristics—being nocturnal, semi-terrestrial, a good tree climber, having lunar phobia and significant edge effect—are likely affecting its genetic structure and differentiation. The high genetic diversity and population structure award R. spectabilis a significant conservation value. Our results can serve as a basis for future research and conservation of the species, particularly considering the problems the island is facing from habitat perturbation, urbanization and introduction of exotic species. In view of the structure and genetic variability observed, it is essential to establish and reinforce protected areas and management programs for the conservation of the endemic and endangered Cozumel Harvest mice.     

AFLP markers suggest low population genetic differentiation of the black rockfish Sebastes schlegelii

AFLP markers were used to investigate the population genetic differentiation among populations of Sebastes schlegelii from China and Japan. A total of 405 bands were amplified for 180 individuals from 9 populations by 3 pairs of selective primers. S. schlegelii exhibited high Nei's gene diversity with an average value of 0.29 for all populations. No significant genealogical branches or clusters corresponding to sampling localities were detected by UPGMA tree. The results of AMOVA analysis and pairwise F_ST values showed no genetic divergence among different geographic populations. The result of STRUCTURE demonstrated all populations of S. schlegelii examined in the study shared one single gene pool.     

Genetic structure in an expanding cervid population after population reduction

The Norwegian red deer population (Cervus elaphus) was from the mid eighteenth to the early twentieth century drastically reduced in size and distribution but has the last century expanded both demographically and spatially. We have investigated genetic variation, differentiation and admixture in this spatially expanding ungulate population, using 14 microsatellites. The present genetic structure is moderate to strong with an average F _ST = 0.08. Low M-ratios indicate loss of genetic variation in all localities and signals of a recent bottleneck was identified in 14 of 15 localities. Genetic distances between the localities indicate two main routes of dispersal during expansion, from the north–west and south–west, respectively. Bayesian assignment tests verify a break of the dataset in two, and demonstrate 99.9% probability for the existence of five sub-populations, which coincide well with five relict populations described by historic records. Computer simulations suggest that the observed genetic differentiation is recent rather than ancient, and that it may be explained by models of fragmentation or of founder events and subsequent merging rather than by models of recent bottlenecks in some particular demes within an ancient genetic structure.     

Genetic diversity of the entomopathogenic fungus Cordyceps tenuipes in forests and butterfly gardens in Quindío,Colombia

Cordyceps tenuipes is an entomopathogenic fungus that infects mostly pupae of several lepidopteran families. In Colombia the species has been reported in non-disturbed tropical rain forests and more recently in butterfly gardens. The aim of this study was to assess the genetic diversity in populations of C. tenuipes present in natural (forests) and artificial (e.g. butterfly gardens) environments in the department of Quindío, Colombia, using three molecular nuclear markers ITS, TEF-1α and RPB1. All the samples evaluated corresponded morphologically and phylogenetically to C. tenuipes. The butterfly garden of Quindio Botanical Garden (QBG) showed the highest genetic diversity among all sampling localities and was very similar to that of its adjacent forest. The Amaranta Butterfly Garden (ABG), located north of QBG, showed lower genetic diversity as well as little genetic differentiation with QBG, consistent with the hypothesis of a pathogen transfer from QBG to ABG. Higher F_ST values were observed for TEF-1α and ITS, revealing genetic differentiation between all demes and the southern forest population. Our research constitutes the first study of the intraspecific diversity of C. tenuipes in Colombia and can serve as the first step in identifying diversity reservoirs and management of epizootic episodes caused by this fungal species.     

Population genetic diversity of mud crab (Scylla paramamosain) in Hainan Island of China based on mitochondrial DNA

In this paper, we analyzed population genetic diversity of Scylla paramamosain in Hainan Island of China based on COI gene sequence. Totally 92 individuals were collected from six localities: Haikou, Wenchang, Wanning, Sanya, Dongfang and Danzhou. A 761 bp fragment was sequenced, defining 32 different haplotypes. H4 was the most frequent haplotype, existing in all six localities, while the majority of haplotypes were rare ones, existing in only one or two individuals. Haplotype diversity (h) and nucleotide diversity (π) ranged from 0.625 to 0.914 and from 0.001 to 0.003, with an average of 0.841 and 0.002, respectively. Genetic distance ranged from 0.001 to 0.003 within localities and from 0.002 to 0.003 between localities. The AMOVA analysis indicated a low level of genetic differentiation among six localities (F_ST = 0.0176, P > 0.05). Neutrality tests and mismatch analysis implied a potential population expansion event for this crab species.     

Allozyme data reveal genetic diversity and isolation by distance in sympatric Glyphidrilus Horst, 1889 (Oligochaeta: Almidae) of the Lower Mekong River Basin

The genus Glyphidrilus, comprised of semi-aquatic freshwater earthworms that live in an ecotone between terrestrial and freshwater ecosystems, are widely distributed along riverbanks and rice paddy systems. Two Glyphidrilus species (Glyphidrilus vangviengensis and Glyphidrilus mekongensis) are endemic in the Lower Mekong River Basin and are sympatric from Northern Thailand to Southern Laos. However, species delimitation among the Mekong Glyphidrilus remains unclear because the key morphological traits in semi-aquatic earthworms are highly polymorphic. This study assessed the distinction between G. vangviengensis and G. mekongensis using allozyme electrophoresis. A total of 752 individuals collected from 33 localities were screened for 10 putative loci from seven enzymatic systems, revealing that G. vangviengensis and G. mekongensis are two distinct species, according to their different allelic patterns and high genetic distance. A low genetic differentiation within each species was indicated by the pairwise Nei's D and F_ST analyses, and the absence of population structure was detected by AMOVA and Bayesian structure analyses. However, a significant isolation by distance, but not vicariance, was observed, which is probably due to the river current causing translocation downstream and so gene flow between adjacent localities. The genetic diversity of the Mekong Glyphidrilus was relatively high and comparable to other earthworm taxa, and several localities showed deviation from Hardy–Weinberg equilibrium. An additional cryptic species from Ban Hat Khamphi, Loei, Thailand, was inferred.     

Genetic Population Structure of Macridiscus multifarius (Mollusca: Bivalvia) on the Basis of Mitochondrial Markers: Strong Population Structure in a Species with a Short Planktonic Larval Stage

The clam Macridiscus multifarius with a planktonic larval stage of about 10 days is an ecologically and economically important species in the coastal regions of China. In this study, 3 mt-DNA markers (COI, 12S rRNA, and ND1) were used to investigate the population structure and demography of wild M. multifarius populations in 3 coastal localities of the East China Sea (ZS and ZP populations) and Beibu Gulf in the South China Sea (BH population). Sequences of 685 bp in COI, 350 bp in 12S rRNA, and 496 bp in ND1 were determined. High level and significant F _ST values were obtained among the different localities on the basis of either COI (F _ST = 0.100–0.444, p < 0.05) or 12S rRNA (F _ST = 0.199–0.742, p < 0.05) gene, indicating a high degree of genetic differentiation among the populations. F _ST values were significant but weak for the ND1 gene because it is highly conservative. The median-joining network suggested an obvious genetic differentiation between ZS and BH populations, and the finding is consistent with the results of our demographic analyses using the unweighted pair group method with arithmetic mean. Our study unraveled the extant population genetic structure of M. multifarius and explained the strong population structure of a species with a short planktonic larval stage species; this information could be useful for fishery management measures, including artificial breeding and conservation.     

Genetic variability of anchovy in the Azov-Black Sea basin

The intraspecific structure of the European anchovy (Engraulis encrasicolus) was studied on the basis of mitochondrial cytochrome b gene (cytb) fragment variability in 84 individuals from seven localities of the Black Sea and the Sea of Azov. The data on haplotype and nucleotide diversity and the values of neutrality tests suggested expansive growth of anchovy populations in the Azov-Black Sea basin. All samples from anchovy populations demonstrated a high level of haplotype diversity (Hd = 0.962). Two dominant haplotypes were identified, the frequencies of which were not directional, and they were present in all localities. Sequence analysis of the mitochondrial cytb gene fragment showed no differentiation between the Sea of Azov and the Black Sea subspecies.     

A molecular approach to understand the riddle of the invasive success of the tarantula,Brachypelma vagans,on Cozumel Island,Mexico

Invasive populations typically demonstrate genetic isolation which results in a loss of genetic diversity and a reduction in invasion success. This study focused on the genetic population of a successful invasive species of tarantula. Individuals were sampled in two mainland localities of the Yucatan Peninsula (Zoh-Laguna and Raudales), in addition to two island localities (El Cedral and Rancho Guadalupe on Cozumel Island). All populations present high genetic diversity (mean: H_e = 0.23, P = 99%), with significant differences between the Raudales and Rancho Guadalupe localities. The AMOVA analysis revealed a significant population structure (14.5% variation among populations), consistent with the gene differentiation coefficient (G_ST = 0.21), and spatial analysis of population structure. Our results suggested that the original introduced population did not suffer a loss of genetic diversity during establishment on the island, possibly a result of different biological conditions. Population structure analysis leads us to suggest that one island population is similar to the original genetic profile, whereas the genotypic profile of the other island population reflects recent introductions from the mainland. We identified a potential risk of extinction for one local mainland population, suggesting that this species may be a successful invader in a new environment but endangered in some parts of its natural area.     

Genetic variation in Aechmea winkleri,a bromeliad from an inland Atlantic rainforest fragment in Southern Brazil

We investigated the genetic diversity and structure of Aechmea winkleri Reitz, an endemic bromeliad found in Southern Brazilian Atlantic rainforest. Seven nuclear microsatellite markers were used to analyze 162 samples from four localities sampled throughout the entire geographic distribution of the species. Results indicate relatively high levels of genetic diversity with an average of allelic richness of 3.57, and observed and expected heterozygosity of 0.559 and 0.608, respectively. The within-inbreeding coefficient was low, ranging from −0.011 to 0.094. All localities significantly deviated from Hardy–Weinberg equilibrium with three of them showing heterozygosites deficiency. Most of the genetic variation (96.64%) was found within localities. No reduction in population size (bottleneck) was detected. Low levels of genetic differentiation among localities were found with pairwise F_ST comparisons varying from 0.021 to 0.075. Bayesian analyses revealed that A. winkleri is composed by two genetic groups. The number of migrants per generation was high (>1), which maintain localities' cohesion and gene flow. Despite genetic erosion was not detected in the present study, our results revealed that the four localities sampled actually represent one population, the only known so far in nature. Management strategies for A. winkleri conservation should be undertaken as it is an endemic species which occurs in a biome that has gone through major deforestation and fragmentation. This would avoid the increase of inbreeding rates and the loss of genetic diversity.     

Dams and canyons disrupt gene flow among populations of a threatened riparian plant

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Genetic diversity of sharpnose mullet <Emphasis Type="Italic">Liza saliens</Emphasis> introduced in southern Caspian Sea in comparison with one native Aegean Sea population

Sharpnose mullet, Liza saliens (Risso, 1810) is one of the valuable species in Caspian shoreline and it was first introduced to Caspian Sea from Black Sea between 1930 and 1934. In the present study, we used six microsatellite markers to obtain genetic information for L. saliens from four localities of southern Caspian Sea and for one native population from Greece coastline (northern Aegean Sea). Results showed lower number of alleles (Na = 5.7–6) and higher observed heterozygosity (Ho = 0.74–0.83) in Caspian Sea samples, related to the native Aegean population (Na = 8, Ho = 0.68). Significant deviations from Hardy-Weinberg expectations were detected in 19 out of 28 tests. Low genetic differentiation (provided Fst values) among samples was detected, but Behshahr sample was significantly differentiated from all the others. The UPGMA tree revealed three major clusters: the Behshahr sample and Greek population were clustered in two different clades, and the remaining three samples formed another cluster. The low genetic variation and spatial differentiation among Caspian Sea samples may be justified by the recent establishment.     

Genetic relationships between Atlantic and Pacific populations of the notothenioid fish Eleginops maclovinus: the footprints of Quaternary glaciations in Patagonia

The genetic relationships between the Pacific and the Atlantic populations of marine coastal biota in Southern South America have been analyzed in few studies, most of them relying on a single mitochondrial locus. We analyzed 10 polymorphic microsatellite loci, isolated from a dinucleotide-enriched Eleginops maclovinus genomic library, in a total of 240 individuals (48 from each of 5 sampled sites: 2 Atlantic, 2 Pacific and 1 in Beagle Channel). The results were contrasted against a previous work on the same species with mitochondrial DNA (mtDNA). Observed heterozygosity within localities ranged from 0.85 to 0.88 with the highest overall number of alleles observed at the northernmost locality on the Pacific side (Concepción), but no clear geographic pattern arose from the data. On the other hand, the number of private alleles was negatively correlated with latitude (Spearman''s r_s test, P=0.017). Among-population variance was low but significant (1.35% P<0.0001, analysis of molecular variance (AMOVA)) and low genetic differentiation between populations was observed (pairwise F_ST values ranged from 0 to 0.021). A Mantel test revealed a significant correlation between geographic distances and F_ST (r=0.56, P=0.047). This could be partially accounted by the Atlantic versus Pacific population differentiation detected in three different analyses (STRUCTURE, SAMOVA (Spatial Analysis of MOlecular VAriance) and a population phylogeny). The observed pattern is compatible with a history of separation into two glacial refugia that was better captured by the multilocus microsatellite data than by the mtDNA analysis.     

Genetic diversity,population structure and phenotypic variation in European Salix viminalis L. (Salicaceae)

To investigate the potential of association genetics for willow breeding, Salix viminalis germplasm was assembled from UK and Swedish collections (comprising accessions from several European countries) and new samples collected from nature. A subset of the germplasm was planted at two sites (UK and Sweden), genotyped using 38 SSR markers and assessed for phenological and biomass traits. Population structure, genetic differentiation (F _ST ) and quantitative trait differentiation (Q _ST ) were investigated. The extent and patterns of trait adaptation were assessed by comparing F _ST ?and Q _ST parameters. Of the 505 genotyped diploid accessions, 27 % were not unique. Genetic diversity was high: 471 alleles was amplified; the mean number of alleles per locus was 13.46, mean observed heterozygosity was 0.55 and mean expected heterozygosity was 0.62. Bayesian clustering identified four subpopulations which generally corresponded to Western Russia, Western Europe, Eastern Europe and Sweden. All pairwise F _ST values were highly significant (p?F _ST ???=???0.12), and the smallest between the Swedish and Eastern European populations (F _ST ??=??0.04). The Swedish population also had the highest number of identical accessions, supporting the view that S. viminalis was introduced into this country and has been heavily influenced by humans. Q _ST values were high for growth cessation and leaf senescence, and to some extent stem diameter, but low for bud burst time and shoot number. Overall negative clines between longitudinal coordinates and leaf senescence, bud burst and stem diameter were also found.     

A comparison of variation between a MHC pseudogene and microsatellite loci of the little greenbul (<Emphasis Type="Italic">Andropadus virens</Emphasis>)

Background  

We investigated genetic variation of a major histcompatibility complex (MHC) pseudogene (Anvi -DAB1) in the little greenbul (Andropadus virens) from four localities in Cameroon and one in Ivory Coast, West Africa. Previous microsatellite and mitochondrial DNA analyses had revealed little or no genetic differentiation among Cameroon localities but significant differentiation between localities in Cameroon and Ivory Coast.     

Fine-grained spatial genetic structure in the bivalve Gemma gemma from Maine and Virginia (USA), as revealed by Inter-Simple Sequence Repeat markers

Gemma gemma is a small ovoviviparous bivalve distributed in shallow sand flats along the North American Atlantic and Gulf of Mexico coasts. Genetic variation in G. gemma was analysed by means of Inter-Simple Sequence Repeats (ISSRs) at the following levels: (i) between localities (Maine and Virginia), (ii) among 10-m-diameter patches within localities, and (iii) within patches. Thirty individuals/patch and three patches/locality were analysed. Individuals were genotyped for 67 ISSR polymorphic loci from five primers. The portion of the genetic variation found between localities (2%) was small compared to that found either among patches within localities (37%) or within patches (61%). ISSRs in G. gemma allowed the detection of significant differentiation at individual and patch levels. By contrast, a low degree of genetic variability was found between localities. The small-scale genetic heterogeneity does not follow a simple, consistent pattern. Our results contrast with the generally accepted rule that aplanic species are locally homogeneous and globally heterogeneous and teleplanic species are the inverse.     

Genetic diversity and population structure analysis of Qinghai-Tibetan plateau schizothoracine fish (Gymnocypris dobula) based on mtDNA D-loop sequences

Gymnocypris dobula is a commercially important fishery species and mostly distributed in the freshwater of Tibetan plateau. In this study, genetic diversity and intraspecific population differentiation were examined by using mitochondrial DNA D-loop sequences in 97 individuals sampled from three localities (Pali, Lasa and Yanghu) in the Tibetan plateau. Two hundred and fourteen polymorphic sites and 50 haplotypes were defined among the three localities. Genetic diversity analysis showed that the highest genetic diversity level was found in Pali population. Phylogenetic relationships analysis results indicated that closer phylogenetic relationships were found between the Yanghu and Lasa populations. Genetic population differentiation analysis indicated that the majority of variation (84.91%) was attributed to variations among populations and the largest differentiation was found between Pali and Lasa localities (F_st = 0.874, Nm = 0.036). Moreover, the historical demographic events were assessed by implementing the mismatch distribution analysis, Fajima's D test and Fu's Fs test. The results indicated that the Pali population had undergone a demographic expansion, possibly within the last 0.163 MYA (Million Years Ago). Our study firstly identified the population genetic structure of the G. dobula, which could be helpful for artificial breeding, fishery stock identification and resource conservation for this species.