Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific

Due to the lack of visible barriers to gene flow, it was a long-standing assumption that marine coastal species are widely distributed, until molecular studies revealed geographically structured intraspecific genetic differentiation in many taxa. Historical events of sea level changes during glacial periods are known to have triggered sequential disjunctions and genetic divergences among populations, especially of coastal organisms. The Parasesarma bidens species complex so far includes three named plus potentially cryptic species of estuarine brachyuran crabs, distributed along East to Southeast Asia. The aim of the present study is to address phylogeography and uncover real and hidden biological diversity within this complex, by revealing the underlying genetic structure of populations and species throughout their distribution ranges from Japan to West Papua, with a comparison of mitochondrial COX1 and 16S rRNA gene sequences. Our results reveal that the P. bidens species complex consists of at least five distinct clades, resulting from four main cladogenesis events during the mid to late Pleistocene. Among those clades, P. cricotum and P. sanguimanus are recovered as monophyletic taxa. Geographically restricted endemic clades are encountered in southeastern Indonesia, Japan and China respectively, whereas the Philippines and Taiwan share two clades. As individuals of the Japanese clade can also be found in Taiwan, we provide evidence of a third lineage and the occurrence of a potential cryptic species on this island. Ocean level retreats during Pleistocene ice ages and present oceanic currents appear to be the main triggers for the divergences of the five clades that are here addressed as the P. bidens complex. Secondary range expansions converted Taiwan into the point of maximal overlap, sharing populations with Japan and the Philippines, but not with mainland China.

Detection of Cryptic Sex in Automictic Populations: Theoretical Expectations and a Case Study in Cataglyphis Desert Ants

Reproductive strategies are diverse and a whole continuum of mixed systems lies between strict sexuality and strict clonality (apomixis), including automixis, a parthenogenetic mode of reproduction involving a meiosis and increasing homozygosity over generations. These various systems impact the genetic structure of populations, which can therefore be used to infer reproductive strategies in natural populations. Here, we first develop a mathematical model, validated by simulations, to predict heterozygosity and inbreeding in mixed sexual-automictic populations. It highlights the predominant role of the rate of heterozygosity loss experienced during automixis (γ), which is locus dependent. When γ is low, mixed populations behave like purely sexual ones until sex becomes rare. In contrast, when γ is high, the erosion of genetic diversity is tightly correlated to the rate of sex, so that the individual inbreeding coefficient can inform on the ratio of sexual/asexual reproduction. In the second part of this study, we used our model to test the presence of cryptic sex in a hybridogenetic Cataglyphis ant where new queens are produced parthenogenetically, leaving males with an apparent null fitness while they are essential to colony development as sperm is required to produce workers. Occasional sexual production of queens could resolve this paradox by providing males some fertile progeny. To determine whether this occurs in natural populations, we simulated genotypic datasets in a population under various regimes of sexual vs. asexual reproduction for queen production and compared the distribution of inbreeding, expected heterozygosity and inter-individual relatedness coefficients with those observed in a natural population of Cataglyphis mauritanica using microsatellites. Our simulations show that the distribution of inter-individual relatedness coefficients was particularly informative to assess the relative rate of sexual/asexual reproduction, and our dataset was compatible with pure parthenogenesis but also with up to 2% sexual reproduction. Our approach, implemented in an R script, should be useful to assess reproductive strategies in other biological models.

Genetic Variability and the Potential Range of Darevskia rostombekowi in Transcaucasia

Abstract— The results of the analysis of the genetic variability of parthenogenetic Darevskia rostombekowi (Darevsky, 1957) species using four microsatellite-containing loci are presented. Based on 118 records with geographical coordinates of the presence of this species in Transcaucasia, the maps of potential range were created. The analysis of the genetic structure of populations demonstrated that despite the established multiclonality (seven clonal lines in four populations), D. rostombekowi was formed as a result of a single act of hybridization between closely related bisexual species. The predicted distribution of D. rostombekowi using the modelling of potential range revealed new suitable habitats, where the presence of the species has not been reported previously. The results of this study and the absence of multiple acts of hybridization during the formation of these clones may indicate a regression of population size of the species. Consequently, the estimation of the conservation status of this parthenogenetic species seems to be justified.

Deforestation is the turning point for the spreading of a weedy epiphyte: an IBM approach

The rapid spread of many weeds into intensely disturbed landscapes is boosted by clonal growth and self-fertilization strategies, which conversely increases the genetic structure of populations. Here, we use empirical and modeling approaches to evaluate the spreading dynamics of Tillandsia recurvata (L.) L. populations, a common epiphytic weed with self-reproduction and clonal growth widespread in dry forests and deforested landscapes in the American continent. We introduce the TRec model, an individual-based approach to simulate the spreading of T. recurvata over time and across landscapes subjected to abrupt changes in tree density with the parameters adjusted according to the empirical genetic data based on microsatellites genotypes. Simulations with this model showed that the strong spatial genetic structure observed from empirical data in T. recurvata can be explained by a rapid increase in abundance and gene flow followed by stabilization after ca. 25 years. TRec model’s results also indicate that deforestation is a turning point for the rapid increase in both individual abundance and gene flow among T. recurvata subpopulations occurring in formerly dense forests. Active reforestation can, in turn, reverse such a scenario, although with a milder intensity. The genetic-based study suggests that anthropogenic changes in landscapes may strongly affect the population dynamics of species with ‘weedy’ traits.

Genetic structure of the water frog (Pelophylax esculentus complex) populations in the south of the Central Russian Upland

BACKGROUND: The water frog (Pelophylax esculentus complex) is hybrid in composition. In view of the fact that a large number of data on the species composition of the water frog and very scarce material on the genetic structure of populations are available in the literature, we aimed to analyze the genetic structure of populations of the water frog in the southern part of the Middle Russian upland, which was one of the refugia for many species during the glacial epoch and the center of dispersion in the postglacial time, based on DNA microsatellite markers. MATERIALS AND METHODS: The study involved 36 local populations. DNA variability was analyzed by multiplex SSR-PCR. Seven loci (Res 14, Res 15, Res 17, Res 22, Rrid059A, Rrid082A, and Rrid171A) were used for amplification. Fragment analysis of PCR products was performed on an ABI PRISM 3500 automated capillary DNA sequencer (Applied Biosystems, USA). RESULTS: The total number of alleles detected ranged from 13 to 41. The effective number of alleles (Ae) averaged 4.569 0.219, the Chenon index (I) 1.567 0.04, level of expected heterozygosity (Не) 0.68 0.01. According to Wrights model, the greatest contribution to genetic variability is made by the heterogeneity of individuals within populations, some of which are of a hybrid nature (Fis = 0.281 0.069, Fit = 0.413 0.053, Fst = 0.180 0.017). The average indicator of the intensity of gene exchange between populations (Nm) was 1.212 0.142 individuals per generation. The calculation of the effective abundance using the LD method indicates a high level of viability of the studied groups of the frogs. CONCLUSION: The results demonstrated a high level of genetic diversity and viability of most of the studied groups, which, due to the intense gene exchange between them, can represent a single panmictic population. The data of the genetic analysis support the active adaptation of P. esculentus complex to living in an urbanized environment.

Genetic identification of populations of Bactrocera dorsalis (Diptera Tephritidae) in the Niayes and Lower Casamance areas in Senegal

Objectives: the study examines the effect of the host plant and of the agro-ecological area on the genetic structure of populations of Bactrocera dorsalis in order to apprehend an appropriate period to fight this pest. Methodology and results: this study was conducted in two large areas mango productions Senegal (area Niayes and the forest area South) on 41 individuals of Bactrocera dorsalis with mitochondrial gene sequencing (cytochrome B). Several haplotypes (28) of which 27 individual have been identified with a high level of genetic diversity (Hd 0.972 and Pi 0.1563). The genetic demo tests suggested a population in equilibrium, a moderate expansion and a grouping according to the areas thus revealing a genetic structure linked to the localities. In addition, the haplotype network showed a majority haplotype comprising all areas, 24 individual haplotypes and a typical haplotype to Notto. Conclusion and application of findings : this exploratory study was in addition to having provided information on the genetic characterization of the species Bactrocera dorsalis , describes its structure and its genetic differentiation based on two areas - ecological where mango is practically cultivated in Senegal . It helped to understand the genetic identity card of the species Bactrocera dorsalis, whose purpose will be to know its weakest link and food preferences to provide alternative struggles. Keywords: Bactrocera dorsalis, Niayes, lower Casamance, mangoes, citrus, PCR, sequencing, cytochrome B

Surname regions and dialectal variation in the Asturian linguistic space

Studies on the correlations between spatial distribution of linguistic varieties and genetic structure of populations began by dealing with geographic spaces and extensive linguistic families. In the last two decades, researchers with this type of interdisciplinary approach have also begun to study more reduced linguistic and population domains. This paper examines geolinguistic and onomastic information in a linguistic and administrative space of a limited extension of the Principality of Asturias. The information on the surnames of this region, taken from the inhabitants’ register, is used to identify surname regions and check correlations with dialect areas described in this space. The results obtained in this research show many similarities in the distribution of surname regions with dialect areas recognized by traditional dialectology studies. The conclusions of the study present the results obtained together with some of the explanatory proposals on the historical constitution of the linguistic diversity of this area.

Detecting DNA polymorphism and genetic diversity in a wide pistachio germplasm by RAPD markers

Assessing the genetic diversity in the population is the prerequisite to start and develop plant breeding projects. Pistacia vera is considered as a commercial species of Pistacia genus. In Iran, Pistachio export is in the second place in terms of non-oil exports and in the first place among horticultural crops. Therefore, we collected and analyzed 11 pistachio genotype (Pistacia vera), from two provinces of Iran regions. Our aims were 1) to assess genetic diversity among some of Irainian pistachio cultivars 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Akbari cultivars depicted unbiased expected heterozygosity (UHe) in the range of 0.028. Shannon information was high (0.49) in Seifadini cultivars. Akbari cultivars howed the lowest value, 0.029. The observed number of alleles (Na) ranged from 0.261 to 2.700 in Shahpasand cultivars and Kalehghoochi cultivars. The effective number of alleles (Ne) was in the range of 1.021-1.800 for Akbari cultivars and Moosaabadi cultivars .Gene flow (Nm) was relatively low (0.38) in pistachio cultivars. The Mantel test showed correlation (r = 0.33, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the among some of Irainian pistachio cultivars can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in pistachio cultivars.

Molecular identification and genetic diversity in Hypericum L.: A high value medicinal plant using RAPD markers markers

Genus Hypericum (Guttiferae, Hypericoideae) is perennial, belonging to the Hypericaceae family, having 484 species in forms of trees, shrubs, and herbs, distributed in 36 taxonomic sections. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Hypericum genetic diversity. Therefore, we collected and analyzed six species from five provinces of Iran regions. Overall, seventy plant specimens were collected. Our aims were 1) to assess genetic diversity among Hypericum species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. H. dogonbadanicum depicted unbiased expected heterozygosity (UHe) in the range of 0.10. Shannon information was high (0.32) in H. perforaturm. H. dogonbadanicum showed the lowest value, 0.17. The observed number of alleles (Na) ranged from 0.22 to 0.53 in H. dogonbadanicum and H. elongaturn. Gene flow (Nm) was relatively low (0.87) in Hypericum. The Mantel test showed correlation (r = 0.45, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Hypericum species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Hypericum species.