Historic speciation and recent colonization of Eurasian monkey gobies (Neogobius fluviatilis and N. pallasi) revealed by DNA sequences,microsatellites, and morphology

Aim Hidden diversity within an invasive ‘species’ can mask both invasion pathways and confound management goals. We assessed taxonomic status and population structure of the monkey goby Neogobius fluviatilis across Eurasia, comparing genetic variation across its native and invasive ranges. Location Native populations were analysed within the Black and Caspian Sea basins, including major river drainages (Dnieper, Dniester, Danube, Don and Volga rivers), along with introduced locations within the upper Danube and Vistula river systems. Methods DNA sequences and 10 nuclear microsatellite loci were analysed to test genetic diversity and divergence patterns of native and introduced populations; phylogenetic analysis of mtDNA cytochrome b and nuclear RAG‐1 sequences assessed taxonomic status of Black and Caspian Sea lineages. Multivariate analysis of morphology was used to corroborate phylogenetic patterns. Population genetic structure within each basin was evaluated with mtDNA and microsatellite data using F_ST analogues and Bayesian assignment tests. Results Phylogenetic analysis of mitochondrial and nuclear sequences discerned a pronounced genetic break between monkey gobies in the Black and Caspian Seas, indicating a long‐term species‐level separation dating to c. 3 million years. This pronounced separation further was confirmed from morphological and population genetic divergence. Bayesian inference showed congruent patterns of population structure within the Black Sea basin. Introduced populations in the Danube and Vistula River basins traced to north‐west Black Sea origins, a genetic expansion pattern matching that of other introduced Ponto‐Caspian gobiids. Main conclusions Both genetic and morphological data strongly supported two species of monkey gobies that were formerly identified as subspecies: N. fluviatilis in the Black Sea basin, Don and Volga Rivers, and the Kumo‐Manych Depression, and Neogobius pallasi in the Caspian Sea and Volga River delta. Genetic origins of introduced N. fluviatilis populations indicated a common invasion pathway shared with other introduced Ponto‐Caspian fishes and invertebrates.     

Fish conservation in the land of steppe and sky: Evolutionarily significant units of threatened salmonid species in Mongolia mirror major river basins

Mongolia's salmonids are suffering extensive population declines; thus, more comprehensive fisheries management and conservation strategies are required. To assist with their development, a better understanding of the genetic structure and diversity of these threatened species would allow a more targeted approach for preserving genetic variation and ultimately improve long‐term species recoveries. It is hypothesized that the unfragmented river basins that have persisted across Mongolia provide unobstructed connectivity for resident salmonid species. Thus, genetic structure is expected to be primarily segregated between major river basins. We tested this hypothesis by investigating the population structure for three salmonid genera (Hucho, Brachymystax and Thymallus) using different genetic markers to identify evolutionarily significant units (ESUs) and priority rivers to focus conservation efforts. Fish were assigned to separate ESUs when the combined evidence of mitochondrial and nuclear data indicated genetic isolation. Hucho taimen exhibited a dichotomous population structure forming two ESUs, with five priority rivers. Within the Brachymystax genus, there were three B. lenokESUs and one B. tumensisESU, along with six priority rivers. While B. tumensiswas confirmed to display divergent mtDNA haplotypes, haplotype sharing between these two congeneric species was also identified. For T. baicalensis,only a single ESU was assigned, with five priority rivers identified plus Lake Hovsgol. Additionally, we confirmed that T. nigrescens from Lake Hovsgol is a synonym of T. baicalensis. Across all species, the most prominent pattern was strong differentiation among major river basins with low differentiation and weak patterns of isolation by distance within river basins, which corroborated our hypothesis of high within‐basin connectivity across Mongolia. This new genetic information provides authorities the opportunity to distribute resources for management between ESUs while assigning additional protection for the more genetically valuable salmonid rivers so that the greatest adaptive potential within each species can be preserved.     

Rangewide phylogeography and landscape genetics of the Western U.S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers

Genetic data are increasingly being used in conservation planning for declining species. We sampled both the ecological and distributional limits of the foothill yellow-legged frog, Rana boylii to characterize mitochondrial DNA (mtDNA) variation in this declining, riverine amphibian. We evaluated 1525 base pairs (bp) of cytochrome b and ND2 fragments for 77 individuals from 34 localities using phylogenetic and population genetic analyses. We constructed gene trees using maximum likelihood and Bayesian inference, and quantified genetic variance (using AMOVA and partial Mantel tests) within and among hydrologic regions and river basins. Several moderately supported, geographically-cohesive mtDNA clades were recovered for R. boylii. While genetic variation was low among populations in the largest, most inclusive clade, samples from localities at the edges of the geographic range demonstrated substantial genetic divergence from each other and from more central populations. Hydrologic regions and river basins, which represent likely dispersal corridors for R. boylii, accounted for significant levels of genetic variation. These results suggest that both rivers and larger hydrologic and geographic regions should be used in conservation planning for R. boylii.     

基于细胞色素b基因的中国岩羊不同地理种群遗传差异分析

为了揭示中国岩羊不同地理种群的遗传差异,探讨岩羊亚种分化的分子机制,采用中国岩羊不同地理种群的细胞色素b(Cyt b)基因的全序列,分析了碱基变异情况、遗传距离以及核苷酸序列差异。用最大似然法和贝叶斯法构建分子系统树并对获得的拓扑结构进行分析。结果发现,西藏亚种与四川亚种Cyt b基因平均序列差异为4.2%(±0.007),处于偶蹄目亚种的序列差异范围内,支持了目前对岩羊西藏亚种的分类地位。四川亚种内部各地理种群之间的遗传距离(0.033±0.0 111)与它们分别到西藏种群的遗传距离(0.042±0.007)差异不显著(t=1.824,P=0.084),说明四川亚种内部各地理种群间已经发生较显著的遗传分化。其中,四川、甘肃和青海种群亲缘关系较近,并与四川亚种内部的其它种群已产生了显著的遗传分化。因此认为四川亚种内部各地理种群的种下分化需要深入研究。     

Back from the Brink: The Holocene History of the Carpathian Barbel Barbus carpathicus

As a result of specific adaptations and habitat preferences strongly rheophilic fish species may show high levels of endemism. Many temperate rheophilic fish species were subjected to a series of range contractions during the Pleistocene, and then successfully expanded during the Holocene, colonising previously abandoned areas. The Carpathian barbel (Barbus carpathicus Kotlík, Tsigenopoulos, Ráb et Berrebi 2002) occurs in the montane streams in three basins of the main Central European rivers in the northern part of the Carpathian range. We used genetic variation within 3 mitochondrial and 9 microsatellite loci to determine a pattern of postglacial expansion in B. carpathicus. We found that overall genetic variation within the species is relatively low. Estimate of time to the most recent common ancestor (tMRCA) of mitochondrial sequences falls within the Holocene. The highest levels of genetic variation found in upper reaches of the Tisa river in the Danube basin suggest that glacial refugia were located in the south-eastern part of the species range. Our data suggest that the species crossed different watersheds at least six times as three genetically distinct groups (probably established in different expansion episodes) were found in northern part of the species range. Clines of genetic variation were observed in both the Danube and Vistula basins, which probably resulted from subsequent bottlenecks while colonizing successive habitats (south eastern populations) or due to the admixture of genetically diverse individuals to a previously uniform population (Vistula basin). Therefore, B. carpathicus underwent both demographic breakdowns and expansions during the Holocene, showing its distribution and demography are sensitive to environmental change. Our findings are important in the light of the current human-induced habitats alterations.     

Assessing Genetic Differentiation in Geographic Populations of Labeo calbasu Using Allozyme Markers

The population structure of Labeo calbasu from 11 rivers belonging to the Indus, Ganges, Bhima, Mahanadi, and Godavari basins was investigated using allozyme marker systems. Seven out of 20 allozyme loci (35%) were polymorphic (P < 0.99). Both probability and score tests indicated significant deviation of genotype proportions from Hardy–Weinberg expectations at two loci, XDH* (Mahanadi, Bhima, and Godavari) and G6PDH* (Mahanadi). A pairwise genetic homogeneity test and F _ST values indicated a low-to-moderate level (0.0515) of genetic structuring in the wild population of L. calbasu. AMOVA analysis also indicated moderate differentiation among the samples from different river basins. Analysis for genetic bottleneck was performed under the infinite allele model. The study revealed nine genetic stocks of L. calbasu from the natural population across Indian rivers. Evidence of genetic bottlenecks in some rivers was also revealed.     

Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation,Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L.)

Previous genetic studies of Atlantic swordfish (Xiphias gladius L.) revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs) within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise F _ST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish.     

Australian lungfish (Neoceratodus forsteri: Dipnoi) have low genetic variation at allozyme and mitochondrial DNA loci: a conservation alert?

Genetic variation at allozyme and mitochondrialDNA loci was investigated in the Australianlungfish, Neoceratodus forsteri Krefft1870. Tissue samples for genetic analysis weretaken non-lethally from 278 individualsrepresenting two spatially distinct endemicpopulations (Mary and Burnett rivers), as wellas one population thought to be derived from ananthropogenic translocation in the 1890's(Brisbane river). Two of 24 allozyme lociresolved from muscle tissue were polymorphic.Mitochondrial DNA nucleotide sequence diversityestimated across 2,235 base pairs in each of 40individuals ranged between 0.000423 and0.001470 per river. Low genetic variation atallozyme and mitochondrial loci could beattributed to population bottlenecks, possiblyinduced by Pleistocene aridity. Limited geneticdifferentiation was detected among rivers usingnuclear and mitochondrial markers suggestingthat admixture may have occurred between theendemic Mary and Burnett populations duringperiods of low sea level when the drainages mayhave converged before reaching the ocean.Genetic data was consistent with theexplanation that lungfish were introduced tothe Brisbane river from the Mary river. Furtherresearch using more variable genetic loci isneeded before the conservation status ofpopulations can be determined, particularly asanthropogenic demands on lungfish habitat areincreasing. In the interim we recommend amanagement strategy aimed at conservingexisting genetic variation within and betweenrivers.     

Molecular identification of evolutionarily significant units in the Amazon River dolphin Inia sp. (Cetacea: Iniidae)

The Amazon river dolphin, genus Inia, is endemic to the major river basins of northern South America. No previous studies have focused on the genetic structure of this genus. In this work, 96 DNA samples from specimens of this genus were collected in the Orinoco basin (four rivers), the Putumayo River, a tributary of the Colombian Amazon and the Mamoré, and the Tijamuchí and Ipurupuru rivers in theBolivian Amazon. These samples were used to amplify a fragment of 400 bp of the mitochondrial DNA (mtDNA) control region. In addition, 38 of these samples were also used to sequence 600 bp of the mitochondrial cytochrome b gene. The analysis of the population structure subdivision with an analysis of molecular variance (AMOVA) revealed important aspects about the genetic structure of Inia groups fromthese three geographically separate regions. By comparing the control region DNA and cytochrome b sequences, distinct types of nonshared haplotypes were observed. The net genetic divergence of control region sequences was 6.53% between the Orinoco and Bolivian rivers, 5.32% between the Putumayo and Bolivian rivers, and 2.50% between the Orinoco and Putumayo rivers. For the cytochrome b gene, these values were 2.48%, 2.98%, and 0.06%, respectively. The nucleotide sequences were analyzed phylogenetically using several genetic distance matrices and applying neighbor-joining, maximum likelihood, and maximum parsimony procedures. The results support the proposal to subdivide the Inia genus into at least two evolutionarily significant units: one confined to the Bolivian river basin and the other widely distributed across the Amazon and Orinoco basins.     

Evolutionary history of the alpha2,8-sialyltransferase (ST8Sia) gene family: Tandem duplications in early deuterostomes explain most of the diversity found in the vertebrate ST8Sia genes

Background

The Salangid icefish Neosalanx taihuensis (Salangidae) is an economically important fish, which is endemic to China, restricted to large freshwater systems (e.g. lakes, large rivers and estuaries) and typically exhibit low vagility. The continuous distribution ranges from the temperate region of the Huai and Yellow River basins to the subtropical region of the Pearl River basin. This wide ranging distribution makes the species an ideal model for the study of palaeoclimatic effects on population genetic structure and phylogeography. Here, we aim to analyze population genetic differentiation within and between river basins and demographic history in order to understand how this species responded to severe climatic oscillations, decline of the sea levels during the Pleistocene ice ages and tectonic activity.

Results

We obtained the complete mtDNA cytochrome b sequences (1141 bp) of 354 individuals from 13 populations in the Pearl River, the Yangze River and the Huai River basin. Thirty-six haplotypes were detected. Haplotype frequency distributions were strongly skewed, with most haplotypes (n = 24) represented only in single samples each and thus restricted to a single population. The most common haplotype (H36) was found in 49.15% of all individuals. Analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. Significant levels of genetic subdivision were detected among populations within basins rather than between the three basins. Demographic analysis revealed that the population size in the Pearl River basin has remained relatively constant whereas the populations in the Yangze River and the Huai River basins expanded about 221 and 190 kyr ago, respectively, with the majority of mutations occurring after the last glacial maximum (LGM).

Conclusion

The observed complex genetic pattern of N. taihuensis is coherent with a scenario of multiple unrelated founding events by long-distance colonization and dispersal combined with contiguous population expansion and locally restricted gene flow. We also found that this species was likely severely impacted by past glaciations. More favourable climate and the formation of large suitable habitations together facilitated population expansion after the late Quaternary (especially the LGM). We proposed that all populations should be managed and conserved separately, especially for habitat protection.     

Population genetics and conservation of the threatened southeastern beach mouse (Peromyscus polionotus niveiventris): subspecies and evolutionary units

We investigated genetic diversity within the southeastern beach mouse (SEBM-Peromyscus polionotus niveiventris) and also tested the hypothesis that the subspecies recognition of P.p. niveiventris, based on size and color differences, is congruent with this taxon representing a discrete evolutionary lineage. We used ten polymorphic microsatellite loci and mitochondrial cytochrome-b gene DNA sequences to investigate genetic diversity and population structure within the SEBM, and to determine the level of divergence between the SEBM and the nearest known inland subspecies of the oldfield mouse (Peromyscus polionotus rhoadsi). Moderate genetic distances were observed between the SEBM and the inland oldfield mouse based on microsatellite data, with F _ST values ranging from 0.11 to 0.22 between these taxa. Additionally, mitochondrial DNA haplotypes of the SEBM formed a distinct monophyletic group relative to haplotypes sampled from P. p. rhoadsi. Based on previous estimates of rates of mitochondrial DNA evolution in rodents, we inferred that Pleistocene sea-level fluctuations are likely responsible for the historical isolation of the SEBM lineage from mainland P. polionotus. Our data demonstrate the genetic distinctiveness of the SEBM, justifying the current subspecies designation for the SEBM and its continued protection under the United States Endangered Species Act. We classify the Cape Canaveral and Smyrna Dunes Park populations of SEBM as a single evolutionary significant unit. The two known extant allopatric populations of the SEBM showed some differentiation in microsatellite frequencies and were moderately reciprocally distinguishable based on assignment to distinct genetic clusters by a Bayesian admixture procedure. These results justify the classification of these two extant SEBM populations as distinct management units that should be independent targets of management and conservation attention.     

The genetic diversity of burbot (<Emphasis Type="Italic">Lota lota</Emphasis> L., 1758) of Western Siberia (the analysis of the mtDNA control region polymorphism)

The genetic variability of burbot (Lota lota L., 1758) inhabiting the Ob-Irtysh and Taz river basins in Western Siberia has been studied based on the polymorphism of the hypervariable fragment of mtDNA control region (407 bp). The analysis of 134 fish samples revealed 30 haplotypes, 23 of which were new. Among haplotypes, previously detected in Eurasia and North America, EB30 was the most frequently found in Western Siberia (45.5% frequency). The results of our study are in agreement with previous research pointing to the genetic differentiation of two burbot subspecies, L. l. lota and L. l. maculosa, and indicate that burbot inhabiting the Ob-Irtysh and Taz river basins belong to the Eurasian-Beringian clade (nominative subspecies L. l. lota). However, a high genetic diversity of burbot in Western Siberia, along with a relatively high differentiation of burbot groups within studied territory, points to a regional specificity of burbot population.     

Phylogeography and historical demography of Sicydium salvini in the eastern Pacific

Amphidromy, characterized by freshwater adult and marine larval stages, has been shown to be an important influence on the genetic structure of aquatic populations. Sicydium salvini is a widespread goby species (Teleostei: Gobiidae: Sicydiinae) in the eastern Pacific with a continuous distribution from Mexico to Panama. Here, we use mitochondrial data to infer population genetic and historical demography of this species. Sequences were collected for the mitochondrial gene cytochrome b for 162 specimens sampled across the range of S. salvini with a concentration on rivers in Costa Rica. No genetic structure was detected between regions or rivers in the AMOVA analysis; the phylogeny for this species showed no geographic affinities and very little resolution. Historical demographic analyses indicated a population expansion during the late Pleistocene. These results are consistent with a panmictic population with expansion influenced strongly by Pleistocene glacial cycles and geologic uplift.     

Extensive genetic divergence in the East Asian natricine snake,Rhabdophis tigrinus (Serpentes: Colubridae), with special reference to prominent geographical differentiation of the mitochondrial cytochrome b gene in Japanese populations

We investigated intraspecific phylogenetic relationships in the natricine snake, Rhabdophis tigrinus. A partial sequence of mitochondrial cytochrome b gene (990 bp) was sequenced for 220 individuals from 112 populations. The phylogeny indicated monophyly of the Japanese populations against the continental and Taiwanese populations, sister relationships of the Japanese and continental populations, and monophyly of the whole species. The results strongly suggested substantial genetic divergences among population assemblages from those three regions. We thus consider both lateralis from the continent, which is often synonymized to R. tigrinus, and formosanus from Taiwan, which is usually regarded as a subspecies of the latter, as distinct full species based on the evolutionary species concept. In the Japanese populations, haplotypes were classified to in two major clades (I and II) that were parapatric to each other. Clade I consisted of three distinct subclades (I‐A, I‐B, and I‐C), of which the former two were parapatric with each other, whereas the latter was sympatric with each of the former two subclades. The geographical haplotype structure exhibited by the Japanese populations is likely to have resulted from a series of allopatric differentiations with rapid range extensions of resultant lineages, leading to secondary contact or further admixture of mitochondrial haplotype clades and subclades. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 395–408.     

Population Structure and Dispersal Patterns within and between Atlantic and Mediterranean Populations of a Large-Range Pelagic Seabird

Dispersal is critically linked to the demographic and evolutionary trajectories of populations, but in most seabird species it may be difficult to estimate. Using molecular tools, we explored population structure and the spatial dispersal pattern of a highly pelagic but philopatric seabird, the Cory''s shearwater Calonectris diomedea. Microsatellite fragments were analysed from samples collected across almost the entire breeding range of the species. To help disentangle the taxonomic status of the two subspecies described, the Atlantic form C. d. borealis and the Mediterranean form C. d. diomedea, we analysed genetic divergence between subspecies and quantified both historical and recent migration rates between the Mediterranean and Atlantic basins. We also searched for evidence of isolation by distance (IBD) and addressed spatial patterns of gene flow. We found a low genetic structure in the Mediterranean basin. Conversely, strong genetic differentiation appeared in the Atlantic basin. Even if the species was mostly philopatric (97%), results suggest recent dispersal between basins, especially from the Atlantic to the Mediterranean (aprox. 10% of migrants/generation across the last two generations). Long-term gene flow analyses also suggested an historical exchange between basins (about 70 breeders/generation). Spatial analysis of genetic variation indicates that distance is not the main factor in shaping genetic structure in this species. Given our results we recommend gathering more data before concluded whether these taxa should be treated as two species or subspecies.     

Phylogeography and genetic structure of the endemic cyprinid fish Microphysogobio brevirostris in northern Taiwan

This study used the mitochondrial DNA cytochrome b and control region sequences to examine the population genetic structure of Microphysogobio brevirostris, an endemic cyprinid species in northern Taiwan. In total, 90 specimens were collected from six populations belonging to four major rivers. All haplotypes were identified as two major clades (Clades N and S), exhibiting a southern and a northern distribution. The results of statistical dispersal-vicariance analysis (S-DIVA) revealed that two vicariance events and one dispersal event shaped the phylogeographic pattern of M. brevirostris. These results suggest that the ancestral populations of M. brevirostris are widely distributed throughout northern Taiwan, north of the Miaoli Plateau. The ancestral populations then diverged into two clades (N and S) by the raising of the Taoyuan Plateau. Finally, two major rivers of the S clade diverged and dispersed into adjacent rivers. Besides, our results revealed that Microphysogobio alticorpus and M. brevirostris colonized Taiwan during the same ice age through different colonization routes.     

Differences Between two Subspecies of Dolly Varden, Salvelinus malma, Revealed by RFLP—PCR Analysis of Mitochondrial DNA

Genetic differences between two subspecies of Dolly Varden, northern Salvelinus malma malma and southern Salvelinus malma krascheninnikovi, from rivers of eastern Russia were studied. Mitochondrial DNA was analyzed by restriction fragment length polymorphisms (RFLP) performed on products amplified with polymerase chain reaction. Three adjacent segments (approximately 7670 bp), comprising 47% of the mitochondrial genome were used: two encoding the five complete NADH dehydrogenase subunits and the other the cytochrome b gene and the control region (D-loop). Total composite haplotypes 46 were found among 136 fishes using RFLP analysis with 14 restriction enzymes. The amount of nucleotide divergence between haplotypes of two subspecies of Dolly Varden was estimated to be approximately 4%. The differences in the level of nucleotide diversity, mismatch distribution between haplotypes, and population-genetic structure of two subspecies of Dolly Varden suggest that these two forms have existed separately for a long time.     

Low genetic diversity and limited gene flow in a dominant mangrove tree species (Rhizophora stylosa) at its northern biogeographical limit across the chain of three Sakishima islands of the Japanese archipelago as revealed by chloroplast and nuclear SSR analysis

We examined the genetic diversity, population structure and gene flow in a dominant mangrove tree (Rhizophora stylosa) at its northern biogeographical limit in Sakishima islands of the Japanese archipelago. Simple sequence repeat (SSR) markers from chloroplast (cpSSR) and nuclear DNA were used to analyze 16 populations recovered from various river basins across the chain of three Sakishima islands—Iriomote, Ishigaki and Miyako. The average number of alleles (1.7–2.7) and observed heterozygosities (0.031–0.216) at nuclear SSR and haploid diversity (0.000–0.489) at cpSSR across the populations suggested low genetic diversity in R. stylosa in Sakishima islands. cpSSR analysis identified two haplotypes, and Bayesian clustering analysis (nuclear SSR) revealed two genetic clusters. Analysis of molecular variance (nuclear SSR) showed significant population differentiations. Pairwise tests consistently revealed significant differentiation between most of the population pairs; however, the degrees of differentiations are generally correspondent to the relative geographical distances as suggested from pairwise F _ST and cpSSR genetic distances. Moreover, Mantel tests showed some signals of correlations between genetic distances (nuclear and chloroplast) and geographical distances. These results suggest that combined contribution of gene flow via pollen and propagule dispersal in R. stylosa mostly occurred between neighboring river basins. The appearances of two cpSSR haplotypes (maternal lineages) as well as two nuclear genetic clusters (putative ancestral lineages) at various river basins support the hypothesis that present-day R. stylosa populations across the Sakishima islands were established from few identical founders; however, significant differentiations among various river basins most likely resulted from the limited gene flow and high inbreeding.     

Cryptic species in a Neotropical parrot: genetic variation within the Amazona farinosa species complex and its conservation implications

The application of genetic approaches has enhanced the identification of cryptic species in a wide variety of taxa, often with immediate conservation implications. Here, we employed multilocus DNA analyses to assess genetic variation and its correspondence to taxonomy within the Mealy Amazon (Amazona farinosa), a parrot species found in Central and South America. DNA sequence data from four mitochondrial regions and two nuclear introns were used to infer relationships among all five named subspecies in this species complex. Two reciprocally monophyletic groups with strong nodal support were found; one comprised of the two Central American subspecies guatemalae and virenticeps and one including all three South American subspecies farinosa, chapmani, and inornata. Molecular characters diagnosed distinct Central American and South American lineages, with an estimated divergence time of 1.75–2.70 million years ago as inferred from cytochrome-b (3.5–5.4 % corrected distance). Our data support recognizing Central American and South American Mealy Amazons as separate species worthy of independent conservation management. Furthermore, our results suggest recognition of two separate management units within the South American clade, although further study is required. These findings have important conservation implications as Central American A. farinosa are under increased pressure from habitat destruction and collection for the pet trade, yet are listed as of Least Concern due to their current classification as subspecies’ subsumed within the species complex.     

Mitochondrial DNA sequences suggest unexpected phylogenetic position of Corso-Sardinian grass snakes (<Emphasis Type="Italic">Natrix cetti</Emphasis>) and do not support their species status,with notes on phylogeography and subspecies delineation of grass snakes

We supplement a previously published mitochondrial DNA data set of grass snake sequences (ND1, ND2, ND4, cyt b, in total 3,806 bp) with sequences of Corso-Sardinian and Tuscan specimens and infer their phylogeny using Bayesian, maximum likelihood and maximum parsimony methods. In addition, we estimate divergence times of grass snake clades using a relaxed molecular clock calibrated with fossil evidence, and, in a second approach, the post-Messinian reopening of the Strait of Gibraltar. Recently it was suggested that Corso-Sardinian grass snakes represent a distinct species: Natrix cetti. All tree-building methods revealed well-supported branching patterns and deep divergences among grass snakes. However, sequences of N. natrix were consistently paraphyletic with respect to Corso-Sardinian sequences. The sister group of Corso-Sardinian grass snakes is a clade embracing N. n. helvetica and N. n. lanzai. Extensive gene flow between N. n. helvetica and a more distantly related subspecies (N. n. natrix) is well known, which is why we conclude that the status of Corso-Sardinian grass snakes as subspecies of N. natrix should be reinstated. Many currently recognized grass snake subspecies conflict with mitochondrial clades, suggestive of inappropriate morphological taxon delineation and mitochondrial introgression. Divergences among grass snakes are old, and the results of the two independent dating approaches are largely congruent. Accordingly, the Alpine orogenesis seems to have caused the origin of the oldest clade, corresponding to Iberian N. n. astreptophora. The formation of Corso-Sardinian grass snakes was dated to the Early Pliocene and could result from post-Messinian flooding of the Mediterranean Basin. Another deeply divergent clade of approximately the same age, endemic in central and northern Europe, suggests the Pleistocene survival of grass snakes north of the Alps. At least one glacial refuge in which old lineages survived Pleistocene cold periods was located on each of the three major southern European peninsulas and in Anatolia. Due to pronounced sequence divergences among Italian and southern Swiss grass snakes, we hypothesize multiple refugia south of the Alps and in the Apennine Peninsula, and there is evidence for two refuges on the Balkan Peninsula.