Shallow Genetic Differentiation Research Articles

Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan.

An accurate assessment of species diversity is a cornerstone of biology and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of the most diverse and widespread cursorial spider groups, however their species richness in Asia is highly underestimated. In this study, we revised species diversity with extensive taxon sampling in Taiwan and explored species boundaries based on morphological traits and genetic data using a two-step approach of molecular species delimitation. Firstly, we employed a single COI dataset and applied two genetic distance-based methods: ABGD and ASAP, and two topology-based methods: GMYC and bPTP. Secondly, we further analyzed the lineages that were not consistently delimited, and incorporated H3 to the dataset for a coalescent-based analysis using BPP. A total of eight morphological species were recognized, including five new species, Hamataliwa cordivulva sp. nov., Hamat. leporauris sp. nov., Tapponia auriola sp. nov., T. parva sp. nov. and T. rarobulbus sp. nov., and three newly recorded species, Hamadruas hieroglyphica (Thorell, 1887), Hamat. foveata Tang & Li, 2012 and Peucetia latikae Tikader, 1970. All eight morphological species exhibited reciprocally monophyletic lineages. The results of molecular-based delimitation analyses suggested a variety of species hypotheses that did not fully correspond to the eight morphological species. We found that Hamat. cordivulva sp. nov. and Hamat. foveata showed shallow genetic differentiation in the COI, but they were unequivocally distinguishable according to their genitalia. In contrast, T. parva sp. nov. represented a deep divergent lineage, while differences of genitalia were not detected. This study highlights the need to comprehensively employ multiple evidence and methods to delineate species boundaries and the values of diagnostic morphological characters for taxonomic studies in lynx spiders.

Comparative phylogeography reveals dissimilar genetic differentiation patterns in two sympatric amphibian species.

Global climate change is expected to have a profound effect on species distribution. Due to the temperature constraints, some narrow niche species could shift their narrow range to higher altitudes or latitudes. In this study, we explored the correlation between species traits, genetic structure, and geographical range size. More specifically, we analyzed how these variables are affected by differences in fundamental niche breadth or dispersal ability in the members of two sympatrically distributed stream-dwelling amphibian species (frog, Quasipaa yei; salamander, Pachyhynobius shangchengensis), in Dabie Mountains, East China. Both species showed relatively high genetic diversity in most geographical populations and similar genetic diversity patterns (JTX, low; BYM, high) correlation with habitat changes and population demography. Multiple clustering analyses were used to disclose differentiation among the geographical populations of these two amphibian species. Q. yei disclosed the relatively shallow genetic differentiation, while P. shangchengensis showed an opposite pattern. Under different historical climatic conditions, all ecological niche modeling disclosed a larger suitable habitat area for Q. yei than for P. shangchengensis; these results indicated a wider environment tolerance or wider niche width of Q. yei than P. shangchengensis. Our findings suggest that the synergistic effects of environmental niche variation and dispersal ability may help shape genetic structure across geographical topology, particularly for species with extremely narrow distribution.

Molecular phylogenetic and morphometric analysis of population structure and demography of endangered threadfin fish Eleutheronema from Indo-Pacific waters

The threadfin Eleutheronema are the important fishery resources in Indo-Pacific regions and classified as the endangered species with considerable conservation values. Their genetic diversity and population structure remain essentially unknown but are critical for the proper management and sustainable harvests of such important fisheries. Here, the mitochondrial DNA sequences of CO1 and 16s rRNA were determined from 75 individuals of Eleutheronema tetradactylum and 89 individuals of Eleutheronema rhadinum collected from different locations of South China Sea and Thailand coastal waters. Genetic diversity analysis revealed that both E. tetradactylum (Haplotype diversity, H = 0.105–0.211; Nucleotide diversity, π = 0.00017–0.00043) and E. rhadinum (H = 0.074–0.663, π = 0.00013–0.01088) had low diversity. Population structure analysis demonstrated the shallow genetic differentiation among the South China Sea populations. The limited communication between China and Thailand populations caused the high genetic differentiation in all groups due to the low dispersal ability. Reconstruction of CO1 phylogenetic relationships and demographic studies across Indo-West-Pacific regions provided strong evidence for a shared common origin or ancestor of E. tetradactylum and E. rhadinum. Eleutheronema rhadinum were further subdivided into two distinct genetic lineages, with Clade A dominantly distributing in Thailand and Malaysia and Clade B distributing in China coastal waters. Phenotypic divergence, characterized mainly by the depth of caudal peduncle and length of caudal peduncle, was also observed for all populations, which was possibly associated with specific local adaptations to environmental changes. Our study suggested a strong need for the development of proper fishery management strategies and conservation actions for the imperiled Eleutheronema species.

Correction to: Genome-wide assessment of population structure and genetic diversity of Eucalyptus urophylla based on a multi-species single-nucleotide polymorphism chip analysis

Eucalyptus urophylla is a commercially important wood crop plantation species due to its rapid growth, biomass yield, and use as bioenergy feedstock. We characterized the genetic diversity and population structure of 332 E. urophylla individuals from 19 geographically defined E. urophylla populations with a reliability of 14,468 single-nucleotide polymorphisms (SNPs). We compared the patterns of genetic variation among these 19 populations. High levels of genetic diversity were observed throughout the 19 E. urophylla populations based on genome-wide SNP data (HE = 0.2677 to 0.3487). Analysis with STRUCTURE software, principal component analysis (PCA), and a neighbor-joining (NJ) tree indicated that E. urophylla populations could be divided into three groups, and weak population structure was observed with pairwise genetic differentiation (FST) values ranging from − 0.09 to 0.074. The low genetic diversity and shallow genetic differentiation found within the 19 populations may be a consequence of their pollination system and seed dispersal mechanism. In addition, 55 core germplasms of E. urophylla were constructed according to the genetic marker data. The genome-wide SNPs we identified will provide a valuable resource for further genetic improvement and effective use of the germplasm resources.

Phylogeography of a salmonid fish, masu salmon Oncorhynchus masou subspecies‐complex, with disjunct distributions across the temperate northern Pacific

Abstract Climate oscillations during the Pleistocene had profound effects on the evolutionary history of freshwater fishes now distributed across northern temperate regions. The extent of continental glaciation on the western side of the North Pacific, including areas of East Asia, was more limited as compared with regions of North America, Europe and high‐latitude areas of the North Pacific. Therefore, the effects of climate oscillations might have influenced species in dissimilar ways depending on the species' distribution. We used mitochondrial DNA (mtDNA) and microsatellite DNA (msDNA) markers to clarify the evolutionary history of masu salmon Oncorhynchus masou subspecies‐complex (family Salmonidae) distributed in historically non‐glaciated regions in the western North Pacific. No marked regional or subspecies‐specific mtDNA haplotype associations were recognised, except for O. masou subsp., a lacustrine form endemic to Lake Biwa, an ancient lake in central Honshu. The landlocked subspecies O. masou formosanus, with a disjunct distribution on Taiwan Island, exhibited no diagnostic population features differing from the other subspecies, in either mtDNA or msDNA markers. Mismatch distribution and Bayesian skyline plot analyses indicated relatively recent range expansion and rapid population growth for masu salmon during the last glacial period (c. 0.1–0.15 Ma). Contrary to the mtDNA genealogy, Bayesian clustering using msDNA showed two main genetic clusters, mainly northern populations of the subspecies O. m. masou and populations of the subspecies O. m. ishikawae in southern areas of the Japanese Archipelago. Notably, O. m. formosanus on Taiwan Island was included in the O. m. masou group, and O. masou subsp. was included in the O. m. ishikawae group. Our results suggest that the masu salmon subspecies‐complex in historically non‐glaciated regions of the Temperate Northern Pacific is characterised by weak population structuring and shallow genetic differentiation among the subspecies, except for O. masou subsp. owing to its long isolation in Lake Biwa. Incomplete lineage sorting and historical inter‐subspecies hybridisation, possibly due to secondary contact, seem to be plausible explanations for discrepancies in the mitochondrial DNA genealogy and nuclear DNA genetic structure.

Mitochondrial phylogeography of the Mediterranean horseshoe bat on the Balkan Peninsula

The Balkan Peninsula is identified as one of the major glacial refugia in Europe during the Pleistocene, and it has served as a genetic source for post-glacial recolonization for many temperate species. The aim of this study was to investigate the genetic diversity and phylogeographic patterns of the Mediterranean horseshoe bat, Rhinolophus euryale Blasius 1853, on the Balkan Peninsula. We also analyzed its demographic history and tested the hypothesis that this region was a glacial refugium for this species. We collected 82 samples from 20 localities in the Balkans and Italy and sequenced the mitochondrial D-loop region. Our results revealed low nucleotide but high haplotype diversity, with 20 out of 24 haplotypes reported for the first time. All Balkan and Italian samples belonged to a single genetic clade in the phylogenetic reconstruction, where they clustered together with previously published samples from Turkey, southern France and North Africa. The haplotype network had a star-like pattern that is indicative of recent population expansion. Both mismatch distribution and shallow genetic differentiation also supported the scenario of a sudden demographic expansion. We estimated that expansion within this lineage commenced in the Late Pleistocene. We suggest that the Balkan Peninsula was a glacial refugium for R. euryale.

Genetic diversity of a hitchhiker and prized food source in the Anthropocene: the Asian green mussel Perna viridis (Mollusca, Mytilidae)

Insight into a species’ native and introduced range is essential in understanding the invasion process. Genetic diversity, propagule pressure and environmental conditions all have been recognised as playing a determinant role in invasion success. Here, we aimed to investigate the genetic diversity and population genetic structure (using the COI mtDNA gene region and 22 nDNA microsatellite markers) of the Asian green mussel Perna viridis within its potential native range in Asia and at introduced locations in the USA and the Caribbean. We also analyse genetic data from vessel intercepts and an incursion. By doing so, we aimed to identify genetic signatures that could allow to track vessel samples to their source and provide further insight into potential high-risk invasive populations or areas. Three top hierarchical clusters were identified using the individual-based Bayesian clustering method in STRUCTURE, corresponding to populations in three world regions: (1) USA and Caribbean, (2) India and (3) Southeast Asia. Within Southeast Asia, additional analysis indicate a shallow genetic differentiation of three subgroups consisting of (3a) Thailand, (3b) Taiwan and Hong-Kong, and (3c) a cluster of Singapore–Indonesia samples. Overall, the population structure found in this study suggests that the markers used could be useful in identifying source populations, particularly between the three mains world regions. Most surprisingly however, this study shows that the genetic diversity of samples collected from vessel intercepts and incursions did not differ significantly from established populations in Southeast Asia. In this region, in addition to the high vessel connectivity and number of P. viridis transported, all sampled populations are likely to pose a comparable risk in terms of genetic diversity. The present work represents the most comprehensive population genetic study of P. viridis, and the first to address the potential genetic introduction risk posed by populations of this species. The information and genetic markers in this study constitute a valuable addition to the tools already used to infer on potential high-risk source populations of P. viridis. They should therefore prove useful for biosecurity surveillance and management actions directed at this species.

Spatial patterns of genetic diversity among Australian alpine flora communities revealed by comparative phylogenomics

AbstractAimThe alpine region of mainland Australia is one of the world's 187 biodiversity hotspots. Genetic analyses of Australian alpine fauna indicate high levels of endemism on fine spatial scales, unlike Northern Hemisphere alpine systems where shallow genetic differentiation is typically observed among populations. These discrepancies have been attributed to differences in elevation and influence from glacial activity, and point to a unique phylogeographic history affecting Australian alpine biodiversity. To test generality of these findings across Australian alpine biota, we assessed patterns of genetic structure across plant species.LocationThe Australian Alps, Victoria, eastern Australia.MethodsWe used an economical pooled genotyping‐by‐sequencing (GBS) approach to examine patterns of genetic diversity among seven widespread species including shrubs and forbs from 16 mountain summits in the Australian Alpine National Park. Patterns of genetic structure among summit populations for each species were inferred from an average of 2,778 independent SNP loci using Bayesian phylogenomic inference and clustering approaches.ResultsSNP results were consistent across species in identifying deep evolutionary splits among summit communities from the Northern and Central Victorian Alpine regions. These patterns of genetic structure are also consistent with those previously reported for invertebrate and mammal taxa. However, local genetic structure was less pronounced in the plants, supporting the notion that population connectivity tends to be higher in plant species.Main conclusionThere is deep lineage diversification between the North and Central Victorian Alpine regions, reflecting a high level of endemism. These findings differ from those reported for alpine biodiversity from New South Wales and much of the Northern Hemisphere, and support the notion that genetic diversity is typically greatest in areas least affected by historical ice sheet formation. We discuss the implications of our findings in the context of conservation planning, and highlight the benefits of this rapid and cost‐effective genome scan approach for characterizing evolutionary processes at multispecies and landscape scales.

Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq

Amorphophallus paeoniifolius, is a commercially important vegetable crop because of its high production potential. In this study, we generated a total of 166 Gb of genomic data from 16 wild and 20 cultivated A. paeoniifolius individuals in southwestern China using restriction site associated DNA sequencing (RAD-seq). We compared the genome-wide variations between the wild and cultivated populations. Wild populations exhibited higher genetic diversity than did cultivated populations based on private allele number, expected heterozygosity, observed heterozygosity and nucleotide diversity. STRUCTURE analysis, principal component analysis (PCA) and a maximum likelihood (ML) tree indicated that A. paeoniifolius populations could be divided into three groups (a cultivated group and two wild groups) with significant genetic differentiation. The low genetic diversity and shallow genetic differentiation found within cultivated populations are likely caused by continuous selection and the clonal propagation methods used during domestication. The significant differentiation between the wild populations may suggest strong genetic drift due to small populations and human disturbance. The genome-wide single nucleotide polymorphisms (SNPs) identified in our study will provide a valuable resource for further breeding improvement and effective use of the germplasm.

Historical abiotic events or human-aided dispersal: inferring the evolutionary history of a newly discovered galaxiid fish.

Range expansion of obligate freshwater fishes in the Cape Floristic Region (CFR) of South Africa has mostly been attributed to river capture events and confluence of rivers following sea-level regression. The role of low drainage divides and interbasin water transfers has received less attention. This study analyzed mitochondrial and nuclear DNA sequences to assess the processes that could have influenced the phylogeographic patterns of a newly discovered lineage of Galaxias zebratus (hereafter Galaxias zebratus “Joubertina”) that occurs across two currently isolated river systems close to the Joubertina area in the eastern CFR. Results from both analyses revealed that observed genetic differentiation cannot be explained by isolation between the two river systems. No genetic differentiation was found between the Krom River system and a population from one of the Gamtoos tributaries. Shallow genetic differentiation was found between the Krom and the other Gamtoos populations. Historical river capture events and sea-level changes do not explain the present distribution of Galaxias zebratus “Joubertina” across the Krom and Gamtoos River systems. Interbasin dispersal during pluvial periods, recent river capture, or recent human-mediated translocation seems to be the most plausible explanations.

High population connectivity and Pleistocene range expansion in the direct-developing plough shell Bullia rhodostoma along the South African coast

Pleistocene climatic and oceanographic changes have influenced the distribution of marine biodiversity in southern Africa. Most evidence, however, has been derived from rocky shore or demersal taxa; data on sandy shore species are limited, despite severe threats to many sandy beach ecosystems. To test the effects of past climatic changes on sandy shore species, we sampled 140 smooth plough shell Bullia rhodostoma individuals from eight localities and generated phylogeographic data derived from the mtDNA cytochrome c oxidase subunit 1 (COI) marker. Nuclear markers (ATPSα, ATPSβ, ANT, SRPS4, TBP, LTRS and ZMP) showed no sequence variation. Bullia rhodostoma exhibited shallow genetic differentiation (ΦST = 0.07, p < 0.05) across its range. Isolation-by-distance suggests a stepping-stone model of migration, which is expected given the species’ direct-development life-history strategy. Demographic reconstruction suggests a post-LGM (Last Glacial Maximum) range expansion, concordant with the signal of shallow genetic differentiation. Phylogeographic patterns obtained suggest that, during lower sea levels than current, B. rhodostoma could have been restricted to the South-West Coast, the central Agulhas Bioregion and probably also the East Coast. When climatic conditions changed and temperatures began to rise after the LGM, the species began a rapid westward range expansion from these refugial regions.

Genetic structure and differentiation of four populations of Afghan Pika (Ochotona rufescens) in Iran based on mitochondrial cytochrome b gene

The population genetics of the Afghan Pika (Ochotona rufescens) was studied in Northern Khorasan Province, Iran. For prediction of the genetic differentiation of four populations, the DNA of mitochondrial cytochrome b of 32 individuals from four areas was sequenced and a Bayesian analysis based on the HKY model was constructed. In total, 15 polymorphic sites, 1125 conserved sites (98.7%) and 14 different haplotypes were found. The phylogenetic tree resulting from the Bayesian analysis and network analysis showed that all samples were clustered in two major groups and the haplotypes of the four populations did not separate geographically. An analysis of molecular variance (AMOVA) indicated that a large majority of the genetic variance was due to the variance within populations. The results of fixation indices showed significant genetic structure among populations in both methods. The pairwise Fst revealed that two northern populations have a significant genetic differentiation from two southern populations, but no significance pairwise Fst value was demonstrated between the closed populations. Nei's genetic distances between closed populations were not significant, while significant values occurred between distant populations. It seems that there is not a major discontinuity between populations of Afghan Pika based on cyt-b mitochondrial gene. However, phylogenetic analysis did not separate populations and a large majority of the genetic variance was found within populations. However, AMOVA analysis showed a significant level of genetic structure among populations (p < 0.001) and between groups (p < 0.5). It seems that these results suggest shallow genetic differentiation between populations of different geographic groups.

Phylogeography and demographic history of two widespread Indo-Pacific mudskippers (Gobiidae: Periophthalmus)

This study provides a first description of the phylogeographic patterns and evolutionary history of two species of the mudskipper genus Periophthalmus. These amphibious gobies are distributed throughout the whole Indo-Pacific region and Atlantic coast of Africa, in peritidal habitats of soft-bottom coastal ecosystems. Three sequence datasets of two widely distributed species, Periophthalmus argentilineatus and P. kalolo, were obtained by amplifying and sequencing two mtDNA markers (D-loop and 16S rDNA) and the nDNA rag1 region. The three datasets were then used to perform phylogeographic, demographic and population genetic analyses. Our results indicate that tectonic events and past climatic oscillations strongly contributed to shape present genetic differentiation, phylogeographic and demographic patterns. We found support for the monophyly of P. kalolo, and only shallow genetic differentiation between East-African and Indo-Malayan populations of this species. However, our collections of the morphospecies P. argentilineatus include three molecularly distinct lineages, one of them more closely related to P. kalolo. The presence of Miocenic timings for the most recent common ancestors of some of these morphologically similar clades, suggests the presence of strong stabilising selection in mudskippers’ habitats. At population level, demographic analyses and palaeoecological records of mangrove ecosystems suggest that Pleistocene bottlenecks and expansion plus secondary contact events of the studied species were associated with recurrent sea transgressions during interglacials, and sea regressions or stable regimes during glacials, respectively.

Gene flow vs. pollution pressure: Genetic diversity of Mytilus galloprovincialis in eastern Adriatic

Environmental pollution may modify all the evolutionary processes involved in shaping the genetic patterns of exposed populations. In order to evaluate the pollution impact on the genetic diversity of Mediterranean mussel Mytilus galloprovincialis ten populations inhabiting differently polluted sites along the eastern Adriatic coast, from pristine bays to heavily trafficked harbours, were studied. Pollution pressure was assessed through an integrated study of biological effects and responses across different levels of biological organization. Eight microsatellite markers were analysed to assess genetic diversity of investigated populations. Both the principal component analysis (PCA) of the biomarker data set as well as the biomarker response index (BRI) confirmed substantial pollution pressure at the highly polluted sites, and very low pollution exposure at the three reference sites. Very shallow genetic differentiation was found in respect to maritime distances or pollution status, and this was attributed to a high gene flow among the populations. However, populations inhabiting polluted sites exhibited higher levels of genetic diversity and evolutionary mechanisms underlying this phenomenon are discussed.

Oceanic circulation, local upwelling and palaeoclimatic changes linked to the phylogeography of the Cape sea urchin Parechinus angulosus

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 468:203-215 (2012) - DOI: https://doi.org/10.3354/meps09956 Oceanic circulation, local upwelling and palaeoclimatic changes linked to the phylogeography of the Cape sea urchin Parechinus angulosus Cornelius M. Muller1, Sophie von der Heyden1, Rauri C. K. Bowie2, Conrad A. Matthee1,* 1Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa 2Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Science Building, University of California, Berkeley, California 94720, USA *Email: cam@sun.ac.za ABSTRACT: To enhance our current understanding of the evolution of intertidal marine species, we investigated the phylogeographic population structure of the Cape sea urchin Parechinus angulosus using cytochrome c oxidase subunit I (COI) mitochondrial and receptor for egg jelly protein 9 (SpREJ9) nuclear DNA (nDNA) sequence data. The species shows variation in colour form, has a wide distribution along the southern African coastline, a broadcast mode of reproduction and probably a fairly long post larval development. Despite the prediction that species with such life history traits will show shallow genetic differentiation among sampling sites, high levels of population differentiation were obtained among many of the 18 sampling localities. The trend was particularly strong along the west coast Namaqua biogeographic province of southern Africa where the structure was also correlated with local upwelling. Larval dispersal broadly corresponded with oceanic currents and 2 distinct geographic genetic groupings were detected. The first grouping represents most individuals sampled along the cool temperate west coast, while the second comprises individuals sampled from the south and east coasts of southern Africa. The genetic separation of P. angulosus individuals is in the vicinity of a recognized biogeographic barrier (Cape Point), and is supported by geneflow analyses, parsimony haplotype networks for both nDNA and mtDNA data, and a mtDNA Bayesian analyses of population structure. Expansion events for the Cape sea urchin, and the divergence time estimates between the 2 assemblages, centre around the last glacial maximum and provide substantial support that glaciations and associated lowering and rising of sea levels significantly affected marine rocky shore organisms along the southern African coastline. KEY WORDS: Southern Africa · Echinodermata · Phylogeography · Geneflow · Sea-level change · SpREJ · mtDNA COI Full text in pdf format PreviousNextCite this article as: Muller CM, von der Heyden S, Bowie RCK, Matthee CA (2012) Oceanic circulation, local upwelling and palaeoclimatic changes linked to the phylogeography of the Cape sea urchin Parechinus angulosus. Mar Ecol Prog Ser 468:203-215. https://doi.org/10.3354/meps09956 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 468. Online publication date: November 14, 2012 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2012 Inter-Research.

Shallow Genetic Differentiation inMiniopterus schreibersii(Chiroptera: Vespertilionidae) Indicates a Relatively Recent Re-Colonization of Europe from a Single Glacial Refugium

In this study we analyzed 547 sequences of the first hypervariable domain of the control region of Miniopterus schreibersii sampled in colonies located in the western- and eastern-most borders of its distribution. We assessed genetic diversity of these colonies, quantified differences between them, and pointed out to their putative ancestral origin. Our results suggest that the extant European populations of M. schreibersii are descendants of the ancestors that survived the last glacial maximum in a single glacial refugium, probably located in the north-western Anatolia. According to our model, a rapid population expansion and major re-colonization events started after the climatic change that followed the end of the last glacial maximum. Our suggestions are supported by the shallow genetic differentiation between the eastern and western colonies of M. schreibersii, high genetic diversity observed in the eastern colonies, and population expansion time estimated for ca. 15.6 kyr BP.

Evolutionary diversification of cryophilic Grylloblatta species (Grylloblattodea: Grylloblattidae) in alpine habitats of California

BackgroundClimate in alpine habitats has undergone extreme variation during Pliocene and Pleistocene epochs, resulting in repeated expansion and contraction of alpine glaciers. Many cold-adapted alpine species have responded to these climatic changes with long-distance range shifts. These species typically exhibit shallow genetic differentiation over a large geographical area. In contrast, poorly dispersing organisms often form species complexes within mountain ranges, such as the California endemic ice-crawlers (Grylloblattodea: Grylloblattidae: Grylloblatta). The diversification pattern of poorly dispersing species might provide more information on the localized effects of historical climate change, the importance of particular climatic events, as well as the history of dispersal. Here we use multi-locus genetic data to examine the phylogenetic relationships and geographic pattern of diversification in California Grylloblatta.ResultsOur analysis reveals a pattern of deep genetic subdivision among geographically isolated populations of Grylloblatta in California. Alpine populations diverged from low elevation populations and subsequently diversified. Using a Bayesian relaxed clock model and both uncalibrated and calibrated measurements of time to most recent common ancestor, we reconstruct the temporal diversification of alpine Grylloblatta populations. Based on calibrated relaxed clock estimates, evolutionary diversification of Grylloblatta occurred during the Pliocene-Pleistocene epochs, with an initial dispersal into California during the Pliocene and species diversification in alpine clades during the middle Pleistocene epoch.ConclusionsGrylloblatta species exhibit a high degree of genetic subdivision in California with well defined geographic structure. Distinct glacial refugia can be inferred within the Sierra Nevada, corresponding to major, glaciated drainage basins. Low elevation populations are sister to alpine populations, suggesting alpine populations may track expanding glacial ice sheets and diversify as a result of multiple glacial advances. Based on relaxed-clock molecular dating, the temporal diversification of Grylloblatta provides evidence for the role of a climate-driven species pump in alpine species during the Pleistocene epoch.

Microsatellite markers reveal shallow genetic differentiation between cohorts of the common sea urchin Paracentrotus lividus (Lamarck) in northwest Mediterranean

Temporal variability was studied in the common sea urchin Paracentrotus lividus through the analysis of the genetic composition of three yearly cohorts sampled over two consecutive springs in a locality in northwestern Mediterranean. Individuals were aged using growth ring patterns observed in tests and samples were genotyped for five microsatellite loci. No reduction of genetic diversity was observed relative to a sample of the adult population from the same location or within cohorts across years. F(ST )and amova results indicated that the differentiation between cohorts is rather shallow and not significant, as most variability is found within cohorts and within individuals. This mild differentiation translated into estimates of effective population size of 90-100 individuals. When the observed excess of homozygotes was taken into account, the estimate of the average number of breeders increased to c. 300 individuals. Given our restricted sampling area and the known small-scale heterogeneity in recruitment in this species, our results suggest that at stretches of a few kilometres of shoreline, large numbers of progenitors are likely to contribute to the larval pool at each reproduction event. Intercohort variation in our samples is six times smaller than spatial variation between adults of four localities in the western Mediterranean. Our results indicate that, notwithstanding the stochastic events that take place during the long planktonic phase and during the settlement and recruitment processes, reproductive success in this species is high enough to produce cohorts genetically diverse and with little differentiation between them. Further research is needed before the link between genetic structure and underlying physical and biological processes can be well established.

Wild stock structure of Girella punctata in Japan revealed shallow genetic differentiation but subtle substructure in subsidiary distributions

Twelve populations of Girella punctata, from widespread locations of the species’ range in Japan and Korea, were screened for sequence variability within the mitochondrial DNA (mtDNA) control region (n = 128) and at five polymorphic microsatellite loci (n = 547) to determine the genetic structure maintaining population integrity. mtDNA variability of 132 variable sites within a 334-bp region reveals shallow genetic differentiation across populations. The weak differentiation of G. punctata was partly supported by the screening of five polymorphic microsatellite loci. However, hierarchical analysis of molecular variance and principal component analysis on the basis of allele frequencies in microsatellite loci extracted a subtle substructure in a subsidiary population and in near-subsidiary populations in the semi-enclosed Seto Inland Sea.

Genetic structuring in the threatened “Lagartijo del Bosque Seco” ( Anolis cooki) from Puerto Rico

Species with restricted geographic distributions consisting of isolated populations are particularly susceptible to extinction because these demes face an increased risk of disappearing due to environmental, demographic, and genetic stochasticity. We used partial DNA sequences of the cytochrome b (1083 bp) and ND2 (1041 bp) mitochondrial genes to investigate the phylogeography and population genetics of Anolis cooki, a threatened lizard endemic to the southwestern coast of the Caribbean Island of Puerto Rico. Maximum likelihood and Bayesian methods revealed relatively shallow genetic differentiation among 27 unique haplotypes (from 52 individuals) from the known extant populations of A. cooki in mainland Puerto Rico. Despite this pattern, specimens from the same geographic area tended to nest together. The most basal division within A. cooki is between haplotypes from the three westernmost populations (Punta Águila, Morrillos, Playa Santa) and the remainder demes (Bahía Ballena, La Cueva, Punta Verraco). The three westernmost populations of A. cooki are separated from their conspecific demes by the Guánica Bay and the Loco River drainage system, which together may represent a physiographic barrier for A. cooki. Each population of A. cooki only has private haplotypes; in other words, there are no shared mitochondrial types between populations. Because the number of private haplotypes can be used as an indirect measure of gene flow, this finding suggests that currently there is no migration among demes, and that each is an independent demographic unit, despite the relatively short distances (ca. 2 km) that separate some of them. Pairwise F ST values and spatial analyses of molecular variation confirmed the existence of distinct groups of genetically defined sampling areas, and of significant molecular variation among populations within groups and within populations. The conservation status of the populations of A. cooki varies greatly. The demes from Punta Águila, Morrillos, and Bahía Ballena inhabit protected areas, and are larger, genetically diverse, and seemingly stable. The population from Playa Santa showed a high level of genetic diversity, but it occurs in an area that has been intensively developed for residential and touristic purposes, and its long-term survival is uncertain. A. cooki is also known from Caja de Muertos, an island off the southcentral coast of Puerto Rico. Surveys conducted on September 2006 and March 2007 did not produce any specimens, and a thorough assessment of Caja de Muertos is needed to determine the present status of A. cooki on the island.