Mitochondrial DNA diversity and phylogeography of endangered green turtle (Chelonia mydas) populations in Africa

We analysed the genetic structure of seven nesting sites of the endangered green turtle (Chelonia mydas) in Africa using mitochondrial DNA control region sequences. Tissue samples were collected from 188 nesting females at six sites in West Africa and one in the Indian Ocean. A 488 bp fragment of the control region revealed 14 different haplotypes, 10 of which are previously undescribed. The most common haplotype (CM8) was observed in 157 individuals. All other haplotypes were closely related, except two divergent lineages: CM38, removed by four substitutions, and the three Indian Ocean haplotypes, distinguished by 31 substitutions. Significant differences in haplotype and nucleotide diversity were observed between Atlantic rookeries and among ocean basins. Analysis of molecular variance revealed high levels of differentiation between the Atlantic and the Indian Ocean populations but a much shallower Atlantic substructuring. Green turtle population genetic structure is thought to have been shaped by a dynamic succession of extinction and recolonisation of rookeries, by natal homing and occasional breakdown in nest-site fidelity. Mismatch distributions of pairwise differences between haplotypes at each rookery were found to be consistent with recent population expansion. We argue that demographic histories can be explained by scenarios at several temporal scales, including geological events, sea level fluctuations and more recent patterns of exploitation. We discuss management and conservation implications of our results for these threatened populations, identifying two ESUs (one in the Atlantic and one in the Indian ocean) and three MUs within the Atlantic.     

Is the Gibraltar Strait a barrier to gene flow for the bat Myotis myotis (Chiroptera: Vespertilionidae)?

Because of their role in limiting gene flow, geographical barriers like mountains or seas often coincide with intraspecific genetic discontinuities. Although the Strait of Gibraltar represents such a potential barrier for both plants and animals, few studies have been conducted on its impact on gene flow. Here we test this effect on a bat species (Myotis myotis) which is apparently distributed on both sides of the strait. Six colonies of 20 Myotis myotis each were sampled in southern Spain and northern Morocco along a linear transect of 1350 km. Results based on six nuclear microsatellite loci reveal no significant population structure within regions, but a complete isolation between bats sampled on each side of the strait. Variability at 600 bp of a mitochondrial gene (cytochrome b) confirms the existence of two genetically distinct and perfectly segregating clades, which diverged several million years ago. Despite the narrowness of the Gibraltar Strait (14 km), these molecular data suggest that neither males, nor females from either region have ever reproduced on the opposite side of the strait. Comparisons of molecular divergence with bats from a closely related species (M. blythii) suggest that the North African clade is possibly a distinct taxon warranting full species rank. We provisionally refer to it as Myotis cf punicus Felten 1977, but a definitive systematic understanding of the whole Mouse-eared bat species complex awaits further genetic sampling, especially in the Eastern Mediterranean areas.     

Restricted dispersal in a continuously distributed marine species: common bottlenose dolphins Tursiops truncatus in coastal waters of the western North Atlantic

The marine environment provides an opportunity to examine population structure in species with high dispersal capabilities and often no obvious barriers to genetic exchange. In coastal waters of the western North Atlantic, common bottlenose dolphins, Tursiops truncatus, are a highly mobile species with a continuous distribution from New York to Florida. We examine if the highly mobile nature coupled with no obvious geographic barriers to movement in this region result in a large panmictic population. Mitochondrial control region sequences and 18 microsatellite loci indicate dolphins are partitioning the habitat both latitudinally and longitudinally. A minimum of five genetically differentiated populations were identified among 404 samples collected in the range of New Jersey to northern Florida using both genetic marker types, some inhabiting nearshore coastal waters and others utilizing inshore estuarine waters. The genetic results reject the hypothesis of a single stock of coastal bottlenose dolphins put forth after the 1987–1988 epizootic that caused a large‐scale die‐off of dolphins and suggest instead the disease vector was transferred from one population to the next as a result of seasonal migratory movements of some populations. These coastal Atlantic populations also differ significantly from bottlenose dolphin samples collected in coastal waters of the northern Gulf of Mexico, implying a long‐term barrier to movement between the two basins.     

Riverine effects on mitochondrial structure of Bornean orangutans (Pongo pygmaeus) at two spatial scales

We examined mitochondrial DNA control region sequences of 73 Kinabatangan orang-utans to test the hypothesis that the phylogeographical structure of the Bornean orang-utan is influenced by riverine barriers. The Lower Kinabatangan Wildlife Sanctuary contains one of the most northern populations of orang-utans ( Pongo pygmaeus ) on Borneo and is bisected by the Kinabatangan River, the longest river in Sabah. Orang-utan samples on either side of the river were strongly differentiated with a high Φ_ST value of 0.404 ( P <  0.001). Results also suggest an east–west gradient of genetic diversity and evidence for population expansion along the river, possibly reflecting a postglacial colonization of the Kinabatangan floodplain. We compared our data with previously published sequences of Bornean orang-utans in the context of river catchment structure on the island and evaluated the general relevance of rivers as barriers to gene flow in this long-lived, solitary arboreal ape.     

Genetic variation across the historical range of the wild turkey (Meleagris gallopavo)

Genetic differences within and among naturally occurring populations of wild turkeys (Meleagris gallopavo) were characterized across five subspecies' historical ranges using amplified fragment length polymorphism (AFLP) analysis, microsatellite loci and mitochondrial control region sequencing. Current subspecific designations based on morphological traits were generally supported by these analyses, with the exception of the eastern (M. g. silvestris) and Florida (M. g. osceola) subspecies, which consistently formed a single unit. The Gould's subspecies was both the most genetically divergent and the least genetically diverse of the subspecies. These genetic patterns were consistent with current and historical patterns of habitat continuity. Merriam's populations showed a positive association between genetic and geographical distance, Rio Grande populations showed a weaker association and the eastern populations showed none, suggesting differing demographic forces at work in these subspecies. We recommend managing turkeys to maintain subspecies integrity, while recognizing the importance of maintaining regional population structure that may reflect important adaptive variation.     

Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.     

Mitochondrial DNA phylogeography reveals marked population structure in the common vampire bat, Desmodus rotundus (Phyllostomidae)

Desmodus rotundus (Chiroptera: Phyllostomidae; Desmodontinae) is the most common vampire bat and has a broad distribution, ranging from southern Mexico to central Chile in the west, and Paraguay and northern Argentina in the east of South America ( Koopman 1988 ). Because of its feeding habit, this bat is considered the main source of rabies transmission to cattle. Although this species has a large spectrum of morphological variability throughout its range, thus far no study has examined the distribution of genetic lineages over its geographic range. Four geographically circumscribed clades of D. rotundus were described in the Brazilian territory on the basis of mitochondrial sequence analyses: southern Atlantic forest (SAF), northern Atlantic forest (NAF), Pantanal (PAN) and Amazon plus Cerrado (AMC) clade. The differentiation among these clades is strongly supported statistically, although the phylogenetic relationship between them remains uncertain. The extremely high levels of sequence divergence that were found between clades (ranging from 6% to 11%) are the highest ever described for a Neotropical bat species and cannot be explained by female philopatry alone. This indicates that D. rotundus comprises two or more distinct, possibly cryptic species. The biogeographic pattern described for this bat is similar to those described for other bats and terrestrial mammals, suggesting geographical congruence between historical vicariant processes, including likely vicariant events between north and south Atlantic Forest and between the Atlantic Forest and the Amazon.     

Genetic structure among continental and island populations of gyrfalcons

Little is known about the possible influence that past glacial events have had on the phylogeography and population structure of avian predators in the Arctic and sub-Arctic. In this study, we use microsatellite and mitochondrial control region DNA variation to investigate the population genetic structure of gyrfalcons (Falco rusticolus) throughout a large portion of their circumpolar distribution. In most locations sampled, the mtDNA data revealed little geographic structure; however, five out of eight mtDNA haplotypes were unique to a particular geographic area (Greenland, Iceland, or Alaska) and the Iceland population differed from others based on haplotype frequency differences (F(ST)). With the microsatellite results, significant population structure (F(ST), principal components analysis, and cluster analysis) was observed identifying Greenland and Iceland as separate populations, while Norway, Alaska and Canada were identified as a single population consistent with contemporary gene flow across Russia. Within Greenland, differing levels of gene flow between western and eastern sampling locations was indicated with apparent asymmetric dispersal in western Greenland from north to south. This dispersal bias is in agreement with the distribution of plumage colour variants with white gyrfalcons in much higher proportion in northern Greenland. Lastly, because the mtDNA control region sequence differed by only one to four nucleotides from a common haplotype among all gyrfalcons, we infer that the observed microsatellite population genetic structure has developed since the last glacial maximum. This conclusion is further supported by our finding that a closely related species, the saker falcon (Falco cherrug), has greater genetic heterogeneity, including mtDNA haplotypes differing by 1-16 nucleotide substitutions from a common gyrfalcon haplotype. This is consistent with gyrfalcons having expanded rapidly from a single glacial-age refugium to their current circumpolar distribution. Additional sampling of gyrfalcons from Fennoscandia and Russia throughout Siberia is necessary to test putative gene flow between Norway and Alaska and Canada as suggested by this study.     

Population genetic structure of Chilo suppressalis (Walker) (Lepidoptera: Crambidae): strong subdivision in China inferred from microsatellite markers and mtDNA gene sequences

Chilo suppressalis (Walker) displays significant geographical differences in ecological preference that may be congruent with patterns of molecular variation. To test this, we collected and analysed 381 individuals of this species from cultivated rice at 18 localities in China during the rice-growing season of 2005–2006. We used four microsatellite DNA markers and four mitochondrial DNA gene fragments. We found that this species is highly differentiated, coupled with an estimated population expansion date of at least 60 000  bp . Phylogenetic analyses, Bayesian clustering, and phylogeographical analyses of statistical parsimony haplotype network consistently divided the populations into three clades: a central China (CC) clade, a northern plus northeastern China (NN) clade and a southwestern China (SW) clade. Analysis of molecular variance indicated a high level of geographical differentiation at different hierarchical levels [ F _ST for microsatellite markers, COI, COII, 16S and ND1 is 0.06004 ( P  < 0.0001), 0.27607 ( P  < 0.0001), 0.22949 ( P  < 0.0001), 0.19485 ( P  < 0.0001) and 0.29285 ( P  < 0.0001), respectively]. Isolation by distance appeared among the samples from within China ( r  = 0.404, P  = 0.0002); N_em values estimated using a coalescent-based method were small (< 2 migrants per generation), suggesting that the observed levels of differentiation are a result of migration–drift equilibrium. Our results imply that the genetic differentiation of this borer, which is approximately in accordance with its observed number of generations per year in different Chinese geographical regions, is probably attributed to climatic and/or geological events (e.g. the last glacial maximum) and subsequently strengthened by the domestication of rice.     

Fine-scale diversity and specificity in the most prevalent lineage of symbiotic dinoflagellates (Symbiodinium, Dinophyceae) of the Caribbean

The success of coral reefs is due to obligate mutualistic symbioses involving invertebrates and photosynthetic dinoflagellate symbionts belonging to the genus Symbiodinium. In the Caribbean, the vast majority of octocorals and other invertebrate hosts associate with Symbiodinium clade B, and more selectively, with a single lineage of this clade, Symbiodinium B1/B184. Although B1/B184 represents the most prevalent Symbiodinium in the Caribbean, there is little evidence supporting fine-scale diversity and host-alga specificity within this lineage. We explored simultaneously the questions of diversity and specificity in Symbiodinium B1/B184 by sequencing the flanking regions of two polymorphic microsatellites from a series of Symbiodinium clade B cultures along with Symbiodinium B1/B184 populations of the octocorals Pseudopterogorgia elisabethae, P. bipinnata and Gorgonia ventalina. Seven unique sequence variants were identified based on concatenation of the two loci. Phylogenetic analyses of these variants, which we refer to as phylotypes, recognized five as belonging to B1/B184, thus providing the first evidence of distinct taxa within this Symbiodinium lineage. Furthermore, sympatric P. elisabethae and P. bipinnata at San Salvador in the Bahamas were found to harbour distinct Symbiodinium B1/B184 phylotypes, demonstrating unequivocally the existence of fine-scale specificity between Caribbean octocorals and these algae. Taken together, this study exemplifies the complex nature of Symbiodinium biodiversity and specificity.     

Microsatellite genetic variation reveals extensive introgression between wild and introduced stocks, and a new evolutionary unit in French pike Esox lucius L.

The genetic variability of 11 French pike Esox lucius populations from rivers or extensive aquaculture ponds was analysed using seven microsatellite markers. The fish stocking of eastern European pike in French rivers is widespread, so five supplementary populations from this region were also analysed. Genetic variability within the French population was small, and similar to that previously found in Europe for this species. French populations from stocked rivers and extensive farms formed a genetically homogeneous group, and did not diverge from most eastern European samples, which may reflect either ancestral polymorphism or a complete introgression of French populations by introduced stocks. Bayesian analysis of the admixture between populations enabled identification of the French populations that were likely to be affected by introduced stocks (of local or foreign origin). Three genetically distinct evolutionary branches were identified: continental Europe, Danube basin, and south‐western France. The last is a new finding in the species which needs to be further explored by comparisons with wild populations at other sites.