The genetic population structure of the gray mouse lemur (<Emphasis Type="Italic">Microcebus murinus), </Emphasis>a basal primate from Madagascar

The genetic structure of a population is closely connected to fundamental evolutionary processes and aspects of social behavior. Information on genetic structure is therefore instrumental for the interpretation of social behavior and evolutionary reconstructions of social systems. Gray mouse lemurs (Microcebus murinus) are basal primates endemic to Madagascar whose social organization is characterized by solitary foraging at night and communal resting during the day. Conflicting reports about population structure based on behavioral observations led us to examine the genetic structure of one population in detail in order to: (1) identify natural genetic units in this solitary primate, and (2) to test the assumption of current models of primate social evolution that solitary primates are organized in matrilines. DNA was extracted from tissue samples of 85 individuals from Kirindy forest to determine their variability at a 530 bp fragment of the mitochondrial D-loop and at six microsatellite loci. We found that this population was characterized by a great general diversity among mtDNA haplotypes, a pronounced sex difference in mtDNA haplotype diversity and spatial clustering of females with a particular haplotype, but low average relatedness among members of haplotype clusters. Specifically, we identified 13 different haplotypes, which were unevenly distributed among individuals. About 80% of all individuals, most of which were females or juvenile males, shared a single haplotype. Rare haplotypes were almost exclusively represented by single adult males, who apparently migrated into this population. One other haplotype was represented by a small group of females living at one edge of the study area. Microsatellite analysis revealed above-average relatedness among females with overlapping home ranges, as well as no signs of inbreeding, implying that male dispersal results in high levels of gene flow among matrilineal groups. We conclude that gray mouse lemur populations are hierarchically organized in small family units of closely related females that form stable sleeping groups, several of which are connected through a common mtDNA haplotype and form spatially distinct clusters. The presence of such matrilines supports a basic assumption of current models of primate social evolution.     

Microsatellite data reveal fine genetic structure in male Guiana dolphins (<Emphasis Type="Italic">Sotalia guianesis)</Emphasis> in two geographically close embayments at south-eastern coast of Brazil

A large macrogeographic differentiation has been observed among Sotalia guianensis populations along the South American coast. However, no genetic structure has been detected so far in closely distributed populations of this species, even though it has been observed in other cetaceans. Here, we examined the fine scale population structure for the largest populations of S. guianensis inhabiting Sepetiba and Paraty embayments at the south-eastern coast of Rio de Janeiro, Brazil. Analysis of mitochondrial DNA (mtDNA) control region sequences failed to detect variability among sequences. Conversely, evidence of significant male population structure was found on the basis of ten nuclear microsatellite loci. Surprisingly, the microsatellite markers were able to distinguish between individuals from the two embayments located 60 km apart. The results suggest that differences in habitat type and behavioral specializations are likely to explain the patterns of genetic structure. These findings should provide baselines for the management of communities exposed to increasing human-driven habitat loss.     

Mitochondrial phylogeography of the killifish Aphanius fasciatus (Teleostei, Cyprinodontidae) reveals highly divergent Mediterranean populations

We studied the genetic structure of the Mediterranean killifish Aphanius fasciatus. Analysis of the sequence variation in a 372-bp portion of the mitochondrial control region in 623 fish from 27 sampling sites along the species’ distributional range (Tyrrhenian coast, Sardinia, Sicily, Adriatic coast, Malta, Tunisia, and Greece) yielded 120 distinct haplotypes. Most of the haplotypes are unique, and only 15 % are shared among different populations. The high F _ST value (=0.80) suggests a strong population genetic structuring. The phylogenetic analysis based on Bayesian inference, maximum likelihood and maximum parsimony, and the median-joining network show a sharp separation of the Southeastern Sicilian populations (belonging to the Hyblean region) and of the fluvial Tunisian population of Rio Melah from the others. The Adriatic, the Eastern Sicilian, and the Greek populations are well differentiated, while the group of populations from the Central-Western Mediterranean does not show a clear pattern of differentiation. Our findings indicate that the current genetic structuring of A. fasciatus reflects historical geographical patterns occurring within the Mediterranean basin from the Late Miocene to the Pleistocene. The presence of divergent evolutionary entities in the Hyblean region and the Tunisian Rio Melah supports their inclusion as target areas for the conservation of A. fasciatus.     

Phylogeography of the European stalked barnacle (Pollicipes pollicipes): identification of glacial refugia

The alternation of glacial and interglacial events during the Pleistocene has produced changes in species distribution ranges leading to bottlenecks and alterations of patterns of gene flow. The European stalked barnacle, Pollicipes pollicipes, is a sessile pedunculate cirripede that inhabits the rocky intertidal frame, from Senegal to the northwestern coast of France. In this work, we have analyzed a fragment of the mitochondrial gene cytochrome c oxidase subunit I for 569 individuals of P. pollicipes in order to investigate whether the shifts in climatic conditions that occurred during the Pleistocene influenced the current pattern of distribution of genetic variation of P. pollicipes. A pre-last glacial maximum pattern of demographic expansion was found, in concordance with many other North Atlantic marine species. On the other hand, three potential glacial refugia were identified: North African coasts, northwestern Iberian Peninsula and English Channel/Brittany.     

Genetic population structure of the seagrass Thalassodendron ciliatum in sandy and rocky habitats in southern Mozambique

The genetic diversity of the dioecious seagrass Thalassodendron ciliatum in six populations in southern Mozambique was studied by means of random amplified polymorphic DNA (RAPD). Samples were taken from sandy and rocky habitats over a span of 880 km. Analysis of molecular variance (AMOVA) showed that most of the genetic variability (71.6% of total genetic variation) was observed within populations. There were also significant genetic differences among populations within each habitat (sandy and rocky). We did not find any significant overall genetic difference between sandy versus rocky populations, indicating that the morphological differences between plants from these two habitats are not maintained by reproductive isolation. There was no significant correlation between geographical and genetic distance, which is discussed in the light of current patterns along the coast. All sampled populations consisted of several genetically distinct individuals, indicating that sexual reproduction is widespread.     

Phylogeography of the Southwestern Atlantic menhaden genus <Emphasis Type="Italic">Brevoortia</Emphasis> (Clupeidae,Alosinae)

Among pelagic fish, the Southwestern Atlantic menhaden genus Brevoortia (Clupeidae, Alosinae) constitutes an important species model to investigate the patterns of genetic differentiation. It is abundant in the Río de la Plata estuary and in the Atlantic coastal lagoons system from Uruguay and Southern Brazil. To access in the taxa discrimination and population structure in Brevoortia we perform a phylogeographic approach based on mitochondrial cytochrome b (cyt-b) sequences including 240 individuals from 16 collecting sites. Among the 720 bp cyt-b sequenced, 199 correspond to variables and 88 to phylogenetically informative sites. High values of haplotype diversity (h = 1.000) and nucleotide diversity (π = 0.061), as well as an average of 0.084 polymorphic segregating sites and 46 different haplotypes were found. Maximum likelihood analysis based on the GTR + I + G model and Bayesian inference strongly support the idea that B. aurea is the only species of the genus inhabiting the Southwestern Atlantic region. Our analyses revealed a complex population pattern characterized by the existence of long-term highly structured genetic assemblages of mixed stocks. Each monophyletic entity included individuals from different collecting sites, different age groups and collected in different years. Our data also suggest that the recruitment of unrelated mtDNA haplotypes carried out by individuals within schools could be occurring in the same nursery areas revealing the existence of many different maternal lineages. A scenario where different simultaneously and successively mixed mtDNA lineages remain historically connected through basal haplotypes among different clades could explains more accurately the complex and ordered metapopulation dynamic found in this pelagic fish.     

Population genetic structure of escolar (<Emphasis Type="Italic">Lepidocybium flavobrunneum</Emphasis>)

Escolar (Lepidocybium flavobrunneum) is a large, mesopelagic fish that inhabits tropical and temperate seas throughout the world, and is a common bycatch in pelagic longline fisheries that target tuna and swordfish. Few studies have explored the biology and natural history of escolar, and little is known regarding its population structure. To evaluate the genetic basis of population structure of escolar throughout their range, we surveyed genetic variation over an 806 base pair fragment of the mitochondrial control region. In total, 225 individuals from six geographically distant locations throughout the Atlantic (Gulf of Mexico, Brazil, South Africa) and Pacific (Ecuador, Hawaii, Australia) were analyzed. A neighbor-joining tree of haplotypes based on maximum likelihood distances revealed two highly divergent clades (δ = 4.85%) that were predominantly restricted to the Atlantic and Indo-Pacific ocean basins. All Atlantic clade individuals occurred in the Atlantic Ocean and all but four Pacific clade individuals were found in the Pacific Ocean. The four Atlantic escolar with Pacific clade haplotypes were found in the South Africa collection. The nuclear ITS-1 gene region of these four individuals was subsequently analyzed and compared to the ITS-1 gene region of four individuals from the South Africa collection with Atlantic clade haplotypes as well as four representative individuals each from the Atlantic and Pacific collections. The four South Africa escolar with Pacific mitochondrial control region haplotypes all had ITS-1 gene region sequences that clustered with the Pacific escolar, suggesting that they were recent migrants from the Indo-Pacific. Due to the high divergence and geographic separation of the Atlantic and Pacific clades, as well as reported morphological differences between Atlantic and Indo-Pacific specimens, consideration of the Atlantic and Indo-Pacific populations as separate species or subspecies may be warranted, though further study is necessary.     

The cockle <Emphasis Type="Italic">Cerastoderma edule</Emphasis> at Northeast Atlantic shores: genetic signatures of glacial refugia

The cockle Cerastoderma (Cardium) edule (L.) ranges from NW Africa to northern Scandinavia. Abundance in shallow coastal sediment is often high, and it attracts commercial harvest. In this study, a complex genetic pattern has been revealed by mitochondrial DNA in 383 individuals from 19 sampling sites. Parsimony network analysis of 79 haplotypes identified two dominant central haplotypes separated by low divergence. One is characteristic for a homogenous southwestern group of populations from Africa to the British Isles. The other is characteristic for a heterogeneous northern group with a deviant Arctic population. At the entrance of the Baltic Sea, a mixture zone of the dominant haplotypes was found. The estimated population expansion time for the northern haplotype group predates that of the southwestern one, suggesting northern glacial refugia and a subsequent southern expansion of C. edule populations.     

Interspecific variation in thermal denaturation of proteins in the congeneric musselsMytilus trossulus andM. galloprovincialis: evidence from the heat-shock response and protein ubiquitination

The genetic population structure of the precominant zooplankter, the copepod Calanus finmarchicus (Gunnerus), was examined to determine whether genetically distinct populations exist in the Gulf of Maine. C. finmarchicus was sampled in three regions of the Gulf of Maine (Great South Channel, spring 1989; northern Gulf of Maine, winter 1990; Great South Channel and Georges Bank, spring 1990). Copepods from seven locations in the Great South Channel, five in the northern Gulf of Maine and four on or near Georges Bank were assayed for allozyme variation and mitochondrial DNA variation of amplified 16S rRNA and cytochrome b genes. Restriction fragment length polymorphism (RFLP) analyses of both mitochondrial DNA genes revealed no variation among any of the individuals assayed. Analysis of five polymorphic allozyme loci revealed that genetic variation among the three geographic regions was low, and genetic identities were high between all locations (I>0.97). Most of the genetic variation was among locations regardless of region. Chi-square tests were used to examine genetic similarity between specific pairs of locations within and between regions. In the northern Gulf of Maine, genetic homogeneity occurred over larger spatial scales (hundreds of km) than in either the Great South Channel or Georges Bank (tens of km). Only copepods from the Bay of Fundy and Nova Scotian Shelf locations were genetically distinct from Wilkinson Basin copepods at two loci. Copepod populations from the northern locations may have been partially isolated or they may represent immigrant populations (e.g., from the Gulf of St. Lawrence). Several pairs of locations were genetically distinct at one or more loci in the two southern regions. Differences between locations in these regions may represent distinct populations advected into the areas at different times or from different sources (e.g., genetic variation may represent a mixture of genetically distinct northern and southern copepod populations). These results suggest extensive gene flow among populations of C. finmarchicus in the Gulf of Maine with some evidence of genetic population subdivision near the Gulf's northeastern and southern boundaries.     

Mitochondrial DNA analysis of native and selectively inbred Chesapeake Bay oysters,Crassostrea virginica

Mitochondrial DNA (mtDNA) genotypes were examined in 1989 in threeCrassostrea virginica (Gmelin) populations native to Chesapeake Bay, USA, and in one population selectively inbred for rapid growth for ten generations. We wished to determine whether this character would be useful as a genetic marker for distinguishing between the inbred line and the native oysters and to determine whether detectable genetic differences exist among present-day native populations ofC. virginica. Thirty mtDNA haplotypes were identified. The average percentage nucleotide difference between native haplotypes was 1.8%. Inbred oysters were characterized by mtDNA haplotypes distinctly different from ancestral native oysters, indicating a high degree of genetic differentiation between the two groups (average percentage mtDNA nucleotide sequence divergence,=21.8%). The common native haplotype was not present in the selectively inbred sample, and six of the seven haplotypes detected in the inbred oysters were not found in the survey of native oysters. Chi-square tests on haplotype frequencies indicated that the native populations were not significantly different from one another. However, the distribution and relatedness of haplotypes suggest that significant change in the oyster gene pool may have occurred over the past few decades.     

Genetic heterogeneity among <Emphasis Type="Italic">Eurytemora affinis</Emphasis> populations in Western Europe

Evolutionary diversification of the broadly distributed copepod sibling species complex Eurytemora affinis has been documented in the northern hemisphere. However, the fine scale geographic distribution, levels of genetic subdivision, evolutionary, and demographic histories of European populations have been less explored. To gain information on genetic subdivision and to evaluate heterogeneity among European populations, we analyzed samples from 8 locations from 58° to 45°N and 0° to 23°E, using 549 base pairs of the mitochondrial cytochrome oxidase subunit I (COI) gene. We discovered three distinct lineages of E. affinis in Western Europe, namely the East Atlantic lineage, the North Sea/English Channel (NSEC) lineage, and the Baltic lineage. These geographically separated lineages showed sequences divergence of 1.7–2.1%, dating back 1.9 million years (CI: 0.9–3.0 My) with no indication of isolation by distance. Genetic divergence in Europe was much lower than among North American lineages. Interestingly, genetic structure varied distinctively among the three lineages: the East Atlantic lineage was divided between the Gironde and the Loire populations, the NSEC lineage comprised one single population unit spanning the Seine, Scheldt and Elbe rivers and the third lineage was restricted to the Baltic Proper (Sweden). We revealed high haplotype diversity in the East Atlantic and the Baltic lineages, whereas in the NSEC lineage haplotype diversity was comparatively low. All three lineages showed signs of at least one demographic expansion event during Pleistocene glaciations that marked their genetic structure. These results provide a preliminary overview of the genetic structure of E. affinis in Europe.     

Association patterns and kinship in female Indo-Pacific bottlenose dolphins (Tursiops aduncus) of southeastern Australia

Kinship has been shown to be an important correlate of group membership and associations among many female mammals. In this study, we investigate association patterns in female Indo-Pacific bottlenose dolphins (Tursiops aduncus) inhabiting an embayment in southeastern Australia. We combine the behavioral data with microsatellite DNA and mitochondrial DNA data to test the hypotheses that genetic relatedness and maternal kinship correlate with associations and social clusters. Mean association between females was not significantly different from a random mean, but the standard deviation was significantly higher than a random standard deviation, indicating the presence of nonrandom associates in the dataset. A neighbor-joining tree, based on the distance of associations between females, identified four main social clusters in the area. Mean genetic relatedness between pairs of frequent female associates was significantly higher than that between pairs of infrequent associates. There was also a significant correlation between mtDNA haplotype sharing and the degree of female association. However, the mean genetic relatedness of female pairs within and between social clusters and the proportion of female pairs with the same and different mtDNA haplotypes within and between clusters were not significantly different. This study demonstrates that kinship correlates with associations among female bottlenose dolphins, but that kinship relations are not necessarily a prerequisite for membership in social clusters. We hypothesize that different forces acting on female bottlenose dolphin sociality appear to promote the formation of flexible groups which include both kin and nonkin.     

Genetic differentiation of the California spiny lobster Panulirus interruptus (Randall, 1840) along the west coast of the Baja California Peninsula, Mexico

Identifying reproductive stocks in commercial species is relevant to fishery management strategies. We obtained muscle samples of California spiny lobster (Panulirus interruptus) from six localities along the west coast of the Baja California Peninsula and analyzed the genetic structure using mtDNA RFLPs. Our results indicated that all localities shared the same major haplotypes and showed a spatial homogeneity in the distribution of haplotype frequencies. An analysis of molecular variance indicated that only 0.84% of the genetic variability was explained by differences among localities and was not significantly different from zero. Weak divergences were found between Bahía Magdalena, the most southerly locality, in relation to other populations. Major oceanographic processes along this coast, combined with a long larval period that supports passive transport among localities, are suggested to explain the results.     

Low levels of genetic variation in mtDNA sequences over the western Mediterranean and Atlantic range of the sponge<Emphasis Type="Italic"> Crambe crambe</Emphasis> (Poecilosclerida)

Crambe crambe is a common encrusting sponge found in the Mediterranean and Atlantic littoral. An analysis of a partial sequence (535 bp) of the mitochondrial DNA (mtDNA) gene cytochrome oxidase subunit I (COI) was conducted in an attempt to determine population structure in this species. This is the first study of population genetics using this kind of marker in the phylum. Samples (N=86) were taken in eight populations separated by distances from 20 to 3,000 km, spanning from the western Mediterranean to the Atlantic. Low variability of this gene was found, as only two haplotypes were identified, along with low nucleotide diversity (=0.0006). However, the different frequencies found among populations revealed genetic structure and low gene flow between close populations, as expected from the dispersal biology of the species. The low variability found in sponges is in agreement with reports on cnidarians and points to a high conservation of mtDNA in diploblastic phyla.     

Genetic structure,lack of sex-biased dispersal and behavioral flexibility in the pair-living fat-tailed dwarf lemur, <Emphasis Type="Italic">Cheirogaleus medius</Emphasis>

Mating system and dispersal patterns influence the spatio-genetic structure within and between populations. Among mammals, monogamy is rare, and its socio-genetic consequences have not been studied in detail before. The goal of our study was to investigate population history, demographic structure, and dispersal patterns in a population of pair-living fat-tailed dwarf lemurs, Cheirogaleus medius, a small, nocturnal primate from western Madagascar, and to infer their underlying behavioral mechanisms. Tissue samples for DNA extraction were obtained from a total of 140 individuals that were captured in two subpopulations about 3 km apart. Analyses of mtDNA variability at the population level revealed very low levels of genetic variability combined with high haplotype diversity, which is indicative of a recent population bottleneck. We found no evidence for spatial clustering of same-sexed individuals with identical haplotypes within each of two subpopulations but significant clustering between them. Thus, a high level of local subpopulation differentiation was observed (F _ST = 0.230). The sexes showed equal variances in the number of individuals representing each haplotype, as well as equal levels of aggregation of identical haplotypes. Hence, both sexes disperse from their natal area, one pattern expected in a pair-living mammal. There is a possibility of behavioral and social flexibility in this species, however, because we documented pronounced differences in density and sex ratio between the two subpopulations, suggesting that single study sites or populations may not be representative of a given local population or even species.     

Phylogeographic structure of <Emphasis Type="Italic">Octopus vulgaris</Emphasis> in South Africa revisited: identification of a second lineage near Durban harbour

In a previous study that investigated genetic structure of Octopus vulgaris along the South African coast by sequencing the mitochondrial cytochrome oxidase III gene (COIII), all sequences generated were identical. Such a finding is unusual, because mitochondrial DNA mutates quickly, and several marine invertebrates present in southern Africa show considerable genetic variation and structure. We reanalysed the samples using two different mitochondrial markers, namely cytochrome oxidase I (COI) and the large ribosomal subunit (16S rRNA). Sequences of both these markers showed variation. The conclusion of the previous study, that South Africa’s O. vulgaris population is characterised by a lack of genetic structure along the coast, is rejected. Some specimens from Durban (southeast Africa) were genetically more different from those found in the remainder of the country than were specimens from other regions (Tristan da Cunha and Senegal). We suggest that the lineage in Durban may have been recently introduced.     

Phylogeography of the sub-Antarctic notothenioid fish Eleginops maclovinus: evidence of population expansion

Phylogeography studies add insights into the geographic and evolutionary processes that underline the genetic divergence of populations. This work examines the geographic genetic structure of the Patagonian blennie, Eleginops maclovinus, a notothenioid (Perciformes) endemic to South American temperate and sub-Antarctic waters, using mitochondrial DNA cytochrome b sequences. We found 58 haplotypes in the analysis of 261 individual sequences of 833 base pairs in length. Among-population variance was very low (1.62%) and many haplotypes were shared between several populations across the species geographic range. Genetic differentiation was not consistent with a simple model of isolation by distance, possibly suggesting a lack of equilibrium between gene flow and local genetic drift. The analysis of mismatch distributions, neutrality tests, and the Bayesian Skyline Plot showed a pattern consistent with a recent population expansion event that may have taken place during the Middle Pleistocene.     

Impact of Hybridization on a Threatened Trout of the Southwestern United States

Trouts native to the American Southwest provide an excellent example of the plight of endangered fishes from this region. The native species, Apache trout and Gila trout ( Oncorhynchus apache and O. gilae , respectively) have faced drastic reduction in habitat and detrimental interactions with introduced species, resulting in a dramatic decrease in numbers and sizes of populations. We used biochemical methods to identify diagnostic markers for the estimation of genetic relatedness and analysis of hybridization among native trouts and introduced cutthroat and rainbow trouts ( O. clarki and O. mykiss , respectively). Restriction endonuclease analysis of mitochondrial DNA (mtDNA) indicated that Apache and Gila trout were very similar to each other, and more similar to rainbow trout than cutthroat. Diagnostic allozyme marker loci indicated that Apache trout hybridized extensively with rainbows in four populations and provided no evidence for reproductive isolation between the forms. Analysis of mtDNA, however, indicated that introduced haplotypes were rare in these same individuals, identifying a bias in the direction of gene exchange between species. The potential reproductive isolation and lack of information concerning population structure necessitate further study of Apache trout to determine the appropriate management strategy for this threatened species. This case demonstrates that extreme care must be exercised when considering elimination of any contaminated population lest the unique genetic identity of the native taxon be lost forever.     

Hierarchical population genetic structure in the commercially exploited shrimp <Emphasis Type="Italic">Crangon crangon</Emphasis> identified by AFLP analysis

The coastal shrimp Crangon crangon is an ecologically and commercially important species but there is limited knowledge of its genetic population structure. We utilised amplified fragment length polymorphisms (AFLPs) to investigate population differentiation among eight sampling locations comprising paired sites from north- and south-western Britain, the eastern English Channel and the Baltic Sea. Initial AMOVA and cluster analysis suggested strong differentiation, but outlier analysis identified three loci that might be subject to selection, one of which showed significant latitudinal variation in allele frequencies. Following exclusion of these outlier loci, and also of a divergent, genetically-impoverished sample from the UK Bristol Channel, cluster analysis revealed three major groupings, corresponding to geographical regions: western Britain, the eastern English Channel and the Baltic Sea. AMOVA identified significant differentiation both within and among these regions, with similar variation explained by each hierarchical level. C. crangon shows greater genetic structuring than has been found in many decapod crustaceans studied to date, and our results are consistent with unstable population sizes and gene flow restricted by distance and probably also hydrographic features. Further investigation of temporal stability in population structure is required, but broad-scale homogeneity of fishery stocks should not be assumed.