Analysis of the genetic structure of European eel (Anguilla anguilla) using microsatellite DNA and mtDNA markers

The spawning population of European eel (Anguilla anguilla L.) has been considered panmictic on the basis of genetic markers and morphometric studies. This hypothesis was tested by screening glass eel from five locations (Ireland, Italy, Morocco, Sweden and U.K.), belonging to two cohorts at the cytochrome b (cyt b) locus (392 bp) of the mitochondrion and at five nuclear microsatellite loci. Seventeen cyt b haplotypes were detected, of which ten were singletons; the most common haplotype occurred in 47% of all fish. Haplotype number increased significantly with latitude. Phylogeographical structure based on the cytoplasmic marker was weak (F_ST=0.014) and non-significant. Close similarity was revealed between British and Irish glass eel populations, and weak differentiation among the British/Irish, Atlantic Moroccan, Italian and Swedish Baltic populations, respectively. No hierarchical genetic structure was obvious. Levels of genetic variation detected with five microsatellites were much higher levels than found with allozymes in previous studies (mean number of alleles per locus=11.1; mean expected heterozygosity=0.68). Overall among-population microsatellite variance was low but significant (F_ST=0.004), and caused by the linked microsatellite loci Aan03 and Aan04. The Hardy-Weinberg-Castle equilibrium and the absence of gametic disequilibria at these loci in the Moroccan population might point to its genetic isolation, although the impact of just two out of five loci is puzzling. Given the weak differentiation typical for marine species and the limitations of our data, the results should be interpreted with caution. However, combined with recent evidence from a related study, the paradigm that the European eel constitutes a panmictic population becomes difficult to maintain.     

Mitochondrial DNA variation in Eritrean hamadryas baboons (Papio hamadryas hamadryas): life history influences population genetic structure

The hamadryas baboon, Papio hamadryas hamadryas, represents a rare exception from the pattern of female philopatry and male-biased dispersal predominant in mammals including primates. To elucidate the possible consequences of the dispersal pattern on the population genetic structure of hamadryas baboons, we sequenced the maternally transmitted mitochondrial hypervariable region I of 74 individuals from ten sampling locations in different ecogeographic zones of Eritrea. To this end, individual fecal samples were collected at sleeping cliffs. Upon comparing the individual sequences by means of phylogenetic tree reconstructions and AMOVA, we could not detect a population genetic structure corresponding to a geographic pattern. Tree reconstructions revealed the existence of two profoundly different lineages both present at most of the sampling locations. These findings and Mantel correlations of genetic distances and the frequency of shared haplotypes to geographic distances point to the presence of female dispersal. Female-mediated gene flow is detectable over geographic distances exceeding those between neighboring subpopulations. Our study therefore corroborates local behavioral observations on a broad geographic scale. After inclusion of geographically closely situated olive baboons, P. h. anubis, in the analyses, all anubis sequences fell within one hamadryas clade. Possible scenarios leading to this situation including long-term hybridization processes are discussed.     

Climate change and population genetic structure of marine species

Climate change influences populations by reducing or extirpating local populations, by disrupting patterns of migration and by shifting geographical distributions. These events can affect genetic population structure in several ways. Molecular markers have been used in numerous population genetic and phylogeographical studies of marine species and have detected population responses to climate change in the last few decades, such as range expansions, adaptative shifts and declines or increases in abundance. Little is known, however, about the molecular and physiological basis of adaptive responses to climate change in marine Mediterranean species. The Mediterranean Sea ecosystem is a ‘living laboratory’ with native species that are challenged by environmental change and by invasive species and a ‘gene-climate’ approach should be adopted as a way of focusing on the relationship between climate warming and genetic diversity.     

Population genetic structure of the prosobranch Nassarius reticulatus (L.) in a ria seascape (NW Iberian Peninsula) as revealed by RAPD analysis

Randomly amplified polymorphic DNA (RAPD) banding patterns were compared between samples of the netted dogwhelk Nassarius reticulatus from 11 locations along the NW Iberian Peninsula coast. To detect if rias (estuaries formed by drowned river valleys) might promote genetic differentiation, five sampling sites were located within a ria (ria of Muros) and the remaining six were scattered along open-coast areas at increasing distances from the ria mouth. Population differentiation statistics (Φ-values) were estimated using a hierarchical analysis of molecular variance (AMOVA) with samples sorted into two groups: open-coast and ria populations. Despite a high potential to disperse, AMOVA demonstrated a modest, statistically significant genetic heterogeneity among N. reticulatus populations. Most of the genetic structure resided in differences among open-coast populations; ria populations were genetically homogeneous. No obvious geographical pattern was detected for the pairwise genetic distances (non-metric multidimensional scaling; UPGMA tree; Mantel test). Unlike previous studies with other species at a variety of estuarine systems other than rias, there was no evidence that the ria of Muros may enhance the genetic divergence of N. reticulatus populations. This discrepancy is discussed in relation to the biological features of the species (high dispersal potential and a preference for mid-low estuarine habitat) and the strong hydrographic connectivity between ria and neighbouring off-shore waters.     

Phenotypic assortative mating and genetic population structure in the crab Trapezia digitalis

Colonies of Pocillopora spp. containing the crab Trapezia digitalis were collected from Hawaii in summer of 1979 and of 1980. Individuals of T. digitalis in Hawaii vary extensively in coloration of the carapace: crabs were separated into phenotypic classes by their degree of carapace reticulation. When presented with two females of different phenotype, males preferentially paired with the female which was similar to them in reticulation. The genetic population structure of T. digitalis was unusual by comparison with other species of Trapezia. Previously reported homozygote excesses at esterase-4, hexokinase-1, phosphoglucoseisomerase, and general protein-2 cannot be explained by the single-locus Wahlund effect, since there was not significant genetic differentiation among phenotypic classes, as measured by Wright's F _ST statistic. There was significant variation among classes in allele frequencies at a fifth locus, hexokinase-2. Two pairs of loci were in significant gametic disequilibrium. Gametic disequilibrium was not detected in seven other species of Trapezia. It is suggested that multi-locus genetic analysis and an increased geographic sampling range are needed to determine the genetic population structure of T. digitalis in relation to observed variation in coloration.     

Mode of larval development and genetic population structure inNodilittorina africana knysnaensis (Prosobranchia: Littorinidae)

We examined electrophoretic variation in the supralittoral gastropod,Nodilittorina africana knysnaensis, along the coast of South Africa in 1989. There was little allozyme variation in nine samples collected over 1 500 km for three highly polymorphic loci,Est, Gpi, andPgm, and Wahlund's effect was absent in the pooled sample. A gene diversity analysis showed that 98.1% of total genic diversity, on average, was contained within populations, and that only 1.9% was due to allozyme frequency differences among populations. Since the mode of larval development has not yet been described for this species, we suggest that the lack of strong allozyme frequency differences over long distances indicates thatN. a. knysnaensis has a planktonic mode of larval development.     

Seamount endemism questioned by the geographic distribution and population genetic structure of marine invertebrates

Previous studies have suggested that the high diversity associated with the Norfolk seamounts (Southwest Pacific) could reflect endemism resulting from limited dispersal due to hydrological phenomena. Crustaceans of the family Galatheidae are thoroughly studied in the New Caledonia economic zone permitting the analysis of species distribution pattern between the New Caledonia slope and Norfolk ridge seamounts. This analysis has shown that, qualitatively, the same species are sampled on seamounts and on the New Caledonia slope. Local endemism was never detected. However, on each seamount, and therefore on a small surface, a very high number of species are usually sampled, suggesting that seamounts are biodiversity hot spots. Then, to evaluate whether the seamounts constitute patches of isolated habitat, we explore the pattern of genetic diversity within several species of crustaceans and gastropods. Analysis of the intra-specific genetic structure using the mitochondrial marker COI reveals that populations of two Galatheidae species (Munida thoe and Munida zebra), polymorphic for this marker, are genetically not structured, both among seamounts and between the seamounts and the island slope. The genetic structure over a similar sampling scheme of two Eumunida species (Chirostylidae, the sister family of Galatheidae) and a planktotrophic gastropod (Sassia remensa) reveals a similar pattern. Population structure is observed only in Nassaria problematica, a non-planktotrophic gastropod with limited larvae dispersal. Thus, the limitation of gene flow between seamounts appears to be observed only for species with limited dispersal abilities. Our results suggest that the Norfolk seamounts rather than functioning as areas of endemism, instead, may be highly productive zones that can support numerous species in small areas.     

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.     

Comparative population genetic structure of marine gastropods (Littorina spp.) with and without pelagic larval dispersal

 Population genetic theory predicts that marine animal species with planktonic larvae will have less genetic structure than those with direct development. We compared the genetic structure of four species of littorinid snails – two with planktonic egg capsules that hatch as planktonic larvae and two with benthic egg masses that hatch as crawl-away juveniles. We used DNA sequencing and single stranded conformational polymorphism (SSCP) to assess sequence variation in a 480 bp fragment of the mitochondrial cytochrome b gene and then used an analysis of molecular variance (AMOVA) to estimate Φ_st for populations from the northeastern Pacific coast. One of the two direct-developing species, Littorina subrotundata, had a moderate amount of population structure (Φ_st=0.209) as expected but the other direct-developing species, L. sitkana, was nearly fixed for a single haplotype that made it impossible to precisely estimate Φ_st. One of the two planktonic-developing species, L. scutulata, did not show any significant population structure (Φ_st=0.004). In contrast to our expectations, the other planktonic-developing species, L. plena, showed some weak but statistically significant population structure (Φ_st=0.052). We discuss how differences in population genetic structure between species with the same type of development may reflect differences in their historical demography. Received: 22 December 1999 / Accepted: 24 July 2000     

Phylogeny and biogeographic history of hake (genus Merluccius), inferred from mitochondrial DNA control-region sequences

 Phylogenetic analyses of the left domain of the mitochondrial DNA control-region sequence have been used to examine the relationships among species of the genus Merluccius (Rafinesque, 1810), and to compare these with hypotheses based on morphological, meristic and allozyme characters. Analysis of aligned sequences revealed that transition bias was much lower than in mammalian mtDNA, and that nucleotide composition of control-region sequences was biased toward A and T. We have roughly calibrated a molecular clock for the genus, based on the rise of the Isthmus of Panamá, which is believed to have created a barrier to dispersal between marine species of the Atlantic and Pacific Oceans. Our mtDNA-based phylogeny was highly congruent with allozyme-based phylogenies, but poorly so with a previously described phylogeny based on morphology. Specifically, our phylogeny resolved two well-supported principal clades, one of American (west Atlantic and east Pacific) species and the other of Euro–African (east Atlantic) species. This suggests an evolutionary history during which the ancestral lineage of Merluccius was divided between two geographic regions, with subsequent dispersal and vicariant events resulting in the evolution and distribution of extant taxa. However, the relationships between some taxa within the American clade could not be resolved. We suggest that this is consistent with an hypothesis of a rapid origin and radiation of these taxa. Received: 12 December 1998 / Accepted: 15 October 1999     

Small-scale spatial and temporal genetic structure of the Atlantic sea scallop (Placopecten magellanicus) in the inshore Gulf of Maine revealed using AFLPs

Despite long planktonic durations, many species of broadcast spawning invertebrates exhibit genetic structure at small spatial and temporal scales. Amplified fragment length polymorphisms were used to assess genetic variation in the sea scallop, Placopecten magellanicus, among four inshore and one offshore location in the Gulf of Maine and temporal genetic variation among age classes of sea scallops at one site. Our results indicated that genetic structure for P. magellanicus exists on smaller spatial scales (tens to hundreds of kilometers) than expected given the 40-day planktonic larval period. In addition, genetic differences among age classes may be influenced by inter-annual differences in larval supply or reproductive success. Future genetic studies should sample multiple age classes prior to comparison among locations.     

Alternative reproductive tactics in the queen-size-dimorphic ant Leptothorax rugatulus (Emery) and their consequences for genetic population structure

We report the results of a comprehensive investigation of the queen size dimorphism in the North American ant Leptothorax rugatulus. Employing allozymes and microsatellites as genetic markers, we found no evidence that the gene pools of large (macrogynes) and small (microgynes) queens are distinct. Queens in polygynous colonies are related to each other, supporting the hypothesis that colonies with more than one queen commonly arise by the adoption of daughter queens into their natal colonies. The higher fat content of macrogynes, their predominance in monogynous societies and in small founding colonies, and their greater flight activity favor the view that macrogynes predominantly found colonies independently, while microgynes are specialized for dependent colony founding by readoption. When comparing the genetic structure of three different subpopulations, we found that the alternative life histories had no significant effect on population viscosity at the scale investigated.     

Levels of social behaviors and genetic structure in a population of round-tailed ground squirrels (Xerospermophilus tereticaudus)

Ground-dwelling sciurids exhibit a continuum of sociality and several models predict levels of sociality within this taxon. Models of ground squirrel sociality predict round-tailed ground squirrels (Xerospermophilus tereticaudus) to be solitary; however, previous behavioral studies suggest round-tailed ground squirrels have a matrilineal social structure. To resolve this discrepancy, we combined behavioral observations with genetic analyses of population structure. We assessed levels of agonistic and amicable behaviors combined with fine-scale population genetic structure of round-tailed ground squirrels in a multi-year study in AZ. Only 45 agonistic and 40 amicable interactions were observed between adults in over 137 h of observations. Overall rates of agonistic or amicable interactions between adults were low (≤0.69/h), with no relationship between relatedness of individuals and rates of either amicable or agonistic interactions. Interactions between juvenile littermates were predominantly amicable. Population substructure was not evident with Bayesian analyses, global or pairwise F _ST values; average relatedness among females was not different from males. However, in 2006, the year after a population reduction through targeted animal elimination, a population bottleneck was detected within at least five of seven loci. Contrary to previous behavioral studies, this population of round-tailed ground squirrels, although aggregated spatially, did not exhibit high levels of social behavior nor subpopulation genetic structure. Analyses of the genetic relationships and sociality along a continuum, particularly within aggregates of individuals, may lead to insights into the origin and maintenance of social behaviors by elucidating the mechanisms by which aggregates with intermediate social levels are formed and maintained.     

Population genetic structure of the brown tiger prawn, Penaeus esculentus, in tropical northern Australia

Eight polymorphic microsatellite loci were analysed in six population samples from four locations of the Australian endemic brown tiger prawn, Penaeus esculentus. Tests of Hardy–Weinberg equilibrium were generally in accord with expectations, with only one locus, in two samples, showing significant deviations. Three samples were taken in different years from the Exmouth Gulf. These showed no significant heterogeneity, and it was concluded that they were from a single panmictic population. A sample from Shark Bay, also on the west coast of Australia, showed barely detectable differentiation from Exmouth Gulf (F _ST = 0 to 0.0014). A northeast sample from the Gulf of Carpentaria showed low (F _ST = 0.008) but significant differentiation from Moreton Bay, on the east coast. However, Exmouth Gulf/Shark Bay samples were well differentiated from the Gulf of Carpentaria/Moreton Bay (F _ST = 0.047–0.063). The data do not fit a simple isolation by distance model. It is postulated that the east–west differentiation largely reflects the isolation of east and west coast populations that occurred at the last glacial maximum when there was a land bridge between north-eastern Australia and New Guinea.     

RFLP analysis of the mtDNA control region in white shrimp (Litopenaeus vannamei) populations from the eastern Pacific

White shrimp (Litopenaeus vannamei) population genetic structure from the eastern Pacific was determined by restriction fragment length polymorphism analysis of the mitochondrial DNA control region. Four localities were surveyed with four endonucleases (Alu I, Taq I, Spe I, Ssp I) yielding 48 composite haplotypes. White shrimp showed high average within-locality haplotype (0.823) and nucleotide (5.41%) diversities and also high average nucleotide divergence between all pairs of localities (0.73%). A mismatch analysis of pairwise differences between haplotypes indicated that white shrimp does not fit the sudden population expansion model. An analysis of molecular variance showed significant geographic variation in the frequencies of haplotypes (Φ_ST=0.1382, P<0.0001). Population differentiation may be maintained by a combination of physical, oceanographic, and biological factors acting as barriers to gene flow among localities. Because of its high polymorphism, the control region might be useful as a genetic marker for monitoring genetic diversity in aquaculture stocks.     

Hydrology influences population genetic structure and connectivity of the intertidal amphipod Corophium volutator in the northwest Atlantic

The mechanisms driving genetic structure in marine systems are elusive due to the difficulty of identifying temporal and spatial barriers to dispersal. By studying marine invertebrate species with limited dispersal potential, genetic structure can be directly related to physical and biological factors restricting connectivity. In the northwest Atlantic, the benthic brood-rearing amphipod Corophium volutator is distributed across basins with distinct circulation patterns and has the potential to disperse passively during its adult stage. We analyzed spatial genetic variation and migration rates across C. volutator’s North American range with sequence data for mitochondrial DNA and three novel nuclear markers using frequency and coalescent-based methods. We found low genetic differentiation within basins, but strong subdivision within the Bay of Fundy and a striking biogeographic break between the Bay of Fundy and Gulf of Maine, suggesting that genetic drift may act on populations in which connectivity is restricted due to the limitation of passive dispersal by hydrological patterns.     

A biochemical genetic study of population structure in queen scallop (Chlamys opercularis) stocks in the Northern Irish Sea

Electrophoresis was used to survey a number of enzymes for loci of potential value as stock markers in Chlamys opercularis (L.). Two loci, Pgi and Pgd, were then studied in larger samples from each of two localities around the Isle of Man. One Pgi allele was found to be restricted to a particular year-class in both populations. This was confirmed by subsequent studies of three further populations, in each of which the same allele occurred only in the one year-class. Otherwise, no significant differences in allele frequencies were found between year-classes or between populations in any of the samples used. From the results it is concluded that there is temporal variation in the sources of recruitment of C. opercularis stocks around the Isle of Man. Possible origins of larvae contributing to these stocks are discussed in the light of what is known of current circulation patterns in the northern Irish Sea.     

Effects of brooding and broadcasting reproductive modes on the population genetic structure of two Antarctic gastropod molluscs

Life-history characteristics exert a profound influence upon the population structure of many marine organisms. However, relatively few genetic studies have compared direct with indirect-developing species in the same ecosystem or geographical region, and none to our knowledge within an Antarctic setting. To address this issue, we have collected novel amplified fragment length polymorphism (AFLP) data from the direct-developing top shell Margarella antarctica to form a comparison with previously published data for the broadcast-spawning Antarctic limpet Nacella concinna. We scored 270 loci in 240 M. antarctica individuals sampled from five populations spanning the full length of the Antarctic Peninsula. Profound differences were identified in the strength and pattern of population structure between the two species, consistent with gene flow being highly restricted in M. antarctica relative to N. concinna.     

Population structure of the widely dispersing marine bryozoan Membranipora membranacea (Cheilostomata): implications for population history, biogeography, and taxonomy

Morphologically plastic, cryptic, or geographically widespread species pose similar challenges to the evolutionary biologist: their taxonomic status is often unclear yet must be known to study almost any aspect of their biology, ecology, evolution, or biogeography. The marine bryozoan Membranipora membranacea (L.) is morphologically plastic and geographically widespread in temperate oceans of the Northern and Southern Hemispheres, and its taxonomy is unclear. This study examined genetic relationships among allopatric populations and sympatric morphs of this species, or species complex. Colonies were collected from 1992 to 1995. Allozymes were used to elucidate the relationships among four widely separated populations, two in the North Atlantic and two in the North Pacific Ocean. Allozymes and mtDNA sequencing were used to clarify the genetic relationships among three sympatric morphs that might correspond to the species M. villosa Hincks and M. membranacea in the northeastern Pacific (Washington State). Populations in the North Atlantic and North Pacific had no fixed allelic differences at the loci tested but were separated by an average Nei's genetic distance of 0.581, suggesting their near-sibling species status. Populations from Friday Harbor (Washington) and Catalina Island (California) were not significantly differentiated, which was attributed to high gene flow. Populations on either side of the North Atlantic were genetically indistinguishable, which is most likely due to the recent establishment of the West Atlantic populations from European founders. At Friday Harbor, sympatric morphs varying in their spination and spine inducibility were genetically indistinguishable, supporting the hypothesis that M. villosa is an induced phenotype of M. membranacea and not a distinct species in the northeastern Pacific. Since such phenotypic plasticity is common in cheilostome bryozoans, the morphospecies concept must be used with caution. Received: 31 August 1998 / Accepted: 10 August 1999