Genetic diversity and relatedness of the mangrove Rhizophora mangle L. (Rhizophoraceae) using amplified fragment polymorphism (AFLP) among locations in Florida, USA and the Caribbean

Rhizophora mangle L. is a widespread mangrove species in the Western Hemisphere. Mangrove habitat loss and their importance to coastal and reef ecosystems make greater understanding of their genetic structure useful for conservation and management. An amplified fragment polymorphism (AFLP) analysis was performed on samples from Florida and the Caribbean to discover the genetic structure present. R. mangle had variable genetic diversity not related to latitude; P ranged 7 %–92 %. Some other factor, perhaps human impact, has caused low genetic diversity in some populations. Across Florida R. mangle populations varied in genetic diversity with less diversity (G_st?=?0.195) and greater gene flow on the Atlantic coast (Nm =2.07) than on the Gulf coast (G_st?=?0.717, Nm?=?0.197). Gene flow between Caribbean islands was low (Nm?=?0.386) compared to continental populations (Nm?=?1.40), indicating that long distance dispersal is not common between islands. Analysis of molecular variance (AMOVA) analysis showed significant deviations from Hardy-Weinberg expectations at the level of region among subpopulations and overall genetic difference among subpopulations for R. mangle. One implication for management is that small continental populations and island populations may be genetically isolated and distinct from each other.     

Allozyme variation in European populations of the oyster Ostrea edulis

Variations at 22 enzyme coding loci were surveyed in 11 populations of the oyster Ostrea edulis L., which were sampled between 1988 and 1990 along the Atlantic and Mediterranean coasts of Europe. Atlantic oyster beds suffered a steady decline during the last century, and restocking of beds with oysters of foreign origin has probably resulted in a high degree of interbreeding of natural oyster stocks from all Atlantic Europe. Our study confirms the low levels of genetic variability previously reported for the oyster populations from the Atlantic coasts, and extends it to the Mediterranean coasts. The locus arginine-kinase (ARK ^*) exhibited a high degree of interpopulation differentiation (F _ST=0.289), resulting from extensive variation in gene frequencies along a geographical cline. However, the overall genetic differentiation between populations was slight, and similar to that reported for other local populations of bivalves (mean genetic distance between populations is 0.010, mean F _ST=0.062). A general pattern of increasing differentiation along the coastline in an Atlantic-mediterranean direction emerged; but genetic differentiation among the Atlantic populations was not significantly lower than that observed among the Mediterranean populations. This and other results suggest that the effects of extensive transplantation of oysters among various areas in Europe are detectable only in some particular localities. The geographical distribution of low-frequency alleles suggests a restriction to gene flow outwards from the Mediterranean Sea, across the Straits of Gibraltar.     

Genetic and environmental effects on the growth rate of Littorina saxatilis

Transfer experiments with two morphs of Littorina saxatilis Olivi (=L. rudis) typically inhabiting exposed and sheltered localities, showed a between-morph difference in shell growth in the same type of habitat, and a withinmorph difference between exposed and sheltered environments. The former indicates a genetic difference between the two morphs, although growth rate has an environmental component as shown by the latter. Juvenile snails of the exposed morph were on average slightly larger than sheltered morph juveniles on hatching, but at 20 wk, when raised in identical environments, the sheltered morph juveniles had grown significantly larger than the exposed ones. A rise in temperature from 5° to 10°C enhanced growth rate for snails raised in the laboratory. Temperature alone could not however explain increased growth during the spring and summer in natural populations.     

Multivariate morphometric analysis of two varieties of Littorina saxatilis from the Swedish west coast

Shell variation in Littorina saxatilis Olivi (=L. rudis) is examined with different techniques of multivariate analysis (canonical variate-, multiple discriminant-, principal component-, and principal coordinate analysis). In bivariate projections of the analyses, two populations, spatially only 60 m apart, but from different habitats, showed a phenotypic separation without overlap. One habitat is a boulder shore, while the other is a rocky cliff. A sample, geographically and environmentally intermediate to the exposed and sheltered populations, covered completely the morphologic gap between the two former groups, indicating a clinal variation in morphology over the environmental gradient exposed — sheltered. From this it is concluded that the two phenotypically distinct populations belong to the same species.     

Pathogen-induced hatching and population-specific life-history response to waterborne cues in brown trout (Salmo trutta)

Hatching is an important niche shift, and embryos in a wide range of taxa can either accelerate or delay this life-history switch in order to avoid stage-specific risks. Such behavior can occur in response to stress itself and to chemical cues that allow anticipation of stress. We studied the genetic organization of this phenotypic plasticity and tested whether there are differences among populations and across environments in order to learn more about the evolutionary potential of stress-induced hatching. As a study species, we chose the brown trout (Salmo trutta; Salmonidae). Gametes were collected from five natural populations (within one river network) and used for full-factorial in vitro fertilizations. The resulting embryos were either directly infected with Pseudomonas fluorescens or were exposed to waterborne cues from P. fluorescens-infected conspecifics. We found that direct inoculation with P. fluorescens increased embryonic mortality and induced hatching in all host populations. Exposure to waterborne cues revealed population-specific responses. We found significant additive genetic variation for hatching time, and genetic variation in trait plasticity. In conclusion, hatching is induced in response to infection and can be affected by waterborne cues of infection, but populations and families differ in their reaction to the latter.     

Genetic differentiation in populations of two Palaemon prawn species at the Atlantic east coast: does gene flow prevent local adaptation?

Two Palaemon prawn species, P. adspersus Rathke and P. squilla (L.), occur along the European Atlantic coast. In areas heavily affected by tides (Netherlands and France), one species, P. squilla, inhabits the intertidal zone, and P. adspersus is found subtidally in the Zostera marina meadows. In areas with small tidal ranges (Sweden) both species occur in the Z. marina zone, and here the body size of P. squilla is reduced, something that in turn reduces reproductive output in this species. Is adaptive improvement in non-tidal P. squilla populations prevented by too extensive gene flow from tidal areas? To wanswer this, genetic differentiation was studied by horizontal starch gel electrophoresis. Each of the two species was sampled at five sites along the European Atlantic coast. Twenty-two enzymes representing 25 loci were scored. Significant genetic heterogeneity between sites was found in both species. Thus the extensive gene flow hypothesis was not supported by the results, and non-tidal populations ought to have the possibility to adapt to local conditions.     

Genetic evidence for the occurrence of a cryptic species with the littoral nemerteans Lineus ruber and L. viridis (Nemertea: Anopla)

Lineus ruber and L. viridis are common intertidal heteronemerteans found on the coasts of northern Europe and the east coast of North America. The two species resemble each other morphologically and were synonymised for many years prior to being separated on the basis of larval development. In this study, specimens of L. ruber and L. viridis were collected from sites along the west and southwest coast of Britain, northern France and the east coast of North America. The external morphology and allele frequencies of isozymes of the two species were compared from all sites. The external morphology of L. ruber and L. viridis was similar but they could generally be separated by colour. Allele frequencies for up to 13 enzyme loci between sympatric populations of L. ruber and L. viridis indicated that these two species are genetically very different (Nei's genetic identity=0.090 to 0.083). Allele-frequency data also indicated the presence of a third genetic type occurring sympatrically with populations of both L. ruber and L. viridis on the coasts of Britain and France but not on the coast of North America. Fixed differences in allele frequencies between populations of the third genetic type and sympatric populations of L. ruber and L. viridis were observed across multiple loci. Genetic identity between the third genetic type and sympatric populations of L. ruber and L. viridis were extremely low (Nei's genetic identity =<0.078). Such large genetic differences between populations indicate a barrier to gene flow and reproductive isolation. The aberrant type, which exhibits sufficient morphological variation to prevent individuals being distinguished from those of both L. ruber and L. viridis, therefore represents a separate species. The low genetic identities found in intrageneric comparisons of species found in this study have been found in other studies on nemerteans. They may indicate systematic problems within these groups or other phenomena such as morphological stasis.     

Population genetic variation in the New Zealand greenshell mussel: locus-dependent conflicting signals of weak structure and high gene flow balanced against pronounced structure and high self-recruitment

A pronounced north–south multitaxon genetic discontinuity occurs in central New Zealand (NZ). Polymorphic microsatellite markers have been used to test the location and structure of this discontinuity in the endemic greenshell mussel, Perna canaliculus. Nine neutral loci revealed limited evidence of genetic structure, but one outlier locus (Pcan1-27) which may be under selection provided evidence of the discontinuity in central NZ. Whilst the limited multilocus evidence of structure is assumed to result from high levels of gene flow among populations of this continuously distributed species, assignment tests indicated high to very high mean levels of self-recruitment within the 14 populations and the north and south regions. The nine neutral loci were unable to provide further clarification as to the geographic location of the discontinuity, whereas the Pcan1-27 locus was particularly informative. These results highlight a tension between limited evidence of genetic structure and presumptive high gene flow among populations versus high levels of self-recruitment and pronounced structure depending on microsatellite loci and analyses in question. Evidence from all 10 loci indicates that the genetic discontinuity is maintained by high levels of self-recruitment, and evidence from Pcan1-27 suggests that selection may also be important in explaining the existence of the discontinuity.     

Transplantation of the Subshrub Lotus scoparius: Testing the Home-Site Advantage Hypothesis

Abstract: The long-term success of restored populations may be jeopardized by the collection locality of transplants if they are ill matched to their new environment. The home-site advantage hypothesis predicts that the relative success of introduced populations will decrease as their genetic and environmental distance to the local native population increases. We evaluated this hypothesis for a geographically variable shrub, Lotus scoparius , in southern Californian coastal sage scrub by planting two common-garden experiments with seedlings from 12 source populations. The common-garden sites differed in environment and were each home to different source populations of the two taxonomic varieties, L. s. var. scoparius or L. s . var. brevialatus . We used allozyme data from each source population to calculate genetic distances between populations, and a combination of climatic data and soil traits to calculate environmental distances. At the more mesic, coastal common garden, cumulative fitness of transplants (survival × flower production) was inversely related to genetic distance between source and resident populations. At the more xeric, inland common garden, cumulative fitness (survival × size) decreased significantly with both genetic and environmental distance after one taxonomic variety was excluded from analyses. Geographic distance was only weakly correlated with genetic distance and had little value in predicting cumulative fitness of transplants. Our data support the home-site advantage hypothesis and the idea that mis-matching source populations of these genetically differentiated seed sources may result in lowered success of restored or constructed populations. The genetic and environmental similarities of source populations should be considered when source materials are chosen for transplantation.     

Correlation between pelagic larval duration and realised dispersal: long-distance genetic connectivity between northern New Zealand and the Kermadec Islands archipelago

The extent to which marine populations are “open” (panmixia) or “closed” (self-recruitment) remains a matter of much debate, with recent reports of high levels of genetic differentiation and self-recruitment among populations of numerous species separated by short geographic. However, the interpretation of patterns of gene flow (connectivity) is often based on a stepping stone model of dispersal that can genetically homogenise even distant populations and blur genetic patterns that may better reflect realised dispersal. One way in which realised long-distance dispersal can be accurately determined is by examination of gene flow of taxa between isolated archipelagos and a mainland where there is no possible stepping stone dispersal across the open ocean. We investigated the genetic structuring of populations of the intertidal gastropod Nerita melanotragus from the subtropical Kermadec Islands and temperate New Zealand’s North Island (the mainland), separated by 750 km of open ocean and characterised by contrasting environmental conditions. Analyses of seven microsatellite markers revealed an absence of genetic structuring with low F _ST and Jost’s D values (from 0.000 to 0.007 and from 0.000 to 0.015, respectively) over large geographic distances and no evidence of isolation by distance among all populations. These results indicate that the realised dispersal of N. melanotragus is of at least 750 km, this species exhibits a very “open” form of connectivity and its larvae exhibit sufficient phenotypic plasticity to settle successfully in different environmental conditions, ranging from subtropical to cool temperate.     

Genetic diversity,clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular,fragmented reef system

Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation was detected both between and within islands, but when a single sample per MLG was included in the analyses, the populations turned out to be nearly panmictic. These observations provide further evidence of the marked variability in reproductive strategies and genetic structure of P. damicornis throughout its geographic range; comparison with results previously obtained for the congeneric species Pocillopora meandrina underlines the importance of life history traits in shaping the genetic structure of coral populations.     

Multi-marker estimate of genetic connectivity of sole (Solea solea) in the North-East Atlantic Ocean

A thorough knowledge on the genetic connectivity of marine populations is important for fisheries management and conservation. Using a dense population sampling design and two types of neutral molecular markers (10 nuclear microsatellite loci and a mtDNA cytochrome b fragment), we inferred the genetic connectivity among the main known spawning grounds of sole (Solea solea L.) in the North-East Atlantic Ocean. The results revealed a clear genetic structure for sole in the North-East Atlantic Ocean with at least three different populations, namely the Kattegat/Skagerrak region, the North Sea and the Bay of Biscay, and with indications for a fourth population, namely the Irish/Celtic Sea. The lack of genetically meaningful differences between biological populations within the southern North Sea is likely due to a large effective population size and sufficient connection (gene flow) between populations. Nevertheless, an isolation-by-distance pattern was found based on microsatellite genotyping, while no such pattern was observed with the cytochrome b marker, indicating an historical pattern prevailing in the latter marker. Our results demonstrate the importance of a combined multi-marker approach to understand the connectivity among marine populations at region scales.     

Effects of habitat fragmentation on the genetic structure and connectivity of the black-lipped pearl oyster Pinctada margaritifera populations in French Polynesia

Habitat destruction leading to increased fragmentation is detrimental to species by reducing population size and genetic diversity and by restraining population connectivity. However, little is known about the effects of naturally fragmented habitats on wild populations, especially when it comes to marine benthic invertebrates with long pelagic larval duration. In this framework, we investigated the connectivity and genetic diversity variation among nine wild populations of the black-lipped pearl oyster, Pinctada margaritifera, throughout French Polynesia using ten microsatellite DNA markers. Despite the naturally fragmented habitat (South Pacific oceanic islands), we found high values of genetic diversity and population admixture, indicating connectivity at small and large spatial scales within sampled sites of the Tuamotu, and between the Society and Tuamotu Archipelagos. In the meantime, habitat geomorphology increased genetic drift in populations occurring in small, closed lagoons. Significant genetic structure not correlated to geographic distance was detected mainly between closed and open lagoons. The Marquesas Islands hosted the most divergent populations, likely a result of vicariance. Our results also highlight that migration patterns among lagoons are not symmetrical. Altogether, the general pattern of gene flow, nonsymmetrical migration rates among populations, absence of isolation by distance and absence of recent extinction events found in our study strongly suggest that P. margaritifera populations of French Polynesia follow an asymmetrical island model of dispersal.     

Genetic analysis of shell-shape variation in Littorina saxatilis on an environmental cline

Three shell-shape parameters of Littorina saxatilis were measured and found to vary in a regular pattern with distance up an estuary. The translation rate of the shell increased, the rate of whorl expansion decreased and the circularity of the aperture decreased proceeding from the exposed shore to the protected shore. The genetic variance of these traits was estimated from the full-sib covariance and the motheroffspring covariance. The genetic variance of the translation rate and the circularity of the aperture was low in all populations, but the genetic variance of the rate of whorl expansion was high on the exposed shore and low on the protected shore. It is argued that the change in mean phenotype of these traits is the result of natural selection produced by varying degrees of wave action and desiccation. The observed genetic variance is consistent with the theory that a trait under selection will show little additive genetic variance.     

Effects of isolation by distance and geographical discontinuity on genetic subdivision of Littoraria cingulata

Littoraria cingulata (Philippi, 1846) is a Western Australian, mangrove littorine snail, represented by two morphologically distinct subspecies, whose distributions are separated by >300 km. The southern subspecies, L. cingulata pristissini, is distinguished from the northern subspecies, L. cingulata cingulata, by having a thinner, keelless shell with more primary grooves, and lower and much more numerous ribs. In contrast with these striking differences, L. cingulata cingulata is morphologically very similar to another species, L. sulculosa, with which it also shares a nearly coincident geographic range. Allozyme comparisons at 22 presumptive loci confirmed a large genetic distance between L. cingulata and L. sulculosa, and the apparent conspecificity of the morphologically divergent subspecies of L. cingulata. Based on geological evidence, the geographical separation of the morphologically divergent forms of L. cingulata has developed within the past 5000 to 10 000 yr. The extensive continuous distribution of the northern subspecies, L. cingulatacingulata, and the large geographic disjunction between the northern and Shark Bay subspecies, L. cingulata pristissini, allowed a test of the genetic importance of this relatively recent disjunction. Within the continuous distribution of the two subspecies, a pattern of isolation by distance was visible up to distances of 300 km. Beyond 300 km, genetic subdivision, measured by pairwise G _ST (the proportion of genetic diversity due to differences between populations), averaged 0.028, whereas subdivision between Shark Bay and northern populations averaged 0.055 over the same range of distances. Although the relative paucity of barriers to gene flow tends to limit genetic subdivision in marine species with planktotrophic larvae, the results for L. cingulata suggest that subdivision can occur within a continuous distribution, but that special events leading to major disjunctions can substantially increase divergence, even over a relatively short period of time. Received: 16 February 1998 / Accepted: 23 April 1998     

No reproductive character displacement in male advertisement signals of Hyla japonica in relation to the sympatric H. suweonensis

Reproductive interaction between closely related taxa may leave a distinctive signature in which populations of interacting taxa are more dissimilar in sympatry than in allopatry. An ideal condition for such a pattern of reproductive character displacement (RCD) may occur when a population has limited gene flow and experiences strong selection pressure, exerted by an interacting taxon in areas of sympatry. In Korea, there are two closely related treefrog species: Hyla japonica, which is distributed widely throughout the country, and Hyla suweonensis, which occurs sympatrically in a narrow strip of western coastal plains. H. suweonensis is only found within the distribution of H. japonica. These two species have a similar single-note call structure. Here, we tested the possibility of RCD in H. japonica by examining geographic variation in advertisement calls. Although means of temporal and spectral characters were significantly different between the two species, sympatric populations of H. japonica and H. suweonensis overlapped in distributions of most characters. Furthermore, allopatric and sympatric H. japonica populations did not differ in all call characters. Weak genetic differentiation between sympatric and allopatric populations of H. japonica implied either substantial gene flow or recent genetic isolation. Possible explanations for no RCD in male advertisement calls of H. japonica include a difference in fine temporal characteristics between the two species, migration between sympatric and allopatric localities in H. japonica, RCD in female preferences in H. japonica, and weak selection pressure by H. suweonensis.     

Population differentiation in megrim (<Emphasis Type="Italic">Lepidorhombus whiffiagonis</Emphasis>) and four spotted megrim (<Emphasis Type="Italic">Lepidorhombus boscii</Emphasis>) across Atlantic and Mediterranean waters and implications for wild stock management

Megrim, Lepidorhombus whiffiagonis, and four spot megrim, Lepidorhombus boscii, are two marine fish species of high commercial interest. Despite their quite heavy exploitation little is known on the genetic structure of their populations. The present work aimed at characterizing the first seven microsatellites markers available for the two megrim species. These new markers were in a second step employed to describe the population structure of the two species among their almost entire habitat range (Atlantic and Mediterranean samples). Our study confirmed the existence of a strong genetic difference between Atlantic and Mediterranean megrim species already described in the literature for L. whiffiagonis on the basis of variations at ribosomal genes. Additionally our analysis gave the first evidences of a strong genetic differentiation among Atlantic populations in both megrim species (within Atlantic global F_ST in L. whiffiagonis and L. boscii were respectively 0.158 and 0.145). When describing megrim population structure, the comparison between allele-frequency-based tests (F_ST comparisons) and genotype-based inferences (Bayesian approach) gave evidences of a hierarchical structure of the populations. In conclusion, our work enlighten the existence of two different stocks within the Atlantic Ocean and one in the Mediterranean Sea that will clearly need to be managed separately. As the present results do not fully support the current megrim stock boundaries they will surely help to rethink megrim management policies in the future.     

Do dominants have higher heterozygosity? Social status and genetic variation in brown trout, Salmo trutta

A key question of evolutionary importance is what factors influence who becomes dominant. Individual genetic variation has been found to be associated with several fitness traits, including behaviour. Could it also be a factor influencing social dominance? We investigated the association between social status and the amount of intra-individual genetic variation in juvenile brown trout (Salmo trutta). Genetic variation was estimated using 12 microsatellite loci. Dominant individuals had higher mean heterozygosity than subordinates in populations with the longest hatchery background. Heterozygosity–heterozygosity correlations did not find any evidence of inbreeding; however, single-locus analysis revealed four loci that each individually differed significantly between dominant and subordinate fish, thus giving more support to local than general effect as the mechanism behind the observed association between genetic diversity and a fitness-associated trait. We did not find any significant relation between mean d ² and social status, or internal relatedness and social status. Our results suggest that individual genetic variation can influence dominance relations, but manifestation of this phenomenon may depend on the genetic background of the population.     

Determining the community structure of the coral Seriatopora hystrix from hydrodynamic and genetic networks

The exchange of genetic information between coral reefs through the transport of larvae can be described in terms of networks that capture the linkages between distant populations. A key question arising from these networks is the determination of the highly connected modules (communities). Communities can be defined using genetic similarity or distance statistics between multiple samples but due to limited specimen sampling capacity the boundaries of the communities for the known coral reefs in the seascape remain unresolved. In this study we use the microsatellite composition of individual corals to compare sample populations using a genetic dissimilarity measure (F_ST) which is then used to create a complex network. This network involved sampling 1025 colonies from 22 collection sites and examining 10 microsatellites loci. The links between each sampling site were given a strength that was created from the pair wise F_ST values. The result is an undirected weighted network describing the genetic dissimilarity between each sampled population. From this network we then determined the community structure using a leading eigenvector algorithm within graph theory. However, given the relatively limited sampling conducted, the representation of the regional genetic structure was incomplete. To assist with defining the boundaries of the genetically based communities we also integrated the communities derived from a hydrodynamic and distance based networks. The hydrodynamic network, though more comprehensive, was of smaller spatial extent than our genetic sampling. A Bayesian Belief network was developed to integrate the overlapping communities. The results indicate the genetic population structure of the Great Barrier Reef and provide guidance on where future genetic sampling should take place to complete the genetic diversity mapping.     

Phylogeography of the seaweed Ishige okamurae (Phaeophyceae): evidence for glacial refugia in the northwest Pacific region

Although benthic marine algae are essential components of marine coastal systems that have been influenced profoundly by past and present climate change, our knowledge of seaweed phylogeography is limited. The brown alga Ishige okamurae Yendo occurs in the northwest Pacific, where it occupies a characteristic belt in the exposed intertidal zone. To understand the patterns of genetic diversity and the evolutionary history of this species, we analyzed mitochondrial cox3 from 14 populations (221 individuals) throughout its range. The 17 haplotypes found in this study formed five distinct clades, indicating significant genetic structure. The high differentiation and number of unique (private) haplotypes may result from the recolonization of the species from glacial refugia. Three putative refugia, each with high genetic diversity, were identified: southern Korea (including Jeju Island), northern Taiwan, and central Pacific Japan. Recolonization of I. okamurae was probably determined by ocean currents and changes in sea level during the last glacial period.