Genetic variation in deep-sea invertebrate populations: The bathyal gastropod Bathybembix bairdii

Five populations of the bathyal trochid gastropod Bathybembix bairdii (Dall) taken from depths of 579 to 1156 m in the Southern California Continental Borderland were surveyed for levels of genetic variability at 18 presumptive gene loci, using techniques of starch gel electrophoresis. All the populations were highly similar genetically; none of the populations possessed unique alleles. Four of 5 polymorphic loci scored in all the populations displayed statistically significant heterogeneity of allelic frequencies among stations. Only the diallelic fumarase (FUM) locus displayed a trend with depth. The geographic and depth patterns of the genetic variability in these populations do not support the hypothesis that the high levels of genetic variability observed in bathyal populations are an artifact of gene flow between populations differentiated with depth. The 16.2% of the loci heterozygous per individual of B. bairdii is of the same order as the average heterozygosities reported for other deep-sea invertebrate taxa. These reports of high genetic variability in a physically constant and seasonless environment are reviewed and discussed in the context of the trophic-stability hypothesis of Ayala and Valentine and the time, size and divergence hypothesis of Soulé. Evidence is presented that despite the observed correlation of average heterozygosities in benthic marine invertebrates with seasonality of the trophic regime, this is not apparent for an enzyme system (leucine amino peptidase) which might be expected to display this trend if it reflected a genetic strategy to cope with trophic seasonality. The time, size and divergence hypothesis, focusing on population size, accounts for the general features of levels of genetic variability in deep-sea invertebrates.     

Genetic structure and allozyme variation of sea bass (Dicentrarchus labrax and D. punctatus) in the Mediterranean Sea

This paper reports data on 28 allozyme loci in wild and artificially reared sea bass (Dicentrarchus labrax) samples, originating from either coastal lagoon or marine sites in the Mediterranean Sea. F _ST analysis (θ estimator) indicated strong genetic structuring among populations; around 34% of the overall genetic variation is due to interpopulation variation. Pairwise θ estimates showed that, on average, the degree of genetic structuring was much higher between marine populations than between samples from lagoons. Six polymorphic loci showed differences in allele frequencies between marine and lagoon samples. Multivariate analyses of individual allozymic profiles and of allele frequencies suggested that different arrays of genotypes prevail in lagoons compared to marine samples, particularly at those loci that, on the basis of previous acclimation experiments, had been implicated in adaptation to freshwater. On the other hand, variation at “neutral” allozyme loci reflects to a greater extent the geographic location of populations. Allozyme differentiation was also studied in a D. labrax population from the Portuguese coast. Average genetic distance between this population and the Mediterranean populations was quite high (Nei's D = 0.236) and calls into question the taxonomic status of the Portuguese population. Finally, genetic relationships between D. labrax and D. punctatus were evaluated. Average Nei's D was 0.648, revealing high genetic differentiation between the two species, even for two sympatric populations of these species in Egypt; thus gene flow was not indicated between species. Received: 24 October 1996 / Accepted: 27 November 1996     

High levels of genetic subdivision of marine and estuarine populations of the estuarine catfishCnidoglanis macrocephalus (Plotosidae) in southwestern Australia

The cobblerCnidoglanis macrocephalus (Valenciennes) is an endemic marine and estuarine catfish from southern Australia. Conflicting views on the degree of isolation of the estuarine populations underscore general questions about genetic divergence in coastal species. Although estuaries are widely recognized as ecologically important, little work has been done on their role in favouring genetic divergence. In order to estimate the extent of genetic subdivision among nearshore marine and estuarine populations, electrophoretic variation of enzymes was examined in seven marine and six estuarine populations of cobbler from sites spanning 1500 km along the southwest Australian coastline. Among all populations, the mean standardized variance in allelic frequencies (F _ST) for six polymorphic loci was 0.277, a high value comparable to those of other shallow-water teleosts whose life-history characteristics and habitat preferences restrict their dispersal capability. The pattern of genetic identities between populations showed divergence between west and south coast sites. Within these regional groups, however, there was substantial heterogeneity, much of which was associated with estuaries. Among all six estuarine sites, the averageF _ST was 0.333, 40% higher than the value of 0.237 for the marine sites. Low estimates of the genetically effective number of migrants suggest population subdivision between marine and estuarine environments and between similar habitat types. This study indicates the importance of habitat in affecting the connectedness of populations, even in apparently open marine systems.     

Genetic structure of local populations and divergence between growth forms in a clonal invertebrate,the Caribbean octocoral Briareum asbestinum

Although the genetic structure of many populations of marine organisms show little deviation from panmixia, in those marine species with limited larval dispersal, patterns of microgeographic genetic differentiation may be common. The octocoral Briareum asbestinum should show local population differentiation because colonies reproduce asexually by fragmentation, most matings occur between colonies in very close proximity, and the sexually produced larvae and sperm appear to disperse only short distances. Variability in secondary chemistry of individual B. asbestinum colonies from different populations in close proximity also suggests local population differentiation. We determined the genetic composition of local populations by surveying allozyme variation of three shallow and two deep populations within a 300 m² area at San Salvador Island, Bahamas and at a site 161 km away on Little San Salvador, Bahamas in July 1990. As B. asbestinum occurs as either an erect branching form or an encrusting mat often at the same sites, we sampled both morphs to examine the extent of genetic exchange between them. Five of 21 loci were polymorphic and most populations showed a deficit of heterozygotes. Allele frequencies differed significantly between morphs at each site where they occurred together. The mean genetic distance (D=0.065) between morphs is consistent with the interpretation that the two morphs are genetically isolated. Despite the close spatial proximity of the San Salvador populations, both the branching and encrusting morphs showed significant genetic heterogeneity among neighboring populations. Similarly, pooled allelic frequencies for samples collected from the islands of San Salvador and Little San Salvador differed significantly at 1 locus for the branching morph and at 3 out of 5 loci for the encrusting morph.     

Sibling species in interstitial flatworms: a case study using<Emphasis Type="Italic"> Monocelis lineata</Emphasis> (Proseriata: Monocelididae)

The genetic relationships between morphologically indistinguishable marine and brackish-water populations of Monocelis lineata (O.F. Müller, 1774) (Proseriata: Monocelididae) were analysed by means of allozyme electrophoresis. Fifteen samples of M. lineata (13 from the Mediterranean and two from the Atlantic) from coastal marine and brackish-water habitats were examined for variation at 18 loci. Eleven loci were polymorphic in at least one population of M. lineata. Low levels of within-population genetic variability were found, with average observed and expected heterozygosity values ranging from H_o=0.015±0.015 to 0.113±0.044, and from H_e=0.028±0.028 to 0.138±0.054, respectively. The occurrence of a number of private alleles indicated a marked genetic divergence among populations of M. lineata, with Rogers genetic distances ranging from D_R=0.003 to 0.676 and a highly significant F_ST value (0.918±0.012, P<0.001). UPGMA (unweighted pair-group method using arithmetic average) cluster analysis and multidimensional scaling showed a clear genetic divergence between marine and brackish-water populations. Moreover, Atlantic and Mediterranean populations were sharply separated. Our results suggest that M. lineata is a complex of sibling species.Communicated by R. Cattaneo-Vietti, Genova     

Genetic variance in Ophiomusium lymani (Ophiuroidea: Echinodermata) from lower bathyal depths in the Rocklall Trough (northeast Atlantic)

Specimens of the deep-sea brittle-star Ophiomusium lymani were collected from six sites in the Rockall Trough (northeast Atlantic_. Four monomorphic and four polymorphic loci were detected, with up to 75 individuals screened at any one locus. The results showed little difference in allele frequencies between sites and, consequently, estimates of genetic identity indicated no significant genetic differentiation between the populations sampled. Deficits of heterozygotes were observed at all polymorphic loci, but the deficiencies were only significant at the phosphoglucose isomerase locus from two locations. The deficit of heterozygotes was not the same across loci, suggesting that inbreeding is not the cause of the excess homozygosity. No relationship between heterozygosity and depth was observed.     

Allozyme variation in global populations of striped mullet, Mugil cephalus (Pisces: Mugilidae)

The striped mullet, Mugil cephalus Linnaeus, 1758, is one of the few species of marine shore fish with a worldwide circumtropical distribution. Because of this distribution and the dependency of M. cephalus on coastal waters during various phases of its life cycle, as well as nearshore living habits, questions have been raised regarding levels of genetic divergence and gene flow among transoceanic populations. To cast more light on this, allozyme variation at 27 presumptive gene loci was investigated in ten globally diverse populations. The observed heterozygosity ranged from 0.018 (Hawaii) to 0.081 (Florida), averaging 0.050. The proportion of polymorphic loci showed a similar trend. Several populations were characterised by fixed allelic differences. Estimated gene diversities were very high, the allele frequency variation among populations was found to be 68%; genetic distances reached 0.242, with an average of 0.117. Estimated rates of gene flow were high among Mediterranean populations (Nm = 7.26), and between Mediterranean and East Atlantic populations (Nm= 2.86), but extremely low between non-contiguous populations within the Indian, Pacific and Atlantic Oceans, where Nm ranged from 0.03 to 0.05. Received: 7 April 1997 / Accepted: 4 February 1998     

Is Syllis gracilis (Polychaeta: Syllidae) a species complex? An allozyme perspective

The genetic relationships between morphologically indistinguishable marine and brackish populations of Syllis gracilis Grube, 1840 (Polychaeta: Syllidae) were studied by means of allozyme electrophoresis. Samples of S. gracilis from marine coastal and brackish-water habitats were examined for variation at 13 presumptive loci. In addition, a sample of the closely related species S. prolifera (Krohn, 1852) was analysed. Five loci were multiallelic in at least one population of S. gracilis and eight loci in S. prolifera. Low to moderate levels of within-population genetic variability were found, with average expected heterozygosity values ranging from H = 0.068 (±0.043 SE) to 0.187 (±0.069 SE) in the populations of S. gracilis; higher values were found in S. prolifera (H = 0.325 ± 0.076). The presence of various private alleles indicated a marked genetic divergence among populations of S. gracilis, with Nei's genetic distances ranging from D = 0.000 to 0.833 and a highly significant F _ST value. Furthermore, evidence for strong genetic heterogeneity between two sympatric marine populations was found. UPGMA cluster analysis and multidimensional scaling pointed out a clear genetic divergence between brackish and marine populations. At least two genetically divergent entities occurred in marine and brackish habitats. This could be due to local adaptation of individuals coming from marine populations to brackish habitats, but more presumably to the occurrence of a species complex within S. gracilis. Received: 6 June 1999 / Accepted: 7 February 2000     

Genetic variability and differentiation of sporophytes and gametophytes in populations of Gelidium arbuscula (Gelidiaceae: Rhodophyta) determined by isozyme electrophoresis

Genetic differentiation and genetic variability of sporophytic and gametophytic populations of Gelidium arbuscula (Bory) from three localities sampled in 1989 and 1990 in the Canary Islands (Spain) were examined by isozyme electrophoresis. Twenty-three to 29 putative alleles corresponding to 22 gene loci, were compared. High deviations in Hardy-Weinberg equilibrium, and significant differences between allelic frequencies of sporophytic and gametophytic subpopulations at the same locality were found, suggesting a predominant asexual reproduction of G. arbuscula. The genetic variability (percentage of polymorphic loci, mean number of alleles per locus and average gene diversity) of haploid subpopulations was lower than that of diploid subpopulations at all three localities, being the lowest described for seaweeds. No correlation between genetic and geographical distance was found. The high genetic differentiation coefficient between all subpopulations suggests a very reduced genetic flow between subpopulations of the same and of different localities. These results suggest that the genetic structure of the populations of G. arbuscula from the Canary Islands is due to a founder-effect combined with a predominance of asexual reproduction. This is the first report comparing allelic frequencies between sporophytic and gametophytic subpopulations of seaweeds.     

Population structure of the common sole (<Emphasis Type="Italic">Solea solea</Emphasis>) in the Northeastern Atlantic and the Mediterranean Sea: revisiting the divide with EPIC markers

Spatial and temporal population genetic structures of the common sole, Solea solea, were studied in Northeastern Atlantic and Mediterranean Sea populations, using three polymorphic exon-primed intron-crossing (EPIC) markers. Results demonstrated significant multilocus differentiation among Eastern Mediterranean and a group composed by Western Mediterranean and Atlantic populations (θ = 0.150, P < 0.001), but also suggested unrecorded genetic differentiation of the Adriatic Sea population. No pattern of isolation-by-distance was recorded across the range covered by sampling, from the Kattegat to the Aegean Sea. Conversely to genetically structured Mediterranean populations, Atlantic populations ranging from Denmark to Portugal could be considered as representative of the same panmictic unit (θ = 0.009, not significant). Results further demonstrated stability of multilocus genetic structure among temporarily replicated cohort samples [0+, 1+, subadults] from several coastal and estuarine locations from Bay of Biscay, excepted for the amylase locus Am2B3-2 at one location (Pertuis d’Antioche). Despite coherence of such observed patterns of multilocus differentiation with previous allozymic surveys in sole, and with patterns generally obtained for other marine fish species, single-locus results from EPICs indicated divergent coalescence schemes supporting a complex response to ecology and history of sole’s populations. Results stress the use of nuclear genes such as EPIC markers to investigate population structure, but also historical, demographic, and possibly selective processes in marine fishes.     

Identification and validation of novel SNP markers in European populations of marine Mytilus mussels

Mussels of the genus Mytilus are widespread in both northern and southern hemispheres. Mytilus taxa are very important components of marine coastal ecosystems, but are difficult to differentiate morphologically. Sequencing and Sequenom MassARRAY iPLEX genotyping technology was used to identify and verify novel SNP markers in three European taxa of Mytilus: M. edulis, M. galloprovincialis, and M. trossulus. SNPs were localized in coding and non-coding sequences of some functionally important genes. Eight SNPs located in genes of the histone family, hsp70 and p53, were discovered and applied as novel markers for Mytilus taxa on a large European scale. Five of these differentiated the M. trossulus genome, two M. galloprovincialis, and one M. edulis. Other SNPs differentiated populations within taxa. The new SNPs will be a valuable tool for population studies of European Mytilus mussels. The percentage of polymorphic SNPs ranged from 19 to 100 % in 24 samples of mussels studied. Populations from Scotland, Mecklenburg Bight, and Norway had over 90 % polymorphic loci. Most loci were in Hardy–Weinberg equilibrium in all samples except for the one from Scotland. The highest percentages of heterozygotes were observed in the Atlantic (Banyuls and Vigo) and North Sea (Tjarno and Westerschelde) populations. An excess of homozygotes was observed in samples from Scotland, Norway, and the Barents Sea. Correspondence and Structure analysis also demonstrated the great heterogeneity of these three samples.     

Population structure of <Emphasis Type="Italic">Symbiodinium</Emphasis> sp. associated with the common sea fan, <Emphasis Type="Italic">Gorgonia ventalina</Emphasis>, in the Florida Keys across distance,depth, and time

Numerous marine invertebrates form endosymbiotic relationships with dinoflagellates in the genus Symbiodinium. However, few studies have examined the fine-scale population structure of these symbionts. Here, we describe the genetic structure of Symbiodinium type “B1/B184” inhabiting the gorgonian Gorgonia ventalina along the Florida Keys. Six polymorphic microsatellite loci were utilized to examine 16 populations along the Upper, Middle, and Lower Keys spanning a range of ~200 km. Multiple statistical tests detected significant differentiation in 54–92% of the 120 possible pairwise comparisons between localities, suggesting low levels of gene flow in these dinoflagellates. In general, populations clustered by geographic region and/or reefs in close proximity. Some of the sharpest population differentiation was detected between Symbiodinium from deep and shallow sites on the same reef. In spite of the high degree of population structure, alleles and genotypes were shared among localities, indicating some connectivity between Symbiodinium populations associated with G. ventalina. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Population structure of the giant tiger prawn Penaeus monodon in Australian waters, determined using microsatellite markers

 We describe three highly polymorphic microsatellite loci which have been isolated from the giant tiger prawn Penaeus monodon. The number of alleles present among 312 samples at the loci Pmo9, Pmo25 and Pmo27 were 84, 34 and 35, respectively, with heterozygosities all >90%. Analyses of the distribution of length variation at three microsatellite loci among five Australian P. monodon populations revealed strong differentiation between populations from the west and those from the northern and eastern coasts. Tests for population differentiation (F st) values and an analogous measure for microsatellite loci (R st) all demonstrated that Western Australian P. monodon are a separate genetic stock which exhibits reduced genetic variation relative to the other populations. Reduced variability is consistent with a recent population bottleneck or colonization by a small founding population from the east when sea links between Indonesia, New Guinea and Australia were re-established following the last ice age. The results of this study are in agreement with previous surveys of P. monodon conducted with allozymes and mtDNA. Received: 18 December 1998 / Accepted: 27 August 1999     

Population genetics of the blue crabCallinectes sapidus: modest population structuring in a background of high gene flow

To determine the genetic population structure of blue crabs (Callinectes sapidus Rathbun), electrophoretic allozyme analysis was performed on 750 individuals collected from 16 nearshore locations ranging from New York to Texas, USA. Twenty enzymes and non-enzymatic proteins coded by 31 presumptive loci were examined. Twenty-two loci were either monomorphic or polymorphic at less than theP ₉₅ level; alleles for these polymorphic loci were geographically dispersed. Allele frequencies for three of the remaining polymorphic loci were homogeneous over all populations, as were levels of polymorphism and heterozygosity. Phenograms generated by the UPGMA (unweighted pair-group method using arithmetic averages) and distance Wagner methods exhibited no geographic pattern in the clustering of populations. Estimates ofN _em (effective number of migrants per generation between populations) indicated substantial gene flow, with aalues sufficiently high to infer panmixia between all blue crab populations from New York to Texas. However, despite this high level of gene flow, two striking patterns of geographic differentiation occurred: genetic patchiness and clinal variation. Allele frequencies atEST-2, GP-1, IDHP-2, DPEP-1, DPEP-2, andTPEP exhibited genetic patchiness on local and range-wide geographic scales, and allele frequencies atEST-2 varied temporally. Genetic patchiness in blue crabs is likely to be the result of the pre-settlement formation and subsequent settlement of genetically heterogeneous patches of larvae; allele frequencies of those larval patches may then be further modified through ontogeny by localized selection. In the Atlantic Ocean, a regional latitudinal cline ofEST-2 allele frequencies was superimposed on the range-wide genetic patchiness exhibited by that locus. This pattern against a background of high gene flow is highly likely to be maintained by selection. In estuaries along the Atlantic Ocean coast, a combination of low adult long-distance migration and a high retention rate of locally spawned larvae could serve to segregate populations and allow for the development of the geographic cline inEST-2. The Gulf of Mexico showed no apparent cline, perhaps due to long-distance migration of females in some regions of the Gulf, or to masking by genetic patchiness. These results emphasize the importance of both ecological and evolutionary time scales and structuring mechanisms in determining genetic population structure.     

Genetic evidence for cryptic speciation in the marine bryozoan Alcyonidium gelatinosum

The common subtidal marine bryozoan Alcyonidium gelatinosum (L.) is one of the most confusing species of a taxonomically very difficult genus. It shows massive variation for almost all morphological characters. A number of sympatric colonies collected off the coast of Lundy (Bristol Channel) could be clearly divided on morphological grounds into two quite distinct types. Using starch gel electrophoresis the products of a range of genetic enzyme loci were compared between the two morphotypes and also between these and other Bristol Channel populations of A. gelatinosum. Minimal differences were observed between one Lundy morphotype and the other allopatric populations, which it was consequently concluded were conspecific. The second morphotype showed considerable genetic differentiation [genetic identity (Nei, 1972) =0.417] from the other Lundy population, with no common alleles at some loci. The probability of obtaining the observed results by chance in a single population is significantly low (P<10^–14). It is therefore concluded that the two morphotypes of A. gelatinosum from Lundy are not conspecific.     

Population genetics of the family ostreidae. I. Intraspecific studies of Crassostrea gigas and Saccostrea commercialis

The levels of genetic variation and estimates of genetic similarity and distance were determined for populations of Crassostrea gigas (Thunberg) and Saccostrea commercialis (Iredale and Roughley). The proportion of polymorphic loci in Japanese populations of C. gigas ranged from 0.58 to 0.63, while the individual heterozygosities ranged from 0.20 to 0.22. The proportion of polymorphic loci in Australian populations of S. commercialis ranged from 0.43 to 0.46, the individual heterozygosities from 0.17 to 0.19. The genetic similarity between different geographical populations of both species was approximately 99%. The genetic distance and similarity data derived from this investigation has resulted in some provisional reclassifications. The Portuguese oyster C. angulata (Lamarck) appears to be more appropriately regarded as a recent colonized isolate of C. gigas. The New Zealand oyster S. glomerata (Gould) is considered a subspecies of the eastern Australian rock oyster S. commercialis. The Japanese Kumamoto population of C. gigas warrants reclassification as the non-sibling species C. sikamea.     

High self-recruitment levels in a Mediterranean littoral fish population revealed by microsatellite markers

Self-recruitment rates are essential parameters in the estimation of connectivity among populations, having important consequences in marine conservation biology. Using ten highly polymorphic microsatellite loci, we estimate, over 3 years, the self-recruitment in a population of Tripterygion delaisi in the NW Mediterranean. Six previously described source populations were used for the assignment (Costa Brava, Columbretes, Formentera, Cabo de Palos, Cabo de Gata and Tarifa). Even though this species has a 16–21 day larval duration, a mean of 66.4 ± 1.4% of the recruits settled in their natal population. When refining in a more local scale the origin of individuals self-recruited to Costa Brava, using as source the three sampling localities that conform this population (Cap de Creus, Tossa and Blanes), the highest percentage (40.6 ± 8.9%) was self-assigned to the adult source locality (Blanes) where recruits were sampled each year. Our results suggest that a high proportion of the larvae of T. delaisi remained close to, or never leave, their natal spawning area. This observation can be extrapolated to other species with similar early life-history traits and low adult mobility and can have important implications for the conservation and management of Mediterranean littoral fishes.     

Genetic consequences of long larval life in the starfish Linckia laevigata (Echinodermata: Asteroidea) on the Great Barrier Reef

Gene flow between populations of the asteroid Linckia laevigata (Linnaeus) was investigated by examining over 1000 individuals collected from ten reefs throughout the Great Barrier Reef (GBR), Australia, for genetic variation at seven polymorphic enzyme loci. Despite geographic separations in excess of 1000 km, Nei's unbiased genetic distance (0 to 0.003) and standardised genetic variation between populations (F _ST) values (mean 0.0011) were small and not significant. Genetic homogeneity among L. laevigata populations is consistent with the long-distance dispersal capability of its 28 d planktonic larval phase, and is greater than that observed for other asteroid species, including another high-dispersal species, Acanthaster planci, which has a 14 d larval phase. Variation within populations was also higher than previously recorded for asteroids (mean heterozygosity=0.384; number of alleles per locus ranged from 5.1 to 6.0 in each population). Among asteroids, dispersal ability is positively correlated with gene flow and levels of variation, and negatively correlated with levels of differentiation.     

Fitness in the Endangered Gila Topminnow

The Gila topminnow (Poeciliopsis o. occidentalis) is a small, live-bearing, endangered fish extant in a maximum of nine locales in four separate watersheds in the United States. To determine if these populations differed in their fitness, we obtained samples from the four watersheds and examined them for four fitness correlates: survival, growth rate, fecundity, and bilateral asymmetry. Earlier research found that one population, Sharp Spring, had higher allozyme heterozygosity than the other three and had higher survival, growth rate, and fecundity and lower bilateral asymmetry than a sample from one of the other populations with no polymorphic allozyme loci, Monkey Spring. We also verified that Sharp Spring fish were polymorphic for the same allozyme loci whereas the Monkey Spring population was not. We did not, however, find positive associations of allozyme heterozygosity with the four fitness correlates for the four samples. Because the earlier study had much lower survival, it is likely that the differences resulted from differential response of the two populations to a stressful laboratory environment. Whether this unknown stress occurs in natural environments or its effect is predictive of other stresses remains unresolved. As a result, we concur with suggestions in the draft recovery plan that topminnows from nearby sources be used for reintroductions and that the Sharp Spring stock not be used outside the upper Santa Cruz River drainage.