Evidence for independent origin of two spring‐spawning ciscoes (Salmoniformes: Coregonidae) in Germany

Combined analyses of mitochondrial DNA (mtDNA) and microsatellite loci were performed to assess the genetic differentiation of two spring‐spawning ciscoes from each other and from sympatric Coregonus albula in two German lakes. Polymorphism was screened at six microsatellite loci and mtDNA for a total of 247 and 94 ciscoes, respectively. Microsatellite data showed a weak differentiation between spring‐spawning Coregonus fontanae and sympatric C. albula in Lake Stechlin ( F _ST = 0–0·008), whereas a significant differentiation was observed between spring‐spawning Coregonus lucinensis and sympatric C. albula in Lake Breiter Luzin ( F _ST = 0·013–0·039). A more pronounced genetic difference was observed between both spring‐spawning species ( F _ST = 0·05–0·128). Shared mtDNA haplotypes among sympatric species within both Lake Stechlin and Lake Breiter Luzin were observed, whereas no haplotype was shared between C. fontanae and C. lucinensis . These results suggest an independent origin for spring‐spawning ciscoes in each lake. Evidence is also provided for mtDNA introgression of Coregonus sardinella into C. lucinensis and C. albula in Lake Breiter Luzin. Postglacially, this species or at least a population which showed mtDNA introgression has colonized the Baltic Sea basin up to the glacial margin that was located between Lakes Stechlin and Breiter Luzin.     

Population structure and phylogeography of Aphyocypris kikuchii (Oshima) based on mitochondrial DNA variation

Aphyocypris kikuchii is a cyprinid species endemic to northern and eastern Taiwan and is the only primary freshwater fish native east of the Coastal Mountain Range. In total, 92 individuals of A. kikuchii from seven populations in three regions of the island were surveyed for mitochondrial DNA (mtDNA) variation. High haplotype diversity ( h = 0·989) and low nucleotide diversity ( π = 0·009) of mtDNA were detected. Negative values of Tajima's D and unimodal mismatch distributions probably reflect a history of recent demographic expansions from small populations. Three major haplotype clusters displayed geographically non-overlapping distributions, indicating a long-term isolation between regions. Hierarchical analysis of molecular variance showed significant genetic structuring among populations ( Φ _ST= 0·66). Significant haplotype heterogeneity was also detected among populations within regions ( Φ _SC= 0·41, P < 0·001) and among regions ( Φ _CT= 0·43, P < 0·05). Molecular clock estimates of coalescence in the three major mtDNA lineages indicated coalescence in the most recent common ancestor c. 0·11–0·39 million years ago. Haplotypes of cluster B nested as interior nodes in the haplotype network, indicating that migrations from Shueilian (SL) populations to the northern region (cluster A) and to the eastern region (cluster C) may have occurred independently. Lineages A and B + C should be managed as two distinct evolutionarily significant units, while the northern, SL and southern groups should be managed as separate management units.     

POPULATION STRUCTURE IN AN INSHORE CETACEAN REVEALED BY MICROSATELLITE AND mtDNA ANALYSIS: BOTTLENOSE DOLPHINS (TURSIOPS SP.) IN SHARK BAY, WESTERN AUSTRALIA

We examined population substructure of bottlenose dolphins ( Tursiops sp). in Shark Bay, Western Australia, using 10 highly polymorphic microsatellite loci, and mitochondrial DNA (mtDNA). For microsatellite analysis, 302 different animals were sampled from seven localities throughout the bay. Analysis of genetic differentiation between sampling localities showed a significant correlation between the number of migrants ( Nm ) calculated from F _ST, R _ST and private alleles, and distance between localities–a pattern of isolation-by-distance. For mtDNA, 220 individuals from all seven localities were sequenced for a 351 base pair fragment of the control region, resulting in eight haplotypes, with two distinct clusters of haplotypes. Values of F _ST and (φ)_ST for mtDNA yielded statistically significant differences, mostly between localities that were not adjacent to each other, suggesting female gene flow over a scale larger than the sampled localities. We also observed a significant correlation between the number of female migrants calculated from F _ST and φ_ST and the distance of sampling localities. Our results indicate that dispersal in female dolphins in Shark Bay is more restricted than that of males.     

A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes

Electrophoretic data were analysed from 49 species of freshwater fish, 57 species of marine fish, and seven anadromous species. For each species, at least 15 individuals had been assayed for at least 15 loci in two or more subpopulations. The results showed that while average total heterozygosity ( _T ) was approximately equal in freshwater and marine species (0·062 and 0·064 respectively), subpopulation heterozygosity ( _s ) was significantly less in the former group (0·046 and 0·059 respectively). Consequently the average degree of genetic subpopulation differentiation ( _ST ) was significantly greater for freshwater species (0·222 v. 0·062). On average, it is likely that marine subpopulations exchange between 10 and 100 times more migrants per generation than freshwater subpopulations, presumably because of the relative absence of barriers to dispersal in the marine environment. The reduced values of H_s in freshwater species are likely to reflect reduced effective subpopulation sizes relative to marine species. The few andromous species that have been analysed show intermediate levels of G_ST .     

Microsatellite variation in cod Gadus morhua throughout its geographic range

Previous genetic studies using neutral markers such as allozymes, mtDNA and minisatellite loci have demonstrated varying amounts of population structure in cod Gadus morhua throughout the Atlantic. Microsatellite loci, which are potentially the most informative of presently available neutral genetic markers, have been applied extensively within western and eastern Atlantic areas but not on a range-wide basis. In the present study, six microsatellite DNA loci were used to screen cod samples from nine locations throughout the geographic range from the Scotian Shelf in the West Atlantic to the Barents and Baltic Seas in the east. Overall F _ST value was 0·03 ( P = < 0·001) across all samples. Statistically significant population differences over all loci combined were evident between more geographically distant samples, using either heterogeneity tests or F _ST analysis, with at least one locus showing significant differences between all samples (prior to Bonferroni correction). A significant correlation was observed between genetic and geographical distance, suggesting a higher level of historical and contemporary gene flow between adjacent populations than more distant populations. Samples from either end of the geographic range (Scotian Shelf and Baltic Sea) were particularly distinct when analysed using the STRUCTURE programme and also showed a high level of self-assignment when individuals of either the Scotian Shelf or Baltic Sea were tested against the entire data set. The present microsatellite study demonstrates a high level of geographic population structure between the western Atlantic, middle and eastern Atlantic and Baltic Sea, and thus, the findings should be useful in devising overall management and conservation strategies for the species.     

Subtle population structuring within a highly vagile marine invertebrate, the veined squid Loligo forbesi, demonstrated with microsatellite DNA markers

Microsatellite DNA markers were applied for the first time in a population genetic study of a cephalopod and compared with previous estimates of genetic differentiation obtained using allozyme and mitochondrial DNA (mtDNA) markers. Levels of genetic variation detected with microsatellites were much higher than found with previous markers (mean number of alleles per locus=10.6, mean expected heterozygosity ( H _E)=0.79; allozyme H _E=0.08; mtDNA restriction fragment length polymorphism (RFLP) H _E=0.16). In agreement with previous studies, microsatellites demonstrated genetic uniformity across the population occupying the European shelf seas of the North East Atlantic, and extreme genetic differentiation of the Azores population ( R _ST/ F _ST=0.252/0.245; allozyme F _ST=0.536; mtDNA F _ST=0.789). In contrast to other markers, microsatellites detected more subtle, and significant, levels of differentiation between the populations of the North East Atlantic offshore banks (Rockall and Faroes) and the shelf population ( R _ST=0.048 and 0.057). Breakdown of extensive gene flow among these populations is indicated, with hydrographic (water depth) and hydrodynamic (isolating current regimes) factors suggested as possible barriers to migration. The demonstration of genetic subdivision in an abundant, highly mobile marine invertebrate has implications for the interpretation of dispersal and population dynamics, and consequent management, of such a commercially exploited species. Relative levels of differentiation indicated by the three different marker systems, and the use of measures of differentiation (assuming different mutation models), are discussed.     

Microsatellite data reveals weak population substructuring in Copadichromis sp.'virginalis kajose', a demersal cichlid from Lake Malawi, Africa

Small but significant differences were found in allele frequencies among five populations (overall F _ST estimate (θ)=0·004, P=0·006; overall R _ST estimate (RHO)=0·019, P <0·00001) of the demersal cichlid Copadichromis sp.'virginalis kajose', collected from five locations in Lake Malawi. Pairwise F _ST estimates revealed significant differences between the most southerly population (Cape Maclear), and the three most northerly populations (Mbamba Bay, Metangula and Chilola). Pairwise R _ST estimates also revealed significant differences between some populations, but no geographical pattern was discernible. There was no evidence of isolation by distance using either the shortest straight-line distance between samples, or the distance around the shoreline following a 50 m depth contour. F _ST estimates were considerably lower than found in previous studies on the mbuna (rock-dwelling species), but higher than those found in a study of three pelagic cichlid species from Lake Malawi. Substructuring in C. sp.'virginalis kajose' appears to be on a similar scale to the Atlantic cod.     

Population divergence in the amphicarpic species Amphicarpaea edgeworthii Benth. (Fabaceae): microsatellite markers and leaf morphology

Comparative analyses of the genetic differentiation in microsatellite markers ( F _ST) and leaf morphology characters ( Q _ST) of Amphicarpaea edgeworthii Benth. were conducted to gain insight into the roles of random processes and natural selection in the population divergence. Simple sequence repeat analyses on 498 individuals of 19 natural populations demonstrate that a significant genetic differentiation occurs among populations (mean F _ST = 0.578), and A. edgeworthii is a highly self-fertilized species (mean selfing rate s  = 0.989). The distribution pattern of genetic diversity in this species shows that central populations possess high genetic diversity (e.g. population WL with H _E = 0.673 and population JG with H _E = 0.663), whereas peripheral ones have a low H _E as in population JD (0.011). The morphological divergence of leaf shape was estimated by the elliptical Fourier analysis on the data from 11 natural and four common garden populations. Leaf morphology analyses indicate the morphological divergence does not show strong correlation with the genetic differentiation ( R  = 0.260, P  = 0.069). By comparing the 95% confidence interval of Q _ST with that of F _ST, Q _ST values for five out of 12 quantitative traits are significantly higher than the average F _ST value over eight microsatellite loci. The comparison of F _ST and Q _ST suggests that two kinds of traits can be driven by different evolutionary forces, and the population divergence in leaf morphology is shaped by local selections.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 505–516.     

Structural and functional connectivity of marine fishes within a semi-enclosed Newfoundland fjord

The interplay between structural connectivity ( i.e. habitat continuity) and functional connectivity ( i.e. dispersal probability) in marine fishes was examined in a coastal fjord (Holyrood Pond, Newfoundland, Canada) that is completely isolated from the North Atlantic Ocean for most of the year. Genetic differentiation was described in three species (rainbow smelt Osmerus mordax , white hake Urophycis tenuis and Atlantic cod Gadus morhua ) with contrasting life histories using seven to 10 microsatellite loci and a protein-coding locus, Pan I ( G. morhua ). Analysis of microsatellite differentiation indicated clear genetic differences between the fjord and coastal regions; however, the magnitude of difference was no more elevated than adjacent bays and was not enhanced by the fjord's isolation. Osmerus mordax was characterized by the highest structure overall with moderate differentiation between the fjord and St Mary's Bay ( F _ST c. 0·047). In contrast, U. tenuis and G. morhua displayed weak differentiation ( F _ST < 0·01). Nonetheless, these populations did demonstrate high rates (< 75%) of Bayesian self-assignment. Furthermore, elevated differentiation was observed at the Pan I locus in G. morhua between the fjord and other coastal locations. Interestingly, locus-specific genetic differentiation and expected heterozygosity were negatively associated in O. mordax , in contrast to the positive associations observed in U. tenuis and G. morhua . Gene flow in these species is apparently unencumbered by limited structural connectivity, yet the observed differentiation suggests that population structuring exists over small scales despite high dispersal potential.     

Population genetic structure and effective population size of ayu (Plecoglossus altivelis), an amphidromous fish

The temporal and spatial population genetic structure of ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae), an amphidromous fish, was examined using analysis of variation at six microsatellite DNA loci. Intracohort genetic diversities, as measured by the number of alleles and heterozygosity, were similar among six cohorts (2001–2006) within a population (Nezugaseki River), with the mean number of alleles per cohort ranging from 11·0 to 12·5 and the expected heterozygosity ranging from 0·74 to 0·77. Intrapopulational genetic diversities were also similar across the three studied populations along the 50 km coast, with the mean number of alleles and the expected heterozygosity ranging from 11·33 to 11·67 and from 0·75 to 0·76, respectively. The authors observed only one significant difference in pair-wise population differentiation ( F _ST-value) between the cohorts within a population and among three populations. Estimates of the effective population size ( N _e) based on maximum-likelihood method yielded small values (ranging from 94·8 to 135·5), whereas census population size ranged from c. 4800 to 24 000. As a result, the ratio of annual effective population sizes to census population size ( N _e/ N ) ranged from 0·004 to 0·023. These estimates of N _e/ N agree more closely with estimates for marine fishes than that of the larger estimates for freshwater fishes. The present study suggests that ayu which is highly fecund and shows low survival during the early life stages is also characterized by having low value of N _e/ N , similar to marine species with a pelagic life cycle.     

Mitochondrial DNA analysis of the geographic structure of Indian scad mackerel in the Indo-Malay archipelago

Sequence analysis of a fragment of the cytochrome b gene in Decapterus russelli sampled from the Indo-Malay archipelago revealed two distinct mitochondrial clades (mean nucleotide divergence=2·2%) whose geographic distribution was heterogeneous (Nei's G _ST=0·416). This pointed to a complex pattern of genetic differentiation and demonstrated limited genetic exchange between populations in this highly mobile species.     

Effects of a founder event and supplementary introductions on genetic variation in a captive breeding population of the endangered Spanish killifish

Twelve polymorphic allozyme loci were employed to assess the genetic change in a captive breeding population of the endangered killifish Aphanius baeticus in the Doñana National Park, south‐western Spain. The initial founder event did not significantly reduce the allelic richness or the expected heterozygosity. No genetic bottleneck signature was detected by tests for deviation from mutation‐drift equilibrium. The F _ST between the wild source and captive population, however, was relatively high (0·053 or 0·122 when excluding or including the locus IDHP‐1 * respectively), after just two to three generations in captivity. Two generations after the incorporation of 68 new wild specimens (greater than five generations after founding) decreased the genetic differences and the F _ST(0·041 excluding IDHP‐1 *). The restoration efforts appeared to be helpful and the study of 12 polymorphic loci and a sensitive parameter such as F _ST were useful for monitoring genetic changes in captivity. Nonetheless, future monitoring should include additional highly polymorphic loci (microsatellites) to achieve higher power to detect genetic change. Such restoration and monitoring efforts should help to avoid rapid inbreeding, adaptation to captivity, and to maintain the long‐term evolutionary potential in small isolated populations.     

Genetic differentiation in pikeperch (Sander lucioperca): the relative importance of gene flow, drift and common history

To investigate the relative importance of homogenizing factors, such as gene flow, and diversifying factors, such as drift, genetic variation in pikeperch ( Sander lucioperca ) in two Fennoscandian regions (North and South) was analysed with microsatellites. Allelic richness and the degree of differentiation were significantly higher in the North ( F _ST= 0·20) than in the South ( F _ST= 0·064). In northern areas, assignments of genotypes were almost exclusively to the population of origin, but in southern areas, the proportion of correct assignments was significantly lower. Most samples exhibited significant heterozygote deficits, and the level of relatedness was higher than expected from randomness. These combined results suggest that there has been more gene flow between populations in southern areas than in northern areas, where the importance of genetic drift has been greater. Effective population sizes were small ( c. 100) and did not differ between areas. The effect of a common history appears minor, and thus processes such as genetic drift and gene flow have been more influential in shaping the patterns of genetic diversity in this species.     

Growth rates of juvenile smalltooth sawfish Pristis pectinata Latham in the western Atlantic

The growth rates of juvenile smalltooth sawfish Pristis pectinata collected in Florida waters between 1999 and 2006 were investigated using length-frequency and tag-recapture data. Stretched total length ( L _ST) data from 144 smalltooth sawfish (690–4960 mm) and 28 recaptures (775–2150 mm) were used for the analyses. Both methods indicated that growth was rapid during the first 2 years after birth. The L _ST increased by 650–850 mm in the first year, and by 480–680 mm in the second year. Data for animals >2200 mm were limited, so growth beyond 2 years of age was uncertain. The von Bertalanffy growth parameters estimated from L _ST frequency data were L _∞= 6000 mm, K = 0·140 year⁻¹ and t ₀=−0·863 years. Growth rates over the size range for which tag-recapture data were available were similar to that from L _ST frequency data. The growth rates reported are substantially faster than those previously assumed for this species and may have important implications for the recovery of this endangered species. There are conflicting data regarding the growth rates of older P. pectinata which need to be resolved with more data from the wild population before a complete understanding of the conservation implications can be obtained.     

Countergradient variation in growth and food conversion efficiency of juvenile turbot

Growth performance of a high latitude (Norway) population of juvenile turbot Scophthalmus maximus , was superior to that of two other lower latitude populations (Scotland, France) especially at 18° and 22° C. Overall these results lend some support to the hypothesis of countergradient variation in growth. The Norwegian population had the highest estimated temperature optimum for growth ( T _opt.G, ±S.E.) (23·0±0·9°C) and food conversion efficiency ( T _opt.Ec) (17·5±0·3), followed by the French ( T _opt.G 21·1±1·0; T _opt.Ec, 16·7±0·1) population, whereas the Scottish population had the lowest optimum ( T _opt.G, 19·6±0·6; T _{opt Ec}, 16·5±0·1°C). These results have two major implications: firstly, for turbot culture, particularly in selection work focusing on growth performance; secondly, if countergradient variation in growth performance takes place within a species one cannot assume automatically that one set of physiological parameters, in this case growth-related parameters, is satisfactory to predict growth for a species throughout its range as different populations might show a difference in response towards different physiological parameters.     

Genetic differentiation among populations of the shortfinned eel Anguilla australis from East Australia and New Zealand

Variability at seven microsatellite loci was used to survey the genetic population structure of the shortfinned eel Anguilla australis . Samples were collected from six estuaries along the east coast of Australia and from three estuaries around New Zealand. Hierarchical analysis of molecular variance of the five loci with good fit to Hardy–Weinberg genotypic proportions detected highly significant differences among samples ( F _ST= 0·016, P < 0·001). The fixation index between countries ( F _CT= 0·012, P < 0·001) was more than double the index among samples within countries ( F _SC= 0·005, P < 0·05). An unweighted pair-group method with arithmetic mean (UPGMA) tree also supported the separation of Australian and New Zealand populations, as did assignment tests, which correctly assigned 80 and 84% of the individuals to Australia and New Zealand, respectively. Isolation-by-distance appeared among samples overall ( r = 0·807, P < 0·001), but not among samples within countries ( r = 0·027, P > 0·05 in Australia; r = 0·762, P > 0·05 in New Zealand). These findings indicate that populations of A. australis in East Australia and in New Zealand may be reproductively isolated from one another. Genetic differentiation among populations of A. australis was two- to 10-fold higher than that among populations of other temperate eels in the North Atlantic Ocean, suggesting that two group of A. australis may reflect sub-species. Anguilla australis in the two countries have different genetic structures and thus require separate management. Genetic isolation between Australian and New Zealand populations indicates that juveniles recruit independently into these two regions from geographically or temporally isolated spawning areas.     

Genetic variability in Irish populations of the invasive zebra mussel, Dreissena polymorpha: discordant estimates of population differentiation from allozymes and microsatellites

1. The recent arrival and explosive spread of the zebra mussel, Dreissena polymorpha (Pallas), in Ireland provided a rare opportunity to study the population genetics of an invasive species.
2. Eight polymorphic allozyme loci ( ACO-1, ACO-2 , EST-D, GPI, IDH-2, MDH, OPDH and PGM ) were used to investigate genetic diversity and population structure in five Irish populations, and the results were compared with those from a previous microsatellite study on the same samples.
3. The mean number of alleles per locus (2.7 ± 0.1) was similar to the mean for the same loci in European populations, suggesting that Irish founder populations were large and/or multiple colonization events took place after foundation. A deficiency of heterozygotes was observed in all populations, but was uneven across loci.
4. Pairwise comparisons, using Fisher's exact tests and F _ST values, revealed significant genetic differentiation among populations. The overall multilocus F _ST estimate was 0.118 ± 0.045, which contrasted with an estimate of 0.015 ± 0.007 from five microsatellite loci on the same samples in a previous study.
5. Assuming that microsatellites can be used as a neutral baseline, the discordant results from allozymes and microsatellites suggest that selection may be acting on some allozyme loci, specifically ACO-1, ACO-2 , IDH-2 and MDH, which contributed most to the significant differentiation between samples.     

Morphological and genetic differentiation in anadromous smelt Osmerus mordax (Mitchill): disentangling the effects of geography and morphology on gene flow

Morphological analyses were combined with genetic analyses at nine microsatellite loci to examine the determinants of gene flow at 21 spawning locations of rainbow smelt Osmerus mordax along the east coast of Canada. Associations between morphology, geography and gene flow were examined using a computational geometric approach and partial Mantel tests. Significant barriers to gene flow and discontinuities in morphology were observed between Newfoundland and mainland Canada, as well as within Newfoundland samples. On regional scales, contrasting patterns were present with restricted gene flow between Newfoundland populations ( F _ST= c . 0·11) and high gene flow between mainland populations ( F _ST= c . 0·017). Within Newfoundland populations, geographic distance was significantly associated with gene flow ( r = 0·85, P < 0·001) contrasting mainland samples where gene flow was most associated with phenotypic divergence ( r = 0·33, P < 0·001). At large spatial scales, weak ( r = 0·19, P = 0·02) associations between gene flow and geographic distance were observed, and moderate associations were also observed between gene flow and morphology ( r = 0·28, P < 0·001). The presence of significant genetic isolation by distance in Newfoundland samples and the clear discontinuity associated with the Cabot Strait suggest geography may be the primary determinant of gene flow. Interestingly, the association between genetic and morphological divergence within mainland samples and overall, supports the hypothesis that gene flow may be moderated by morphological divergence at larger spatial scales even in high gene flow environments.     

Comparative effects of long-term hypoxia on growth, feeding and oxygen consumption in juvenile turbot and European sea bass

When juvenile turbot Scophthalmus maximus and sea bass Dicentrarchus labrax were fed to satiation, growth and food intake were depressed under hypoxia (3·2±0·3 and 4·5±0·2 mg O₂ l^-1). However, no significant difference in growth was observed between fishes maintained in hypoxia and fed to satiation and fishes reared in normoxia (7·4±0·3 mg O₂ l^-1) and fed restricted rations (same food intake of fishes at 3·2 mg O₂ l^-1). Routine oxygen consumption of fishes fed to satiation was higher in normoxia than in hypoxia due to the decrease in food intake in the latter. Of the physiological parameters measured, no significant changes were observed in the two species maintained in hypoxia. This study confirms the significant interaction between environmental oxygen concentrations, feeding and growth in fishes. Decrease in food intake could be an indirect mechanism by which prolonged hypoxia reduces growth in turbot and sea bass, and may be a way to reduce energy and thus oxygen demand.     

Contrasting genetic patterns and population histories in three threatened redfin species (Cyprinidae) from the Olifants River system, western South Africa

Differentiation occurred in different areas of the same river system in Pseudobarbus phlegethon and two sister species of the serrated redfin lineage ( Barbus calidus and Barbus erubescens ) of the Western Cape region of South Africa. In an analysis of 27 allozyme loci a deep divergence was found within P. phlegethon between the Olifants and Doring catchments (seven fixed allelic differences; 0·338 <  D  < 0·366; F _ST = 0·925). In contrast, speciation in the serrated redfin lineage occurred within the Doring catchment between B. calidus and B. erubescens (one fixed allelic difference; 0·008 <  D  < 0·052; F _ST = 0·760). Different niche preferences, behaviour and morphology probably played an important role in the formation of these contrasting patterns of genetic structure and suggest that B. calidus may have been better able to disperse between the Olifants and Doring catchments (no fixed allelic differences; 0 <  D  < 0·040; F _ST = 0·281) than P. phlegethon .