Natal origin and migration pathways of Mekong catfish (Pangasius krempfi) using strontium isotopes and trace element concentrations in environmental water and otoliths

To improve our knowledge of the migration pathway of a highly threatened fish species along the Mekong River, strontium isotope ratios (87Sr/86Sr) and 18 trace element concentrations were measured in the water and in the otoliths of an anadromous catfish, Pangasius krempfi, to infer its natal origin and potential migration pathways. Water was sampled at 18 locations along the mainstream, tributaries and distributaries of the Mekong River. To check for accuracy and precision, measurements of the 87Sr/86Sr ratios and trace element concentrations were then compared in two laboratories that use different analytical methods. Differences in trace element concentrations between locations were not significant and could not, therefore, be used to discriminate between migration pathways. However, the Mekong mainstream, tributaries and distributaries could all be discriminated using Sr isotopes. The 87Sr/86Sr profiles recorded in P. krempfi otoliths showed that there were three contingents with obligate freshwater hatching and variable spawning sites along the Mekong mainstream, from Phnom Penh (Cambodia) to Nong Khai (Thailand) or further. After hatching, the fish migrated more or less rapidly to the Mekong Delta and then settled for most of their lifetime in brackish water. Spawning habitats and migration routes may be threatened by habitat shifts and the increasing number of hydropower dams along the river, especially the contingents born above Khone Falls (Laos). The conservation of P. krempfi, as well as other migratory fish in the Mekong River, requires agreements, common actions and management by all countries along the Mekong River. This study highlighted the importance of using both Sr/Ca and 87Sr/86Sr ratios to understand life history of anadromous fishes as the 87Sr/86Sr ratio in the water was shown to be less effective than the Sr/Ca ratio in identifying movements between different saline areas.

Genetic diversity and structure of circumtropical almaco jack, Seriola rivoliana: tool for conservation and management

The almaco jack, Seriola rivoliana, is a circumtropical pelagic fish of importance both in commercial fisheries and in aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed using mtDNA sequence data and single nucleotide polymorphisms (SNPs) from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of cytochrome c oxidase subunit 1 and 3678 neutral SNPs were recovered. Three genetic groups were identified, with both marker types distributed in different oceanic regions: Pacific-1 in central Pacific, Pacific-2 in eastern Pacific and Atlantic in western Atlantic. Nonetheless, the analysis of SNP identified a fourth population in the Pacific coast of Baja California Sur, Mexico (Pacific-3), whereas that of mtDNA did not. This mito-nuclear discordance is likely explained by a recently diverged Pacific-3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian Ocean with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with _r m < 0.2, whereas in the eastern Pacific it was asymmetric and higher from south to north (_r m > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management.

Acanthopagrus datnia (Hamilton, 1822), a senior synonym of Acanthopagrus longispinnis (Valenciennes, 1830) (Perciformes: Sparidae)

The taxonomic status of the Bay of Bengal nominal sparid species Coius datnia Hamilton, 1822 and Acanthopagrus longispinnis (Valenciennes, 1830) are reviewed and investigated both morphologically and genetically. Because of inadequate description and no type specimen, Coius datnia has recently been considered to belong to Sparidentex, a genus without molarifom teeth. Critical examination of the original description and examination of specimens from the type locality and adjacent areas reveal that Coius datnia belongs to Acanthopagrus, a genus with an inner series of molars. Furthermore, examination of specimens previously recognized as Acanthopagrus longispinnis (Valenciennes 1830), and recent collection of fresh specimens from lower Ganges estuary in Bangladesh, show that morphological differences between Acanthopagrus datnia and A. longispinnis are minor, and they are genetically identical. The longer second anal-fin spine in A. longispinnis (>21% SL) is, in fact, a feature of some younger A. datnia. Accordingly, A. datnia is regarded as a senior synonym of A. longispinnis, and is distinguished from its congeners by the presence of 12 dorsal-fin spines (rarely 11 or 13), 3½ scale rows between the fifth dorsal-fin spine base and lateral line, pelvic and anal-fins pale yellow to yellow with black streaks present in the interradial membranes of anal-fin rays, and caudal fin grey or yellowish grey. A neotype (and neogenotype) has been designated for Acanthopagrus datnia (Hamilton, 1822).

Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron

Preliminary studies conducted on the human gastro-intestinal tract have revealed that enteric viral communities play a preponderant role in microbial homeostatis. However to date, such communities have never been investigated in the fish gut. Herein, we examined the main ecological traits of viruses in the digestive tract of a euryhaline fish, the tilapia Sarotherodon melanotheron. Individuals were collected at 8 different sites in Senegal covering a salinity gradient from 3 to 104‰, and showing large disparities in their organic pollutant concentrations. Results showed that the gut of S. melanotheron is home to a highly abundant viral community (0.2-10.7 × 10⁹ viruses ml^-1), distinct from the surrounding water, and essentially composed of phages of which a substantial proportion is temperate (the fraction of lysogenized cells-FLC ranging from 8.1 to 33.0%). Also, a positive and significant correlation was detected between FLC and the concentrations of polycyclic aromatic hydrocarbon in sediment, while no clear relationships were found between salinity and any of the microbial parameters considered. Finally, our data suggest that virus-bacteria interactions within the fish intestine are likely sensitive to the presence of particular xenobiotics, which may compromise the balance in the gut microbiota, and subsequently affect the health of their host.

DNA barcoding post-larvae can improve the knowledge about fish biodiversity: an example from La Reunion, SW Indian Ocean

The aim of this study was to demonstrate that fish larvae identified using their COI sequences offer a unique opportunity for improving the knowledge of local fish richness. Fish larvae were sampled at the end of their pelagic phase using light-traps set off the West Coast of La Reunion Island, southwestern Indian Ocean, once per month from October 2014 to March 2015. Among the 5174 larvae caught, 214 morphologically different specimens were selected, 196 successfully barcoded, giving a total of 101 different Barcode Index Numbers (BINs). Among these BINs, 55 had never been recorded in La Reunion exclusive economic zone (EEZ), and 13 were new for the BOLD database. Even if the sampling effort for collecting fish post-larvae during this study was relatively low, it allowed adding at least nine new species to an updated checklist of fishes of La Reunion EEZ.

Diversity and distribution of cryptic species within the Mugil cephalus species complex in Vietnam

Mugil cephalus sensu lato is a globally distributed complex of cryptic species whose distribution range and evolutionary history remains largely unknown. In the North West (NW) Pacific three species have been identified genetically among fish described morphologically as M. cephalus. Their distribution ranges are largely parapatric and has been proposed to mirror different thermal preferences. To date, few samples have been analyzed from South China Sea, which limits inferences on the evolutionary history of the species complex. We sampled fish identified morphologically as M. cephalus along Vietnamese shores and characterized them using the sequence polymorphism of two mitochondrial genes, the cytochrome oxidase I and cytochrome b. This demonstrated that all three species described in the NW Pacific are present in both northern and southern Vietnamese waters. Although the difference in species abundance reflects those observed in the NW Pacific, no phylogeographic pattern was revealed. In addition, no population structure was observed whatever the species or the distribution range considered, which indicates a significant level of gene flow that maintains genetic homogeneity of the three species. It is also conceivable that each species experienced a recent population expansion from a single ancestral population. Finally we suggest that if the cold waters of the NW Pacific present a physiologic challenge leading to the almost parapatric distribution of the three species, then it is likely that the warm surface temperatures of the South China Sea negate this barrier.

Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy

The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera.

Next generation sequencing yields the complete mitochondrial genome of the largescale mullet, Liza macrolepis (Teleostei: Mugilidae)

In this study, the complete mitogenome sequence of largescale mullet (Teleostei: Mugilidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome, consisting of 16,832 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region of D-loop. D-loop which has a length of 1094 bp is located between tRNA-Pro and tRNA-Phe. The overall base composition of largescale mullet is 27.8% for A, 30.1% for C, 16.2% for G, and 25.9% for T. The complete mitogenome may provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Mugilidae.

A comparative study of Ligophorus uruguayense and L. saladensis (Monogenea: Ancyrocephalidae) from Mugil liza (Teleostei: Mugilidae) in southern Brazil

Representatives of Ligophorus Euzet et Suriano, 1977 were found on the gills of Mugil liza Valenciennes caught in southern Brazil. They were identified as Ligophorus uruguayense Failla Siquier et Ostrowski de Núñez, 2009 and Ligophorus saladensis Marcotegui et Martorelli, 2009, even though specific identification proved to be difficult due to inconsistencies in some diagnostic features reported for these two species. Therefore, a combined morphological and molecular approach was used to critically review the validity of these species, by means of phase contrast and confocal fluorescence microscopical examination of sclerotised hard parts, and assessing the genetic divergence between L. saladensis, L. uruguayense and their congeners using rDNA sequences. The main morphological differences between the two species relate to the shape of the accessory piece of the penis and the median process of the ventral bar. The accessory piece in L. uruguayense is shorter than in L. saladensis, has a cylindrical, convex upper lobe and straight lower lobe (vs with the distal tip of the lower lobe turning away from the upper lobe in the latter species). The ventral bar has a V-shaped anterior median part in L. uruguayense (vs U-shaped in L. saladensis). The two species are suggested to be part of a species complex together with L. mediterraneus Sarabeev, Balbuena et Euzet, 2005. We recommend to generalise such comparative assessment of species of Ligophorus for a reliable picture of the diversity and diversification mechanisms within the genus, and to make full use of its potential as an additional marker for mullet taxonomy and systematics.

Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii

The black-chinned tilapia Sarotherodon melanotheron heudelotii Rüppell 1852 (Teleostei, Cichlidae) displays remarkable acclimation capacities. When exposed to drastic changes of salinity, which can be the case in its natural habitat, it develops quick physiological responses and keeps reproducing. The present study focused on the physiological impact of salinity on male reproductive capacities, using gene expression as a proxy of acclimation process. Two series of experimental fish were investigated: the first one was composed of fish maintained in freshwater for several generations and newly acclimated to salinities of 35 and 70, whereas the second one consisted of the descendants of the latter born and were raised under their native salinity. Expression patterns of 43 candidate genes previously identified from the testes of wild males was investigated in the three salinities and two generations. Twenty of them showed significant expression differences between salinities, and their predicted function revealed that most of them are involved in the osmotic tolerance of sperm cells and/or in the maintenance of sperm motility. A high level of expression variation was evidenced, especially for fish maintained in freshwater. In spite of this, gene expression patterns allowed the differentiation between fish raised in freshwater and those maintained in hypersaline water in both generations. Altogether, the results presented here suggest that this high variability of expression is likely to ensure the reproductive success of this species under varying salinities.

Ligophorus species (Monogenea: Ancyrocephalidae) from Mugil cephalus (Teleostei: Mugilidae) off Morocco with the description of a new species and remarks about the use of Ligophorus spp. as biological markers of host populations

Gill monogenean species of Ligophorus Euzet et Suriano, 1977 were studied from the teleost Mugil cephalus Linneaus (Mugilidae) from the Mediterranean and Atlantic coasts of Morocco. We report the presence of L. mediterraneus from both the Mediterranean and Atlantic coast and L. cephali and L. maroccanus sp. n. from the Atlantic coast only. The latter species, which is described herein as new, resembles L. guanduensis but differs from this species mainly in having a shorter penis compared to the accessory piece, a proportionally longer extremity of the accessory piece and a less developed heel. The utility of Ligophorus spp. as markers of cryptic species of the complex M. cephalus is discussed in the context of species diversity and geographical distribution of these monogeneans on this host around the world. Presence of different species of Ligophorus on M. cephalus sensu stricto from the Atlantic and Mediterranean coast of Morocco demonstrates the usefulness of these species as fine resolution markers of genetic populations of their host, which are known to inhabit those coasts.

Pelagic life and depth: coastal physical features in West Africa shape the genetic structure of the Bonga Shad, Ethmalosa fimbriata

The bonga shad, Ethmalosa fimbriata, is a West African pelagic species still abundant in most habitats of its distribution range and thought to be only recently affected by anthropogenic pressure (habitat destruction or fishing pressure). Its presence in a wide range of coastal habitats characterised by different hydrodynamic processes, represents a case study useful for evaluating the importance of physical structure of the west African shoreline on the genetic structure of a small pelagic species. To investigate this question, the genetic diversity of E. fimbriata was assessed at both regional and species range scales, using mitochondrial (mt) and nuclear DNA markers. Whereas only three panmictic units were identified with mtDNA at the large spatial scale, nuclear genetic markers (EPIC: exon-primed intron-crossing) indicated a more complex genetic pattern at the regional scale. In the northern-most section of shad’s distribution range, up to 4 distinct units were identified. Bayesian inference as well as spatial autocorrelation methods provided evidence that gene flow is impeded by the presence of deep-water areas near the coastline (restricting the width of the coastal shelf), such as the Cap Timiris and the Kayar canyons in Mauritania and Senegal, respectively. The added discriminatory power provided by the use of EPIC markers proved to be essential to detect the influence of more subtle, contemporary processes (e.g. gene flow, barriers, etc.) acting within the glacial refuges identified previously by mtDNA.

Mitochondrial haplotypes indicate parapatric-like phylogeographic structure in blue-spotted maskray (Neotrygon kuhlii) from the Coral Triangle region

Phylogeographic structure was investigated in the blue-spotted maskray, Neotrygon kuhlii, focusing on the Coral Triangle region. We used as genetic marker a 519-bp fragment of the cytochrome c-oxidase subunit I (COI) gene, sequenced in a total of 147 individuals from 26 sampling locations. The parsimony network of COI haplotypes was split into seven distinct clades within the Coral Triangle region. Different clades had exclusive but contiguous geographic distributions, indicating parapatric-like phylogeographic structure. Strong genetic differences were also inferred between local populations within a clade, where reciprocal monophyly between geographically adjacent samples was observed on several instances. Nearly 25% of the total molecular variance could be ascribed to differences between geographic samples within a clade, whereas interclade variation accounted for >65% of the total variance. The strong phylogeographic structure observed within a clade can be explained by either sedentarity or female philopatry. We interpret the parapatric distribution of clades as the joint result of 1) expansion from refuge populations at times of low sea level, and 2) possible enhanced competition between individuals from different clades, or assortative mating, or hybrid zones, along lines of secondary contact. The parapatric-like structure uncovered in the present study parallels regional differences at nuclear marker loci, thus pointing to incipient speciation within Coral Triangle N. kuhlii.

Permanent genetic resources added to molecular ecology resources database 1 December 2012-31 January 2013

This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba.

Multiparametric approach for assessing environmental quality variations in West African aquatic ecosystems using the black-chinned tilapia (Sarotherodon melanotheron) as a sentinel species

The study highlights the potential of the black-chinned tilapia to be used as a sentinel to assess environmental contaminants based on the use of a set of biomarkers. The usefulness of fish species as sentinels for assessing aquatic environment contamination was tested using a set of biomarkers in Senegalese environments characterized by multi-pollution sources. The black-chinned tilapia (Sarotherodon melanotheron) was selected as a sentinel because of its abundance, wide distribution in all coastal aquatic ecosystems and physiological properties. The potential influence of confounding factors such as salinity on biomarker in the tilapia has been examined. Individuals were sampled during two seasons (dry and wet) in eight sites characterized by various degrees of anthropogenic contamination and different salinities (from 0 to 102 psu). Biomarkers-including growth rate (GR), condition factor (CF), biotransformation enzymes such as 7-ethoxyresorufin-O-deethylase (EROD) and glutathione-S-transferase (GST), lipid peroxidation (TBARS) and acetylcholinesterase (AChE)-were measured. Chemical contaminant [polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs)] levels showed different sources of contamination with relatively high concentrations of PAHs in the Hann Bay and Foundiougne locations. The most sensitive biomarker present in different sites according to the principal component analysis is EROD. Few variations of the AChE activity and TBARS levels were found. No clear relationship was found between biomarker responses and salinity, but GR and CF were lower in hypersaline conditions. Tilapia is responsive to environmental contaminants such as PAHs, OCPs and PCBs. The S. melanotheron multiparametric approach showed a better discrimination of sites.

Impact of environmental DDT concentrations on gill adaptation to increased salinity in the tilapia Sarotherodon melanotheron

Estuaries of tropical developing countries suffering from severe droughts induced by climate change are habitats to fish, which face drastic salinity variations and the contact with pollutants. The Western Africa tilapia Sarotherodon melanotheron is highly resistant to hypersalinity, but the effect of human-released xenobiotics on its adaptation is barely known. Controlled experiments were conducted to observe S. melanotheron gill adaptation to abrupt salinity variations in the presence of waterborne DDT, at concentrations detected in their natural habitat. The gills appeared as an important site of DDT conversion to DDD and/or depuration. A 12-days DDT exposure resulted in decreased gill epithelium thickness at all salinities (from fresh- to hypersaline-water), and the structure of gills from freshwater fish was particularly altered, relative to controls. No unbalance in tilapia blood osmolality was observed following DDT exposure, which however caused a decrease in branchial Na(+)-K(+)-ATPase (NKA) activity. Gill cellular NKA expression was reduced in salt-water, together with the expression of the CFTR chloride channel in hypersaline water. Although S. melanotheron seems very resistant (especially in seawater) to short-term waterborne DDT contamination, the resulting alterations of the gill tissue, cells and enzymes might affect longer term respiration, toxicant depuration and/or osmoregulation in highly fluctuating salinities.

Plio-Pleistocene sea level and temperature fluctuations in the northwestern Pacific promoted speciation in the globally-distributed flathead mullet Mugil cephalus

BACKGROUND

The study of speciation in the marine realm is challenging because of the apparent absence of physical barriers to dispersal, which are one of the main drivers of genetic diversity. Although phylogeographic studies using mitochondrial DNA (mtDNA) information often reveal significant genetic heterogeneity within marine species, the evolutionary significance of such diversity is difficult to interpret with these markers. In the northwestern (NW) Pacific, several studies have emphasised the potential importance of sea-level regression during the most recent glaciations as a driver of genetic diversity in marine species. These studies have failed, however, to determine whether the period of isolation was long enough for divergence to attain speciation. Among these marine species, the cosmopolitan estuarine-dependent fish Mugil cephalus represents an interesting case study. Several divergent allopatric mtDNA lineages have been described in this species worldwide, and three occur in sympatry in the NW Pacific.

RESULTS

Ten nuclear microsatellites were surveyed to estimate the level of genetic isolation of these lineages and determine the role of sea-level fluctuation in the evolution of NW Pacific M. cephalus. Three cryptic species of M. cephalus were identified within this region (NWP1, 2 and 3) using an assignment test on the microsatellite data. Each species corresponds with one of the three mtDNA lineages in the COI phylogenetic tree. NWP3 is the most divergent species, with a distribution range that suggests tropical affinities, while NWP1, with a northward distribution from Taiwan to Russia, is a temperate species. NWP2 is distributed along the warm Kuroshio Current. The divergence of NWP1 from NWP2 dates back to the Pleistocene epoch and probably corresponds to the separation of the Japan and China Seas when sea levels dropped. Despite their subsequent range expansion since this period of glaciation, no gene flow was observed among these three lineages, indicating that speciation has been achieved.

CONCLUSIONS

This study successfully identified three cryptic species in M. cephalus inhabiting the NW Pacific, using a combination of microsatellites and mitochondrial genetic markers. The current genetic architecture of the M. cephalus species complex in the NW Pacific is the result of a complex interaction of contemporary processes and historical events. Sea level and temperature fluctuations during Plio-Pleistocene epochs probably played a major role in creating the marine species diversity of the NW Pacific that is found today.

Differential expression of the heat shock protein Hsp70 in natural populations of the tilapia, Sarotherodon melanotheron, acclimatised to a range of environmental salinities

Background

The relationship between environmental variation and induction of heat shock proteins (Hsps) has been much documented under experimental conditions. However, very little is known about such induction in natural populations acclimatised to prevailing environmental conditions. Furthermore, while induction of stress proteins has been well documented in response to environmental contaminants and thermal stressors, little is known about whether factors, such as extreme salinity, are also potential inductors. The black-chinned tilapia Sarotherodon melanotheron is unusual for its ability to colonise estuarine environments in West Africa that are characterised by extremely high salinities. The relationships between mRNA levels of the 70 kDa heat shock protein (Hsp70) and Na⁺, K⁺-ATPase1α (Naka) in the gills, environmental salinity, and a life-history trait (condition factor) were investigated in wild populations of this species sampled from three locations in the Saloum estuary, at salinities ranging from 40 to 100 psu.

Results

The highest Hsp70 and Naka mRNA levels, and the poorest condition factors were recorded in the most saline sampling site (100 psu). The Hsp70 and Naka mRNA were correlated amongst themselves and showed a direct positive correlation with environmental salinity, and a negative correlation with fish condition factor. Thus, the Hsp70 is constitutively overexpressed by S. melanotheron acclimatised to extreme hypersalinity.

Conclusions

These results indicate that, although S. melanotheron can colonise extremely saline environments, the overexpression of Hsp70 combined with the higher Naka mRNA expression reveals that this represents a chronic stress. The induction of Hsp70 was, therefore, a biomarker of chronic hyper-osmotic stress which presumably can be linked to the impaired growth performance and precocious reproduction that have been demonstrated in the populations at the extremely saline sites.

Cytochrome b barcoding, molecular systematics and geographic differentiation in rabbitfishes (Siganidae)

The fish genus Siganus (Siganidae) is widely distributed in the coastal habitats of all the tropical Indo-Pacific, with 28 nominal species recognized so far, based on general morphology and coloration patterns. A mitochondrial phylogeny of 16 Siganidae species, based on the partial nucleotide sequences of the cytochome b gene, was produced. Individual haplotypes of given nominal species generally clustered at the extremity of long branches, thus validating the current taxonomy. However, S. lineatus haplotypes formed a paraphyletic group including S. guttatus, while S. fuscescens haplotypes were apparently splitted in two groups, calling for further investigation. S. woodlandi and S. argenteus formed a monophyletic group, as expected from their close morphological relatedness, although they were separated by a substantial, 14.5-16.3% nucleotide distance. Among eight species sampled from different locations across the Indo-West Pacific, S. argenteus and S. spinus showed the lowest degree of geographic differentiation, a result that correlated well with their extended pelagic larval stage. Fixation index estimates were high in all six other species tested (S. doliatus, S. fuscescens, S. lineatus, S. puellus, S. punctatus, S. vulpinus). The cytochrome b gene fragment chosen here proved useful as a barcode in Siganidae.

Discrepancies in phylogeographical patterns of two European anglerfishes (Lophius budegassa and Lophius piscatorius)

In order to investigate the relative importance of historical processes and life-history traits in shaping the present-day genetic structure of European anglerfishes, 382 Lophius piscatorius and 134 Lophius budegassa were sequenced on the 5' end of the mitochondrial control region. Both species showed a limited genetic structure and some evidence of a demographic expansion that probably occurred not at the end of the Last Glacial Maximum, but earlier in the Pleistocene. The main discrepancy between the two anglerfishes concerned the genetic structure between Atlantic and Mediterranean populations, with weak but significant differentiation observed only in L. budegassa. This genetic structure was congruent with the existence of a phylogeographical break previously reported in several marine species across the Almeria-Oran front. The contrast observed between both anglerfishes was supposed to be induced by a possible more ancient (re)colonisation of the Mediterranean Sea by L. budegassa. Finally, the limited genetic structure and lack of isolation by distance observed in both species suggested high larval dispersal capacities that probably overwhelm the influence of the bathymetric distribution range on migrations of adults and juveniles.

Nuclear-DNA markers confirm the presence of two anchovy species in the Mediterranean

Morphometric, allozymic, and mitochondrial DNA variability previously indicated that the Mediterranean anchovy Engraulis encrasicolus includes two distinct forms, one of the inshore habitat, and the other one of the open-sea habitat. Here, we showed that the two forms significantly differ by several morphological characters. To test the hypothesis, proposed previously, that the two forms are distinct biological species, we used length-polymorphic, exon-primed intronic PCR markers from the creatine-kinase multigenic family and genetically characterized anchovy samples collected in the northwestern Mediterranean and in the eastern Atlantic. Large genetic differences were found between the two forms (Weir and Cockerham's theta = 0.397 to 0.586). In contrast, geographic variation in the open-sea form at the scale of the eastern Atlantic/northwestern Mediterranean was weak (theta = -0.006 to 0.042). This again demonstrated considerable restriction to nuclear gene flow between inshore and open-sea anchovy populations. In addition to previous results from allozymes, this confirmed their status as distinct biological species, namely Engraulis albidus sp. nov. and Engraulis encrasicolus L.

Genetic structure of fragmented populations of a threatened endemic percid of the Rhône river: Zingel asper

Zingel asper is an endemic percid of the Rhône basin considered to be critically endangered. This species was continuously distributed throughout the Rhône in 1900, but today only occupies 17% of its initial area. In the present study, five microsatellite loci were used to assess the level of genetic variability within and among populations localized in different sub-basins. Contrasting results were obtained for the three main populations from the Rhône. A reduced allelic diversity was observed for the two populations displaying the lowest patch sizes (length of the river system occupied); of these, a recent genetic bottleneck was detected for the population showing a particularly low density. However, the third population was characterized by a relatively large spatial extent, high local fish concentrations and an allelic diversity that was twice as high and associated with an equilibrium between mutation and drift. Thus, this population shows an apparently better evolutionary potential for long-term survival. Since 1930, a marked fragmentation of the whole Rhône system has appeared, related to the development of dams, and we assume that the significant genetic differentiation detected between the populations could mainly reflect the impact of this fragmentation. The high turnover of the Z. asper populations, and the major role of dispersal in population persistence (highlighted in a recent population dynamics study), indeed suggest that the differentiation observed could mainly have arisen from habitat fragmentation in recent history.

Identifying main evolutionary mechanisms shaping genetic variation of Leuciscus cephalus L. 1758 (Cyprinidae) in western Greece: discordance between methods

Numerous methods can be used in intraspecific phylogeographic studies to infer the evolutionary mechanisms that shaped observed genetic variation in populations. However, these methods are scarcely used jointly, and the evolutionary outcomes they could propose are not fully compared. In this study, using a chub (Leuciscus cephalus; Cyprinidae) mitochondrial DNA data set (13 populations in Western Greece, 14 haplotypes), we compare three distinct 'historical' methods that could possibly infer relative importance of basic evolutionary mechanisms (isolation vs migration) shaping genetic variation: the nested clade analysis, the psi-test and the 'mismatch distributions'. Taking together, interpretations of these analyses allow to draw a picture of the evolutionary history of chub in Western Greece based on isolation and genetic drift for higher clades. However, results issued each method can differ for low differentiated clades. We discuss such differences and suggest that methods should be used jointly in phylogeographic studies for a better evaluation of the evolutionary mechanisms that shaped genetic variation.

Origin, radiation, dispersion and allopatric hybridization in the chub Leuciscus cephalus

The phylogenetic relationships of 492 chub (Leuciscus cephalus) belonging to 89 populations across the species' range were assessed using 600 base pairs of cytochrome b. Furthermore, nine species belonging to the L. cephalus complex were also analysed (over the whole cytochrome b) in order to test potential allopatric hybridization with L. cephalus sensu stricto (i.e. the chub). Our results show that the chub includes four highly divergent lineages descending from a quick radiation that took place three million years ago. The geographical distribution of these lineages and results of the nested clade analysis indicated that the chub may have originated from Mesopotamia. Chub radiation probably occurred during an important vicariant event such as the isolation of numerous Turkish river systems, a consequence of the uplift of the Anatolian Plateau (formerly covered by a broad inland lake). Dispersion of these lineages arose from the changes in the European hydrographic network and, thus, the chub and endemic species of the L. cephalus complex met by secondary contacts. Our results show several patterns of introgression, from Leuciscus lepidus fully introgressed by chub mitochondrial DNA to Leuciscus borysthenicus where no introgression at all was detected. We assume that these hybridization events might constitute an important evolutionary process for the settlement of the chub in new environments in the Mediterranean area.

Nested clade and phylogeographic analyses of the chub, Leuciscus cephalus (Teleostei, cyprinidae), in Greece: implications for Balkan Peninsula biogeography

Phylogenetic relationships among Greek populations of the chub, Leuciscus cephalus, were investigated using 600 bp of the cytochrome b gene. The aim of this study was to test the assumption that the main difference in ichthyological composition between both sides of the Balkan Peninsula is directly linked to differences in the dispersion mechanisms used by fish in order to extend their distribution range. Phylogenetic and nested clade analyses clearly showed that populations in Greece are significantly differentiated. Greek populations were found to descend from three lineages in three geographical provinces: Western, Central, and Eastern Greece. The chub reached Western Greece at the beginning of the Pleistocene and Eastern Greece during the mid-Pleistocene. Chub dispersion occurred mainly by river confluence due to sea level lowering and river capture in Western Greece and sea dispersal with low-salinity conditions within the Aegean Sea in Eastern Greece. However, in Central Greece, the original mtDNA lineage has presumably been lost owing to a genetic introgression following a second invasion from the Danube during the final stage of the last glaciation. This study provides new elements for a better understanding of the composition of the contemporary ichthyofauna in Greece and highlights possible evolutionary mechanisms responsible for the high endemism rate in the Western Greek biogeographic province.

Phylogeography and postglacial dispersion of the chub (Leuciscus cephalus) in Europe

A phylogeographic analysis of mitochondrial DNA variation was performed in order to test the hypothesis of a postglacial recolonization of mid- and north-European rivers from a Danubian refuge. Over 345 chub specimens from European rivers covering most of the species' native range were investigated using 600 bp of the cytochrome b gene. Chub in European rivers belong to four highly divergent mitochondrial groups (lineages) differing by mean divergence estimates from 5.2% to 7.89%. These four lineages have a largely allopatric distribution, implying four geographical sets: two Mediterranean, and two north-European sets. This pattern provided strong evidence for: (i) the eradication of this species from most of Europe during maximum ice extent; (ii) its survival in four refugia (Adriatic side of the Balkans, eastern Greece (Aegean Rivers), southern tributaries of the Danube, and periphery of Black and Caspian Seas); (iii) a differential postglacial recolonization of mid- and northern Europe from the last two refugia only; (iv) the occurrence of this recolonization in two steps for the Danubian (western) lineage that entered western Europe (Rhine-Rhone-Loire drainages) during the Riss-Würm interglacial period and survived the last glaciation there before colonizing Garonne, UK and German drainages up to the Elbe during the Holocene; and (v) the occurrence of this recolonization in a single step for the Ponto-Caspian (eastern) lineage that entered the Baltic area as far as the Oder in the Holocene. Both lineages came into contact in the River Elbe without evident mixing.

Phylogeography and postglacial dispersion of the chub (Leuciscus cephalus) in Europe

A phylogeographic analysis of mitochondrial DNA variation was performed in order to test the hypothesis of a postglacial recolonization of mid- and north-European rivers from a Danubian refuge. Over 345 chub specimens from European rivers covering most of the species' native range were investigated using 600 bp of the cytochrome b gene. Chub in European rivers belong to four highly divergent mitochondrial groups (lineages) differing by mean divergence estimates from 5.2% to 7.89%. These four lineages have a largely allopatric distribution, implying four geographical sets: two Mediterranean, and two north-European sets. This pattern provided strong evidence for: (i) the eradication of this species from most of Europe during maximum ice extent; (ii) its survival in four refugia (Adriatic side of the Balkans, eastern Greece (Aegean Rivers), southern tributaries of the Danube, and periphery of Black and Caspian Seas); (iii) a differential postglacial recolonization of mid- and northern Europe from the last two refugia only; (iv) the occurrence of this recolonization in two steps for the Danubian (western) lineage that entered western Europe (Rhine-Rhone-Loire drainages) during the Riss-Würm interglacial period and survived the last glaciation there before colonizing Garonne, UK and German drainages up to the Elbe during the Holocene; and (v) the occurrence of this recolonization in a single step for the Ponto-Caspian (eastern) lineage that entered the Baltic area as far as the Oder in the Holocene. Both lineages came into contact in the River Elbe without evident mixing.