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Copyright of Cybium: International Journal of Ichthyology is the property of Societe Francaise d'Ichtyologie (SFI) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align phylogenetic method, newly applied to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions. Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121-96 Mya) and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69-10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving different repeat types. [ABSTRACT FROM AUTHOR]

The occurrence of Alexandrium catenella related to paralytic shellfish poisoning (PSP) in the French Mediterranean Thau lagoon has been known since 1998. Blooms are recurrent and usually occur each year in spring and/or autumn. Taxonomic diversity of resting cysts and vegetative cells has been studied through morphological examination and molecular typing of 558 clonal strains sampled in 2004 and 2007. Sequencing the nuclear rRNA fragment, including ITS1, the 5.8S rRNA gene, ITS2, and the D1/D2 28S rRNA genes, enabled two species to be determined, A. catenella and A. tamarense, which are difficult to distinguish morphologically (cryptic species). In order to carry out extensive and accurate molecular determinations, an original semi-multiplex PCR method, using new ribotype-specific primers targeting the 18S–28S rRNA ITS region, has been developed. The relative abundance of each species was then established in seawater in 2007 and in the sediment collected in 2004. The co-occurrence of A. catenella (Group IV), which is known as the main species responsible for toxic PSP events since 1998 and of A. tamarense (Group III) (non-toxic) that was not formally recognized by microscopic observation since 1995, was examined for several months. [ABSTRACT FROM AUTHOR]

Abstract: Freshwater fauna of ancient lakes frequently contain endemic taxa thought to have originated during the long existence of these lakes, yet uncertainties remain as to whether they represent distinct genetic lineages with respect to more widespread relatives and to the relative roles of isolation and dispersal in their evolution. Phylogenetic analyses of sequence variation at nuclear and mitochondrial genes were used to examine these issues for the freshwater fish genus Barbus in two European ancient lake systems on the Balkan Peninsula. The nuclear and mitochondrial data yielded concordant phylogeographic patterns though incomplete sorting of nuclear haplotypes between some mitochondrial clades was detected. The distributions of two currently recognized species investigated here do not match the distributions of evolutionary lineages revealed by phylogenetic analyses. The Prespa barbel, Barbus prespensis, is not endemic to the lakes Prespa as previously thought but is instead found to be widespread in the south-eastern Adriatic Sea basin, with a distribution largely corresponding to the basin of the now extinct Lake Maliq historically connected with Lake Prespa. On the other hand, a cryptic phylogenetic subdivision in a widespread species, B. rebeli, was discovered to be more distant from B. rebeli than from other Barbus species and to be endemic to the system of connected lakes Ohrid and Shkodra. The division coincides with the hydrogeographical boundary delimiting distributions of other freshwater fishes, and we suggest that this newly discovered evolutionary lineage represents a distinct species. These findings support the emerging pattern that endemic taxa have evolved not through isolation of individual lakes, but in systems of currently and historically interconnected lakes and their wider basins. [Copyright &y& Elsevier]

Abstract: Sicyopterus lagocephalus is the most abundant sicydiine (amphidromous gobiid) in the rivers of volcanic islands in the south-western Indian Ocean. The species occurs in the Mascarene (Mauritius and La Réunion) and Comoros islands (Anjouan, Mayotte, etc.) and the post-larvae supply an economically important fishery. Because of the scarcity of available ecological and biological data, a genetic survey has been undertaken at the scale of the south-western Indian Ocean using intron-length polymorphism. Samples from La Réunion, Mauritius and Mayotte were used to assess the population genetic structure within islands and between nearby and remote islands. No genetic divergences were observed in samples at these different geographical scales. A lower number of rare alleles were observed in Mayotte samples suggesting a slight effect of their peripheral geographical position. However, no recent bottleneck was evidenced for these populations. High temporal divergences have been demonstrated in La Réunion as in previous studies indicating a temporal Wahlund effect. In the light of these results, the dispersion abilities, the connectivity of populations and the metapopulation functioning are discussed in relation to the regional environmental factors (dispersal barriers, habitat colonization, cyclones, long distance dispersal). [Copyright &y& Elsevier]

Populations of the marble trout (Salmo marmoratus) are critically declining due to introgression by brown trout (S. Trutta) strains. Hybrids between the two forms are fertile and presently predominant in most rivers of the species’ range. The involved hybridization mechanisms have been studied through two large scale in-stream experiments (Driselpoh and Stopnikarca) as 50% of each species have been stocked at the age of one year in fishless streams, each fish being individually marked. Diagnostic molecular markers were applied to test a partial reproductive isolation between the two species. Emphasis was put on survival and growth patterns of stocked fish (parental generation) as well as on fish hatched within the stream (F1 generation). No evidence of a partial reproductive barrier between the two species was observed. Survival of the parental generation depended on the year in both streams, as well as on the species in Stopnikarca, but was identical for both species in Driselpoh. In both streams survival of instream hatched individuals measured from 0+ to 2+ was lower for brown trout. In Driselpoh, F1 0+, 1+ and 2+ hybrids were larger than pure individuals. Larger hybrids were only observed in Stopnikarca when analyses focused on individuals in inter-specific competition suggesting that heterosis and stress effects may explain the observed size differences. Our results point out important ecological differences between marble and brown trout and have shown that hybridization can easily take place. The findings indicate that high F1 hybrid presence, survival and heterosis effects may impede marble trout rehabilitation in the area. [Copyright &y& Elsevier]

Background: The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are microsatellites and mitochondrial markers that lack replicability among laboratories, and a large genome coverage. An alternative that may be particularly efficient and universal is the development of small to large panels of Single Nucleotide Polymorphism markers (SNPs). Here, we used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned on the brown trout linkage map and suitable for population genetics studies. Then, we used this novel resource to develop a cost-effective array of 192 SNPs (96 × 2) evenly spread on this map. This array was tested for genotyping success in five independent rivers occupied by two main brown trout evolutionary lineages (Atlantic -AT- and Mediterranean -ME-) on a total of 1862 individuals. Moreover, inference of admixture rate with domestic strains and population differentiation were assessed for a small river system (the Taurion River, 190 individuals) and results were compared to a panel of 13 microsatellites. Results: A high genotyping success was observed for all rivers (< 1% of non-genotyped loci per individual), although some initially used SNP failed to be amplified, probably because of mutations in primers, and were replaced. These SNPs permitted to identify patterns of isolation-by-distance for some rivers. Finally, we found that microsatellite and SNP markers yielded very similar patterns for population differentiation and admixture assessments, with SNPs having better ability to detect introgression and differentiation. Conclusions: The novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations. [ABSTRACT FROM AUTHOR]

The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression., (© 2022 Fisheries Society of the British Isles.)

Selection, genetic drift, and gene flow affect genetic variation within populations and genetic differences among populations. Both drift and selection tend to decrease variation within populations and increase differences among populations, whereas gene flow increases variation within populations but leads to populations being related. In brown trout (Salmo trutta L.), the most important factor in population fragmentation is disrupted river-segment connectivity. The main goal of the study was to use genetic analysis to estimate the level of gene flow among resident and migratory brown trout in potential hybridization areas located downstream of impassable barriers in one river basin in the southern Baltic Sea region. First, spawning redds were counted in the upper river basin downstream of impassable barriers. Next, samples were collected from juveniles in spawning areas located downstream of barriers and from adults downstream and upstream of barriers. Subsequently, genetic analysis was performed using a panel of 13 microsatellite loci and the Salmo trutta 5 K SNP microarray. The genetic differentiation estimated between the resident form sampled upstream of the barriers and the anadromous specimens downstream of the barriers was high and significant. Analysis revealed that gene flow occurred between the two forms in the hybridization zone investigated and that isolated resident specimens shared spawning grounds with sea trout downstream of the barriers. The brown trout population from the river system investigated was slightly, internally diversified in the area accessible to migration. Simultaneously, the isolated part of the population was very different from that in the rest of the basin. The spawning areas of the anadromous form located downstream of the barriers were in a hybridization zone and gene flow was confirmed to be unidirectional. Although they constituted a small percentage, the genotypes typical upstream of the barriers were admixed downstream of them. The lack of genotypes noted upstream of the barriers among adult anadromous individuals might indicate that migrants of upstream origin and hybrids preferred residency., (© 2021. The Author(s).)

There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations., (Copyright © 2021. Published by Elsevier Inc.)

Physiological plasticity gives HABs species the ability to respond to variations in the surrounding environment. The aim of this study was to examine morphological and physiological variability in Alexandrium pacificum R.W. Litaker (Group IV) (former Alexandrium catenella) blooming in Annaba bay, Algeria. Monoclonal cultures of up to 30 strains of this neurotoxic dinoflagellate were established by the germination of single resting cysts from the surface sediment of this southern Mediterranean marine ecosystem. Ribotyping confirmed formally for the first time that A. pacificum is developing in Eastern Algerian waters. Toxin analyses of A. pacificum strains revealed substantial intraspecific variability in both the profile and toxin amount. However, the toxin profile of most strains is characterized by the dominance of GTX6 (up to 96 mol %) which is the less toxic paralytic molecule. The toxin concentrations in the isolated strains varied widely between 3.8 and 30.82 fmol cell -1 . We observed an important variation in the growth rate of the studied A. pacificum strains with values ranging from 0.05 to 0.33 d -1 . The lag time of the studied strains varied widely and ranged from 4 to 20 days. The intraspecific diversity could be a response to the selection pressure which may be exerted by different environmental conditions over time and which can be genetically and in turn physiologically expressed. This study highlights, for the first time, that the sediment of a limited area holds an important diversity of A. pacificum cysts which give when germinate populations with noticeable physiological plasticity. Consequently, this diversified natural populations allow an exceptional adaptation to specific environmental conditions to outcompete local microalgae and to establish HABs which could explain why this dinoflagellate is successful and expanding worldwide., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well., Competing Interests: The authors have declared that no competing interests exist.

Understanding the evolutionary consequences of human-mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make-up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double-digested restriction site-associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data., (© 2018 John Wiley & Sons Ltd.)

High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout ( Salmo trutta ), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar , revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar / S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout., (Copyright © 2017 Leitwein et al.)

The European sturgeon (Acipenser sturio) was once a common species throughout Europe, but the sole remaining natural population presently inhabits the Gironde Estuary in France (Atlantic coast). The species was classified as 'Critically Endangered' in 1996, and the Gironde population is now on the verge of extinction. In this setting, and for the first time, we present the past phylogeographical features of this species throughout Europe along with an assessment of its former genetic diversity. This study was based on a molecular analysis (mtDNA CR sequencing) of 10 living specimens from the Gironde Estuary, 55 museum specimens that had been caught along 19th and 20th centuries, and 59 archaeological remains dating back to 260-5000years BP, from which mitochondrial DNA was extracted and amplified. Although discontinuous, the produced data provided a realistic image of the former structure of A. sturio in Europe. Reconstruction of the phylogenetic trees and haplotypes network led to the identification of several clades. The mitochondrial genetic diversity of this species was found to be much greater at the core (Iberian Peninsula, Mediterranean and Adriatic regions) than along the margins (Atlantic-Northern Europe, Black Sea) of its range. A series of hypotheses on the dates and causes of changes in the species' major structures are put forward on the basis of these data. Finally, competition with A. oxyrinchus, a sibling species whose presence in Northern Europe was recently reconsidered, is presented as a major factor in the evolution of this species., (Copyright © 2015 Elsevier Inc. All rights reserved.)

The intra-specific diversity and genetic structure within the Alexandrium pacificum Litaker (A. catenella - Group IV) populations along the Temperate Asian coasts, were studied among individuals isolated from Japan to China. The UPGMA dendrogram and FCA revealed the existence of 3 clusters. Assignment analysis suggested the occurrence of gene flows between the Japanese Pacific coast (cluster-1) and the Chinese Zhejiang coast (cluster-2). Human transportations are suspected to explain the lack of genetic difference between several pairs of distant Japanese samples, hardly explained by a natural dispersal mechanism. The genetic isolation of the population established in the Sea of Japan (cluster-3) suggested the existence of a strong ecological and geographical barrier. Along the Pacific coasts, the South-North current allows limited exchanges between Chinese and Japanese populations. The relationships between Temperate Asian and Mediterranean individuals suggested different scenario of large-scale dispersal mechanisms., (Copyright © 2015. Published by Elsevier Ltd.)

Sturgeons (family Acipenseridae) are one of the most endangered groups of animals. Two hundred million years of evolution and multiple ploidy levels make this group a unique subject for studying the evolution of polyploidy in animals. As most sturgeon species have gone through significant functional diploidization, 2 scales of ploidy levels can be distinguished: the "evolutionary scale," which indicates the maximum ploidy level achieved and the "recent scale," which indicates the current functional ploidy level. This study analyzes published and new microsatellites to check the ploidy level and to determine the degrees of functional diploidization in 10 sturgeon species from Europe and Asia. We screened 50 primer pairs newly developed for Acipenser gueldenstaedtii and 40 primer pairs previously developed in other studies for other sturgeon species. The maximal number of alleles per individual of a given species was assessed at 20 microsatellite loci, which showed consistent amplification in most of the 10 analyzed species. Taken together, our data on the percentage of disomic loci in different species suggest that functional diploidization is an ongoing process in sturgeons. We observed lower levels of diploidization in tetraploid species from the Atlantic clade than in the species from the Pacific clade, which can be explained by the more recent genome duplication in tetraploid species from the Atlantic clade. Based on the recent findings and results of this study, we propose that the evolution of sturgeons has been affected by at least 3 different polyploidization events., (© The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Alexandrium catenella (group IV) and Alexandrium tamarense (group III) (Dinophyceae) are two cryptic invasive phytoplankton species belonging to the A. tamarense species complex. Their worldwide spread is favored by the human activities, transportation and climate change. In order to describe their diversity in the Mediterranean Sea and understand their settlements and maintenances in this area, new microsatellite markers were developed based on Thau lagoon (France) samples of A. catenella and A. tamarense strains. In this study twelve new microsatellite markers are proposed. Five of these microsatellite markers show amplifications on A. tamarense and ten on A. catenella. Three of these 12 microsatellite markers allowed amplifications on both cryptic species. Finally, the haplotypic diversity ranged from 0.000 to 0.791 and 0.000 to 0.942 for A. catenella and A. tamarense respectively., (Copyright © 2014. Published by Elsevier Ltd.)

It has been previously established that the Leopard Whipray, Himantura leoparda, consists of two genetically isolated, cryptic species, provisionally designated as 'Cluster 1' and 'Cluster 4' (Arlyza et al., Mol. Phylogenet. Evol. 65 (2013) [1]). Here, we show that the two cryptic species differ by the spotting patterns on the dorsal surface of adults: Cluster-4 individuals tend to have larger-ocellated spots, which also more often have a continuous contour than Cluster-1 individuals. We show that H. leoparda's holotype has the typical larger-ocellated spot pattern, designating Cluster 4 as the actual H. leoparda. The other species (Cluster 1) is described as Himantura tutul sp. nov. on the basis of the nucleotide sequence of a 655-base pair fragment of its cytochrome-oxidase I gene (GenBank accession No. JX263335). Nucleotide synapomorphies at this locus clearly distinguish H. tutul sp. nov. from all three other valid species in the H. uarnak species complex, namely H. leoparda, H. uarnak, and H. undulata. H. tutul sp. nov. has a wide distribution in the Indo-West Pacific, from the shores of eastern Africa to the Indo-Malay archipelago. H. leoparda under its new definition has a similarly wide Indo-West Pacific distribution., (Copyright © 2013 Académie des sciences. Published by Elsevier SAS. All rights reserved.)

In the marine environment, differential gene exchange between partially reproductively isolated taxa can result in introgression that extends over long distances due to high larval dispersal potential. However, the degree to which this process contributes to interlocus variance of genetic differentiation within introgressed populations remains unclear. Using a genome-scan approach in the Indo-Pacific eel Anguilla marmorata, we investigated the degree of interpopulation genetic differentiation, the rate of introgression, and within-population genetic patterns at 858 AFLP markers genotyped in 1117 individuals. Three divergent populations were identified based on clustering analysis. Genetic assignments of individuals revealed the existence of different types of hybrids that tended to co-occur with parental genotypes in three population contact zones. Highly variable levels of genetic differentiation were found between populations across the AFLP markers, and reduced rates of introgression were shown at some highly differentiated loci. Gene flow across semipermeable genetic barriers was shown to generate spatial introgression patterns at some loci which define within-population structure over long distances. These results suggest that differential introgression in subdivided populations may be relevant when interpreting spatial variation patterns displayed by outlying loci in other marine fish populations., (© 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.)

The objectives of the study were to determine the phylogeographic structure of brown trout (Salmo trutta) in Morocco, elucidate their colonization patterns in North-West Africa and identify the mtDNA lineages involved in this process. We also aimed to resolve whether certain brown trout entities are also genetically distinct. Sixty-two brown trout from eleven locations across the Mediterranean and the Atlantic drainages in Morocco were surveyed using sequence analysis of the mtDNA control region and nuclear gene LDH, and by genotyping twelve microsatellite loci. Our study confirms that in Morocco both the Atlantic and Mediterranean basins are populated by Atlantic mtDNA lineage brown trout only, demonstrating that the Atlantic lineage (especially its southern clade) invaded initially not only the western part of the Mediterranean basin in Morocco but also expanded deep into the central area. Atlantic haplotypes identified here sort into three distinct groups suggesting Morocco was colonized in at least three successive waves (1.2, 0.4 and 0.2-0.1 MY ago). This notion becomes more pronounced with the finding of a distinct haplotype in the Dades river system, whose origin appears to coalesce with the nascent stage of the basal mtDNA evolutionary lineages of brown trout. According to our results, Salmo akairos, Salmo pellegrini and "green trout" from Lake Isli do not exhibited any character states that distinctively separate them from the other brown trout populations studied. Therefore, their status as distinct species was not confirmed., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Validation of parental allocation using PAPA software (Duchesne P, Godbout MH, Bernatchez L. 2002. PAPA (package for the analysis of parental allocation): a computer program for simulated and real parental allocation. Mol Ecol Notes. 2:191-193.) was investigated under the assumption that only a small proportion of potential breeders contributed to the offspring sample. Inbreeding levels proved to have a large impact on allocation error rate. Consequently, simulations from artificial, unrelated parents may strongly underestimate allocation error, and so, whenever possible, simulations based on the actual parental genotypes should be run. An unexpected and interesting finding was that ambiguity (the highest likelihood is shared by several parental pairs) rates below 10% stood very close to exact allocation error rates (true proportions of wrong allocations). Hence, the ambiguity rate statistic may be viewed as a ready-made indicator of the resolution power of a specific parental allocation run and, if not exceeding 10%, used as an estimate of allocation error rate. It was found that the PAPA simulator, even with few contributing breeders, can be trusted to output reasonably accurate estimates of allocation error as long as those estimates do not exceed 15%. Indeed, most discrepancies between exact and estimated error then stood below 3%. Reproductive success variance had little impact on error estimate discrepancies within the same range. Finally, a (focal set) method was described to correct the estimated family sizes computed directly from parental allocations. Essentially, this method makes use of the detailed structure of the allocation probabilities associated with each parental pair with at least 1 allocated offspring. The allocation probabilities are expressed in matrix form, and the subsequent calculations are run based on standard matrix algebra. On average, this method provided better estimates of family sizes for each investigated combination of parameter values. As the size of offspring samples increased, the corrections improved until a plateau was finally reached. Typically, samples comprising 250, 500, and 1000 offspring would bring corrections in the order of 10-20%, 20-30%, and 30-40%, respectively.

Genetic variability of Trichomycterus from the region of Torotoro (Bolivia, Upper Amazon), distributed in the same watershed where the habitat is structured by waterfalls, canyons and a cave, was studied by allozyme (twelve putative loci) and RFLP-mtDNA (DLoop and cytochrome b) analyses. Alloenzymatic variation studied by Correspondence Analysis and Maximum Likelihood Analysis revealed a four-group structure, which was largely congruent with the distribution of the 14 mtDNA haplotypes. Two of these four clusters (I and II) were differentiated by two diagnostic loci (IDH and G3PDH), two semi-diagnostic loci (PGM and 6PGDH) and consequently a very high F(st )value (estimator theta = 0.77). Therefore, clusters I and II are reproductively isolated. The distribution limit of these two (sibling) species does not correspond to those of the morphological species of Trichomycterus identified in this region: the epigean T. cf. barbouri and the hypogean T. chaberti. However, hypogean fish exhibited two mtDNA haplotypes, a private one and another shared with the epigean Trichomycterus from upstream reaches.

The barb Barbus petenyi is a cyprinid widely distributed throughout the mountain regions in the Danube River basin. Phylogenetic analysis of the DNA sequence variation at the mitochondrial cytochrome b gene over much of this range yielded three deep-branching (5.9-9.4% average divergence), well-supported haplotype clades with mutually exclusive geographic distributions and divergence times estimated to be in the Tertiary. The clades did not form an altogether monophyletic group as the most divergent one coalesced more recently with haplotypes of phylogenetically close species than with the other B. petenyi haplotypes. This pattern was supported by bootstrap and log-likelihood Shimodaira-Hasegawa tests. The other two were sister clades, but their distinctiveness was supported by previous allozyme data. Hence, from a taxonomic point of view, the current recognition of B. petenyi is erroneous, as it does not represent a single evolutionary lineage, and we suggest that three species be recognized instead. Substantial phylogeographic differences were evident among the three putative species, the two more southerly ones displaying significant structure, which suggested that they each survived in several glacial refugia throughout the Pleistocene. The phylogeographic pattern of multiple populations of rheophilic barbs with a history of long-term persistence and separation within the Danube River basin is novel within fishes and provides a hypothesis against which phylogeographic patterns among other similarly distributed rheophilic species may be compared.