Deep genetic divergence and recent radiations in sand goby <i>Pomatoschistus minutus</i> along European coasts

Understanding evolutionary patterns is more complex in marine compared to continental species because marine species have high effective population sizes and high levels of dispersal due to an apparent lack of barriers. Moreover, phylogeographical breaks in the marine realm such as the Atlantic-Mediterranean transition remain controversial. Therefore a new high-quality phylogeographic analysis was realized for a marine demersal fish, the sand goby Pomatoschistus minutus (Gobiidae, Teleostei). Sand gobies of 12 locations along the full European distribution range were analyzed by sequencing a large fragment of the mitochondrial cytochrome b gene.The phylogenetic results show that P. minutus comprises two deep genealogical lineages, the Mediterranean Sea Clade (MS-Clade) and the Atlantic Ocean Clade (AOClade), that date back to the Early Pleistocene (1.6-0.8 MYA). Even though the sand goby occurs only in a few northern locations in the Mediterranean, the MS-Clade contains the Significant Units (ESU), one off the Western Iberian Peninsula and the other in the marine systems of the North Atlantic (Bay of Biscay, North Sea, Irish Sea and Baltic Sea). This is consistent with two separate palaeorefugia during the Pleistocene glaciations: the Iberian Peninsula and the Bay of Biscay. Less haplotypes were shared among the marine systems of the North Atlantic, indicating a low present-day gene flow. The network analysis showed a recent radiation in each marine system, even in the northern Baltic Sea where the recolonization of P. minutus occurred only 8000 years ago. This phylogeographic pattern will be compared with putatively adaptive loci in order to study the characteristics of local adaptation in the marine environment

Exploring glacial and present evolutionary patterns of a marine goby, <i>Pomatoschistus minutus</i>

A classical understanding of marine fishes is that they have high effective population sizes and high levels of dispersal due to an apparent lack of barriers in the marine environment. The realization of a genetic population structure is therefore thought to be a slow process. To gain insights in this process, it is a challenge to disentangle the interaction between selection, gene flow, population history and genetic drift. The sand goby (Pomatoschistus minutus), which is an important ecological but noncommercial species, was chosen to distinguish between natural and anthropologically induced processes. A spatio-temporal analysis with samples from different localities throughout the species distribution and with two types of genetic markers was performed to assess the neutral genetic population structure. Phylogeographical patterns were studied by sequence cytochrome b (mtDNA). Nine new nuclear microsatellites were developed and used to describe the current genetic diversity and population structure. The genetic structure of the sand goby is best explained by a combination of present and historic factors. Due to its high potential for dispersion and high effective population size, it shows the typical features of a marine fish with a high level of diversity and a limited degree of genetic differentiation. The large genetic distance between the Venetian and all other samples shows that the sand gobies from the Adriatic Sea should be considered as a distinct cryptic species of the genus Pomatoschistus. Low but significant differentiation is observed between Atlantic and western Mediterranean P. minutus. In the Atlantic and Baltic basins, there is evidence for a postglacial range expansion and a weak pattern of isolation-by-distance. Furthermore the results support the hypothesis of a glacial refugium and a fine-scale genetic structure in the southern North Sea. The neutral genetic pattern will be compared with putatively adaptive loci in order to study the genomic characteristics of local adaptation in the marine environment. This should provide a better understanding of how fish respond to changes in the environment

Development and characterization of nine polymorphic microsatellite markers in the sand goby <i>Pomatoschistus minutus</i> (Gobiidae)

A microsatellite-enriched genomic library was constructed for the sand goby, Pomatoschistus minutus (Pallas 1770), and nine polymorphic DNA microsatellite markers of high quality were successfully optimized. Characterization of 96 individuals from the Vaccarès lagoon (France) showed moderate to high levels of polymorphism (two to 54 alleles). All the markers conformed to Hardy-Weinberg equilibrium and showed no evidence of null alleles, large allele dropout, stuttering and linkage disequilibrium between pairs of loci. These markers successfully amplify in three closely related species and can be employed to investigate population genetic structure and to clarify paternity in Pomatoschistus species

Thermal refugia and the survival of species in changing environments: new evidence from a nationally extinct freshwater fish

Variation in global climate during the Quaternary has helped shape current species distributions. The stenohaline fish fauna of the British Isles is generally thought to have colonised eastern England via a landbridge following the last glacial maximum. This theory is investigated using the nationally extinct burbot, Lota lota, as a model species. Samples were collected from 15 museum specimens of known English provenance and analysed for differences in the mitochondrial DNA control region. The DNA analysis produced eight sequences of 270 base pairs, with one sample reaching 420 base pairs in length. Genetic analysis suggests the extinct English population of the burbot was a distinct lineage, differing from those previously described from across the species’ global distribution. Despite this, network analysis suggests that the English lineage is closely related to populations in western Europe, supporting colonisation via a postglacial landbridge. The rate of genetic divergence suggests that the timing of L. lota's colonisation of English rivers was prior to the last glacial maximum. Lota lota appears to have survived the last glacial maximum in refugia within the British Isles. This study adds to the evidence for a British freshwater refugia and furthers our understanding of the colonisation history of British freshwater fishes. These results also provide valuable information for conservation strategies for L. lota indicating the western European clade as most genetically appropriate for potential future reintroductions to English rivers

Indications for a recent Holarctic expansion of pike based on a preliminary study of mtDNA variation

An extremely limited haplotypic diversity within populations and a strikingly low divergence between European and Canadian haplotypes were found in pike Esox lucius. Certain haplotypes were associated with a particular geographical region in Europe: a widespread European and a restricted Hungarian–Norwegian type. The low haplotypic intraspecific divergence suggests a late Pleistocene expansion from an ancestral population

Distributional and demographic consequences of Pleistocene climate fluctuations for a marine demersal fish in the north-eastern Atlantic

Aim: The Pleistocene glaciations were the most significant historical event during the evolutionary life span of most extant species. However, little is known about the consequences of these climate changes for the distribution and demography of marine animals of the north-eastern Atlantic. The present study focuses on the phylogeographic and demographic patterns of the sand goby, Pomatoschistus minutus (Teleostei: Gobiidae), a small marine demersal fish.Location: North-eastern Atlantic, Mediterranean, Irish, North and Baltic seas.Methods: Analysis was carried out by sequencing the mtDNA cytochrome b gene of sand gobies from 12 localities throughout the species' range, and using this information in combination with published data of allozyme markers and mtDNA control region sequences. Several phylogenetic methods and a network analysis were used to explore the phylogeographic pattern. The historical demography of P. minutus was studied through a mismatch analysis and a Bayesian skyline plot.Results: Reciprocal monophyly was found between a Mediterranean Sea (MS) clade and an Atlantic Ocean (AO) clade, both with a Middle Pleistocene origin. The AO Clade contains two evolutionary significant units (ESUs): the Iberian Peninsula (IB) Group and the North Atlantic (NA) Group. These two groups diverged during Middle Pleistocene glacial cycles. For the NA Group there is evidence for geographic sorting of the ancestral haplotypes with recent radiations in the Baltic Sea, Irish Sea, North Sea and Bay of Biscay. The demographic histories of the Mediterranean Clade and the two Atlantic ESUs were influenced mainly by expansions dated as occurring during the Middle Pleistocene glaciations and post-Eem, respectively.Main conclusions: The pre-LGM (Last Glacial Maximum) subdivision signals were not erased for P. minutus during the LGM. Middle Pleistocene glaciations yielded isolated and differently evolving sets of populations. In contrast to the case for most other taxa, only the northern Atlantic group contributed to the post-glacial recolonization. The historical demography of Mediterranean sand gobies was influenced mainly by Middle Pleistocene glaciations, in contrast to that of the Atlantic populations, which was shaped by Late Pleistocene expansions

High molecular diversity in the rhodopsin gene in closely related goby fishes: a role for visual pigments in adaptive speciation?

The spectral tuning mechanism of visual pigments is an excellent model to elucidate the mechanisms of adaptive evolution and the importance of selection as an evolutionary force. Therefore, we use a phylogenetic approach to determine whether there is evidence for differential adaptive molecular evolution on the rhodopsin (RH1) gene among closely related ‘sand goby’ species (Teleostei, Gobiidae). Fragments of the RH1 gene (868 bp) were sequenced and analyzed for nine ‘sand goby’ species that inhabit different photic environments. A high level of interspecific polymorphism at the RH1 gene was observed, including non-synonymous mutations on amino acids known as spectral tuning sites. Clear indications for positive Darwinian selection were provided by three independent methods: (1) by linking functional variation on the RH1 gene to specific light environments of the different fish habitats; (2) by constructing and comparing phylogenies based on RH1 and the ‘neutral’ 12S and 16S mtDNA fragments; and (3) by performing statistical tests to detect signatures of directional selection on the RH1 gene. This study shows an unusual high variability in the gobiid visual RH1 pigment, and we therefore suggest a possible role for sensory genes in the adaptive radiation of ‘sand goby’ species

Mito-nuclear discordance in the degree of population differentiation in a marine goby

An increasing number of phylogeographic studies on marine species shows discordant patterns in the degree of population differentiation between nuclear and mitochondrial markers. To understand better which factors have the potential to cause these patterns of discordance in marine organisms, a population genetic study was realized on the sand goby Pomatoschistus minutus (Pallas 1770; Gobiidae, Teleostei). Sand gobies from eight European locations were genotyped at eight microsatellite markers. Microsatellites confirmed the global phylogeographical pattern of P. minutus observed with mitochondrial DNA (mtDNA) markers and nuclear allozyme markers. Three groups consistent with the mitochondrial lineages were defined (the Mediterranean, Iberian and North Atlantic groups) and indications of a recent founder event in the northern Baltic Sea were found. Nevertheless, differences in the degree of population differentiation between the nuclear and mitochondrial markers were large (global FST-values for microsatellites=0.0121; for allozymes=0.00831; for mtDNA=0.4293). Selection, sex-biased dispersal, homoplasy and a high effective population size are generally accepted as explanations for this mitonuclear discrepancy in the degree of population differentiation. In this study, selection on mtDNA and microsatellites, male-biased dispersal and homoplasy on microsatellite markers are unlikely to be a main cause for this discrepancy. The most likely reason for the discordant pattern is a recent demographical expansion of the sand goby, resulting in high effective population sizes slowing down the differentiation of nuclear DNA