Genetic architecture of the marbled goby Pomatoschistus marmoratus (Perciformes, Gobiidae) in the Mediterranean Sea

Unstable environment of coastal lagoons drives genetic variation in the amphipod Quadrivisio lutzi

The freshwater/brackish amphipod Quadrivisio lutzi inhabits coastal lagoons, highly unstable environments subject to sudden inflow of marine water. Our aim was to evaluate how the genetic composition varies in these populations. Brazilian populations were compared by 16S rRNA and COI gene sequences. The genetic structure of four Rio de Janeiro amphipod populations was evaluated during the period of 2011-2019 by COI. Rio de Janeiro population was compared with Alagoas and São Paulo populations, which was genetically distinct, at species level (16S, d > 7%; COI, d >14%). The genetic structure in Rio de Janeiro showed the Imboassica subpopulation as the most divergent (Imboassica & Carapebus, F ST = 0.238), followed by Lagamar population (Lagamar & Carapebus, F ST = 0.049). The geographic distance and urbanization around these lagoons explain the degree of genetic isolation of these amphipod subpopulations. Paulista and Carapebus populations were not structured. Temporal variation in haplotype number and frequency were evident in both populations that were evaluated (Carapebus and Imboassica). Changes in salinity and water volume variation at these lagoons may be responsible for the observed changes in genetic composition, which may be the results of genetic drift effects over temporally fluctuating size subpopulations, without loss of genetic diversity.

Population Genetic Diversity of Two Marine Gobies (Gobiiformes: Gobiidae) from the North-Eastern Atlantic and the Mediterranean Sea

Gobies (Gobiiformes: Gobiidae) are the most species-rich family of fishes in general, and the most abundant fish group in the European seas. Nonetheless, our knowledge on many aspects of their biology, including the population genetic diversity, is poor. Although barriers to gene flow are less apparent in the marine environment, the ocean is not a continuous habitat, as has been shown by studies on population genetics of various marine biota. For the first time, European marine goby species which cannot be collected by common fishery techniques were studied. The population genetic structure of two epibenthic species, Gobius geniporus and Gobius cruentatus, from seven localities across their distribution ranges was assessed, using one mitochondrial (cytochrome b) and one nuclear gene (first intron of ribosomal protein gene S7). Our results showed that there is a great diversity of haplotypes of mitochondrial gene cytochrome b in both species at all localities. Global fixation indices (FST) indicated a great differentiation of populations in both studied gobies. Our results did not show a geographic subdivision to individual populations. Instead, the data correspond with the model of migration which allow divergence and recurrent migration from the ancestral population. The estimated migration routes coincide with the main currents in the studied area. This matches well the biology of the studied species, with adults exhibiting only short-distance movements and planktonic larval stages.

Next-generation phylogeography of the cockle Cerastoderma glaucum: Highly heterogeneous genetic differentiation in a lagoon species

AIM

Coastal lagoons form an intriguing example of fragmented marine habitats. Restricted gene flow among isolated populations of lagoon species may promote their genetic divergence and may thus provide a first step toward speciation. In the present study, the population genetic structure of the lagoon cockle Cerastoderma glaucum has been investigated to clarify the complex phylogeographic pattern found in previous studies, to localize major genetic breaks, and to discuss their origin and maintenance.

LOCATION

The Atlantic and Mediterranean coasts, including the Baltic, North Sea, and Black Sea.

METHODS

A total of 204 C. glaucum individuals from 14 populations were genotyped using restriction site-associated DNA sequencing (RADseq). The genetic diversity, divergence, and structure were analyzed using genome-wide single nucleotide polymorphisms (SNPs). Phylogenetic relationships were inferred under a coalescent model using svdquartets.

RESULTS

The RADseq approach allowed inferring phylogeographic relationships with an unprecedented resolution. Three deeply divergent lineages were identified within C. glaucum that are separated by many genetic barriers: one lineage in the Aegean-Black Sea region, one in the Ionian Sea, and the last one widely distributed from the Western Mediterranean to the Baltic Sea. The nested branching pattern displayed on the species tree largely agrees with the likely scenario of C. glaucum postglacial expansion from the Mediterranean to the Baltic Sea.

MAIN CONCLUSION

The genetic differentiations between geographically separated lagoons proved to be strong, highlighting the evolutionary influence of these naturally fragmented habitats. The postglacial expansion created complex patterns of spatial segregation of genetic diversity with allele frequency gradients in many outlier loci, but also discrepancies between the nuclear and mitochondrial genetic markers that probably arose from genetic surfing of mitochondrial variation.

A new species of Gobius (Perciformes: Gobiidae) from the Mediterranean Sea and the redescription of Gobius bucchichi

A new species of the gobiid genus Gobius (Gobiidae, Perciformes), Gobius incognitus sp. nov. is described from the Mediterranean Sea, and its most morphologically similar species Gobius bucchichi is redescribed. The new species is distinguished from its congeners by: scales in lateral series 51-59; predorsal scales 25-35; opercle scaled in adults with 10-16 scales present; pectoral fin with ray count 18-20 and free tips on upper rays well developed and on the first ray longer than two thirds of the entire ray length; pelvic disc complete and with well-developed anterior membrane without lateral lobes; anterior oculoscapular canal with pore α at rear of orbit; oculoscapular row x(1) not extending forwards to pore β; suborbital row d discontinuous with large gap below suborbital rows 3 and 4; eye diameter 1·08-1·32 in snout length; by pigment rows on cheek and pigmentation on pectoral-fin base.

Gene flow, population growth and a novel substitution rate estimate in a subtidal rock specialist, the black-faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the Adriatic Sea

Population histories depend on the interplay between exogeneous and endogeneous factors. In marine species, phylogeographic and demographic patterns are often shaped by sea level fluctuations, water currents and dispersal ability. Using mitochondrial control region sequences (n = 120), we infer phylogeographic structure and historic population size changes of a common littoral fish species, the black-faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the north-eastern Adriatic Sea. We find that Adriatic T. delaisi are differentiated from conspecific populations in the remaining Mediterranean, but display little phylogeographic structure within the Adriatic basin. The pattern is consistent with passive dispersal of planktonic larvae along cyclonic currents within the Adriatic Sea, but limited active dispersal of adults. Demographic reconstructions are consistent with recent population expansion, probably triggered by rising sea levels after the last glacial maximum (LGM). Placing the onset of population growth between the LGM and the warming of surface waters (18 000-13 000 years BP) and employing a novel expansion dating approach, we inferred a substitution rate of 2.61-3.61% per site per MY. Our study is one of only few existing investigations of the genetic structure of animals within the Adriatic basin and is the first to provide an estimate for mitochondrial control region substitution rates in blennioid fishes.

DNA barcoding for species assignment: the case of Mediterranean marine fishes

BACKGROUND

DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity.

METHODOLOGY/PRINCIPAL FINDINGS

A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%), most of them of high commercial relevance, suggesting possible cryptic species.

CONCLUSION/SIGNIFICANCE

We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity.

New light on the evolutionary history of the common goby (Pomatoschistus microps) with an emphasis on colonization processes in the Mediterranean Sea

Through the study of the phylogeographic structure and demographic history of the common goby, Pomatoschistus microps, the influence of Quaternary climatic changes on the evolutionary history of coastal and marine fishes is investigated. Because of its sedentary life cycle in Mediterranean lagoons, it is also a good model to study more specifically if the formation of lagoons during the Holocene had an impact on population structure and demography. Mitochondrial sequences of Northeastern Atlantic and Western Mediterranean specimens were used for phylogenetic reconstructions as well as divergence time estimates, demographic history and population structure analyses. Pomatoschistus microps was a highly supported monophyletic clade including four lineages. It may have appeared 77,000 yr ago, and the divergence of its lineages likely occured shortly thereafter (between 61,000 and 54,000 yr). Most lineages had polytomic topologies, low nucleotide diversity and demographic analyses providing evidence of population expansion. Each lineage was characterized by a large number of private haplotypes. Most haplotypes found in Mediterranean localities were endemic, and one was dominant. Complex reticulated relationships connecting North European, Atlantic and Mediterranean haplotypes were observed. Moderate to high population structure was underlined. Contrary to previous published studies, no significant differentiation was observed between Atlantic and Mediterranean populations, indicating that the Gibraltar Strait is not a phylogeographic break for P. microps. Indeed, molecular dating combined with the tree topologies, phylogeographic and demographic analyses as well as high haplotype diversity underline a recent and rapid population divergence during the last glacial. However, population structure indicates that differentiation is an ongoing process. From an ancestral population trapped in the Atlantic, this goby colonized first northern Europe and later the Mediterranean Sea. Shared haplotypes could have dispersed in the western Mediterranean basin before the lagoon formation, while most private haplotypes, evidencing a recent isolation, probably diverged in lagoons after their closure.

Isolation By Distance (IBD) signals in the deep-water rose shrimp Parapenaeus longirostris (Lucas, 1846) (Decapoda, Panaeidae) in the Mediterranean Sea

The identification of boundaries of genetic demes is one of the major goals for fishery management, and few Mediterranean commercial species have not been studied from a genetic point of view yet. The deep-water rose shrimp Parapenaeus longirostris (Lucas, 1846) is one of the most important components of commercial landings in Mediterranean, its fishery aspects have received much attention, regrettably without any concern for the genetic architecture of its populations. The population structure in the central and eastern Mediterranean Sea (captures from six Italian and two Greek landings) has been analysed on the basis of surveys carried out with mitochondrial and AFLP markers. Data revealed the presence of a gradual discrepancy along a west-east axis. This species, occurring mainly at a depth of between 100 and 400 m, is not strongly confined in isolated demes, but it demonstrates an 'Isolation By Distance' model, within the Mediterranean Sea, which includes geographical areas with a some degree of isolation. The role of hydrodynamic forces, such as currents, water fronts, is discussed; and a further evidence of the 'Levantine isolation' within Mediterranean basin is shown.

Genetic connectivity between land and sea: the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea

INTRODUCTION

We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces.

RESULTS

Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set.

CONCLUSIONS

We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.

A legacy of contrasting spatial genetic structure on either side of the Atlantic-Mediterranean transition zone in a marine protist

The mechanisms that underpin the varied spatial genetic structures exhibited by free-living marine microorganisms remain controversial, with most studies emphasizing a high dispersal capability that should redistribute genetic diversity in contrast to most macroorganisms whose populations often retain a genetic signature of demographic response to historic climate fluctuations. We quantified the European phylogeographic structure of the marine flagellate Oxyrrhis marina and found a marked difference in spatial genetic structure, population demography, and genetic diversity between the northwest Atlantic and Mediterranean Sea that reflects the persistent separation of these regions as well as context-dependent population responses to contrasting environments. We found similar geographic variation in the level of genetic diversity in the sister species Oxyrrhis maritima. Because the capacity for wide dispersal is not always realized, historic genetic footprints of range expansion and contraction persist in contemporary populations of marine microbes, as they do in larger species. Indeed, the well-described genetic effects of climatic variation on macroorganisms provide clear, testable hypotheses about the processes that drive genetic divergence in marine microbes and thus about the response to future environmental change.

Overlapping patterns of morphometric and genetic differentiation in the Mediterranean goby Pomatoschistus tortonesei Miller, 1968 (Perciformes, Gobiidae) in Tunisian lagoons

The genetic and morphological variations of Pomatoschistus tortonesei Miller, 1968 were studied in samples collected from three Tunisian lagoons. The morphological analysis included 18 morphometric measurements and was based on linear discriminant analysis (LDA), whereas the genetic analysis was based on the 16S-rRNA and COI mitochondrial genes. Both analyses differentiated the populations and demonstrated consistently a well-supported differentiation between the western Mediterranean samples (Bizerta and Tunis South lagoons) and the eastern Mediterranean sample (El Bibane lagoon). The observed differentiation could be explained in terms of the geographic isolation of the various populations and the influence of environmental factors, which differ greatly between the different sites. The molecular results revealed that the populations are characterised by unique haplotypes which are well defined in relation to limited gene flow and restricted dispersal abilities. Additionally, it seems that local selective pressures have modelled biometrical variation. Morphological results can reflect a differential habitat use revealed in the cephalic features and a different response to hydrodynamic constraints developed in dissimilar dorsal and pelvic fin lengths.