Valerio Ketmaier

Phylogeography and molecular rates of subterranean aquatic Stenasellid Isopods with a peri-Tyrrhenian distribution.

The subterranean Isopods belonging to the genus Stenasellus have an interesting disjunct distribution in the peri‐Tyrrhenian area with morphologically closely related taxa occurring in Sardinia, Corsica, Tuscany and in the Pyrenees phreatic and interstitial waters. Because the dispersal capacities of these organisms are limited, their distribution has been associated traditionally with the tectonic events leading to the separation of the Sardinia–Corsica microplate from the Pyrenees and its subsequent movement towards the Italian peninsula. We sequenced a fragment of the mtDNA cytochrome oxidase I gene (COI) for multiple populations of the S. racovitzai species‐group (Corsica, Sardinia, Tuscany) and S. virei (Pyrenees). We found that multiple phylogenetic analyses always gave the same topology, which is consistent with the genetic relations found using allozyme data, and with the palaeogeography of the area. The molecular data suggest that a combination of vicariance and dispersal events explain most effectively the present distribution pattern of these organisms. We also calculated COI rates and calibrated them against absolute time, taking advantage of the availability of two geologically based time estimates. Rates on all substitutions are similar to those published for other crustaceans for the same COI fragment, including taxonomically and ecologically distant groups. Rates on third codon positions or on transversions are generally lower than those found in other crustaceans.

Adaptive radiation in African weakly electric fish (Teleostei: Mormyridae: Campylomormyrus): a combined molecular and morphological approach

We combined multiple molecular markers and geometric morphometrics to revise the current taxonomy and to build a phylogenetic hypothesis for the African weakly electric fish genus Campylomormyrus. Genetic data (2039 bp DNA sequence of mitochondrial cytochrome b and nuclear S7 genes) on 106 specimens support the existence of at least six species occurring in sympatry. We were able to further confirm these species by microsatellite analysis at 16 unlinked nuclear loci and landmark‐based morphometrics. We assigned them to nominal taxa by comparisons to type specimens of all Campylomormyrus species recognized so far. Additionally, we showed that the shape of the elongated trunk‐like snout is the major source of morphological differentiation among them. This finding suggests that the radiation of this speciose genus might have been driven by adaptation to different food sources.

Contrasting signals from multiple markers illuminate population connectivity in a marine fish

Recent advances in molecular biology and bioinformatics have helped to unveil striking and previously unrecognized patterns of geographic genetic structure in marine populations. Largely driven by the pressing needs of fisheries management and conservation, studies on marine fish populations have played a pivotal role in testing the efficiency of a range of approaches to explore connectivity and dispersal at sea. Here, we employed nuclear and mitochondrial DNA markers and parasitic infestations to examine the nature and patterns of population structure in a warm‐temperate coastal marine teleost across major putative biogeographic barriers in the Mediterranean Sea and Eastern Atlantic Ocean. We detected deep genetic divergence between mitochondrial lineages, likely caused by dramatic climatic and geological transformations before and during the Pleistocene. Such long‐diverged lineages later came into secondary contact and can now be found in sympatry. More importantly, microsatellite data revealed that these lineages, after millions of years of independent evolution, now interbreed extensively. By combining genetic and parasite data, we were able to identify at least five independent demographic units. While the different genetic and parasite‐based methods produce notably contrasting signals and may complicate the reconstruction of connectivity dynamics, we show that by tailoring the correct interpretation to each of the descriptors used, it is possible to achieve a deeper understanding of the micro‐evolutionary process and, consequently, resolve population structure.

Isolation by distance in equilibrium and nonequilibrium populations of four talitrid species in the Mediterranean Sea.

Abstract Allozymic variation at 21–23 loci was studied in 28 populations of Talitrus saltator, 23 populations of Orchestia montagui, 13 populations of O. stephenseni, and five populations of Platorchestia platensis from the Mediterranean Basin. Different levels of gene flow (Nmθ) were detected within each species at the scale of the whole Mediterranean: O. montagui and P. platensis had low population structure, with levels of Nmθ 1, whereas the T. saltator and O. stephenseni populations have values of Nmθ < 1. The relationship between Nmθ and geographic distance was analyzed to test for the presence of an isolation by distance pattern in the spatial genetic variation within each species. A model of isolation by distance is useful to describe the pattern of genetic structuring of study species at the scale of the whole Mediterranean: geographic distance explained from 28% to 70% of the variation in gene flow. In the Aegean area all species showed an island model of genetic structuring regardless of the levels of gene flow.

Mitochondrial Control Region and microsatellite analyses on harbour porpoise (Phocoena phocoena) unravel population differentiation in the Baltic Sea and adjacent waters

The population status of the harbour porpoise (Phocoena phocoena) in the Baltic area has been a continuous matter of debate. Here we present the by far most comprehensive genetic population structure assessment to date for this region, both with regard to geographic coverage and sample size: 497 porpoise samples from North Sea, Skagerrak, Kattegat, Belt Sea, and Inner Baltic Sea were sequenced at the mitochondrial Control Region and 305 of these specimens were typed at 15 polymorphic microsatellite loci. Samples were stratified according to sample type (stranding vs. by-caught), sex, and season (breeding vs. non-breeding season). Our data provide ample evidence for a population split between the Skagerrak and the Belt Sea, with a transition zone in the Kattegat area. Among other measures, this was particularly visible in significant frequency shifts of the most abundant mitochondrial haplotypes. A particular haplotype almost absent in the North Sea was the most abundant in Belt Sea and Inner Baltic Sea. Microsatellites yielded a similar pattern (i.e., turnover in occurrence of clusters identified by STRUCTURE). Moreover, a highly significant association between microsatellite assignment and unlinked mitochondrial haplotypes further indicates a split between North Sea and Baltic porpoises. For the Inner Baltic Sea, we consistently recovered a small, but significant separation from the Belt Sea population. Despite recent arguments that separation should exceed a predefined threshold before populations shall be managed separately, we argue in favour of precautionary acknowledging the Inner Baltic porpoises as a separate management unit, which should receive particular attention, as it is threatened by various factors, in particular local fishery measures.

Large-scale mitochondrial phylogeography in the halophilic fairy shrimp Phallocryptus spinosa (Milne-Edwards, 1840) (Branchiopoda: Anostraca)

Abstract.In this study we analyzed patterns of sequence divergence in about 1kb of mitochondrial DNA coding for two genes (16S rRNA and Cytochrome Oxidase I, COI) in 15 populations and 61 individuals of the halophilic fairy shrimp Phallocryptus spinosa (Milne-Edwards, 1840). Populations were sampled in saline and hypersaline water bodies from Spain, France, Italy, Greece, Turkey, Ukraine, Iran, Uzbekistan, Cyprus, Algeria, Morocco and Botswana. Our genetic findings suggest complex phylogeographic relationships and pronounced genetic differentiation among populations. Multiple phylogenetic methods and nested clade analysis revealed the existence of four highly divergent maternal lineages with strong phylogeographic patterns and signatures of either allopatric fragmentation or restricted gene flow with isolation by distance. These results are further supported by the hierarchical analysis of molecular variance (AMOVA) and pairwise FST values, which indicate that most of detected genetic heterogeneity is apportioned among populations. Genetic relationships among haplotypes fit geographical hypotheses in most cases but one. Indeed, one haplotype is shared among French, Iranian and Uzbekistan populations. We hypothesize that this peculiar occurrence might be due to an avian-mediated long distance passive dispersal event.

Molecular systematics, phylogeny and biogeography of roaches (Rutilus, Teleostei, Cyprinidae)

In this study we used sequence data from the entire mtDNA cytochrome b gene to reconstruct patterns and times of diversification in the roach genus Rutilus. The genus is present with numerous endemic species in the Eastern peri-Mediterranean area and with a few widespread species in Central Europe. Our phylogenetic results do not support the subdivision into two subgenera proposed on morphological grounds. Within R. pigus and R. rutilus we identify highly divergent and allopatric mitochondrial lineages. The deeper splits in the genus phylogeny date back to the middle Miocene; the main diversification took place at the Miocene-Pliocene boundary.

Variation of genetic and behavioural traits in the sandhopper Talitrus saltator (Crustacea Amphipoda) along a dynamic sand beach

In an attempt to unravel the possible relationships among coastal stability, genetic variability and orientation behaviour in the sandhopper Talitrus saltator, we have screened four subpopulations of this species. Sandhoppers along 3 km of a dynamic sand beach were studied for orientation performance (i.e. adherence to the seaward theoretical escape direction (TED)) and sequence variation for a fragment of the mitochondrial (mt) gene encoding for the cytochrome oxidase subunit I (COI). The sampling sites differed in the stability of the shoreline (from severely eroded to accreting). Analysis of molecular variance (AMOVA) revealed significant subdivisions among the four locations. The subpopulation sampled at the most eroded point showed no haplotype diversity and had the highest scatter in orientation. Genetic diversity increased with decreasing erosion. Orientation performances were best where the beach is in dynamic equilibrium, and were progressively more scattered at the accreting points. Multiple linear regression analyses demonstrated that the variables and factors that affected orientation significantly were daytime, global solar radiation, sex of individuals and haplotype diversity. Environmental factors are likely to influence sandhopper behaviour on a short and medium time scale (i.e. from single individual life span to a few generations). The data also suggest that temporal stability of the shoreline has a positive effect on the genetic variability of the resident sandhopper populations.

Exploratory analysis of talitrid population genetics as an indicator of the quality of sandy beaches

Allozymic variation was studied at 23 loci in 10 populations of Talitrus saltator, two populations of Talorchestia deshayesii and two populations of Talorchestia brito from the Mediterranean and Baltic Seas. Levels of genetic differentiation among the three species showed a close relationship between T. saltator and T. deshayesii, whereas T. brito was more genetically differentiated. Within T. saltator, it was possible to recognise two main clusters, the first grouping consisting of Baltic, Tyrrhenian and North African populations, the second comprising Adriatic and East Mediterranean populations. Talitrus saltator populations were generally characterised by low levels of gene flow (Nm < 1). The relationship between Nm and geographic distances was analysed to test for an isolation by distance pattern in the spatial genetic variation. Isolation by distance was detected at the scale of the whole Mediterranean, with geographic distance explaining about 50% of the variance in gene flow. The North African populations showed an island model of genetic structuring; this result is mainly due to the anomalous genetic pattern of a population from a Tunisian beach (Tabarka) highly exploited for tourism. Human activities, which may influence T. saltator population dynamics, are believed to be responsible for the observed pattern of genetic variation in North Africa.

Allozymic variability and biogeographic relationships in two Leuciscus species complexes (Cyprinidae) from southern Europe, with the rehabilitation of the genus Telestes Bonaparte

Abstract Genetic variability was assessed in eight populations belonging to the Leuciscus souffla complex and in nine populations of Leuciscus cephalus, sampled in France, Italy and Greece and in one population of Leuciscus lucumonis, endemic to Italy. Twenty‐six enzymatic loci were analysed in order to clarify the genetic relationships, the patterns of colonisation of peri‐Mediterranean area and the taxonomic positions. Results indicate a more ancient penetration of the Leuciscus souffia complex in southern Europe (possibly during the Messinian ‘Lago Mare’ phase of the Mediterranean), whereas L. cephalus and L. lucumonis seem to have quite recently reached these regions (about 1Myr). These evidences are discussed in relation to the two main proposed models of primary freshwater fishes colonisation of peri‐Mediterranean area. In addition, the genetic distance suggests a generic separation between the two complexes. The genus Telestes Bonaparte, is rehabilitated to include members of the Leuciscus souffia ...