Allometric differences on the shell shape of two scorched mussel species along the Atlantic South American Coast

Scorched mussels (Bivalvia: Mytilidae) are an important component of rocky shore assemblages around the world. The mussel beds of the mid-intertidal coasts of the south-western Atlantic are composed of two species of scorched mussels, which dominate the physiognomy and structure of the rocky shore communities. The present study investigates the variation in the shell-shape allometric trajectories of both species of mussels throughout their distributional range in the southwestern Atlantic coast, from latitude 34°S to 53°S. Shells of Brachidontes rodriguezii were collected at two Uruguayan localities and four Argentinean localities, while shells of Perumytilus purpuratus were collected at six Argentinean localities. Shell shapes of the specimens were studied by geometric morphometrics using landmark and semi-landmark methods. Different evolutionary histories and thermal regimes characterize these two species. Brachidontes rodriguezii seems to have a long history in the region and is present in a restricted area, the warm temperate region of the south-western Atlantic, while P. purpuratus seems to have a recent history and is present in a wide thermal range, involving the cold-temperate regions of the south-western Atlantic and south-eastern Pacific and the warm-temperate region of the south-eastern Pacific. Based on these considerations, we prompt the hypothesis that allometric trajectories of P. purpuratus shell shape is more variable and adapted to a specific habitat than B. rodriguezii. The impact of allometry was larger in P. purpuratus than in B. rodriguezii. Graphical evidence was gathered, showing that these two species differ in allometric growth forms and that the allometric shell morphology changes reflect environmental constraints and adaptation. While the intertidal mussel beds of the South American coasts are ecologically similar in appearance, we found that the allometric variation of the scorched mussels occurs in response to diverging evolutionary processes such as phenotypic plasticity in P. purpuratus and canalization in B. rodriguezii.     

Shape Variation in the Dermatocranium of the Greater Short-Horned Lizard <Emphasis Type="Italic">Phrynosoma hernandesi</Emphasis> (Reptilia: Squamata: Phrynosomatidae)

Dermatocranial shape and horn morphology display great disparity among the species of Phrynosoma. Ontogenetic change in dermatocranial shape in a series of 79 specimens of the short-horned Phrynosoma hernandesi (54F: 25M) was examined using geometric morphometric techniques. A multivariate ANCOVA of Procrustes residuals with sex as a factor and ln(centroid size) as the covariate indicated sexual shape dimorphism. Separate multivariate regressions of Procrustes residuals on ln(centroid size) for each sex indicated that allometry accounts for ~52–54% of the total sample shape variance. Comparisons of ontogenetic shape change between sexes indicate that sexual shape dimorphism is minimal and of uncertain biological significance. Groupings of multivariate regression coefficients by magnitude and sign suggest that allometric integration of the dermatocranium is not uniform over the dermatocranium. Principal component analysis of the landmark configurations corrected for sex and allometry yields a first principal component which describes shape variance concentrated in the posterolateral and posterior regions of the dermatocranium, and again is indicative of non-uniform shape variation over the dermatocranium. Our findings for P. hernandesi indicate that the adult shape of the dermatocranium may contribute to a passive defence against predation. We hypothesize that the complexity in dermatocranial shape demonstrated here for P. hernandesi indicates parcellation of shape variance, which may contribute to explanations of the pronounced dermatocranial disparity exhibited by the species of Phrynosoma.     

Craniomandibular Variation in the Taxonomically Problematic Gerbil Genus <Emphasis Type="Italic">Gerbillus</Emphasis> (Gerbillinae,Rodentia): Assessing the Influence of Climate,Geography, Phylogeny,and Size

The taxonomy of Gerbillus, the most speciose gerbil genus, is highly debated. Of particular contention is the relationship of Dipodillus to Gerbillus; some consider it to be a closely related genus, while others synonymize it with Gerbillus—either with or without recognizing it as a subgenus. The main objective of this study is to test the validity of common taxonomic groupings within the Gerbillus-Dipodillus species complex, which was achieved by using geometric morphometrics to examine cranial and mandibular variation in 34 out of the 52 Gerbillus-Dipodillus species. Craniomandibular size and shape were highly correlated, indicating strong allometric patterns in shape variation. The common taxonomic groups were significantly different in craniomandibular size and shape, yet they did overlap considerably in morphospace. A notable exception was the extreme divergence of Monodia (G. mauritaniae) from all other species in the occlusal view of the mandible. Morphospace overlap is likely a consequence of both phylogenetic history and environmental adaptation. Only the ventral cranium was associated with climate, particularly in areas related to resource acquisition. Geographic distance was not significantly associated with craniomandibular morphometric distance, and the groups overlapped greatly in their geographic range. Cranial and mandibular regions differed in discrimination power—the ventral cranium had among the highest, while the dorsal cranium and the occlusal mandible had the lowest. Craniomandibular regions varied in association with climate, phylogeny, and size—previous studies suggest this difference may be a consequence of different genetic controls for shape variation.     

Conservation genetics of the short-beaked common dolphin (<Emphasis Type="Italic">Delphinus delphis</Emphasis>) in the Mediterranean Sea and in the eastern North Atlantic Ocean

Mediterranean Sea common dolphins have recently been listed as ‘endangered’ in the IUCN Red list, due to their reported decline since the middle of the 20th century. However, little is know about the number or distribution of populations in this region. We analysed 118 samples from the Black Sea, Mediterranean Sea and eastern North Atlantic at nine microsatellite nuclear loci and for 428 bps of the mtDNA control region. We found small but significant population differentiation across the basin between the eastern and the western Mediterranean populations at both nuclear and mtDNA markers (microsatellite F _ST = 0.052, mtDNA F _ST = 0.107, P values ≤ 0.001). This matched the differential distribution and habitat use patterns exhibited by this species in the eastern and the western parts of the Mediterranean Sea. The assignment test of a small number of samples from the central Mediterranean could not exclude further population structure in the central area of the basin. No significant genetic differentiation at either marker was observed among the eastern north Atlantic populations, though the Alboran population (inhabiting the Mediterranean waters immediately adjacent the Atlantic ocean) showed significant mtDNA genetic differentiation compared to the Atlantic populations. Directional estimates of gene flow suggested movement of females out of the Mediterranean, which may be relevant to the population decline. Phylogenetic analysis suggested that the observed population structure evolved recently.     

Phenetic relationships among four Apodemus species (Rodentia, Muridae) inferred from skull variation

Phenetic relationships among four Apodemus species (A. agrarius, A. epimelas, A. flavicollis and A. sylvaticus) inferred from skull (mandible and cranium) variation were explored using landmark-based geometric morphometrics. Analysis of size variation revealed that mandibles and crania of A. epimelas were the largest, followed by those of A. flavicollis, while A. agrarius and A. sylvaticus had the smallest ones. Phenetic relationships inferred from mandible shape variation better reflected phylogenetic relationships among the analyzed Apodemus species than those inferred from cranial differences. Concerning cranial shape variation, the most differentiated species was A. epimelas, whose ecology clearly differs from the other three species. Thus, differentiation of the mandible provided a pattern fully concordant with the phylogeny, while the cranium differentiation was in agreement with ecology expectations. The most evident shape changes of mandible and cranium involved the angular process and facial region, respectively. We also found that allometry had a significant influence on shape variation and that size-dependent shape variation differed among the analyzed species. Moreover, mandible and cranium are differently influenced by allometric changes. Different phenetic relationships inferred from mandible and cranium shape variation imply that phylogeny, ecology, together with factors related to size differences are all involved in the observed morphological divergence among the analyzed Apodemus species.     

Effect of salinity on vegetative growth and sexual reproduction of algae from the genus <Emphasis Type="Italic">Ardissonea</Emphasis> de Notaris (Bacillariophyta)

Effect of salinity on vegetative growth and sexual reproduction was investigated in laboratory cultures of a benthic diatom Ardissonea crystallina (C. Agardh) Grunow from the Black Sea and vegetative growth of Ardissonea sp. from the coast of Martinique, the Atlantic Ocean. Typical water salinity in the places where the populations inhabit differs two times. It was shown that the clones of both populations have a broad tolerance and great ability to adapt to changes in salinity. Cells of different size (i.e., in different stages of the life cycle) responded differently to desalination. Salinities optimal for vegetative growth of these species were not the same. Ardissonea from the coast of Martinique was more sensitive to low levels of salinity as compared with A. crystallina from the Black Sea. It was surprising that salinity optimal for vegetative growth and sexual reproduction of the Black Sea species did not coincide with the real salinity level of the Black Sea. Position of physiological optimums indicates an oceanic (or Mediterranean) origin of the Black Sea population of A. crystallina.     

Otolith variation in Pacific herring (<Emphasis Type="Italic">Clupea pallasii</Emphasis>) reflects mitogenomic variation rather than the subspecies classification

Pacific herring (Clupea pallasii) is divided into three subspecies: two in northeast Europe and one in the north Pacific Ocean. Genetic studies have indicated that the populations in northeast Europe have derived from the northwest Pacific herring recently, or during the last 10–15 kyr, and that they are distinct from the population in the northeast Pacific. In addition, hybridization between the Pacific herring and the Atlantic herring has been documented. Otolith variation has been considered to be largely affected by environmental variation, but here we evaluate whether the genetic differentiation is reflected in otolith shape differences. A clear difference in otolith shape was observed between the genetically differentiated herring species Clupea harengus from the Atlantic and C. pallasii. The otolith shape of C. p. suworowi in the Barents Sea was different from the shape of C. pallasii in northern Norway and C. p. pallasii from the Pacific. Populations of C. p. pallasii, sampled east and west of the Alaska Peninsula, which belong to two genetically different clades of the C. p. pallasii in the Pacific Ocean, show a clear difference in otolith shape. C. p. suworowi and the local C. pallasii peripheral population in Balsfjord in northern Norway are more similar to the northwest Pacific herring (C. p. pallasii) than to the northeast Pacific herring (C. p. pallasii), both genetically and in otolith shape. The Balsfjord population, known to be influenced by introgression of mtDNA from the Atlantic herring, does not show any sign of admixture in otolith shape between the two species. A revised classification, considering the observed genetic and morphological evidence, should rather group the northwest Pacific herring in the Bering Sea together with the European populations of C. pallasii than with the northeast Pacific herring in the Gulf of Alaska.     

Diagnostic features and taxonomy of the Mediterranean species of the big-scale sand smelts belonging to <Emphasis Type="Italic">Atherina boyeri</Emphasis> group (Atherinidae)

Morphological studies of the big-scale sand smelt from the group Atherina boyeri sensu lato were carried out using the materials of the museum collections from the Mediterranean Sea, the Black Sea, and the Sea of Azov. It has been shown that low-raker sand smelt belonging to the species A. boyeri sensu stricto, and multi-raker sand smelt, referred to the A. mochon species, are differentiated by a complex of morphological features: the number of gill rakers, the shape of scales, the length of the ascending process of praemaxillare, and the shape of the lower margin of maxillare. The key for their identification is presented. It is assumed that A. mochon is not a native Black Sea species but belongs to the invasive species originating from the Mediterranean Sea. The isolation of two cryptic species is discussed. The neotype of A. pontica is designated.     

The Effect of Pleistocene Climate Fluctuations on Distribution of European Abalone (<Emphasis Type="Italic">Haliotis tuberculata</Emphasis>), Revealed by Combined Mitochondrial and Nuclear Marker Analyses

The genetic differentiation among the populations of the European abalone Haliotis tuberculata was investigated using different markers to better understand the evolutionary history and exchanges between populations. Three markers were used: mitochondrial cytochrome oxidase I (COI), the sperm lysin nuclear gene, and eight nuclear microsatellites. These markers present different characteristics concerning mutation rate and inheritance, which provided complementary information about abalone history and gene diversity. Genetic diversity and relationships among subspecies were calculated from a sample of approximately 500 individuals, collected from 17 different locations in the north-eastern Atlantic Ocean, Macaronesia, and Mediterranean Sea. COI marker was used to explore the phylogeny of the species with a network analysis and two phylogenetic methods. The analysis revealed 18 major haplotypes grouped into two distinct clades with a pairwise sequence divergence up to 3.5 %. These clades do not correspond to subspecies but revealed many contacts along Atlantic coast during the Pleistocene interglaciations. The sperm lysin gene analysis separated two different subtaxa: one associated to Macaronesian islands, and the other to all other populations. Moreover, a small population of the northern subtaxon was isolated in the Adriatic Sea—probably before the separation of the two lineages—and evolved independently. Microsatellites were analyzed by different genetics methods, including the Bayesian clustering method and migration patterns analysis. It revealed genetically distinct microsatellite patterns among populations from Mediterranean Sea, Brittany and Normandy, Morocco, and Canary and Balearic islands. Gene flow is asymmetric among the regions; the Azores and the Canary Islands are particularly isolated and have low effective population sizes. Our results support the hypothesis that climate changes since the Pleistocene glaciations have played a major role in the geographic distribution of the European abalone. Traces of these events related to maternal inheritance were shown on COI marker.     

Geographic Cline in the Shape of the Moose Mandible: Indications of an Adaptive Trend

Intra-specific geographic variation is probably one of the most common patterns studied in ungulate morphology. However, the shape of the mandible, a crucial feature with regard to feeding, has been greatly understudied in this context. Here, we utilized a museum collection of moose (Alces alces) mandibles to investigate whether we could detect significant variation in this species, and test for the existence of geographic patterns and associations with population genetic structure. We applied a landmark-based geometric morphometrics approach, analyzing shape data with principal component analysis and linear mixed models. A significant geographic shift in the shape of the moose mandible was revealed. The main pattern was similar in both sexes; however, there was a consistent difference in shape between males and females over the latitudinal scale. The main changes included an enlargement in the attachment surfaces of the muscles controlling biting and mastication, suggesting more effective mastication towards the north, plausibly as an adaptive response to a harder and tougher wintertime diet. Additionally, more subtle, yet statistically significant age-related shape variation was discovered. Interestingly, no or only a weak association between the morphometric variation and the genetic population structure was detected with neutral molecular markers.     

Morphological and Genetic Divergences in a Coral Reef Damselfish, Pomacentrus coelestis

Population differentiation is one of the main topics in evolutionary biology. Except the exploration of color variation, few studies focused on morphological divergences among populations of coral reef fishes. In this work, we studied morphological and genetic differentiation among populations of the damselfish, Pomacentrus coelestis, in the northwestern Pacific Ocean. The shapes of the mandible and the premaxilla were explored using geometric morphometric methods and the genetic structure was investigated using microsattelites. Various tests revealed significant shape variation among most P. coelestis populations for both skeletal units. Morphological variation of the mandible accompanies a genetic break between populations of mainland Japan and Okinawa-Taiwan. However, Mantel and Procrustes tests revealed no congruence between morphological and genetic structures. We illustrate that phenotypic plasticity and adaptive divergence are potential evolutionary mechanisms underlying shape difference among P. coelestis populations. An ecomorphological approach suggests that various diet could be related to shape variation of oral jaws.     

When invasion biology meets taxonomy: <Emphasis Type="Italic">Clavelina oblonga</Emphasis> (Ascidiacea) is an old invader in the Mediterranean Sea

Taxonomic issues often confound the study of invasive species, which sometimes are unrecognized as introduced in newly colonized areas. Clavelina oblonga Herdman, 1880 is an abundant ascidian species along the southeastern coast of the United States and the Caribbean Sea. It was introduced into the eastern Atlantic and Brazil decades ago. In the Mediterranean Sea, a similar species had been described as C. phlegraea Salfi 1929 and reported from southern Italy and Corsica. In the last few years a species of Clavelina has proliferated in the embayments of the Ebro Delta (NW Mediterranean), a zone of active bivalve culture industry where it has smothered mussel spat, leading to economic loss. We here report the morphological and genetic identity of this species, synonymizing the Atlantic C. oblonga and the Mediterranean C. phlegraea (the latter therefore is a synonym of the former). Thus, C. oblonga has existed in the Mediterranean for over 80 years, but was known under a different name. We also found this species in natural habitats in the Iberian Atlantic coast close to the Strait of Gibraltar, raising concerns about an ongoing expansion. In order to obtain information relevant for management, we monitored growth, reproductive cycles and settlement patterns of this ascidian on bivalve cultures in the Ebro Delta. Its biological cycles were markedly seasonal, with peak abundance and reproduction during the warmest months, followed by regression during the cold season. The settlement period was short, mostly concentrated in a single month each year. Avoidance of mussel and oyster seeding during late summer and early autumn can readily reduce the damage caused by this species.     

Craniometric variation of some Mediterranean and Atlantic populations of Stenella coeruleoalba (Mammalia,Delphinidae): A three‐dimensional geometric morphometric analysis

The variability of cranial features of Atlantic and Mediterranean samples of Stenella coeruleoalba was examined using a three‐dimensional geometric morphometric approach. Data were collected on 79 skulls from the upper and middle Mediterranean Sea, the Atlantic French coasts, and Scotland. Three‐dimensional x, y, and z coordinates of 27 landmarks were recorded on each left half skull using a Microscribe 3‐D digitizer. All configurations were rotated, centered, and scaled, and residuals from the mean configuration were analyzed through multivariate analyses of variance. Mahalanobis distances among populations were used to evaluate phenetic relationships. Consensus configurations were compared to visualize shape differences among samples. Analyses revealed significant differences among populations, a clear distinction of the Scottish coasts dolphins from the other samples, and a closer relationship of the dolphins from the French coasts to the Mediterranean populations than to the Scottish one. Shape differences are mainly concentrated in the rostral and in the occipital regions of the skull. Phylogenetic and adaptive factors were invoked as possible causes of the variation patterns.     

Spatio‐temporal patterns of genetic diversity in the Mediterranean striped dolphin (Stenella coeruleoalba)

Comparing the genetic composition of wild animals between geographic regions with distinct environments is common in evolutionary studies. However, genetic composition can also change through time in response to environmental changes but studies examining this are carried out less often. In this study, we characterize striped dolphin genetic composition in the Mediterranean Sea across both geography and time. We provide genotype data for 15 microsatellite loci and 919 bp of mtDNA control region, collected over 21 years across all main Mediterranean Sea basins. We investigated spatial genetic structure using both classical and Bayesian population structure methods, and compared it with temporal patterns of genetic change using time‐series statistics. We integrated the temporal datasets with known environmental pressures and data on social structure, to infer potential drivers of observed changes. Geographic analyses suggest weak differentiation for striped dolphin in the Mediterranean Sea, with evidence for a recent expansion. Temporal analyses show significant cyclical fluctuations in genetic composition over 21 years, which correspond well with recurrent morbillivirus epizootics. Similarly, social group composition shows changes in the relative number of juveniles and adults per group, and an overall increase in the number of adults per group relative to juveniles over the time period. We suggest that the observed changes in genetic and group composition could relate to specific dynamics of morbillivirus resistance. Overall, our study highlights the importance of tracking long‐term genetic variation and the potential for this species as a model in studying genetic adaptation to environmental stress.     

The Role of Geographical and Ecological Factors on Population Divergence of the Neotropical otter <Emphasis Type="Italic">Lontra longicaudis</Emphasis> (Carnivora,Mustelidae)

The geographic distribution of the populations of a species are influenced by the spatial structure of the ecosystems, the environmental factors and the presence of geographic barriers. The Neotropical otter, Lontra longicaudis, is widely distributed throughout the Americas, where a wide range of environmental conditions and geographical features could promote genetic and morphological variation on the three currently recognized subspecies. In this study, we combined phylogeographic, morphometric and environmental niche modelling analyses to examine whether: (1) genetic variation is associated with the presence of barriers to gene flow and/or hydrography; (2) genetic and morphologic variation are associated with environmental variation; and (3) the observed variation in L. longicaudis populations corresponds to the previously defined subspecies. We found strong phylogeographic structure between the northern (L. l. annectens) and the two-southern subspecies (L. l. longicaudis and L. l. enudris), and although shallower, we also detected genetic differentiation between the two South American subspecies. Such genetic differentiation corresponds to the hydrography and to the geographical barriers characteristic of the distributional area of the species. We found a correlation between the shape of the skull and mandible with the environmental variation through the distribution of the species, and we rejected the hypothesis of niche equivalency and similarity between the three identified genetic lineages, suggesting adaptations to different environmental conditions. Our results support that the variation in environmental conditions, in concert with geographical barriers to gene flow and hydrography, have led to population divergence of L. longicaudis along the Neotropics. These results have important taxonomic implications for the species and its conservation.     

Marked mitochondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius

Restriction analysis of mitochondrial DNA (mtDNA) from 204 individuals of swordfish (Xiphias gladius) revealed no differentiation among samples from three sites in the Mediterranean Sea (Greece, Italy, Spain), but a high degree of differentiation between Mediterranean samples and a sample from the Gulf of Guinea. A fifth sample from the Atlantic side of the Straits of Gibraltar (Tarifa) consisted mostly of mitotypes that are common in the Mediterranean, but contained several of mtDNA types of the Guinea sample not found in the Mediterranean. We conclude that, in spite of free migration of swordfish across the Straits of Gibraltar, little genetic exchange occurs between the populations inhabiting the Mediterranean Sea and the tropical Atlantic ocean. This is the first evidence of genetic differentiation among geographic populations of this highly mobile species that supports a world-wide fishery.     

Evolutionary Lability of Integration in Cambrian Ptychoparioid Trilobites

Phenotypic integration can influence evolutionary rate and direction by channeling variation into few dimensions. The extent to which that channeling serves as a constraint over macroevolutionary timescales is determined in part by the evolutionary lability of phenotypic integration. Evolutionary change in patterns of pleiotropy, potentially reducing that constraint, is thought to be more readily achieved when pleiotropy is structured by variation arising in parallel along different developmental pathways rather than by variation arising from direct interactions within and between those pathways. Herein we test two predictions that follow from that hypothesis: (1) that clades undergoing dramatic diversification are characterized by integration that is weakly influenced by direct interactions; and (2) that the structure of integration arising from direct interactions is more conservative than that arising from parallel variation. We examine integration of the cranidium of two Cambrian ptychoparioid trilobites, Crassifimbra walcotti and Eokochaspis nodosa, comparing them to each other and to a previously studied species, C.? metalaspis. Shape variation is decomposed into components representing variation among individuals and variation due to direct interactions. In all three species, variation among individuals was only weakly influenced by direct interactions, suggesting that integration was unlikely to have been a long-term constraint on the Cambrian diversification of ptychoparioids. Phenotypic integration of E. nodosa is no more similar than expected by chance to either Crassifimbra species, but the component due to direct interactions is more similar than expected by chance to that of C.? metalaspis. Conversely, the two Crassifimbra species are generally similar (although not identical) in phenotypic integration, but markedly differ in their structure of direct interactions. Integration arising from direct interactions was therefore not immune to restructuring over even short evolutionary timescales, and was not always more conservative than that arising from parallel variation.     

Ecogeographical Variation in Skull Shape of South-American Canids: Abiotic or Biotic Processes?

Species morphological changes can be mutually influenced by environmental or biotic factors, such as competition. South American canids represent a quite recent radiation of taxa that evolved forms very disparate in phenotype, ecology and behaviour. Today, in the central part of South America there is one dominant large species (the maned wolf, Chrysocyon brachyurus) that directly influence sympatric smaller taxa via interspecific killing. Further south, three species of similar sized foxes (Lycalopex spp.) share the same habitats. Such unique combination of taxa and geographic distribution makes South American dogs an ideal group to test for the simultaneous impact of climate and competition on phenotypic variation. Using geometric morphometrics, we quantified skull size and shape of 431 specimens belonging to the eight extant South American canid species: Atelocynus microtis, Cerdocyon thous, Ch. brachyurus, Lycalopex culpaeus, L. griseus, L. gymnocercus, L. vetulus and Speothos venaticus. South American canids are significantly different in both skull size and shape. The hypercarnivorous bush dog is mostly distinct in shape from all the other taxa while a degree of overlap in shape—but not size—occurs between species of the genus Lycalopex. Both climate and competition impacts interspecific morphological variation. We identified climatic adaptations as the main driving force of diversification for the South American canids. Competition has a lower degree of impact on their skull morphology although it might have played a role in the past, when canid community was richer in morphotypes.     

Phylogeography of the planktonic chaetognath Sagitta setosa reveals isolation in European seas

Numerous planktonic species have disjunct distribution patterns in the world's oceans. However, it is unclear whether these are truly unconnected by gene flow, or whether they are composed of morphologically cryptic species. The marine planktonic chaetognath Sagitta setosa Müller has a discontinuous geographic distribution over the continental shelf in the northeastern Atlantic, Mediterranean Sea, and Black Sea. Morphological variation between these populations has been described, but overlaps and is therefore unsuitable to determine the degree of isolation between populations. To test whether disjunct populations are also genetically disjunct, we sequenced a 504-bp fragment of mitochondrial DNA comprising the cytochrome oxidase II region of 86 individuals. Sequences were highly variable; each represented a different haplotype. Within S. setosa, sequence divergence ranged from 0.2 to 8.1% and strong phylogeographic structure was found, with four main groups corresponding to the northeastern Atlantic, Mediterranean Sea (including Ligurian Sea, Tyrrhenian Sea and Gulf of Gabes), Adriatic Sea, and Black Sea. Two of these (Atlantic and Black Sea) were resolved as monophyletic clades, thus gene flow between disjunct populations of S. setosa has been extremely limited and lineage sorting has taken place. The deepest divergence was between Atlantic and Mediterranean/Black Sea populations followed by a split between Mediterranean and Black Sea populations. The Mediterranean/Black Sea clade comprised three groups, with the Adriatic Sea as the most likely sister clade of the Black Sea. These data are consistent with a colonization of the Black Sea from the Mediterranean. Furthermore, a possible cryptic species was found in the Black Sea with 23.1% sequence divergence from S. setosa. Two possibilities for the evolutionary origin of this species are proposed, namely, that it represents a relict species from the ancient Paratethys, or that it represents another chaetognath species that colonized the Black Sea more recently. Even though the exact timing of disjunction of S. setosa populations remains unclear, on the basis of the geological and paleoclimatic history of the European basins and our estimates of net nucleotide divergence, we suggest that disjunct populations arose through vicariance resulting from the cyclical changes in temperature and sea levels during the Pleistocene. We conclude that these populations have remained disjunct, not because of limited dispersal ability, but because of the inability to maintain viable populations in suboptimal, geographically intermediate areas.