An exhaustive phylogeny of the combtooth blenny genus Salaria (Pisces, Blenniidae) shows introgressive hybridization and lack of reciprocal mtDNA monophyly between the marine species Salaria basilisca and Salaria pavo

Chromosome-level genome assembly of the highly-polymorphic peacock blenny (Salaria pavo)

The peacock blenny Salaria pavo is notorious for its extreme male sexual polymorphism, with large males defending nests and younger reproductive males mimicking the appearance and behavior of females to parasitically fertilize eggs. The lack of a reference genome has, to date, limited the understanding of the genetic basis of the species phenotypic plasticity. Here, we present the first reference genome assembly of the peacock blenny using PacBio HiFi long-reads and Hi-C sequencing data. The final assembly of the S. pavo genome spanned 735.90 Mbp, with a contig N50 of 3.69 Mbp and a scaffold N50 of 31.87 Mbp. A total of 98.77% of the assembly was anchored to 24 chromosomes. In total, 24,008 protein-coding genes were annotated, and 99.0% of BUSCO genes were fully represented. Comparative analyses with closely related species showed that 86.2% of these genes were assigned to orthogroups. This high-quality genome of S. pavo will be a valuable resource for future research on this species' reproductive plasticity and evolutionary history.

Phylogenetic review of the comb-tooth blenny genus Hypleurochilus in the northwest Atlantic and Gulf of Mexico

As some of the smallest vertebrates, yet largest producers of consumed reef biomass, cryptobenthic reef fishes serve a disproportionate role in reef ecosystems and are one of the most poorly understood groups of fish. The blenny genera Hypleurochilus and Parablennius are currently considered paraphyletic and the interrelationships of Parablennius have been the focus of recent phylogenetic studies. However, the interrelationships of Hypleurochilus remain understudied. This genus is transatlantically distributed and comprises 11 species with a convoluted taxonomic history. In this study, relationships for ten Hypleurochilus species are resolved using multi-locus nuclear and mtDNA sequence data, morphological data, and mined COI barcode data.  Mitochondrial and nuclear sequence data from 61 individuals collected from the western Atlantic and northern Gulf of Mexico (N. GoM) delimit seven species into a temperate clade, a tropical clade, and a third distinct lineage. This lineage, herein referred to as H. cf. aequipinnis, may represent a species of Hypleurochilus whose range has expanded into the N. GoM. Inclusion of publicly available COI sequence for an additional three species provides further phylogenetic resolution. H. bananensis forms a new eastern Atlantic clade with H. cf. aequipinnis, providing further evidence for a western Atlantic range expansion. Single marker COI delimitation was unable to elucidate the relationships between H. springeri/H. pseudoaequipinnis and between H. multifilis/H. caudovittatus due to incomplete lineage sorting. Mitochondrial data are also unable to accurately resolve the placement of H. bermudensis. However, a comprehensive approach using multi-locus phylogenetic and species delimitation methods was able to resolve these relationships. While mining publicly available sequence data allowed for the inclusion of an increased number of species in the analysis and a more comprehensive phylogeny, it was not without drawbacks, as a handful of sequences are potentially mis-identified. Overall, we find that the recent divergence of some species within this genus and potential introgression events confound the results of single locus delimitation methods, yet a combination of single and multi-locus analyses has allowed for insights into the biogeography of this genus and uncovered a potential transatlantic range expansion.

Two new freshwater blennies from the Eastern Mediterranean basin (Teleostei: Blenniidae)

Two new species of Salariopsis are described from the Eastern Mediterranean basin. Salariopsis burcuae, new species, from the Bay of Antalya east to the Jordan, is characterised by having a short cirrus, usually not overlapping the 9th circum-orbital sensory pore, and many tiny black dots on the cheek not organised in rows or bands. The new species shows a 4.1% K2P sequence divergence on the cytochrome-c-oxidase subunit 1 (COI) barcoding region from its closest relative, S. fluviatilis. Salariopsis renatorum, new species, from the upper Ceyhan drainage and a coastal stream in Arsuz, is distinguished by having an unbranched supraocular tentacle, black lateral line pores, a short snout, and no black dots on the upper part of the flank and on the cheek. It is also distinguished from its geographically closest congener, S. burcuae, by a molecular distance of 8.8% K2P in its COI barcode region.

Disentangling cryptic species in Parastenocarididae (Copepoda: Harpacticoida) with an integrative approach: the case of Stammericaris similior sp. nov. and Stammericaris destillans Bruno & Cottarelli 2017

Stammericaris similior sp. nov. is described combining light microscopy, scanning electron microscopy, and genetic barcoding. The new species was collected from rimstone pools in Scrivilleri Cave, a cave in Sicily with so far unexplored microcrustacean fauna. The new species is particularly interesting because it is morphologically very similar to Stammericaris destillans, an epikarstic parastenocaridid endemic to a different Sicilian cave; however, the phylogenetic analysis based on the mitochondrial COI gene of sixteen parastenocaridids shows that these two Stammericaris are two distinct species, with an uncorrected p-distance of 22.9, and the sequences of Stammericaris similior sp. nov. cluster together in a well-supported monophyletic clade, with two different haplotypes. To our knowledge, the presence of different species of almost identical morphology had not been recorded before for the genus Stammericaris. The integrated molecular and morphological analysis, the latter conducted with the support of SEM, allows disentangling the affinities of the new species and identifying a few distinctive characters: the males of the new species are characterized by the caudal rami shorter than the anal somite; the morphology of the P3, which is thin and slightly arched, with three proximal spinules on exp-1; the peculiar structure of the P4 enp; the P4 basis ornamented with two spinules of different length, the one closest to the endopod being the shortest one, and a half-moon shaped lamella. The new species differs from S. destillans for its larger size, the presence of: three spinules, instead of two, on the P3 exp-1; the half-moon shaped lamella on the P4 basis; a row of spinules along the inner margin of P4 exp-1. We also provide data on the ecology and distribution of the new species, a list of the other copepod species collected, and a dichotomic key for the males of all species presently assigned to the genus.

Mitochondrial DNA of Sardinian and North-West Italian Populations Revealed a New Piece in the Mosaic of Phylogeography and Phylogeny of Salariopsis fluviatilis (Blenniidae)

The genus Salariopsis (Blenniidae) comprises freshwater blenny fish that inhabits Mediterranean Sea, Black Sea, and north-east Atlantic areas. Three species were formally described to date: Salariopsis fluviatilis. S. economidisi, and S. atlantica. In this study, 103 individuals were collected from different Italian regions (Sardinia, Liguria, Piedmont, Lombardy) and analyzed using the mtDNA Control Region and the ribosomal 16s gene. We aimed (i) to depict the phylogeographic patterns of S. fluviatilis in northern Italy and Sardinia and (ii) to compare the genetic structure of Italian samples with those from other Mediterranean regions. Results obtained showed the presence of a well-supported genetic structuring among Italian S. fluviatilis populations, shedding new light on the phylogeographic patterns of northern Italian populations of S. fluviatilis sensu stricto across the Ligurian Alpine ridge and the Sardinia Island-mainland dispersal patterns. Furthermore, our species delimitation analysis was consistent in supporting results of previous research about the presence of genetic differentiation among S. fluviatilis, evidencing: (i) a large group of S. fluviatilis sensu stricto that includes two sub-groups (Occidental and Oriental), (ii) one group comprising populations from the Middle East of a taxonomic entity corresponding to Salariopsis cf. fluviatilis, and (iii) one group of Iberian individuals from the Guadiana River.

The Inland Water Copepod Fauna of a Traditional Rural Landscape in a Mediterranean Island (Crustacea, Copepoda)

Although the Mediterranean area is a well-known hotspot of biological diversity, the crustacean assemblages inhabiting inland waters of the Mediterranean islands are to date unevenly known, and detailed information is missing for most taxa and areas. In the frame of this paper, we provide a checklist and a characterization of the copepod fauna of the lentic water bodies occurring in a traditional rural landscape of Sicily, where the co-existence of agriculture, woodlands, and pastoral activities lead to the presence of a wide range of different aquatic habitats. Overall, 22 copepod species belonging to the orders Calanoida, Cyclopoida, and Harpacticoida have been found in the 92 surveyed sites, stressing the conservation value of the area. In the study area, species widespread in the west Palaearctic region co-exist with strictly Mediterranean elements and a small but biogeographically significant group of species with northern or Balkan affinities, which support the role of the investigated area as a refugium for species that colonised Sicily during Pleistocene climate fluctuations and are now restricted to the more wet parts of the island. A single non-native species has been found, and its distribution is currently limited to permanent, man-made reservoirs.

The genus Diaphanosoma (Diplostraca: Sididae) in Greece: morphological and molecular assessment

For the genus Diaphanosoma Fischer (Cladocera) the species name D. brachyurum has been widely used for many decades to identify other species belonging to this genus. To clarify the diversity of the genus in Greek lakes in the present study, we morphologically and genetically identified the Diaphanosoma species occurring in eight lakes. Three hundred twenty-nine Diaphanosoma individuals were morphologically examined, while for the genetic analyses the mtDNA COI gene was sequenced in 48 individuals. Combining the morphological and genetic results, we verified the occurrence of D. mongolianum, D. orghidani and D. macedonicum in our study area. We could not confirm prior records of D. brachyurum and D. lacustris while we provide the molecular identity of D. macedonicum. Furthermore, we highlight the need to check whether the European D. mongolianum populations are characterised of mitochondrial discordance and hybridization as the individuals from the Asian type locality of the species. Our results support the importance of combining both approaches to correctly identify taxonomic species, despite the extra effort and cost during the sample analysis.

Molecular Cytogenetic Characterization of the Sicilian Endemic Pond Turtle Emys trinacris and the Yellow-Bellied Slider Trachemys scripta scripta (Testudines, Emydidae)

Turtles, a speciose group consisting of more than 300 species, demonstrate karyotypes with diploid chromosome numbers ranging from 2n = 26 to 2n = 68. However, cytogenetic analyses have been conducted only to 1/3rd of the turtle species, often limited to conventional staining methods. In order to expand our knowledge of the karyotype evolution in turtles, we examined the topology of the (TTAGGG)_n telomeric repeats and the rDNA loci by fluorescence in situ hybridization (FISH) on the karyotypes of two emydids: the Sicilian pond turtle, Emys trinacris, and the yellow-bellied slider, Trachemys scripta scripta (family Emydidae). Furthermore, AT-rich and GC-rich chromosome regions were detected by DAPI and CMA₃ stains, respectively. The cytogenetic analysis revealed that telomeric sequences are restricted to the terminal ends of all chromosomes and the rDNA loci are localized in one pair of microchromosomes in both species. The karyotype of the Sicilian endemic E. trinacris with diploid number 2n = 50, consisting of 13 pairs of macrochromosomes and 12 pairs of microchromosomes, is presented here for first time. Our comparative examination revealed similar cytogenetic features in Emys trinacris and the closely related E. orbicularis, as well as to other previously studied emydid species, demonstrating a low rate of karyotype evolution, as chromosomal rearrangements are rather infrequent in this group of turtles.