Karyotype and genome size of Iberochondrostoma almacai (Teleostei, Cyprinidae) and comparison with the sister-species I.lusitanicum

This study aimed to define the karyotype of the recently described Iberian endemic Iberochondrostoma almacai, to revisit the previously documented chromosome polymorphisms of its sister species I.lusitanicum using C-, Ag-/CMA3 and RE-banding, and to compare the two species genome sizes. A 2n = 50 karyotype (with the exception of a triploid I.lusitanicum specimen) and a corresponding haploid chromosome formula of 7M:15SM:3A (FN = 94) were found. Multiple NORs were observed in both species (in two submetacentric chromosome pairs, one of them clearly homologous) and a higher intra and interpopulational variability was evidenced in I.lusitanicum. Flow cytometry measurements of nuclear DNA content showed some significant differences in genome size both between and within species: the genome of I. almacai was smaller than that of I.lusitanicum (mean values 2.61 and 2.93 pg, respectively), which presented a clear interpopulational variability (mean values ranging from 2.72 to 3.00 pg). These data allowed the distinction of both taxa and confirmed the existence of two well differentiated groups within I. lusitanicum: one that includes the populations from the right bank of the Tejo and Samarra drainages, and another that reunites the southern populations. The peculiar differences between the two species, presently listed as “Critically Endangered”, reinforced the importance of this study for future conservation plans

A Ranking System for Reference Libraries of DNA Barcodes: Application to Marine Fish Species from Portugal

BACKGROUND: The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal. METHODOLOGY/PRINCIPAL FINDINGS: Specimens (n = 659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A-E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E). CONCLUSION/SIGNIFICANCE: We highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the continuous revision and annotation required in taxonomic work

A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids

A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose.

Reproductive success of nuclear nonhybrid males of Squalius alburnoides hybridogenetic complex (Teleostei, Cyprinidae): An example of interplay between female choice and ecological pressures?

The hybridogenetic fish complex Squalius alburnoides comprises diploid males with non-hybrid nuclear genomes and several hybrid forms varying in ploidy and relative proportions of the parental genomes. In this paper, we present evidence that in captivity females prefer to mate with non-hybrid males. We suggest that female choice combined with different ecological requirements of hybrid and non-hybrid males may explain the extreme variation in the relative abundance of male types among drainages

Mitochondrial and nuclear intraspecific variation in the rusty blenny (Parablennius sanguinolentus, Blenniidae)

The genetic structure of Parablennius sanguinolentus from the northeastern Atlantic and Mediterranean was assessed using sequences from the mitochondrial control region (CR) and the first intron of the nuclear S7 ribosomal protein gene (S7). Our data show high genetic diversity for the central Mediterranean populations, contrasting with very low diversity in the Atlantic populations and in the westernmost Mediterranean population of Cabo de Gata. Both CR mismatch analysis and neutrality tests provide evidence of demographic and spatial expansion for the Atlantic and central Mediterranean populations. The significant correlation between genetic and geographic distances supported isolation-by-distance for the S7, but not for the CR, suggesting a complex scenario for the history of the rusty blenny in the Mediterranean Sea. The pattern of genetic structure displayed by P. sanguinolentus could be explained as the result of a post-glacial colonization of the Atlantic coast of Europe from the Mediterranean Sea