Stingrays genus Hypanus currently encompasses nine valid species from the Atlantic and Pacific oceans, though the phylogenetic relationships amongst some of them were based on a single mitochondrial gene and did not involve all putative Hypanus species. To address the monophyly of the genus and its relationship to other Dasyatinae genera, we sequenced the whole mitochondrial genomes of all species that supposedly belong to this genus and representatives of Dasyatinae, Neotrygoninae, and, as an outgroup, Fontitrygon (Urogymninae). Based on phylogenetic analyses, Hypanus is the sister-genus to all other Dasyatinae, and this subfamily is closely-related to Neotrygoninae within the family Dasyatidae. The species F. geijskesi is closely related to H. guttatus rather than to its congeners and should be allocated to Hypanus as H. geijskesi for the genus monophyly. After lineage delimitation analyses, we identified three species complexes composed of H. americanus, H. guttatus, and H. say, with two distinct evolutionary lineages within each, leaving the genus with 13 evolutionary units, of which six are currently under threat and only H. sabinus is of least concern. The urgency in identifying these new lineages lies in the fact they might already be under threat before being formally described.

The Thorny Skate (Amblyraja radiata) is a vulnerable species displaying a discrete size-polymorphism in the northwest Atlantic Ocean (NWA). We conducted whole genome sequencing of samples collected across its range. Genetic diversity was similar at all sampled sites, but we discovered a ~ 31 megabase bi-allelic supergene associated with the size polymorphism, with the larger size allele having introgressed in the last ~160,000 years B.P. While both Gulf of Maine (GoM) and Canadian (CAN) populations exhibit the size polymorphism, we detected a significant deficit of heterozygotes at the supergene and longer stretches of homozygosity in GoM population. This suggests inbreeding driven by assortative mating for size in GoM but not in CAN. Coalescent-based demographic modelling reveals strong migration between regions maintaining genetic variability in the recombining genome, preventing speciation between morphs. This study highlights short-term context-dependent evolutionary consequences of a size-determining supergene providing new insights for the management of vulnerable species.

Fishes in the cypriniform family Catostomidae (suckers) are evolutionary tetraploids. The use of nuclear markers in the phylogenetic study of this important group has been greatly hindered by the challenge of identifying paralogous copies of genes. In the present study, we used two different methods to separate the gene copies of five single-copy nuclear genes (i.e., RAG1, EGR2B, EGR3, IRBP2, and RAG2). For each gene, all sequences of Copy I formed a clade that was sister to the clade formed by all sequences of Copy II in the phylogenetic trees. The maternal and paternal progenitor of the tetraploid ancestor of the Catostomidae could not be determined. We also constructed a mitochondrial tree to reflect the maternal relationships among major catostomid lineages. Our data appear to support a sister relationship between Catostominae and a monophyletic group composed of Myxocyprininae, Cycleptinae, and Ictiobinae. However, within Catostominae, there is significant conflict between mitochondrial and nuclear data regarding the relationships among Erimyzonini, Catostomini, and Moxostomatini/Thoburnini. Many indels, unexpected stop codons, and possible gene loss were identified in one gene copy of RAG1, RAG2, and IRBP2. We believe that additional nuclear genome data are needed to better resolve the phylogenetic relationships within the family Catostomidae.

A new species of hornshark is described from northwestern Australia based on six whole specimens and a single egg case. Heterodontus marshallae n. sp. was previously considered to be conspecific with H. zebra from the Western Pacific. The new species differs from H. zebra in the sequence of its NADH2 gene, several morphological characters, egg case morphology and key coloration features. Despite the coloration being similar between H. marshallae n. sp. and H. zebra, i.e., pale background with 22 dark brown bands and saddles, they differ consistently in two key aspects. Firstly, the snout of H. marshallae n. sp. has a dark semicircular bar, usually bifurcated for most of its length vs. a pointed, triangular shaped dark marking in H. zebra. Secondly, H. zebra has a dark bar originating below the posterior gill slits and extending onto anterior pectoral fin, which is absent in H. marshallae n. sp. The Heterodontus marshallae n. sp. is endemic to northwestern Australia and occurs in deeper waters (125–229 m) than H. zebra (0–143 m).

Botiidae is a small family of freshwater fishes distributed across Southeast Asia, South Asia, and East Asia. It comprises two subfamilies: the diploid Leptobotiinae and the tetraploid Botiinae. Whether species in the Botiinae are autotetraploids or allotetraploids and how many polyploidization events occurred during the evolution of this subfamily remain open questions. The phylogenetic relationships and biogeography of the Botiidae also require further investigation. In the current study, we compared phylogenetic trees constructed using DNA sequences from the mitochondrial genome and five phased nuclear genes. We also performed whole genome sequencing for two tetraploid species: Chromobotia macracanthus and Yasuhikotakia modesta. Genome profiling of five botiine species suggests that they are likely of allotetraploid origin. Nuclear gene tree topologies indicate that the tetraploidization of the Botiinae occurred only once in the common ancestor of this subfamily. Although the possible maternal progenitor and paternal progenitor of the Botiinae cannot be determined, the subfamily Leptobotiinae can be excluded as a progenitor. The gene trees built in this study generally agree on the following sister group relationships: Leptobotiinae/Botiinae, Leptobotia/Parabotia, Chromobotia/Botia, Yasuhikotakia/Syncrossus, and Sinibotia/Ambastaia. Clades formed by the last two generic pairs are also sisters to each other. Timetree analyses and ancestral range reconstruction suggest that the family Botiidae might have originated in East Asia and Mainland Southeast Asia approximately 51 million years ago and later dispersed to South Asia and the islands of Southeast Asia.