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Differentiation of the frog sculpin Myoxocephalus stelleri Tilesius, 1811 (Actinopterygii, Cottidae) based on mtDNA and karyotype analyses.

ABSTRACT: A molecular genetic and karyological study of the frog sculpin Myoxocephalus stelleri Tilesius, 1811 was carried out on an extensive sample from a large area of the species' range. A total of 42 specimens was sampled from the Sea of Japan, Sea of Okhotsk, and coastal waters off the southern Kuril Islands, which makes this sampling scheme the most comprehensive to date. The level of mtDNA polymorphism was found to be low. The haplotypes of the species formed three phylogenetic groups. The unique M. stelleri haplotype from the coast of Shikotan Island linked all the studied groups, indicating that it is likely ancestral. Robertsonian polymorphism was identified in the species. In all five cytotypes (I - 2n = 44, II - 2n = 43, III - 2n = 42, IV - 2n = 41, V - 2n = 40; NF = 44+2) were identified, all of which were present in the Sea of Japan. Only one (cytotype I) was found in the Sea of Okhotsk, which is probably the closest to the ancestral karyotype. The significant chromosomal polymorphism and the presence of common haplotypes in the studied samples indicate their recent origin from a common ancestor and/or relatively recent contacts within the range. The discrepancies between mtDNA and karyotypes in assigning the ancestral M. stelleri to the coastal waters off Shikotan Island (southern Kuril Islands) and the Sea of Okhotsk, respectively, can be explained by the different inheritance mechanisms and the rates of evolution of molecular genetic and karyological traits.

SUBMITTER: Moreva IN

PROVIDER: S-EPMC8217076 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin Myoxocephalus quadricornis and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group. A comparison of the My. quadricornis mt genomes obtained by us with other complete mt genomes available in GenBank has revealed a surprisingly low divergence (3.06 ± 0.12%) with Megalocottus platycephalus and, at the same time, a significantly higher divergence (7.89 ± 0.16%) with the species of the genus Myoxocephalus. Correspondingly, phylogenetic analyses have shown that My. quadricornis is clustered with Me. platycephalus but not with the Myoxocephalus species. Completely consistent patterns of divergence and tree topologies have been obtained based on nuclear rDNA. Thus, the multi-gene data in the present work indicates obvious contradictions in the relationships between the Myoxocephalus and Megalocottus species studied. An extensive phylogenetic analysis has provided evidence for a closer affinity of My. quadricornis with the species of the genus Megalocottus than with the species of the genus Myoxocephalus. A recombination analysis, along with the additional GenBank data, excludes introgression and/or incorrect taxonomic identification as the possible causative factors responsible for the observed closer affinity between the two species from different genera. The above facts necessitate realignment of the genera Myoxocephalus and Megalocottus. The genetic data supports the two recognized genera, Myoxocephalus and Megalocottus, but suggests changing their compositions through transferring My. quadricornis to the genus Megalocottus. The results of the present study resolve the relationships within a complex group of sculpin fishes and show a promising approach to phylogenetic systematics (as a key organizing principle in biodiversity research) for a better understanding of the taxonomy and evolution of fishes and for supplying relevant information to address various fish biodiversity conservation and management issues.

Project description:Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250-283 Ma and ∼120-133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.

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Differentiation of the frog sculpin Myoxocephalus stelleri Tilesius, 1811 (Actinopterygii, Cottidae) based on mtDNA and karyotype analyses.

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