The incomplete history of mitochondrial lineages between two rockfishes, Sebastes longispinis and Sebastes hubbsi (Scorpaeniformes: Scorpaenidae)

Allopatric origin, secondary contact and subsequent isolation of sympatric rockfishes (Sebastidae: Sebastes) in the north-western Pacific

Understanding how speciation occurs is central to biology. Gene flow between diverging taxa is correlated with geography and other aspects of speciation; therefore, the examination of gene flow during divergence is a potent approach to understanding the nature of speciation. Here, we inferred the speciation process of the sympatric rockfishes Sebastes steindachneri and Sebastes wakiyai in the north-western Pacific and its marginal seas based on genome-wide single nucleotide polymorphism and mitochondrial DNA data. Model-based demographic inference showed that gene flow between the two species was absent in the initial and late stages of divergence and present only in the middle stage. Population expansion occurred before or during the period of gene flow. The estimated timings of the initial divergence and population expansion fell within the Pleistocene, during which the seas currently inhabited by the two species were repeatedly isolated and reconnected. Contemporary isolation was supported by the absence of hybrids and the shared mitochondrial DNA haplotypes. Our results suggest that the two species initially diverged in allopatry, followed by secondary contact and introgression and by the completion of reproductive isolation. Given that complete isolation following secondary contact has rarely been tested or documented in marine organisms, we highlight the importance of careful consideration of alternative divergence scenarios to be tested, which should take into account the geological and environmental settings.

Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome

Delimiting intraspecific genetic variation in harvested species is crucial to the assessment of population status for natural resource management and conservation purposes. Here, we evaluated genetic population structure in lingcod (Ophiodon elongatus), a commercially and recreationally important fishery species along the west coast of North America. We used 16,749 restriction site-associated DNA sequencing (RADseq) markers, in 611 individuals collected from across the bulk of the species range from Southeast Alaska to Baja California, Mexico. In contrast to previous population genetic work on this species, we found strong evidence for two distinct genetic clusters. These groups separated latitudinally with a break near Point Reyes off Northern California, and there was a high frequency of admixed individuals in close proximity to the break. F-statistics corroborate this genetic break between northern and southern sampling sites, although most loci are characterized by low FST values, suggesting high gene flow throughout most of the genome. Outlier analyses identified 182 loci putatively under divergent selection, most of which mapped to a single genomic region. When individuals were grouped by cluster assignment (northern, southern, and admixed), 71 loci were fixed between the northern and southern cluster, all of which were identified in the outlier scans. All individuals identified as admixed exhibited near 50:50 assignment to northern and southern clusters and were heterozygous for most fixed loci. Alignments of RADseq loci to a draft lingcod genome assembly and three other teleost genomes with chromosome-level assemblies suggest that outlier and fixed loci are concentrated on a single chromosome. Similar genomic patterns have been attributed to chromosomal inversions in diverse taxonomic groups. Regardless of the evolutionary mechanism, these results represent novel observations of genetic structure in lingcod and designate clear evolutionary units that could be used to inform fisheries management.

Whole genome resequencing data for three rockfish species of Sebastes

Here we report Illumina-based whole genome sequencing of three rockfish species of Sebastes in northwest Pacific. The whole genomic DNA was used to prepare 350-bp pair-end libraries and the high-throughput sequencing yielded 128.5, 137.5, and 124.8 million mapped reads corresponding to 38.54, 41.26, and 37.43 Gb sequence data for S. schlegelii, S. koreanus, and S. nudus, respectively. The k-mer analyses revealed genome sizes were 846.4, 832.5, and 813.1 Mb and the sequencing coverages were 45×, 49×, and 46× for three rockfish, respectively. Comparative genomic analyses identified 46,624 genome-wide single nucleotide polymorphisms (SNPs). Phylogenetic analysis revealed closer relationships of the three species, compared to other six rockfish species. Demographic analysis identified contrasting changes between S. schlegelii and other two species, suggesting drastically different response to climate changes. The reported genome data in this study are valuable for further studies on comparative genomics and evolutionary biology of rockfish species.

Design Type(s)	species comparison design • sequence analysis objective
Measurement Type(s)	whole genome sequencing assay
Technology Type(s)	DNA sequencing
Factor Type(s)
Sample Characteristic(s)	Sebastes schlegelii • Sebastes koreanus • Sebastes nudus

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Upwelling and eddies affect connectivity among local populations of the goldeye rockfish, Sebastes thompsoni (Pisces, Scorpaenoidei)

The goldeye rockfish, Sebastes thompsoni, commercial rockfish catch in the Northwest Pacific Ocean, may influence its population structure. To clarify the population genetic structure of Korean S. thompsoni and its degree of hybridization with the most close species, Sebastes joyneri, we analyzed a mitochondrial (mt) DNA control region and eleven polymorphic microsatellite (ms) loci. S. joyneri individuals were clearly distinguished from S. thompsoni by the mtDNA control region and ms loci results, with single interspecific hybridization between two species suggesting no impact on genetic structure of S. thompsoni. Analysis of mtDNA revealed no population structure within S. thompsoni, suggesting the survival of a single population in southern refugia during the glacial period. The ms loci results, in contrast, showed two genetically distinct clusters within S. thompsoni: One was predominant throughout Korean coasts (from the Yellow Sea, via the Korea Strait to the East Sea); the other was predominant at Dokdo Island in the East Sea; and both occurred in similar ratios at Wangdolcho Reef in the East Sea. A possible factor that restricts gene flow between Korean coastal and offshore populations in the East Sea may be related to the complex oceanic current patterns such as eddies and upwelling, which represent impermeable barriers to population connectivity for this species. Our findings highlight that these two populations might be representative of two separate stock within Korean waters and maintain their geographically related genetic structure.

Complete mitochondrial genome of Sebastes longispinis (Scorpaenidae, Scorpaeniformes) from the East Sea, Korea

Sebastes longispinis is considered to be a valid species despite its incomplete mitochondrial lineage. To obtain basic information of this species, the complete mitochondrial DNA sequence of S. longispinis was determined by next-generation sequencing. The complete sequence is 16,445 bp in length and comprised of 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and a control region. The complete mitogenome contains 28.0% A, 26.7% T, 17.1% G and 28.3% C nucleotides, with a slight AT bias (54.6%). The start codon of each PCG is ATG, except for COX1 (GTG). The stop codons found in the PCGs are mainly TAA, except for ND1 (TAG), ND3 (TAG), ND4 (AGA), and Cytb (incomplete termination codon, T). The tRNAs have a typical cloverleaf form, except for tRNA(Ser (AGY)), which lacks the DHU arm. The mitogenome of S. longispinis can be used to address the incomplete mitochondrial lineages in allied species of the Scorpaenidae.

Species identification and evolutionary inference of the genera Megalobrama and Parabramis (Cyprinidae: Cultrinae) in China

The species boundaries and evolutionary relationships of two closely related genera, Megalobrama and Parabramis, were inferred from the partial mitochondrial cytochrome oxidase subunit I (COI) gene, NADH dehydrogenase subunit 2 (ND2) gene and their concatenated segment. Phylogenetic reconstructions showed that among the three breams, Megalobrama amblycephala and Megalobrama skolkovii are more closely related to each other than either is to Megalobrama terminalis. The taxonomy of M. pellegrini should be reconsidered. The divergence time estimation based on the assumption of a global molecular clock indicated that speciation and dispersal of the two genera might have occurred at approximately Pliocene to Late Pleistocene, due to major paleo-environmental events associated with monsoon evolution and the formation of the Three Gorges of the Yangtze River.