Crossing the Pacific: Genomics Reveals the Presence of Japanese Sardine (Sardinops melanosticta) in the California Current Large Marine Ecosystem.

Recent increases in frequency and intensity of warm water anomalies and marine heatwaves have led to shifts in species ranges and assemblages. Genomic tools can be instrumental in detecting such shifts. In the early stages of a project assessing population genetic structure in Pacific Sardine (Sardinops sagax), we detected the presence of Japanese Sardine (Sardinops melanosticta) along the west coast of North America for the first time.

Upwelling-level acidification and pH/pCO variability moderate effects of ocean acidification on brain gene expression in the temperate surfperch, Embiotoca jacksoni.

Acidification-induced changes in neurological function have been documented in several tropical marine fishes. Here, we investigate whether similar patterns of neurological impacts are observed in a temperate Pacific fish that naturally experiences regular and often large shifts in environmental pH/pCO . In two laboratory experiments, we tested the effect of acidification, as well as pH/pCO variability, on gene expression in the brain tissue of a common temperate kelp forest/estuarine fish, Embiotoca jacksoni.

Strong population differentiation in lingcod () 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 (), 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.

Evolutionary origin of the Atlantic Cabo Verde nibbler (Girella stuebeli), a member of a primarily Pacific Ocean family of antitropical herbivorous reef fishes.

Nibblers (family Girellidae) are reef fishes that are mostly distributed in the Indo-Pacific, with one exception: Girella stuebeli, which is found in the Cabo Verde Archipelago, in the Atlantic Ocean. We capitalized on this unusual distribution to study the evolutionary history of the girellids, and determine the relationship between G. stuebeli and the remaining nibbler taxa.

Molecular phylogenetics of snailfishes (Cottoidei: Liparidae) based on MtDNA and RADseq genomic analyses, with comments on selected morphological characters.

Phylogenetic relationships of snailfishes of the family Liparidae were analyzed on the basis of two sets of molecular sequence data: one from the mitochondrial DNA cytochrome c oxidase subunit one gene (COI) and another from restriction-site associated genome-wide sequences (RADseq). The analysis of COI sequence data from at least 122 species of 18 genera from the Pacific, Atlantic, and Southern oceans resulted in a moderately well-resolved phylogeny among the major clades, albeit with significant polytomy among central clades. Nectoliparis was the sister of all other members of the family, followed by Liparis.

Taxonomic revisions within Embiotocidae (Teleostei, Perciformes) based on molecular phylogenetics.

Embiotocidae, a unique family within the Perciformes that has evolved a complex viviparous natural history, has lacked full resolution and strong support in several interspecific relationships until recently. Here we propose three taxonomic revisions within embiotocid surfperches based on recent molecular phylogenetic analyses that robustly resolve all interspecific relationship in the Eastern Pacific species: Hypsurus caryi (Agassiz, 1853) resurrected to its original name Embiotoca caryi Agassiz, 1853, Rhacochilus vacca (Girard, 1855) shifted into the genus Phanerodon Girard, 1854, and Hyperprosopon anale Agassiz, 1861 separated into the available genus Hypocritichthys Gill, 1862. The proposed changes would leave three previously paraphyletic groups monophyletic (Embiotoca, Hyperprosopon, and Phanerodon) and would maintain the current number of genera at 13.

, a new brooding damselfish (Teleostei, Perciformes, Pomacentridae) from Busuanga Island, Philippines.

A new species of damselfish, is described from specimens collected in shallow water (1-8m depth) off Busuanga Island, Palawan Province, Philippines. It differs from the other two species in the genus, and , in various features including having golden upper body lacking dark edges of dorsal and caudal fins, higher modal number of tubed lateral line scales, as well as differences in two mitochondrial markers, one nuclear marker, and RAD markers.

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae).

The complete 16,515bp nucleotide sequence of the mitochondrial genome was determined for the black surfperch, Embiotoca jacksoni (Perciformes: Embiotocidae). The black surfperch mitochondrial genome contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and the non-coding control region (D-loop), the gene order of which is identical to that observed in most vertebrates. The protein-coding gene sequences of E.

Tempo and mode of speciation in Holacanthus angelfishes based on RADseq markers.

In this study we estimated the timing of speciation events in a group of angelfishes using 1186 RADseq markers corresponding to 94,880 base pairs. The genus Holacanthus comprises seven species, including two clades of Panama trans-Isthmian geminates, which diverged approximately 3-3.5Mya.

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies.

Background: Phylogenetic and population genetic studies often deal with multiple sequence alignments that require manipulation or processing steps such as sequence concatenation, sequence renaming, sequence translation or consensus sequence generation. In recent years phylogenetic data sets have expanded from single genes to genome wide markers comprising hundreds to thousands of loci. Processing of these large phylogenomic data sets is impracticable without using automated process pipelines.

Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality.

In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S.