Cryptic Diversity and Patterns of Structure in Nine Species of North Pacific Rockfishes (Sebastes spp. and Sebastolobus spp.).
8 affiliations
- 1Auke Bay Laboratories, Alaska Fisheries Science Center, NOAA, Juneau, Alaska, USA.
- 2Pacific States Marine Fisheries Commission, Portland, Oregon, USA.
- 3University of Alaska Fairbanks, Juneau, Alaska, USA.
- 4Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA.
- 5Alaska Department of Fish and Game, Juneau, Alaska, USA.
- 6Southwest Fisheries Science Center, NOAA, La Jolla, California, USA.
- 7Northwest Fisheries Science Center, NOAA, Seattle, Washington, USA.
- 8Department of Biology, University of Victoria, Victoria, British Columbia, Canada.
Abstract
Understanding how habitat and life history traits contribute to population genetic structure is critical for evaluating conservation risks and identifying optimal management of wild populations. Species derived from adaptive radiations can provide a useful model for studying such patterns because the presence of some consistent traits allows for closer examination of attributes which differ. Here, we examine population structure in rockfishes (genera Sebastes and Sebastolobus), a group of speciose, recently diverged marine fishes that exhibit a continuum of genetic structure, from cryptic species to putative genetic panmixia. In this study, we analyse low-coverage whole genome resequencing data from nine rockfish species and identify four major types of genetic differentiation: cryptic diversity, isolation-by-distance (IBD), no detectable structure (putative panmixia) and no detectable structure with a single genomic region putatively underlying local adaptation. Two species, Dark (Sebastes ciliatus) and Northern (S. polyspinis) rockfishes, each exhibited cryptic diversity consisting of two sympatric groups differentiated at every chromosome throughout the genome. Black rockfish in Southeast Alaska also had two genetic groups, despite an overall signal of IBD from the West Coast of North America through the Gulf of Alaska (GOA). Five species showed evidence of genetic panmixia throughout the sampled range, while Yelloweye Rockfish exhibited high gene flow across ~4000 km, from southern California to the GOA, but had strong differentiation between the Salish Sea and the outer coast. Of the species in which no structure was detected, only Blackspotted Rockfish had one outlier region exhibiting signatures of potential local adaptation. Our results highlight how multiple mechanisms likely promote genetic structure in rockfishes, hinting at tentative links to depth distributions and offshore habitats that might influence patterns of differentiation in rockfishes more broadly. Further, this study provides genetic data for some of the most abundant rockfishes in commercial fisheries in the Northeast Pacific, enhancing the scientific information available for informing fisheries management.
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BibTeX
@article{baetscher2026cryptic,
title = {{Cryptic Diversity and Patterns of Structure in Nine Species of North Pacific Rockfishes (Sebastes spp. and Sebastolobus spp.).}},
author = {Diana S Baetscher and Natasha Howe and Laura E Timm and Runyang Nicolas Lou and Wei Cheng and John R Hyde and Krista M Nichols and Gregory L Owens and Peter H Sudmant and Wes Larson},
journal = {Molecular ecology},
year = {2026},
month = oct,
doi = {10.1111/mec.70601},
url = {https://europepmc.org/article/MED/42908379},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Cryptic Diversity and Patterns of Structure in Nine Species of North Pacific Rockfishes (Sebastes spp. and Sebastolobus spp.).
AU - Diana S Baetscher
AU - Natasha Howe
AU - Laura E Timm
AU - Runyang Nicolas Lou
AU - Wei Cheng
AU - John R Hyde
AU - Krista M Nichols
AU - Gregory L Owens
AU - Peter H Sudmant
AU - Wes Larson
PY - 2026
DA - 2026/10/01
JO - Molecular ecology
DO - 10.1111/mec.70601
UR - https://europepmc.org/article/MED/42908379
AB - Understanding how habitat and life history traits contribute to population genetic structure is critical for evaluating conservation risks and identifying optimal management of wild populations. Species derived from adaptive radiations can provide a useful model for studying such patterns because the presence of some consistent traits allows for closer examination of attributes which differ. Here, we examine population structure in rockfishes (genera Sebastes and Sebastolobus), a group of speciose, recently diverged marine fishes that exhibit a continuum of genetic structure, from cryptic species to putative genetic panmixia. In this study, we analyse low-coverage whole genome resequencing data from nine rockfish species and identify four major types of genetic differentiation: cryptic diversity, isolation-by-distance (IBD), no detectable structure (putative panmixia) and no detectable structure with a single genomic region putatively underlying local adaptation. Two species, Dark (Sebastes ciliatus) and Northern (S. polyspinis) rockfishes, each exhibited cryptic diversity consisting of two sympatric groups differentiated at every chromosome throughout the genome. Black rockfish in Southeast Alaska also had two genetic groups, despite an overall signal of IBD from the West Coast of North America through the Gulf of Alaska (GOA). Five species showed evidence of genetic panmixia throughout the sampled range, while Yelloweye Rockfish exhibited high gene flow across ~4000 km, from southern California to the GOA, but had strong differentiation between the Salish Sea and the outer coast. Of the species in which no structure was detected, only Blackspotted Rockfish had one outlier region exhibiting signatures of potential local adaptation. Our results highlight how multiple mechanisms likely promote genetic structure in rockfishes, hinting at tentative links to depth distributions and offshore habitats that might influence patterns of differentiation in rockfishes more broadly. Further, this study provides genetic data for some of the most abundant rockfishes in commercial fisheries in the Northeast Pacific, enhancing the scientific information available for informing fisheries management.
SN - 0962-1083
SN - 1365-294X
ER -