Do Genetically Distinct Rougheye Rockfish Sibling Species Differ Phenotypically? A. J. GHARRETT* Juneau Center, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 11120 Glacier Highway, Juneau, Alaska 99801, USA C. W. MECKLENBURG Point Stephens Research, Post Office Box 210307, Auke Bay, Alaska 99821, USA L. W. SEEB Gene Conservation Laboratory, Alaska Department of Fish and Game, 333 Raspberry Road, Anchorage, Alaska 99518-1599, USA Z. LI, A. P. MATALA, 1 AND A. K. GRAY 2 Juneau Center, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 11120 Glacier Highway, Juneau, Alaska 99801, USA J. HEIFETZ National Marine Fisheries Service, Auke Bay Laboratory, 11305 Glacier Highway, Juneau, Alaska 99801, USA Abstract.—Two cryptic species of rougheye rockfish Sebastes aleutianus, which we refer to as types I and II, have been identified independently from DNA (microsatellite and mitochondrial DNA [mtDNA]) markers and from distributions of allozyme allele frequencies. Visual differences that discriminate between these species in the field would improve their conservation and management. To delineate species, we used two microsatellite loci, lSma6 and lSma7, in conjunction with mtDNA site differences for the restriction enzymes Cfo I in the region of NADH dehydrogenase (ND) subunits 3 and 4 and Mbo I in the region of ND subunits 5 and 6. We compared meristic characters and morphological dimensions of the genetically determined species and observed that although all parameters had overlapping distributions, type II rougheye rockfish have slightly fewer and shorter gill rakers and deeper bodies. Discriminant analysis of morphological characteristics accurately delineated the species (.94%). Rougheye rockfish have two color forms: light and dark. We examined the correlation between coloration and genotype and observed that most type II fish had the light coloration, but type I fish were either light or dark and the proportion of each color form changed geographically. We also demonstrated that frequency differences in the distributions of allozyme markers are concordant with diagnostic differences at microsatellite loci and mtDNA markers, although the allozyme markers are not diagnostic. The rougheye rockfish Sebastes aleutianus is a commercially valuable species that is caught in- cidentally in Alaskan longline and trawl fisheries. It is targeted by fishermen when possible and is often harvested to the maximum level allowed by regulation. Both trawl and longline surveys are conducted by the National Marine Fisheries Service (NMFS) to assess abundance of rougheye rockfish in the Gulf of Alaska (GOA) and Bering Sea. Recently, it was discovered that the rougheye rockfish includes two genetically distinct species, as determined independently from DNA markers (Gharrett et al. 2005) and allozyme markers (Hawkins et al. 2005). The two forms are often caught in the same hauls (Gharrett et al. 2005). Delineation of the two species in the laboratory is straightforward and rapid using genetic analysis; however, the species are similar in external appearance, and previously the existence of a single species was assumed. Identification of diagnostic phenotypic char- acters that would allow visual differentiation of the two rougheye rockfish species in the field is desirable * Corresponding author: ffajg@uaf.edu 1 Present address: U.S. Fish and Wildlife Service, Aberna- thy Fish Technology Center, 1440 Abernathy Creek Road, Longview, Washington 98632, USA. 2 Present address: National Marine Fisheries Service, Auke Bay Laboratory, 11305 Glacier Highway, Juneau, Alaska 99801, USA. Received May 21, 2005; accepted December 26, 2005 Published online June 6, 2006 792 Transactions of the American Fisheries Society 135:792–800, 2006 Ó Copyright by the American Fisheries Society 2006 DOI: 10.1577/T05-136.1 [Article]