Vincent P. Buonaccorsi

Influence of habitat discontinuity, geographical distance, and oceanography on fine-scale population genetic structure of copper rockfish (Sebastes caurinus)

The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range‐wide study of the population‐genetic structure of copper rockfish revealed a pattern consistent with isolation‐by‐distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly–spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole‐coast scale (~2200 km), significant population subdivision (FST = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (~450 km, FST = 0.001). Hierarchical amova identified a weak but significant 130‐km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (Nem) is half that of the coast‐wide average. However, individual‐based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow.

Genomic characterization of sex-identification markers in Sebastes carnatus and Sebastes chrysomelas rockfishes.

Fish have evolved a variety of sex‐determining (SD) systems including male heterogamy (XY), female heterogamy (ZW) and environmental SD. Little is known about SD mechanisms of Sebastes rockfishes, a highly speciose genus of importance to evolutionary and conservation biology. Here, we characterize the sex determination system in the sympatrically distributed sister species Sebastes chrysomelas and Sebastes carnatus. To identify sex‐specific genotypic markers, double digest restriction site – associated DNA sequencing (ddRAD‐seq) of genomic DNA from 40 sexed individuals of both species was performed. Loci were filtered for presence in all of the individuals of one sex, absence in the other sex and no heterozygosity. Of the 74 965 loci present in all males, 33 male‐specific loci met the criteria in at least one species and 17 in both. Conversely, no female‐specific loci were detected, together providing evidence of an XY sex determination system in both species. When aligned to a draft reference genome from Sebastes aleutianus, 26 sex‐specific loci were interspersed among 1168 loci that were identical between sexes. The nascent Y chromosome averaged 5% divergence from the X chromosome and mapped to reference Sebastes genome scaffolds totalling 6.9Mbp in length. These scaffolds aligned to a single chromosome in three model fish genomes. Read coverage differences were also detected between sex‐specific and autosomal loci. A PCR‐RFLP assay validated the bioinformatic results and correctly identified sex of five additional individuals of known sex. A sex‐determining gene in other teleosts gonadal soma‐derived factor (gsdf) was present in the model fish chromosomes that spanned our sex‐specific markers.

Vision and change through the genome consortium for active teaching using next-generation sequencing (GCAT-SEEK).

Development of the Genome Consortium on Active Teaching using Next Generation Sequencing (GCAT-SEEK) is described. Workshops, educational modules, assessment resources, data analysis software and computer hardware available for faculty are described.

GCAT-SEEKquence: Genome Consortium for Active Teaching of Undergraduates through Increased Faculty Access to Next-Generation Sequencing Data

To transform undergraduate biology education, faculty need to provide opportunities for students to engage in the process of science. The rise of research approaches using next-generation (NextGen) sequencing has been impressive, but incorporation of such approaches into the undergraduate curriculum remains a major challenge. In this paper, we report proceedings of a National Science Foundation–funded workshop held July 11–14, 2011, at Juniata College. The purpose of the workshop was to develop a regional research coordination network for undergraduate biology education (RCN/UBE). The network is collaborating with a genome-sequencing core facility located at Pennsylvania State University (University Park) to enable undergraduate students and faculty at small colleges to access state-of-the-art sequencing technology. We aim to create a database of references, protocols, and raw data related to NextGen sequencing, and to find innovative ways to reduce costs related to sequencing and bioinformatics analysis. It was agreed that our regional network for NextGen sequencing could operate more effectively if it were partnered with the Genome Consortium for Active Teaching (GCAT) as a new arm of that consortium, entitled GCAT-SEEK(quence). This step would also permit the approach to be replicated elsewhere.

Characterization of a genomic divergence island between black-and-yellow and gopher Sebastes rockfishes

Islands of high genomic divergence that contain genes of evolutionary significance may form between diverging species. The gopher rockfish, Sebastes carnatus, and black‐and‐yellow rockfish, S. chrysomelas, are sympatrically distributed temperate marine species inhabiting rocky reefs and kelp forests on the west coast of the United States. Prior studies documented low levels of genetic divergence between the two species, except at a single microsatellite locus that displayed high divergence, Sra.7‐2. To better characterize genome wide divergence, we scored 25 additional microsatellite loci. Mean neutral divergence between species (FST = 0.01) changed little from prior estimates. Sra.7‐2 continued to be an extreme divergence outlier. Five novel microsatellites within ± 15 kb of Sra.7‐2 were characterized. High divergence, consistently low diversity in S. chrysomelas, and linkage disequilibrium were detected at these loci, suggesting the influence of recent selection. However, coalescent modelling of divergence at neutral and Sra.7‐2 regions showed that initial divergence at Sra.7‐2 was ancient, likely predating divergence at neutral regions. It is therefore unlikely that Sra.7‐2 divergence represents solely recent ecological divergence within one species and may represent the action of recurrent selection. Introgressive gene flow (2NEm) was much higher (>>1) at neutral than Sra.7‐2 regions (<<1) despite evidence that two S. carnatus individuals have recently mixed ancestry at the Sra.7‐2 region. The Sra.7‐2 genomic region is likely one of several regions containing genes involved in initiating and maintaining species integrity. Completion of the final stages of speciation appears to be a slow and ongoing process for these species.

Comparative Population Genetic Analysis of Bocaccio Rockfish Sebastes paucispinis Using Anonymous and Gene-Associated Simple Sequence Repeat Loci

Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high gene-flow marine species off the west coast of North America that experienced strong population decline over the past 3 decades. We used 18 anonymous and 13 gene-associated simple sequence repeat (SSR) loci (expressed sequence tag [EST]-SSRs) to characterize range-wide population structure with temporal replicates. No F(ST)-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between F(ST) and variation or marker class was observed. General linear model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates but did not affect the observed pattern of population structure.

Development of metabolic-process EST-SSR PCR primers within the bocaccio rockfish Sebastes paucispinis

The bocaccio rockfish has historically supported an important fishery on the west coast of North America, and experienced a severe population collapse in the past several decades. Here we report development of 13 EST-SSR PCR primer pairs developed from previously published Sebastes EST databases. All loci are involved in metabolic processes. Diversity in a collection of bocaccio rockfish from off central California ranged from 2 to 17 alleles, with heterozygosities of 0.24–0.92. The loci will be informative in further resolving stock structure issues and possible local adaptation along the species’ broad latitudinal range.

Lack of Mother–Offspring Relationships in White-Tailed Deer Capture Groups

Abstract Behavioral studies of white-tailed deer (Odocoileus virginianus) often assign mother–offspring relationships based on common capture of juveniles with adult deer, assuming that fawns associate closely with mothers. We tested this assumption using genetic parentage to assess mother–offspring relationships within capture groups based on data from 10 polymorphic microsatellite loci. At the 80% confidence level, we assigned maternity to 43% and 51% of juveniles captured with an adult female in 2 respective study areas. Capture with their mother did not differ by sex of juveniles in either study area, and limiting our analysis to capture groups that most represent family groups (i.e., one ad F with 1–3 juv) did not increase maternity assignment (35%). Our results indicate that common capture may be a poor indicator of mother–offspring relationships in many field settings. We recommend genetic verification of family relationships.

Complete mitochondrial genome sequences of five rockfishes (Perciformes: Sebastes)

Abstract Rockfishes of the genus Sebastes rank among the longest-lived vertebrate animals. In order to facilitate comparative genomic research in animal longevity, the complete mitochondrial genome sequences are presented for Sebastes aleutianus, Sebastes minor, Sebastes nigrocinctus, Sebastes rubrivinctus, and Sebastes steindachneri.

Population Genomic Analysis of Brook Trout in Pennsylvania’s Appalachian Region

AbstractInformed conservation of stream fishes requires detailed understanding of the effects of both natural processes and anthropogenic activities on genetic diversity. Brook Trout Salvelinus fontinalis, a salmonid native to eastern North America, typically resides in cold, high-quality stream ecosystems. The species has not only faced historical anthropogenic pressures, but also confronts current and future pressures. In a genetic analysis we used a reduced representation sequencing method (ddRADseq) to characterize 63 individuals from 23 streams where Brook Trout are native in the Appalachian region of Pennsylvania. A total of 2,590 loci passed filtering criteria, and 53% displayed significant association with a major stream drainage basin (Susquehanna or Allegheny; mean FST = 0.085). Mapping of the sequencing reads to the Atlantic Salmon Salmo salar genome revealed no clustering of high interdrainage FST values to specific genome regions. Evidence for genetic heterogeneity within each drainage basin ...