Genetic And Demographic Consequences Of Lake And River Habitat Fragmentation On Fishes In Vermont

Globally, habitat fragmentation has had a major impact on the conservation and management of many species and is one of the primary causes of species extinction. Habitat fragmentation is loosely defined as a process in which a continuous habitat is reduced to smaller, disconnected patches as the result of habitat loss, restriction of migration or the construction of barriers to movement. Aquatic systems are particularly vulnerable to habitat fragmentation, and today an estimated 48% of rivers are fragmented worldwide. My dissertation evaluates how habitat fragmentation has influenced the populations of four different species of fish in the Lake Champlain basin. In chapter 1 I summarize the current state of habitat fragmentation research, I broadly describe habitat fragmentation, review how habitat fragmentation pertains to population genetics, and describe the legacy of habitat fragmentation in the Lake Champlain basin. In chapters 2, 3 and 4 I evaluate and discuss the impact of nine lake causeways on the population structure of slimy sculpin (Cottus cognatus), rainbow smelt (Osmerus mordax), and lake whitefish (Coregonus clupeaformis). The genetic effects of causeways are limited. However, causeways appear to have had a significant influence on rainbow smelt demographics, and the genetic structure observed in lake whitefish may be a product of reduced effective population size resulted from commercial harvest in the late 1800s. In chapter 5 I evaluate how the basin-wide population of tessellated darters (Etheostoma olmstedi) is naturally structured throughout Lake Champlain and three different major tributaries and evaluates the effect that different types of habitat fragmentation (dams, causeways, and natural fall lines) have on tessellated darter populations. Tessellated darters appear to be highly structured by river drainage but not by dams, causeways or fall lines. My dissertation highlights how comparative population genetic studies can be used to identify patterns of isolation within large populations. My results stress the value of reporting both the presence and absence of barrier induced population sub-structuring

A New GTSeq Resource to Facilitate Multijurisdictional Research and Management of Walleye Sander Vitreus

Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research, which relies on data about specific markers in an organism\u27s genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact of this issue and provide a common starting place for new research. Genotyping-in-thousands (GTSeq) is one approach used to create standardized marker panels for nonmodel organisms. Here, we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye (Sander vitreus) from the Great Lakes region of North America. High genome-coverage sequencing conducted using RAD capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype markers were chosen, which were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave-one-out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false-positive rates of parent-offspring and full-sibling kinship identification were found to be low. Finally, genotypes could be consistently scored among separate sequencing runs \u3e94% of the time. Results indicate that the GTSeq panel that we developed should perform well for multijurisdictional walleye research throughout the Great Lakes region

Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research

Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA‐based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome‐db.org) provides an intuitive solution for maintaining links between genetic datasets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDC’s sequence read archive (SRA) while maintaining persistent links to standards‐compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Background: Yellow perch, Perca flavescens, is an ecologically and commercially important species native to a large portion of the northern United States and southern Canada. It is also a promising candidate species for aquaculture. No yellow perch reference genome, however, has been available to facilitate improvements in both fisheries and aquaculture management practices. Findings: By combining Oxford Nanopore Technologies long-reads, 10X genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). Genome annotation identified 41.7% (366 Mb) of repeated elements and 24,486 genes including 16,579 genes (76.3%) significantly matching with proteins in public databases. We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping test which accurately differentiates XY genetic males (amhr2by+) from XX genetic females (amhr2by−). Conclusions: Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries, and aquaculture research. In addition, the characterization of the amhr2by gene as a candidate sex determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes