Daniel Gómez Uchida

 Nye beach Newport OR   Gros Morne National Park Newfoundland Canada   Peggy's Cove Halifax Canada   Greenlake Seattle WA



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My research uses genetic and genomic data to address ecological and evolutionary questions among natural populations. Although I have hitherto focused on nonmodel aquatic organisms (mostly fishes), next generation sequencing technology is now enabling unprecedented access to genomic resources that a decade ago were exclusive to a few model species. Molecular bioinformation allows inference of past and contemporary factors responsible for the origin and maintenance of genetic diversity, which can be natural (climate, landscape, habitat quality and quantity, life-history) or anthropogenic in nature (overexploitation, habitat and population fragmentation). Collectively, they will  affect a population's genetic properties - namely size, gene flow, and inbreeding - and thus its persistence and ability to adapt. Assessing and understanding these factors can help conservation biologists and resource managers ensure long-term sustainability of ecologically and economically important wild populations. So far my research has developed along three main lines:

Population Genomics

Fall ChinookDuring my tenure at the International Program for Salmon Ecological Genetics (IPSEG),  School of Aquatic and Fishery Sciences (SAFS) of the University of Washington, I developed and applied genomic tools that can further our understanding on how salmon populations diverge and adapt to discrete environments wherein they reproduce. One initiative involves next generation sequencing of Chinook salmon (Oncorhynchus tshawytscha) transcriptomes for single nucleotide polymophisms (SNPs) characterization. In partnership with the Washington Department of Fish and Wildlife (WDFW), this research seeks to address fundamental management questions, such as ascertaining the origin of Puget Sound Chinook salmon populations known to have a shallow evolutionary history. Other projects encompass spatial and temporal analyses of SNP diversity among sockeye (Oncorhynchus nerka) and chum salmon populations (Oncorhynchus keta) from Alaska. This is a joint initiative between IPSEG, SAFS, and the Alaska Department of Fish and Game (ADFG) to answer population-level questions related to (i) philopatry/dispersal, (ii) local adaptation in the face of gene flow, and (iii) temporal population stability and effective population size (Ne), all using  a combination of population-, individual-, and coalescent-based methods. 

Molecular Ecology

Landlocked Arctic charr Landscape, habitat, and ecological attributes shape the genetic properties of freshwater fish populations. I addressed this topic using single and multispecies approaches. Firstly, I analyzed the degree of reproductive isolation between sympatric morphs of Arctic charr (Salvelinus alpinus) from Gander Lake, Newfoundland. Divergent forms (also known as ‘morphotypes’, or ‘ecotypes’) within populations are characterized by incomplete speciation and large differences in resource use (e.g., food, habitat, spawning grounds, and/or migratory routes). Genetic monitoring of this and other species complexes can help us understand how speciation occurs and biodiversity is maintained. Secondly, I studied a pristine community of three salmonids (brook trout Salvelinus fontinalis, Atlantic salmon Salmo salar, and Arctic charr Salvelinus alpinus) distributed in seven interconnected ponds in the highlands of Gros Morne National Park (Newfoundland, Canada). Such comparative framework can gauge the importance of life-history and landscape attributes impacting genetic diversity and population size. In addition, holistic approaches to conservation of wildlife involving community- and ecosystem-based frameworks have been increasingly advertised as viable solutions in the sustainability of biological systems. This work is part of an ongoing collaboration with Daniel E. Ruzzante and Thomas W. Knight that started during my tenure at Dalhousie University (Canada) as Visiting Postdoctoral Fellow for Parks Canada.

Conservation Genetics

Canary rockfishWorldwide declines of economically important marine populations have primed the development of multidisciplinary approaches to conservation. Among these disciplines, molecular population genetics provides an efficient and inexpensive way to measure spatial scales of dispersal and local adaptation, as well as estimates of effective population size (Ne). Such information is pivotal for the implementation of spatial planning in order to mitigate losses of abundance and genetic diversity. I utilized a variety of molecular tools (allozymes, AFLPs, and microsatellites) to investigate these and related topics in populations of Chilean hairy edible crab (Cancer setosus) during my master of science program at Universidad de Concepcion (Chile) and The University of Hull (UK), and subsequently in species of Pacific rockfishes (genus Sebastes) during my doctoral program at Oregon State University (USA). Here I focused on darkblotched (Sebastes crameri), canary (Sebastes pinniger), and black rockfish (Sebastes melanops) to address questions regarding population connectivity employing genetic as well as ecological methods (e.g., otolith microchemistry). Much of this work was done cooperatively with my major professor, Michael A. Banks, Jessica A. Miller, and the Trawl Survey Team from NOAA Fisheries at the Hatfield Marine Science Center in Newport, Oregon. Currently I am joining expertise with Vince P. Buonaccorsi (Juniata College) to gauge the importance of Ne influencing gene flow and genetic diversity in a coastal rockfish assemblage off California.