Daniel Gomez-Uchida

daniel.gomez-uchida@lifetime.oregonstate.edu

Research Interests:

In general, my scientific interests encompass (and mix) several disciplines in evolutionary biology such as population genetics, molecular biology and population ecology. I have a special focus on the evolutionary processes that shape the genetic diversity and demography of marine populations with emphasis in fishery-exploited stocks.
I am currently investigating two rockfish species that inhabit the northeastern Pacific—canary (Sebastes pinniger) and darkblotched rockfish (S. crameri). Rockfishes are a highly speciose group and one of the few marine examples of explosive radiation. They have been also the targets of a historical fishery since the 1940s. In recent years, biomass of some representatives including canary and darkblotched has shrunk considerably, even below sustainable levels.

Specific topics of my investigation include:

Dispersal and connectivity among populations—Tracking movements of marine organisms in real time is difficult and requires costly technology. The combination of theoretical population genetics and molecular tools provides an inexpensive way to measure the historical (past and contemporary) connectivity among local populations. One big revelation from the steady development of new molecular “tracers” is that, for many species, oceans are not a homogeneous “soup”; instead, organisms with supposedly high potential to disperse show that this connectivity decays with geographic separation (isolation by distance), suggesting subtle oceanographic and/or behavioral mechanisms of larval and/or adult retention.

Demographic genetics of populations—The combination of components from life history theory (e.g., age structure, survivorship, mortality and reproduction) and genotypic data has provided us with a quantitative measure of effective population size (Ne). Ne is a parameter of great evolutionary interest, as it represents the number of successful breeders in a population and dictates the pace of temporal genetic change. The genetic evidence hitherto shows that marine populations have effective sizes several orders of magnitude smaller than census sizes. While this difference could be explained by a large variance in reproductive success among individuals, I additionally investigated potential methodological constraints that might affect precision in Ne estimates.

Genetic effects of historical fishing—Polymerase Chain Reaction (PCR) in molecular biology has enabled to explore genome sequences of interest in diverse areas—e.g., forensics and phylogenetics—from small amounts of DNA recovered from tissue left in a crime scene or stored in a museum. Likewise, scale and otolith collections are commonplace in fishery research facilities, since the application of statistical age-based models. These biological structures literally represent an “ancient genetic library”, and can allow a temporal comparison of fish stocks before and after intense harvesting. At present, I am analyzing an archived collection of canary rockfish (S. pinniger) otoliths dating from 1970 to 1990, a period wherein canary rockfish’s abundance shrank considerably.

Genomic analyses of microsatellite flanking regions (MFR)—Sequences where microsatellite primers anneal (or “flank”) can reveal interesting evolutionary patterns at the molecular level. Unlike microsatellites themselves, these regions do not experience high mutation rates and can be fairly conserved across millions of year of evolution. They are therefore attractive from a phylogenetic standpoint. My objective is to explore the use of these MFR for the study of rockfish evolution and speciation. A summer intern and I will be researching some of these sequences in canary and black rockfish.

Publications:

Submitted:

Gomez-Uchida, D. & M. A. Banks. (2005) Integrating Temporal and Spatial Scales in Rockfish Genetics: Shaping Conservation and Management Goals. In: Biology, Assessment, and Management of North Pacific Rockfishes. Proceedings from the 23rd Lowell Wakefield Symposium in Anchorage. Alaska Sea Grant.

Gomez-Uchida, D. & M. A. Banks (2005) All microsatellites are not created equal: bias and precision in temporal estimates of effective population size for darkblotched rockfish Sebastes crameri. Conservation Genetics.

Peer-Reviewed:

Miller, J. A., M. A. Banks, D. Gomez-Uchida & A. L. Shanks (2005) Population structure in black rockfish (Sebastes melanops): a comparison between otolith microchemistry and microsatellite DNA. Canadian Journal of Fisheries and Aquatic Sciences 62: 2189-2198.

Gomez-Uchida, D. & M. A. Banks (2005) Microsatellite analyses of spatial genetic structure in darkblotched rockfish (Sebastes crameri): is pooling samples safe? Canadian Journal of Fisheries and Aquatic Sciences 62: 1874-1886.

Gomez-Uchida, D., E. A. Hoffman, W. R. Ardren & M. A. Banks (2003) Microsatellite markers for the heavily exploited canary (Sebastes pinniger) and other rockfish species. Molecular Ecology Notes 3:387-389.

Gomez-Uchida, D., D. Weetman, L. Hauser, R. Galleguillos & M. Retamal (2003) Allozyme and AFLP analysis of genetic population structure in the hairy edible crab Cancer setosus from the Chilean coast. Journal of Crustacean Biology 23(2): 486-494 (pdf).

Aliaga, B., D. Gomez-Uchida & S. Neira (2001) Bioeconomic analysis of pacific sardine (Sardinops sagax) y anchovy (Engraulis ringens) fishery from northern Chile. Invest. Mar. Valparaíso 29(2): 15-23 (available at http://www.scielo.cl).

Non-Refereed:

Gomez-Uchida, D. & M. A. Banks (2005) Microsatellites reveal regional genetic structure and effective population size in darkblotched rockfish (Sebastes crameri). In Conservation of Pacific Rockfishes: Ecological Genetics and Stock Structure. Paul Moran (ed.) NOAA Technical Report (in press).

AWARDS AND SCHOLARSHIPS

Mia J Tegner Award, MCBI (California) (US$ 3,000) 2004
Richard Carlson Scholarship, Dept. Fisheries & Wildlife (US$ 1,500) 2004
American Fisheries Society, Student Travel Award (US$ 500) 2003
Mamie Markham Award, Hatfield Marine Science Center (US$ 9,400) 2002-03
Research fellowship (M.S.), Universidad de Concepcion 1998-99
INTERCAMPUS scholarship, Spanish Cooperation Agency 1996
“Facultad de Ciencias Naturales y Oceanograficas”, best graduate 1996
“Dr. Parmenio Yanez”, Dept of Zoology, Universidad de Concepcion 1996
“Universidad de Concepcion”, Summa Cum Laude 1995

MEETINGS/ WORKSHOPS

135th American Fisheries Society annual meeting, Anchorage 2005
(Speaker)
Gomez-Uchida, D. & M. A. Banks. (2005) Integrating Temporal and
Spatial Scales in Rockfish Genetics: Shaping Conservation and
Management Goals. 23rd Lowell Wakefield Symposium.

American Association for the Advancement of Science 2005
Annual Meeting Symposium “New findings Challenge
Foundations of Fisheries Management” (Invited speaker)
Gomez-Uchida, D. Successful breeders are surprisingly few and far between:
Implications for fisheries management.

National Marine Fisheries Service Workshop (Seattle, US) 2004
Conservation of Pacific Rockfishes: Ecological Genetics
and Stock Structure (Invited speaker)
Gomez-Uchida, D. and Michael Banks. Population genetics and demography of darkblotched rockfish: Sampling issues, oceanographic barriers and low effective
size.

13th Western Groundfish Conference (Victoria, Canada) 2004
Gomez-Uchida, D. and Michael Banks. Microsatellites reveal genetic structure,
effective population size and species misidentification of darkblotched rockfish
(Sebastes crameri) in the northeastern Pacific.

133rd American Fisheries Society annual meeting (Quebec, Canada) 2003
Gomez-Uchida, D. and Michael Banks. Fishing effects upon molecular variation
in overfished rockfish species: Demographic genetics of darkblotched rockfish
Sebastes crameri.

132nd American Fisheries Society annual meeting (Baltimore, US) 2002
Gomez-Uchida, D. and Michael Banks. Genetic and ecological inference on
ranges and limits of stock structure among four rockfish life-history types. I.
Microsatellite analysis of genetic population structure in canary rockfish
Sebastes pinniger off Washington and Oregon coast.

XXI Marine Science meeting - Universidad de Valparaiso (Chile) 2001
Gomez-Uchida, D., R. Galleguillos and Marco A. Retamal. Genetic population
structure of the Hairy Edible crab Cancer setosus Molina in the Chilean coast.
I. Analysis of allozyme variation.

XXIII Annual meeting of the Chilean Genetics Society 2000
Organization committee

XVI Marine Science meeting - Universidad de Concepcion (Chile) 1996
Gómez-Uchida, D., Galleguillos, R. & C. Oyarzún. “Genetic variability of the rock cod Eleginops maclovinus (Valenciennes, 1830) (Pisces, Perciformes, Eleginopsidae)”