Evolution Behind Barriers

Evolution Behind Barriers

Summary

For nearly a century, man-made dams have land-locked salmonids in many Pacific Northwest Rivers, preventing these anadromous fish from completing their natural life cycle. Anadromous fish are born in rivers and migrate to the ocean as smolts. After maturing to the adult stage, these fish return to their native streams and mate. Inevitably, the creation of dams forces them into alternate life history strategies. Upstream fish cannot outmigrate to the sea and downstream fish are blocked from reaching upriver spawning habitat. Dams created two populations of fish: one group that is land-locked (upstream residents) and a second that retains its anadromy, but over time, their natural abundance has dwindled. Oncorhynchus mykiss, steelhead/rainbow trout populations have been divided by dams in many PNW rivers and may have become adapted to these different environments. Life history variance between each population of fish could prove to be maladaptive when the dams are removed. Whether these changes are due to environmental differences or genetic divisions is not known. My research aims to elucidate the genetic underpinnings of these life history changes. I propose to study the genetic basis of adaptive differentiation between populations of O. mykiss living both above and below artificial barriers. I will use a population genomics approach that employs molecular markers to identify functional differences between populations. By understanding the influence of genetic changes and environmental influences between land-locked and anadromous fish, resource managers can better plan restoration and recolonization efforts in areas such as the Elwha River.

Background

At the beginning of the twentieth century, many dams were constructed in the Pacific Northwest, primarily to harness local hydropower energy and to store water for human usage. However, the creation of these artificial barriers re-engineered the ecosystem and caused landscape-level environmental effects. Dams change both above and below barrier flow, sediment, chemical, and thermal regimes, and introduce different pathogen/parasite loads, and these alterations, in turn, affect the biota of the system (Bu and Seng 1997; Poff and Hart 2002; Thompson et al. 2002).

Currently, a trend exists to either remove ageing dams or restore fish passage. For example, in 2008, the 96 year old Elwha Dam will be breeched and in 2006 the 95 year old Tacoma Water Diversion Dam will restore fish passage. Research shows dams create substantial life-history impacts on anadromous fish species trapped (Hoffman and Winter 1996). Without an opportunity to migrate to food-rich marine waters, residents, above barrier fish, are forced to forage and grow in the less productive riverine ecosystem (Morita et al. 2000). Resident fish are often smaller, mature at different rates, demonstrate different movement patterns, and spawn at different times from their anadromous conspecifics (Morita 2001; Northcote 1992). Over time, these types of genetic life history changes in resident fish could prevent a natural readjustment to an anadromous life cycle. Additionally, it is likely that either dam removal or fish ladders will press upstream and downstream fish into similar spawning habitats within a river. Thus, breeding between these populations could create fish that are ill-suited for anadromy, hindering restoration efforts.

A 2004 research study (Thrower et al. 2004) mated wild anadromous steelhead with recently isolated lake-derived resident steelhead populations that shared the same river drainage ninety years ago. The progeny showed substantial differences in size, growth, smoltification (the time when salmon first migrate from fresh water to marine waters), and maturation when compared to parental populations. In addition, smolts derived from anadromous parents survived better in the marine environment than the smolts of the lake derived fish (Thrower et al. 2004). These data suggest that recent division of O. mykiss populations can lead to genetic differentiation that affects critical life-history strategies important for survival.

Research Questions & Objectives

Conservation biology depends on data that can be used to make informed decisions to ensure the long-term survival of a species. Traditional genetics investigates inheritance and the genes involved with heritable traits, and thus the divergence of characteristics. Conservation genetics brings these non-disparate fields together and supplies resource managers with data regarding a population’s biology, which has historically been collected with neutral molecular markers. These markers may reveal gene flow, bottleneck events, effective population sizes, population origin of individuals, individual inbreeding levels, sex-specific gene flow, founder contribution, and historical/geographical relationships between groups (Avise 2004). This information is critical in modern conservation biology and policy-making.

Interpreting differences between populations’ neutral marker data may not correctly assume adaptive differentiation between populations. Differences in the frequency of neutral markers, however, tell us little about local adaptation, as shifts at adaptive loci can occur much faster than changes in neutral loci (Miller 2001). Local adaptation is a key component to preserving an organism’s survival and reproduction within a particular environment. The field of adaptive genetics aims to bridge a gap within traditional conservation genetics research by understanding functional genetic diversity between populations. Adaptive genetics searches for molecular markers that are linked to complex life history traits. Once identified, these markers can be used to discern adaptive differentiation between populations (Vasemägi & Primmer 2005). Identifying adaptive genetic diversity between populations is a key element in identifying unique populations within a species’ range and will greatly inform management decisions.

My research uses adaptive markers to study above and below dam O. mykiss populations in five different river systems. By using these markers in various river systems, my research seeks to find a dam’s unique genetic impact on above and below barrier O. mykiss populations. A dam’s influence within a short time span (~100 years) can cause rapid evolutionary changes, affecting critical life history strategies.

Two approaches can identify adaptive genes. First, a direct candidate gene approach selects functionally important genes that are likely to be experiencing selection [e.g., the major histocompatibility complex, MHC, which has been associated with pathogen/parasite resistance and mate choice in fishes (Landry et al. 2001; Edwards et al. 1998)]. Second, a population genomics approach takes a genome-wide screen of microsatellite markers found within expressed sequence tags (ESTs) (Li et al. 2004). ESTs are known to have functional importance, and may be involved with metabolic enzymes, structural and storage proteins, disease signaling, and transcription factors (Li et al. 2004). Additionally, microsatellites, a neutral molecular marker, are embedded within ESTs. Consequently, if ESTs are responding to selection, the embedded microsatellite will also demonstrate signatures of selection (Vasemägi et al. 2005). By screening EST-linked microsatellites across multiple river systems, my results will reveal specific traits within O. mykiss that have been influenced by barriers.

My objectives for this study are to

· Employ a multi-locus genomic screen of ~100 EST-linked microsatellites of O. mykiss above and below artificial barriers an

· Use population genomics to identify functionally important adaptive genes

Methodology

Field Collections

We collected fin clip samples from juvenile and adult O. mykiss at sites above and below barriers in the Elwha, Green, Klickitat, Walla Walla, and Russian rivers. Fin clips were collected from above and below dam populations of resident steelhead, rainbow trout, wild steelhead, and any hatchery fish. Tissue was acquired through fish electroshocking, hook and line, or archived hatchery DNA samples.

Elwha River

Collaborative sampling efforts with the National Park Service, Lower Elwha Klallam Tribe and NOAA Fisheries will continue in 2006.

Green River

Current data sets only include two above dam and two below dam locations in this system. Through a collaborative effort with the City of Tacoma Water Group and NOAA Fisheries, expanded sampling will occur in 2006.

Klickitat River

Dr. Shawn Narum of Columbia River Inter-Tribal Fish Commission will be providing above and below barrier O. mykiss tissue samples.

Russian River

Dr. Derek Girman and Kristy Denier have provided tissue samples from O. mykiss populations both above and below natural/artificial barriers in California.

Walla Walla River

Dr. Shawn Narum of Columbia River Inter-Tribal Fish Commission will be providing samples of sympatric rainbow trout and steelhead populations.

Genetic Studies

Currently, I am screening ~50 EST-linked microsatellite markers on above/below dam populations (Vasemägi et al. 2005; Caird 2005). Some markers have been mapped on the O. mykiss genome map (Nichols et al. 2003), which ensures that my markers cover different chromosomes. Prior to running the population genetic analyses, I will test the genetic diversity found at microsatellites to ensure that basic assumptions of microsatellite theory are not violated (Raymond and Rousset 2001; Van Oosterhout 2001). Statistical analyses will identify outlier loci (e.g., F_ST > 2σ) and then use genome maps/BAC libraries to identify adaptive genes of interest (Luikart et al. 2003).

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