Research | research

Salmonid Conservation Projects

Evaluating intraspecific diversity in Central Valley Chinook salmon over the past 20 years

E.E. Collins, T. Thompson, P. Goertler, M.R. Baerwald, M.H. Meek

Intraspecific diversity allows populations to contend with stochastic and extreme environmental conditions. One system that is representative of notable intraspecific diversity is Chinook salmon in the Central Valley of California, USA. It is the only place in the species range where four adult migration timings (Winter, Spring, Fall, Late-fall) co-occur. These populations are declining and are of serious conservation import; with Winter run listed as Endangered and Spring run listed as Threatened under the Endangered Species Act (ESA). To assess intraspecific diversity of the different runs in the Central Valley, we used RAD-sequencing to genotype outmigrating juveniles every year for over 20 years of sampling. Individuals were assigned to migration timings and subpopulations of origin using a baseline of samples with known origins. We aimed to determine changes in genetic health over time by estimating effective population size (Ne) for each population. Population level genetic health is described by Ne as an estimate of existing genetic variation influenced by genetic drift, selection, mutation, and gene flow of a population. This study provides managers with insights into how anthropogenic forces have impacted the genetic diversity of ESA listed Chinook salmon populations over the past 20 years. Moreover, this study demonstrates a broader example of how an organism with a genetically heritable trait, adapted to stochastic environmental conditions, struggles to persist when faced with an altered habitat and changing climate.

Genetic monitoring of steelhead in the Klickitat River to estimate productivity, straying, and migration timing

E.E. Collins, J.E. Hess, S. Bechtol, N. Romero, S.R. Narum, J.S. Zendt

Salmonids with complex life history variation present challenges for conservation management, but genetic approaches alongside fisheries monitoring can address questions regarding viability of natural populations. We genotyped adult (n=3,108) and juvenile (n=2,624) samples of anadromous Oncorhynchus mykiss that were collected in the Klickitat River, WA, USA at traps in the lower drainage to examine tributary level productivity, straying from outside sources and variation in adult migration timing. Genetic assignment of steelhead from this system indicated that the majority were produced within or near tributaries of the middle Klickitat River (juvenile mean = 72.8%; adult mean = 87.3%). Analyses with parentage-based tagging identified that most hatchery-origin adults assigned to the Skamania Hatchery (80.8%) as expected since this has been the release stock for decades within the Klickitat River drainage. Hatchery-origin adults were also identified from programs operating outside the Klickitat River, which were primarily strays from Snake River hatcheries. Most natural-origin steelhead assigned to the Klickitat River, but there were also natural-origin fish identified as strays from other regions of the Columbia River (22.3% of natural returns). We also examined genes known to be associated with migration timing in adult steelhead observed at the trap and observed a strong relationship between migration date and alleles for early and late migration, but individual outliers were detected across seasons. Our results indicate that genetic variation of steelhead in the Klickitat River has been influenced by hatchery programs as well as natural-origin straying from other sub-basins, but genetic diversity remains high throughout the sub-basin, and both early and late migration alleles are maintained. The genetic diversity present in Klickitat River steelhead may enable this Endangered Species Act listed (threatened) species to better adapt to stochastic environmental conditions compared to less diverse populations.

Whole-genome resequencing to evaluate life history variation in anadromous migration of Oncorhynchus mykiss

E.E. Collins, N. Romero, J.S. Zendt, S.R. Narum

Anadromous fish experience physiological modifications necessary to migrate between vastly different freshwater and marine environments, but some species such as Oncorhynchus mykiss demonstrate variation in life history strategies with some individuals remaining exclusively resident in freshwater, while others undergo anadromous migration. Since there is limited understanding of genes involved in this life history variation across populations of this species, we evaluated the genomic difference between known anadromous (n=39) and resident (n=78) Oncorhynchus mykiss collected from the Klickitat River, WA, USA with whole-genome resequencing methods. Sequencing of these collections yielded 5.64 million single nucleotide polymorphisms (SNPs) that were tested for significant differences between resident and anadromous groups along with previously identified candidate gene regions. While a few regions of the genome were marginally significant, there was one region on chromosome Omy12 that provided the most consistent signal of association with anadromy near two annotated genes in the reference assembly: COP9 signalosome complex subunit 6 (CSN6) and NACHT, LRR and PYD domains-containing protein 3 (NLRP3). Previously identified candidate genes for anadromy within the inversion region of chromosome Omy05 in coastal steelhead and rainbow trout were not informative for this population as shown in previous studies. Results indicate that the significant region on chromosome Omy12 may represent a minor effect gene for male anadromy and suggests that this life history variation in Oncorhynchus mykiss is more strongly driven by other mechanisms related to environmental rearing such as epigenetic modification, gene expression, and phenotypic plasticity. Further studies into regulatory mechanisms of this trait are needed to understand drivers of anadromy in populations of this protected species.

Distribution of genetic variation underlying migration timing in steelhead of the Columbia River basin

E.E. Collins, J.S. Hargrove, T.A. Delomas, and S.R. Narum

Fish migrations are energetically costly, especially when moving between freshwater and saltwater, but are a viable strategy for Pacific salmon and trout (Oncorhynchus spp.) due to the advantageous resources available at various life stages. Anadromous steelhead (O. mykiss ) migrate vast distances and exhibit variation for adult migration phenotypes that have a genetic basis at candidate genes known as greb1L and rock1 . We examined the distribution of genetic variation at 13 candidate markers spanning greb1L, intergenic, and rock1 regions versus 226 neutral markers for 113 populations (n = 9,471) of steelhead from inland and coastal lineages in the Columbia River. Patterns of population structure with neutral markers reflected genetic similarity by geographic region as demonstrated in previous studies, but candidate markers clustered populations by genetic variation associated with adult migration timing. Mature alleles for late migration had the highest frequency overall in steelhead populations throughout the Columbia River, with only 9 of 113 populations that had a higher frequency of premature alleles for early migration. While a single haplotype block was evident for the coastal lineage, we identified multiple haplotype blocks for the inland lineage. The inland lineage had one haplotype block that corresponded to candidate markers within the greb1L gene and immediately upstream in the intergenic region, and the second block only contained candidate markers from the intergenic region. Haplotype frequencies had similar patterns of geographic distribution as single markers, but there were distinct differences in frequency between the two haplotype blocks for the inland lineage. This may represent multiple recombination events that differed between lineages where phenotypic differences exist between freshwater entry versus arrival timing as indicated by Micheletti et al. (2018a). Redundancy analyses were used to model environmental effects on allelic frequencies of candidate markers, and significant variables were migration distance, temperature, isothermality, and annual precipitation. This study improves our understanding of the spatial distribution of genetic variation underlying adult migration timing in steelhead as well as associated environmental factors and has direct conservation and management implications.

Antarctic Projects

Species diversity of adult and larval spionids (Spionidae; Polychaeta) in the Southern Ocean

E.E. Collins, K.M. Halanych, and A.R. Mahon

While commonly found in the plankton, our current understanding of spionid biodiversity in Antarctica is limited by the difficulties of sampling the region and a lack of taxonomic expertise in the identification of spionid species, particularly for larval life history stages. With difficulties utilizing morphological characters to determine species diversity within the Spionidae, we chose to use DNA barcoding as a tool for taxonomic identification. Samples from throughout the Western Antarctic, including the Peninsula, Bellingshausen, Amundsen, and Ross Seas were collected, DNA was extracted, and standard genetic barcoding methods were applied. A fragment of the mitochondrial cytochrome c oxidase subunit I (COI) was used as our barcode marker to connect our knowledge of larval populations to adults collected from throughout the region. Additionally, the genetic barcodes generated in this study will also help determine if any of the collected organisms are cryptic species of spionids or potentially previously unrecorded species from the regions sampled. Future directions will include expanded sampling for both adults and larvae from other regions of the Southern Ocean and also to potentially utilize genetic and morphological characters to describe new species of spionids from the region.

Phylogeography of Ammothea (Arthropoda, Pycnogonida) in the Southern Ocean

E.E. Collins, K.M. Halanych, and A.R. Mahon

Pycnogonids, or sea spiders, are obligate marine arthropods distributed across all oceans. Geographic and subsequently biological isolation has occurred in the Southern Ocean since the creation of the Antarctic Circumpolar Current (ACC) approximately 41 million years ago resulting in many taxa that are endemic to the region. Sea spiders in Antarctic waters are exceedingly diverse (20% of all species are present) and many are only found in the Southern Ocean (64% of all Antarctic sea spiders are endemic). The use of molecular tools has provided a greater understanding of sea spider biodiversity, particularly for those groups thought to have circumpolar distributions. This study employs mitochondrial and nuclear markers to investigate diversity and phylogeographic relationships within the Ammotheidae, a common sea spider family in the Southern Ocean. Sampling throughout the Western Antarctic Peninsula and seas (Bellingshausen, Amundsen, and Ross Seas) provides new insight for both the biodiversity and potential cryptic species within the family and also for population connectivity across large distances around the continent.

Phylogeography of Nymphon australe (Pycnogonida, Nymphonidae) Populations in the Southern Ocean

E.E. Collins, M.P. Galaska, K.M. Halanych, and A.R. Mahon

Within the Southern Ocean, the Antarctic Circumpolar Current is hypothesized to facilitate a circumpolar distribution for many taxa, even though some, such as pycnogonids, are assumed to have limited ability to disperse, based on brooding life histories and adult ambulatory capabilities. With a number of contradictions to circumpolarity reported in the literature for other pycnogonids, alternative hypotheses have been explored, particularly for Nymphon australe, the most common species of Pycnogonida (sea spider) in the Southern Ocean. Glacial events have been hypothesized to impact the capacity of organisms to colonize suitable areas without ice coverage as refuge and without the eurybathic capacity to colonize deeper areas. In this study, we examine populations of one presumed circumpolar species, the pycnogonid N. australe, from throughout the Western Antarctic, using a 2b-RAD approach to detect genetic variation with single-nucleotide polymorphisms. Using this approach, we found that N. australe included two distinct groups from within >5000-km sampling region. By using a discriminant analysis of principle components, sparse nonnegative matrix factorization, and admixture coefficient analysis, two distinctive populations were revealed in the Western Antarctic: one covered distances greater than 5000 km (Weddell, Western Antarctic Peninsula, and Ross Sea), and the other shared limited connectivity entrained within the Amundsen Sea. Under further scrutiny of the 3086 single-nucleotide polymorphisms in the data set, only 78 loci had alignment stacks between the two populations. We propose that the populations analyzed are divergent enough to constitute two different species from within this common Antarctic genus known for its phenotypic plasticity.

Phylogeny of all Pycnogonid Families Determined with Mitochondrial Genomes

E.E. Collins, K.M. Halanych, and A.R. Mahon

Pycnogonids (common name: sea spiders) are widely distributed globally and are a speciose basal class in Arthropoda. There are ten putative families and over 1,300 described species of pycnogonids. The phylogenetic place of sea spiders within Arthropoda has long been disputed and remains unresolved due to morphological oddities and extremely reduced forms. The most recent studies are in agreement that sea spiders have evolved within Chelicerata (Subphylum of the Arthropoda phylum) based on evolutionary relationships discerned from morphological and molecular traits. The resolution of evolutionary patterns within Pycnogonida is even murkier. To resolve sea spider evolutionary relationships at the family level, the mitochondrial genome for at least one individual from all putative families was sequenced. The mitochondrial genome was chosen because it is conserved enough to resolve deeper node relationships. In comparison to nuclear genes, which deal with the expression of traits, mitochondrial genes are more conserved because they code for basic functions of cellular energy production. These sequences will produce a dataset robust enough to inform pycnogonid evolutionary relationships at the family level with more confidence than previous studies.