Craig A. Steele

Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus)

Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species’ phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath‐Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20 000 years ago), mid‐Pleistocene (800 000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath‐Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid‐Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid‐Pleistocene. Tests for expanding populations using mismatch distributions and ‘g’ distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.

Influence of life-history variation on the genetic structure of two sympatric salamander taxa

Life‐history characteristics are an important determinant of a species’ dispersal abilities. We predict that variation in life history can influence population‐level genetic patterns. To test this prediction, we estimate population‐level genetic structure for two sympatric species of stream‐breeding salamander. The Copes giant salamander (Dicamptodon copei) rarely metamorphoses into a terrestrial adult, thereby limiting overland dispersal and potentially gene flow. In contrast, the Pacific giant salamander (D. tenebrosus) commonly metamorphoses, which is expected to facilitate overland dispersal and gene flow. Three sets of analyses based on microsatellite data support these hypotheses, showing that D. tenebrosus displays minimal population‐level genetic structuring and no pattern of isolation by distance, whereas D. copei displays a high degree of population‐level genetic structure and significant isolation by distance. Specifically, nearly all pairwise FST values were significantly different from 0 between populations of D. copei, with fewer than half the pairwise FST values significant from 0 in D. tenebrosus. Additionally, Structure analyses indicated eight genetic clusters for D. copei but only one genetic cluster for D. tenebrosus. Finally, Mantel tests showed significant correlations between stream and overland distance with genetic distance for D. copei but no significant correlations of either landscape feature for D. tenebrosus at the scale of the study. These results provide a case study of the link between life‐history variation and population genetic patterns while controlling for phylogeny and environmental variation.

Universal mtDNA primers for species identification of degraded bony fish samples

We developed primers for amplifying and sequencing highly degraded mtDNA from diverse fish species. The primers flank a variable 148‐bp fragment within the 12S region of mtDNA. We screened and sequenced 82 samples of bony fishes representing 17 families to confirm cross‐species amplification and identification. Salmonid species were analysed and demonstrate 13 species‐specific SNPs within this region. Based on alignments of additional deposited sequences, these primers are conserved in many other species, making them useful for species identification using degraded DNA samples such as archaeological specimens.

Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout.

Y-chromosome and mitochondrial DNA markers can reveal phylogenetic patterns by allowing tracking of male and female lineages, respectively. We used sequence data from a recently discovered Y-linked marker and a mitochondrial marker to examine phylogeographic structure in the widespread and economically important rainbow trout (Oncorhynchus mykiss). Two distinct geographic groupings that generally correspond to coastal and inland subspecies were evident within the Y-marker network while the mtDNA haplotype network showed little geographic structure. Our results suggest that male-specific behavior has prevented widespread admixture of Y haplotypes and that gene flow between the coastal and inland subspecies has largely occurred through females. This new Y marker may also aid conservation efforts by genetically identifying inland populations that have not hybridized with widely stocked coastal-derived hatchery fish.

Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead

Effective population size (Ne) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate Ne directly. Consequently, genetic methods to estimate Ne have been developed. Two Ne estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers. We challenged the software COLONY with 2,599,961 known relationships and demonstrated that reconstruction of full‐sib and unrelated pairs was greater than 95% and 99% accurate, respectively. However, reconstruction of half‐sib pairs was poor (<5% accurate). Despite poor half‐sib reconstruction, both estimators provided accurate estimates of the effective number of breeders (Nb) when sample sizes were near or greater than the true Nb and when assuming a monogamous mating system. We further demonstrated that both methods provide roughly equivalent estimates of Nb. Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating Nb in steelhead populations in the region.

Maximum Likelihood Estimation of the Proportion of Hatchery-Origin Fish on Spawning Grounds Using Coded Wire Tagging and Parentage-Based Tagging

AbstractFor salmon populations in the Columbia River and Snake River basins, many of which are listed under the U.S. Endangered Species Act of 1973, reliable estimates of the proportion of hatchery-origin adults in spawning areas (p) are needed to assess population status and the genetic and demographic interactions of hatchery- and natural-origin fish. Some hatchery fish receive visible marks, coded wire tags (CWTs), parentage-based tags (PBTs), or all three. This allows one to identify whether fish recovered after release are of hatchery origin. Parentage-based tagging involves genotyping hatchery broodstock and uses parentage assignments as “tags” that identify the origin and brood year of their progeny. We derived a maximum likelihood estimator of p and applied it to the 2012 and 2013 carcass survey data for spring–summer Chinook Salmon Oncorhynchus tshawytscha in the South Fork Salmon River, Idaho. Maximum likelihood estimation was also applied to CWT data and, for investigating the importance of exp...

Polymorphic tetranucleotide microsatellites for Cope's giant salamander (Dicamptodon copei) and Pacific giant salamander (Dicamptodon tenebrosus)

We present primers and amplification conditions for 15 microsatellite loci developed for the Copes giant salamander (Dicamptodon copei), 14 of which are tetranucleotide repeats. Cross‐species amplification revealed 10 of these loci to also be polymorphic in the Pacific giant salamander (Dicamptodon tenebrosus). Several loci produced nonoverlapping allelic ranges between the two species and may be useful in species identification. These polymorphic microsatellite loci are potentially useful for future studies of population genetics in dicamptodontid salamanders.

Comparative genome mapping reveals evidence of gene conversion between Sox9 paralogs of rainbow trout (Oncorhynchus mykiss)

Considerable evidence suggests that one genome duplication event preceded the divergence of teleost fishes and a second genome duplication event occurred before the radiation of teleosts of the family Salmonidae. Two Sox9 genes have been isolated from a number of teleosts and are called Sox9a and Sox9b. Two Sox9 gene copies have also been isolated from rainbow trout, a salmonid fish and are called Sox9 and Sox9?2. Previous evaluations of the evolutionary history of rainbow trout Sox9 gene copies using phylogenetic reconstructions of their coding regions indicated that they both belong to the Sox9b clade. In this study, we determine the true evolutionary history of Sox9 gene copies in rainbow trout. We show that the locus referred to as Sox9 in rainbow trout is itself duplicated. Mapping of the duplicated Sox9 gene copies indicates that they are co-orthologs of Sox9b while mapping of Sox9?2 indicates that it is an ortholog of Sox9a. This relationship is supported by phylogenetic reconstruction of Sox9 gene copies in teleosts using their 3? untranslated regions. The conflicting phylogenetic topology of Sox9 genes in rainbow trout indicates the occurrence of gene conversion events between Sox9 and Sox9?2 which is supported by a number of recombination analyses.