selected publications
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academic article
- The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest. Molecular Ecology. 31:4402-4416. 2022
- Genomic evidence of an ancient inland temperate rainforest in the Pacific Northwest of North America. Molecular Ecology. 31:2985-3001. 2022
- Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity. MBio. 13. 2022
- Genomic resolution of cryptic species diversity in chipmunks. Evolution. 2022
- Comparative phylogeography of two Northern Rocky Mountain endemics: the widespread Anguispira kochi occidentalis and the narrow-range Anguispira nimapuna (Gastropoda: Discidae). Biological Journal of the Linnean Society. 133:817-834. 2021
- Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). Systematic Biology. 2021
- No evidence for phylosymbiosis in western chipmunk species. FEMS Microbiology Ecology. 96. 2020
- Phylogeography, Genetic Diversity, and Connectivity of Brown Bear Populations in Central Asia. PLOS One. 14:e0220746. 2019
- Integrating life history traits into predictive phylogeography. Molecular Ecology. 28:2062-2073. 2019
- A carnivores' oasis? An isolated fisher (Pekania pennanti) population provides insight on persistence of a metapopulation. Conservation Genetics. 20:585-596. 2019
- The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. PeerJ. 7:e6334. 2019
- Predicting plant conservation priorities on a global scale. Proceedings of the National Academy of Sciences of the United States of America. 115:13027-13032. 2018
- Taxonomy and biogeography of Hemphillia (Gastropoda: Pulmonata: Arionidae) in North American rainforests, with description of a new species (Skade’s jumping-slug, Hemphillia skadei sp. nov.). Canadian Journal of Zoology. 96:305-316. 2018
- Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Molecular Ecology. 27:1012-1024. 2018
- Testing for the presence of cryptic diversity in tail-dropper slugs (Prophysaon) using molecular data. Biological Journal of the Linnean Society. 124:518-532. 2018
- Demographic Model Selection using Random Forests and the Site Frequency Spectrum.. Molecular Ecology. 26:4562-4573. 2017
- Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias). Genome Biology and Evolution. 9:7-19. 2017
- Identifying cryptic diversity with predictive phylogeography. Proceedings of the Royal Society B: Biological Sciences. 283. 2016
- Genetic Structure across Broad Spatial and Temporal Scales: Rocky Mountain Tailed Frogs (Ascaphus montanus; Anura: Ascaphidae) in the Inland Temperate Rainforest. Journal of Heredity. 106:700-710. 2015
- Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees.. Molecular Biology and Evolution. 30:154-166. 2013
- Species limits and integrated taxonomy of the Idaho ground squirrel (Urocitellus brunneus): genetic and ecological differentiation. Journal of Mammalogy. 93:589-604. 2012
- Generalized Mixture Models for Molecular Phylogenetic Estimation. Systematic Biology. 61:12-21. 2012
- Phylogeny Estimation of the Radiation of Western North American Chipmunks (Tamias) in the Face of Introgression Using Reproductive Protein Genes. Systematic Biology. 61:44-62. 2012
- A Toxoplasma gondii protein with homology to intracellular type Na+/H+ exchangers is important for osmoregulation and invasion. Experimental Cell Research. 317:1382-1396. 2011
- Approximating Model Probabilities in Bayesian Information Criterion and Decision-Theoretic Approaches to Model Selection in Phylogenetics. Molecular Biology and Evolution. 28:343-349. 2011
- Examination of nuclear loci across a zone of mitochondrial introgression between Tamias ruficaudus and T. amoenus. Journal of Mammalogy. 91:1389-1400. 2010
- Assessment of Substitution Model Adequacy Using Frequentist and Bayesian Methods. Molecular Biology and Evolution. 27:2790-2803. 2010
- Sexual Signal Evolution Outpaces Ecological Divergence during Electric Fish Species Radiation. American Naturalist. 176:335-356. 2010
- Effects of parameter estimation on maximum-likelihood bootstrap analysis. Molecular Phylogenetics and Evolution. 56:642-648. 2010
- Introgression at differentially aged hybrid zones in red-tailed chipmunks. Genetica. 138:869-883. 2010
- Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudus). Molecular Ecology. 18:3097-3109. 2009
- The Golden Rule of Reviewing. American Naturalist. 173:E155-E158. 2009
- Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular Ecology. 17:1313-1327. 2008
- Does choice in model selection affect maximum likelihood analysis?. Systematic Biology. 57:76-85. 2008
- The complete nuclear estrogen receptor family in the rainbow trout: Discovery of the novel ER alpha 2 and both ER beta isoforms. Gene. 392:164-173. 2007
- Allozyme and mitochondrial DNA variation in the tailed frog (Anura : Ascaphus): The influence of geography and gene flow. Herpetologica. 62:235-258. 2006
- Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata : Dicamptodontidae). Molecular Phylogenetics and Evolution. 36:90-100. 2005
- Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation. Molecular Biology and Evolution. 22:691-703. 2005
- A multi-compartmented glacial refugium in the northern Rocky Mountains: Evidence from the phylogeography of Cardamine constancei (Brassicaceae). Conservation Genetics. 6:895-904. 2005
- Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Molecular Ecology. 14:255-265. 2005
- Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Molecular Biology and Evolution. 22:1386-1392. 2005
- Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: Hypothesis testing within a comparative phylogeographic framework. Evolution. 59:1639-1652. 2005
- Model selection in phylogenetics. Annual Review of Ecology Evolution and Systematics. 36:445-466. 2005
- Testing population genetic structure using parametric bootstrapping and MIGRATE-N. Genetica. 124:71-75. 2005
- Exploring population genetic structure in three species of Lesser Antillean bats. Molecular Ecology. 13:2557-2566. 2004
- Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Systematic Biology. 53:781-792. 2004
- Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology. 52:674-683. 2003
- Phylogeography and introgressive hybridization: Chipmunks (genus Tamias) in the northern Rocky Mountains. Evolution. 57:1900-1916. 2003
- Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia : Sciuridae), and phylogeographic inferences for northwest North America. Molecular Phylogenetics and Evolution. 26:389-408. 2003
- Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data. Molecular Biology and Evolution. 19:762-776. 2002
- Phylogeography of the red-tailed chipmunk (Tamias ruficaudus), a northern Rocky Mountain endemic. Molecular Ecology. 10:2683-2695. 2001
- Phylogeography of the tailed frog (Ascaphus truei): Implications for the biogeography of the Pacific Northwest. Evolution. 55:147-160. 2001
- Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?. Systematic Biology. 50:723-729. 2001
- Phylogeography of Peromyscus furvus (Rodentia; Muridae) based on cytochrome b sequence data. Molecular Ecology. 9:2129-2135. 2000
- Comparative phylogeography of mesoamerican highland rodents: Concerted versus independent response to past climatic fluctuations. American Naturalist. 155:755-768. 2000
- The emerging statistical perspective in systematics: A comment on Mares and Braun. Journal of Mammalogy. 81:260-270. 2000
- Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA. Molecular Phylogenetics and Evolution. 13:82-92. 1999
- Phylogeny of the deuterostomes: A molecular analysis of large and small subunit ribosomal RNA gene sequences. American Zoologist. 39:135A-135A. 1999
- The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models. Molecular Biology and Evolution. 16:1347-1356. 1999
- 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes. Molecular Biology and Evolution. 15:1706-1718. 1998
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book section
- Maximum-likelihood methods for phylogeny estimation. Ed. 395. 2005
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chapter
- Phylogeny inference based on parsimony and other methods using PAUP*. Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing. 267-312. 2009
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dataset