Publications
For the most up-to-date list of lab publications, visit our Google Scholar pages! Here you will find additional information and links for each publication.
2024
Lotterhos KE. Principles in experimental design for evaluating genomic forecasts. In Press at Methods in Ecology and Evolution. http://doi.org/10.1111/2041-210X.14379
Lotterhos KE, Bernal MA, Phifer-Rixey M, Hanley T. Lighting pathways to success in STEM: A virtual Lab Meeting Program (LaMP) mutually benefits mentees and host labs. Proceedings of the Royal Society B: Biological Sciences. A Biological Practices Paper. Press
Lotterhos KE. Interpretation issues with “genomic vulnerability” arise from conceptual issues in local adaptation and maladaptation. Evolution Letters. https://doi.org/10.1093/evlett/qrae004 . Blog Post
2023
Lotterhos KE. 2023. The paradox of adaptive trait clines with non-clinal patterns in the underlying genes. Proceedings of the National Academy of Sciences
Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Mitchell ED, Peichel CL, Rafajlovic M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology.
Bogan S, Johns J, Griffiths J, Davenport D, Smith S, Schaal S, Downey-Wall A, Lou N, Lotterhos KE, Guidry M, Rivera H, McGirr J, Puritz JB, Roberts S, Silliman K. A dynamic web resource for robust and reproducible genomics in nonmodel species: marineomics.io. Methods in Ecology and Evolution.
Puritz J, Guo X, Hare Matthew, He Y, Hillier L, Jin S, Lotterhos KE, Liu M, Minx P, Modak T, Proestou D, Rice E, Tomlinson C, Warren W, Witkop E, Zhao H, Gomez-Chiarri M. A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference. Molecular Ecology Resources
Guo X, Puritz J, Wang Z, Proestou D, Allen S Jr., Small J, Verbyla K, Zhao H, Haggard J, Chriss N, Zeng D, Lundgren K, Allam B, Bushek D, Carnegie R, Gomez-Chiarri M, Hare M, Hollenbeck C, La Peyre J, Liu M, Lotterhos KE, Plough L, Rawson P, Saillant E, Rikard S, Varney R, Wikfors G, Wilbur A. Development and evaluation of high-density SNP arrays for the eastern oyster Crassostrea virginica. Marine Biotechnology. 25, 174–191
2022
McNally EM, Downey-Wall A, Titmuss F, Cortina C, Lotterhos KE, and Ries JB. 2022. Parental exposure of Eastern oysters (Crassostrea virginica) to ocean acidification mitigates negative effects of elevated pCO2 on larval shell growth and morphology. Limnology and Oceanography.
Schaal SM and Lotterhos KE. 2022. Inversion Invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow. Phil. Trans. B. (Special Issue on Supergenes) [Research featured in Quanta Magazine's article on supergenes]
Berdan EL, Flatt T, Kozak GM, Lotterhos KE, Wielstra B. 2022. Genomic architecture of supergenes: Connecting form to function. Phil. Trans. B. (Special Issue on Supergenes)
Lotterhos KE, Fitzpatrick MC, Blackmon H. 2022. Simulation Tests of Methods in Evolution, Ecology, and Systematics: Pitfalls, Progress, and Principles. Annual Reviews in Ecology, Evolution, and Systematics. 53:113-136.
Láruson AJ, Haller B, Keller S, Fitzpatrick MC, and Lotterhos KE. 2022. A critical assessment of measuring genomic vulnerability with gradient forests. Evolutionary Applications. 15(3): 403–416.
Albecker MA, Trussell GC, Lotterhos KE. 2022 A novel analytical framework to quantify co-gradient and countergradient variation. Ecology Letters.
2021
Lotterhos KE, Albecker MA, Trussell GC. 2021. Evolution in Changing Seas. Proceedings of the Royal Society B 288: 20212443 (Special Feature on Evolution in Changing Seas)
Albecker MA, Wilkins LGE, Krueger-Hadfield SA, Bashevkin SM, Hahn MW, Hare MP, Kindsvater HK, Sewell MA, Lotterhos KE, Reitzel AM. 2021. Does a complex life cycle promote or constrain adaptation to environmental change? Genome-informed approaches and insights for characterizing selection across stages of a life cycle. Proceedings of the Royal Society B 288: 20212122 (Special Feature on Evolution in Changing Seas)
Unzueta-Martínez A, Downey-Wall AM, Cameron LP, Agar JN, Ries JB, Lotterhos KE, Bowen JL. Ocean acidification alters the diversity and structure of oyster associated microbial communities. Limnology and Oceanography Letters 6: 348-359
Trigg SA, Venkataraman YR, Gavery MR, Roberts SB, Bhattacharya D, Downey-Wall A, Eirin-Lopez J, Johnson KM, Lotterhos KE, Puritz JB, and Putnam HM. 2021. Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Molecular Ecology Resources.
Schaal SM*, Lotterhos KE. 2021. Comparative thermal performance among four young-of-the-year temperate reef fish species. ICES Journal of Marine Science fsab072
Bitter M, Wong J, Dam H, Donelan S, Kenkel C, Komoroske L, Nickols K, Rivest E, Salinas S, Burgess S, Lotterhos KE. Fluctuating selection and global change: a synthesis and review on disentangling the roles of climate amplitude, predictability, and novelty. In press at Proceedings of the Royal Society B (Evolution in Changing Seas Special Issue) [Link]
Lotterhos KE, Láruson AJ*, Jiang LQ. 2021. Novel and disappearing climates in the global sea surface from 1800 to 2100. Nature Scientific Reports 11, 15535. [NOAA press release][Dryad][Top 100 Ecology paper; Top 100 Earth Science paper; Editor's choice: Climate Change]
2020
Downey-Wall AM*, Cameron LP, Ford BM, McNally EM, Venkataraman YR, Roberts SB, Ries JB, Lotterhos KE. 2020. Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica). Frontiers in Marine Science 7:566419. (Special Issue in Marine Environmental Epigenetics) [Link][Dryad]
Láruson AJ*, Yeaman S, Lotterhos KE. 2020. The importance of genetic redundancy in evolution. Trends in Ecology and Evolution 35:809-822. [Link]
Venkataraman YR, Downey-Wall AM, Ries J, Westfield I, White SJ, Roberts SB, Lotterhos KE. 2020. General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica). Frontiers in Marine Science 7:523697 (Special Issue in Marine Environmental Epigenetics) [Link]
2019
Lotterhos, KE. 2019. The effect of neutral recombination variation on genome scans for selection. G3: Genes | Genomes | Genetics 9:1851-1867 [Link][Dryad]
Lotterhos, KE. 2019. Characterizing the multivariate physiogenomic response to environmental change. Molecular Ecology https://doi.org/10.1111/mec.15129 [Link]
2018
Lotterhos KE, Moore JH, Stapleton A. Analysis Validation has been neglected in the Age of Reproducibility. PloS Biology. https://doi.org/10.1371/journal.pbio.3000070
Lotterhos KE, Yeaman S, Degner J, Aitken S, Hodgins K. 2018. Modularity of genes involved in local adaptation to climate despite physical linkage. Genome Biology 19:157. (Preprint “Recommended” by PCI Evolutionary Biology) [Link][Dryad]
Fitzpatrick MC, SR Keller, and KE Lotterhos. 2018. Comment on “Genomic signals of selection predict climate-driven population declines in a migratory bird.” Science 361 (6401), eaat7279. [Link]
Puritz JB and KE Lotterhos. 2018. Expressed Exome Capture Sequencing (EecSeq): a method for cost-effective exome sequencing for all organisms with or without genomic resources. Molecular Ecology Resources 18:1209-1222. [Link]
2017
Lotterhos KE, DC Card, SM Schaal, L Wang, C Collins, R Verity. 2017. Composite measures of selection can improve the signal-to-noise ratio in genome scans. Methods in Ecology and Evolution 8: 717–727. Special Feature ‘How to Measure Natural Selection.’ (product of NESCent working group). [Link][Dryad]
Verity R+, C Collins+, DC Card, SM Schaal, L Wang, KE Lotterhos. MINOTAUR: A platform for the analysis and visualization of multivariate results from genome scans with R Shiny. Molecular Ecology Resources, doi:10.1111/1755-0998.12579. (product of NESCent working group). [Link][R Package on GitHub]
Lowry DB, S Hoban, JL Kelley, KE Lotterhos, LK Reed, MF Antolin, A Storfer. 2017. Responsible RAD: Striving for best practices in population genomic studies of adaptation. Molecular Ecology Resources 17:366-369. [Link]
Markel RW+, KE Lotterhos+, and CLK Robinson. Temporal variability in the environmental and geographic predictors of spatial patterns of recruitment in nearshore rockfishes. Marine Ecology Progress Series. 574:97-111 [Link][Dryad]
Haggarty DR, KE Lotterhos, and JB Shurin. 2017. Young-of-the-year recruitment does not predict the abundance of older age classes in black rockfish in Barkley Sound, British Columbia, Canada. Marine Ecology Progress Series. 574:113-126. [Link]
Lowry DB, S Hoban, JL Kelley, KE Lotterhos, LK Reed, MF Antolin, A Storfer. 2017. Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation. Molecular Ecology Resources 17:142-152. [Link]
2016
Yeaman SY+, Hodgins KA+, Lotterhos KE, H Suren, S Nadeau, JC Degner, KA Nurkowski, P Smets, T Wang, LK Gray,6 KJ Liepe, A Hamann, JA Holliday, MC Whitlock, LH Rieseberg, SN Aitken. Convergent local adaptation to climate in distantly related conifers. Science, 353:1431-1433. [Link] [Science Perspective by Angela Hancock] [Press][Dryad]
Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation. In press at Molecular Ecology Resources. [Link]
Hoban S+, JL Kelley+, KE Lotterhos+, MF Antolin, G Bradburd, DB Lowry, ML Poss, LK Reed, A Storfer, MC Whitlock. Finding the genomic basis of local adaptation: pitfalls, practical solutions and future directions. American Naturalist 188(4): doi: 10.1086/688018. [Link] [Press] F1000-recommended
Sherman CDH, KE Lotterhos, MF Richardson, CK Tepolt, LA Rollins, SR Palumbi, and AD Miller. What are we missing about marine invasions? Filling in the gaps with evolutionary genomics. Marine Biology 163:198. doi: 10.1007/s00227-016-2961-4. [Link]
2015
Whitlock MC and KE Lotterhos 2015. Reliable detection of loci responsible for local adaptation: Inference of a neutral model through trimming the distribution of FST. American Naturalist: 186(S1): S24-S36. [Link] [R Package on GitHub] F1000-recommended (Special Issue: Local Adaptation)
Lotterhos KE and MC Whitlock. 2015. The relative power of genome scans depends on sampling design and statistical method. Molecular Ecology 24(5): 1031-1046. [Link] [Dryad repository]
2014
Lotterhos KE and MC Whitlock. 2014. Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests. Molecular Ecology 23(9): 2178-2192. [Link] [Dryad respository]
Lotterhos KE, SJ Dick and DR Haggarty. 2014. Evaluation of Rockfish Conservation Area networks in the US and Canada relative to the dispersal distance for black rockfish (Sebastes melanops). Evolutionary Applications 7(2): 238-259. [Link] [Press] [Dryad respository]
Hughes AR and KE Lotterhos. 2014. Genotypic diversity at multiple spatial scales in the foundation marsh species, Spartina alterniflora. Marine Ecology Progress Series 497: 105-117. [Link]
2013
Travis J and KE Lotterhos. 2013. Using experiments and models to untangle direct and indirect effects in a ”simple” food web: is there hope for understanding fishery systems? Bulletin of Marine Science 89(1): 317-335. [Link]
2012
Lotterhos KE 2012. Non-significant isolation-by-distance implies limited dispersal. Molecular Ecology 21: 5637-5639. [Link]
Lotterhos KE and RW Markel. 2012. Oceanographic drivers of offspring abundance may increase or decrease reproductive variance in a temperate marine fish. Molecular Ecology 21: 5009-5026. [Link] [Dryad repository]
2011
Reuter KE, KE Lotterhos, RN Crim, CA Thompson, and CDG Harley. 2011. Elevated pCO2 increases sperm limitation and risk of polyspermy in the red sea urchin Strongylocentrotus franscicanus. Global Change Biology 17: 163-171. [Link]
Lotterhos KE 2011. The context-dependent effect of multiple paternity on effective population size (Ne). Evolution 65(6): 1693-1706. [Link]
Levitan DR, ND Fogarty, J Jara, KE Lotterhos and N Knowlton. 2011. Genetic, spatial and temporal components to precise spawning synchrony in reef building corals of the Montastraea annularis species complex. Evolution 65(5): 1254-1270. [Link]
2010 and prior
Lotterhos KE and DR Levitan. 2010. Gamete release and spawning behavior in broadcast spawning marine invertebrates. pp 99-120 in: The Evolution of Primary Sexual Characters in Animals. A. Crdoba-Aguilar and J.L. Leonard, eds.
Barber J and KE Lotterhos. 2007. Causes and costs of injury in trapped Dungeness crabs, in Piatt, J.F., and Gende, S.M., eds., Proceedings of the Fourth Glacier Bay Science Symposium: U.S. Geological Survey Scientific Investigations Report 2007-5047, p. 181-182.
Knox RS, D Glen, and KE Lotterhos, 2002. Effect of inhomogeneous broadening on the fluorescence anisotropy of a square-symmetric molecule. Chemical Physics Letters 361: 285-290.