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.

Advisees and mentees are marked with an asterisk *

2025

1. Lind B* and Lotterhos KE.  2024. The limits of predicting maladaptation to future environments with genomic data. Molecular Ecology Resources.  COVER Volume 25, Issue 4, May 2025

2. Albecker MA*, Bittar TB, Trussell GC, Lotterhos, KE. Meta-analysis reveals patterns of cogradient and countergradient variation. Accepted at American Naturalist

3. Alvarez Caraveo B, Guillermic M, Downey-Wall A*, Cameron LP, Sutton JN, Ries JB, Lotterhos KE, Eagle RA. Magnesium (Mg/Ca, δ26Mg), boron (B/Ca, δ11B), and calcium ([Ca2+]) geochemistry of Arctica islandica and Crassostrea virginica extrapallial fluid and shell. Accepted in Biogeosciences 

4. Titmuss D*, Albecker MA*, Lotterhos KE. Responses of Littorina spp. intertidal snails to thermal extremes indicate countergradient variation in fitness. In Press at Ecology and Evolution. 

2024

5. Lotterhos KE. 2024b. Principles in experimental design for evaluating genomic forecasts. Methods in Ecology and Evolution 15(9):1466-1482.

6. Lotterhos KE✝, Bernal MA✝, Phifer-Rixey M✝, Hanley T✝. 2024.  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

7. Lotterhos KE. 2024.  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 

8. Venkataraman YR, Huffmyer AS, White SJ, Downey-Wall A*, Ashey J, Becker DM, Bengtsson Z, Putnam H, Strand E, Rodríguez-Casariego JA, Wanamaker SA, Lotterhos KE, Roberts S. DNA methylation modulates transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica). Environtmental Epigenetics 10(1) dvae018. https://doi.org/10.1093/eep/dvae018 

9. Hardy D, Gaither MR, Lotterhos KE, Greaves S, Cipolla K, Kerns EV, Prieto A, Gilg MR. Asymmetrical hybridization rates and multiple environmental factors influence the spatial genetic structure of a killifish hybrid zone. Evolution. qpae160, https://doi.org/10.1093/evolut/qpae160 

2023

5. Lotterhos KE. 2023. The paradox of adaptive trait clines with non-clinal patterns in the underlying genes. Proceedings of the National Academy of Sciences 120 (12) e2220313120.

   1. Note: The length of linkage groups was misreported in this article as 50cM. The correct length is 5cM. PNAS declined to publish a correction because the error did not impact the conclusions in the article (the population-scaled recombination rate was correctly reported, and that parameter is what drives the level of genetic diversity observed in the simulations). Here is a copy of the erratum that explains how to calculation cM from a recombination rate and distance between base pairs. 

6. 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. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology 36(12):1761-1782

7. 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. 2023. A dynamic web resource for robust and reproducible genomics in nonmodel species: marineomics.io. Methods in Ecology and Evolution 14:2709-2716.

8. 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 24:e13801.

9. 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

7. 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. 67(8): 1732-1745

8. 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. 377:1856 10.1098/rstb.2021.0200 (Special Issue on Supergenes) [Research featured in Quanta Magazine's article on supergenes]

9. Berdan EL, Flatt T, Kozak GM, Lotterhos KE, Wielstra B. 2022. Genomic architecture of supergenes: Connecting form to function. Phil. Trans. B. 10.1098/rstb.2021.0192 (Special Issue on Supergenes)

10. 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.

11. Láruson AJ*, Haller B, Keller S, Fitzpatrick MC, and Lotterhos KE. 2022. Seeing the forest for the trees: Assessing genetic offset predictions from gradient forests. Evolutionary Applications. 15(3): 403–416.

12. Albecker MA*, Trussell GC, Lotterhos KE. 2022 A novel analytical framework to quantify co-gradient and countergradient variation. Ecology Letters. 25(6) 1521-1533.

2021

13. 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)

14. 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 affect adaptation to environmental change? Genome-informed insights for characterizing selection across complex life cycle. Proceedings of the Royal Society B 288: 20212122 (Special Feature on Evolution in Changing Seas)

15. 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

16. 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. 22(4): 1247-1261

17. Schaal SM*, Haller B, Lotterhos KE. 2021. Comparative thermal performance among four young-of-the-year temperate reef fish species. ICES Journal of Marine Science fsab072, 

18. 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. Proceedings of the Royal Society B 288: 20210727 (Special Feature on Evolution in Changing Seas)

19. Lotterhos KE, Láruson AJ*, Jiang LQ. 2021. Novel and disappearing climates in the global sea surface from 1800 to 2100.  Nature Scientific Reports 11, 1-16. https://doi.org/10.1038/s41598-021-94872-4. Top 100 Ecology, Top 100 Earth Science, Editor’s Choice: Climate Change

2020

20. 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)

21. Láruson AJ*, Yeaman S, Lotterhos KE. 2020. The importance of genetic redundancy in evolution. Trends in Ecology and Evolution 35:809-822.

22. 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)

2019

23. Lotterhos KE. 2019. The effect of neutral recombination variation on genome scans for selection. G3: Genes | Genomes | Genetics 9:1851-1867

24. Lotterhos KE. 2019. Characterizing the multivariate physiogenomic response to environmental change. Molecular Ecology 28:2711-2714.

2018

25. 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

26. 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)

27. 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.

28. 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.

2017

29. 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).

30. 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).

31. 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.

32. KE Lotterhos✝, Markel RW✝, and CLK Robinson. 2017. Temporal variability in the environmental and geographic  predictors of spatial patterns of recruitment in nearshore rockfishes. Marine Ecology Progress Series. 574:97-111

33. 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

34. 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. “Top downloaded” paper.

2016

35. Sherman CDH, KE Lotterhos, MF Richardson, CK Tepolt, LA Rollins, SR Palumbi, and AD Miller. 2016. 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

36. Yeaman S✝, KA Hodgins✝, KE Lotterhos, H Suren, S Nadeau, JC Degner, KA Nurkowski, P Smets, T Wang, LK Gray, KJ Liepe, A Hamann, JA Holliday, MC Whitlock, LH Rieseberg, and SN Aitken. 2016. Convergent local adaptation to climate in distantly related conifers. Science 353:1431-1433.

37. KE Lotterhos✝, Hoban S✝, JL Kelley✝, MF Antolin, G Bradburd, DB Lowry, ML Poss, LK Reed, A Storfer, MC Whitlock. 2016. Finding the genomic basis of local adaptation: pitfalls, practical solutions and future directions. American Naturalist 188: 379-397. (Product of NimBios Landscape Genomics Working Group). 

2015

38. Whitlock MC and KE Lotterhos. 2015. Reliable detection of loci responsible for local adaptation: inference of a null model through trimming the distribution of FST. American Naturalist 186(S1): S24-S36 (Special Issue on local adaptation). 

39. Lotterhos KE and MC Whitlock. 2015. The relative power of genome scans to detect local adaptation depends on sampling design and statistical method. Molecular Ecology 24(5):1031-1046. 

2014

40. Lotterhos KE and S Schaal*. 2014. Genome scans for the contemporary response to selection in quantitative traits. Molecular Ecology 23(18): 4435-7. 

41. 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.

42. 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. 

43. 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. 

2013

44. 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. 

2012

45. Lotterhos KE. 2012. Non-significant isolation-by-distance implies limited dispersal. Molecular Ecology 21: 5637-5639. 

46. Lotterhos KE and R Markel. 2012. Oceanographic drivers of offspring abundance may increase or decrease reproductive variance in a temperate marine fish. Molecular Ecology 21: 5009-5026. 

2011

47. Reuter KE*, KE Lotterhos, RN Crim, CA Thompson, and CDG. Harley. 2011. Ocean acidification increases sperm limitation and risk of polyspermy in the red sea urchin Strongylocentrotus franscicanus. Global Change Biology 17: 163-171. 

48. Lotterhos KE. 2011. The context-dependent effect of multiple paternity on effective population size (Ne). Evolution 65(6): 1693-1706. 

49. 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. 

2010 and prior

50. 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. Cordoba-Aguilar and J.L. Leonard, eds. Oxford University Press.

51. Knox RS, D Gulen, and KE Lotterhos. 2002. Effect of inhomogeneous broadening on the fluorescence anisotropy of a square-symmetric molecule. Chemical Physics Letters 361: 285-290. 

Data Publications

1. Lotterhos, K. (2023) Output model data from paradox of adaptive trait clines with non-clinal patterns in the underlying genes (Model Validation Program project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-02-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.889769.1 

2. Lotterhos KE (2023). Code from: "The paradox of adaptive trait clines with non-clinal patterns in the underlying genes”. https://zenodo.org/record/7622893#.ZCLNzezMJUI 

3. Schaal S, Haller B, Lotterhos KE. (2022) Data from: Inversion Invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow. Dryad, Dataset, https://doi.org/10.5061/dryad.mkkwh712q 

4. Albecker MA and Lotterhos KE. (2022). Archived data and code from: A novel analytical framework to quantify co-gradient and countergradient variation. https://zenodo.org/record/6470547#.Y7V6HOzMJUI 

5. Downey-Wall A (2020). Data from: Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica). doi:10.5061/dryad.8cz8w9gnk  

6. Lotterhos, Katie E (2019), Data from: The effect of neutral recombination variation on genome scans for selection, Dryad, Dataset, https://doi.org/10.5061/dryad.rj0kj10

7. Lotterhos, Katie E. et al. (2018), Data from: Modularity of genes involved in local adaptation to climate despite physical linkage, Dryad, Dataset, https://doi.org/10.5061/dryad.r67hd7t

8. Lotterhos, Katie E. et al. (2018), Data from: Composite measures of selection can improve the signal-to-noise ratio in genome scans, Dryad, Dataset, https://doi.org/10.5061/dryad.bp11m 

9. Markel, Russell W. et al. (2018), Data from: Temporal variability in the environmental and geographic predictors of spatial-recruitment in nearshore rockfishes, Dryad, Dataset, https://doi.org/10.5061/dryad.11j13

10. Yeaman, Sam et al. (2016), Data from: Convergent local adaptation to climate in distantly related conifers, Dryad, Dataset, https://doi.org/10.5061/dryad.0t407 

11. Lotterhos, Katie E.; Whitlock, Michael C. (2015), Data from: The relative power of genome scans to detect local adaptation depends on sampling design and statistical method, Dryad, Dataset, https://doi.org/10.5061/dryad.mh67v

12. Lotterhos, Katie E.; Whitlock, Michael C. (2014), Data from: Evaluation of demographic history and neutral parameterization on the performance of Fst outlier tests, Dryad, Dataset, https://doi.org/10.5061/dryad.v8d05

13. Lotterhos, Katie E.; Dick, Stefan J.; Haggarty, Dana R. (2013), Data from: Evaluation of rockfish conservation area networks in the United States and Canada relative to the dispersal distance for black rockfish (Sebastes melanops), Dryad, Dataset, https://doi.org/10.5061/dryad.m0p56

14. Lotterhos, Katie E.; Markel, Russell W. (2012), Data from: Oceanographic drivers of offspring abundance may increase or decrease variance in reproductive success in a temperate marine fish, Dryad, Dataset, https://doi.org/10.5061/dryad.hg6vs