Publications

Names in bold are current or former Kelley Lab members.

Preprints

• Greenway R., Brown A.P., Camarillo H., Delich C., McGowan K.L., Nelson J., Arias-Rodriguez L., Kelley J.L., Tobler M. Convergent adaptation and ecological speciation result from unique genomic mechanisms in sympatric extremophile fishes. bioRxiv.
  

2022

• Armstrong E.E., Perry B.W., Huang Y., Garimella K.V., Jansen H.T., Robbins C.T., Tucker N.R., and Kelley J.L. A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos). Genome Biology and Evolution. DOI: 10.1093/gbe/evac125
• Coffin J.L., Kelley J.L., Jeyasingh P.D., Tobler M. (2022) Impacts of heavy metal pollution on the ionomes and transcriptomes of Western mosquitofish (Gambusia affinis). Molecular Ecology. DOI: 10.1111/mec.16342

2019

• McGowan, K.L.*, Passow, C.N., Arias-Rodriguez, L., Tobler, M. Kelley, J.L. Expression analyses of cave mollies (Poecilia mexicana) reveal key genes involved in the early evolution of eye regression. Biol Lett. 15(10):1-7. *Corresponding author [github]
• Fraik, A.K., Quackenbush, C., Margres, M.J., Comte, S., Hamilton, D.G., Kozakiewicz, C.P., Jones, M., Hamede, R., Hohenlohe, P.A., Storfer, A., Kelley, J.L. (2019) Transcriptomics of tasmanian devil (Sarcophilus harrisii) ear tissue reveals homogeneous gene expression patterns across a heterogeneous landscape. Genes, 10, 801. *Corresponding author [github]
• James S., Jennings G., Kwon Y.M., Stammnitz M., Fraik A.K., Storfer A., Comte S., Pemberton D., Pye R., Woods G., Hohenlohe P.A., McCallum H., Siddle H., Thomas F., Ujvari B., Murchison E.P., Jones M., Hamede R. (2019) Tracing the rise of malignant cell lines: distribution, epidemiology and evolutionary interactions of two transmissible cancers in Tasmanian devils. Evolutionary Applications. 12.9. https://doi.org/10.1111/eva.12831
• Jansen, H.T. ^†*, Trojahn, S.^* , Saxton, M.^*, Quackenbush, C.R., Evans Hutzenbiler, B.D. Nelson, O.L., Cornejo, O.E., Robbins, C.T., Kelley, J.L.^† (2019) Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear. Communications Biology. 2:336. ^*co-first author ^†Corresponding authors [github]
• Ren, Z.*, Martyniuk, N.*, Oleksy, I.A.*, Swain, A.*, & Hotaling, S.† (2019) Ecological stoichiometry of the mountain cryosphere. Frontiers in Ecology and Evolution 7:360. *co-first author; †corresponding author
• Hotaling, S., Kelley, J.L., Weisrock, D.W. (2019) Nuclear and mitochondrial genomic resources for the meltwater stonefly, Lednia tumana (Plecoptera: Nemouridae) Aquatic Insects 1-8. [preprint]
• Hotaling, S.,  Shain, D.H., Lang, S.A., Bagley, R.K., Lusha M., Weisrock, D.W., Kelley, J.L. (2019) Long-distance dispersal, ice sheet dynamics, and mountaintop isolation underlie the genetic structure of glacier ice worms Proceedings of the Royal Society B [github]
• Brown, A.P., McGowan, K.L., Schwarzkopf, E.J., Greenway, R., Arias-Rodriguez, L., Tobler, M., Kelley, J.L. (2019) Local ancestry analysis reveals genomic convergence in extremophile fishes. Philosophical Transactions of the Royal Society B. [github]
• Hotaling, S., Foley, M.E., Zeglin, L.H., Finn, D.S., Tronstad, L.M., Giersch, J.J., Muhlfeld, C.C. and Weisrock, D.W. (2019) Microbial assemblages reflect environmental heterogeneity in alpine streams. Global Change Biology. https://doi.org/10.1111/gcb.14683
• Hotaling, S., Kelley, J.L. (2019) The rising tide of high-quality genomic resources. News and Views for Molecular Ecology Resources. 19:567–569
  • Perspective on: Lehmann et al. Finding Nemo’s Genes: A chromosome‐scale reference assembly of the genome of the orange clownfish Amphiprion percula
• Hotaling, S., Quackenbush, C.R., Bennett Ponsford, J., New, D.D., Tobler, M., Kelley, J.L. (2019) Bacterial diversity in replicated hydrogen sulfide-rich springs. Microbial Ecology. 77: 559–573.

2018

2017

• Cribbin, K., Quackenbush, C.R., Taylor, K., Arias Rodriguez, L., Kelley, J.L. (2017) Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar. BMC Genomics. 18:283
• Lowry, D.B., Hoban, S., Kelley, J.L., Lotterhos, K.E., Reed, L.K., Antolin, M.F., Storfer, A., (2017) Responsible RAD: Striving for best practices in population genomic studies of adaptation. Molecular Ecology Resources. doi: 10.1111/1755-0998.12677
  Write-up in about the RAD-seq “debate” in The Molecular Ecologist: http://www.molecularecologist.com/2017/04/to-radseq-or-not-to-radseq/

2016

• Lowry, D.B., Hoban, S., Kelley, J.L., Lotterhos, K.E., Reed, L.K., Antolin, M.F, Storfer, A. (2016) Breaking RAD: An Evaluation of The Utility Of Restriction Site Associated DNA Sequencing For Genome Scans Of Adaptation. Molecular Ecology Resources. doi: 10.1111/1755-0998.12596
• Hoban, S.*, Kelley, J.L.*†, Lotterhos, K.E.*, Antolin, M.F., Bradburd, G., Lowry, D.B., Poss, M.L., Reed, L.K., Storfer, A., Whitlock, M.C. (2016) Finding the genetic basis of local adaptation in non-model organisms: pitfalls, practical solutions and future directions. American Naturalist. doi: 10.1086/688018.
  *Contributed equally. †Corresponding author.
  F1000 recommended article
• Kelley, J.L., Brown, A.P., Overgaard Therkildsen, N., Foote, A. (2016) The life aquatic: advances in marine vertebrate genomics. Nature Reviews Genetics. 17: 523–534 doi:10.1038/nrg.2016.66
  
• Kelley, J.L., Yee, M.C., Brown, A.P., Richardson, R., Taternkov, A., Lee, C., Harkins, T., Bustamante, C.D., Earley, R.L. (2016) The genome of the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus: a model for studying phenotypic plasticity and adaptations to extreme environments. Genome Biology and Evolution. 8 (7): 2145-2154. doi: 10.1093/gbe/evw145
  Genome assembly [link to Genbank]
  Gene annotation [link to GFF file]
• Tobler, M., Passow, C.N, Greenway, R, Kelley, J.L., Shaw, J.H. (2016) The evolutionary ecology of animals inhabiting hydrogen sulfide rich environments. Annual Review of Ecology, Evolution, and Systematics. doi: 10.1146/annurev-ecolsys-121415-032418 Direct link to pdf of article.
• Benestan, L., Ferchaud, A.-L., Hohenlohe, P., Garner, B.A., Naylor, G.J.P. , Baums, I., Schwartz, M., Kelley, J.L., Luikart, G. (2016) Conservation genomics of natural and managed populations: building a conceptual and practical framework. Molecular Ecology. doi:10.1111/mec.13647.
• Culumber, Z.W., Hopper, G. W., Barts, N., Passow, C.N., Morgan, S., Brown, A.,  Arias-Rodriguez L., Tobler, M. (2106) Habitat use of two extremophile, highly endemic, and critically endangered fish species (Gambusia eurystoma and Poecilia sulphuraria; Poeciliidae). Aquatic Conservation – Marine and Freshwater Ecosystems. doi: 10.1002/aqc.2640.
• Kelley, J.L., Passow, C.N., Arias Rodriguez, L., Patacsil Martin, D., Yee, M.C., Bustamante, C.D., Tobler, M. (2106) Mechanisms underlying adaptation to life in hydrogen sulfide rich environments. Molecular Biology and Evolution. doi:10.1093/molbev/msw020.
  In the news: ScienceDaily, K-state, WSU News
• Cooke, T.F., Yee, M.C., Muzzio, M., Adams, A., Bell, R., Cornejo, O.E., Kelley, J.L., Bailliet, G., Bravi, C.M., Bustamante, C.D., and E.E. Kenny. (2016) GBStools: A unified approach for reduced representation sequencing and genotyping. PLoS Genetics. 2016 12(2): e1005631. doi: 10.1371/journal.pgen.1005631.

• Daubert, D.M., Kelley, J.L., Udod, Y.G., Habor, C., Kleist, C.G., Furman, I.K., Tikonov, I.N., Swanson, W.J., Roberts F.A. (2016) Human Enamel Thickness and ENAM Polymorphism. International Journal of Oral Science. doi: 10.1038/ijos.2016.1.

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2015

• Stevison, L.S., Woerner, A.E., Kidd, J.M., Kelley, J.L., Veeramah, K., McManus, K.F., Great Ape Genome Project, Bustamante, C.D., Hammer, M.F., Wall, J.D. (2015) The Time-Scale of Recombination Rate Evolution in Great Apes. Molecular Biology and Evolution. doi: 10.1093/molbev/msv331.
• McManus, K.F.*, Kelley, J.L.*, Song, S.*, Veeramah, K., Woerner, A.E., Stevison, L.S., Ryder, O.A., Great Ape Genome Project, Kidd, J.M., Wall, J.D., Bustamante, C.D, Hammer, M.F. (2015) Inference of Gorilla demographic and selective history from whole genome sequence data. Molecular Biology and Evolution. 32 (3): 600-612. doi: 10.1093/molbev/msu394. * contributed equally

• Nam K, Munch K, Hobolth A, Dutheil JY, Veeramah KR, Woerner AE, Hammer MF, Great Ape Genome Diversity Project, Mailund T, Schierup MH. (2015) Extreme selective sweeps independently targeted the X chromosomes of the great apes. Proceedings of the National Academy of Sciences 112 (20), 6413-6418.

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2014

• Kelley, J.L., Peyton, J.T.*, Fiston-Lavier, A.-S.*, Teets N.M., Yee M.C., Bustamante, C.D., Lee, R.E. and D.L. Denlinger. (2014) Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nature Communications. 5:4611. doi:10.1038/ncomms5611. * contributed equally
  Link to Belgica CDS
  Link to Belgica ProteinsLink to Name Map
  Link to Belgica GFF
• McCoy, R.C., Taylor, R.W., Blauwkamp, T.A., Kelley, J.L., Kertesz, M., Pushkarev, D., Petrov, D.A., and Fiston-Lavier, A-S. (2014) Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements. PLoS ONE 9(9): e106689. doi:10.1371/journal.pone.0106689.
• Tobler, M., Henpitaa, C.R., Bassett, B, Kelley, J.L., Shaw, J.H. (2014) H2S exposure elicits differential expression of candidate genes in fish adapted to sulfidic and non-sulfidic environments. Comparative Biochemistry and Physiology Part A. 175:7-14. doi: 10.1016/j.cbpa.2014.04.012.
• Pfenninger, M., Lerp, H., Passow, C., Kelley, J.L., Tobler, M., Funke, E., Greshake, B., Erkoc, U.K., Berberich, T., and M. Plath. (2014) Parallel evolution of cox-genes in H2S -tolerant fish: a key adaptation facilitates repeated niche shifts. Nature Communications. 5:3873. doi:10.1038/ncomms4873.

• McCoy, R., Garud, N., Kelley, J.L., Boggs, C. and D.A. Petrov. (2014) Genomic inference accurately predicts the timing and severity of a recent bottleneck in a non-model insect population. Molecular Ecology doi: 10.1111/mec.12591.

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2013

• Ma, X., Kelley J.L., Eilertson, K., Musharoff, S., Degenhardt, J.D., Martins, A.L., Vinar, T., Kosiol, C., Siepel, A., Gutenkust, R.N. and C.D. Bustamante. (2013) Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). PLoS ONE 8(10): e77175. doi:10.1371/journal.pone.0077175.
• Prado-Martinez, J.*, Sudmant, P.H.*, Kidd, J.M., Li, H., Kelley, J.L., Lorente-Galdos, B., Veeramah, K., Woerner, A., O’Connor, T.D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A.E., Malig, M., Hernandez-Rodriguez, J., Hernando-Herraez, I., Prüfer, K., Pybus, M., Johnstone, L., Lachmann, M., Alkan, C., Twigg, D., Petit, N., Baker, C., Hormozdiari, F., Fernandez-Callejo, M., Dabad, M., Wilson, M.L., Stevison, L., Camprubí, C., Carvalho, T., Ruiz-Herrera, A., Vives, L., Mele, M., Abello, T., Kondova, I., Bontrop, R.E., Pusey, A., Lankester, F., Kiyang, J.A., Bergl, R.A., Lonsdorf, E., Myers, S., Ventura, M., Gagneux, P., Comas, D., Siegismund, H., Blanc, J., Agueda-Calpena, L., Gut, M., Fulton, L., Tishkoff, S.A., Mullikin, J.C., Wilson, R.K., Gut, I.G., Gonder, M.K., Ryder, O.A., Hahn, B.H., Navarro, A., Akey, J.M., Bertranpetit, J., Reich, D., Mailund, T., Schierup M.H., Hvilsom, C., Andrés, A.M., Wall, J., Bustamante, C.D., Hammer, M., Eichler, E.E.+, Marques-Bonet, T+. (2013) Great ape genetic diversity and population history. Nature. doi:10.1038/nature12228. * and + contributed equally
  
• Ségurel, L., Austerlitz, F., Toupance, B., Gautier, M., Kelley J.L., Pasquet P., Lonjou, C., Georges, M., Voisin, S., Cruaud, C., Couloux, A., Hegay, T., Aldashev, A., Vitalis, R.and E. Heyer. (2013) Positive selection of protective variants for type 2 diabetes from the Neolithic onward: a case study in Central Asia. European Journal of Human Genetics. doi:10.1038/ejhg.2012.295.
  In the news: http://sciencelife.uchospitals.edu/2013/03/07/how-type-2-diabetes-survived-evolution/

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2012

• Teets, N.M, Peyton, J.T., Colinet, H., Renault, D., Kelley, J.L., Kawarasaki , Y., Lee Jr., R.E., and D.L. Denlinger. (2012) Gene expression changes governing extreme dehydration tolerance in an Antarctic insect. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1218661109.
  Data access: Gene transcripts
  In the news: Miami University news office, F1000 recommended article 
• Kelley, J.L., Passow, C., Plath, M., Rodrigues, L.A., Yee, M.C., and M. Tobler. (2012) Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome. BMC Genomics. 13:652.
  Data access: http://www.sulfide-life.info/mtobler/databases
• Kelley, J.L. (2012) Biased estimates of dating selection pressures in recent human evolution. Frontiers in Evolutionary and Population Genetics. 3:165.

• Kelley, J.L., Yee, M.C., Lee, C., Levandowsky, E., Shah, M., Harkins, T., Earley, R.L., and C.D. Bustamante. (2012) The possibility of de novo assembly of a genome and population genomics of the mangrove rivulus Kryptolebias marmoratus. Integrative and Comparative Biology. 52:737-42.

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2011

• Hernandez, R.D., Kelley, J.L., Elyashiv, E., Melton, S.C., Auton, A., McVean, G., Sella, G., Przeworski, M., and 1000 Genomes Project Consortium. (2011) Classic selective sweeps were rare in recent human evolution. Science 331: 920-24.
  F1000 recommended article 

• Zakai, N., Lange, L., Longstreth, W.T. Jr., O’Meara, E.S., Kelley, J.L., Fornage, M., Nickerson, D., Cushman, M., Reiner, A.P. (2011) Association of Coagulation and Inflammation Related Genes and Factor VIIc Levels with Stroke: The Cardiovascular Health Study. Journal of Thrombosis and Haemostasis 9(2):267-74.

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Earlier publications

• 1000 Genomes Project Consortium, Abecasis G.R., Altshuler D.L., Auton A., Brooks L.D., Durbin R.M., Gibbs R.A., Hurles M.E., McVean G.A. (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061-73.
•  Kelley, J.L., Aagaard, J., MacCoss, M. and W. Swanson. (2010) Functional diversification and evolution of antifreeze proteins in the Antarctic fish Lycodichthys dearborni. Journal of Molecular Evolution 71:111-118.
• Kosova, G., Pickrell, J.K., Kelley, J.L., McArdle, P.F., Shuldiner, A.R., Abney, M. and C Ober. (2010) The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate. PLoS Genetics. 6(6): e1000947.
• Kelley, J.L., Turkheimer, K., Haney, M., and W. Swanson. (2009) Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations. Human Molecular Genetics. 18: 779-84.
  
• Kelley, J.L. and W. Swanson. (2008) Positive selection in the human genome: from genome scans to biological significance. Annual Review of Genomics and Human Genetics. 9:143-60.
• Kelley, J.L. and W. Swanson. (2008) Dietary change and adaptive evolution of enamelin in human and among primates. Genetics. 178(3):1595-603.
  Link to primer details.
• Kelley, J.L., Madeoy, J., Calhoun, J., Swanson, W. and J. Akey. (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Research. 16(8):980-9.
• Thomas, J., Kelley, J.L., Roberston, H., Ly, K., and W. Swanson. (2005) Adaptive evolution in the SRZ chemoreceptor families of C. elegans and C. briggsae. Proceedings of the National Academy of Sciences. 102(12): 4476 – 4481.
• Kelley, J.L.*, Stinchcombe, J.R.*, Weinig, C. and J. Schmitt. (2005) Soft and hard selection on plant defense traits in Arabidopsis thaliana. Evolutionary Ecology Research. 7(2): 287 – 302. *authors contributed jointly