Names in bold are current or former Kelley Lab members.
Preprints
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
2021
- , , Evans Hutzenbiler B.D., Trojahn S., Kingham B.,
- Towards a genome sequence for every animal: where are we now? Proceedings of the National Academy of Sciences. 118 (52). DOI: 10.1073/pnas.2109019118 , ,
- Hotaling S., Sproul J.S., Heckenhauer J., Powell A., Larracuente A.M., Pauls S.U., Kelley J.L., Frandsen P.B. (2021) Long reads are revolutionizing 20 years of insect genome sequencing. Genome Biology and Evolution. 13 (8). DOI: 10.1093/gbe/evab138
- Schweizer R.M., Saarman N., Ramstad K.M., Forester B.R., Kelley J.L., Hand B.K., Malison R.L., Ackiss A.S., Watsa M., Nelson T.C., Beja-Pereira A., Waples R.S., Funk W.C., Luikart G. (2021) Big data in conservation genomics: Boosting skills, hedging bets, and staying current in the field. Journal of Heredity. 112 (4), 313-327. DOI: 10.1093/jhered/esab019
- Deemer B.R., Hotaling S., Poulson-Ellestad K., Falkenberg L.J., Cloern J.E., Soranno P.A. (2021) Engaging the next generation of editorial talent through a hands-on fellowship model. Ecology Letters. 24 (7), 1297-1301. DOI: 10.1111/ele.13758
- Kelley J.L., Tobler M., Beck D., Sadler-Riggleman I., Quackenbush C.R., Arias Rodriguez L., Skinner M.K. (2021) Epigenetic inheritance of DNA methylation changes in fish living in hydrogen sulfide-rich springs. Proceedings of the Natural Academy of Sciences. 118 (26). DOI: 10.1073/pnas.2014929118
- Jansen H.T., Evans Hutzenbiler B., Hapner H.R., McPhee M.L., Carnahan A.M., Kelley J.L., Saxton M.W., Robbins C.T. (2021) Can offsetting the energetic cost of hibernation restore an active season phenotype in grizzly bears (Ursus arctos horribilis)? Journal of Experimental Biology. 224 (12). DOI: 10.1242/jeb.242560
- Hotaling S., Borowiec M.L., Lins L.S.F., Desvignes T., Kelley J.L. (2021) The biogeographic history of eelpouts and related fishes: Linking phylogeny, environmental change, and patterns of dispersal in a globally distributed fish group. Molecular Phylogenetics and Evolution. 162 (107211). DOI: 10.1111/1755-0998.13312
- Whibley A., Kelley J.L., Narum S.R. (2021) The changing face of genome assemblies: Guidance on achieving high-quality reference genomes.Molecular Ecology Resources. 21 (3), 641-652. DOI: 10.1111/1755-0998.13312
- Everson K.M., Gray L.N., Jones A.G., Lawrence N.M., Foley M.E., Sovacool K.L., Kratovil J.D., Hotaling S., Hime P.M., Storfer A., Parra-Olea G., Percino-Daniel R., Aguilar-Miguel X., O’Neill E.M., Zambrano L., Shaffer H.B., Weisrock D.W. (2021) Geography is more important than life history in the recent diversification of the tiger salamander complex. Proceedings of the National Academy of Sciences. 118 (17). DOI: 10.1073/pnas.2014719118
- Fraik A.K., McMillan J.R., Liermann M., Bennett T., McHenry M.L., McKinney G.J., Wells A.H., Winans G., Kelley J.L., Pess G.R., Nichols K.M. (2021) The impacts of dam construction and removal on the genetics of recovering steelhead (Oncorhynchus mykiss) populations across the Elwha River watershed. Genes. 12 (1), 89. DOI: 10.3390/genes12010089
- Brighenti S.*, Hotaling S.*, Finn D.S., Fountain A.G., Hayashi M., Herbst D., Saros J.E., Tronstad L.M., Millar C.I. (2021) Rock glaciers and related cold rocky landforms: overlooked climate refugia for mountain biodiversity. Global Change Biology. DOI: 10.1111/gcb.15510; *contributed equally
- Kelley J.L., Desvignes T., McGowan K.L., Perez M., Rodriguez L.A., Brown A.P., Culumber Z., Tobler M. (2020) microRNA expression variation in a natural system as a potential molecular mechanism contributing to adaptation to hydrogen sulfide. Journal of Evolutionary Biology. 34 (6), 977-988. DOI: 10.1111/jeb.13727
- Marden E., Abbott R.J., Austerlitz F., Ortiz-Barrientos D., Baucom R.S., Bongaerts P., Bonin A., Bonneaud C., Browne L., Alex Buerkle C., Caicedo A.L., Coltman D.W., Cruzan M.B., Davison A., DeWoody J.A., Dumbrell A.J., Emerson B.C., Fountain-Jones N.M., Gillespie R., Giraud T., Hansen M.M., Hodgins K.A., Heuertz M., Hirase S., Hooper R., Hohenlohe P., Kane N.C., Kelley J.L., Kinziger A.P., McKenzie V.J., Moreau C.S., Nazareno A.G., Pelletier T.A., Pemberton J.M., Qu Y., Renaut S., Riginos C., Rodríguez-Ezpeleta N., Rogers S.M., Russell J.A., Schoville S.D., Shi S., Smith M., Sork V.L., Stone G.N., Taberlet P., Videvall E., Waits L., Warschefsky E., Wayne R.K., Whibley A., Willoughby J., Yoder J.B., Zinger L., Sibbett B., Narum S., Rieseberg L.H. (2021) Sharing and reporting benefits from biodiversity research.Molecular Ecology. 30 (5), 1103-1107. DOI: 10.1111/mec.15702
2020
- Whibley A., Kelley J., Narum S. (2020) The changing face of genome assemblies: guidance on achieving high‐quality reference genomes. Molecular Ecology Resources. DOI: 10.1111/1755-0998.13312
- Hotaling S., Kelley J.L., Frandsen P.B. (2020) Aquatic insects are dramatically underrepresented in genomic research. Insects. 11, 601. DOI: 10.3390/insects11090601
- Elser J.J., Wu C., Gonzalez A.L., Shain D.H., Smith H.J., Sommaruga R., Williamson C.E., Brahney J., Hotaling S., Vanderwall J., Aizen E., Aizen V., Battin T., Camassa R., Dong Z., Feng X., Jiang H., Li J., Lu L., Qu J.J., Ren Z., Tan W., Wen J., Wen L., Woods H.A., Xiong X., Xu J., Yu G., Yu J., Harper J.T., Saros J.E. (2020) Key rules of life and the fading alpine cryosphere: Impacts in alpine lakes and streams. Global Change Biology. 26, 6644-6656. DOI: 10.1111/gcb.15362
- Birrell J.H., Shah A.A., Hotaling S., Giersch J.J., Williamson C.E., Jacobsen D., Woods H.A. (2020) Insects in high-elevation streams: life in extreme environments imperiled by climate change. Global Change Biology. 26, 6667-6684. DOI: 10.1111/gcb.15356
- Deemer B.R., Hotaling S., Poulson-Ellestad K., Falkenberg L.J., Cloern J.E. (2020) Virtual networking between editors and early career researchers: benefits, silver linings, and lessons learned. Limnology and Oceanography Bulletin. 29, 141-144. DOI: 10.1002/lob.10407
- To composite or replicate: how sampling method and protocol differences alter stream bioassessment metrics.Environmental Monitoring and Management. 192 (531). DOI: 10.1101/847327 , , ,
- Hotaling S.*, Shah A.A.*, Dillon M.E., Giersch J.J., Tronstad L.M., Finn D.S., Woods H.A., Kelley J.L. (2020) Cold tolerance of mountain stoneflies (Plecoptera: Nemouridae) from the high Rocky Mountains. Western North American Naturalist. DOI: 10.1101/2020.06.25.171934 In press; *contributed equally
- Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments. Proceedings of the National Academy of Sciences , , , , , , , , , , , , ,
- Hotaling S., Shah A.A., McGowan K.L., Tronstad L.M., Giersch J.J., Finn D.S., Woods H.A., Dillon M.E., Kelley J.L. (2020) Mountain stoneflies may tolerate warming streams: evidence from organismal physiology and gene expression. Global Change Biology. 26, 5524-5538. DOI: 10.1111/gcb.15294
-
Margres M. J., R-Aravena M., Hamede R., Chawla K., Patton A., Lawrance M.F., Fraik A.K., Davis B.W., Ostrander E.A., Jones M.E., McCallum H., Paddison P.J., Hohenlohe P.A., Hockenbery D., Storfer A. (2020) Spontaneous tumor regression in Tasmanian devils associated with RASL11A activation.Genetics. 215 (4), 1143-1152. DOI: 10.1534/genetics.120.303428
- Fraik A.K., Margres M.J., Epstein B., Barbosa S., Jones M., Hendricks S., Schönfeld B., Stahlke A.R., Veillet A., Hamede R., McCallum H., Lopez‐Contreras E., Kallinen S.J., Hohenlohe P.A., Kelley J.L., Storfer A. (2020) Disease swamps molecular signatures of genetic‐environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii ) populations. Evolution. 74 (7), 1392-1408. DOI: 10.1111/evo.14023
- Hotaling S. (2020) Simple rules for concise scientific writing. Limnology & Oceanography Letters. 5, 379-383. DOI: 10.1002/lol2.10165
- Headwaters fed by subterranean ice: potential climate refugia for mountain stream communities? Western North American Naturalist. 80 (3), 395-407. DOI: 10.3398/064.080.0311; *contributed equally , , ,
- Rolling stones gather moss: movement and longevity of moss balls on an Alaskan glacier. Polar Biology. 43, 735-744. DOI: 10.1007/s00300-020-02675-6 , ,
- Muhlfeld C.C.*, Cline T.J.*, Giersch J.J.*, Peitzsch E., Florentine C., Jacobsen D., Hotaling S. (2020) Specialized meltwater biodiversity persists despite widespread deglaciation. PNAS. 117 (22), 12208-12214. DOI: 10.1073/pnas.2001697117; *contributed equally
- Kelley J.L., Gilad Y. (2020) Effective study design for comparative functional genomics. Nature Reviews Genetics. 21, 385-386. DOI: 10.1038/s41576-020-0242-z
- Shah A.A., Dillon M.E., Hotaling S., Woods H.A. (2020) High elevation insect communities face shifting ecological and evolutionary landscapes. Current Opinion in Insect Science. 41, 1-6. DOI: 10.1016/j.cois.2020.04.002
- Stibal M., Bradley J.A., Edwards A., Hotaling S., Zawierucha K., Rosvold J., Lutz S., Cameron K.A., Mikucki J.A., Kohler T.J., Sabacka M., Anesio A.M. (2020) Glacial ecosystems are essential to understanding biodiversity responses to glacier retreat. Nature Ecology & Evolution. 4, 686-687. DOI: 10.1038/s41559-020-1163-0
- Poulson-Ellestad K., Hotaling S., Falkenberg L., Soranno P. (2020)Illuminating a black box of the peer review system: demographics, experiences, and career benefits of associate editors.Limnology and Oceanography Bulletin. 29 (1), 11-17. DOI: 10.1002/lob.10362
- Jordan S., Hand B.K., Hotaling S., DelVecchia A., Malison R., Nissley C., Stanford J., Luikart G. (2020) Genomic data reveal similar genetic differentiation in aquifer species with different dispersalcapacities and life histories. Biological Journal of the Linnean Society. 129 (2), 315-322. DOI: 10.1093/biolinnean/blz173
- Hotaling S.*, Wimberger P.H., Kelley J.L., Watts, H.E. (2020) Macroinvertebrates on glaciers: a key resource for terrestrial food webs?Ecology. 101 (4). DOI: 10.1002/ecy.2947; *Corresponding author
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
- Storfer A., Patton A., Fraik A.K. (2018) Navigating the interface from landscape genetics to landscape genomics. Frontiers in Genetics. 9.68, doi.org/10.3389/fgene.2018.00068
- Storfer A., Hohenlohe P.A., Margres M., Patton A., Fraik A.K., Lawrance M., Ricci L., Stahlke A., McCallum H.I., Jones M.E. (2018) The devil is in the details: Genomics of transmissible cancers in Tasmanian devils. PLOS Pathogens. 14.8, doi.org/10.1371/journal.ppat.1007098
- Margres M.J., Jones M., Epstein B., Comte S., Fox S., Fraik A.K., Hendricks S.A., Huxtable S., Lachish S., Lazenby B., O’Rourke S.M., Stahlke A.R., Wiench C.G., Hamede R., Schonfeld B., McCallum H., Miller M.R., Hohenlohe P.A., Storfer A. (2018) Large‐effect loci affect survival in Tasmanian devils (Sarcophilus harrisii ) infected with a transmissible cancer. Molecular Ecology. doi.org/10.1111/mec.14853
-
Hotaling, S., Giersch, J.J., Finn, D.S., Tronstad, L.M., Jordan, S., Serpa, L.E., Call, R.G., Muhlfeld, C.C., Weisrock, D.W. (2018) Congruent population genetic structure but differing depths of divergence for three alpine stoneflies with similar ecology and geographic distributions. Freshwater Biology, doi.org/10.1111/fwb.13223
-
Brown, A.P., Arias-Rodriguez, L., Yee, M.C, Tobler, M., Kelley, J.L. (2018) Concordant changes in gene expression and nucleotides underlie independent adaptation to extremely sulfidic environments. Genome Biology and Evolution. doi: 10.1093/gbe/evy198 [github]
-
Hotaling, S., Muhlfeld, C.C., Giersch, J.J., Miller, M.R., Ali, O.A., Jordan, S.P., Luikart, G., Weisrock, D.W. (2018). Demographic modeling reveals a history of divergence with gene flow for a glacially-tied stonefly in a changing post-Pleistocene landscape. Journal of Biogeography. 45:304-317.
-
Hotaling, S. (2018) Publishing papers while keeping everything in balance: Practical advice for a productive graduate school experience. Ideas in Ecology and Evolution. vol 11.
-
Tobler, M., Kelley, J.L., Plath, M., Riesch, R. (2018) Extreme environments and the origins of biodiversity: adaptation and speciation in sulfide spring fishes. Molecular Ecology. 27:843–859.
-
Barts, N., Greenway, R., Passow, C.N., Arias-Rodriguez, L., Kelley, J.L, Tobler, M. (2018) Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich environments. Genome. 61: 273–286. [github]
-
Lins, L.S.F, Trojahn, S., Sockell, A., Yee, M-C, Tatarenkov, A., Bustamante, C.D., Earley, R.L., Kelley, J.L. (2018) Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate. Genome. 61: 241–247. [github]
2017
-
Passow, C.N., Henpita, C., Shaw, J.H., Quakenbush, C.R., Warren, W.C., Schartl, M., Arias-Rodriguez, L., Kelley, J.L.*, Tobler, M*. (2017) The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish. Molecular Ecology. doi:10.1111/mec.14360. *co-supervised research [github]
-
Brown, A.P., Greenway, R., Morgan, S., Quackenbush, C.R., Giordani, L., Arias Rodriguez, L., Tobler, M., Kelley, J.L. (2017) Genome-scale data reveals that endemic Poecilia populations from small sulfidic springs display no evidence of inbreeding. Molecular Ecology. doi: 10.1111/mec.14249. [github]
- Passow, C.N., Brown, A.P., Arias-Rodriguez, L., Yee, M.-C., Sockell, A., Schartl, M., Warren, W.C., Bustamante, C., Kelley, J.L.*, Tobler, M*. (2017) Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae) Molecular Ecology. doi: 10.1111/mec.14198. *co-supervised research [github]
- Fu, Z., Epstein, B., Kelley J.L., Zheng, Q., Bergland, A.O., Castillo Carrillo, C.I., Jensen, A.S., Dahan, J., Karasev, A.V., Snyder, W.E. (2017) Using NextRAD sequencing to infer movement of herbivores among host plants. PLOS ONE. 12(5): e0177742.
- Kelley, J.L. (2017) Detecting Natural Selection in the Genome. Oxford Bibliographies in Evolutionary Biology. Ed. Karin Pfennig. New York: Oxford University Press. doi: 10.1093/obo/9780199941728-0088
-
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: 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.
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.
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.
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/
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.
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.
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