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Joanna L. Kelley, Ph.D. - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
 Washington State University, Pullman, WA, United States 
 2022- University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
reproductive protein evolution, genomics of adaptation,
Website:
https://evogenomes.sites.ucsc.edu/people/lab-members/
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71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Wilson EJ, Barts N, Coffin JL, Johnson JB, Rodríguez Peña CM, Kelley JL, Tobler M, Greenway R. Gene expression signatures between Limia perugiae (Poeciliidae) populations from freshwater and hypersaline habitats, with comparisons to other teleosts. Plos One. 19: e0315014. PMID 39637050 DOI: 10.1371/journal.pone.0315014  0.37
2024 Greenway R, De-Kayne R, Brown AP, Camarillo H, Delich C, McGowan KL, Nelson J, Arias-Rodriguez L, Kelley JL, Tobler M. Integrative analyses of convergent adaptation in sympatric extremophile fishes. Current Biology : Cb. PMID 39395416 DOI: 10.1016/j.cub.2024.09.027  0.485
2024 Hermosilla-Albala N, Silva FE, Cuadros-Espinoza S, Fontsere C, Valenzuela-Seba A, Pawar H, Gut M, Kelley JL, Ruibal-Puertas S, Alentorn-Moron P, Faella A, Lizano E, Farias I, Hrbek T, Valsecchi J, et al. Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism. Communications Biology. 7: 1283. PMID 39379612 DOI: 10.1038/s42003-024-06901-3  0.408
2024 De-Kayne R, Perry BW, McGowan KL, Landers J, Arias-Rodriguez L, Greenway R, Rodríguez Peña CM, Tobler M, Kelley JL. Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes. Genome Biology and Evolution. 16. PMID 38788745 DOI: 10.1093/gbe/evae087  0.372
2024 Armstrong EE, Bissell KL, Fatima HS, Heikkinen MA, Jessup A, Junaid MO, Lee DH, Lieb EC, Liem JT, Martin EM, Moreno M, Otgonbayar K, Romans BW, Royar K, Adler MB, ... ... Kelley JL, et al. Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae. G3 (Bethesda, Md.). PMID 38366575 DOI: 10.1093/g3journal/jkae034  0.316
2023 Sproul J, Hotaling S, Heckenhauer J, Powell A, Marshall D, Larracuente AM, Kelley J, Pauls SU, Frandsen PB. 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges. Genome Research. PMID 37739812 DOI: 10.1101/gr.277387.122  0.329
2023 Ryan K, Greenway R, Landers J, Arias-Rodriguez L, Tobler M, Kelley JL. Selection on standing genetic variation mediates convergent evolution in extremophile fish. Molecular Ecology. PMID 37548336 DOI: 10.1111/mec.17081  0.708
2023 Pawar H, Rymbekova A, Cuadros-Espinoza S, Huang X, de Manuel M, van der Valk T, Lobon I, Alvarez-Estape M, Haber M, Dolgova O, Han S, Esteller-Cucala P, Juan D, Ayub Q, Bautista R, ... Kelley JL, et al. Ghost admixture in eastern gorillas. Nature Ecology & Evolution. PMID 37500909 DOI: 10.1038/s41559-023-02145-2  0.343
2023 Juan D, Santpere G, Kelley JL, Cornejo OE, Marques-Bonet T. Current advances in primate genomics: novel approaches for understanding evolution and disease. Nature Reviews. Genetics. PMID 36599936 DOI: 10.1038/s41576-022-00554-w  0.363
2022 Armstrong EE, Perry BW, Huang Y, Garimella KV, Jansen HT, Robbins CT, Tucker NR, Kelley JL. A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos). Genome Biology and Evolution. PMID 35929770 DOI: 10.1093/gbe/evac125  0.339
2022 Hotaling S, Desvignes T, Sproul JS, Lins LSF, Kelley JL. Pathways to polar adaptation in fishes revealed by long-read sequencing. Molecular Ecology. PMID 35561000 DOI: 10.1111/mec.16501  0.379
2021 Hotaling S, Kelley JL, Frandsen PB. Toward a genome sequence for every animal: Where are we now? Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34862323 DOI: 10.1073/pnas.2109019118  0.329
2021 Hotaling S, Sproul JS, Heckenhauer J, Powell A, Larracuente AM, Pauls SU, Kelley JL, Frandsen PB. Long-reads are revolutionizing 20 years of insect genome sequencing. Genome Biology and Evolution. PMID 34152413 DOI: 10.1093/gbe/evab138  0.328
2021 Fraik AK, McMillan JR, Liermann M, Bennett T, McHenry ML, McKinney GJ, Wells AH, Winans G, Kelley JL, Pess GR, Nichols KM. The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead () Populations across the Elwha River Watershed. Genes. 12. PMID 33450806 DOI: 10.3390/genes12010089  0.305
2020 Whibley A, Kelley J, Narum S. The changing face of genome assemblies: guidance on achieving high-quality reference genomes. Molecular Ecology Resources. PMID 33326691 DOI: 10.1111/1755-0998.13312  0.31
2020 Fu Z, Meier AR, Epstein B, Bergland AO, Castillo Carrillo CI, Cooper WR, Cruzado RK, Horton DR, Jensen AS, Kelley JL, Rashed A, Reitz SR, Rondon SI, Thinakaran J, Wenninger EJ, et al. Host plants and shape the population genetics of sympatric herbivore populations. Evolutionary Applications. 13: 2740-2753. PMID 33294020 DOI: 10.1111/Eva.13079  0.439
2020 Hotaling S, Kelley JL, Frandsen PB. Aquatic Insects Are Dramatically Underrepresented in Genomic Research. Insects. 11. PMID 32899516 DOI: 10.3390/Insects11090601  0.428
2020 Hotaling S, Shah AA, McGowan KL, Tronstad LM, Giersch JJ, Finn DS, Woods HA, Dillon ME, Kelley JL. Mountain stoneflies may tolerate warming streams: evidence from organismal physiology and gene expression. Global Change Biology. PMID 32698241 DOI: 10.1111/Gcb.15294  0.315
2020 Greenway R, Barts N, Henpita C, Brown AP, Arias Rodriguez L, Rodríguez Peña CM, Arndt S, Lau GY, Murphy MP, Wu L, Lin D, Tobler M, Kelley JL, Shaw JH. Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments. Proceedings of the National Academy of Sciences of the United States of America. PMID 32586956 DOI: 10.1073/Pnas.2004223117  0.488
2020 Fraik AK, Margres MJ, Epstein B, Barbosa S, Jones M, Hendricks S, Schönfeld B, Stahlke AR, Veillet A, Hamede R, McCallum H, Lopez-Contreras E, Kallinen SJ, Hohenlohe PA, Kelley JL, et al. Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. Evolution; International Journal of Organic Evolution. PMID 32445281 DOI: 10.1111/Evo.14023  0.447
2020 Kelley JL, Gilad Y. Effective study design for comparative functional genomics. Nature Reviews. Genetics. PMID 32332928 DOI: 10.1038/S41576-020-0242-Z  0.333
2019 McGowan KL, Passow CN, Arias-Rodriguez L, Tobler M, Kelley JL. Expression analyses of cave mollies () reveal key genes involved in the early evolution of eye regression. Biology Letters. 15: 20190554. PMID 31640527 DOI: 10.1098/Rsbl.2019.0554  0.333
2019 Fraik AK, Quackenbush C, Margres MJ, Comte S, Hamilton DG, Kozakiewicz CP, Jones M, Hamede R, Hohenlohe PA, Storfer A, Kelley JL. Transcriptomics of Tasmanian Devil () Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape. Genes. 10. PMID 31614864 DOI: 10.3390/Genes10100801  0.382
2019 Hotaling S, Shain DH, Lang SA, Bagley RK, Tronstad LM, Weisrock DW, Kelley JL. Long-distance dispersal, ice sheet dynamics and mountaintop isolation underlie the genetic structure of glacier ice worms. Proceedings. Biological Sciences. 286: 20190983. PMID 31213183 DOI: 10.1098/Rspb.2019.0983  0.346
2019 Brown AP, McGowan KL, Schwarzkopf EJ, Greenway R, Rodriguez LA, Tobler M, Kelley JL. Local ancestry analysis reveals genomic convergence in extremophile fishes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 374: 20180240. PMID 31154969 DOI: 10.1098/Rstb.2018.0240  0.587
2019 Hotaling S, Kelley JL. The rising tide of high-quality genomic resources. Molecular Ecology Resources. 19: 567-569. PMID 31004471 DOI: 10.1111/1755-0998.12964  0.348
2019 Hotaling S, Kelley JL, Weisrock DW. Nuclear and mitochondrial genomic resources for the meltwater stonefly (Plecoptera: Nemouridae), Lednia tumana (Ricker, 1952) Aquatic Insects. 40: 362-369. DOI: 10.1080/01650424.2019.1639764  0.366
2018 Brown AP, Arias-Rodriguez L, Yee MC, Tobler M, Kelley JL. Concordant changes in gene expression and nucleotides underlie independent adaptation to hydrogen-sulfide-rich environments. Genome Biology and Evolution. PMID 30215710 DOI: 10.1093/Gbe/Evy198  0.493
2018 Hotaling S, Quackenbush CR, Bennett-Ponsford J, New DD, Arias-Rodriguez L, Tobler M, Kelley JL. Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams. Microbial Ecology. PMID 30105506 DOI: 10.1007/S00248-018-1237-6  0.373
2018 Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: adaptation and speciation in sulfide spring fishes. Molecular Ecology. PMID 29368386 DOI: 10.1111/Mec.14497  0.453
2017 Lins LSF, Trojahn S, Sockell A, Yee MC, Tatarenkov A, Bustamante CD, Earley RL, Kelley JL. Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate. Genome. PMID 29268023 DOI: 10.1139/Gen-2017-0188  0.484
2017 Barts N, Greenway R, Passow CN, Arias-Rodriguez L, Kelley JL, Tobler M. Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs. Genome. PMID 29227751 DOI: 10.1139/Gen-2017-0051  0.389
2017 Passow CN, Henpita C, Shaw JH, Quackenbush CR, Warren WC, Schartl M, Arias-Rodriguez L, Kelley JL, Tobler M. The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish. Molecular Ecology. PMID 28926156 DOI: 10.1111/Mec.14360  0.452
2017 Brown AP, Greenway R, Morgan S, Quackenbush CR, Giordani L, Arias-Rodriguez L, Tobler M, Kelley JL. Genome-scale data reveals that endemic Poecilia populations from small sulfidic springs display no evidence of inbreeding. Molecular Ecology. PMID 28731545 DOI: 10.1111/Mec.14249  0.432
2017 Passow CN, Brown AP, Arias-Rodriquez L, Yee MC, Sockell A, Schartl M, Warren WC, Bustamante C, Kelley JL, Tobler M. Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Molecular Ecology. PMID 28598519 DOI: 10.1111/Mec.14198  0.464
2017 Fu Z, Epstein B, Kelley JL, Zheng Q, Bergland AO, Castillo Carrillo CI, Jensen AS, Dahan J, Karasev AV, Snyder WE. Using NextRAD sequencing to infer movement of herbivores among host plants. Plos One. 12: e0177742. PMID 28505182 DOI: 10.1371/Journal.Pone.0177742  0.327
2017 Cribbin KM, Quackenbush CR, Taylor K, Arias-Rodriguez L, Kelley JL. Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar. Bmc Genomics. 18: 283. PMID 28388875 DOI: 10.1186/S12864-017-3652-3  0.371
2017 Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Responsible RAD: Striving for best practices in population genomic studies of adaptation. Molecular Ecology Resources. PMID 28382730 DOI: 10.1111/1755-0998.12677  0.346
2017 Stinchcombe JR, Kelley JL, Conner JK. How to measure natural selection Methods in Ecology and Evolution. 8: 660-662. DOI: 10.1111/2041-210X.12816  0.317
2016 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. Molecular Ecology Resources. PMID 27860289 DOI: 10.1111/1755-0998.12635  0.535
2016 Hoban S, Kelley JL, Lotterhos KE, Antolin MF, Bradburd G, Lowry DB, Poss ML, Reed LK, Storfer A, Whitlock MC. Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions. The American Naturalist. 188: 379-397. PMID 27622873 DOI: 10.1086/688018  0.509
2016 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. Molecular Ecology Resources. PMID 27618670 DOI: 10.1111/1755-0998.12596  0.423
2016 Kelley JL, Brown AP, Therkildsen NO, Foote AD. The life aquatic: advances in marine vertebrate genomics. Nature Reviews. Genetics. PMID 27376488 DOI: 10.1038/Nrg.2016.66  0.505
2016 Daubert DM, Kelley JL, Udod YG, Habor C, Kleist CG, Furman IK, Tikonov IN, Swanson WJ, Roberts FA. Human enamel thickness and ENAM polymorphism. International Journal of Oral Science. 8: 93-7. PMID 27357321 DOI: 10.1038/Ijos.2016.1  0.647
2016 Kelley JL, Yee MC, Brown AP, Richardson RR, Tatarenkov A, Lee CC, Harkins TT, Bustamante CD, Earley RL. 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. PMID 27324916 DOI: 10.1093/Gbe/Evw145  0.483
2016 Benestan L, Ferchaud AL, Hohenlohe P, Garner BA, Naylor GJ, Baums I, Schwartz M, Kelley JL, Luikart G. Conservation genomics of natural and managed populations: building a conceptual and practical framework. Molecular Ecology. PMID 27086132 DOI: 10.1111/Mec.13647  0.421
2016 Kelley JL, Arias-Rodriguez L, Martin DP, Yee MC, Bustamante CD, Tobler M. Mechanisms underlying adaptation to life in hydrogen sulfide rich environments. Molecular Biology and Evolution. PMID 26861137 DOI: 10.1093/Molbev/Msw020  0.473
2016 Cooke TF, Yee MC, Muzzio M, Sockell A, Bell R, Cornejo OE, Kelley JL, Bailliet G, Bravi CM, Bustamante CD, Kenny EE. GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data. Plos Genetics. 12: e1005631. PMID 26828719 DOI: 10.1371/Journal.Pgen.1005631  0.442
2016 Tobler M, Passow CN, Greenway R, Kelley JL, Shaw JH. The Evolutionary Ecology of Animals Inhabiting Hydrogen Sulfide–Rich Environments Annual Review of Ecology, Evolution, and Systematics. 47: 239-262. DOI: 10.1146/Annurev-Ecolsys-121415-032418  0.334
2015 Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Bustamante CD, Hammer MF, Wall JD. The Time-Scale Of Recombination Rate Evolution In Great Apes. Molecular Biology and Evolution. PMID 26671457 DOI: 10.1093/Molbev/Msv331  0.421
2015 McManus KF, Kelley JL, Song S, Veeramah KR, Woerner AE, Stevison LS, Ryder OA, Ape Genome Project G, Kidd JM, Wall JD, Bustamante CD, Hammer MF. Inference of gorilla demographic and selective history from whole-genome sequence data. Molecular Biology and Evolution. 32: 600-12. PMID 25534031 DOI: 10.1093/Molbev/Msu394  0.519
2014 McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA, Fiston-Lavier AS. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. Plos One. 9: e106689. PMID 25188499 DOI: 10.1371/Journal.Pone.0106689  0.412
2014 Kelley JL, Peyton JT, Fiston-Lavier AS, Teets NM, Yee MC, Johnston JS, Bustamante CD, Lee RE, Denlinger DL. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nature Communications. 5: 4611. PMID 25118180 DOI: 10.1038/Ncomms5611  0.464
2014 Pfenninger M, Lerp H, Tobler M, Passow C, Kelley JL, Funke E, Greshake B, Erkoc UK, Berberich T, Plath M. Parallel evolution of cox genes in H2S-tolerant fish as key adaptation to a toxic environment. Nature Communications. 5: 3873. PMID 24815812 DOI: 10.1038/Ncomms4873  0.408
2014 Tobler M, Henpita C, Bassett B, Kelley JL, Shaw JH. H2S exposure elicits differential expression of candidate genes in fish adapted to sulfidic and non-sulfidic environments. Comparative Biochemistry and Physiology. Part a, Molecular & Integrative Physiology. 175: 7-14. PMID 24813672 DOI: 10.1016/J.Cbpa.2014.04.012  0.398
2014 McCoy RC, Garud NR, Kelley JL, Boggs CL, Petrov DA. Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population. Molecular Ecology. 23: 136-50. PMID 24237665 DOI: 10.1111/Mec.12591  0.485
2013 Ma X, Kelley JL, Eilertson K, Musharoff S, Degenhardt JD, Martins AL, Vinar T, Kosiol C, Siepel A, Gutenkunst RN, Bustamante CD. Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). Plos One. 8: e77175. PMID 24194868 DOI: 10.1371/Journal.Pone.0077175  0.554
2013 Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, et al. Great ape genetic diversity and population history. Nature. 499: 471-5. PMID 23823723 DOI: 10.1038/Nature12228  0.494
2013 Ségurel L, Austerlitz F, Toupance B, Gautier M, Kelley JL, Pasquet P, Lonjou C, Georges M, Voisin S, Cruaud C, Couloux A, Hegay T, Aldashev A, Vitalis R, Heyer E. Positive selection of protective variants for type 2 diabetes from the Neolithic onward: a case study in Central Asia. European Journal of Human Genetics : Ejhg. 21: 1146-51. PMID 23340510 DOI: 10.1038/Ejhg.2012.295  0.459
2012 Teets NM, Peyton JT, Colinet H, Renault D, Kelley JL, Kawarasaki Y, Lee RE, Denlinger DL. Gene expression changes governing extreme dehydration tolerance in an Antarctic insect. Proceedings of the National Academy of Sciences of the United States of America. 109: 20744-9. PMID 23197828 DOI: 10.1073/Pnas.1218661109  0.394
2012 Kelley JL, Passow CN, Plath M, Arias Rodriguez L, Yee MC, Tobler M. Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome. Bmc Genomics. 13: 652. PMID 23170846 DOI: 10.1186/1471-2164-13-652  0.514
2012 Kelley JL. Systematic underestimation of the age of selected alleles. Frontiers in Genetics. 3: 165. PMID 22969791 DOI: 10.3389/Fgene.2012.00165  0.507
2012 Kelley JL, Yee MC, Lee C, Levandowsky E, Shah M, Harkins T, Earley RL, Bustamante CD. The possibility of de novo assembly of the genome and population genomics of the mangrove rivulus, Kryptolebias marmoratus. Integrative and Comparative Biology. 52: 737-42. PMID 22723055 DOI: 10.1093/Icb/Ics094  0.509
2011 Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M. Classic selective sweeps were rare in recent human evolution. Science (New York, N.Y.). 331: 920-4. PMID 21330547 DOI: 10.1126/Science.1198878  0.513
2010 Kelley JL, Aagaard JE, MacCoss MJ, Swanson WJ. Functional diversification and evolution of antifreeze proteins in the antarctic fish Lycodichthys dearborni. Journal of Molecular Evolution. 71: 111-8. PMID 20686757 DOI: 10.1007/S00239-010-9367-6  0.623
2010 Kosova G, Pickrell JK, Kelley JL, McArdle PF, Shuldiner AR, Abney M, Ober C. The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate. Plos Genetics. 6: e1000974. PMID 20532200 DOI: 10.1371/Journal.Pgen.1000974  0.419
2009 Kelley JL, Turkheimer K, Haney M, Swanson WJ. 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. PMID 19060005 DOI: 10.1093/Hmg/Ddn399  0.723
2008 Kelley JL, Swanson WJ. Positive selection in the human genome: from genome scans to biological significance. Annual Review of Genomics and Human Genetics. 9: 143-60. PMID 18505377 DOI: 10.1146/Annurev.Genom.9.081307.164411  0.693
2008 Kelley JL, Swanson WJ. Dietary change and adaptive evolution of enamelin in humans and among primates. Genetics. 178: 1595-603. PMID 18245370 DOI: 10.1534/Genetics.107.077123  0.702
2006 Kelley JL, Madeoy J, Calhoun JC, Swanson W, Akey JM. Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Research. 16: 980-9. PMID 16825663 DOI: 10.1101/Gr.5157306  0.723
2005 Thomas JH, Kelley JL, Robertson HM, Ly K, Swanson WJ. Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae. Proceedings of the National Academy of Sciences of the United States of America. 102: 4476-81. PMID 15761060 DOI: 10.1073/Pnas.0406469102  0.607
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