PUBLICATIONS

2024

Jordan Little, Maria Chikina, Nathan L Clark (2024) Evolutionary rate covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions eLife 2024. 12:RP93333

Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E; Zoonomia Consortium**; Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science 2024: eabn3263. PMID: 38422184 PDF

Ruby Redlich, Amanda Kowalczyk, Michael Tene, Heather H Sestili, Kathleen Foley, Elysia Saputra, Nathan Clark, Maria Chikina, Wynn K Meyer, Andreas Pfenning. RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution. bioRxiv 2023

Emily EK Kopania, Gregg WC Thomas, Carl R Hutter, Sebastian ME Mortimer, Colin M Callahan, Emily Roycroft, Anang S Achmadi, William G Breed, Nathan L Clark, Jacob A Esselstyn, Kevin C Rowe, Jeffrey M Good. Molecular evolution of male reproduction across species with highly divergent sperm morphology in diverse murine rodents. bioRxiv, 2023.08. 30.555585

2023

Sarah A.M. Lucas, Allie M Graham, Jason S Presnell, Nathan L Clark. Highly Dynamic Gene Family Evolution Suggests Changing Roles for PON Genes Within Metazoa. Genome Biology and Evolution, 2023; 15(2): evad011 PDF

Allie M Graham, Jerrica M Jamison, Marisol Bustos, Clement E Furlong, Rebecca Richter, Judit Marsillach, Jason S Presnell, Dan Crocker, Lorrie Rea, Alexis Michaels, Ari Fustukjian, Wynn K Meyer, and Nathan L Clark. Reduction of Paraoxonase expression followed by inactivation across semiaquatic mammals suggests adaptive benefit of gene loss. MBE 2023; 40(5): msad104 PDF

Marlen C Rice, Jordan H Little, Dale L Forrister, Julane Machado, Nathan L Clark, James A Gagnon. Gadusol is a maternally provided sunscreen that protects fish embryos from DNA damage. Current Biology 2023; 33(1): P3229-3237.E4.

2022

Amanda Kowalczyk, Maria Chikina, Nathan Clark. Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness. eLife. 2022; 11:e76911. Featured in an eLife Digest by Matt Dean

Wang X-P, Balchak DM, Gentilcore C, Clark NL, Kashlan OB. Activation by Cleavage of the Epithelial Na+ Channel α and γ Subunits Independently Coevolved with the Vertebrate Terrestrial Migration. eLife. 2022; 11: e75796. PMC8791634

Catalina Pereira, Gerardo A. Arroyo-Martinez, Matthew Z. Guo, Michael S. Downey, Emma R. Kelly, Kathryn J. Grive, Shantha K. Mahadevaiah, Jennie Sims, Vitor Marcel Faça, Charlton Tsai, Carl J. Schiltz, Niek Wit, Heinz Jacobs, Nathan L. Clark, Raimundo Freire, James M. A. Turner, Amy M. Lyndaker, Miguel A. Brieño-Enríquez, Paula E. Cohen, Marcus B. Smolka, Robert S. Weiss. Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis. eLife. 2022; 11: e68677. PMC8824475

Jana Vondrakova, Michaela Frolikova, Lukas Ded, Jiri Cerny, Pavla Postlerova, Veronika Palenikova, Ondrej Simonik, Krystof Basus, Eliska Valaskova, Radek Machan, Allan Pacey, Zuzana Holubcova, Pavel Koubek, Zuzana Ezrova, Zuzana Nahacka, Soojin Park, Ruiwu Liu, Raghavendran Partha, Nathan Clark, Jiri Neuzil, Masahito Ikawa, Kent Erickson, Kit S. Lam, Harry Moore & Katerina Komrskova. MAIA, Fc receptor-like 3, supersedes JUNO as IZUMO1 receptor during human fertilization. Science Advances. 2022; 8: eabn0047.

2021

Saputra E, Kowalczyk A, Cusick L, Clark NL, Chikina M. Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations between phenotypes and genetic elements in a phylogenetic context. Molecular Biology and Evolution. 2021; msab068. PDF

Furman CM, Elbashir R, Pannafino G, Clark NL, Alani E. Experimental exchange of paralogous domains in the MLH family provides evidence of sub-functionalization after gene duplication. G3 Genes| Genomes|Genetics. 2021. jkab111.

Keeble S, Firman RC, Sarver BAJ, Clark NL, Simmons LW, Dean MD. Evolutionary, proteomic, and experimental evidence that the extracellular matrix of cumulus cells impacts fertilization outcomes. Biology of Reproduction. 2021. PDF

Kowalczyk A, Gbadamosi O, Kolor K Sosa Jahree, St Croix C, Gibson G, Chikina M, Aizenman E, Clark NL, Kiselyov K. Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter. Biochemical Journal. 2021. 478 (17): 3205-3220. PDF

Amanda Kowalczyk, Maria Chikina, Nathan L Clark. A cautionary tale on proper use of branch-site models to detect convergent positive selection. bioRxiv 2021.10.26.465984;

2020

Kowalczyk, A, Partha R, Clark NL, and Chikina M. Pan-mammalian analysis of molecular constraints underlying extended lifespan. eLife. 2020; 9: e51089.

Talsness DM, Owings KG, Coelho E, Mercenne G, Pleinis JM, Partha R, Hope KA, Zuberi AR, Clark NL, Lutz CM, Rodan AR, Chow CY. A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency. eLife. 2020;9 e57831.

Jen-Wei Huang, Ananya Acharya, Angelo Taglialatela, Tarun Nambiar, Raquel Cuella-Martin, Giuseppe Leuzzi, Samuel Hayward, Sarah Joseph, Gregory Brunette, Roopesh Anand, Rajesh Soni, Nathan Clark, Kara Bernstein, Petr Cejka, and Alberto Ciccia. MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage. Nature Communications. 2020; 11: 2928

2019

Sackton TB and Clark NL. Convergent evolution in the genomics era: new insights and directions. Philosophical Transactions of the Royal Society B. 2019; 374(1777): Article ID 20190102.

Kowalczyk A, Meyer WK, Partha R, Mao W, Clark NL, Chikina M. RERconverge: an R package for associating evolutionary rates with convergent traits. Bioinformatics. 2019; 1-3: btz468. PDF

Partha R, Kowalczyk A, Clark NL, Chikina M. Robust methods for detecting convergent shifts in evolutionary rates. Molecular Biology and Evolution. 2019; 36(8): 1817-1830. PDF

Plakke MS, Walker JL, Lombardo JB, Goetz BJ, Pacella GN, Durrant JD, Clark NL, Morehouse NI. Characterization of Female Reproductive Proteases in a Butterfly from Functional and Evolutionary Perspectives. Physiol Biochem Zool. 2019; 92(6): 579-590. https://doi.org/10.1086/705722 PDF

Raza Q, Choi JY, Li Y, O’Dowd RM, Watkins SC, Hong Y, Clark NL, Kwiatkowski AV. Evolutionary rate covariation identifies the GTPase activating protein Raskol as a signaling component of the cadherin adhesion network in Drosophila. PLOS Genetics. 2019; 15(2): e1007720. Featured in Perspective by Jeffrey Colgren and Scott Nichols. Evolution as a guide for experimental cell biology.

Brunette GJ, Jamalruddin MA, Baldock RA, Clark NL, Bernstein KA. Evolution-based screening enables genome-wide prioritization and discovery of DNA repair genes. Proceedings of the National Academy of Sciences, USA. 2019; 116(39): 19593-19599. PDF

Hill JA, Neethiraj R, Rastas P, Clark NL, Morehouse NI, de la Paz Celorio-Mancera M, Cols JC, Dircksen H, Meslin C, Sikkink K, Vives M, Vogel H, Wiklund C, Boggs CL, Nylin, Wheat CW. A butterfly chromonome reveals selection dynamics during extensive and cryptic chromosomal reshuffling. Science Advances. 2019; 12:5(6):eaau3648. PDF

Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark NL, Chen V, Lu S Chen L, Yu L, Hochheiser HS, Jiang X, Wang J, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLOS Computational Biology. 2019; 15(7): e1007088.

2018

Wynn K. Meyer, Jerrica Jamison, Rebecca Richter, Stacy E. Woods, Charles Kronk, Raghavendran Partha, Amanda Kowalczyk, Maria Chikina, Robert K. Bonde, Joseph Gaspard, Janet M. Lanyon, Clement E. Furlong, and Nathan L. Clark. Ancient convergent losses of Paraoxonase 1 yield deleterious consequences for modern marine mammals. Science. 2018; 361(6402): 591-594. PDF

Sumitha Nallu, Jason Hill, Kristine Don, Carlos Sahagun, Wei Zhang, Camille Meslin, Emilie Snell-Rood, Nathan L. Clark, Nathan I. Morehouse, Joy Bergelson, Christopher W. Wheat and Marcus R. Kronforst. The molecular genetic basis of herbivory between butterflies and their host-plants. Nature: Ecology and Evolution. 2018; 2: 1418-1427. PDF

2017

Partha R, Chauhan BK, Worman-Ferreria Z, Robinson JD, Lathrop K, Nischal KK, Chikina M*, Clark NL*. Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling. eLife. 2017; 6: e25884.

Meslin C, Cherwin TS, Plakke MS, Small BS, Goetz BJ, Morehouse NI, Clark NL. Structural complexity and molecular heterogeneity of a butterfly ejaculate reflect a complex history of selection. Proceedings of the National Academy of Sciences, USA. 2017; 114(27): E5406–E5413. Featured in The Atlantic. PDF

2016

Clancy CJ, Meslin C, Badrane H, Cheng S, Losada LC, Nierman WC, Vergidis P, Clark NL, Nguyen MH. Candida albicans transcriptional profiling within biliary fluid from a patient with cholangitis, before and after antifungal treatment and surgical drainage. Open Forum Infectious Diseases. 2016; 3(3):ofw120. PDF

Chikina M, Robinson JD, Clark NL. Hundreds of genes experienced convergent shifts in selective pressure in marine mammals. Molecular Biology and Evolution. 2016. 33(9): 2182-2192. PDF

Böhm S, Szakal B, Herken BW, Sullivan MR, Mihalevic MJ, Kabbinavar FF, Branzei D, Clark NL, Bernstein KA. The budding yeast ubiquitin protease Ubp7 is a novel component involved in S-phase progression. Journal of Biological Chemistry. 2016; 291(9): 4442-52. PDF

Ziegler A, Augustin H, Clark NL, Berthelot-Grosjean M, Simonnet M, Steinert J, Geillon F, Maniere G, Featherstone D, and Grosjean Y. The Amino Acid Transporter JhI-21 Coevolves with Glutamate Receptors, Impacts NMJ Physiology, and Influences Locomotor Activity in Drosophila Larvae. Scientific Reports. 2016. 6:19692. PDF

2015

Wolfe NW, Clark NL. ERC Analysis: web-based inference of gene function via Evolutionary Rate Covariation. Bioinformatics. 2015. doi:10.1093/bioinformatics/btv454. PDF

Mangels R, Young B, Keeble S, Ardekani R, Meslin C, Ferreira Z, Clark NL, Good JM, Dean MD. Genetic and phenotypic influences on copulatory plug survival in mice. Heredity. 2015. 115, 496-502. PDF

Plakke MS, Deutsch AB, Meslin C, Clark NL, Morehouse NI. Dynamic digestive physiology of a female reproductive organ in a polyandrous butterfly. Journal of Experimental Biology. 2015. 218, 1548-1555. Featured in “Inside JEB”. PDF

Hancks DC, Hartley MK, Hagan C, Clark NL, Elde NC. Overlapping Patterns of Rapid Evolution in the Nucleic Acid Sensors cGAS and OAS1 Suggest a Common Mechanism of Pathogen Antagonism and Escape. PLOS Genetics. 2015. 11(5): e1005203

Godin SK, Meslin C, Bratton-Palmer DS, Hornack C, Mihalevic MJ, Yoshida K, Kabbinavar F, Sullivan M, Clark NL*, Bernstein KA*. Evolutionary and functional analysis of the invariant SWIM domain in the conserved Shu2/SWS1 protein family from Saccharomyces cerevisiae to Homo sapiens. Genetics. 2015. 199(4): 1023-1033. Selected for Issue Highlight & Featured by Saccharomyces Genome Database Blog. PDF

Meslin C, Plakke MS, Deutsch AB, Small BS, Morehouse NI, Clark NL. Digestive Organ in the Female Reproductive Tract Borrows Genes from Multiple Organ Systems to Adopt Critical Functions. Molecular Biology and Evolution. 2015. 32(6): 1567-1580. PDF

Priedigkeit NM, Wolfe NW, Clark NL. Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene networks. PLOS Genetics. 2015; 11(2): e1004967.

2014

Findlay GD, Sitnik JL, Wang W, Aquadro CF, Clark NL, Wolfner MF. Evolutionary Rate Covariation Identifies New Members of a Protein Network Required for Drosophila Female Post-Mating Responses. PLOS Genetics. 2014; 10(1): e1004108. Featured in Faculty of 1000.

2009

Clark NL, Gasper J, Sekino M, Springer SA, Aquadro CF, Swanson WJ. Coevolution of interacting fertilization proteins. PLOS Genetics 2009; 5(7): e1000570.

Dean MD, Clark NL, Findlay GD, Karn RC, Yi X, Swanson WJ, MacCoss MJ, Nachman MJ. Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus). Molecular Biology and Evolution. 2009; 26(8): 1733. PDF

2008

Clark NL. Adaptive evolution of primate sperm proteins. In: Encyclopedia of Life Sciences (ELS). 2008. John Wiley and Sons, Ltd: Chichester. PDF

Karn RC, Clark NL, Nguyen ED, Swanson WJ. Adaptive evolution in rodent seminal vesicle proteins. Molecular Biology and Evolution. 2008; 25(11): 2301. PDF

2007

Clark NL, Findlay GD, Yi X, MacCoss MJ, Swanson WJ. Duplication and selection on abalone sperm lysin in an allopatric population. Molecular Biology and Evolution. 2007; 24(9): 2081. PDF

2006

Panhuis, TM, Clark, NL & Swanson, WJ. Rapid evolution of reproductive proteins in abalone and Drosophila. Philosophical Transactions of the Royal Society B. 2006; 361: 261-268. PDF

Clark NL, Aagaard JE, Swanson WJ. Evolution of reproductive proteins from animals and plants. Reproduction 2006; 131(1): 11-22. PDF

2005

Clark NL, Swanson WJ. Pervasive adaptive evolution in primate seminal proteins. PLOS Genetics. 2005; 1(3): e35.

Stewart MK, Clark NL, Merrihew G, Galloway EM, Thomas JH. High genetic diversity in the chemoreceptor superfamily of Caenorhabditis elegans. Genetics. 2005; 169(4): 1985-1996. PDF