Profile picture of Clayton Small

Clayton Small

Research Assistant Professor
Data Science
Phone: 541-346-4232
Office: 319 Pacific Hall
Office Hours: Tuesday 3-4:30
Research Interests: Evolutionary Genomics, Computational Biology, Data Science


Clay Small is an evolutionary genomicist who studies the genetic underpinnings of traits and host-microbe interactions in animals, especially bony fishes. He currently works as a Research Assistant Professor in the Department of Data Science. Clay received his B.S. in Zoology from the University of Idaho in 2003, and after working as a wildlife ecologist for a few years he began graduate study with renowned evolutionary geneticist Adam Jones at Texas A&M University. His dissertation work on the evolution of reproductive proteins (particularly those associated with male pregnancy in seahorses and their relatives) coincided with the advent of next-generation sequencing. Clay did his postdoctoral work in Bill Cresko's Lab at the UO, and he continues collaborative work with the Institute of Ecology and Evolution to date. Since joining the University of Oregon Clay has enjoyed working on a diversity of genomics research projects and teaching graduate students about genomics, R, statistical inference, and data visualization, including several years with the Knight Campus Bioinformatics and Genomics Master's Program.


Ph.D., Zoology - Texas A&M University, College Station, TX

B.S., Zoology, cum laude - University of Idaho, Moscow, ID


I am an evolutionary genomicist interested in the repeatability of evolution, specifically with respect to phenotypic novelties and host-microbe interactions. My research integrates across the fields of computational biology, evo-devo, and microbial ecology, united under the theme of understanding how the "genomic rules" of adaptation predict biodiversity at molecular, phenotypic and community levels.


To address these questions I mostly focus on diversity within several clades of ray-finned fishes. I currently work on three primary study systems: 1. The genomic basis of male pregnancy, including the repeated evolution of complex pregnancy, in seahorses, pipefishes, and seadragons; 2. The evolution of fish-associated microbiomes, particularly how host genetic variation shapes, constrains, and facilitates the predictability of microbial community assembly and molecular evolution; and 3. The developmental genetic underpinnings of a novel, non-mineralized bone tissue type which has evolved repeatedly in sculpin fishes and their relatives.


My training is unique in its breadth, marked by a few career highlights. As a graduate student I developed the first next-generation transcriptomic resources for pipefishes, and I have since been a leader on several genome projects for this group of fishes, including the Gulf pipefish genome (2016) and the leafy and weedy seadragon genomes (2022). As a postdoc I played key roles in developing the threespine stickleback fish as a model for the study of host-microbe interactions, experimental and analytical work that I continue today.


Ramesh B, Small CM, Healey HM, Johnson B, Barker E, Currey MC, Bassham S, Myers M, Cresko WA, Jones AG. 2023. Improvements to the Gulf pipefish Syngnathus scovelli genome. GigaByte10.46471/gigabyte.76.


Frantz SI, Small CM, Cresko WA, Singh ND. 2023. Ovarian transcriptional response to Wolbachia infection in D. melanogaster in the context of between-genotype variation in gene expression. G310.1093/g3journal/jkad047.


Small CM, Healey HM, Currey MC, Beck EA, Catchen J, Lin ASP, Cresko WA, Bassham S. 2022. Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes. PNAS 119:e2119602119 (cover article).


Johnson BD, Anderson AP, Small CM, Rose E, Flanagan SP, Hendrickson-Rose C, Jones AG. 2022. The evolution of the testis transcriptome in pregnant male pipefishes and seahorses. Evolution76:2162-2180.


Petersen AM, Small CM, Yan Y, Wilson C, Bremiller RA, Buck LC, von Hippel FA, Cresko WA, Postlethwait JH. 2022. Evolution and developmental expression of the sodium iodide symporter (NIS, slc5a5) gene family: Implications for perchlorate toxicology. Evolutionary Applications 15:1079-1098.


Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. 2021. Advancing human disease research with fish evolutionary mutant models. Trends in Genetics 38:22-44.


Beck EA, Currey M, Small CM, Cresko WA. 2020. QTL mapping of intestinal neutrophil variation in threespine stickleback reveals possible gene targets connecting intestinal inflammation and systemic health. G3 g3.119.400685.


Small CM, Currey M, Beck EA, Bassham S, Cresko WA. 2019. Highly reproducible 16S sequencing facilitates measurement of host genetic influences on the stickleback gut microbiome. mSystems4:e00331-19.


Cytrynbaum EG, Small CM, Kwon RY, Boaz H, Kent D, Yan Y, Knope ML, Bremiller RA, Desvignes T, Kimmel CB. 2019. Developmental tuning of mineralization drives morphological diversity of gill cover bones in sculpins and their relatives. Evolution Letters 3:374-391.


Kimmel CB, Small CM, Knope ML. 2017. A rich diversity of opercle bone shape among teleost fishes. PLoS One 12:e188888.


Small CM, Milligan-Myhre K, Bassham S, Guillemin K, Cresko WA. 2017. Host genotype and microbiota contribute asymmetrically to transcriptional variation in the threespine stickleback gut. Genome Biology and Evolution 9:504-520.


Small CM, Bassham S, Catchen J, Amores A, Fuiten AF, Brown RS, Jones AG, Cresko WA. 2016. The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biology17:258


Milligan-Myhre K, Small CM, Mittge EK, Agarwal M, Cresko WA, Guillemin K. 2016. Innate immune responses to gut microbiota differ between threespine stickleback populations. Disease Models and Mechanisms 9:187-198.


Rose E, Small CM, Saucedo HA, Harper C, Jones AG. 2014. Genetic evidence for monogamy in the dwarf seahorse, Hippocampus zosterae. Journal of Heredity 105:828-833.


Small CM, Harlin-Cognato AD, Jones AG. 2013. Functional similarity and molecular divergence of a novel reproductive transcriptome in two male-pregnant Syngnathus pipefish species. Ecology and Evolution 3:4092-4108.


Mobley KB, Small CM, Jones AG. 2011. Molecular insights into syngnathid biology: the genetics and genomics of pipefishes, seahorses, and seadragons. Journal of Fish Biology 78:1624-1646.


Mobley KB, Small CM, Jue NK, Jones AG. 2010. Population structure of the dusky pipefish (Syngnathus floridae) from the Atlantic and Gulf of Mexico, as revealed by mitochondrial DNA and microsatellite analyses. Journal of Biogeography 37:1363-1377.


Jones AG, Small CM, Paczolt KA, Ratterman NL. 2010. A practical guide to methods of parentage analysis.  Molecular Ecology Resources 10:6-30.


Small CM, Carney GE, Mo Q, Vannucci M, Jones AG. 2009. A microarray analysis of sex- and gonad-biased gene expression in the zebrafish: evidence for masculinization of the transcriptome.BMC Genomics 10:579.