Publications

2025

Quantitative genetics of microbiome-mediated traits

Week B, Ralph PL, Tavalire HF, Cresko WA, Bohannan BJM. Evolution qpaf171.

Attendance of Underserved Populations at Field-Based Health Services Events

Leve LD, DeGarmo DS, Searcy J, Budd EL, Ramírez García JI, Mauricio AM, Cresko WA. Prevention Science 1-11.

Signatures and likely sources of the male pregnancy microbiome in wild bay pipefish

Barker EM, Small CM, Bassham S, Beck EA, Currey MC, Healey HM, Johnson BD, Cresko WA, Jones AG. Animal Microbiome 7(1):112.

Single-cell sequencing provides clues about the developmental genetic basis of evolutionary adaptations in syngnathid fishes

Healey HM, Penn HB, Small CM, Bassham S, Goyal V, Woods MA, Cresko WA. eLife 13:RP97764.

Predator induced phenotypes are inherited over four generations in genetically identical Daphnia lumholtzi

Snyder SN, Meyer WC, Jorgenson SL, Contreras EB, Bland T, Cresko WA. bioRxiv and in review at Evolution.

Spontaneous mutant in threespine stickleback connects endosome trafficking disorders and inflammatory bowel diseases

Beck EA, Smith CA, Currey MC, Small CM, Bohannan BJM, Cresko WA. bioRxiv and in review at G3.

2024

Chromosome-scale genome assemblies for 10 syngnathiform fishes produced using a standardized sequencing and annotation workflow

Ramesh B, Small CM, Bassham S, Johnson B, Barker E, Rose E, Currey MC, Healey HM, Myers M, Ahnesjö I, Kvarnemo L, Monteiro N, Cresko WA, Jones AG. bioRxiv and in review at Molecular Ecology.

2023

Host genomic variation shapes gut microbiome diversity in threespine stickleback fish

Small CM, Beck EA, Currey MC, Tavalire HF, Bassham S, Cresko WA. mBio 14:e0021923.

Genome-wide analysis facilitates estimation of male contribution in meiotic gynogenesis

Currey MC, Walker C, Bassham S, Healey HM, Beck EA, Cresko WA. Journal of Fish Biology 102(4):844-855.

Improvements to the Gulf pipefish genome

Ramesh B, Small CM, Healey HM, Johnson B, Barker E, Currey MC, Bassham S, Myers M, Cresko WA, Jones AG. GigaByte 2023:gigabyte76.

Reaching Latinx communities with algorithmic optimization for SARS-CoV-2 testing locations

Searcy JA, Cioffi CC, Tavalire HF, Budd EL, Cresko WA, DeGarmo DS, Leve LD. Prevention Science 24:1249-1260.

Ovarian transcriptional response to Wolbachia infection in D. melanogaster

Frantz SI, Small CM, Cresko WA, Singh ND. G3: Genes|Genomes|Genetics 13(5):jkad047.

2022

Extreme intraspecific divergence in mitochondrial haplotypes makes threespine stickleback an emerging evolutionary model

Beck EA, Bassham S, Cresko WA. Frontiers in Genetics 13:925786.

Leafy and weedy seadragon genomes connect genic and repetitive DNA to syngnathid biology

Small CM, Healey HM, Currey MC, Beck EA, Catchen J, Lin ASP, Cresko WA, Bassham S. PNAS 119(26):e2119602119.

Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

Healey HM, Bassham S, Cresko WA. Genetics 220(3):iyac017.

Advancing human disease research with fish evolutionary mutant models

Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Trends in Genetics 38:22-44.

Development and design of a culturally tailored intervention to address COVID-19 disparities

Budd EL, McWhirter EH, De Anda S, Mauricio AM, Mueller MV, Cioffi CC, Nash A, Van Brocklin K, Yarris K, Jackson A, Terral H, García JR, Cresko WA, DeGarmo DS, Leve LD. Frontiers in Public Health 10:962862.

Effects of a health education intervention for COVID-19 prevention in Latinx communities

De Anda S, Budd EL, Halvorson S, Mauricio AM, McWhirter EH, Cioffi CC, García JR, Cresko WA, Leve LD, DeGarmo DS. American Journal of Public Health 112:S923-S927.

Effectiveness of a COVID-19 testing outreach intervention for Latinx communities

DeGarmo DS, De Anda S, Cioffi CC, Tavalire HF, Searcy JA, Budd EL, McWhirter EH, Mauricio AM, Halvorson S, Beck EA, Fernandes L, Currey MC, García JR, Cresko WA, Leve LD. JAMA Network Open 5:e2216796.

Evolution and developmental expression of the sodium-iodide symporter gene family

Petersen AM, Small CM, Yan YL, Wilson C, Batzel P, Bremiller RA, Buck CL, von Hippel FA, Cresko WA, Postlethwait JH. Evolutionary Applications 15:1079-1098.

2021

Shared environment and genetics shape the gut microbiome after infant adoption

Tavalire HF, Christie DM, Leve LD, Ting N, Cresko WA, Bohannan BJM. mBio 12(2):e00548-21.

Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance

O’Connor CH, Sikkink KL, Nelson TC, Fierst JL, Cresko WA, Phillips PC. G3: Genes|Genomes|Genetics 11(4):jkab045.

Evolutionary divergence of a Hoxa2b hindbrain enhancer in syngnathids

Fuiten AM, Cresko WA. Development, Genes and Evolution 231:57-71.

Genome-wide single nucleotide polymorphism markers reveal population structure

Rengefors K, Gollnisch R, Sassenhagen I, Härnström Aloisi K, Svensson M, Lebret K, Čertnerová D, Cresko WA, Bassham S, Ahrén D. Molecular Ecology 30:912-925.

A highly contiguous nuclear genome assembly of the mandarinfish

Stervander M, Cresko WA. G3: Genes|Genomes|Genetics 11(12):jkab306.

2020

QTL mapping of intestinal neutrophil variation in threespine stickleback

Beck EA, Currey MC, Small CM, Cresko WA. G3: Genes|Genomes|Genetics 10(2):613-622.

A few stickleback suffice for the transport of alleles to new lakes

Galloway J, Cresko WA, Ralph P. G3: Genes|Genomes|Genetics 10(2):505-514.

2019

Highly reproducible 16S sequencing facilitates measurement of host genetic influences on the stickleback gut microbiome

Small CM, Currey MC, Beck EA, Bassham S, Cresko WA. mSystems 4(4):e00331-19.

Genetic divergence outpaces phenotypic evolution among threespine stickleback populations

Currey MC, Bassham S, Cresko WA. Biological Journal of the Linnean Society 128(2):415-434.

Population genetic divergence and environment influence the gut microbiome

Steury RA, Currey MC, Cresko WA, Bohannan BJM. Genes 10(7):484.

Selection, linkage, and population structure interact to shape genetic variation

Nelson TC, Crandall JG, Ituarte CM, Catchen JM, Cresko WA. Genetics 212:1367-1382.

Environmental and evolutionary drivers of the modular gene regulatory network

Sikkink KL, Reynolds RM, Ituarte CM, Cresko WA, Phillips PC. G3: Genes|Genomes|Genetics 9(3):969-982.

Determining the contributions of stress and inflammation to child health

Tavalire HF, Cresko WA, Leve LD. Behavior Genetics 49(6):504-505.

2018

Repeated selection of alternatively adapted haplotypes creates sweeping genomic remodeling

Bassham S, Catchen J, Lescak E, von Hippel FA, Cresko WA. Genetics 209(3):921-939.

Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations

Nelson TC, Cresko WA. Evolution Letters 2(1):9-21.

Naturalistic experimental designs as tools for understanding the role of genes and the environment

Leve LD, Neiderhiser JM, Harold GT, Natsuaki MN, Bohannan BJM, Cresko WA. Prevention Science 19(1):68-78.

2017

Host genotype and microbiota contribute asymmetrically to transcriptional variation

Small CM, Milligan-Myhre K, Bassham S, Guillemin K, Cresko WA. Genome Biology and Evolution 9(3):504-520.

Exogenous iodide ameliorates perchlorate-induced thyroid phenotypes in stickleback

Gardell AM, von Hippel FA, Adams EM, Dillon DM, Petersen AM, Postlethwait JH, Cresko WA, Buck CL. General and Comparative Endocrinology 243:60-69.

Developmental timing differences underlie armor loss across threespine stickleback populations

Currey MC, Bassham S, Perry S, Cresko WA. Evolution and Development 19(6):231-243.

Ancient three-spined stickleback mtDNA lineages are not associated with phenotypic or nuclear genetic variation

Lescak EA, Wund MA, Bassham S, Catchen J, Prince DJ, Lucas R, Dominguez G, von Hippel FA, Cresko WA. Biological Journal of the Linnean Society 122(3):579-588.

2016

The genome of the Gulf pipefish enables understanding of evolutionary innovations

Small CM, Bassham S, Catchen J, Amores A, Fuiten AM, Brown RS, Jones AG, Cresko WA. Genome Biology 17:258.

Innate immune responses to gut microbiota differ between threespine stickleback populations

Milligan-Myhre K, Small CM, Agarwal M, Mittge EK, Cresko WA, Guillemin K. Disease Models and Mechanisms 9(2):187-198.

Perchlorate exposure reduces primary germ cell number in female stickleback

Petersen AM, Earp N, Redmond M, Postlethwait JH, von Hippel FA, Buck CL, Cresko WA. PLoS One 11(7):e0157792.

2015

Evolution of stickleback in 50 years on earthquake-uplifted islands

Lescak EA, Bassham S, Catchen J, Gelmond O, Sherbick ML, von Hippel FA, Cresko WA. PNAS 112(52):E7204-E7212.

Perchlorate disrupts embryonic androgen synthesis without changing thyroid hormone

Petersen AM, Dillon D, Bernhardt RR, Torunsky R, Postlethwait JH, von Hippel FA, Buck CL, Cresko WA. General and Comparative Endocrinology 210:130-144.

Environmentally induced changes in correlated responses to selection reveal variable pleiotropy

Sikkink KL, Reynolds RM, Cresko WA, Phillips PC. Evolution 69:1128-1142.

Effects of crossovers between homeologs on inheritance and population genomics in polyploid-derived salmonid fishes

Allendorf FW, Bassham S, Cresko WA, Limborg MT, Seeb LW, Seeb JE. Journal of Heredity 106:217-227.

2014

Rapid evolution of phenotypic plasticity and shifting thresholds of genetic assimilation

Sikkink KL, Reynolds RM, Ituarte CM, Cresko WA, Phillips PC. G3: Genes|Genomes|Genetics 4(6):1103-1112.

The transgenerational effects of heat stress in the nematode Caenorhabditis remanei

Sikkink KL, Ituarte CM, Reynolds RM, Cresko WA, Phillips PC. Genomics 104:438-446.

2013

The population structure and recent colonization history of Oregon threespine stickleback

Catchen J, Bassham S, Wilson T, Currey MC, O’Brien C, Yeates Q, Cresko WA. Molecular Ecology 22(11):2864-2883.

Stacks: an analysis tool set for population genomics

Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA. Molecular Ecology 22(11):3124-3140.

Geography of the circadian gene clock and photoperiodic response in western North American populations

O’Brien CS, Unruh L, Zimmerman C, Bradshaw WE, Holzapfel CM, Cresko WA. Journal of Fish Biology 82(3):827-839.

2012

Developmental dissociation in morphological evolution of the stickleback opercle

Kimmel CB, Hohenlohe PA, Ullmann B, Currey MC, Cresko WA. Evolution and Development 14(4):326-337.

Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes

Hohenlohe PA, Bassham S, Currey MC, Cresko WA. Philosophical Transactions of the Royal Society B 367(1587):395-408.

Population genomic analysis of model and nonmodel organisms using sequenced RAD tags

Hohenlohe PA, Catchen J, Cresko WA. Methods in Molecular Biology 888:235-260.

Independent axes of genetic variation and parallel evolutionary divergence of opercle bone shape

Kimmel CB, McGuigan K, Phillips PC, Ullmann B, Currey MC, von Hippel FA, Kristjánsson BK, Gelmond O, Cresko WA. Evolution 66(2):419-434.

Conservation of the photoperiodic neuroendocrine axis among vertebrates

O’Brien CS, Bourdo R, Bradshaw WE, Holzapfel CM, Cresko WA. General and Comparative Endocrinology 178:19-27.

2011

Cryptic genetic variation and body size evolution in threespine stickleback

McGuigan K, Nishimura N, Currey MC, Hurwit D, Cresko WA. Evolution 65:1203-1211.

SNP discovery and genotyping for evolutionary genetics using RAD sequencing

Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA. Methods in Molecular Biology 772:157-178.

Stacks: building and genotyping loci de novo from short-read sequences

Catchen JM, Amores A, Hohenlohe PA, Cresko WA, Postlethwait JH. G3: Genes|Genomes|Genetics 1:171-182.

Local de novo assembly of RAD paired-end contigs using short sequencing reads

Etter P, Preston J, Bassham S, Cresko WA, Johnson EA. PLoS One 6(4):e18561.

Distinct lineages of Schistocephalus parasites in threespine and ninespine stickleback hosts

Nishimura N, Heins D, Anderson R, Barber I, Cresko WA. PLoS One 6(7):e22505.

2010

Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags

Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA. PLoS Genetics 6(2):e1000862.

Using population genomics to detect selection in natural populations

Hohenlohe PA, Phillips PC, Cresko WA. International Journal of Plant Sciences 171(9):1059-1071.

Resolving postglacial phylogeography using high-throughput sequencing

Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM. PNAS 107(37):16196-16200.

Quantitative genetic variation in static allometry in threespine stickleback

McGuigan K, Nishimura N, Currey MC, Hurwit D, Cresko WA. Integrative and Comparative Biology 50(6):1067-1080.

2009

Evolutionary mutant models for human disease

Albertson RC, Cresko WA, Dietrich HW III, Postlethwait JH. Trends in Genetics 25(2):74-81.

Latitudinal variation in photoperiodic response of the three-spined stickleback

Yeates-Burghart QS, O’Brien CS, Cresko WA, Holzapfel CM, Bradshaw WE. Journal of Fish Biology 75:2075-2081.

2008

Rapid SNP discovery and genetic mapping using sequenced RAD markers

Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. PLoS One 3(10):e3376.

Armor Development and Fitness

Cresko WA. Science 322:204-206.

Special issue on stickleback behavior and evolution: Preface

Cresko WA. Behaviour 145:409-411.

Heterotopy explains opercular shape evolution in Alaskan threespine sticklebacks

Kimmel CB, Ullmann B, Currey MC, Aguirre WE, Cresko WA. Behaviour 145:669-691.

Female-specific increases in primordial germ cells marks sex differentiation in threespine stickleback

Lewis ZR, McClellan MC, Postlethwait JH, Cresko WA, Kaplan RH. Journal of Morphology 269:909-921.

2007

Rapid and cost-effective polymorphism identification and genotyping using RAD markers

Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. Genome Research 17(2):240-248.

Developmental basis of microevolution in threespine stickleback

Cresko WA, McGuigan K, Phillips PC, Postlethwait JH. Genetica 129(1):105-126.

2006

Perchlorate induces hermaphroditism in threespine stickleback

Bernhardt RR, von Hippel FA, Cresko WA. Environmental Toxicology and Chemistry 25(8):2087-2096.

2005

Evolution and development of facial bone morphology in threespine sticklebacks

Kimmel CB, Ullmann B, Walker C, Wilson C, Currey MC, Phillips PC, Bell MA, Postlethwait JH, Cresko WA. PNAS 102(16):5791-5796.

The origin of subfunctions and modular gene regulation

Force A, Cresko WA, Pickett FB, Proulx SR, Amemiya C, Lynch M. Genetics 170:433-446.

2004

Parallel genetic basis for repeated evolution of armor loss in Alaskan threespine stickleback

Cresko WA, Amores A, Wilson C, Murphy J, Currey MC, Phillips P, Bell MA, Kimmel CB, Postlethwait JH. PNAS 101(16):6050-6055.

Evolutionary and developmental consequences of teleost genome duplication

Postlethwait JH, Amores A, Cresko WA, Yan Y. Trends in Genetics 20(10):481-490.

2003

Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish

Cresko WA, Yan Y, Baltrus D, Amores A, Singer A, Rodriguez-Mari A, Postlethwait JH. Developmental Dynamics 228:480-489.

2000

The ecology and geography of speciation: A case study using an adaptive radiation of threespine stickleback in Alaska

Cresko WA. PhD Dissertation, Clark University, Worcester, MA.

1998

Nested biological variation and speciation

Foster SA, Scott R, Cresko WA. Philosophical Transactions of the Royal Society of London B 353:207-218.

1997

Diamondback terrapin mortality in crab pots

Roosenburg WM, Cresko WA, Modesitte M, Robbins MB. Conservation Biology 11:1166-1172.

1996

Two morphotypes of lacustrine threespine stickleback in Benka Lake, Alaska

Cresko WA, Baker JA. Environmental Biology of Fishes 45:343-350.

Nesting biology and foraging patterns of the solitary bee Melissodes rustica

Cameron S, Whitfield J, Hulslander C, Cresko WA, Isenberg S, King R. Journal of the Kansas Entomological Society 69(4):260-273.

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100+ publications | 15,000+ citations | h-index: 52 | Google Scholar

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