Catherine Linnen

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  • Associate Professor
  • Behavior
  • Bioinformatics and Computational Biology
  • Biology
  • Ecology and Evolutionary Biology
  • Genetics and Genomics
204E TH Morgan
Research Interests:

PH.D. Harvard University., 2007


Genomics of Adaptation and Speciation

My research is motivated by a desire to understand the mechanisms responsible for generating biodiversity. Biologists have long sought to understand how changes in DNA sequences (genotype) give rise to changes in the appearance and/or behavior of organisms (phenotype). To date, most of our successes in linking genotype to phenotype have been in a handful of model organisms in the lab (e.g., worms, yeast, fruit flies, and lab mice); however, recent advances in sequencing technologies and novel statistical methods are now making it possible to study this connection in a wide range of organisms in nature. This allows us to understand not only how genetic variation contributes to phenotypic variation, but also how evolutionary processes such as natural selection act on this variation to shape its distribution in space and time in the wild.

Using an integrative approach that combines lab and fieldwork and applies the tools of molecular phylogenetics, ecological genetics, and population genomics, I am linking genotype and phenotype in two systems: the deer mouse, Peromyscus maniculatus, and the pine-sawfly genus Neodiprion (order Hymenoptera; family Diprionidae). Deer mice and sawflies share several features that make them excellent study organisms, including: they are abundant and easy to find in nature; they can be kept under controlled laboratory conditions; crosses can be made between divergent populations and species; and they have many traits that are variable within and between species. To gain insight into how organisms adapt to their environment and why this process sometimes leads to the formation of new species, I specifically focus on those traits that impact the ability of individuals to survive and reproduce (e.g., cryptic coat color in deer mice) and/or contribute to reproductive barriers between populations and species (e.g., host use in sawflies). My long-term research goals in both systems are to: (1) identify the genes, mutations, and molecular mechanisms responsible for phenotypic differences between populations and species, (2) measure the strength of natural selection acting on those phenotypes and their underlying genes, (3) reconstruct the histories of ecologically important genes (gene trees) and the populations in which they occur (population/species trees), and (4) determine the extent to which the course of evolution varies across different organisms and traits.


PubMed Publications*: 
  • Linnen, CR ;Brandvain, Y ;Unckless, RL "Theme: Recent work in speciation research by women authors." Evolution; international journal of organic evolution 76, 6 (2022): 1100-1103. Details.
  • Lindstedt, C ;Bagley, RK ;Calhim, S ;Jones, M.;Linnen, CR "The impact of life stage and pigment source on the evolution of novel warning signal traits." Evolution; international journal of organic evolution 76, 3 (2022): 554-572. Details.
  • Bendall, EE ;Bagley, RK ;Sousa, VC ;Linnen, CR "Faster-haplodiploid evolution under divergence-with-gene-flow: Simulations and empirical data from pine-feeding hymenopterans." Molecular ecology 31, 8 (2022): 2348-2366. Details. Full text
  • Herrig, DK ;Vertacnik, KL ;Kohrs, AR ;Linnen, CR "Support for the adaptive decoupling hypothesis from whole-transcriptome profiles of a hypermetamorphic and sexually dimorphic insect, Neodiprion lecontei." Molecular ecology 30, 18 (2021): 4551-4566. Details. Full text
  • Harris, RB ;Irwin, K ;Jones, MR ;Laurent, S ;Barrett, RDH ;Nachman, MW ;Good, JM ;Linnen, CR ;Jensen, JD ;Pfeifer, SP "The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards." Heredity 124, 1 (2020): 1-14. Details. Full text
  • Linnen, CR ;O'Quin, CT ;Shackleford, T ;Sears, CR ;Lindstedt, C "Genetic Basis of Body Color and Spotting Pattern in Redheaded Pine Sawfly Larvae (<i>Neodiprion lecontei</i>)." Genetics 209, 1 (2018): 291-305. Details. Full text
  • Linnen, CR "Predicting evolutionary predictability." Molecular ecology 27, 12 (2018): 2647-2650. Details. Full text
  • Pfeifer, SP ;Laurent, S ;Sousa, VC ;Linnen, CR ;Foll, M ;Excoffier, L ;Hoekstra, HE ;Jensen, JD "The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow." Molecular biology and evolution 35, 4 (2018): 792-806. Details. Full text
  • Mallarino, R ;Linden, TA ;Linnen, CR ;Hoekstra, HE "The role of isoforms in the evolution of cryptic coloration in Peromyscus mice." Molecular ecology 26, 1 (2017): 245-258. Details. Full text
  • Bagley, RK ;Sousa, VC ;Niemiller, ML ;Linnen, CR "History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei)." Molecular ecology 26, 4 (2017): 1022-1044. Details. Full text
  • Bendall, EE ;Vertacnik, KL ;Linnen, CR "Oviposition traits generate extrinsic postzygotic isolation between two pine sawfly species." BMC evolutionary biology 17, 1 (2017): 26. Details. Full text
  • Vertacnik, KL ;Linnen, CR "Evolutionary genetics of host shifts in herbivorous insects: insights from the age of genomics." Annals of the New York Academy of Sciences 1389, 1 (2017): 186-212. Details. Full text
  • JW, 2nd Terbot;Gaynor, RL ;Linnen, CR "Gregariousness does not vary with geography, developmental stage, or group relatedness in feeding redheaded pine sawfly larvae." Ecology and evolution 7, 11 (2017): 3689-3702. Details. Full text
  • Glastad, KM ;Arsenault, SV ;Vertacnik, KL ;Geib, SM ;Kay, S ;Danforth, BN ;Rehan, SM ;Linnen, CR ;Kocher, SD ;Hunt, BG "Variation in DNA Methylation Is Not Consistently Reflected by Sociality in Hymenoptera." Genome biology and evolution 9, 6 (2017): 1687-1698. Details. Full text
  • Harper, KE ;Bagley, RK ;Thompson, KL ;Linnen, CR "Complementary sex determination, inbreeding depression and inbreeding avoidance in a gregarious sawfly." Heredity 117, 5 (2016): 326-335. Details. Full text
  • Thompson, KL ;Linnen, CR ;Kubatko, L "Tree-based quantitative trait mapping in the presence of external covariates." Statistical applications in genetics and molecular biology 15, 6 (2016): 473-490. Details. Full text
  • Patten, MM ;Carioscia, SA ;Linnen, CR "Biased introgression of mitochondrial and nuclear genes: a comparison of diploid and haplodiploid systems." Molecular ecology 24, 20 (2015): 5200-10. Details. Full text
  • Brady, CM ;Asplen, MK ;Desneux, N ;Heimpel, GE ;Hopper, KR ;Linnen, CR ;Oliver, KM ;Wulff, JA ;White, JA "Worldwide populations of the aphid Aphis craccivora are infected with diverse facultative bacterial symbionts." Microbial ecology 67, 1 (2014): 195-204. Details. Full text
  • Linnen, CR ;Poh, YP ;Peterson, BK ;Barrett, RD ;Larson, JG ;Jensen, JD ;Hoekstra, HE "Adaptive evolution of multiple traits through multiple mutations at a single gene." Science (New York, N.Y.) 339, 6125 (2013): 1312-6. Details. Full text
  • Manceau, M.;Domingues, VS ;Linnen, CR ;Rosenblum, EB ;Hoekstra, HE "Convergence in pigmentation at multiple levels: mutations, genes and function." Philosophical transactions of the Royal Society of London. Series B, Biological sciences 365, 1552 (2010): 2439-50. Details. Full text
  • Weber, JN ;Peters, MB ;Tsyusko, OV ;Linnen, CR ;Hagen, C.;Schable, NA ;Tuberville, TD ;McKee, AM ;Lance, SL ;Jones, KL ;Fisher, HS ;Dewey, MJ ;Hoekstra, HE ;Glenn, TC "Five Hundred Microsatellite Loci for Peromyscus." Conservation genetics (Print) 11, 3 (2010): 1243-1246. Details.
  • Linnen, CR ;Farrell, BD "A test of the sympatric host race formation hypothesis in Neodiprion (Hymenoptera: Diprionidae)." Proceedings. Biological sciences 277, 1697 (2010): 3131-8. Details. Full text
  • Linnen, CR ;Kingsley, EP ;Jensen, JD ;Hoekstra, HE "On the origin and spread of an adaptive allele in deer mice." Science (New York, N.Y.) 325, 5944 (2009): 1095-8. Details. Full text
  • Linnen, CR ;Farrell, BD "Comparison of methods for species-tree inference in the sawfly genus Neodiprion (Hymenoptera: Diprionidae)." Systematic biology 57, 6 (2008): 876-90. Details. Full text
  • Linnen, CR ;Farrell, BD "Phylogenetic analysis of nuclear and mitochondrial genes reveals evolutionary relationships and mitochondrial introgression in the sertifer species group of the genus Neodiprion (Hymenoptera: Diprionidae)." Molecular phylogenetics and evolution 48, 1 (2008): 240-57. Details. Full text
  • Linnen, CR ;Farrell, BD "Mitonuclear discordance is caused by rampant mitochondrial introgression in Neodiprion (Hymenoptera: Diprionidae) sawflies." Evolution; international journal of organic evolution 61, 6 (2007): 1417-38. Details.
  • Linnen, CR ;Hoekstra, HE "Measuring natural selection on genotypes and phenotypes in the wild." Cold Spring Harbor symposia on quantitative biology 74, (0): 155-68. Details. Full text
* Publications are automatically pulled from based on a user-specific query. Results may include incorrect citations. See: Tutorial on improving PubMed results.
Current Research Opportunities

Students (undergraduate and graduate) and postdocs interested in joining my lab are encouraged to contact me via email: See here for more details on ongoing research in the lab.