Matthew Rockman

Our goal is to understand the relationship between the molecular mechanisms that shape phenotypes within individuals and the evolutionary mechanisms that generate and maintain phenotypic variation within populations. This project requires that we identify the functional allelic variants that segregate in nature, understand their molecular mechanisms, characterize their population genetic dynamics, and build models that explain these dynamics in terms of molecular biology and ecology.

We use molecular and quantitative genetics to discover the alleles that underlie phenotypic variation. Our primary model system is C. elegans, a bacteria-eating nematode widely distributed across the globe. Natural isolates of this species harbor variation for development, morphology, behavior, and physiology (indeed, for almost any trait we can measure). A particular focus of our research is the genetic basis of gene expression variation; insofar as spatial and temporal regulation of gene activity underlies development, genetic analysis of gene expression variation provides a unique window into the substrate of developmental evolution. Moreover, by measuring thousands of gene expression traits simultaneously, we can leverage their correlation structure to infer the causal networks that constitute the genotype-phenotype map, potentially a major shaper of phenotypic divergence.

Our genome-scale analyses form the basis for our studies of the evolutionary causes of heritable variation. We are studying in particular the roles of dominance, epistasis, and linkage. C. elegans is an especially powerful system for studying the effects of linked selection because of its relatively low rate of outcrossing. We hope to study global patterns of epistasis by characterizing the additive and epistatic effects of large numbers of loci underlying gene expression traits that are under stabilizing selection. Alternate models for the mechanism of stabilizing selection — compensatory evolution and fluctuating neutral space — will be directly testable.

To incorporate ecological context into our understanding of heritable variation, we are planning extensive field work to characterize spatial and temporal dynamics of functional allele frequencies in C. elegans. In parallel, we are initiating work on a new model system, a widely distributed polychaete species with abundant heritable variation for developmental phenotypes. We can collect the polychaetes from sites across the exceptional marine and estuarine setting of the New York area and we are developing molecular tools to discover the loci underlying developmental variation and their distributions in nature.

Date of these PubMed search results: March 24 2020
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1. Hybridization promotes asexual reproduction in Caenorhabditis nematodes.
   PLoS Genet (2019 Dec) PMC6946170 free full-text archive
   Lamelza P, Young JM, Noble LM, Caro L, Isakharov A, Palanisamy M, Rockman MV, Malik HS, Ailion M
2. Tightly linked antagonistic-effect loci underlie polygenic phenotypic variation in C. elegans.
   Evol Lett (2019 Oct) PMC6791183 free full-text archive
   Bernstein MR, Zdraljevic S, Andersen EC, Rockman MV
3. Comparative genomics of 10 new Caenorhabditis species.
   Evol Lett (2019 Apr) PMC6457397 free full-text archive
   Stevens L, Felix MA, Beltran T, Braendle C, Caurcel C, Fausett S, Fitch D, Frezal L, Gosse C, Kaur T, Kiontke K, Newton MD, Noble LM, Richaud A, Rockman MV, Sudhaus W, Blaxter M
4. Decoupled maternal and zygotic genetic effects shape the evolution of development.
   Elife (2018 Sep 10) PMC6168281 free full-text archive
   Zakas C, Deutscher JM, Kay AD, Rockman MV
5. Polygenicity and Epistasis Underlie Fitness-Proximal Traits in the Caenorhabditis elegans Multiparental Experimental Evolution (CeMEE) Panel.
   Genetics (2017 Dec) PMC5714472 free full-text archive
   Noble LM, Chelo I, Guzella T, Afonso B, Riccardi DD, Ammerman P, Dayarian A, Carvalho S, Crist A, Pino‑Querido A, Shraiman B, Rockman MV, Teotonio H
6. The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length.
   Genetics (2016 Sep) PMC5012401 free full-text archive
   Cook DE, Zdraljevic S, Tanny RE, Seo B, Riccardi DD, Noble LM, Rockman MV, Alkema MJ, Braendle C, Kammenga JE, Wang J, Kruglyak L, Felix MA, Lee J, Andersen EC
7. Fine-Scale Crossover Rate Variation on the Caenorhabditis elegans X Chromosome.
   G3 (Bethesda) (2016 Jun 1) PMC4889672 free full-text archive
   Bernstein MR, Rockman MV
8. The Expendables: Natural selection driving reduced gene function (Comment on DOI 10.1002/bies.201500083).
   Bioessays (2015 Nov) PMID: 26488529
   Bernstein MR, Rockman MV
9. Natural Variation in plep-1 Causes Male-Male Copulatory Behavior in C. elegans.
   Curr Biol (2015 Oct 19) PMC4618159 free full-text archive
   Noble LM, Chang AS, McNelis D, Kramer M, Yen M, Nicodemus JP, Riccardi DD, Ammerman P, Phillips M, Islam T, Rockman MV
10. Wild worm embryogenesis harbors ubiquitous polygenic modifier variation.
    Elife (2015 Aug 22) PMC4569889 free full-text archive
    Paaby AB, White AG, Riccardi DD, Gunsalus KC, Piano F, Rockman MV
11. Gene-based polymorphisms reveal limited genomic divergence in a species with a heritable life-history dimorphism.
    Evol Dev (2015 Jul-Aug) PMID: 26174100
    Zakas C, Rockman MV
12. Dimorphic development in Streblospio benedicti: genetic analysis of morphological differences between larval types.
    Int J Dev Biol (2014) PMID: 25690973
    Zakas C, Rockman MV
13. Cryptic genetic variation: evolution's hidden substrate.
    Nat Rev Genet (2014 Apr) PMC4737706 free full-text archive
    Paaby AB, Rockman MV
14. Multigenic natural variation underlies Caenorhabditis elegans olfactory preference for the bacterial pathogen Serratia marcescens.
    G3 (Bethesda) (2014 Feb 19) PMC3931561 free full-text archive
    Glater EE, Rockman MV, Bargmann CI
15. Crossover heterogeneity in the absence of hotspots in Caenorhabditis elegans.
    Genetics (2014 Jan) PMC3872180 free full-text archive
    Kaur T, Rockman MV
16. Pleiotropy: what do you mean? Reply to Zhang and Wagner.
    Trends Genet (2013 Jul) PMID: 23746964
    Paaby AB, Rockman MV
17. Resistance to germline RNA interference in a Caenorhabditis elegans wild isolate exhibits complexity and nonadditivity.
    G3 (Bethesda) (2013 Jun 21) PMC3689805 free full-text archive
    Pollard DA, Rockman MV
18. Long-range regulatory polymorphisms affecting a GABA receptor constitute a quantitative trait locus (QTL) for social behavior in Caenorhabditis elegans.
    PLoS Genet (2012) PMC3527333 free full-text archive
    Bendesky A, Pitts J, Rockman MV, Chen WC, Tan MW, Kruglyak L, Bargmann CI
19. The many faces of pleiotropy.
    Trends Genet (2013 Feb) PMC3558540 free full-text archive
    Paaby AB, Rockman MV
20. More than the sum of its parts: a complex epistatic network underlies natural variation in thermal preference behavior in Caenorhabditis elegans.
    Genetics (2012 Dec) PMC3512158 free full-text archive
    Gaertner BE, Parmenter MD, Rockman MV, Kruglyak L, Phillips PC
21. Patterns of nuclear genetic variation in the poecilogonous polychaete Streblospio benedicti.
    Integr Comp Biol (2012 Jul) PMID: 22659203
    Rockman MV
22. The QTN program and the alleles that matter for evolution: all that's gold does not glitter.
    Evolution (2012 Jan) PMC3386609 free full-text archive
    Rockman MV
23. A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits.
    BMC Evol Biol (2011 Nov 21) PMC3277298 free full-text archive
    Kiontke KC, Felix MA, Ailion M, Rockman MV, Braendle C, Penigault JB, Fitch DH
24. A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans.
    PLoS Biol (2011 Jul) PMC3144186 free full-text archive
    Seidel HS, Ailion M, Li J, van Oudenaarden A, Rockman MV, Kruglyak L
25. Catecholamine receptor polymorphisms affect decision-making in C. elegans.
    Nature (2011 Apr 21) PMC3154120 free full-text archive
    Bendesky A, Tsunozaki M, Rockman MV, Kruglyak L, Bargmann CI
26. Selection at linked sites shapes heritable phenotypic variation in C. elegans.
    Science (2010 Oct 15) PMC3138179 free full-text archive
    Rockman MV, Skrovanek SS, Kruglyak L
27. Multiple Functional Variants in cis Modulate PDYN Expression.
    Mol Biol Evol (2010 Feb) PMID: 19910384
    Babbitt CC, Silverman JS, Haygood R, Reininga JM, Rockman MV, Wray GA
28. Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors.
    Neuron (2009 Mar 12) PMC2772867 free full-text archive
    McGrath PT, Rockman MV, Zimmer M, Jang H, Macosko EZ, Kruglyak L, Bargmann CI
29. Recombinational landscape and population genomics of Caenorhabditis elegans.
    PLoS Genet (2009 Mar) PMC2652117 free full-text archive
    Rockman MV, Kruglyak L
30. Reverse engineering the genotype-phenotype map with natural genetic variation.
    Nature (2008 Dec 11) PMID: 19079051
    Rockman MV
31. Molecular basis of the copulatory plug polymorphism in Caenorhabditis elegans.
    Nature (2008 Aug 21) PMC2597896 free full-text archive
    Palopoli MF, Rockman MV, TinMaung A, Ramsay C, Curwen S, Aduna A, Laurita J, Kruglyak L
32. Tinker where the tinkering's good.
    Trends Genet (2008 Jul) PMC2887039 free full-text archive
    Rockman MV, Stern DL
33. Breeding designs for recombinant inbred advanced intercross lines.
    Genetics (2008 Jun) PMC2429860 free full-text archive
    Rockman MV, Kruglyak L
34. Widespread genetic incompatibility in C. elegans maintained by balancing selection.
    Science (2008 Feb 1) PMC2421010 free full-text archive
    Seidel HS, Rockman MV, Kruglyak L
35. Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region.
    Proc Natl Acad Sci U S A (2006 Oct 31) PMC1637582 free full-text archive
    Loisel DA, Rockman MV, Wray GA, Altmann J, Alberts SC
36. Genetics of global gene expression.
    Nat Rev Genet (2006 Nov) PMID: 17047685
    Rockman MV, Kruglyak L
37. Ancient and recent positive selection transformed opioid cis-regulation in humans.
    PLoS Biol (2005 Dec) PMC1283535 free full-text archive
    Rockman MV, Hahn MW, Soranzo N, Zimprich F, Goldstein DB, Wray GA
38. Positive selection on MMP3 regulation has shaped heart disease risk.
    Curr Biol (2004 Sep 7) PMID: 15341739
    Rockman MV, Hahn MW, Soranzo N, Loisel DA, Goldstein DB, Wray GA
39. Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans.
    Genetics (2004 Jun) PMC1470926 free full-text archive
    Hahn MW, Rockman MV, Soranzo N, Goldstein DB, Wray GA
40. Analysis of common IL-6 promoter SNP variants and the AnTn tract in humans and primates and effects on plasma IL-6 levels following coronary artery bypass graft surgery.
    Biochim Biophys Acta (2004 Mar 2) PMID: 14990346
    Kelberman D, Fife M, Rockman MV, Brull DJ, Woo P, Humphries SE
41. Positive selection on a human-specific transcription factor binding site regulating IL4 expression.
    Curr Biol (2003 Dec 2) PMID: 14654003
    Rockman MV, Hahn MW, Soranzo N, Goldstein DB, Wray GA
42. The evolution of transcriptional regulation in eukaryotes.
    Mol Biol Evol (2003 Sep) PMID: 12777501
    Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA
43. Idiomatic (gene) expressions.
    Bioessays (2003 May) PMID: 12717811
    Rockman MV
44. Abundant raw material for cis-regulatory evolution in humans.
    Mol Biol Evol (2002 Nov) PMID: 12411608
    Rockman MV, Wray GA
45. Episodic chromosomal evolution in Planipapillus (Onychophora: Peripatopsidae): a phylogenetic approach to evolutionary dynamics and speciation.
    Evolution (2002 Jan) PMID: 11913667
    Rockman MV, Rowell DM
46. Phylogenetics of Planipapillus, lawn-headed onychophorans of the Australian Alps, based on nuclear and mitochondrial gene sequences.
    Mol Phylogenet Evol (2001 Oct) PMID: 11603941
    Rockman MV, Rowell DM, Tait NN