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[some articles are listed in multiple categories]
[PubMed] [ISI ResearcherID] [Google Scholar]
Trainee co-authors underlined, *equal contribution

[Evolutionary Genomics]    [Population Genetics]    [Speciation]    [Biodiversity and Ecology]
[Phenotypic Evolution and Adaptation]    [Breeding System and Sex Ratio Evolution

Evolutionary Genomics

Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis.
Jovelin, R., A. Krizus, B. Taghizada, J.C. Gray, P.C. Phillips, J.M. Claycomb, & A.D. Cutter. 2016. RNA. In press.

Hitting two birds with one stone: the unforeseen consequences of nested gene knockouts in Caenorhabditis elegans.
Jovelin, R. & A.D. Cutter. 2016. Worm. 5: e1156835.

When natural selection gives gene function the cold shoulder.
Cutter, A.D. & R. Jovelin. 2015. Bioessays. 37: 1169-1173. [pdf]
[Bioessays opinion]

Reproductive mode and the evolution of genome size and structure in Caenorhabditis nematodes.
Fierst, J.L., J.H. Willis, C.G. Thomas, W. Wang, R.M. Reynolds, T. Ahearne, A.D. Cutter & P.C. Phillips. 2015. PLoS Genetics. 11: e1005323. [pdf]
[F1000] [Unz]

Full-genome evolutionary histories of selfing, splitting and selection in Caenorhabditis.
Thomas, C.G.*, W. Wang*, R. Jovelin, R. Ghosh, T. Lomasko, Q. Trinh, L. Kruglyak, L.D. Stein & A.D. Cutter. 2015. Genome Research. 25: 667-678. [pdf] [supplement] [VCF data]

Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes.
Tu, S., M. Wu, J. Wang, A.D. Cutter, Z. Weng & J.M. Claycomb. 2015. Nucleic Acids Research43: 208-224. [pdf] [supplemental data]

Microevolution of nematode miRNAs reveals diverse modes of selection.
Jovelin, R. & A.D. Cutter. 2014. Genome Biology & Evolution. 6: 3049-3063. [pdf]

Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri.
Dey, A., C.K.W. Chan, C.G. Thomas & A.D. Cutter. 2013. PNAS. 110: 11056-11060. [pdf]
[Seeds of Science Blog] [First Look Blog] [F1000]

Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory.
Cutter, A.D. 2013. Molecular Phylogenetics and Evolution. 69: 1172-1185. [free pdf] [pdf]

Genomic signatures of selection at linked sites: unifying the disparity among species.
Cutter, A.D. & B.A. Payseur. 2013. Nature Reviews Genetics. 14: 262-274. [pdf]

Molecular hyperdiversity and evolution in very large populations.
Cutter, A.D., R. Jovelin & A. Dey. 2013. Molecular Ecology. 22: 2074-2095. [pdf]

Fifteen years of evolutionary genomics in Caenorhabditis elegans.
Jovelin, R.
, A. Dey, & A.D. Cutter. 2013. In: Encyclopedia of Life Sciences. John Wiley & Sons (Chichester). [pdf]

Gene duplication in the evolution of sexual dimorphism.
Wyman, M.J., A.D. Cutter & L. Rowe. 2012.  Evolution. 66: 1556-1566. [pdf]

Polymorphism, divergence and the role of recombination in Saccharomyces cerevisiae genome evolution.
Cutter, A.D. & A.M. Moses. 2011.  Molecular Biology and Evolution. 28: 1745-1754. [pdf] [supplementary data]

Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae
Cutter, A.D. & J.Y. Choi. 2010. Genome Research. 20: 1103-1111. [pdf]

The evolutionary dynamics of operon distributions in eukaryote genomes.
Cutter, A.D. & A.F. Agrawal. 2010. Genetics. 185: 685-693.[pdf

Molecular evolution inferences from the C. elegans genome
Cutter, A.D. 2010. In: WormBook, The C. elegans Research Community, ed. doi/10.1895/wormbook.1.149.1 [pdf]

Evolution of the C. elegans genome
Cutter, A.D., A. Dey & R.L. Murray. 2009. Molecular Biology and Evolution. 26: 1199-1234. [pdf
 

Germline expression influences operon organization in the C. elegans genome.
Reinke, V. & A.D. Cutter. 2009. Genetics. 181: 1219-1228. [pdf] [supplementary data]

Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate.
Cutter, A.D. 2008.  Molecular Biology & Evolution. 25: 778-786. [pdf] [supplementary tables]

Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing.
Cutter, A.D., J.D. Wasmuth & N.L. Washington. 2008.  Genetics. 178: 2093-2104. [pdf] [supplementary data] [F1000 review]

The evolution of biased codon and amino acid usage in nematode genomes.
Cutter, A.D., J. Wasmuth & M. Blaxter. 2006. Molecular Biology and Evolution. 23: 2303-2315. [pdf] [supplementary figures]

Transposable element orientation bias in the Drosophila melanogaster genome.
Cutter, A.D., J.M. Good, C. Pappas, M.A. Saunders, D. Starrett, & T.J. Wheeler. 2005. Journal of Molecular Evolution. 61: 733-741. [pdf] [supplementary table]

Sexual and temporal dynamics of molecular evolution in C. elegans development.
Cutter, A.D. & S. Ward. 2005.  Molecular Biology and Evolution. 22: 178-188. [pdf] [supplementary figures]

Clustered organization of reproductive genes in the C. elegans genome.
Miller, M.A., A.D. Cutter, I. Yamamoto, S. Ward, & D. Greenstein. 2004. Current Biology. 14: 1284-1290. [pdf]

Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans.
Cutter, A.D., B.A. Payseur, T. Salcedo, A.M. Estes, J.M. Good, E. Wood, T. Hartl, H. Maughan, J. Strempel, B. Wang, A.C. Bryan, & M. Dellos. 2003. Genome Research. 13: 2651-2657. [pdf] [supplementary table]

Selection at linked sites in the partial selfer Caenorhabditis elegans.
Cutter, A.D. & B.A. Payseur. 2003.  Molecular Biology and Evolution. 20: 665-673. [pdf]

Rates of deleterious mutation and the evolution of sex in Caenorhabditis.
Cutter, A.D. & B.A. Payseur. 2003. Journal of Evolutionary Biology. 16: 812-822. [pdf]

Searching for evidence of positive selection in the human genome using patterns of microsatellite variability.
Payseur, B.A., A.D. Cutter, & M.W. Nachman. 2002.  Molecular Biology and Evolution. 19: 1143-1153. [pdf]

 

Population Genetics

Full-genome evolutionary histories of selfing, splitting and selection in Caenorhabditis.
Thomas, C.G.*, W. Wang*, R. Jovelin, R. Ghosh, T. Lomasko, Q. Trinh, L. Kruglyak, L.D. Stein & A.D. Cutter. 2015. Genome Research. 25: 667-678. [pdf] [supplement] [VCF data]

Microevolution of nematode miRNAs reveals diverse modes of selection.
Jovelin, R. & A.D. Cutter. 2014. Genome Biology & Evolution. 6: 3049-3063. [pdf]

A recent selective sweep on the age-1 PI3 kinase regulator of the insulin-like signaling pathway within Caenorhabditis remanei.
Jovelin, R., J.S. Comstock, A.D. Cutter & P.C. Phillips. 2014. G3 (Genes, Genomes, Genetics). 4: 1123-1133. [pdf] [cover photo] [GSA blog]

Specialist versus generalist life histories and nucleotide diversity in Caenorhabditis nematodes.
Li, S.*, R. Jovelin*, T. Yoshiga, R. Tanaka & A.D. Cutter. 2014. Proceedings B (Royal Society of London). 281: In press. [pdf]

Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri.
Dey, A., C.K.W. Chan, C.G. Thomas & A.D. Cutter. 2013. PNAS. 110: 11056-11060. [pdf] [Seeds of Science Blog] [First Look Blog] [F1000]

Outbreeding depression with low genetic variation in selfing Caenorhabditis nematodes.
Gimond, C., 
R. JovelinS. Han, C. Ferrari, A.D. Cutter & C. Braendle. 2013. Evolution. 67: 3087-3101.  [pdf]

Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory.
Cutter, A.D. 2013. Molecular Phylogenetics and Evolution. 69: 1172-1185. [free pdf] [pdf]

Genomic signatures of selection at linked sites: unifying the disparity among species.
Cutter, A.D. & B.A. Payseur. 2013. Nature Reviews Genetics. 14: 262-274. [pdf]

Fine-scale signatures of molecular evolution reconcile models of indel-associated mutation.
Jovelin, R. & A.D. Cutter. 2013. Genome Biology and Evolution. 5: 978-986. [pdf]

Molecular hyperdiversity and evolution in very large populations.
Cutter, A.D., R. Jovelin & A. Dey. 2013. Molecular Ecology. 22: 2074-2095. [pdf]

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest.
Felix, M.A., 
R. Jovelin, C. Ferrari, S. Han, Y.R. Cho, E.C. Andersen, A.D. Cutter & C. Braendle. 2013.  BMC Evolutionary Biology. 13: 10. [pdf]

Global population genetic structure of Caenorhabditis remanei reveals incipient speciation
Dey, A.
, Y. Jeon, G.-X. Wang & A.D. Cutter. 2012. Genetics. 191: 1257-1269. [pdf]

Influence of finite-sites mutation, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversity
Cutter, A.D.,
G.-X. Wang, H. Ai, & Y. Peng. 2012.  Molecular Ecology. 21: 1345-1359. [pdf]

MicroRNA sequence variation potentially contributes to within-species functional divergence in the nematode Caenorhabditis briggsae.
Jovelin, R. & A.D. Cutter. 2011. Genetics. 189: 967-976. [pdf]

Polymorphism, divergence and the role of recombination in Saccharomyces cerevisiae genome evolution
Cutter, A.D. & A.M. Moses. 2011. Molecular Biology and Evolution. 28: 1745-1754. [pdf] [supplementary data]

Extremely high molecular diversity within the East Asian nematode Caenorhabditis sp. 5.
Wang, G.-X., S. Ren, Y. Ren, H. Ai & A.D. Cutter. 2010. Molecular Ecology. 19: 5022-5029. [pdf] 

Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae.
Cutter, A.D. & J.Y. Choi. 2010.  Genome Research. 20: 1103-1111. [pdf]

Molecular population genetics and phenotypic sensitivity to ethanol for a globally diverse sample of the nematode Caenorhabditis briggsae.
Cutter, A.D., W. Yan, N. Tsvetkov, S. Sunil & M.A. Felix. 2010.  Molecular Ecology. 19: 798-809.  [pdf

Population frequencies of transposable elements in selfing and outcrossing Caenorhabditis nematodes.
Dolgin, E.S., B. Charlesworth & A.D. Cutter. 2008.  Genetics Research. 90: 317-329.  [pdf

Multilocus patterns of polymorphism and selection across the X-chromosome of Caenorhabditis remanei.
Cutter, A.D. 2008.  Genetics. 178: 1661-1672. [pdf] [supplementary tables]

Hakuna nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae.
Dolgin, E.S., M.A. Felix & A.D. Cutter. 2007. Heredity. 100: 304-315. [pdf] [supplementary figures]

High nucleotide polymorphism and the decay of linkage disequilibrium in wild populations of Caenorhabditis remanei.
Cutter, A.D., S.E. Baird & D. Charlesworth. 2006.  Genetics. 174: 901-913. [pdf]

Patterns of nucleotide polymorphism distinguish temperate and tropical wild isolates of Caenorhabditis briggsae.
Cutter, A.D., M.A. Felix, A. Barriere & D. Charlesworth. 2006.  Genetics. 173: 2021-2031. [pdf]

Integrating patterns of polymorphism at SNPs and STRs.
Payseur, B.A. & A.D. Cutter. 2006. Trends in Genetics. 22: 424-429. [pdf]

Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans.
Cutter, A.D. 2006. Genetics. 172: 171-184. [pdf] [supplementary table and figure]

Selection at linked sites in the partial selfer Caenorhabditis elegans.
Cutter, A.D. & B.A. Payseur. 2003.  Molecular Biology and Evolution. 20: 665-673. [pdf]

Searching for evidence of positive selection in the human genome using patterns of microsatellite variability.
Payseur, B.A., A.D. Cutter, & M.W. Nachman. 2002. Molecular Biology and Evolution. 19: 1143-1153. [pdf]

 

Speciation

Sexual conflict and speciation.
Ting, J.J. & A.D. Cutter. 2016. In: Encyclopedia of Evolutionary Biology (R. Kliman, ed). Academic Press (Oxford). Volume 4, pp. 192-199.

Gametic selection, developmental trajectories and extrinsic heterogeneity in Haldane's rule.
Bundus, J.D.
, R. Alaei & A.D. Cutter. 2015. Evolution. 69: 2005-2017. [pdf]

Repeatability, ephemerality, and inconvenient truths in the speciation process. (Commentary)
Cutter, A.D. 2015. Molecular Ecology. 24: 1643-1644. [pdf]

Gonad morphogenesis defects drive hybrid male sterility in asymmetric hybrid breakdown of Caenorhabditis nematodes.
Dey, A., Q. Jin, Y.-C. Chen & A.D. Cutter. 2014. Evolution & Development. 16: 362-372. [F1000]

Intense sperm-mediated sexual conflict promotes gametic isolation in Caenorhabditis nematodes.
Ting, J.J.*, G.C. Woodruff*, G. Leung, N.-R. Shin, A.D. Cutter & E.S. Haag. 2014. PLoS Biology. 12: e1001915. [pdf] [supplemental info] [supplemental movie 1] [Primer in PLoS] [Washington Post] [National Geographic] [LA Times] [Wired UK] [New Scientist] [The Verge] [The Hindu] [Popular Science] [Chicago Tribune] [Int'l Business Times] [Nature's Nether Regions Blog[Science Codex] [Tech Times] [Huffington Post UK] [Austrian Tribune]
[Guardian Liberty Voice] [Nature World News] [IFL Science] [LaborWelt] [Rosa Rubicondior blog] [The Varsity] [Seeds of Science blog] [EcuaVisa] [BECTN] [UofT News] [F1000]

A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species.
Felix, M.-A., C. Braendle & A.D. Cutter. 2014. PLoS One. 9: e94723. [pdf]

Outbreeding depression with low genetic variation in selfing Caenorhabditis nematodes.
Gimond, C., 
R. JovelinS. Han, C. Ferrari, A.D. Cutter & C. Braendle. 2013. Evolution. 67: 3087-3101.  [pdf]

Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory.
Cutter, A.D. 2013. Molecular Phylogenetics and Evolution. 69: 1172-1185. [free pdf] [pdf]

Global population genetic structure of Caenorhabditis remanei reveals incipient speciation.
Dey, A.
, Y. Jeon, G.-X. Wang & A.D. Cutter. 2012. Genetics. 191: 1257-1269. [pdf]

The polymorphic prelude to Bateson-Dobzhansky-Muller incompatibilities.
Cutter, A.D. 2012. Trends in Ecology & Evolution. 27: 209-218. [pdf]

Genetic variation for post-zygotic reproductive isolation between Caenorhabditis briggsae and Caenorhabditis sp. 9.
Kozlowska, J.L., A.R. Ahmad, E. Jahesh & A.D. Cutter. 2012. Evolution. 66: 1180-1195. [pdf]


Biodiversity and Ecology

Caenorhabditis evolution in the wild.
Cutter, A.D. 2015. Bioessays. 37: 983-995. [pdf]

Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory.
Cutter, A.D. 2013. Molecular Phylogenetics and Evolution. 69: 1172-1185. [free pdf] [pdf]

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest.
Felix, M.A., 
R. Jovelin, C. Ferrari, S. Han, Y.R. Cho, E.C. Andersen, A.D. Cutter & C. Braendle. 2013.  BMC Evolutionary Biology. 13: 10. [pdf]

Fossil leaf economics quantified: calibration, Eocene case study, and implications.
Royer, D.L., L. Sack, P. Wilf, C.H. Lusk, G.J. Jordan, Ü. Niinemets, I.J. Wright, M. Westoby, B. Cariglino, P.D. Coley, A.D. Cutter, K.R. Johnson, C.C. Labandeira, A.T. Moles, M.B. Palmer and F. Valladares. 2007.  Paleobiology. 33: 574-589. [pdf]

Insect herbivory, plant defense, and early Cenozoic climate change.
Wilf, P., C.C. Labandeira, K. Johnson, P.D. Coley, & A.D. Cutter. 2001. Proceedings of the National Academy of Sciences USA. 98: 6221-6226. [pdf]

Response of rainforest ant communities in Australia's humid tropics to disturbance: validation of the functional group model.
King, J.R., A.N. Andersen, & A.D. Cutter. 1998. Biodiversity and Conservation 7: 1627-1638. [pdf]


Phenotypic Evolution and Adaptation

Convergent evolution of sperm gigantism and the developmental origins of sperms size variability in Caenorhabditis nematodes.
Vielle, A., N. Callemeyn-Torre, C. Gimond, N. Poullet, N. Soares, J.C. Gray, A.D. Cutter & C. Braendle.
[bioRxiv]

Mainstreaming C. elegans in experimental evolution.
Gray, J.C. & A.D. Cutter. 2014. Proceedings B (Royal Society of London). 281: 20132858. [pdf]

Temperature-dependent behaviors are genetically variable in the nematode Caenorhabditis briggsae.
Stegeman, G.W., M. Bueno de Mesquita, W.S. Ryu & A.D. Cutter. 2013.  Journal of Experimental Biology. 216: 850-858. [pdf]

Experimental evolution of sperm count in protandrous self-fertilizing hermaphrodites.
Murray, R.L. & A.D. Cutter. 2011.  Journal of Experimental Biology. 214: 1740-1747. [pdf]

Heritable determinants of male fertilization success in the nematode Caenorhabditis elegans.
Murray, R.L., J.L. Kozlowska & A.D. Cutter. 2011. BMC Evolutionary Biology. 11:99. [pdf] [additional data]

Temperature-dependent fecundity associates with latitude in Caenorhabditis briggsae.
Prasad, A., M. Croydon-Sugarman, R.L. Murray & A.D. Cutter. 2011. Evolution. 65: 52-63. [pdf]

Molecular population genetics and phenotypic sensitivity to ethanol for a globally diverse sample of the nematode Caenorhabditis briggsae.
Cutter, A.D., W. Yan, N. Tsvetkov, S. Sunil & M.A. Felix. 2010.  Molecular Ecology. 19: 798-809.  [pdf

Sperm-limited fecundity in nematodes: how many sperm are enough?
Cutter, A.D. 2004. Evolution. 58: 651-655. [pdf]

The kin composition of social groups: Trading group size for degree of altruism.
Avilés, L., J.A. Fletcher, & A.D. Cutter. 2004. American Naturalist. 164: 132-144.  [pdf]

Population ecology, nonlinear dynamics, and social evolution. I. associations among nonrelatives.
Avilés, L., P. Abbot, & A.D. Cutter. 2002. American Naturalist. 159: 115-127. [pdf]


Breeding System and Sex Ratio Evolution

Outbreeding depression with low genetic variation in selfing Caenorhabditis nematodes.
Gimond, C., 
R. JovelinS. Han, C. Ferrari, A.D. Cutter & C. Braendle. 2013. Evolution. 67: 3087-3101.  [pdf]

Experimental evolution of sperm count in protandrous self-fertilizing hermaphrodites.
Murray, R.L. & A.D. Cutter. 2011. Journal of Experimental Biology. 214: 1740-1747. [pdf]

Reproductive evolution: symptom of a selfing syndrome (Dispatch).
Cutter, A.D. 2008. Current Biology. 18: R1056-R1058. [pdf]

On the potential for extinction by Muller's ratchet in Caenorhabditis elegans.
Loewe, L. & A.D. Cutter. 2008. BMC Evolutionary Biology. 8: 125. [pdf]

Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing.
Cutter, A.D., J.D. Wasmuth & N.L. Washington. 2008. Genetics. 178: 2093-2104. [pdf] [supplementary data] [F1000 review]

Inbreeding and outbreeding depression in Caenorhabditis nematodes.
Dolgin, E.S., B. Charlesworth, S.E. Baird & A.D. Cutter. 2007.  Evolution. 61: 1339-1352. [pdf]

Post-copulatory sexual selection reduces genetic diversity in experimental populations of C. elegans.
LaMunyon, C., O. Bouban & A.D. Cutter. 2007. Journal of Heredity. 98: 67-72. [pdf]

Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans.
Cutter, A.D. 2006. Genetics. 172: 171-184. [pdf] [supplementary table and figure]

Mutation and the experimental evolution of outcrossing in Caenorhabditis elegans.
Cutter, A.D. 2005.  Journal of Evolutionary Biology. 18: 27-34. [pdf]

Sperm-limited fecundity in nematodes: how many sperm are enough?
Cutter, A.D. 2004. Evolution. 58: 651-655. [pdf]

Rates of deleterious mutation and the evolution of sex in Caenorhabditis.
Cutter, A.D. & B.A. Payseur. 2003.  Journal of Evolutionary Biology. 16: 812-822. [pdf]

The proximate determinants of sex ratio in C. elegans populations.
Cutter, A.D., L. Avilés, & S. Ward. 2003. Genetical Research. 81: 91-102. [pdf]

Precise, highly female-biased sex ratios in a social spider.
Avilés, L., J. McCormack, A. Cutter, & T. Bukowski. 2000. Proceedings: Biological Sciences (Royal Society of London). 267: 1445-1449. [pdf]

 

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text & photos © 2006-2016 by asher d. cutter. design © 2006 by yee-fan sun