{"id":596,"date":"2015-01-09T19:25:20","date_gmt":"2015-01-09T19:25:20","guid":{"rendered":"http:\/\/blogs.rochester.edu\/larracuente\/?page_id=596"},"modified":"2025-05-21T03:50:26","modified_gmt":"2025-05-21T03:50:26","slug":"publications","status":"publish","type":"page","link":"http:\/\/blogs.rochester.edu\/larracuente\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Complete List of Published Work in MyBibliography:\u00a0\u00a0 http:\/\/www.ncbi.nlm.nih.gov\/sites\/myncbi\/amanda.larracuente.1\/bibliography\/40318594\/public\/?sort=date&direction=descending<\/a><\/p>\n

ORCID: https:\/\/orcid.org\/0000-0001-5944-5686<\/a><\/p>\n

2025<\/strong><\/p>\n

Edvalson, L. T. and A.M. Larracuente. 2025. Consequences of drive on the evolution of genomes and species<\/a>. G3: Genes|Genomes|Genetics DOI:10.1093\/g3journal\/jkaf076.<\/p>\n

Mart\u00ed, E. and A.M. Larracuente. 2025. An innovation in host responses to escalating genomic conflicts.<\/a> Trends in Genetics. https:\/\/doi.org\/10.1016\/j.tig.2025.03.001.<\/p>\n

2024<\/strong><\/p>\n

Courret, C., Hemmer, L. , Wei,X. , Patel, P.D., Chabot, B., Fuda, N.J. Geng,X., Chang, C-H, Mellone, B., Larracuente, A.M. 2024. Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila
\n<\/a>\u00a0PLOS Biology 22(11): e3002911. https:\/\/doi.org\/10.1371\/journal.pbio.3002911<\/p>\n

Chabot, B., Sun, R., Amjad, A., Hoyt, S.J., Ouyang, L., Courret, C., Drennan, R., Leo L., Larracuente A.M., Core, L., O\u2019Neill, R.J., Mellone, B.G. Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape.\u00a0 2024 May. https:\/\/doi.org\/10.1186\/s13059-024-03433-1<\/a>\u00a0 Genome Biology. 25, 295.<\/p>\n

2023<\/strong><\/p>\n

Courret, C.& and A.M. Larracuente. 2023. High levels of intra-strain structural variation in Drosophila simulans X pericentric heterochromatin. GENETICS. iyad176. https:\/\/doi.org\/10.1093\/genetics\/iyad176<\/a>.<\/p>\n

Arkhipova, I.R, Burns, K.H., Chiappinelli, K. B., Chuong, E.B., Goubert, C., Guarn\u00e9, A., Larracuente, A.M., and H.L. Levin. Meeting Report: Transposable Elements at the Crossroads of Evolution, Health and Disease 2023. Mobile DNA. Accepted. In press.<\/p>\n

Courret, C., Wei, X., and Larracuente, A.M. 2023. New perspectives on the causes and consequences of male meiotic drive. Curr Opinion Gen & Dev. https:\/\/doi.org\/10.1016\/j.gde.2023.102111<\/a>.<\/p>\n

Mart\u00ed, E. and A.M. Larracuente. 2023. Genetic conflict and the origin of multigene families: implications for sex chromosome evolution. Proc R. Soc. B. https:\/\/doi.org\/10.1098\/rspb.2023.1823<\/a>.<\/p>\n

Courret, C, Ogereau, G, Larracuente,A.M., and C. Montchamp-Moreau. 2023. The evolutionary history of Drosophila simulans Y chromosomes reveals molecular signatures of resistance to sex ratio meiotic drive.<\/a> BioRxiv. https:\/\/doi.org\/10.1101\/2022.12.22.521550.\u00a0 Molecular Biology and Evolution 40(7):msad152. https:\/\/doi.org\/10.1093\/molbev\/msad152<\/a><\/p>\n

Sproul, J.S.S., Hotaling,S., Heckenhauer,J., Powell,A., Larracuente,A.M., Kelley,J.L., Pauls, S.U., Frandsen, P.B. 2023. Repetitive elements in the era of biodiversity genomics: insights from 600+ insect genomes.<\/a> BioRxiv 2022.06.02.494618; Genome Research. https:\/\/doi.org\/10.1101\/gr.277387.122<\/a><\/p>\n

2022<\/strong><\/p>\n

Lucas W Hemmer, Sherif Negm, Xuewen Geng, C\u00e9cile Courret, Beatriz Navarro-Dom\u00ednguez, Iain Speece, Xiaolu Wei, Eddyson Altidor, James Chaffer, John S. Sproul, Amanda M Larracuente. 2022. Centromere-associated retroelement evolution in Drosophila melanogaster<\/em> reveals an underlying conflict<\/a>. BioRxiv https:\/\/doi.org\/10.1101\/2022.11.25.518008<\/a>.<\/p>\n

Hanlon, S.L., Larracuente, A.M. When it comes to genetics, cheaters do prosper<\/a>. Chromosome Res (2022). https:\/\/doi.org\/10.1007\/s10577-022-09705-5<\/p>\n

Navarro-Dom\u00ednguez, B., Chang, C-H, Brand, C, Muirhead, C., Presgraves, D.C., and A.M. Larracuente. 2022 Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load<\/a>. BioRxiv 12\/23\/21 doi:10.1101\/2021.12.22.473781. eLife 2022;11:e78981 DOI: 10.7554\/eLife.78981<\/p>\n

Chen, T., Wei, X., Courret, C., Cui, M., Cheng, L., Wu, J., Ahmad, K., Larracuente, A.M., Rong, Y. 2022. The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila<\/a>. BIORXIV 4\/22\/22. PLoS Genet 18(9): e1010351. https:\/\/doi.org\/10.1371\/journal.pgen.1010351<\/p>\n

Chang, C-H., Gregory, L.E., Gordon, K.E., Meiklejohn, C.D., Larracuente, A.M. 2022. Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes.<\/a>\u00a0 eLife 2022;11:e75795 DOI: 10.7554\/eLife.75795<\/p>\n

2021<\/strong><\/p>\n

Wei,X., Eickbush,D.G., Speece,I., A.M. Larracuente. 2021. Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster<\/em> female germline<\/a>. eLife 2021;10:e62375. doi: 10.7554\/eLife.62375<\/a><\/p>\n

Herbette M, X Wei, C-H Chang, A.M. Larracuente, B Loppin, R Dubruille. 2021. Distinct spermiogenic phenotypes underlie sperm elimination in the Segregation Distorter<\/em> meiotic drive system<\/a>. PLoS Genet 17(7): e1009662. https:\/\/doi.org\/10.1371\/journal.pgen.1009662<\/p>\n

Heckenhauer, J., Frandsen, P.B., Sproul, J.S.&, Li, Z., Paule, J. Larracuente,A.M. ,Maughan, P.J., Barker, M.S.,Schneider, J.V., Pauls, S.V. 2021. Genome size evolution in the diverse insect order Trichoptera<\/a>. BioRxiv 5\/10\/21. https:\/\/doi.org\/10.1101\/2021.05.10.443368.<\/p>\n

Hotaling S, Sproul J.S.&, Heckenhauer J., Powell A., Larracuente A.M., Pauls S.U., Kelley J.L., and P.B. Frandsen. 2021. Long-reads are revolutionizing 20 years of insect genome sequencing.<\/a> BioRxiv 2\/15\/21. https:\/\/doi.org\/10.1101\/2021.02.14.431146. Accepted, Genome Biology and Evolution<\/em>.<\/p>\n

Chakraborty, C-H Chang, D. E. Khost, J. Vedanayagam, J.R. Adrion, Y. Liao, K. Montooth, C.D. Meiklejohn, A.M. Larracuente<\/strong>, J.J. Emerson. 2021. Evolution of genome structure in the Drosophila simulans<\/em> species complex.<\/a> Genome Research. 31: 380-396. doi: 10.1101\/gr.263442.120 \"Faculty<\/p>\n

2020<\/strong><\/p>\n

Sherif Negm, Anya D. Greenberg, Amanda M. Larracuente, John S. Sproul. 2020. RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles<\/a>. \u00a0Molecular Ecology Resources, 2020;00:1\u201313. https:\/\/doi.org\/10.1111\/1755-0998.13305<\/a>.<\/p>\n

Price, T.A.R., Windbichler, N., Unckless, R.L., Sutter, A., Runge, J-N, Ross P.A., Pomiankowski, A., Nuckolls,N., Montchamp-Moreau, C., Mideo, N., Martin, O.Y., Manser, A., Larracuente, A.M.,<\/strong> Holman, L., Godwin, J., Gemmell, N., Courret, C.&<\/sup>,Buchman, A, Lindholm, A.K. 2020. Resistance to Natural and Synthetic Gene Drive Systems.<\/a> Journal of Evolutionary Biology<\/em>. 33(10): 1345-1360. https:\/\/doi.org\/10.1111\/jeb.13693.<\/p>\n

Sproul, J., Khost, D.E.*, Eickbush, D.G., Negm, S., Wei, X., Wong, I., and A.M. Larracuente 2020. Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster<\/em> and the simulans clade.<\/a> BIORXIV\/2019\/846238,\u00a0 Molecular Biology and Evolution.\u00a0 37(8)2241-2256, https:\/\/doi.org\/10.1093\/molbev\/msaa078<\/p>\n

2019<\/strong><\/p>\n

Courret, C. , Chang, C-H., Wei, K., Montchamp-Moreau, C., Larracuente, A.M.\u00a02019.Meiotic drive mechanisms: lessons from Drosophila. In press. Proceedings of the Royal Society B<\/em>.<\/p>\n

Chang, C-H, Chavan, A, Palladino, J., Wei, X., Martins, N.M.C., Santinello, B., Chen, C-C, Erceg, J., Beliveau, B.J., Wu, C-T, Larracuente, A.M., and Mellone, B.G. 2019. Islands of retroelements are major components of Drosophila melanogaster<\/em> centromeres.<\/a> BioRxiv Epub 2\/1\/2019. PLoS Biology https:\/\/doi.org\/10.1371\/journal.pbio.3000241.\"Access<\/a><\/p>\n

Chang, C-H. and A.M. Larracuente. 2019.\u00a0Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome.<\/a> GENETICS 211: 333-348. doi: 10.1534\/genetics.118.301765. BioRxiv 07\/25\/2018.
\n-featured in GENETICS highlights 1\/1\/2019 http:\/\/www.genetics.org\/content\/211\/1\/NP\"Access<\/a><\/p>\n

2018<\/strong><\/p>\n

Fallon, T.R., Lower, S.E., Chang, C-H, Bessho-Uehara, M., Martin, G.J., Bewick, A.J., Behringer, M., Debat, H.J., Wong, I., Day, J.C. , Suvorov, A., Silva, C.J., Hall, D.W., Schmitz, R.J., Nelson, D.R., Lewis, S., Shigenobu,S., Bybee, S.M., Larracuente, A.M., Oba, Y., Weng, J-K. 2017. Firefly genomes illuminate the origin and evolution of bioluminescence.<\/a> \u00a0BioRxiv 12\/21\/17.\u00a0Elife Oct 16;7. pii: e36495. doi: 10.7554\/eLife.36495.<\/p>\n

2017<\/strong><\/p>\n

Khost, D.E., D. Eickbush, A.M. Larracuente. 2017. Single molecule long read sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster.<\/em>\u00a0 Genome Research . Advanced Access. 4\/3\/17. http:\/\/www.genome.org\/cgi\/doi\/10.1101\/gr.213512.116.<\/a> \"Access<\/a><\/p>\n

Chang, C-H. and A.M. Larracuente. 2017. Structural changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura<\/em>. Evolution. 71-5:1285-1296. http:\/\/dx.doi.org\/10.1111\/evo.13229.<\/a><\/p>\n

2016<\/strong><\/p>\n

Larracuente, A.M. 2016.\u00a0FISH in Drosophila in<\/em> Fluorescence in situ<\/em> Hybridization (FISH) \u2013 Application Guide, T Liehr (Editor), 2nd Ed., Springer, Berlin, 2017, ISBN: 978-3662529577.<\/p>\n

Larracuente, A.M. and V.H. Meller. 2016. Host\u2013Symbiont Interactions: Male- Killers Exposed.<\/a> Current Biology 26, R408\u2013R431, May 23, 2016. http:\/\/dx.doi.org\/10.1016\/j.cub.2016.03.057<\/p>\n

Lindholm, A. K., Dyer, K. A., Firman, R. C., Fishman, L., Forstmeier, W., Holman, L., Johannesson, H., Knief, U., Kokko, H., Larracuente, A. M., Manser, A., Montchamp-Moreau, C., Petrosyan, V. G., Pomiankowski, A., Presgraves, D. C., Safronova, L. D., Sutter, A., Unckless, R. L., Verspoor, R. L., Wedell, N., Wilkinson, G. S. & Price, T. A. R. 2016. The ecology and evolutionary dynamics of meiotic drive. <\/a>Trends in Ecology & Evolution. http:\/\/dx.doi.org\/10.1016\/j.tree.2016.02.001
\n<\/em><\/p>\n

2015<\/strong><\/p>\n

Hales, K.G., C.A. Korey, A.M. Larracuente and D.M. Roberts. 2015. Genetics on the fly: a primer on the Drosophila<\/em> model system.<\/a> GENETICS. 201(3):815-842. doi: 10.1534\/genetics.115.183392 \"Access<\/a><\/em><\/p>\n

Brand, C.B., A.M. Larracuente and D.C. Presgraves. 2015.\u00a0<\/em>Origin, evolution, and population genetics of the selfish Segregation distorter<\/em> gene duplication in European and African populations of Drosophila melanogaster<\/em>.<\/a> Evolution. 69-5: 1271\u20131283. <\/em>DOI: 10.1111\/evo.12658. *\"Access<\/a><\/p>\n

Unckless, R., A.M. Larracuente, and A.G. Clark. 2015. Sex-ratio meiotic drive and Y-linked resistance in Drosophila affinis<\/em>.<\/a> Genetics. Online 1\/8\/2015.10.1534\/genetics.114.173948<\/p>\n

Larracuente, A.M. and P.M. Ferree. 2015. Simple method for fluorescence DNA in situ<\/em> hybridization to squashed chromosomes<\/a>. J. Vis. Exp. 95, e52288. doi:10.3791\/52288.<\/p>\n

2014<\/strong><\/p>\n

Larracuente, A.M. 2014. The organization and evolution of the Responder<\/em> satellite in species of the Drosophila melanogaster<\/em> group: dynamic evolution of a target of meiotic drive<\/a>. BMC Evol. Biol.14:233. doi:10.1186\/s12862-014-0233-9<\/p>\n

Larracuente, A.M. and A.G. Clark. 2014. Recent selection on the Y-to-dot translocation in<\/a> Drosophila pseudoobscura<\/em>. Mol. Biol. Evol. 31(4):846-856. doi 10.1093\/molbev\/msu002.<\/p>\n

2005-2013<\/strong><\/p>\n

Larracuente, A.M. and A.G. Clark. 2013. Surprising differences in the variability of Y chromosomes in African and Cosmopolitan populations of<\/a> Drosophila melanogaster<\/em>. Genetics. 193:201-214.<\/p>\n

Larracuente, A.M. and D.C. Presgraves. 2012. The selfish Segregation Distorter<\/em> gene complex of Drosophila melanogaster<\/em><\/a>. Genetics. 192: 1-21.<\/p>\n

Larracuente, A.M., M.A.F. Noor, A.G. Clark. 2010. Translocation of Y-linked genes to the dot chromosome in Drosophila pseudoobscura<\/em><\/a>. Mol. Biol. Evol. 27(7): 1612-1620.<\/p>\n

Singh, N.D., A.M. Larracuente, T.B. Sackton, A.G. Clark. 2009. Comparative genomics on the Drosophila Phylogenetic Tree<\/a>. Annu. Rev. Ecol. Evol. Syst. 40:459\u201380.<\/p>\n

Larracuente, A.M., T.B. Sackton*, A.J. Greenberg, A. Wong, N.D. Singh, D. Sturgill, Y. Zhang, B. Oliver, A.G. Clark. 2008. Evolution of protein-coding genes in Drosophila<\/a>. Trends Genet. 24(3): 114-123.<\/p>\n

Singh N.D., A.M. Larracuente*, A.G. Clark. 2008. Contrasting the efficacy of selection on the X and autosomes in Drosophila<\/a>. Mol. Biol. Evol. 25(2):454-467.<\/p>\n

Drosophila 12 Genomes Consortium: A.G. Clark, M.B. Eisen, D.R. Smith, C.M. Bergman, B. Oliver, T.A. Markow, T.C. Kaufman, M. Kellis, W. Gelbart, V.N. Iyer, D.A. Pollard, T.B. Sackton, A.M. Larracuente et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny<\/a>. Nature. 450(7167): 203-218.<\/p>\n

Morris, S.R., A.M. Larracuente, K.M. Covino, M.S. Mustillo, K.E. Mattern, D.A. Liebner, H.D. Sheets. 2006. Limitations posed by parameter estimability in open population models: a case study using migratory stopover. Wilson Journal of Ornithology. 118(4): 513-526.<\/p>\n

Morris, S.R., H.D. Sheets, E.M. Turner, D.A. Liebner, A.M. Larracuente. 2005. Problems associated with pooling mark-recapture data prior to estimating stopover length for migratory passerines. Pages 670-673 in Bird Conservation Implementation and Integration in the Americas: Proceedings of the Third International Partners in Flight Conference 2002 (C.J. Ralph and T.D. Rich, eds.). U.S.D.A. Forest Service Technical report, GTR-PSW-191, Albany, CA.<\/p>\n

Morris, S.R., D.A. Liebner, A.M. Larracuente, E.M.Turner, H.D. Sheets. 2005. Multiple day constancy as an alternative to pooling for mark-recapture stopover estimates for nearctic-neotropical migrant landbirds. The Auk 122 (1):319-328.* indicates co-first author<\/p>\n

Drosophila image in header taken by Mr.Checker.<\/p>\n","protected":false},"excerpt":{"rendered":"

Complete List of Published Work in MyBibliography:\u00a0\u00a0 http:\/\/www.ncbi.nlm.nih.gov\/sites\/myncbi\/amanda.larracuente.1\/bibliography\/40318594\/public\/?sort=date&direction=descending ORCID: https:\/\/orcid.org\/0000-0001-5944-5686 2025 Edvalson, L. T. and A.M. Larracuente. 2025. Consequences of drive on the evolution of genomes and species. G3: Genes|Genomes|Genetics DOI:10.1093\/g3journal\/jkaf076. Mart\u00ed, E. and A.M. Larracuente. 2025. An innovation in host responses to escalating genomic conflicts. Trends in Genetics. https:\/\/doi.org\/10.1016\/j.tig.2025.03.001. 2024 Courret, C., Hemmer, L. … Continue reading Publications<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":26,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/full-width.php","meta":{"footnotes":""},"class_list":["post-596","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/blogs.rochester.edu\/larracuente\/wp-json\/wp\/v2\/pages\/596","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.rochester.edu\/larracuente\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/blogs.rochester.edu\/larracuente\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.rochester.edu\/larracuente\/wp-json\/wp\/v2\/users\/26"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.rochester.edu\/larracuente\/wp-json\/wp\/v2\/comments?post=596"}],"version-history":[{"count":82,"href":"https:\/\/blogs.rochester.edu\/larracuente\/wp-json\/wp\/v2\/pages\/596\/revisions"}],"predecessor-version":[{"id":10702,"href":"https:\/\/blogs.rochester.edu\/larracuente\/wp-json\/wp\/v2\/pages\/596\/revisions\/10702"}],"wp:attachment":[{"href":"https:\/\/blogs.rochester.edu\/larracuente\/wp-json\/wp\/v2\/media?parent=596"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}