Lab Publications

  • Akopyan M, Jacobs A, Rick J, Wilder AP, Baumann Z, Conover D, Baumann H, Therkildsen N. Multiple chromosomal inversions modulate continuous local adaptation along a steep thermal cline.. 2026. Science. 10.1126/science.ady6774
  • John CAS, Carlson DM, Holst LK, Therkildsen N, McIntyre PB. Overcoming barriers to conservation of species complexes: integrating ecology with affordable whole genome methods to define conservation units in imperiled fishes. 2025. Biodiversity and Conservation. 10.1007/s10531-025-03139-1
  • Dimens PV, Franckowiak RP, Iqbal A, Grenier JK, Munn PR, Therkildsen N. Harpy: a pipeline for processing haplotagging linked-read data. 2025. Bioinformatics Advances. 10.1093/bioadv/vbaf133
  • Zarri LJ, Kraft CE, McIntyre P, Baetscher DS, Jirka KJ, Randall EA, Marcy‐Quay B, John CAS, Sethi SA, Airey M, Detmer T, Flecker A, Therkildsen N. Eradication efforts catalyze rapid evolution in an invasive predatory fish. 2025. Proceedings of the National Academy of Sciences of the United States of America. 10.1073/pnas.2424067122
  • Ortiz-Pachar J, Ramírez-González J, Moity N, Andrade-Vera S, Rivadeneira WD, Therkildsen N. A chromosome-level genome assembly for the brown sea cucumber from the Galápagos Islands, Isostichopus fuscus. 2025. Scientific Data. 10.1038/s41597-025-06422-6
  • Zarri LJ, Franckowiak RP, Bogdanowicz S, Kurata NP, Pacheco F, Therkildsen N, Flecker A. Do tributary dams pose a greater conservation threat than main-stem dams for nonmigratory freshwater fishes?. 2025. Transactions of the American Fisheries Society. 10.1093/tafafs/vnaf031
  • Akopyan M, Tigano A, Jacobs A, Wilder AP, Therkildsen N. Genetic Differentiation is Constrained to Chromosomal Inversions and Putative Centromeres in Locally Adapted Populations With Higher Gene Flow. 2024. Molecular Biology and Evolution. 10.1093/molbev/msaf092
  • Rodenbiker J, Therkildsen N, Ruan E, Su K. Advancing One Health in Urban Seafood Markets: A Genetic and Social Analysis of Dried Sea Cucumber in Three New York City Chinatowns. 2024. Sustainability. 10.3390/su16093589
  • Monteiro HJA, Bekkevold D, Pacheco G, Mortensen S, Lou R, Therkildsen N, Tanguy A, Robert C, Wit PRd, Meldrup D, Laugen AT, Ermgassen PZz, Strand Å, Saurel C, Hemmer-Hansen J. Genome‐Wide Population Structure in a Marine Keystone Species, the European Flat Oyster (Ostrea edulis). 2024. Molecular Ecology. 10.1111/mec.17573
  • Velotta JP, Iqbal A, Glenn E, Franckowiak RP, Formenti G, Mountcastle J, Balacco JR, Tracey A, Sims Y, Howe K, Fedrigo O, Jarvis ED, Therkildsen N. A Complete Assembly and Annotation of the American Shad Genome Yields Insights into the Origins of Diadromy. 2024. Genome Biology and Evolution. 10.1093/gbe/evae276
  • Rodenbiker J, Therkildsen N, Li CC. Global shark fins in local contexts: multi-scalar dynamics between Hong Kong markets and Mid-Atlantic fisheries. 2023. Ecology and Society. 10.5751/es-14229-280305
  • Baetscher DS, Locatelli NS, Won E, Fitzgerald T, McIntyre PB, Therkildsen N. Optimizing a metabarcoding marker portfolio for species detection from complex mixtures of globally diverse fishes. 2023. Environmental DNA. 10.1002/edn3.479
  • Jacobs A, Velotta JP, Tigano A, Wilder AP, Baumann H, Therkildsen N. Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside. 2022. bioRxiv. 10.1101/2022.04.27.489786
  • Therkildsen N, Pinsky M. A long evolutionary reach for fishing nets. 2022. Science. 10.1126/science.abo6512
  • Akopyan M, Tigano A, Jacobs A, Wilder AP, Baumann H, Therkildsen N. Comparative linkage mapping uncovers recombination suppression across massive chromosomal inversions associated with local adaptation in Atlantic silversides. 2022. Molecular Ecology. 10.1111/mec.16472
  • Lou R, Therkildsen N. Batch effects in population genomic studies with low-coverage whole genome sequencing data: causes, detection, and mitigation.. 2021. Molecular ecology resources. 10.22541/au.162791857.78788821/v2
  • Tigano A, Jacobs A, Wilder AP, Nand A, Zhan Y, Dekker J, Therkildsen N. Erratum to: Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. 2021. Genome Biology and Evolution. 10.1093/gbe/evab163
  • Akopyan M, Tigano A, Jacobs A, Wilder AP, Baumann H, Therkildsen N. Comparative linkage mapping uncovers massive chromosomal inversions that suppress recombination between locally adapted fish populations. 2021. bioRxiv. 10.1101/2021.10.18.464892
  • Baetscher DS, Locatelli N, Won E, Fitzgerald T, McIntyre P, Therkildsen N. Optimizing a metabarcoding primer portfolio for species-level detection of taxa in complex mixtures of diverse fishes. 2021. 10.22541/au.163861686.62434613/v1
  • Lou R, Jacobs A, Wilder AP, Therkildsen N. A beginner's guide to low‐coverage whole genome sequencing for population genomics. 2020. Molecular Ecology. 10.1111/mec.16077
  • Locatelli N, McIntyre P, Therkildsen N, Baetscher DS. GenBank's reliability is uncertain for biodiversity researchers seeking species-level assignment for eDNA.. 2020. Proceedings of the National Academy of Sciences of the United States of America. 10.1073/pnas.2007421117
  • Lou R, Therkildsen N, Messer PW. The Effects of Quantitative Trait Architecture on Detection Power in Short-Term Artificial Selection Experiments. 2020. G3: Genes|Genomes|Genetics. 10.1534/g3.120.401287
  • Tigano A, Jacobs A, Wilder AP, Nand A, Zhan Y, Dekker J, Therkildsen N. Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. 2020. Genome Biology and Evolution. 10.1093/gbe/evab098
  • Marcy‐Quay B, Sethi S, Therkildsen N, Kraft C. Expanding the feasibility of fish and wildlife assessments with close‐kin mark–recapture. 2020. Ecosphere. 10.1002/ecs2.3259
  • Wilder AP, Palumbi S, Conover D, Therkildsen N. Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome. 2020. Evolution Letters. 10.1002/evl3.189
  • Dehasque M, Ávila-Arcos M, Díez-del-Molino D, Fumagalli M, Guschanski K, Lorenzen E, Malaspinas A, Marquès-Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen N, Wegmann D, Dalén L, Foote A. Inference of natural selection from ancient DNA. 2020. Evolution Letters. 10.1002/evl3.165
  • Therkildsen N, Baumann H. A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia.. 2020. Marine genomics. 10.1016/j.margen.2019.100738
  • Lowndes J, Froehlich H, Horst A, Jayasundara N, Pinsky M, Stier A, Therkildsen N, Wood CL. Supercharge your research: a ten-week plan for open data science.. 2019. Nature. 10.1038/d41586-019-03335-4
  • Jacobs A, Therkildsen N. Excavating ghost footprints and tangled trees from modern genomes. 2019. Molecular Ecology. 10.1111/mec.15141
  • Clucas GV, Lou R, Therkildsen N, Kovach A. Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing. 2019. Evolutionary Applications. 10.1111/eva.12861
  • Lou R, Therkildsen N, Messer PW. The Effects of Quantitative Trait Architecture on Detection Power in Artificial Selection Experiments. 2019. bioRxiv. 10.1101/672683
  • Therkildsen N, Wilder AP, Conover D, Munch S, Baumann H, Palumbi S. Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing. 2019. Science. 10.1126/science.aaw7271
  • Lou R, Fletcher NK, Wilder AP, Conover D, Therkildsen N, Searle J. Full mitochondrial genome sequences reveal new insights about post-glacial expansion and regional phylogeographic structure in the Atlantic silverside (Menidia menidia). 2018. Marine Biology. 10.1007/s00227-018-3380-5
  • Lou R, Fletcher NK, Wilder AP, Conover D, Therkildsen N, Searle J. Full mitochondrial genome sequences reveal new insights about post-glacial expansion and regional phylogeographic structure in the Atlantic silverside (Menidia menidia). 2018. Marine Biology. 10.1007/S00227-018-3380-5
  • Fairweather R, Bradbury I, Helyar S, Bruyn Md, Therkildsen N, Bentzen P, Hemmer-Hansen J, Carvalho G. Range‐wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod. 2018. Ecology and Evolution. 10.1002/ece3.4672
  • Rudman SM, Barbour MA, Csilléry K, Gienapp P, Guillaume F, Hairston N, Hendry A, Lasky J, Rafajlović M, Räsänen K, Schmidt P, Seehausen O, Therkildsen N, Turcotte MM, Levine J. What genomic data can reveal about eco-evolutionary dynamics. 2017. Nature Ecology & Evolution. 10.1038/s41559-017-0385-2
  • Bernatchez L, Wellenreuther M, Araneda C, Ashton DT, Barth JM, Beacham T, Maes G, Martinsohn J, Miller K, Naish KA, Ovenden J, Primmer C, Suk HY, Therkildsen N, Withler R. Harnessing the Power of Genomics to Secure the Future of Seafood.. 2017. Trends in ecology & evolution. 10.1016/j.tree.2017.06.010
  • Therkildsen N, Palumbi S. Practical low‐coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. 2017. Molecular Ecology Resources. 10.1111/1755-0998.12593
  • Kelley JL, Brown AP, Therkildsen N, Foote A. The life aquatic: advances in marine vertebrate genomics. 2016. Nature Reviews Genetics. 10.1038/nrg.2016.66
  • Mensa I, Banaszkiewicz P, Michonneau F, Buske OJ, Latornell D, Ma EJ, Bonnie J, Steinbach P, Allen JE, Mills B, Stimberg M, Standage DS, Soranzo N, Brown A, Barmby P, Lijnzaad P, Howe A, Teleńczuk B, Kelly T, Perry A, Bekolay T, Srinath A, Jennings ME, Gray N, White E, Milhans J, Marwaha K, Madin JS, Simpkin S, Olson R, Walt A, Fontenelle H, Kim JT, Gidden M, Shattow GM, Duckles J, Mayes A, Jackson M, Schloss P, Middleson R, Emonet R, Vollmer D, Brase R, Linden JVD, Keipert K, Blischak J, Lake S, Smith B, Baird D, Harstad E, Mashchenko S, Nielsen DE, Hansen M, Chung K, Poisot T, Silva R, Povall T, Hagh VF, Staton ME, Palamartchouk K, Rydbeck H, Sadjadi M, Boardman S, Beagrie R, Koch C, Fernandes F, McTavish E, Dolson EL, Blin K, Brunson D, Nederbragt L, Keener A, Willing C, Bell J, Ross N, Pourreza H, Pipitone J, Simpson JW, Marini C, O'Leary A, Turner S, Waterfall J, Orr AJ, King WT, Gacenga F, Eyers D, Richie-Halford AC, Konrad BP, Schyndel Jv, Alexander H, Jones D, Seyffert B, Ritchie S, Alsheikh-Hussain AS, Wilson G, González I, Irving DB, Imamoglu F, Miotto A, Boughton A, Timbers T, Walker A, Therkildsen N, Thoele F, Mount S, Zamparo L, Boissoneault M, Chen D, Belikov E, Young L, Devenyi GA, Winston D. Software Carpentry: The Unix Shell. 2015. 10.5281/zenodo.27355
  • Bonanomi S, Pellissier L, Therkildsen N, Hedeholm R, Retzel A, Meldrup D, Olsen S, Nielsen A, Pampoulie C, Hemmer-Hansen J, Wisz M, Grønkjær P, Nielsen E. Archived DNA reveals fisheries and climate induced collapse of a major fishery. 2015. Scientific Reports. 10.1038/srep15395
  • Orbit, Hemmer J, Therkildsen N. Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges. 2014. The Biological Bulletin. 10.1086/BBLv227n2p117
  • Hemmer-Hansen J, Therkildsen N, Pujolar J. Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges. 2014. The Biological Bulletin. 10.1086/BBLv227n2p117
  • Hemmer-Hansen J, Therkildsen N, Meldrup D, Nielsen E. Conserving marine biodiversity: insights from life-history trait candidate genes in Atlantic cod (Gadus morhua). 2014. Conservation Genetics. 10.1007/s10592-013-0532-5
  • Bothwell H, Bisbing S, Therkildsen N, Crawford LA, Alvarez N, Holderegger R, Manel S. Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach. 2013. Conservation Genetics. 10.1007/s10592-012-0411-5
  • Hemmer-Hansen J, Therkildsen N, Meldrup D, Nielsen E. Conserving marine biodiversity: insights from life-history trait candidate genes in Atlantic cod (Gadus morhua). 2013. Conservation Genetics. 10.1007/s10592-013-0532-5
  • Therkildsen N, Hemmer-Hansen J, Hedeholm R, Wisz M, Pampoulie C, Meldrup D, Bonanomi S, Retzel A, Olsen S, Nielsen E. Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of Atlantic cod Gadus morhua. 2013. Evolutionary Applications. 10.1111/eva.12055
  • Therkildsen N, Hemmer-Hansen J, Als T, Swain D, Morgan M, Trippel E, Palumbi S, Meldrup D, Nielsen E. Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod. 2013. Molecular Ecology. 10.1111/mec.12260
  • Heino M, Baulier C, Boukal D, Ernande B, Johnston F, Fabian, Mollet M, Pardoe H, Therkildsen N, Uusi‐Heikkilä S, Vainikka A, RobertArlinghaus, Dankel D, Dunlop E, AnneMariaEikeset, Enberg K, Georg, Engelhard H, Jørgensen C, Laugen AT, Matsumura S, Nusslé S, Urbach D, Whitlock R, Rijnsdorp A, Dieckmann U. Can fisheries-induced evolution shift reference points for fisheries management?. 2013. Ices Journal of Marine Science. 10.1093/ICESJMS/FST077
  • Hemmer-Hansen J, Nielsen E, Therkildsen N, Taylor MI, Ogden R, Geffen A, Bekkevold D, Helyar S, Pampoulie C, Johansen T, Carvalho G. A genomic island linked to ecotype divergence in Atlantic cod. 2013. Molecular Ecology. 10.1111/mec.12284
  • Behrens J, Gräns A, Therkildsen N, Neuenfeldt S, Axelsson M. Correlations between hemoglobin type and temperature preference of juvenile Atlantic cod Gadus morhua. 2012. Journal of Experimental Marine Biology and Ecology. 10.1016/J.JEMBE.2011.11.019
  • Bothwell H, Bisbing S, Therkildsen N, Crawford LA, Alvarez N, Holderegger R, Manel S. Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach. 2012. Conservation Genetics. 10.1007/s10592-012-0411-5
  • Laugen AT, Engelhard G, Whitlock R, Arlinghaus R, Dankel D, Dunlop E, Eikeset AM, Enberg K, Jørgensen C, Matsumura S, Nusslé S, Urbach D, Baulier L, Boukal D, Ernande B, Johnston F, Mollet F, Pardoe H, Therkildsen N, Uusi‐Heikkilä S, Vainikka A, Heino M, Rijnsdorp A, Dieckmann U. Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management. 2012. Fish and Fisheries (Oxford, England). 10.1111/faf.12007
  • Wit P, Pespeni MH, Ladner J, Barshis D, Seneca F, Jaris H, Therkildsen N, Morikawa MK, Palumbi S. The simple fool's guide to population genomics via RNA‐Seq: an introduction to high‐throughput sequencing data analysis. 2012. Molecular Ecology Resources. 10.1111/1755-0998.12003
  • Therkildsen N, Nielsen E, Swain D, Pedersen JS. Large effective population size and temporal genetic stability in Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence. 2010. Canadian Journal of Fisheries and Aquatic Sciences. 10.1139/F10-084
  • Therkildsen N, Nielsen E, Hüssy K, Meldrup D, Geffen A. Does DNA extraction affect the physical and chemical composition of historical cod (Gadus morhua) otoliths. 2010. Ices Journal of Marine Science. 10.1093/ICESJMS/FSQ016
  • Therkildsen N. Small- versus large-scale fishing operations in New England, USA. 2007. Fisheries Research. 10.1016/J.FISHRES.2006.10.004