​Publications


​Lab members highlighted in bold


Pre-prints:
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  • Runyang, N. L., Jacobs, A., Wilder, A., and Therkildsen, N.O. 2021 A beginner's guide to low-coverage whole genome sequencing for population genomics. Authorea DOI: 10.22541/au.160689616.68843086/v3


Peer-reviewed papers:

  • Tigano, A., Jacobs, A., Wilder, A. P.,  Nand, A., Zhan, Y., Dekker, J., and  Therkildsen, N. O. 2021. Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation. Genome Biology and Evolution 13, evab098.

  • Locatelli, N. S., McIntyre, P. B., Therkildsen, N. O., and Baetscher, D. S. 2020. GenBank’s reliability is uncertain for biodiversity researchers seeking species-level assignment for eDNA. Proceedings of the National Academy of Sciences 117:32211-32212.

  • Riginos, C., Crandall, E. D., Liggins, L., Gaither, M.R., Ewing, R. B., Meyer, C., … Therkildsen, N. O., … et al. [total of 14 authors]. 2020. Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research. Molecular Ecology Resources 20:1458-1469.

  • Marcy-Quay, B., Sethi, S. A., Therkildsen, N. O., and Kraft, C. E. 2020. Expanding the feasibility of fish and wildlife assessments with close-kin mark-recapture. 2020. Ecosphere 11:e03259.

  • Wilder, A. P., Palumbi, S. R., Conover, D. O., and Therkildsen, N. O. 2020. Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome. Evolution letters 4:430-443.

  • Dehasque, M., Ávila-Arcos, M. C., Díez del Molino, D., Fumagalli, M., Guschanski, K., Lorenzen, E. D., ..., N. O. Therkildsen, ..., et al. 2020. Inference of natural selection from ancient DNA. Evolution Letters 4:94–108. 
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  • Therkildsen, N. O. and Baumann, H. 2020. A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia. Marine Genomics 100738.

  • Lou, R. N., Therkildsen, N. O., and Messer, P. W. 2020. The effects of quantitative trait architecture on detection power in short-term artificial selection experiments.. G3: Genes, Genomes, Genetics 10:3213-3227.

  • Clucas, G. V., Lou, R. N., Therkildsen, N. O. and Kovach, A. I. 2019. Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing. Evolutionary Applications 134:1289. 

  • Therkildsen, N. O., Wilder, A. P., Conover, D. O., Munch, S. B., Baumann, H. and Palumbi, S. R. 2019. Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing. Science 365:487–490

  • Jacobs, A. and Therkildsen, N. O. 2019. Excavating ghost footprints and tangled trees from modern genomes. Molecular Ecology, 28:3287–3290.

  • Fairweather, R., Bradbury, I. R., Helyar, S. J., De Bruyn, M., Therkildsen, N. O., Bentzen, P., et al. 2018. Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod. Ecology and Evolution, 8:12140–12152.

  • Lou, R. N., Fletcher, N. K., Wilder, A. P., Conover, D. O., Therkildsen, N. O.* and Searle, J. B.* 2018. Full mitochondrial genome sequences reveal new insights about post-glacial expansion and regional phylogeographic structure in the Atlantic silverside (Menidia menidia). Marine Biology 165:124.
    * equal contribution

  • Rudman, S. M., Barbour, M. A., Csilléry, K., Gienapp, P., Guillaume, F., Hairston, N. G., …Therkildsen, N. O., … et al. 2018. What genomic data can reveal about eco-evolutionary dynamics. Nature Ecology & Evolution, 2:9–15.

  • Bernatchez, L., Wellenreuther, M., Araneda, C., Ashton, D. T., Barth, J. M. I., Beacham, T. D., …Therkildsen, N. O.,… et al. 2017. Harnessing the power of genomics to secure the future of seafood. Trends in Ecology & Evolution, 32:665–680.

  • Therkildsen, N. O. and Palumbi, S. R. 2017. Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. Molecular Ecology Resources 17:194–208.

  • Kelley, J. L., Brown, A. P., Therkildsen, N. O. and Foote, A. D. 2016. The life aquatic: advances in marine vertebrate genomics. Nature Reviews Genetics 17:523-534.

  • Bonanomi, S., Therkildsen, N. O., Retzel, A., Hedeholm, R. B., Pedersen, M. V. Meldrup, D., Pampoulie, C., Hemmer-Hansen, J., Grønkjær, P. and Nielsen, E. E. 2016. Historical DNA documents long distance natal homing in marine fish. Molecular Ecology 25: 2727–2734.

  • Bonanomi, S., Pellissier, L., Therkildsen, N. O., Hedeholm, R. B., Retzel, A., Meldrup, M., Olsen, S. M., Nielsen, A., Pampoulie, C., Hemmer-Hansen, J., Wisz, M. S., Grønkjær, P. and Nielsen, E. E. 2015. Archived DNA reveals fisheries and climate induced collapse of a major fishery. Nature Scientific Reports 5:15395.

  • Hemmer-Hansen, J., Therkildsen, N. O. and Pujolar, J. M. 2014. Population genomics of marine fishes: Next generation prospects and challenges. The Biological Bulletin 227:117-132.

  • Bonanomi, S., Therkildsen, N. O., Hedeholm, R. B., Hemmer-Hansen, J. and Nielsen, E. E. 2014. The use of archived tags in retrospective genetic analysis of fish. Molecular Ecology Resources 14:616-621.

  • Hemmer-Hansen, J., Therkildsen, N. O., Meldrup, D. and Nielsen, E. E. 2014. Conserving marine biodiversity: insights from life-history trait candidate genes in Atlantic cod (Gadus morhua). Conservation Genetics 15:213-228.

  • Laugen, A. T., Engelhard, G. H., Whitlock, R., Arlinghaus, R., Dankel, D. J., Dunlop, E. S., […], Therkildsen, N. O. et al. 2014. Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management. Fish and Fisheries 15:65-96.

  • Heino, M., Baulier, L., Boukal, D. S., Ernande, B., Johnston, F. D., Mollet, M., […], Therkildsen, N. O. et al. 2013. Can fisheries-induced evolution shift reference points for fisheries management? ICES Journal of Marine Science 70:707-721.

  • Hemmer-Hansen. J., Nielsen, E. E., Therkildsen, N. O., Taylor, M. I., Ogden, R., Geffen, A., Bekkevold, D., Helyar, D., Pampoulie, C., Johansen, T., FishPopTrace Consortium and Carvalho, G. R. 2013. A genomic island linked to ecotype divergence in Atlantic cod. Molecular Ecology 22: 2653-2667.

  • Therkildsen, N. O., Hemmer-Hansen, J., Hedeholm, R. B., Wisz, M., Pampoulie, C., Meldrup, D., Bonanomi, S., Retzel, A., Olsen, M. A. and Nielsen, E. E. 2013. Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of Atlantic cod Gadus morhua. Evolutionary Applications 6:690-705.

  • Therkildsen, N. O., Hemmer-Hansen, J, Als, T. D, Swain, D. P., Morgan, J., Trippel, E., Meldrup, D. and Nielsen, E. E. 2013. Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod. Molecular Ecology 22:2424-2440.

  • Bothwell, H., Bisbing, S., Therkildsen, N. O., Crawford, L., Alvarez, N., Holderegger, R. and Manel, S. 2012. Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach. Conservation Genetics 14:467-481.

  • De Wit, P., Pespeni, M. H., Ladner, J. T., Barshis, D. J., Seneca, S., Jaris, H., Therkildsen, N. O., Morikawa, M. and Palumbi, S. R. 2012. The Simple Fool’s Guide to RNA-Seq: Gene expression and SNP data analysis in the age of high-throughput sequencing. Molecular Ecology Resources 12:1058-1067.

  • Behrens, J. W., Gräns, A., Therkildsen, N. O., Neuenfeldt, S. and Axelsson, M. 2012. Correlations between hemoglobin type and temperature preference of juvenile Atlantic cod Gadus morhua. Journal of Experimental Marine Biology and Ecology 413: 71-77.

  • Therkildsen, N. O., Nielsen, E. E., Swain, D. P. and Pedersen, J. S. 2010 Effective population size and temporal genetic stability in Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence. Canadian Journal of Fisheries and Aquatic Sciences 67: 1585-1595.

  • Therkildsen, N. O., Nielsen, E. E., Hüssy, K., Meldrup, M. and Geffen, A. J. 2010. Does DNA extraction affect the physical and chemical composition of historical cod (Gadus morhua) otoliths? ICES Journal of Marine Science 67:1251-1259.

  • Therkildsen, N. O. 2007. Small versus large-scale fishing operations in New England, USA. Fisheries Research 83:285-296.
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  • Therkildsen, N. O. and Petersen, C. W. 2006. A review of the emerging fisheries for the sea cucumber Cucumaria frondosa: biology, policy, and future prospects. Beche-de-Mer Information Bulletin 23:16-25.