Hoban, S., Archer, F. I., Bertola, L. D., Bragg, J. G., Breed, M. F., Bruford, M. W., Coleman, M. A., Ekblom, R., Funk, W. C., Grueber, C. E., Hand, B. K., Jaffé, R., Jensen, E., Johnson, J. S., Kershaw, F., Liggins, L., MacDonald, A. J., Mergeay, J., Miller, J. M., … Hunter, M. E. (2022). Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition. Biological Reviews, 97(4), 1511–1538.
Louis, M., Galimberti, M., Archer, F., Berrow, S., Brownlow, A., Fallon, R., Nykanen, M., O’Brien, J., Roberston, K. M., Rosel, P. E., Simon-Bouhet, B., Wegmann, D., Fontaine, M. C., Foote, A. D., & Gaggiotti, O. E. (2021). Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. Science Advances, 7(44), 13.
Thomson, A. I., Archer, F. I., Coleman, M. A., Gajardo, G., Goodall-Copestake, W. P., Hoban, S., Laikre, L., Miller, A. D., O’Brien, D., Pérez-Espona, S., Segelbacher, G., Serrão, E. A., Sjøtun, K., & Stanley, M. S. (2021). Charting a course for genetic diversity in the UN Decade of Ocean Science. Evolutionary Applications, 14(6), 1497–1518.
Morin, P. A., Archer, F. I., Avila, C. D., Balacco, J. R., Bukhman, Y. V., Chow, W., Fedrigo, O., Formenti, G., Fronczek, J. A., Fungtammasan, A., Gulland, F. M. D., Haase, B., Peter Heide-Jorgensen, M., Houck, M. L., Howe, K., Misuraca, A. C., Mountcastle, J., Musser, W., Paez, S., … Jarvis, E. D. (2021). Reference genome and demographic history of the most endangered marine mammal, the vaquita. Molecular Ecology Resources, 21(4), 1008–1020.
Leslie, M. S., Archer, F. I., & Morin, P. A. (2019). Mitogenomic differentiation in spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) from the eastern tropical Pacific Ocean. Marine Mammal Science, 35(2), 522–551.
Hartmann, A. C., Marhaver, K. L., Klueter, A., Lovci, M. T., Closek, C. J., Diaz, E., Chamberland, V. F., Archer, F. I., Deheyn, D. D., Vermeij, M. J. A., & Medina, M. (2019). Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host. Molecular Ecology, 28(1), 141–155.
Jost, L., Archer, F., Flanagan, S., Gaggiotti, O., Hoban, S., & Latch, E. (2018). Differentiation measures for conservation genetics. Evolutionary Applications, 11(7), 1139–1148.
Milligan, B. G., Archer, F. I., Ferchaud, A.-L., Hand, B. K., Kierepka, E. M., & Waples, R. S. (2018). Disentangling genetic structure for genetic monitoring of complex populations. Evolutionary Applications, 11(7), 1149–1161.
Hartmann, A. C., Petras, D., Quinn, R. A., Protsyuk, I., Archer, F. I., Ransome, E., Williams, G. J., Bailey, B. A., Vermeij, M. J. A., Alexandrov, T., Dorrestein, P. C., & Rohwer, F. L. (2017). Meta-mass shift chemical profiling of metabolomes from coral reefs. Proceedings of the National Academy of Sciences, 114(44), 11685–11690.
Martien, K. K., Leslie, M. S., Taylor, B. L., Morin, P. A., Archer, F. I., Hancock-Hanser, B. L., Rosel, P. E., Vollmer, N. L., Viricel, A., & Cipriano, F. (2017). Analytical approaches to subspecies delimitation with genetic data. Marine Mammal Science, 33, 27–55.
Rosel, P. E., Hancock-Hanser, B. L., Archer, F. I., Robertson, K. M., Martien, K. K., Leslie, M. S., Berta, A., Cipriano, F., Viricel, A., Viaud-Martinez, K. A., & Taylor, B. L. (2017). Examining metrics and magnitudes of molecular genetic differentiation used to delimit cetacean subspecies based on mitochondrial DNA control region sequences. Marine Mammal Science, 33, 76–100.
Leduc, R. G., Archer, F. I., Lang, A. R., Martien, K. K., Hancock-Hanser, B., Torres-Florez, J. P., Hucke-Gaete, R., Rosenbaum, H. C., van Waerebeek, K., Brownell, R. L., & Taylor, B. L. (2017). Genetic variation in blue whales in the eastern pacific: implication for taxonomy and use of common wintering grounds. Mol Ecol, 26(3), 740–751.
Archer, F. I., Adams, P. E., & Schneiders, B. B. (2017). stratag: An r package for manipulating, summarizing and analysing population genetic data. Molecular Ecology Resources, 17(1), 5–11.
Jombart, T., Archer, F., Schliep, K., Kamvar, Z., Harris, R., Paradis, E., Goudet, J., & Lapp, H. (2017). apex: phylogenetics with multiple genes. Mol Ecol Resour, 17(1), 19–26.
Parobek, C. M., Archer, F. I., DePrenger-Levin, M. E., Hoban, S. M., Liggins, L., & Strand, A. E. (2017). skelesim: an extensible, general framework for population genetic simulation in R. Mol Ecol Resour, 17(1), 101–109.
Rosel, P. E., Taylor, B. L., Hancock-Hanser, B. L., Morin, P. A., Archer, F. I., Lang, A. R., Mesnick, S. L., Pease, V. L., Perrin, W. F., Robertson, K. M., Leslie, M. S., Berta, A., Cipriano, F., Parsons, K. M., Viricel, A., Vollmer, N. L., & Martien, K. K. (2017). A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species. Marine Mammal Science, 33(S1), 56–75.
Taylor, B. L., Archer, F. I., Martien, K. K., Rosel, P. E., Hancock-Hanser, B. L., Lang, A. R., Leslie, M. S., Mesnick, S. L., Morin, P. A., Pease, V. L., Perrin, W. F., Robertson, K. M., Parsons, K. M., Viricel, A., Vollmer, N. L., Cipriano, F., Reeves, R. R., Krützen, M., & Baker, C. S. (2017). Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data. Marine Mammal Science, 33(S1), 132–155.
Klueter, A., Trapani, J., Archer, F. I., McIlroy, S. E., & Coffroth, M. A. (2017). Comparative growth rates of cultured marine dinoflagellates in the genus Symbiodinium and the effects of temperature and light. PLOS ONE, 12(11), e0187707.
Morin, P. A., Parsons, K. M., Archer, F. I., Avila-Arcos, M. C., Barrett-Lennard, L. G., Dalla Rosa, L., Duchene, S., Durban, J. W., Ellis, G. M., Ferguson, S. H., Ford, J. K., Ford, M. J., Garilao, C., Gilbert, M. T. P., Kaschner, K., Matkin, C. O., Petersen, S. D., Robertson, K. M., Visser, I. N., … Foote, A. D. (2015). Geographic and temporal dynamics of a global radiation and diversification in the killer whale. Molecular Ecology, 24(15), 3964–3979.
Klueter, A., Crandall, J. B., Archer, F. I., Teece, M. A., & Coffroth, M. A. (2015). Taxonomic and environmental variation of metabolite profiles in marine dinoflagellates of the genus symbiodinium. Metabolites, 5(1), 74–99.
Martien, K. K., Chivers, S. J., Baird, R. W., Archer, F. I., Gorgone, A. M., Hancock-Hanser, B. L., Mattila, D., McSweeney, D. J., Oleson, E. M., Palmer, C., Pease, V. L., Robertson, K. M., Schorr, G. S., Schultz, M. B., Webster, D. L., & Taylor, B. L. (2014). Nuclear and mitochondrial patterns of population structure in North Pacific false killer whales (Pseudorca crassidens). J Hered, 105(5), 611–626.
Rankin, S., Archer, F., & Barlow, J. (2013). Vocal activity of tropical dolphins is inhibited by the presence of killer whales, Orcinus orca. Marine Mammal Science, 29(4), 679–690.
Archer, F. I., Morin, P. A., Hancock-Hanser, B. L., Robertson, K. M., Leslie, M. S., Berube, M., Panigada, S., & Taylor, B. L. (2013). Mitogenomic phylogenetics of fin whales (balaenoptera physalus spp.): Genetic evidence for revision of subspecies. PLOS ONE, 8(5).
Hancock-Hanser, B. L., Frey, A., Leslie, M. S., Dutton, P. H., Archer, F. I., & Morin, P. A. (2013). Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics. Mol Ecol Resour, 13(2), 254–268.
Duchene, S., Archer, F. I., Vilstrup, J., Caballero, S., & Morin, P. A. (2011). Mitogenome Phylogenetics: The Impact of Using Single Regions and Partitioning Schemes on Topology, Substitution Rate and Divergence Time Estimation. PLOS ONE, 6(11).
Perrin, W. F., Thieleking, J. L., Walker, W. A., Archer, F. I., & Robertson, K. M. (2011). Common bottlenose dolphins (Tursiops truncatus) in California waters: Cranial differentiation of coastal and offshore ecotypes. Marine Mammal Science, 27(4), 769–792.
Mesnick, S. L., Taylor, B. L., Archer, F. I., Martien, K. K., Trevino, S. E., Hancock-Hanser, B. L., Medina, S. C. M., Pease, V. L., Robertson, K. M., Straley, J. M., Baird, R. W., Calambokidis, J., Schorr, G. S., Wade, P., Burkanov, V., Lunsford, C. R., Rendell, L., & Morin, P. A. (2011). Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA. Molecular Ecology Resources, 11, 278–298.
Morin, P. A., Archer, F. I., Foote, A. D., Vilstrup, J., Allen, E. E., Wade, P., Durban, J., Parsons, K., Pitman, R., Li, L., Bouffard, P., Nielsen, S. C. A., Rasmussen, M., Willerslev, E., Gilbert, M. T. P., & Harkins, T. (2010). Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Research, 20(7), 908–916.
Morin, P. A., Martien, K. K., Archer, F. I., Cipriano, F., Steel, D., Jackson, J., & Taylor, B. L. (2010). Applied Conservation Genetics and the Need for Quality Control and Reporting of Genetic Data Used in Fisheries and Wildlife Management. Journal of Heredity, 101(1), 1–10.
Archer, F. I., Redfern, J. V., Gerrodette, T., Chivers, S. J., & Perrin, W. F. (2010). Estimation of relative exposure of dolphins to fishery activity. Marine Ecology-Progress Series, 410, 245–255.
Morin, P. A., Leduc, R. G., Archer, F. I., Martien, K. K., Huebinger, R., Bickham, J. W., & Taylor, B. L. (2009). Significant deviations from Hardy-Weinberg equilibrium caused by low levels of microsatellite genotyping errors. Molecular Ecology Resources, 9(2), 498–504.
Roeder, A. D., Archer, F. I., Poiner, H. N., & Morin, P. A. (2004). A novel method for collection and preservation of faeces for genetic studies. Molecular Ecology Notes, 4(4), 761–764.