Evolutionary ecology of marine mammals
Cabrera, Andrea A.
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Cabrera, A. A. (2018). Evolutionary ecology of marine mammals. University of Groningen.
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References
Abdo, Z., Crandall, K. A., & Joyce, P. (2004). Evaluating the performance of likelihood methods for detecting population structure and migration. Molecular Ecology, 13(4), 837-851. doi: 10.1111/j.1365-294X.2004.02132.x
Abrantes, F. (2000). 200 000 yr diatom records from Atlantic upwelling sites reveal maximum productivity during LGM and a shift in phytoplankton community structure at 185 000 yr. Earth and Planetary
Science Letters, 176(1), 7-16. doi: 10.1016/S0012-821x(99)00312-X
Acevedo-Whitehouse, K., Rocha-Gosselin, A., & Gendron, D. (2010). A novel non-invasive tool for disease surveillance of free-ranging whales and its relevance to conservation programs. Animal
Conservation, 13(2), 217-225. doi: 10.1111/j.1469-1795.2009.00326.x
Aeschbacher, S., Beaumont, M. A., & Futschik, A. (2012). A novel approach for choosing summary statistics in Approximate Bayesian Computation. Genetics, 192(3), 1027-1047. doi: 10.1534/genetics.112.143164
Aguilar, A., & Nadal, J. (1984). Obtención de biopsias hipodérmicas de cetáceos en libertad. Investigación
Pesquera, 48(1), 23-29.
Allen, S. (2014). From exploitation to adoration: the historical and contemporary contexts of human-cetacean interactions. In J. Higham, L. Bejder & R. Williams (Eds.), Whale-watching: sustainable tourism
and ecological management (pp. 31-47). United Kingdom: Cambridge University Press.
Allendorf, F. W., Hohenlohe, P. A., & Luikart, G. (2010). Genomics and the future of conservation genetics.
Nature Reviews Genetics, 11(10), 697-709. doi: 10.1038/nrg2844
Alley, R. B., Mayewski, P. A., Sowers, T., Stuiver, M., Taylor, K. C., & Clark, P. U. (1997). Holocene climatic instability: A prominent, widespread event 8200 yr ago. Geology, 25(6), 483-486. doi: 10.1130/0091-7613(1997)025<0483:HCIAPW>2.3.CO;2
Alter, S. E., & Palumbi, S. R. (2009). Comparing evolutionary patterns and variability in the mitochondrial control region and cytochrome b in three species of baleen whales. Journal of Molecular Evolution,
68, 97–111.
Alter, S. E., Rynes, E., & Palumbi, S. R. (2007). DNA evidence for historic population size and past ecosystem impacts of gray whales. Proceedings of the National Academy of Sciences of the United
States of America, 104(38), 15162-15167. doi: 10.1073/pnas.0706056104
Amaral, A. R., Beheregaray, L. B., Bilgmann, K., Freitas, L., Robertson, K. M., Sequeira, M., . . . Müller, L. M. (2012). Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Molecular Ecology,
21(19), 4854-4871.
Amos, B., Barrett, J., & Dover, G. A. (1991). Breeding-behavior of pilot whales reveled by DNA fingerprinting. Heredity, 67, 49-55. doi: 10.1038/hdy.1991.64
Amos, B., & Hoelzel, A. R. (1991). Long-term preservation of whale skin for DNA analysis. Report of the
International Whaling Commission, Special Issue 13, 99-104.
Amos, B., Schlötterer, C., & Tautz, D. (1993). Social-structure of pilot whales revealed by analytical DNA profiling. Science, 260(5108), 670-672. doi: 10.1126/science.8480176
Amos, W., Wilmer, J. W., & Kokko, H. (2001). Do female grey seals select genetically diverse mates? Animal
Behaviour, 62, 157-164. doi: 10.1006/anbe.2001.1739
Anderwald, P., Danielsdottir, A. K., Haug, T., Larsen, F., Lesage, V., Reid, R. J., . . . Hoelzel, A. R. (2011). Possible cryptic stock structure for minke whales in the North Atlantic: Implications for conservation and management. Biological Conservation, 144(10), 2479-2489. doi: 10.1016/j.biocon.2011.07.002
147
Ansmann, I. C., Parra, G. J., Lanyon, J. M., & Seddon, J. M. (2012). Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia. Molecular
Ecology, 21(18), 4472-4485. doi: 10.1111/j.1365-294X.2012.05722.x
Aquadro, C. F., & Greenberg, B. D. (1983). Human mitochondrial DNA variation and evolution: Analysis of nucleotide sequences from seven individuals. Genetics, 103(2), 287.
Archer, F. I., Morin, P. A., Hancock-Hanser, B. L., Robertson, K. M., Leslie, M. S., Bérubé, M., . . . Taylor, B. L. (2013). Mitogenomic phylogenetics of fin whales (Balaenoptera physalus spp.): Genetic evidence for revision of subspecies. PLoS One, 8(5), e63396. doi: 10.1371/journal.pone.0063396 Árnason, Ú., & Gullberg, A. (1993). Comparison between the complete mtDNA sequences of the blue and
the fin whale, two species that can hybridize in nature. Journal of Molecular Evolution, 37(4), 312-322. doi: 10.1007/BF00178861
Árnason, U., Gullberg, A., & Widegren, B. (1991a). The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus. Journal of Molecular Evolution, 33(6), 556-568. doi: 10.1007/bf02102808
Árnason, U., Gullberg, A., & Widegren, B. (1993). Cetacean mitochondrial DNA control region sequences of all extant baleen whales and two sperm whale species. Molecular Biology and Evolution, 10(5), 960-970.
Árnason, U., Spilliaert, R., Pálsdóttir, A., & Árnason, A. (1991b). Molecuar-identification of hybrids between the 2 largest whale species, the blue whale (Balaenoptera musculus) and the fin whale (B. physalus).
Hereditas, 115(2), 183-189.
Au, D. W. K., & Perryman, W. L. (1985). Dolphin habitats in the Eastern Tropical Pacific. Fishery Bulletin,
83(4), 623-643.
Avise, J. C. (1989). Gene trees and organismal histories: A phylogenetic approach to population biology.
Evolution, 43(6), 1192-1208. doi: 10.2307/2409356
Avise, J. C. (2000). Phylogeography: the history and formation of species. Cambridge: Harvard University Press.
Avise, J. C. (2004). Molecular markers, natural history, and evolution. United States of America Sinauer Associates, Incorporated.
Avise, J. C. (2009). Phylogeography: retrospect and prospect. Journal of Biogeography, 36(1), 3-15. doi: 10.1111/j.1365-2699.2008.02032.x
Avise, J. C., Arnold, J., Ball, R. M., Bermingham, E., Lamb, T., Neigel, J. E., . . . Saunders, N. C. (1987). Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 489-522. doi: 10.1146/annurev.ecolsys.18.1.489
Avise, J. C., Giblin-Davidson, C., Laerm, J., Patton, J. C., & Lansman, R. A. (1979). Mitochondrial DNA clones and matriarchal phylogeny within and among geographic populations of the pocket gopher,
Geomys pinetis. Proceedings of the National Academy of Sciences of the United States of America,
76(12), 6694-6698. doi: 10.1073/pnas.76.12.6694
Avise, J. C., Neigel, J. E., & Arnold, J. (1984). Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Journal of Molecular Evolution, 20(2), 99-105. doi: 10.1007/Bf02257369
Bacon, C. D., Silvestro, D., Jaramillo, C., Smith, B. T., Chakrabarty, P., & Antonelli, A. (2015). Biological evidence supports an early and complex emergence of the Isthmus of Panama. Proceedings of the
National Academy of Sciences of the United States of America, 112(19), 6110-6115. doi: 10.1073/pnas.1423853112
Baker, C. S., & Clapham, P. J. (2004). Modelling the past and future of whales and whaling. Trends in
148
Baker, C. S., Dalebout, M. L., Funahashi, N., Ma, Y. U., Steel, D., & Lavery, S. (2004). Market surveys of
whales, dolphins and porpoises in Japan and Korea, 2003-2004, with reference to stock identity of sei whales. SC/56/BC3. Paper presented at the Scientific Committee for the International Whaling Commission.
Baker, C. S., Lambertsen, R. H., Weinrich, M. T., Calambokidis, J., Early, G., & O’Brien, S. J. (1991). Molecular genetic identification of the sex of humpback whales (Megaptera novaeangliae). Reports
of the International Whaling Commission, Special Issue 13, 105-111.
Baker, C. S., Perry, A., Bannister, J. L., Weinrich, M. T., Abernethy, R. B. M. C. J., Lien, J., . . . Palumbi, S. P. (1993). Abundant mitochondrial DNA variation and world-wide population structure in humpback whales. Proceedings of the National Academy of Sciences of the United States of America, 90, 8239-8243.
Baker, C. S., Steel, D., Calambokidis, J., Falcone, E., Gonzalez-Peral, U., Barlow, J., . . . Yamaguchi, M. (2013). Strong maternal fidelity and natal philopatry shape genetic structure in North Pacific humpback whales. Marine Ecology Progress Series, 494, 291-306. doi: 10.3354/Meps10508 Ball, R. M., & Avise, J. C. (1992). Mitochondrial DNA phylogeographic differentiation among avian
populations and the evolutionary significance of subspecies. Auk, 109(3), 626-636.
Banguera-Hinestroza, E., Cárdenas, H., Ruiz-García, M., Marmontel, M., Gaitán, E., Vázquez, R., & García-Vallejo, F. (2002). Molecular identification of evolutionarily significant units in the Amazon River Dolphin Inia sp. (Cetacea:Iniidae). The Journal of Heredity, 93(5), 312-322.
Barber, D. C., Dyke, A., Hillaire-Marcel, C., Jennings, A. E., Andrews, J. T., Kerwin, M. W., . . . Gagnon, J. M. (1999). Forcing of the cold event of 8,200 years ago by catastrophic drainage of Laurentide lakes.
Nature, 400(6742), 344-348.
Beaumont, M. A. (1999). Detecting population expansion and decline using microsatellites. Genetics, 153(4), 2013-2029.
Beaumont, M. A. (2008). Joint determination of topology, divergence time, and immigration in population trees. In S. Matsumura, P. Forster & C. Renfrew (Eds.), Simulation, Genetics and Human Prehistory (pp. 135-154). Cambridge, UK: McDonald Institute Monographs.
Beaumont, M. A., & Rannala, B. (2004). The Bayesian revolution in genetics. Nature Reviews Genetics, 5(4), 251-261. doi: 10.1038/Nrg1318
Beaumont, M. A., Zhang, W. Y., & Balding, D. J. (2002). Approximate Bayesian computation in population genetics. Genetics, 162(4), 2025-2035.
Beerli, P. (2004). Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology, 13(4), 827-836. doi: 10.1111/j.1365-294X.2004.02101.x
Beerli, P. (2009). How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use? In G. Bertorelle, M. W. Bruford, H. C. Hauffe, A. Rizzoli & C. Vernesi (Eds.), Population Genetics
for Animal Conservation (pp. 39-77). United Kingdom: Cambridge University Press.
Beerli, P., & Felsenstein, J. (1999). Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics, 152(2), 763-773. Beerli, P., & Felsenstein, J. (2001). Maximum likelihood estimation of a migration matrix and effective
population sizes in n subpopulations by using a coalescent approach. Proceedings of the National
Academy of Sciences of the United States of America, 98(8), 4563-4568. doi: 10.1073/pnas.081068098
Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B-Methodological, 57(1), 289-300.
149
Bernardi, G., & Lape, J. (2005). Tempo and mode of speciation in the Baja California disjunct fish species
Anisotremus davidsonii. Molecular Ecology, 14(13), 4085-4096. doi: 10.1111/j.1365-294X.2005.02729.x
Bernatchez, L. (1995). A role for molecular systematics in defining evolutionarily significant units in fishes. In J. L. Nielsen (Ed.), Evolution and the Aquatic Ecosystem. Defining Unique Units in Population
Conservation (Vol. 17, pp. 114-132). Bethesda, Maryland: American Fisheries Society Symposium. Berta, A. (2012). Return to the sea: the life and evolutionary times of marine mammals. London, England:
University of California Press, Ltd.
Berta, A., Sumich, J. L., & Kovacs, K. M. (2006). Marine mammals: evolutionary biology. United States of America: Elsevier/Academic Press.
Bertorelle, G., Benazzo, A., & Mona, S. (2010). ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Molecular Ecology, 19(13), 2609-2625. doi: 10.1111/j.1365-294X.2010.04690.x
Bérubé, M., Aguilar, A., Dendanto, D., Larsen, F., Notarbartolo Di Sciara, G., Sears, R., . . . Palsbøll, P. J. (1998). Population genetic structure of North Atlantic, Mediterranean Sea and Sea of Cortez fin whales, Balaenoptera physalus (Linnaeus 1758): analysis of mitochondrial and nuclear loci.
Molecular Ecology, 7(5), 585-599. doi: 10.1046/j.1365-294x.1998.00359.x
Bérubé, M., Jørgensen, H., McEwing, R., & Palsbøll, P. J. (2000). Polymorphic di-nucleotide microsatellite loci isolated from the humpback whale, Megaptera novaeangliae. Molecular Ecology, 9(12), 2181-2183. doi: 10.1046/j.1365-294X.2000.105315.x
Bérubé, M., & Palsbøll, P. (1996a). Erratum of identification of sex in cetaceans by multiplexing with three ZFX and ZFY specific primers. Molecular Ecology, 5(4), 602-602. doi: 10.1111/j.1365-294X.1996.tb00355.x
Bérubé, M., & Palsbøll, P. (1996b). Identification of sex in cetaceans by multiplexing with three ZFX and ZFY specific primers. Molecular Ecology 5(2), 283-287.
Bérubé, M., Rew, M., Skaug, H., Jørgensen, H., Robbins, J., Best, P., . . . Palsbøll, P. (2005). Polymorphic microsatellite loci isolated from humpback whale, Megaptera novaeangliae and fin whale,
Balaenoptera physalus. Conservation Genetics, 6(4), 631-636. doi: 10.1007/s10592-005-9017-5 Bérubé, M., Urban, J., Dizon, A. E., Brownell, R. L., & Palsbøll, P. J. (2002). Genetic identification of a
small and highly isolated population of fin whales (Balaenoptera physalus) in the Sea of Cortez, Mexico. Conservation Genetics, 3(2), 183-190. doi: 10.1023/a:1015224730394
Besnard, G., Dupuy, J., Larter, M., Cuneo, P., Cooke, D., & Chikhi, L. (2014). History of the invasive African olive tree in Australia and Hawaii: evidence for sequential bottlenecks and hybridization with the Mediterranean olive. Evolutionary Applications, 7(2), 195-211. doi: 10.1111/Eva.12110
Best, P. B., Schaeff, C. M., Reeb, D., & Palsbøll, P. J. (2003). Composition and possible function of social groupings of southern right whales in South African waters. Behaviour, 140, 1469-1494. doi: 10.1163/156853903771980675
Bilgmann, K., Parra, G. J., Zanardo, N., Beheregaray, L. B., & Möller, L. M. (2014). Multiple management units of short-beaked common dolphins subject to fisheries bycatch off southern and southeastern Australia. Marine Ecology Progress Series, 500, 265-U300. doi: 10.3354/meps10649
Bintanja, R., van de Wal, R. S. W., & Oerlemans, J. (2005). Modelled atmospheric temperatures and global sea levels over the past million years. Nature, 437(7055), 125-128. doi: 10.1038/Nature03975 Bisconti, R., Canestrelli, D., Colangelo, P., & Nascetti, G. (2011). Multiple lines of evidence for demographic
and range expansion of a temperate species (Hyla sarda) during the last glaciation. Molecular
Ecology, 20(24), 5313-5327. doi: 10.1111/j.1365-294X.2011.05363.x
Boehme, L., Thompson, D., Fedak, M., Bowen, D., Hammill, M. O., & Stenson, G. B. (2012). How many seals were there? The global shelf loss during the Last Glacial Maximum and its effect on the size
150
and distribution of grey seal populations. PLoS One, 7(12), e53000. doi: 10.1371/journal.pone.0053000
Bonnell, M. L., & Selander, R. K. (1974). Elephant seals: genetic variation and near extinction. Science,
184(4139), 908-909. doi: 10.2307/1738190
Bossdorf, O., Richards, C. L., & Pigliucci, M. (2008). Epigenetics for ecologists. Ecology Letters, 11(2), 106-115. doi: 10.1111/j.1461-0248.2007.01130.x
Bowen, W. D. (1997). Role of marine mammals in aquatic ecosystems. Marine Ecology Progress Series,
158, 267-274.
Box, G. E. P. (1976). Science and statistics. Journal of the American Statistical Association, 71(356), 791-799. doi: 10.2307/2286841
Box, G. E. P., & Draper, N. R. (1987). Empirical model-building and response surfaces. New York, United States of America: John Wiley
Brischoux, F., Tingley, R., Shine, R., & Lillywhite, H. B. (2012). Salinity influences the distribution of marine snakes: implications for evolutionary transitions to marine life. Ecography, 35(11), 994-1003. doi: 10.1111/j.1600-0587.2012.07717.x
Briscoe, E., & Feldman, J. (2011). Conceptual complexity and the bias/variance tradeoff. Cognition, 118(1), 2-16. doi: 10.1016/j.cognition.2010.10.004
Brown Gladden, J. G., Ferguson, M. M., & Clayton, J. W. (1997). Matriarchal genetic population structure of North American beluga whales Delphinapterus leucas (Cetacea: Monodontidae). Molecular
Ecology, 6(11), 1033-1046. doi: DOI 10.1046/j.1365-294X.1997.00275.x
Brown, J., Ferrians, J., O.J., Heginbottom, J. A., & Melnikov, E. S. (2002). Circum-Arctic map of permafrost and ground ice conditions, version 2. Downloaded on 4 March 2017. doi: 10.7265/N5K072F8 Bruford, M. W., & Wayne, R. K. (1993). Microsatellites and their application to population genetic studies.
Current opinion in genetics & development, 3(6), 939-943. doi: 10.1016/0959-437x(93)90017-j Burbrink, F. T., Lawson, R., & Slowinski, J. B. (2000). Mitochondrial DNA phylogeography of the polytypic
North American rat snake (Elaphe obsoleta): A critique of the subspecies concept. Evolution, 54(6), 2107-2118. doi: 10.1111/j.0014-3820.2000.tb01253.x
Cahill, J. A., Green, R. E., Fulton, T. L., Stiller, M., Jay, F., Ovsyanikov, N., . . . Shapiro, B. (2013). Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS
Genetics, 9(3), e1003345. doi: 10.1371/journal.pgen.1003345
Caissie, B. E., Brigham-Grette, J., Lawrence, K. T., Herbert, T. D., & Cook, M. S. (2010). Last Glacial Maximum to Holocene sea surface conditions at Umnak Plateau, Bering Sea, as inferred from diatom, alkenone, and stable isotope records. Paleoceanography, 25. doi: 10.1029/2008pa001671 Cammen, K. M., Andrews, K. R., Carroll, E. L., Foote, A. D., Humble, E., Khudyakov, J. I., . . . Van Cise,
A. M. (2016). Genomic methods take the plunge: recent advances in high-throughput sequencing of marine mammals. Journal of Heredity.
Campagna, L., de Groot, P. J. V., Saunders, B. L., Atkinson, S. N., Weber, D. S., Dyck, M. G., . . . Lougheed, S. C. (2013). Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales. Ecology and Evolution, 3(9), 3152-3165. doi: 10.1002/ece3.662
Carapelli, A., Comandi, S., Convey, P., Nardi, F., & Frati, F. (2008). The complete mitochondrial genome of the Antarctic springtail Cryptopygus antarcticus (Hexapoda: Collembola). BMC Genomics, 9(315). doi: 10.1186/1471-2164-9-315
Castellani, C., Lindley, A. J., Wootton, M., Lee, C. M., & Kirby, R. R. (2012). Morphological and genetic variation in the North Atlantic copepod, Centropages typicus. Journal of the Marine Biological
151
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics. Molecular Ecology, 22(11), 3124-3140. doi: 10.1111/mec.12354 Cerchio, S., & Tucker, P. (1998). Influence of alignment on the mtDNA phylogeny of Cetacea: Questionable
support for a Mysticeti/Physeteroidea clade. Systematic Biology, 47(2), 336-344.
Chan, Y. L., Schanzenbach, D., & Hickerson, M. J. (2014). Detecting concerted demographic response across community assemblages using hierarchical Approximate Bayesian Computation. Molecular Biology
and Evolution, 31(9), 2501-2515.
Chen, L., & Yang, G. (2009). A genomic scanning using AFLP to detect candidate loci under selection in the finless porpoise (Neophocaena phocaenoides). Genes Genet Syst, 84(4), 307-313.
Chikina, M., Robinson, J. D., & Clark, N. L. (2016). Hundreds of genes experienced convergent shifts in selective pressure in marine mammals. Molecular Biology and Evolution, 33(9), 2182-2192. Chivers, S. J., Baird, R. W., McSweeney, D. J., Webster, D. L., Hedrick, N. M., & Salinas, J. C. (2007).
Genetic variation and evidence for population structure in eastern North Pacific false killer whales (Pseudorca crassidens). Canadian Journal of Zoology, 85, 783-794.
Clapham, P. J., Aguilar, A., & Hatch, L. T. (2008). Determining spatial and temporal scales for management: lessons from whaling. Marine Mammal Science, 24(1), 183-201. doi: 10.1111/j.1748-7692.2007.00175.x
Clapham, P. J., Palsbøll, P. J., Mattila, D. K., & Vasquez, O. (1992). Composition and dynamics of humpback whale competitive groups in the West Indies. Behaviour, 122, 182-194. doi: 10.1163/156853992x00507
Clark, P. U., Dyke, A. S., Shakun, J. D., Carlson, A. E., Clark, J., Wohlfarth, B., . . . McCabe, A. M. (2009). The Last Glacial Maximum. Science, 325(5941), 710-714. doi: 10.1126/science.1172873
Climap. (1981). Seasonal reconstructions of the Earth's surface at the last glacial maximum. Geological
Society of America, Map and Chart Series MC-36.
Coates, A. G., Jackson, J. B. C., Collins, L. S., Cronin, T. M., Dowsett, H. J., Bybell, L. M., . . . Obando, J. A. (1992). Closure of the Isthmus of Panama: The near-shore marine record of Costa Rica and Western Panama. Geological Society of America Bulletin, 104(7), 814-828. doi: 10.1130/0016-7606 Colbeck, G. J., Turgeon, J., Sirois, P., & Dodson, J. J. (2011). Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus). Molecular Ecology, 20(9), 1976-1987. doi: 10.1111/j.1365-294X.2011.05069.x
Colleoni, F., Wekerle, C., Näslund, J.-O., Brandefelt, J., & Masina, S. (2016). Constraint on the penultimate glacial maximum Northern Hemisphere ice topography (≈140 kyrs BP). Quaternary Science
Reviews, 137, 97-112. doi: 10.1016/j.quascirev.2016.01.024
Cornille, A., Gladieux, P., Smulders, M. J. M., Roldan-Ruiz, I., Laurens, F., Le Cam, B., . . . Giraud, T. (2012). New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genetics, 8(5), e1002703. doi: 10.1371/journal.pgen.1002703
Cornuet, J. M., Pudlo, P., Veyssier, J., Dehne-Garcia, A., Gautier, M., Leblois, R., . . . Estoup, A. (2014). DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data.
Bioinformatics, 30(8), 1187-1189. doi: 10.1093/bioinformatics/btt763
Cornuet, J. M., Ravigne, V., & Estoup, A. (2010). Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). BMC Bioinformatics, 11, 401. doi: 10.1186/1471-2105-11-401
152
Cornuet, J. M., Santos, F., Beaumont, M. A., Robert, C. P., Marin, J. M., Balding, D. J., . . . Estoup, A. (2008). Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics, 24(23), 2713-2719. doi: 10.1093/bioinformatics/btn514
Coulson, M. W., Marshall, H. D., Pepin, P., & Carr, S. M. (2006). Mitochondrial genomics of gadine fishes: implications for taxonomy and biogeographic origins from whole-genome data sets. Genome, 49(9), 1115-1130. doi: 10.1139/G06-083
Crandall, K. A., Bininda-Emonds, O. R. P., Mace, G. M., & Wayne, R. K. (2000). Considering evolutionary processes in conservation biology. Trends in Ecology & Evolution, 15(7), 290-295. doi: 10.1016/S0169-5347(00)01876-0
Croll, D. A., Marinovic, B., Benson, S., Chavez, F. P., Black, N., Ternullo, R., & Tershy, B. R. (2005). From wind to whales: trophic links in a coastal upwelling system. Marine Ecology Progress Series, 289, 117-130. doi: 10.3354/meps289117
Cronin, M. A., Rincon, G., Meredith, R. W., MacNeil, M. D., Islas-Trejo, A., Canovas, A., & Medrano, J. F. (2014). Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U.
arctos), and black bears (U. americanus) derived from genome sequences. The Journal of Heredity,
105(3), 312-323. doi: 10.1093/jhered/est133
Csillery, K., Blum, M. G. B., Gaggiotti, O. E., & Francois, O. (2010). Approximate Bayesian Computation (ABC) in practice. Trends in Ecology & Evolution, 25(7), 410-418. doi: 10.1016/j.tree.2010.04.001 Csillery, K., Francois, O., & Blum, M. G. B. (2012). abc: an R package for approximate Bayesian
computation (ABC). Methods in Ecology and Evolution, 3(3), 475-479. doi: 10.1111/j.2041-210X.2011.00179.x
Dallas, J. F. (1992). Estimation of microsatellite mutation-rates in recombinant inbred strains of mouse.
Mammalian Genome, 3(8), 452-456. doi: 10.1007/Bf00356155
Daníelsdóttir, A. K., Duke, E. J., Joyce, P., & Árnason, A. (1991). Preliminary studies on the genetic variation at enzyme loci in fin whales (Balaenoptera physalus) and sei whales (Balaenoptera borealis) from the North Atlantic. Report of the International Whaling Commission, Special Issue 13, 115-124. Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics
and parallel computing. Nature Methods, 9(8), 772-772.
Darwin, C. (1845). Journal of researches into the natural history and geology of the countries visited during
the voyage of H.M.S. Beagle round the world, under the command of Capt. Fitz Roy. London: John Murray.
Darwin, C. (1859). On the origin of species by means of natural selection, or the preservation of favoured
races in the struggle for life. London: (J. Murray).
Dasmahapatra, K. K., Hoffman, J. I., & Amos, W. (2009). Pinniped phylogenetic relationships inferred using AFLP markers. Heredity, 103(2), 168-177. doi: 10.1038/hdy.2009.25
Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M., & Blaxter, M. L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews
Genetics, 12(7), 499-510. doi: 10.1038/nrg3012
Davidson, A. D., Boyer, A. G., Kim, H., Pompa-Mansilla, S., Hamilton, M. J., Costa, D. P., . . . Brown, J. H. (2012). Drivers and hotspots of extinction risk in marine mammals. Proceedings of the National
Academy of Sciences of the United States of America, 109(9), 3395-3400.
Davies, J. L. (1963). The antitropical factor in cetacean speciation. Evolution, 17(1), 107-116. doi: 10.2307/2406339
Davis, W., Fargions, S., May, Leming, T. D., Baumgartner, M. F., Evans, E., . . . Mullin, K. D. (1998). Physical habitat of cetaceans along the continental slop in the Norrh-Central and Western Gulf of Mexico. Marine Mammal Science, 14(3), 490-507.
153
Dawbin, W. H. (1966). The seasonal migratory cycle of humpback whales. In K. S. Norris (Ed.), Whales,
dolphins and porpoises (pp. 145-170). Berkely, CA: University of California Press.
de Bruyn, M., Hall, B. L., Chauke, L. F., Baroni, C., Koch, P. L., & Hoelzel, A. R. (2009). Rapid Response of a Marine Mammal Species to Holocene Climate and Habitat Change. PLoS Genetics, 5(7). doi: 10.1371/journal.pgen.1000554
Deagle, B. E., Faux, C., Kawaguchi, S., Meyer, B., & Jarman, S. N. (2015). Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water.
Molecular Ecology, 24(19), 4943-4959. doi: 10.1111/mec.13370
Deméré, T. A. (1994). The family Odobenidae: A phylogenetic analysis of fossil and living taxa. Proceedings
of the San Diego Society of Natural History, 29, 99-123.
Deméré, T. A., Berta, A., & Adam, P. J. (2003). Pinnipedimorph evolutionary biogeography. Bulletin of the
American Museum of Natural History(279), 32-76.
Denver, D. R., Morris, K., Lynch, M., Vassilieva, L. L., & Thomas, W. K. (2000). High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science, 289(5488), 2342-2344. doi: 10.1126/science.289.5488.2342
Dizon, A., Lockyer, C., Perrin, W. F., Demaster, D. P., & Sisson, J. (1992). Rethinking the stock concept: a phylogeographyc approach. Conservation Biology, 6(1), 24-36.
Dobzhansky, T. (1937). Genetics and the Origin of Species (Vol. 11). New York, United States of America: Columbia university press.
Dobzhansky, T. (1973). Nothing in biology makes sense except in the light of evolution. The American
Biology Teacher, 35(3), 125-129. doi: 10.2307/4444260
Donovan, G. P. (1991). A review of IWC stock boundaries. Report of the International Whaling Commission,
Special Issue 13, 39-68.
Douzery, E. (1993). Evolutionary relationships among cetacea based on the sequence of the mitochondrial 12s ribosomal-RNA gene - possible paraphyly of toothed-whales (odontocetes) and long separate evolution of sperm whales (physeteridae). Comptes rendus de l'Académie des Sciences - Series III -
Sciences de la Vie, 316(12), 1511-1518.
Drouot, V., Berube, M., Gannier, A., Goold, J. C., Reid, R. J., & Palsboll, P. J. (2004). A note on genetic isolation of Mediterranean sperm whales (Physeter macrocephalus) suggested by mitochondrial DNA. Journal of Cetacean Research and Management, 6(1), 29-32.
Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC
Evolutionary Biology, 7(214). doi: 10.1186/1471-2148-7-214
Durban, J. W., & Pitman, R. L. (2012). Antarctic killer whales make rapid, round-trip movements to subtropical waters: evidence for physiological maintenance migrations? Biology Letters, 8(2), 274-277. doi: DOI 10.1098/rsbl.2011.0875
Ehlers, J., Ehlers, J., Gibbard, P. L., & Hughes, P. D. (2011). Quaternary glaciations-extent and chronology:
a closer look. Oxford, United Kingdom: Elsevier.
Endler, J. A. (2010). Editorial. Evolutionary Ecology, 24(5), 955-956. doi: 10.1007/s10682-010-9398-x Estoup, A., Jarne, P., & Cornuet, J. M. (2002). Homoplasy and mutation model at microsatellite loci and their
consequences for population genetics analysis. Molecular Ecology, 11(9), 1591-1604. doi: 10.1046/j.1365-294X.2002.01576.x
Excoffier, L., & Lischer, H. E. L. (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10(3), 564-567. doi: 10.1111/j.1755-0998.2010.02847.x
154
Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data.
Genetics, 131(2), 479-491.
Excoffier, L., & Yang, Z. H. (1999). Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees. Molecular Biology and Evolution, 16(10), 1357-1368. Fair, P., & Becker, P. (2000). Review of stress in marine mammals. Journal of Aquatic Ecosystem Stress and
Recovery, 7(4), 335-354. doi: 10.1023/a:1009968113079
Falush, D., Stephens, M., & Pritchard, J. K. (2007). Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes, 7(4), 574-578. doi: 10.1111/j.1471-8286.2007.01758.x
Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39(4), 783-791. doi: 10.2307/2408678
Fetterer, F., Knowles, K., Meier, W., Savoie, M., & Windnagel, A. K. (2017). Sea Ice Index, Version 3. Downloaded on 4 March 2017. doi: 10.7265/N5K072F8
Filatova, O. A., Fedutin, I. D., Burdin, A. M., & Hoyt, E. (2006). Using a mobile hydrophone stereo system for real-time acoustic localization of killer whales (Orcinus orca). Applied Acoustics, 67, 1243-1248. Fisher, R. A. (1935). The logic of inductive inference. Journal of the Royal Statistical Society, 98(1), 39-82.
doi: 10.2307/2342435
Flatz, R., Gonzalez-Suarez, M., Young, J. K., Hernandez-Camacho, C. J., Immel, A. J., & Gerber, L. R. (2012). Weak polygyny in California sea lions and the potential for alternative mating tactics. PloS
One, 7(3), e33654. doi: 10.1371/journal.pone.0033654
Fontaine, M. C., Baird, S. J. E., Piry, S., Ray, N., Tolley, K. A., Duke, S., . . . Michaux, J. R. (2007). Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters. BMC Biology, 5. doi: 10.1186/1741-7007-5-30
Fontaine, M. C., Snirc, A., Frantzis, A., Koutrakis, E., Öztürk, B., Öztürk, A. A., & Austerlitz, F. (2012). History of expansion and anthropogenic collapse in a top marine predator of the Black Sea estimated from genetic data. Proceedings of the National Academy of Sciences of the United States of America,
109(38), E2569–E2576. doi: 10.1073/pnas.1201258109
Fontaine, M. C., Tolley, K. A., Michaux, J. R., Birkun, A., Ferreira, M., Jauniaux, T., . . . Baird, S. J. E. (2010). Genetic and historic evidence for climate-driven population fragmentation in a top cetacean predator: the harbour porpoises in European water. Proceedings of the National Academy of Sciences
of the United States of America, 277(1695), 2829-2837.
Foote, A. D., Hofreiter, M., & Morin, P. A. (2012a). Ancient DNA from marine mammals: Studying long-lived species over ecological and evolutionary timescales. Annals of Anatomy - Anatomischer
Anzeiger, 194(1), 112-120.
Foote, A. D., Kaschner, K., Schultze, S. E., Garilao, C., Ho, S. Y. W., Post, K., . . . Gilbert, M. T. P. (2013). Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nature Communications, 4, 1677. doi: 10.1038/ncomms2714
Foote, A. D., Liu, Y., Thomas, G. W. C., Vinar, T., Alfoldi, J., Deng, J., . . . Gibbs, R. A. (2015). Convergent evolution of the genomes of marine mammals. Nature Genetics, 47(3), 272-275. doi: 10.1038/ng.3198
Foote, A. D., Morin, P. A., Durban, J. W., Willerslev, E., Orlando, L., & Gilbert, M. T. P. (2011a). Out of the Pacific and Back Again: Insights into the Matrilineal History of Pacific Killer Whale Ecotypes.
PLoS One, 6(9). doi: 10.1371/journal.pone.0024980
Foote, A. D., Thomsen, P. F., Sveegaard, S., Wahlberg, M., Kielgast, J., Kyhn, L. A., . . . Gilbert, M. T. P. (2012b). Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS One, 7(8), e41781. doi: 10.1371/journal.pone.0041781
155
Foote, A. D., Vijay, N., Avila-Arcos, M. C., Baird, R. W., Durban, J. W., Fumagalli, M., . . . Wolf, J. B. W. (2016). Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nature
Communications, 7. doi: 10.1038/ncomms11693
Foote, A. D., Vilstrup, J. T., De Stephanis, R., Verborgh, P., Abel Nielsen, S. C., Deaville, R., . . . Piertney, S. B. (2011b). Genetic differentiation among North Atlantic killer whale populations. Molecular
Ecology, 20(3), 629-641. doi: 10.1111/j.1365-294X.2010.04957.x
Ford, J. K. B., Ellis, G. M., Barrett-Lennard, L. G., Morton, A. B., Palm, R. S., & Balcomb, K. C. (1998). Dietary specialization in two sympatric populations of killer whales (Orcinus orca) in coastal British Columbia and adjacent waters. Canadian Journal of Zoology, 76(8), 1456-1471. doi: 10.1139/cjz-76-8-1456
Fordyce, R. E. (1980). Whale Evolution and Oligocene Southern-Ocean Environments. Palaeogeography
Palaeoclimatology Palaeoecology, 31(2-4), 319-336. doi: 10.1016/0031-0182(80)90024-3
Fordyce, R. E., & Barnes, L. G. (1994). The Evolutionary History of Whales and Dolphins. Annual Review
of Earth and Planetary Sciences, 22(1), 419-455. doi: 10.1146/annurev.ea.22.050194.002223 Franchini, P., Parera, D. M., Kautt, A. F., & Meyer, A. (2017). quaddRAD: a new high-multiplexing and
PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage. Molecular Ecology, 26(10), 2783-2795. doi: 10.1111/mec.14077
Frankham, R. (1995). Conservation genetics. Annual Review of Genetics, 29, 305-327. doi: 10.1146/annurev.ge.29.120195.001513
Fu, Y. X., & Li, W. H. (1993). Statistical tests of neutrality of mutations. Genetics, 133(3), 693-709. Funk, D. J. (1999). Molecular systematics of cytochrome oxidase I and 16S from Neochlamisus leaf beetles
and the importance of sampling. Molecular Biology and Evolution, 16(1), 67-82.
Funk, D. J., & Omland, K. E. (2003). Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology Evolution
and Systematics, 34, 397-423. doi: 10.1146/annurev.ecolsys.34.011802.132421
Funk, W. C., Mckay, J. K., Hohenlohe, P. A., & Allendorf, F. W. (2012). Harnessing genomics for delineating conservation units. Trends in Ecology & Evolution, 27(9), 489-496. doi: 10.1016/j.tree.2012.05.012 Gambell, R. (1985). Fin whale Balaenoptera physalus (Linnaeus, 1758). In S. H. Ridgway & S. R. Harrison
(Eds.), Handbook of Marine Mammals (pp. 171-192). London, UK: Academic Press Inc.
Garcia-Rodriguez, A. I., Bowen, B. W., Domning, D., Mignucci-Giannoni, A. A., Marmontel, M., Montoya-Ospina, R. A., . . . McGuire, P. M. (1998). Phylogeography of the West Indian manatee (Trichechus manatus): how many populations and how many taxa? Molecular Ecology, 7(9), 1137-1149. doi: 10.1046/j.1365-294x.1998.00430.x
Garza, J. C., & Williamson, E. G. (2001). Detection of reduction in population size using data from microsatellite loci. Molecular Ecology, 10(2), 305-318. doi: 10.1046/j.1365-294x.2001.01190.x Geisser, S., & Eddy, W. F. (1979). A predictive approach to model selection. Journal of the American
Statistical Association, 74(365), 153-160. doi: 10.2307/2286745
Gelman, A. (2013). Two simple examples for understanding posterior p-values whose distributions are far from uniform. Electronic Journal of Statistics, 7, 2595-2602. doi: 10.1214/13-Ejs854
Gelman, A., Carlin, J. B., Stern, H. S., Dunson, D. B., Vejtaro, A., & Rubin, D. B. (2014). Bayesian data
analysis (Vol. 2). FL, United States of America: Taylor & Francis.
Geman, S., Bienenstock, E., & Doursat, R. (1992). Neural networks and the bias/variance dilemma. Neural
Computation, 4(1), 1-58. doi: 10.1162/neco.1992.4.1.1
Gero, S., Bejder, L., Whitehead, H., Mann, J., & Connor, R. C. (2005). Behaviourally specific preferred associations in bottlenose dolphins, Tursiops spp. Canadian Journal of Zoology, 83, 1566-1573.
156
Gersonde, R., Crosta, X., Abelmann, A., & Armand, L. (2005). Sea-surface temperature and sea ice distribution of the Southern Ocean at the EPILOG Last Glacial Maximum - A circum-Antarctic view based on siliceous microfossil records. Quaternary Science Reviews, 24(7-9), 869-896. doi: 10.1016/j.quascirev.2004.07.015
Girod, C., Vitalis, R., Leblois, R., & Freville, H. (2011). Inferring population decline and expansion from microsatellite data: a simulation-based evaluation of the Msvar method. Genetics, 188(1), 165-179. doi: 10.1534/genetics.110.121764
Glover, K. A., Kanda, N., Haug, T., Pastene, L. A., Oien, N., Goto, M., . . . Skaug, H. J. (2010). Migration of Antarctic minke whales to the Arctic. PLoS One, 5(12). doi: 10.1371/journal.pone.0015197 González-Wevar, C. A., Saucede, T., Morley, S. A., Chown, S. L., & Poulin, E. (2013). Extinction and
recolonization of maritime Antarctica in the limpet Nacella concinna (Strebel, 1908) during the last glacial cycle: toward a model of Quaternary biogeography in shallow Antarctic invertebrates.
Molecular Ecology, 22(20), 5221-5236. doi: 10.1111/Mec.12465
Goodall-Copestake, W. P., Perez-Espona, S., Clark, M. S., Murphy, E. J., Seear, P. J., & Tarling, G. A. (2010). Swarms of diversity at the gene cox1 in Antarctic krill. Heredity, 104(5), 513-518. doi: 10.1038/hdy.2009.188
Grant, W. S., & Cheng, W. (2012). Incorporating deep and shallow components of genetic structure into the management of Alaskan red king crab. Evolutionary Applications, 5(8), 820-837. doi: 10.1111/j.1752-4571.2012.00260.x
Graves, J. A., Helyar, A., Biuw, M., Juessi, M., Juessi, I., & Karlsson, O. (2009). Microsatellite and mtDNA analysis of the population structure of grey seals (Halichoerus grypus) from three breeding areas in the Baltic Sea. Conservation Genetics, 10(1), 59-68. doi: 10.1007/s10592-008-9517-1
Griffiths, R. C., & Tavare, S. (1994). Sampling theory for neutral alleles in a varying environment.
Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 344(1310), 403-410. doi: 10.1098/rstb.1994.0079
Haag-Liautard, C., Coffey, N., Houle, D., Lynch, M., Charlesworth, B., & Keightley, P. D. (2008). Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. PLoS Biology, 6(8), 1706-1714. doi: 10.1371/journal.pbio.0060204
Haeckel, E. (1866). Generelle Morphologie der Organismen (Vol. 2). Berlin: Verlag von Georg Reimer. Harland, R., Polovodova Asteman, I., Morley, A., Morris, A., Harris, A., & Howe, J. A. (2016). Latest
Quaternary palaeoceanographic change in the eastern North Atlantic based upon a dinoflagellate cyst event ecostratigraphy. Heliyon, 2(5), e00114. doi: 10.1016/j.heliyon.2016.e00114
Harlin-Cognato, A. D., Markowitz, T., Wuersig, B., & Honeycutt, R. L. (2007). Multi-locus phylogeography of the dusky dolphin (Lagenorhynchus obscurus): passive dispersal via the west-wind drift or response to prey species and climate change? BMC Evolutionary Biology, 7. doi: 10.1186/1471-2148-7-131
Hasegawa, M., Kishino, H., & Yano, T. A. (1985). Dating of the human - ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22(2), 160-174. doi: 10.1007/Bf02101694 Hastings, K. K., Small, R. J., & Pendleton, G. W. (2012). Sex- and age-specific survival of harbor seals
(Phoca vitulina) from Tugidak Island, Alaska. Journal of Mammalogy, 93(5), 1368-1379. doi: 10.1644/11-mamm-a-291.1
Heithaus, M. R., Frid, A., Wirsing, A. J., & Worm, B. (2008). Predicting ecological consequences of marine top predator declines. Trends in Ecology & Evolution, 23(4), 202-210. doi: 10.1016/j.tree.2008.01.003
Heller, R., Chikhi, L., & Siegismund, H. R. (2013). The confounding effect of population structure on bayesian skyline plot inferences of demographic history. PLoS One, 8(5), e62992. doi: 10.1371/journal.pone.0062992
157
Hewitt, G. M. (1996). Some genetic consequences of ice ages, and their role in divergence and speciation.
Biological Journal of the Linnean Society, 58(3), 247-276. doi: 10.1111/j.1095-8312.1996.tb01434.x Hewitt, G. M. (2000). The genetic legacy of the Quaternary ice ages. Nature, 405(6789), 907-913. doi:
10.1038/35016000
Hewitt, G. M. (2004). Genetic consequences of climatic oscillations in the Quaternary. Philosophical
Transactions of the Royal Society of London Series B-Biological Sciences, 359(1442), 183-195. doi: 10.1098/rstb.2003.1388
Hewitt, G. M. (2011). Quaternary phylogeography: the roots of hybrid zones. Genetica, 139(5), 617-638. doi: DOI 10.1007/s10709-011-9547-3
Hewitt, G. M., & Butlin, R. K. (1997). Causes and consequences of population structure. In J. R. Krebs & N. B. Davies (Eds.), Behavioural Ecology: An Evolutionary Approach (pp. 350-372). Oxford: Wiley-Blackwell.
Hey, J., & Nielsen, R. (2004a). Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D-persimilis.
Genetics, 167(2), 747-760. doi: 10.1534/genetics.103.024182
Hey, J., & Nielsen, R. (2004b). Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis.
Genetics, 167(2), 747-760. doi: 10.1534/genetics.103.024182
Hey, J., & Nielsen, R. (2007). Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences of the United
States of America, 104(8), 2785-2790. doi: 10.1073/pnas.0611164104
Hirai, J., Tsuda, A., & Goetze, E. (2015). Extensive genetic diversity and endemism across the global range of the oceanic copepod Pleuromamma abdominalis. Progress in Oceanography, 138, 77-90. doi: 10.1016/j.pocean.2015.09.002
Ho, S. Y. W., Kolokotronis, S.-O., & Allaby, R. G. (2007). Elevated substitution rates estimated from ancient DNA sequences. Biology Letters, 3(6), 702-705.
Hoban, S., Bertorelle, G., & Gaggiotti, O. E. (2012). Computer simulations: tools for population and evolutionary genetics. Nature Reviews Genetics, 13(2), 110-122. doi: 10.1038/Nrg3130
Hoban, S. M., Gaggiotti, O. E., & Bertorelle, G. (2013). The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study.
Molecular Ecology, 22(13), 3444-3450. doi: 10.1111/mec.12258
Hodgkinson, A., & Eyre-Walker, A. (2011). Variation in the mutation rate across mammalian genomes.
Nature Reviews Genetics, 12(11), 756-766. doi: 10.1038/nrg3098
Hoelzel, A. R., & Amos, W. (1988). DNA Fingerprinting and scientific whaling. Nature, 333(6171), 305-305. doi: 10.1038/333305a0
Hoelzel, A. R., Dahlheim, M., & Stern, S. J. (1998). Low genetic variation among killer whales (Orcinus
orca) in the Eastern North Pacific and genetic differentiation between foraging specialists. Journal
of Heredity, 89, 121-128.
Hoelzel, A. R., Hancock, J. M., & Dover, G. A. (1991). Evolution of the cetacean mitochondrial D-loop region. Molecular Biology and Evolution, 8(4), 475-493.
Hoelzel, A. R., Hey, J., Dahlheim, M. E., Nicholson, C., Burkanov, V., & Black, N. (2007). Evolution of population structure in a highly social top predator, the killer whale. Molecular Biology and
Evolution, 24(6), 1407-1415.
Hoelzel, A. R., Le Boeuf, B. J., Reiter, J., & Campagna, C. (1999). Alpha-male paternity in elephant seals.
158
Hoffman, J. I., Forcada, J., Trathan, P. N., & Amos, W. (2007). Female fur seals show active choice for males that are heterozygous and unrelated. Nature, 445(7130), 912-914. doi: 10.1038/nature05558
Hoffman, J. I., Grant, S. M., Forcada, J., & Phillips, C. D. (2011). Bayesian inference of a historical bottleneck in a heavily exploited marine mammal. Molecular Ecology, 20(19), 3989-4008.
Hoffman, J. I., Simpson, F., David, P., Rijks, J. M., Kuiken, T., Thorne, M. A. S., . . . Dasmahapatra, K. K. (2014). High-throughput sequencing reveals inbreeding depression in a natural population.
Proceedings of the National Academy of Sciences of the United States of America, 111(10), 3775-3780. doi: 10.1073/pnas.1318945111
Hoffman, J. I., Thorne, M. A. S., Trathan, P. N., & Forcada, J. (2013). Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal. BMC Genomics, 14. doi: 10.1186/1471-2164-14-52
Hoffman, J. I., Trathan, P. N., & Amos, W. (2006). Genetic tagging reveals extreme site fidelity in territorial male Antarctic fur seals Arctocephalus gazella. Molecular Ecology, 15(12), 3841-3847. doi: 10.1111/j.1365-294X.2006.03053.x
Hoffman, J. I., Tucker, R., Bridgett, S. J., Clark, M. S., Forcada, J., & Slate, J. (2012). Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Molecular Ecology Resources, 12(5), 861-872. doi: 10.1111/j.1755-0998.2012.03158.x
Hofreiter, M., & Stewart, J. (2009). Ecological change, range fluctuations and population dynamics during the Pleistocene. Current Biology, 19(14), R584-R594. doi: 10.1016/j.cub.2009.06.030
Hohn, A. A., Scott, M. D., Wells, R. S., Sweeney, J. C., & Irvine, A. B. (1989). Growth layers in teeth from known-age, free-ranging bottlenose dolphins. Marine Mammal Science, 5(4), 315-342. doi: 10.1111/j.1748-7692.1989.tb00346.x
Hopkins, T. L. (1985). Food web of an Antarctic midwater ecosystem. Marine Biology, 89(2), 197-212. doi: 10.1007/Bf00392890
Howell, A. B. (1930). Aquatic mammals: thier adaptation to life in the water. Springfield: Charles C. Thomas Press.
Howell, N., Smejkal, C. B., Mackey, D. A., Chinnery, P. F., Turnbull, D. M., & Herrnstadt, C. (2003). The pedigree rate of sequence divergence in the human mitochondrial genome: There is a difference between phylogenetic and pedigree rates. American Journal of Human Genetics, 72(3), 659-670. doi: 10.1086/368264
Hudson, R. R. (1990). Gene genealogies and the coalescent process. Oxford surveys in evolutionary biology,
7(1), 44.
Hudson, R. R. (1991). Gene genealogies and the coalescent process In D. Futuyama & J. Antonovics (Eds.),
Oxford surveys in evolutionary biology (Vol. 7, pp. 1-44). USA: Oxford University Press.
Hudson, R. R., & Turelli, M. (2003). Stochasticity overrules the “three-times rule”: genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution, 57(1), 182-190. doi: 10.1111/j.0014-3820.2003.tb00229.x
Humble, E., Martinez-Barrio, A., Forcada, J., Trathan, P. N., Thorne, M. A. S., Hoffmann, M., . . . Hoffman, J. I. (2016). A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them. Molecular Ecololgy Resources, 16(4), 909-921. doi: 10.1111/1755-0998.12502 Ingebrigtsen, A. (1929). Whales caught in the North Atlantic and other seas. Conseil Permanent International
pour l’Exploration de la Mer. Rapports et Proces-Verbaux des Reunions, 56, 123-135.
Ingman, M., Kaessmann, H., Paabo, S., & Gyllensten, U. (2000). Mitochondrial genome variation and the origin of modern humans. Nature, 408(6813), 708-713.
159
Inoue, K., Monroe, E. M., Elderkin, C. L., & Berg, D. J. (2014). Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide ranging, but endangered, freshwater mussel. Heredity, 112(3), 282-290. doi: 10.1038/hdy.2013.104
Jabot, F., Faure, T., & Dumoulin, N. (2013). EasyABC: performing efficient approximate Bayesian computation sampling schemes using R. Methods in Ecology and Evolution, 4(7), 684-687. doi: 10.1111/2041-210x.12050
Jackson, J. A., Steel, D. J., Beerli, P., Congdon, B. C., Olavarría, C., Leslie, M. S., . . . Baker, C. S. (2014). Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae).
Proceedings of the Royal Society of London, Series B: Biological Sciences, 281(1786). doi: 10.1098/rspb.2013.3222
Jarman, S. N., Polanowski, A. M., Faux, C. E., Robbins, J., De Paoli-Iseppi, R., Bravington, M., & Deagle, B. E. (2015). Molecular biomarkers for chronological age in animal ecology. Molecular Ecology,
24(19), 4826-4847. doi: 10.1111/mec.13357
Jeffreys, A. J., Wilson, V., & Thein, S. L. (1985). Hypervariable minisatellite regions in human DNA. Nature,
314(6006), 67-73. doi: 10.1038/314067a0
Jonsgård, Å. (1966). The distribution of Balaenopteridae in the north Atlantic Ocean. In K. S. Norris (Ed.),
Whales, dolphins and porpoises (pp. 114-124). Berkely, CA: University of California Press
Jouzel, J., Masson-Delmotte, V., Cattani, O., Dreyfus, G., Falourd, S., Hoffmann, G., . . . Wolff, E. W. (2007). Orbital and millennial Antarctic climate variability over the past 800,000 years. Science, 317(5839), 793-796. doi: 10.1126/science.1141038
Kanda, N., Goto, M., & Pastene, L. (2006). Genetic characteristics of western North Pacific sei whales,
Balaenoptera borealis, as revealed by microsatellites. Marine Biotechnology, 8(1), 86-93. doi: 10.1007/s10126-005-5130-1
Kanda, N., Goto, M., Yoshida, H., & Pastene, L. A. (2009). Stock structure of sei whales in the North Pacific
as revealed by microsatellite and mitochondrial DNA analyses. SC/J09/JR32 Paper presented at the Scientific Committee for the International Whaling Commission.
Kaplan, M. R., Fogwill, C. J., Sugden, D. E., Hulton, N., Kubik, P. W., & Freeman, S. P. H. T. (2008). Southern Patagonian glacial chronology for the Last Glacial period and implications for Southern Ocean climate. Quaternary Science Reviews, 27(3-4), 284-294. doi: 10.1016/j.quascirev.2007.09.013
Kappe, A. L., Vandezande, L., Vedder, E. J., Bijlsma, R., & Vandelden, W. (1995). Genetic-variation in
Phoca vitulina (the harbor seal) revealed by DNA-fingerprinting and RAPDs. Heredity, 74, 647-653. doi: 10.1038/hdy.1995.88
Kaschner, K., Tittensor, D. P., Ready, J., Gerrodette, T., & Worm, B. (2011). Current and future patterns of global marine mammal biodiversity. PLoS One, 6(5), e19653. doi: 10.1371/journal.pone.0019653 Kato, H., & Fujise, Y. (2000). Dwarf minke whales: morphology, growth and life history with some analyses
on morphometric variation among the different forms and regions. International Whaling Commission Meeting Document SC/52/OS3.
Katona, S., Baxter, B., Brazier, O., Kraus, S., Perkins, J., & Whitehead, H. (1979). Identification of humpback whales by fluke photographs. In H. Winn & B. Olla (Eds.), Behavior of Marine Animals (pp. 33-44): Springer US.
Katona, S. K., & Whitehead, H. P. (1981). Identifying humpaback whales using their natural markings. Polar
Record, 20(128), 439-444.
Kawamura, A. (1980). A review of food of balaenopterid whales. The Scientific Reports of the Whales
160
Keane, M., Semeiks, J., Webb, A. E., Li, Y. I., Quesada, V., Craig, T., . . . de Magalhaes, J. P. (2015). Insights into the evolution of longevity from the bowhead whale genome. Cell Reports, 10(1), 112-122. doi: 10.1016/j.celrep.2014.12.008
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2), 111-120. doi: 10.1007/Bf01731581
Kimura, M., & Ohta, T. (1969). The average number of generations until fixation of a mutant gene in a finite population. Genetics, 61(3), 763-771.
Kimura, M. K., Uchiyama, K., Nakao, K., Moriguchi, Y., San Jose-Maldia, L., & Tsumura, Y. (2014). Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica. Annals of
Botany, 114(8), 1687-1700. doi: 10.1093/aob/mcu197
Kingman, J. F. C. (1980). Mathematics of genetic diversity: Society for Industrial and Applied Mathematics. Kircher, M., & Kelso, J. (2010). High-throughput DNA sequencing - concepts and limitations. Bioessays,
32(6), 524-536. doi: 10.1002/bies.200900181
Kopelman, N. M., Mayzel, J., Jakobsson, M., Rosenberg, N. A., & Mayrose, I. (2015). Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Molecular
Ecology Resources, 15(5), 1179-1191. doi: 10.1111/1755-0998.12387
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014). ANGSD: Analysis of next generation sequencing data. Bmc Bioinformatics, 15. doi: 10.1186/s12859-014-0356-4
Krause, J., Unger, T., Nocon, A., Malaspinas, A.-S., Kolokotronis, S.-O., Stiller, M., . . . Hofreiter, M. (2008). Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evolutionary Biology, 8(1), 220. doi: 10.1186/1471-2148-8-220
Krützen, M., Barre, L. M., Connor, R. C., Mann, J., & Sherwin, W. B. (2004). 'O father: where art thou?' - Paternity assessment in an open fission-fusion society of wild bottlenose dolphins (Tursiops spp.) in Shark Bay, Western Australia. Molecular Ecology, 13(7), 1975-1990. doi: 10.1111/j.1365-294X.2004.02192.x
Kuhner, M. K. (2006). LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics, 22(6), 768-770. doi: 10.1093/bioinformatics/btk051
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357-U354. doi: 10.1038/Nmeth.1923
Larsen, T., Tegelström, H., Juneja, R. K., & Taylor, M. K. (1983). Low protein variability and genetic similarity between populations of the polar bear (Ursus maritimus). Polar Research, 1(1).
Latch, E. K., Dharmarajan, G., Glaubitz, J. C., & Rhodes, O. E. (2006). Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conservation Genetics, 7(2), 295-302. doi: 10.1007/s10592-005-9098-1 Lawton-Rauh, A. (2008). Demographic processes shaping genetic variation. Current Opinion in Plant
Biology, 11(2), 103-109. doi: 10.1016/j.pbi.2008.02.009
Leaché, A. D. (2009). Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus). Systematic Biology, 58(6), 547-559. doi: 10.1093/sysbio/syp057
LeDuc, R. G., Dizon, A. E., Goto, M., Pastene, L. A., Kato, H., Nishiwaki, S., . . . Brownell, R. L. (2007). Patterns of genetic variation in Southern Hemisphere blue whales and the use of assignment test to detect mixing on the feeding grounds. Journal of Cetacean Research and Management, 9(1), 73. LeDuc, R. G., Martien, K. K., Morin, P. A., Hedrick, N., Robertson, K. M., Taylor, B. L., . . . George, J. C.
(2008). Mitochondrial genetic variation in bowhead whales in the western Arctic. Journal of
161
Lessios, H. A. (2008). The Great American Schism: Divergence of marine organisms after the rise of the Central American Isthmus. Annual Review of Ecology Evolution and Systematics, 39, 63-91. doi: 10.1146/annurev.ecolsys.38.091206.095815
Librado, P., & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11), 1451-1452. doi: 10.1093/bioinformatics/btp187
Liepe, J., Barnes, C., Cule, E., Erguler, K., Kirk, P., Toni, T., & Stumpf, M. P. H. (2010). ABC-SysBio-approximate Bayesian computation in Python with GPU support. Bioinformatics, 26(14), 1797-1799. doi: 10.1093/bioinformatics/btq278
Lindgren, A., Hugelius, G., Kuhry, P., Christensen, T. R., & Vandenberghe, J. (2016). GIS-based maps and area estimates of Northern Hemisphere permafrost extent during the Last Glacial Maximum.
Permafrost and Periglacial Processes, 27(1), 6-16. doi: 10.1002/ppp.1851
Lippens, C., Estoup, A., Hima, M. K., Loiseau, A., Tatard, C., Dalecky, A., . . . Brouat, C. (2017). Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times. Heredity. doi: 10.1038/hdy.2017.18
Lipps, J. H., & Mitchell, E. (1976). Trophic model for the adaptive radiations and extinctions of pelagic marine mammals. Paleobiology, 2(2), 147-155. doi: 10.2307/2400357
Lisiecki, L. E., & Raymo, M. E. (2005a). Correction to “A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records”. Paleoceanography, 20(2), 1. doi: 10.1029/2005PA001164 Lisiecki, L. E., & Raymo, M. E. (2005b). A Pliocene-Pleistocene stack of 57 globally distributed benthic
delta O-18 records. Paleoceanography, 20(1). doi: 10.1029/2004pa001071
Liu, S., Lorenzen, E. D., Fumagalli, M., Li, B., Harris, K., Xiong, Z., . . . Wang, J. (2014). Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell, 157(4), 785-794. doi: 10.1016/j.cell.2014.03.054
Liu, X. M., & Fu, Y. X. (2015). Exploring population size changes using SNP frequency spectra. Nature
Genetics, 47(5), 555-U172. doi: 10.1038/ng.3254
Lombaert, E., Guillemaud, T., Thomas, C. E., Handley, L. J. L., Li, J., Wang, S., . . . Estoup, A. (2011). Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis.
Molecular Ecology, 20(22), 4654-4670. doi: 10.1111/j.1365-294X.2011.05322.x Lönnberg, E. (1931). The Skeleton of Balaenoptera brydei Ö. Olsen: Almqvist & Wiksell.
Lopes, J. S., Balding, D., & Beaumont, M. A. (2009). PopABC: a program to infer historical demographic parameters. Bioinformatics, 25(20), 2747-2749. doi: 10.1093/bioinformatics/btp487
Lorance, P., Nedreaas, K., Fernandes, P., Kjellén, N., & Florin, A. (2015). Clupea harengus. The IUCN Red List of Threatened Species 2015. e.T155123A45074983. Retrieved from http://www.iucnredlist.org/details/155123/1
Lorenzen, E. D., Nogues-Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K. A., . . . Willerslev, E. (2011). Species-specific responses of Late Quaternary megafauna to climate and humans. Nature,
479(7373), 359-364. doi: 10.1038/nature10574
Louis, M., Fontaine, M. C., Spitz, J., Schlund, E., Dabin, W., Deaville, R., . . . Simon-Bouhet, B. (2014a). Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator. Proceedings of the Royal Society of London, Series B: Biological Sciences, 281(1795), 20141558. doi: 10.1098/rspb.2014.1558
Louis, M., Viricel, A., Lucas, T., Peltier, H., Alfonsi, E., Berrow, S., . . . Simon-Bouhet, B. (2014b). Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic.
162
Lowther, A. D., Harcourt, R. G., Goldsworthy, S. D., & Stow, A. (2012). Population structure of adult female Australian sea lions is driven by fine-scale foraging site fidelity. Animal Behaviour, 83(3), 691-701. doi: 10.1016/j.anbehav.2011.12.015
Lyrholm, T., Leimar, O., Johanneson, B., & Gyllensten, U. (1999). Sex-biased dispersal in sperm whales: contrasting mitochondrial and nuclear genetic structure of global populations. Proceedings of the
Royal Society of London, Series B: Biological Sciences, 266(1417), 347-354.
Mackintosh, N. A. (1946). The natural history of whalebone whales. Biological Reviews of the Cambridge
Philosophical Society, 21(2), 60-74. doi: 10.1111/j.1469-185X.1946.tb00453.x
Mackintosh, N. A. (1948). The stock of whales. Nature, 162(4108), 148-148. doi: 10.1038/162148a0 Maddison, W. P. (1997). Gene trees in species trees. Systematic Biology, 46(3), 523-536. doi:
10.2307/2413694
Malik, S., Brown, M. W., Kraus, S. D., Knowlton, A. R., Hamilton, P. K., & White, B. N. (1999). Assessment of mitochondrial DNA structuring and nursery use in the North Atlantic right whale (Eubalaena
glacialis). Canadian Journal of Zoology, 77(8), 1217-1222.
Marjoram, P., & Tavare, S. (2006). Modern computational approaches for analysing molecular genetic variation data. Nature Reviews Genetics, 7(10), 759-770. doi: 10.1038/Nrg1961
Martinez, I., Elvevoll, E. O., & Haug, T. (1997). RAPD typing of north-east Atlantic minke whale (Balaenoptera acutorostrata). Ices Journal of Marine Science, 54(3), 478-484. doi: 10.1006/jmsc.1996.0168
Masland, E. D. P., Sweezy, M. A., & Ono, K. A. (2010). Molecular methods for differentiating grey seal (Halichoerus grypus) and harbour seal (Phoca vitulina) scat. Molecular Ecology Resources, 10(1), 214-217. doi: 10.1111/j.1755-0998.2009.02741.x
Matthews, L. H. (1966). Chairman’s Introduction to First Session of the International Symposium on Cetacean Research. In K. S. Norris (Ed.), Whales, Dolphins and Porpoises (pp. 3-6). Berkeley: University of California Press.
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., . . . DePristo, M. A. (2010). The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297-1303. doi: 10.1101/gr.107524.110
Medrano-Gonzalez, L., Aguayolobo, A., Urbanramirez, J., & Baker, C. S. (1995). Diversity and distribution of mitochondrial-DNA lineages among humpback whales, Megaptera novaeangliae, in the Mexican Pacific Ocean. Canadian Journal of Zoology, 73(9), 1735-1743. doi: 10.1139/Z95-205
Melnick, D. J., Hoelzer, G. A., Absher, R., & Ashley, M. V. (1993). MtDNA diversity in rhesus-monkeys reveals overestimates of divergence time and paraphyly with neighboring Species. Molecular
Biology and Evolution, 10(2), 282-295.
Mendel, G. (1866). Versuche über Pflanzen-Hybriden. Naturforsch. Ver. Brünn, 4, 3-47.
Meng, X. P., Shen, X., Zhao, N. N., Tian, M., Liang, M., Hao, J., . . . Zhu, X. L. (2013). Mitogenomics reveals two subspecies in Coelomactra antiquata (Mollusca: Bivalvia). Mitochondrial DNA, 24(2), 102-104. doi: 10.3109/19401736.2012.726620
Miller, W., Schuster, S. C., Welch, A. J., Ratan, A., Bedoya-Reina, O. C., Zhao, F., . . . Lindqvist, C. (2012). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences of the United States of America, 109(36), E2382–E2390.
Mishmar, D., Ruiz-Pesini, E., Golik, P., Macaulay, V., Clark, A. G., Hosseini, S., . . . Wallace, D. C. (2003). Natural selection shaped regional mtDNA variation in humans. Proceedings of the National Academy
of Sciences of the United States of America, 100(1), 171-176. doi: 10.1073/pnas.0136972100 Mizroch, S. A., Rice, D. W., & Breiwick, J. M. (1984). The sei whale, Balaenoptera borealis. Marine