University of Groningen
Divergence and adaptive capacity of marine keystone species Fietz, Katharina
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References
Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP (2016) Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation? Trends Ecol Evol 31, 689-699.
Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. Bmc Bioinformatics 12.
Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19, 1655-1664.
Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nature Reviews Genetics 11, 697-709.
Allendorf FW, Luikart G, Aitken SN (2013) Conservation and the genetics of populations, 2nd edn. Blackwell Publishing, West Sussex, UK.
Alves F, Querouil S, Dinis A, et al. (2013) Population structure of short-finned pilot whales in the oceanic archipelago of Madeira based on photo-identification and genetic analyses:
implications for conservation. Aquatic Conservation-Marine and Freshwater Ecosystems 23, 758-776.
Amano M, Hayano A, Miyazaki N (2002) Geographic variation in the skull of the ringed seal, Pusa hispida. Journal of Mammalogy 83, 370-380.
Amato KR, Yeoman CJ, Kent A, et al. (2013) Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. Isme Journal 7, 1344-1353.
Amos B, Hoelzel AR (1991) Long-term preservation of whale skin for DNA analysis.
Andersen LW, Ruzzante DE, Walton M, et al. (2001) Conservation genetics of harbour porpoises, Phocoena phocoena, in eastern and central North Atlantic. Conservation Genetics 2, 309-324.
Anderson J, Carvalho N, Contini F, Virtanen J (2012) The 2012 Annual Economic Report on the EU Fishing Fleet (STECF-12-10) (ed. Scientific TaECfFS). European Commission. Andersson L, Ryman N, Rosenberg R, Stahl G (1981) Genetic variability in Atlantic herring
(Clupea harengus harengus) - description of protein loci and population data. Hereditas 95, 69-78.
Andrews KR, Karczmarski L, Au WWL, et al. (2010) Rolling stones and stable homes: social structure, habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris). Molecular Ecology 19, 732-748.
Ansmann IC, Lanyon JM, Seddon JM, Parra GJ (2013) Monitoring Dolphins in an Urban Marine System: Total and Effective Population Size Estimates of Indo-Pacific Bottlenose Dolphins in Moreton Bay, Australia. Plos One 8.
Bahr K (1934) Der kleine Sandaal (Ammodytes tobianus L.) der Ostsee. Zeitschr. Fisch. u. d. Hilfswiss. 33.
Baker CS, Clapham PJ (2004) Modelling the past and future of whales and whaling. Trends Ecol Evol 19, 365-371.
Baker CS, Florez-Gonzalez L, Abernethy B, et al. (1998) Mitochondrial DNA variation and maternal gene flow among humpback whales of the southern hemisphere. Marine Mammal Science 14, 721-737.
Baker CS, Palumbi SR, Lambertsen RH, et al. (1990) Influence of seasonal migration on
geographic distribution of mitochondrial DNA haplotypes in humpback whales. Nature 344, 238-240.
Baker CS, Steel D, Calambokidis J, et al. (2013) Strong maternal fidelity and natal philopatry shape genetic structure in North Pacific humpback whales. Marine Ecology Progress Series 494, 291-306.
Barnosky AD, Matzke N, Tomiya S, et al. (2011) Has the Earth's sixth mass extinction already arrived? Nature 471, 51-57.
Bax N, Williamson A, Aguero M, Gonzalez E, Geeves W (2003) Marine invasive alien species: a threat to global biodiversity. Marine Policy 27, 313-323.
Beaumont M (2005) Adaptation and speciation: what can Fst tell us? Trends in Ecology and Evolution 20, 435 - 440.
Beaumont MA (2010) Approximate Bayesian Computation in Evolution and Ecology. In: Annual Review of Ecology, Evolution, and Systematics, Vol 41 (eds. Futuyma DJ, Shafer HB, Simberloff D), pp. 379-406.
Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology 13, 969-980.
Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society B-Biological Sciences 263, 1619-1626. Beaumont MA, Nielsen R, Robert C, et al. (2010) In defence of model-based inference in
phylogeography REPLY. Molecular Ecology 19, 436-446.
Beaumont MA, Zhang WY, Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics 162, 2025-2035.
Beerli P, Felsenstein J (1999) Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152, 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, 4563-4568.
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, 289-300.
Benson AK (2016) The gut microbiome—an emerging complex trait. Nature Genetics 48, 1301-1302.
Berg PR, Jentoft S, Star B, et al. (2015) Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.). Genome Biol Evol 7, 1644-1663.
Bermingham E, McCafferty SS, Martin AP (1997) Fish biogeography and molecular clocks: perspectives from the Panamanian Isthmus. In: Molecular Systematics of Fishes (eds. Kocher TD, Stepien CA), pp. 113-128. NY: Academic Press, New York.
Berta A, Churchill M (2012) Pinniped taxonomy: review of currently recognized species and subspecies, and evidence used for their description. Mammal Review 42, 207-234. Bérubé M, Aguilar A, Dendanto D, et al. (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, 585-599.
Bérubé M, Jorgensen H, Mcewing R, Palsbøll PJ (2000) Polymorphic di-nucleotide microsatellite loci isolated from the humpback whale, Megaptera novaeangliae. Molecular Ecology 9, 2181-2183.
Bérubé M, Palsbøll P (1996) Identification of sex in Cetaceans by multiplexing with three ZFX and ZFY specific primers. Molecular Ecology 5, 283-287.
Bérubé M, Rew MB, Skaug H, et al. (2005) Polymorphic microsatellite loci isolated from humpback whale, Megaptera novaeangliae and fin whale, balaenoptera physalus. Conservation Genetics 6, 631-636.
Best PB (1993) Increase rates in severly depleted stocks of baleen whales. ICES Journal of Marine Science 50, 169-186.
Bjorck S (2008) The late Quaternary development of the Baltic Sea In: Assessment of climate change for the Baltic Sea Basin (ed. Team A), pp. 398-407. Springer Verlag, Berlin Heidelberg.
Blekhman R, Goodrich JK, Huang K, et al. (2015) Host genetic variation impacts microbiome composition across human body sites. Genome Biology 16.
Block BA, Dewar H, Farwell C, Prince ED (1998) A new satellite technology for tracking the movements of Atlantic bluefin tuna. Proceedings of the National Academy of Sciences of the United States of America 95, 9384-9389.
Bolnick DI, Snowberg LK, Hirsch PE, et al. (2014) Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecology Letters 17, 979-987.
Bordenstein SR, Theis KR (2015) Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. Plos Biology 13.
Boskovic R, Kovacs KM, Hammill MO, White BN (1996) Geographic distribution of
mitochondrial DNA haplotypes in grey seals (Halichoerus grypus). Canadian Journal of Zoology-Revue Canadienne De Zoologie 74, 1787-1796.
Boustany AM, Reeb CA, Block BA (2008) Mitochondrial DNA and electronic tracking reveal population structure of Atlantic bluefin tuna (Thunnus thynnus). Marine Biology 156, 13-24. Bouzat JL (2010) Conservation genetics of population bottlenecks: the role of chance, selection,
and history. Conservation Genetics 11, 463-478.
Bouzat JL, Lewin HA, Paige KN (1998) The ghost of genetic diversity past: Historical DNA analysis of the greater prairie chicken. American Naturalist 152, 1-6.
Boye TK, Simon M, Madsen PT (2010) Habitat use of humpback whales in Godthaabsfjord, West Greenland, with implications for commercial exploitation. Journal of the Marine Biological Association of the United Kingdom 90, 1529-1538.
Bradbury IR, Hubert S, Higgins B, et al. (2010) Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature. Proceedings of the Royal Society B-Biological Sciences 277, 3725-3734.
Caporaso JG, Kuczynski J, Stombaugh J, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335-336.
Castro-Prieto A, Wachter B, Sommer S (2011) Cheetah Paradigm Revisited: MHC Diversity in the World's Largest Free-Ranging Population. Mol Biol Evol 28, 1455-1468.
Cato D, CMcCauley R, Rogers T, Noad M- (2006) Passive acoustics for monitoring marine mammals - progress and challenges. Proceedings of ACOUSTICS, 453 - 460.
Chao A, Shen TJ (2003) Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environmental and Ecological Statistics 10, 429-443.
Chapskii KK (1975) Obosnavanie dvukh novykh podvidov nastoyashchikh tyulenei semeistva Phocidae. Trudy Zoologischeskogo Instituta Akademii Nauk SSSR, 53, 282-333.
Christensen A, Mosegaard H, Jensen H (2009) Spatially resolved fish population analysis for designing MPAs: influence on inside and neighbouring habitats. ICES Journal of Marine Science 66, 56-63.
Clapham PJ, Baraff LS, Carlson CA, et al. (1993a) Seasonal occurrence and annual return of humpback whales, Megaptera novaeangliae, in the southern Gulf of Maine. Canadian Journal of Zoology-Revue Canadienne De Zoologie 71, 440-443.
Clapham PJ, Mead JG (1999) Megaptera novaeangliae. Mammalian species 604, 1-9.
Clapham PJ, Palsboll PJ, Mattila DK (1993b) High-energy behaviors in humpback whales as a source of sloughed skin for moluecular analysis. Marine Mammal Science 9, 213-220. Clapham PJ, Young SB, Brownell RL (1999) Baleen whales: conservation issues and the status of
the most endangered populations. Mammal Review 29, 35-60.
Clegg SM, Kelly JF, Kimura M, Smith TB (2003) Combining genetic markers and stable isotopes to reveal population connectivity and migration patterns in a Neotropical migrant, Wilson's warbler (Wilsonia pusilla). Molecular Ecology 12, 819-830.
Cole JR, Wang Q, Fish JA, et al. (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Research 42, D633-D642.
Collette BB, Carpenter KE, Polidoro BA, et al. (2011) High Value and Long Life-Double Jeopardy for Tunas and Billfishes. Science 333, 291-292.
Colston TJ, Jackson CR (2016) Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Molecular Ecology 25, 3776-3800.
Cook BD, Bunn SE, Hughes JM (2007) Molecular genetic and stable isotope signatures reveal complementary patterns of population connectivity in the regionally vulnerable southern pygmy perch (Nannoperca australis). Biological Conservation 138, 60-72.
Cooke GM, Schlub TE, Sherwin WB, Ord TJ (2016) Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis. Plos One 11. Cooke JG, Weller DW, Bradford AL, et al. (2013a) Population assessment of the Sakhalin gray
whale aggregation. Paper SC/65a/BRG27 presented to the International Whaling Commission Scientific Committee.
Cooke SJ, Midwood JD, Thiem JD, et al. (2013b) Tracking animals in freshwater with electronic tags: past, present and future. Animal Biotelemetry 1, 5.
Coop G, Witonsky D, Di Rienzo A, Pritchard JK (2010) Using Environmental Correlations to Identify Loci Underlying Local Adaptation. Genetics 185, 1411-1423.
Corander J, Majander KK, Cheng L, Merila J (2013) High degree of cryptic population
differentiation in the Baltic Sea herring Clupea harengus. Molecular Ecology 22, 2931-2940. Cornuet J-M, Pudlo P, Veyssier J, et al. (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, 1187-1189. Cornuet JM, 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.
Cornuet JM, Santos F, Beaumont MA, et al. (2008) Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics 24, 2713-2719.
Crispo E, Chapman LJ (2010) Temporal Variation in Population Genetic Structure of a Riverine African Cichlid Fish. Journal of Heredity 101, 97-106.
Crow KD, Munehara H, Bernardi G (2010) Sympatric speciation in a genus of marine reef fishes. Molecular Ecology 19, 2089-2105.
Csillery K, Blum MG, Gaggiotti OE, Francois O (2010) Approximate Bayesian Computation (ABC) in practice. Trends Ecol Evol 25, 410-418.
Darling JD, Calambokidis J, Balcomb KC, et al. (1996) Movement of a humpback whale (Megaptera novaeangliae) from Japan to British Columbia and return. Marine Mammal Science 12, 281-287.
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9, 772-772.
Darwin C (1859) On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life John Murray, London.
Dawbin WH (1966) The seasonal migratory cycle of the humpback whale. In: Whales, dolphins and porpoises (ed. Norris KS), pp. 145-170. University of California press, Berkeley.
de Villemereuil P, Gaggiotti OE (2015) A new FST-based method to uncover local adaptation using environmental variables. Methods in Ecology and Evolution 6, 1248-1258.
Derraik JGB (2002) The pollution of the marine environment by plastic debris: a review. Mar Pollut Bull 44, 842-852.
Di Maiuta N, Schwarzentruber P, Schenker M, Schoelkopf J (2013) Microbial population dynamics in the faeces of wood-eating loricariid catfishes. Letters in Applied Microbiology 56, 401-407.
Dieckmann U, Doebeli M (1999) On the origin of species by sympatric speciation. Nature 400, 354-357.
Do C, Waples RS, Peel D, et al. (2014) NEESTIMATOR v2: re-implementation of software for the estimation of contemporary effective population size (N-e) from genetic data. Molecular Ecology Resources 14, 209-214.
Doebeli M (1996) A quantitative genetic competition model for sympatric speciation. Journal of Evolutionary Biology 9, 893-909.
Drummond AJ, Ashton B, Cheung M, et al. (2009) Geneious v4.7. http://www.geneious.com. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26,
2460-2461.
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10, 996-+.
Eichmiller JJ, Hamilton MJ, Staley C, Sadowsky MJ, Sorensen PW (2016) Environment shapes the fecal microbiome of invasive carp species. Microbiome 4.
Ekström E (2016) Beslut om skyddsjakt efter gråsäl för 2016. Swedish Environmental Protection Agency, Stockholm.
Elshire RJ, Glaubitz JC, Sun Q, et al. (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. Plos One 6.
Emeis KC, Struck U, Blanz T, Kohly A, Voss M (2003) Salinity changes in the central Baltic Sea (NW Europe) over the last 10 000 years. Holocene 13, 411-421.
Endler JA (1977) Geographic isolation, speciation and gene flow Princeton University Press, Princeton, NJ.
Engelhard GH, Peck MA, Rindorf A, et al. (2013) Forage fish, their fisheries, and their predators: who drives whom? ICES Journal of Marine Science 71, 90-104.
Estoup A, Jarne P, Cornuet JM (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Molecular Ecology 11, 1591-1604. Excoffier L, Hofer T, Foll M (2009) Detecting loci under selection in a hierarchically structured
population. Heredity (Edinb) 103, 285-298.
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10, 564-567.
Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes - application to human mitochondrial-DNA restriction data. Genetics 131, 479-491.
Falush D, van Dorp L, Lawson D (2016) A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots. bioRxiv.
Feder JL, Berlocher SH, Roethele JB, et al. (2003) Allopatric genetic origins for sympatric host-plant shifts and race formation in Rhagoletis. Proceedings of the National Academy of Sciences of the United States of America 100, 10314-10319.
Feinberg AP, Irizarry RA (2010) Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proceedings of the National Academy of Sciences of the United States of America 107, 1757-1764.
Fietz K, Galatius A, Teilmann J, et al. (2016) Shift of grey seal subspecies boundaries in response to climate, culling and conservation. Molecular Ecology 25, 4097-4112.
Fisher RA (1930) The genetical theory of natural selection, Oxford.
Flather CH, Hayward GD, Beissinger SR, Stephens PA (2011) Minimum viable populations: is there a 'magic number' for conservation practitioners? Trends Ecol Evol 26, 307-316.
Florin AB, Hoglund J (2008) Population structure of flounder (Platichthys flesus) in the Baltic Sea: differences among demersal and pelagic spawners. Heredity (Edinb) 101, 27-38.
Foll M, Gaggiotti O (2008) A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective. Genetics 180, 977-993. Fontaine MC, Roland K, Calves I, et al. (2014) Postglacial climate changes and rise of three
ecotypes of harbour porpoises, Phocoena phocoena, in western Palearctic waters. Mol Ecol 23, 3306-3321.
Foote AD, Newton J, Piertney SB, Willerslev E, Gilbert MTP (2009) Ecological, morphological and genetic divergence of sympatric North Atlantic killer whale populations. Molecular Ecology 18, 5207-5217.
Foote AD, Vijay N, Avila-Arcos MC, et al. (2016) Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nature Communications 7.
Ford JKB, Ellis GM, Barrett-Lennard LG, et al. (1998) Dietary specialization in two sympatric populations of killer whales (Orcinus orca) in coastal British Columbia and adjacent waters. Canadian Journal of Zoology-Revue Canadienne De Zoologie 76, 1456-1471.
Forney KA, Wade P (2005) Worldwide distribution and abundance of killer whales. In: Whales, Whaling and Ocean Ecosystems (ed. Estes J), pp. 145-162. University of California Press, Berkeley, CA.
Frankham R (2005) Genetics and Extinction. Biological Conservation 126, 131 - 140.
Frankham R, Ballou J, Briscoe D (2009) Introduction to conservation genetics. Cambridge Univ Press, Cambridge.
Frankham R, Bradshaw CJA, Brook BW (2014) Genetics in conservation management: Revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biological Conservation 170, 56-63.
Franklin IR (1980) Evolutionary changes in small populations. Soule, M. E., and B. A. Wilcox, ewds. Conservation Biology: An Evolutionary-Ecological Perspective. Sinauer Associates, Sunderland, MA.
Franklin IR, Frankham R (1998) How large must populations be to retain evolutionary potential? Animal Conservation 1, 69-70.
Frederiksen M, Edwards M, Richardson AJ, Halliday NC, Wanless S (2006) From plankton to top predators: bottom-up control of a marine food web across four trophic levels. Journal of Animal Ecology 75, 1259-1268.
Froese R, Zeller D, Kleisner K, Pauly D (2012) What catch data can tell us about the status of global fisheries. Marine Biology 159, 1283-1292.
Furness RW (2002) Management implications of interactions between fisheries and
sandeel-dependent seabirds and seals in the North Sea. ICES Journal of Marine Science 59, 261-269. Gaggiotti OE, Bekkevold D, Jorgensen HBH, et al. (2009) Disentangling the effects of
evolutionary, demographic, and environmental factors influencing genetic structure ofnatural populations: Atlantic herring as a case study. Evolution 63, 2939-2951. Gagnaire PA, Broquet T, Aurelle D, et al. (2015) Using neutral, selected, and hitchhiker loci to
assess connectivity of marine populations in the genomic era. Evol Appl 8, 769-786.
Gardmark A, Ostman O, Nielsen A, et al. (2012) Does predation by grey seals (Halichoerus grypus) affect Bothnian Sea herring stock estimates? ICES Journal of Marine Science 69, 1448-1456.
Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Molecular Ecology 10, 305-318.
Gauld JA (1990) Movements of lesser sandeels (Ammodytes marinus Raitt) tagged in the Northwestern North Sea. Journal Du Conseil 46, 229-231.
Gelman A, Carlin JB, Stern HB, al. e (1995) Bayesian Data Analysis Chapman and Hall, New York.
Gelman A, Rubin DB (1992) Inference from Iterative Simulation Using Multiple Sequences Statistical Science 7, 457-511.
Geweke J (1991) Evaluating the accuracy of sampling-based approaches to calculating posterior moments. In: Bayesian Statistics 4 (eds. Bernado M, Berger JO, Dawid AP, Smith AFM). Clarendon Press, Oxford, UK.
Ghalambor CK, McKay JK, Carroll SP, Reznick DN (2007) Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments. Functional Ecology 21, 394-407.
Gilbert MTP, Moore W, Melchior L, Worobey M (2007) DNA Extraction from Dry Museum Beetles without Conferring External Morphological Damage. Plos One 2.
Givens CE, Ransom B, Bano N, Hollibaugh JT (2015) Comparison of the gut microbiomes of 12 bony fish and 3 shark species. Marine Ecology Progress Series 518, 209-223.
Goodrich JK, Waters JL, Poole AC, et al. (2014) Human Genetics Shape the Gut Microbiome. Cell 159, 789-799.
Goudet J (1995) FSTAT (Version 1.2): A computer program to calculate F-statistics. Journal of Heredity 86, 485-486.
Graves JA, Helyar A, Biuw M, et al. (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, 59-68.
Gunther T, Coop G (2013) Robust Identification of Local Adaptation from Allele Frequencies. Genetics 195, 205-+.
Guo BC, DeFaveri J, Sotelo G, Nair A, Merila J (2015) Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biol 13, 19.
Guo BC, Li ZT, Merila J (2016) Population genomic evidence for adaptive differentiation in the Baltic Sea herring. Molecular Ecology 25, 2833-2852.
Habel JC, Husemann M, Finger A, Danley PD, Zachos FE (2014) The relevance of time series in molecular ecology and conservation biology. Biological Reviews 89, 484-492.
Han Z, Yanagimoto T, Zhang Y, Gao T (2012) Phylogeography Study of Ammodytes personatus in Northwestern Pacific: Pleistocene Isolation, Temperature and Current Conducted Secondary Contact. Plos One 7.
Hansen CHF, Krych L, Nielsen DS, et al. (2012) Early life treatment with vancomycin propagates Akkermansia muciniphila and reduces diabetes incidence in the NOD mouse. Diabetologia 55, 2285-2294.
Harding KC, Harkonen T, Helander B, Karlsson O (2007) Status of Baltic grey seals: population assessment and extinction risk. NAMMCO Scientific Publications 6, 33-56.
Harding KC, Harkonen TJ (1999) Development in the Baltic grey seal (Halichoerus grypus) and ringed seal (Phoca hispida) populations during the 20th century. Ambio 28, 619-627.
Harkonen T, Brasseur S, Teilmann J, et al. (2007) Status of grey seals along mainland Europe from the Southwestern Baltic to France. NAMMCO Scientific Publications 6.
Harwood J, Croxall JP (1988) The assessment of competition between seals and commercial fisheries in the North Sea and the Antarctic. Marine Mammal Science 4, 13-33.
Hasegawa M, Kishino H, Yano TA (1985) Dating of the human ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22, 160-174.
Haug T, Hammill M, Olafsdottir D (2007) Introduction: Grey seals in the North Atlantic and the Baltic. NAMMCO Scientific Publications 6, 7-12.
Hauser L, Carvalho GR (2008) Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts. Fish and Fisheries 9, 333-362.
Heide-Jorgensen MP, Harkonen TJ (1988) Rebuilding seal stocks in the Kattegat-Skagerrak. Marine Mammal Science 4, 231-246.
Helle E (1976) PCB levels correlated with pathological changes in seal uteri. Ambio 6, 261-262. Herlemann DPR, Lundin D, Andersson AF, Labrenz M, Jürgens K (2016) Phylogenetic Signals of
Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea. Frontiers in Microbiology 7.
Herman DP, Burrows DG, Wade PR, et al. (2005) Feeding ecology of eastern North Pacific killer whales Orcinus orca from fatty acid, stable isotope, and organochlorine analyses of blubber biopsies. Marine Ecology Progress Series 302, 275-291.
Hill WG (1981) Estimation of effective population size from data on linkage disequilibrium. Genetical Research 38, 209-216.
Hoegh-Guldberg O, Hoegh-Guldberg H, Veron JEN, et al. (2009) The Coral Triangle and Climate Change: Ecosystems, People, and Societies at Risk, p. 276 pp. WWF Australia, Brisbane. Hoeksema BW (2007) Delineation of the Indo-Malayan Centre of Maximum Marine Biodiversity:
The Coral Triangle. In: Biogeography, Time and Place: Distributions, Barriers and Islands (ed. Renema W), pp. 117 - 178. Springer.
Hoelzel AR (1998) Genetic structure of cetacean populations in sympatry, parapatry, and mixed assemblages: Implications for conservation policy. Journal of Heredity 89, 451-458. Hoelzel AR, Potter CW, Best PB (1998) Genetic differentiation between parapatric 'nearshore' and
'offshore' populations of the bottlenose dolphin. Proceedings of the Royal Society B-Biological Sciences 265, 1177-1183.
Holm S (1979) A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics 6, 65-70.
Holsinger KE (1996) Review: The scope and the limits of conservation genetics. Evolution 50, 2558 - 2561.
Hooker SK, Gerber LR (2004) Marine reserves as a tool for ecosystem-based management: The potential importance of megafauna. Bioscience 54, 27-39.
Hotelling H (1933) Analysis of a complex of statistical variables into principal components. J Educ Psychol 25, 417 - 441.
Hu YOO, Karlson B, Charvet S, Andersson AF (2016) Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea. Frontiers in Microbiology 7.
Huber I, Spanggaard B, Appel KF, et al. (2004) Phylogenetic analysis and in situ identification of the intestinal microbial community of rainbow trout (Oncorhynchus mykiss, Walbaum). Journal of Applied Microbiology 96, 117-132.
Ingebrigtsen A (1929) Whales caught in the North Atlantic and other seas. Rapp. p.-v. réun. - Cons. int. explor. mer 56, 1-26.
Islam MS, Tanaka M (2004) Impacts of pollution on coastal and marine ecosystems including coastal and marine fisheries and approach for management: a review and synthesis. Mar Pollut Bull 48, 624-649.
Jackson JA, Steel DJ, Beerli P, et al. (2014) Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae). Proc Biol Sci 281.
Jackson JBC, Kirby MX, Berger WH, et al. (2001) Historical overfishing and the recent collapse of coastal ecosystems. Science 293, 629-638.
Jamieson IG, Allendorf FW (2012) How does the 50/500 rule apply to MVPs? Trends Ecol Evol 27, 578-584.
Jann B, Allen J, Carrillo M, et al. (2003) Migration of a humpback whale (Megaptera novaeangliae) between the Cape Verde Islands and Iceland. Journal of Cetacean Research and
Management 5, 125-129.
Jansson BO, Dahlberg K (1999) The environmental status of the Baltic Sea in the 1940s, today, and in the future. Ambio 28, 312-319.
Jeffreys H (1948) Theory of Probability 2edn. The Clarendon Press, Oxford.
Jensen H, Rindorf A, Wright PJ, Mosegaard H (2011) Inferring the location and scale of mixing between habitat areas of lesser sandeel through information from the fishery. ICES Journal of Marine Science 68, 43-51.
Jepsen N, Thorstad EB, Havn T, Lucas MC (2015) The use of external electronic tags on fish: an evaluation of tag retention and tagging effects. Animal Biotelemetry 3, 49.
Jiggins CD, Bridle JR (2004) Speciation in the apple maggot fly: a blend of vintages? Trends Ecol Evol 19, 111-114.
Johannesson K, Andre C (2006) Life on the margin: genetic isolation and diversity loss in a peripheral marine ecosystem, the Baltic Sea. Mol Ecol 15, 2013-2029.
Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403-1405.
Jones AG, Moore GI, Kvarnemo C, Walker D, Avise JC (2003) Sympatric speciation as a consequence of male pregnancy in seahorses. Proceedings of the National Academy of Sciences of the United States of America 100, 6598-6603.
Jorgensen HBH, Hansen MM, Loeschcke V (2005) Spring-spawning herring (Clupea harengus L.) in the southwestern Baltic Sea: do they form genetically distinct spawning waves? ICES Journal of Marine Science 62, 1065-1075.
Kandler R (1941) Untersuchungen über Fortpflanzung, Wachstum und Variabilität der Arten des Sandaals in Ost- und Nordsee, mit besonderer Berücksichtigung von Ammodytes tobianus. L. Kieler Meeres. 5, 45-139.
Katona SK, Beard JA (1990) Population Size, Migrations and Feeding Aggregations of the
Humpback Whale (Megaptera novaeangliae) in the Western North Atlantic Ocean. Report of the International Whaling Commission, 295 - 305.
Kim JK, Watson W, Hyde J, et al. (2010) Molecular identification of Ammodytes (PISCES, Ammodytidae) larvae, with ontogenetic evidence on separating populations. Genes & Genomics 32, 437-445.
Kimura M, Crow JF (1964) The Number of Alleles That Can Be Maintained in a Finite Population Genetics 49, 725-738.
Klepaker T (1993) Morphological changes in a marine population of threespined stickleback, Gasterosteus aculeatus, recently isolated in fresh water Canadian Journal of Zoology 71, 1251 - 1258.
Klimova A, Phillips CD, Fietz K, et al. (2014) Global population structure and demographic history of the grey seal. Molecular Ecology 23, 3999-4017.
Knowlton N, Weigt LA (1998) New dates and new rates for divergence across the Isthmus of Panama. Proceedings of the Royal Society B-Biological Sciences 265, 2257-2263.
Kohl KD, Stengel A, Dearing MD (2016) Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets. Environmental Microbiology 18, 1720-1729. Konigson S, Lunneryd SG, Stridh H, Sundqvist F (2009) Grey seal predation in cod gillnet fisheries
in the central Baltic Sea. Journal of Northwest Atlantic Fishery Science 42, 41 - 47. Kool JT, Moilanen A, Treml EA (2013) Population connectivity: recent advances and new
perspectives. Landscape Ecology 28, 165-185.
Kruskal WH, Wallis WA (1952) Use of ranks in one-criterion variance analysis. Journal of the American Statistical Association 47, 583-621.
Kultz D (2015) Physiological mechanisms used by fish to cope with salinity stress. Journal of Experimental Biology 218, 1907-1914.
Kultz D, Li J, Gardell A, Sacchi R (2013) Quantitative Molecular Phenotyping of Gill Remodeling in a Cichlid Fish Responding to Salinity Stress. Molecular & Cellular Proteomics 12, 3962-3975.
Lambertsen RH (1987) A biopsy system for large whales and its use for cytogenetics. Journal of Mammalogy 68, 443-445.
Lamichhaney S, Martinez Barrio A, Rafati N, et al. (2012) Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. Proc Natl Acad Sci U S A 109, 19345-19350.
Lanzen A, Jorgensen SL, Huson DH, et al. (2012) CREST - Classification Resources for Environmental Sequence Tags. Plos One 7.
Laparra JM, Sanz Y (2010) Interactions of gut microbiota with functional food components and nutraceuticals. Pharmacological Research 61, 219-225.
Lawson DJ, Falush D (2012) Population Identification Using Genetic Data. In: Annual Review of Genomics and Human Genetics, Vol 13 (eds. Chakravarti A, Green E), pp. 337-361. Le Moan A, Gagnaire PA, Bonhomme F (2016) Parallel genetic divergence among coastal-marine
ecotype pairs of European anchovy explained by differential introgression after secondary contact. Molecular Ecology 25, 3187-3202.
Lee SM, Robineau D (2004) Les cetacés des gravures rupestres néolithiques de Bangu-dae (Corée du Sud) et les débuts de la chasse á la baleine dans le Pacifique nord-ouest. L'Anthropologie 108, 137 - 151.
Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of theory of selective neutrality of polymorphisms. Genetics 74, 175-195.
Lewy P, Nielsen A, Gislason H (2004) Stock dynamics of sandeel in the North Sea and sub-regions including uncertainties. Fisheries Research 68, 237-248.
Ley RE, Hamady M, Lozupone C, et al. (2008) Evolution of mammals and their gut microbes. Science 320, 1647-1651.
Li XM, Zhu YJ, Yan QY, Ringo E, Yang DG (2014) Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond? Journal of Applied Microbiology 117, 1245-1252.
Limborg MT, Helyar SJ, de Bruyn M, et al. (2012) Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus). Molecular Ecology 21, 3686-3703.
Limborg MT, Pedersen JS, Hemmer-Hansen J, Tomkiewicz J, Bekkevold D (2009) Genetic population structure of European sprat Sprattus sprattus: differentiation across a steep environmental gradient in a small pelagic fish. Marine Ecology Progress Series 379, 213-224.
Llewellyn MS, McPGinnity P, Dionne M, et al. (2016) The biogeography of the atlantic salmon (Salmo salar) gut microbiome. Isme Journal 10, 1280-1284.
Lotterhos KE, Whitlock MC (2014) Evaluation of demographic history and neutral
parameterization on the performance of F-ST outlier tests. Molecular Ecology 23, 2178-2192.
Lowe WH, Allendorf FW (2010) What can genetics tell us about population connectivity? Molecular Ecology 19, 3038-3051.
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R (2011) UniFrac: an effective distance metric for microbial community comparison. Isme Journal 5, 169-172.
Lu F, Lipka AE, Glaubitz J, et al. (2013) Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol. PLoS Genet 9.
Martinez Barrio A, Lamichhaney S, Fan G, et al. (2016) The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. eLife 5.
Mayr E (1942) Systematics and the Origin of Species Columbia University Press, New York. McConnell BJ, Fedak MA, Lovell P, Hammond PS (1999) Movements and foraging areas of grey
McMillan WO, Weigt LA, Palumbi SR (1999) Color pattern evolution, assortative mating, and genetic differentiation in brightly colored butterflyfishes (Chaetodontidae). Evolution 53, 247-260.
McMurdie PJ, Holmes S (2013) phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. Plos One 8.
Menozzi P, Piazza A, Cavalli-Sforza LL (1978) Synthetic maps of human gene frequencies in Europeans. Science 201, 786 - 792.
Merola M (1994) Reassessment of homozygosity and the case for inbreeding depression in the cheetah, Acinonyx jubatus - implications for conservation. Conservation Biology 8, 961-971.
Microsoft (2007) Microsoft Excel. Redmont, Wahsington.
Miller CR, Waits LP (2003) The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): Implications for conservation. Proceedings of the National Academy of Sciences of the United States of America 100, 4334-4339. Mills LS, Allendorf FW (1996) The one-migrant-per-generation rule in conservation and
management. Conservation Biology 10, 1509-1518.
Mills LS, Soule ME, Doak DF (1993) The keystone-species concept in ecology and conservation. Bioscience 43, 219-224.
Minton G, Collins T, Findlay KP, et al. (2011) Seasonal distribution, abundance, habitat use and population identity of humpback whales in Oman. Journal of Cetacean Research and Management (Special Issue) 3, 185-198.
Mitchell E, Reeves RR (1983) Catch history, abundance, and present status of northwest Atlantic humpback whales. Rep. Int. Whal. Commn., 153 - 212.
Miya M, Nishida M (1997) Speciation in the open ocean. Nature 389, 803-804.
Miyake S, Ngugi DK, Stingl U (2015) Diet strongly influences the gut microbiota of surgeonfishes. Molecular Ecology 24, 656-672.
Molnar JL, Gamboa RL, Revenga C, Spalding MD (2008) Assessing the global threat of invasive species to marine biodiversity. Frontiers in Ecology and the Environment 6, 485-492. Morrison JC, Sechrest W, Dinerstein E, Wilcove DS, Lamoreux JF (2007) Persistence of large
mammal faunas as indicators of global human impacts. Journal of Mammalogy 88, 1363-1380.
Munday PL, Jones GP, Caley MJ (1997) Habitat specialisation and the distribution and abundance of coral-dwelling gobies. Marine Ecology Progress Series 152, 227-239.
Munday PL, van Herwerden L, Dudgeon CL (2004) Evidence for sympatric speciation by host shift in the sea. Current Biology 14, 1498-1504.
Narum SR, Hess JE (2011) Comparison of FST outlier tests for SNP loci under selection. Molecular Ecology Resources 11, 184 - 194.
Naturstyrelsen (2014) Forslag om midlertidig ordning til regulering af gråsæl. Naturstyrelsen (2016) Sæljægerkorps skal hjælpe trængte fiskere.
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583-590.
Nei M, Li WH (1979) A mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America 76, 5269-5273.
Neigel JE (2002) Is Fst obsolete? Conservation Genetics 3, 167 - 173.
Nelson JS, Grande TC, Wilson MVH (2016) Fishes of the World, 5 edn. John Wiley & Sons. Nielsen EE, Cariani A, Mac Aoidh E, et al. (2012) Gene-associated markers provide tools for
tackling illegal fishing and false eco-certification. Nature Communications 3.
Nielsen EE, Hemmer-Hansen J, Larsen PF, Bekkevold D (2009a) Population genomics of marine fishes: identifying adaptive variation in space and time. Molecular Ecology 18, 3128-3150.
Nielsen EE, Hemmer-Hansen J, Poulsen NA, et al. (2009b) Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua). BMC Evol Biol 9.
NOAA NOaAAF (2010) BLUE WHALE (Balaenoptera musculus musculus): Western North Atlantic Stock. NOAA Assessment Report.
Obrien SJ, Roelke ME, Marker L, et al. (1985) Genetic basis for species vulnerability in the cheetah. Science 227, 1428-1434.
Oconnell M, Fives JM (1995) The biology of the lesser sand-eel Ammodytes tobianus L in the Galway Bay area. Biology and Environment-Proceedings of the Royal Irish Academy 95B, 87-98.
Ojaveer E, Kalejs M (2005) The impact of climate change on the adaptation of marine fish in the Baltic Sea. ICES Journal of Marine Science 62, 1492-1500.
Oksanen J, Blanchet FG, Friendly M, et al. (2016) vegan: Community Ecology Package. Olsen MT (2012) Molecular ecology of marine mammals, University of Stockholm.
Olsen MT, Andersen LW, Dietz R, et al. (2014) Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units. Molecular Ecology 23, 815-831.
Olsen MT, Galatius A, Biard V, Gregersen K, Kinze CC (2016) The forgotten type specimen of the grey seal Halichoerus grypus (Fabricius, 1791) from the island of Amager, Denmark. Zoological Journal of the Linnean Society 178, 713-720.
Orr JW, Wildes S, Kai Y, et al. (2015) Systematics of North Pacific sand lances of the genus Ammodytes based on molecular and morphological evidence, with the description of a new species from Japan. Fishery Bulletin 113, 129-156.
Padhukasahasram B (2014) Inferring ancestry from population genomic data and its applications. Frontiers in Genetics 5.
Paetkau D, Strobeck C (1994) Microsatellite analysis of genetic variation in black bear populations. Molecular Ecology 3, 489-495.
Palsboll PJ, Berube M, Aguilar A, Notarbartolo-Di-Sciara G, Nielsen R (2004) Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations. Evolution 58, 670-675.
Palsboll PJ, Berube M, Allendorf FW (2007) Identification of management units using population genetic data. Trends Ecol Evol 22, 11-16.
Palsbøll PJ, Bérubé M, Larsen AH, Jorgensen H (1997) Primers for the amplification of tri- and tetramer microsatellite loci in baleen whales. Molecular Ecology 6, 893-895.
Palsbøll PJ, Clapham PJ, Mattila DK, et al. (1995) Distribution of Mtdna Haplotypes in North-Atlantic Humpback Whales - the Influence of Behavior on Population-Structure. Marine Ecology Progress Series 116, 1-10.
Palsboll PJ, Peery MZ, Berube M (2010) Detecting populations in the 'ambiguous' zone: kinship-based estimation of population structure at low genetic divergence. Molecular Ecology Resources 10, 797-805.
Palsbøll PJ, Zachariah Peery M, Olsen MT, Beissinger SR, Bérubé M (2013) Inferring recent historic abundance from current genetic diversity. Mol Ecol 22, 22-40.
Palumbi SR (1992) Marine speciation on a small planet. Trends Ecol Evol 7, 114-118.
Palumbi SR, Baker CS (1994) Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Mol Biol Evol 11, 426-435.
Pastene LA, Goto M, Kanda N, et al. (2007) Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera
Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2, 2074-2093.
Paulson JN, Stine OC, Bravo HC, Pop M (2013) Differential abundance analysis for microbial marker-gene surveys. Nature Methods 10, 1200-+.
Pauly D, Alder J, Bennett E, et al. (2003) The future for fisheries. Science 302, 1359-1361.
Pauly D, Watson R, Alder J (2005) Global trends in world fisheries: impacts on marine ecosystems and food security. Philosophical Transactions of the Royal Society B-Biological Sciences 360, 5-12.
Pedersen SA, Lewy P, Wright P (1999) Assessments of the lesser sandeel (Ammodytes marinus) in the North Sea based on revised stock divisions. Fisheries Research 41, 221-241.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
Proctor R, Wright PJ, Everitt A (1998) Modelling the transport of larval sandeels on the north-west European shelf. Fisheries Oceanography 7, 347-354.
Puebla O (2009) Ecological speciation in marine v. freshwater fishes. Journal of Fish Biology 75, 960-996.
Punt AE, Friday NA, Smith TD (2006) Reconciling data on the trends and abundance of North Atlantic humpback whales within a population modelling framework. Journal of Cetacean Research and Management 8, 145-159.
Purcell S, Neale B, Todd-Brown K, et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81, 559-575. R Development Core Team (2015) R: A language and environment for statistical computing. R
Foundation for Statistical Computing, Vienna, Austria.
Rasmussen K, Palacios DM, Calambokidis J, et al. (2007) Southern Hemisphere humpback whales wintering off Central America: insights from water temperature into the longest mammalian migration. Biology Letters 3, 302-305.
Rawls JF, Mahowald MA, Ley RE, Gordon JI (2006) Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127, 423-433. Rawls JF, Samuel BS, Gordon JI (2004) Gnotobiotic zebrafish reveal evolutionarily conserved
responses to the gut microbiota. Proceedings of the National Academy of Sciences of the United States of America 101, 4596-4601.
Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conservation Biology 17, 230-237.
Reed DL, Carpenter KE, deGravelle MJ (2002) Molecular systematics of the Jacks (Perciformes : Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches. Mol Phylogenet Evol 23, 513-524.
Reich D, Price AL, Patterson N (2008) Principal component analysis of genetic data. Nature Genetics 40, 491-492.
Reilly SB, Bannister JL, Best PB, et al. (2008a) Balaenoptera musculus. http://dx.doi.org/10.2305/IUCN.UK.2008.RLTS.T2477A9447146.en
Reilly SB, Bannister JL, Best PB, et al. (2008b) Eschrichtius robustus (western subpopulation). http://dx.doi.org/10.2305/IUCN.UK.2008.RLTS.T8099A12885692.en
Reissmann J, Burchard H, Feistel R, et al. (2009) State-of-the-art review on vertical mixing in the BalticSea and consequences for eutrophication. Progress in Oceanography 82, 47-80. Rice WR (1989) Analyzing tables of statistical tests. Evolution 43, 223-225.
Rindorf A, Wanless S, Harris MP (2000) Effects of changes in sandeel availability on the reproductive output of seabirds. Marine Ecology Progress Series 202, 241-252.
Robert CP, Chopin N, Rousseau J, et al. (2009) Harold Jeffreys's Theory of Probability Revisited. Statistical Science 24, 141-194.
Roberts CM, McClean CJ, Veron JEN, et al. (2002) Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295, 1280-1284.
Rocha LA, Bowen BW (2008) Speciation in coral-reef fishes. Journal of Fish Biology 72, 1101-1121.
Roeselers G, Mittge EK, Stephens WZ, et al. (2011) Evidence for a core gut microbiota in the zebrafish. Isme Journal 5, 1595-1608.
Roman J, Palumbi SR (2003) Whales before whaling in the North Atlantic. Science 301, 508-510. Rosenbaum HC, Pomilla C, Mendez M, et al. (2009) Population Structure of Humpback Whales
from Their Breeding Grounds in the South Atlantic and Indian Oceans. Plos One 4.
Rosenberg E, Zilber-Rosenberg I (2011) Symbiosis and Development: The Hologenome Concept. Birth Defects Research Part C-Embryo Today-Reviews 93, 56-66.
Rousset F (2008) GENEPOP ' 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8, 103-106.
Rundle HD, Nosil P (2005) Ecological speciation. Ecology Letters 8, 336-352.
Rundle HD, Schluter D (2004) Natural selection and ecological speciation in sticklebacks. In: Adaptive Speciation (eds. Dieckmann U, Doebeli M, Metz JAJ, Tautz D), pp. 192–209. Cambridge University Press, Cambridge.
Ryan C, Wenzel FW, López Suárez P, Berrow SD (2014) An abundance estimate for humpback whales Megaptera novaeangliae breeding ground Boa Vista, Cape Verde Islands. Zoologica Caboverdiana 5, 20-28.
Sanders JG, Powell S, Kronauer DJC, et al. (2014) Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes. Molecular Ecology 23, 1268-1283.
Savolainen O, Lascoux M, Merila J (2013) Ecological genomics of local adaptation. Nature Reviews Genetics 14, 807-820.
Schluter D (2001) Ecology and the origin of species. Trends Ecol Evol 16, 372-380.
Schluter D (2009) Evidence for Ecological Speciation and Its Alternative. Science 323, 737-741. Schluter D, Conte GL (2009) Genetics and ecological speciation. Proceedings of the National
Academy of Sciences of the United States of America 106, 9955-9962.
Semrau J, Ortega Gras JJ (2013) Fisheries in Denmark. European Parliament, Policy Department B: Structural and Cohesion Policies.
Sergio F, Caro T, Brown D, et al. (2008) Top Predators as Conservation Tools: Ecological
Rationale, Assumptions, and Efficacy. Annual Review of Ecology Evolution and Systematics 39, 1-19.
Shafer ABA, Wolf JBW, Alves PC, et al. (2015) Genomics and the challenging translation into conservation practice. Trends Ecol Evol 30, 78-87.
Shannon CE (1948) A Mathematical Theory of Communication University of Illinois Press, Urbana. Sigsgaard EE, Nielsen IB, Bach SS, et al. (2016) Population characteristics of a large whale shark
aggregation inferred from seawater environmental DNA. Nature Ecology & Evolution 1, 0004.
Sigurjónsson S (1988) Operational factors of the Icelandic large whale fishery. Rep Int Whal Comm 38, 327-333.
Simon M, Stafford KM, Beedholm K, Lee CM, Madsen PT (2010) Singing behavior of fin whales in the Davis Strait with implications for mating, migration and foraging. Journal of the Acoustical Society of America 128, 3200-3210.
Skovrind M, Olsen MT, Vieira FG, et al. (2016) Genomic population structure of freshwater-resident and anadromous ide (Leuciscus idus) in north-western Europe. Ecol Evol. Slatkin M (1976) The rate of spread of an advantageous allele in a subdivided population. In:
Population Genetics and Ecology (eds. Karlin S, Nevo E), pp. 767 - 780. Academic Press NY, New York.
Slatkin M (1985) Gene flow in natural populations. Annual Review of Ecology and Systematics 16, 393-430.
Smith TD, Reeves RR (2003) Estimating American 19(th) century catches of humpback whales in the West Indies and Cape Verde Islands. Caribbean Journal of Science 39, 286-297.
Smith TD, Reeves RR (2010) Historical Catches of Humpback Whales, Megaptera novaeangliae, in the North Atlantic Ocean: Estimates of Landings and Removals. Marine Fisheries Review 72, 1 - 43.
Sparholt H (1990) An estimate of the total biomass of fish in the North Sea. Journal Du Conseil 46, 200-210.
Stevick PT, Allen J, Clapham PJ, et al. (2003) North Atlantic humpback whale abundance and rate of increase four decades after protection from whaling. Marine Ecology Progress Series 258, 263-273.
Stevick PT, Neves MC, Johansen F, et al. (2011) A quarter of a world away: female humpback whale moves 10 000 km between breeding areas. Biology Letters 7, 299-302.
Stokesbury MJW, Harvey-Clark C, Gallant J, Block BA, Myers RA (2005) Movement and environmental preferences of Greenland sharks (Somniosus microcephalus) electronically tagged in the St. Lawrence Estuary, Canada. Marine Biology 148, 159-165.
Stone GS, Florezgonzalez L, Katona S (1990) Whale migration record. Nature 346, 705-705. Streelman JT, Alfaro M, Westneat MW, Bellwood DR, Karl SA (2002) Evolutionary history of the
parrotfishes: Biogeography, ecomorphology, and comparative diversity. Evolution 56, 961-971.
Sullam KE, Rubin BER, Dalton CM, et al. (2015) Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies. Isme Journal 9, 1508-1522.
Sumaila UR, Huang L (2012) Managing Bluefin Tuna in the Mediterranean Sea. Marine Policy 36, 502-511.
Syedang H, Andre C, Jonsson P, Elfman M, Limburg KE (2010) Migratory behaviour and otolith chemistry suggest fine-scale sub-population structure within a genetically homogenous Atlantic Cod population. Environmental Biology of Fishes 89, 383-397.
Szefer P, Szefer K, Glasby GP, Pempkowiak J, Kaliszan R (1996) Heavy-metal pollution in surficial sediments from the Southern Baltic Sea off Poland. Journal of Environmental Science and Health Part a-Toxic/Hazardous Substances & Environmental Engineering 31, 2723-2754.
Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
Tavare S, Balding DJ, Griffiths RC, Donnelly P (1997) Inferring coalescence times from DNA sequence data. Genetics 145, 505-518.
Taylor BL, Chivers SJ, Larese J, Perrin WF (2007) Generation length and percent mature estimates for IUCN assessments of cetaceans. Southwest Fisheries Science Centre, National Marine Fisheries Service.
Taylor BL, Wade PR, De Master DP, Barlow J (2000) Incorporating uncertainty into management models for marine mammals. Conservation Biology 14, 1243-1252.
Teilmann J, Carstensen J, Dietz R, Clermont Edrén SM (2004) Effect on seals at Rødsand seal sanctuary from the construction of Nysted Offshore Wind Farm based on aerial surveys. National Environmental Research Institute, Denmark.
Teilmann J, Dietz T, Clermont Edrén SM, Damsgaard Henriksen O, Carstensen J (2003) Aerial surveys of seals at Rødsand seal sanctuary and adjacent haul-out sites. In: Research Notes from NERI, p. 28. National Environmental Research Institute, Denmark.
Thiel R, Knebelsberger T (2016) How reliably can northeast Atlantic sand lances of the genera Ammodytes and Hyperoplus be distinguished? A comparative application of morphological and molecular methods. ZooKeys 617, 139-164.
Thomas E, Booth L, Maslin M, Shackleton NJ (1995) Northeastern Atlantic benthic foraminifera during the last 45,000 years: Changes in productivity seen from the bottom up.
Paleoceanography 10, 545 - 562.
Tremaroli V, Backhed F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 489, 242-249.
Trimble HC, Keeler CE (1938) The inheritance of high uric acis excretion in dogs. Journal of Heredity 29, 281-289.
Turner GF, Burrows MT (1995) A model od sympatric speciation by sexual selection. Proceedings of the Royal Society B-Biological Sciences 260, 287-292.
Valenzuela-Quinonez F (2016) How fisheries management can benefit from genomics? Brief Funct Genomics 15, 352-357.
Valsecchi E, Amos W (1996) Microsatellite markers for the study of cetacean populations. Molecular Ecology 5, 151-156.
Vatanen T, Kostic Aleksandar D, d’Hennezel E, et al. (2016) Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell 165, 842-853.
Via S (2001) Sympatric speciation in animals: the ugly duckling grows up. Trends Ecol Evol 16, 381-390.
Vilas R, Vandamme SG, Vera M, et al. (2015) A genome scan for candidate genes involved in the adaptation of turbot (Scophthalmus maximus). Marine Genomics 23, 77-86.
Walker WA, Center SF (1981) Geographical Variation in Morphology and Biology of Bottlenose Dolphins (Tursiops) in the Eastern North Pacific National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southwest Fisheries Center.
Waples RS (1998) Separating the wheat from the chaff: Patterns of genetic differentiation in high gene flow species. Journal of Heredity 89, 438-450.
Waples RS (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics 7, 167-184.
Waples RS, Do C (2010) Linkage disequilibrium estimates of contemporary N-e using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary Applications 3, 244-262.
Waples RS, Gaggiotti O (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15, 1419-1439.
Warner T (2011) En multidiciplinær undersøgelse af fire sameksisterende tobisarter (Ammodytes tobianus, Ammodytes marinus, Hyperoplus lanceolatus og Gymnammodytes
semisquamatus) ved Horns Rev i Nordseøen, University of Copenhagen.
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38, 1358-1370.
Wenzel FW, Allen J, Berrow S, et al. (2009) Current Knowledge on the Distribution and Relative Abundance of Humpback Whales (Megaptera novaeangliae) off the Cape Verde Islands, Eastern North Atlantic. Aquatic Mammals 35, 502-510.
Westfall PH, Young SS (1993) Resampling-based multiple testing John Wiley & Sons, New York. Whitlock MC, McCauley DE (1999) Indirect measures of gene flow and migration: F-ST not equal
1/(4Nm+1). Heredity (Edinb) 82, 117-125.
Wiecaszek B, Krzykawski S, Antoszek A (2007) Meristic and morphometric characters of small sandeel, Ammodytes tonianus L. (Actinopterygii: Ammodytidae), from the Gulf of Gdansk, Baltic Sea. Acta Ichthyologica et Piscatoria 37, 37-45.
Wilberg MJ, Dreher BP (2004) GENECAP: a program for analysis of multilocus genotype data for non-invasive sampling and capture-recapture population estimation. Molecular Ecology Notes 4, 783-785.
Wilcoxon F (1945) Individual Comparisons by Ranking Methods. Biometrics Bulletin 1, 80-83. Wright S (1931) Evolution in Mendelian populations. Genetics 16, 97-159.
Wright S (1951) The genetical structure of natural populations. Annals of Eugenics 15, 323-354. Yeates DK, Zwick A, Mikheyev AS (2016) Museums are biobanks: unlocking the genetic potential
of the three billion specimens in the world's biological collections. Current Opinion in Insect Science 18, 83-88.
Zeller D, Rossing P, Harper S, et al. (2011) The Baltic Sea: Estimates of total fisheries removals 1950-2007. Fisheries Research 108, 356-363.
