References
Akolkar KS, Asaduzzaman M, Kinoshita S, Asakawa S, Watabe S (2016)
Characterization of Pax3 and Pax7 genes and their expression patterns
during different development and growth stages of Japanese pufferfishTakifugu rubripes . Gene, 575 , 21-28.
Araújo MB, Anderson RP, Barbosa AM, et al . (2019). Standards for
distribution models in biodiversity assessments. Science Advances,5 , eaat4858.
Ashburner MM, Ball CAC, Blake JA, et al. (2000) Gene ontology:
tool for the unification of biology. The Gene Ontology Consortium.
Nature Genetics, 25 , 25-29.
Bierne N, Bonhomme F, David P (2003) Habitat preference and the
marine-speciation paradox. Proc Biol Sci, 270 , 1399-1406.
Blonder B, Lamanna C, Violle C, Enquist BJ (2014) The n-dimensional
hypervolume. Global Ecology and Biogeography, 23 , 595-609.
Blonder B, Morrow CB, Maitner B, Harris DJ (2018) New approaches for
delineating n-dimensional hypervolumes. Methods in Ecology and
Evolution, 9 , 305-319.
Bolnick DI, Stutz WE (2017) Frequency dependence limits divergent
evolution by favouring rare immigrants over residents. Nature,546 , 285-288.
Carvalho JC, Cardoso P (2018) Decomposing the causes for niche
differentiation between species using hypervolumes. bioRxiv.
Chen Y, Chen Y, He D, Sui X (2006) Current Status and Perspective of
Biogeography Study in Taiwan Strait, China. Chinese Journal of Zoology,41 , 118-122.
Chen Z, Zhang Y, Han ZQ, Song N, Gao TX (2017) Morphological characters
and DNA barcoding of Syngnathus schlegeli in the coastal waters
of China. Chinese Journal of Oceanology & Limnology, 1-11.
Cunha RL, Tenorio MJ, Afonso C, Castilho R, Zardoya R (2008) Replaying
the tape: Recurring biogeographical patterns in Cape Verde Conus after
12 million years. Molecular Ecology, 17 , 885-901.
Devictor V, Clavel J, Julliard R, et al. (2010) Defining and
measuring ecological specialization. Journal of Applied Ecology,47 , 15-25.
Dong YW, Wang HS, Han GD, et al. (2012) The impact of Yangtze
River discharge, ocean currents and historical events on the
biogeographic pattern of Cellana toreuma along the China coast. PLoS
ONE, 7 , e36178.
Dormann CF, Elith J, Bacher S, et al. (2013) Collinearity: a
review of methods to deal with it and a simulation study evaluating
their performance. Ecography, 36 , 27-46.
Ellegren H, Sheldon BC (2008) Genetic basis of fitness differences in
natural populations. Nature, 452 , 169-175.
Excofer L, Laval G, Schneider S (2005) Arlequin (version 3.0): an
integrated software package for population genetics data analysis.
Evolutionary Bioinformatics, 1 , 47–50.
Fox LR, Morrow PA (1981) Specialization: Species Property or Local
Phenomenon? Science, 211 , 887-893.
Garant D, Kruuk LE, Wilkin TA, Mccleery RH, Sheldon BC (2005) Evolution
driven by differential dispersal within a wild bird population. Nature,433 , 60-65.
GBIF.org (13 December 2019) GBIF Occurrence Download
https://doi.org/10.15468/dl.ec6hrx
Gillespie RG, Bennett GM, De Meester L, et al. (2020) Comparing
Adaptive Radiations Across Space, Time, and Taxa. Journal of Heredity,111 , 1-20.
Hendry AP, Wenburg JK, Bentzen P, Volk EC, Quinn TP (2000) Rapid
evolution of reproductive isolation in the wild: evidence from
introduced salmon. Science, 290 , 516-519.
Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature,405 , 907-913.
Hewitt GM (2004) Genetic Consequences of Climatic Oscillations in the
Quaternary. Philosophical Transactions of the Royal Society of London
Series B: Biological Sciences, 359 , 183-195.
Kawecki T, Ebert D (2004) Conceptual issues in local adaptation. Ecology
Letters, 7 , 1225-1241.
Landis JR, Koch GG (1977) The measurement of observer agreement for
categorical data. Biometrics, 33 , 159-174.
Li H (2011) A statistical framework for SNP calling, mutation discovery,
association mapping and population genetical parameter estimation from
sequencing data. Bioinformatics, 27 , 2987-2993.
Li H, Durbin R (2009) Fast and accurate short read alignment with
Burrows–Wheeler transform Oxford University Press.
Liu J, Gao T, Shifang WU, Zhang Y (2007) Pleistocene isolation in the
Northwestern Pacific marginal seas and limited dispersal in a marine
fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Molecular
Ecology, 16 , 275-288.
Loosli F, Staub W, Finger-Baier KC, et al. (2003) Loss of eyes in
zebrafish caused by mutation of chokh / rx3 . EMBO Journal,4 , 894–899.
Loxdale HD, Gugs L, Harvey JA (2011) The evolutionary improbability of
‘generalism’ in nature, with special reference to insects. Biological
Journal of the Linnean Society, 103 , 1-18.
Mammola S (2019) Assessing similarity of n -dimensional
hypervolumes: Which metric to use? Journal of Biogeography, 46 ,
1–12.
Mammola S, Arnedo MA, Fišer C, et al. (2020) Environmental
filtering and convergent evolution determine the ecological
specialization of subterranean spiders. Functional Ecology, 34 ,
1064-1077.
Mammola S, Cardoso P (2020) Functional diversity metrics using kernel
density n-dimensional hypervolumes. Methods in Ecology and Evolution,
early view.
Ni G, Li Q, Kong L, Yu H (2014) Comparative phylogeography in marginal
seas of the northwestern Pacific. Molecular Ecology, 23 ,
534-548.
Ni G, Li Q, Kong L, Zheng X, Crandall KA (2012) Phylogeography of
Bivalve Cyclina sinensis : Testing the Historical Glaciations and
Changjiang River Outflow Hypotheses in Northwestern Pacific. PLoS ONE,7 , e49487.
Ogata H, Goto S, Sato K, et al. (2000) KEGG: Kyoto Encyclopedia
of Genes and Genomes. Nucleic Acids Research, 27 , 29-34.
Allouche O, Tsoar A, Kadmon R (2006) Assessing the accuracy of species
distribution models: prevalence, kappa and the true skill statistic
(TSS). Journal of Applied Ecology, 43 , 1223-1232.
Palumbi SR (1994) Genetic Divergence, Reproductive Isolation, and Marine
Speciation. Annual Review of Ecology & Systematics, 25 ,
547-572.
Purcell S, Neale B, Toddbrown 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.
Rocha LA, Bass AL, Robertson DR, Bowen BW (2002) Adult habitat
preferences, larval dispersal, and the comparative phylogeography of
three Atlantic surgeonfishes (Teleostei: Acanthuridae). Molecular
Ecology, 11 , 243-251.
Rocha LA, Robertson DR, Roman J, Bowen BW (2005) Ecological speciation
in tropical reef fishes. Proc Biol Sci, 272 , 573-579.
Sabeti PC, Schaffner SF, Fry B, et al. (2006) Positive natural
selection in the human lineage. Science, 312 , 1614-1620.
Sbrocco EJ (2014) Paleo-MARSPEC: gridded ocean climate layers for the
mid-Holocene and Last Glacial Maximum. Ecology, 95 , 1710.
Sbrocco EJ, Barber PH (2013) MARSPEC: ocean climate layers for marine
spatial ecology: Ecological Archives E094-086.
Shipley LA, Forbey JS, Moore BD (2009) Revisiting the dietary niche:
When is a mammalian herbivore a specialist? Integrative & Comparative
Biology, 3.
Smith TB, Wayne RK, Girman DJ, Bruford MW (1997) A Role for Ecotones in
Generating Rainforest Biodiversity. Science, 276 , 1855-1857.
Swets JA (1988) Measuring the accuracy of diagnostic systems. Science,240 , 1285-1293.
Takahashi H, Takeshita N, Tanoue H, et al. (2015) Severely
depleted genetic diversity and population structure of a large predatory
marine fish (Lates japonicus ) endemic to Japan. Conservation
Genetics, 16 , 1155-1165.
Tamaki K, Honza E (1991) Global tectonics and formation of marginal
basins: Role of the Western Pacific. Translated World Seismology,14 , 224-230.
Tang H, Peng J, Wang P, Risch NJ (2005) Estimation of individual
admixture: Analytical and study design considerations. Genetic
Epidemiology, 28 , 289-301.
Thuiller W, Georges D, Engler R, Breiner F (2020) biomod2:
Ensemble Platform for Species Distribution Modeling. R package version
3.3-7.1. https://CRAN.R-project.org/package=biomod2
Thuiller W, Guéguen M, Renaud J, Karger DN (2019) Uncertainty in
ensembles of global biodiversity scenarios. Nature Communications,10 , 1-9.
Tobler M, Dewitt TJ, Schlupp I, et al. (2008) Toxic hydrogen
sulfide and dark caves: phenotypic and genetic divergence across two
abiotic environmental gradients in Poecilia mexicana . Evolution,62 , 2643-2659.
Todd Streelman J, Danley PD (2003) The stages of vertebrate evolutionary
radiation. Trends in Ecology & Evolution, 18 , 126-131.
Utter F, Seeb J (2010) A perspective on positive relationships between
genetic diversity and abundance in fishes. Molecular Ecology,19 , 4831–4833.
Vilella A, Severin JV, A, Heng L, Durbin R, Birney E (2009)
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees
in vertebrates. Genome Research, 19 , 327-335.
Vincent ACJ, Foster SJ, Koldewey HJ (2011) Conservation and management
of seahorses and other Syngnathidae. Journal of Fish Biology,78 , 1681-1724.
Wainwright PC, Bellwood DR, Westneat MW, Grubich JR, Hoey AS (2004) A
functional morphospace for the skull of labrid fishes: patterns of
diversity in a complex biomechanical system. Biological Journal of the
Linnean Society, 82 , 1-25.
Wainwright PC, McGee MD, Longo SJ, Hernandez LP (2015) Origins,
Innovations, and Diversification of Suction Feeding in Vertebrates.
Integrative and Comparative Biology, 55 , 134-145.
Wang MS, Li Y, Peng MS, et al. (2015) Genomic Analyses Reveal
Potential Independent Adaptation to High Altitude in Tibetan Chickens.
Molecular Biology & Evolution, 32 , 1880-1889.
Wang P (1999) Response of Western Pacific marginal seas to glacial
cycles: Paleoceanographic and sedimentological features. Marine Geology,156 , 5-39.
Wang PX, Sun XJ (1994) Last glacial maximum in China: comparison between
land and sea. Catena, 23 , 341-353.
Watanabe S, Watanabe Y (2001) Brooding season, sex ratio, and brood
pouch development in the seaweed pipefish, Syngnathus schlegeli ,
in Otsuchi Bay, Japan. Ichthyological Research, 48 , 155-160.
Wilson AB, Ahnesjo I, Vincent ACJ, Meyer A (2003) The dynamics of male
brooding, mating patterns, and sex roles in pipefishes and seahorses
(family Syngnathidae). Evolution, 57 , 1374-1386.
Wilson AB, Wegmann A, Ahnesjo I, Goncalves JMS (2020) The evolution of
ecological specialization across the range of a broadly distributed
marine species. Evolution, 74-3 , 629-643.
Xu J, Chan TY, Tsang LM, Chu KH (2009) Phylogeography of the mitten crab
Eriocheir sensu stricto in East Asia: Pleistocene isolation, population
expansion and secondary contact. Molecular Phylogenetics and Evolution,52 , 45-56.
Yang C, Wang L, Siva VS, et al. (2012) A novel cold-regulated
cold shock domain containing protein from scallop Chlamys farreriwith nucleic acid-binding activity. Plos One, 7 , e32012.
Yang J, Lee SH, Goddard ME, Visscher PM (2011) GCTA: A Tool for
Genome-wide Complex Trait Analysis. American Journal of Human Genetics,88 , 76-82.
Yu HX, Zhou YW (2001) Geomorphology and geological features of the
continental shelf in northern and western Taiwan, China. Science in
China (Series D), 31 , 486-495.
Yu M, Liu Y, Li J, et al. (2016) Eyes shut homolog is required
for maintaining the ciliary pocket and survival of photoreceptors in
zebrafish. Biology Open, 5 , 1662-1673.
Zardi GI, Nicastro KR, Costa JF, Serrão EA, Pearson GA (2013) Broad
scale agreement between intertidal habitats and adaptive traits on a
basis of contrasting population genetic structure. Estuarine Coastal &
Shelf Science, 131 , 140-148.
Zhang BD, Xue DX, Wang J, et al. (2016) Development and
preliminary evaluation of a genomewide single nucleotide polymorphisms
resource generated by RAD-seq for the small yellow croaker
(Larimichthys polyactis ). Mol Ecol Resour, 16 , 755-768.
Zhang YH, Qin G, Zhang HX, Wang X, Lin Q (2017) DNA barcoding reflects
the diversity and variety of brooding traits of fish species in the
family Syngnathidae along China’s coast. Fisheries Research,185 , 137-144.