Molecular phylogenetics reveals a pattern of biome conservatism in New World anchovies (family Engraulidae)

Journal of Evolutionary Biology

Volumn 25, Issue 4, 2012, Pages 701-715

  Bloom, D D ^a   Lovejoy, N R ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Anchovies; Biogeography; Freshwater; Habitat transitions; Macroevolution; Marine; Neotropics; Phylogeny; South America

Indexed keywords

AQUATIC ORGANISM; BIOLOGICAL INVASION; BIOME; CLADISTICS; CLUPEOID; COMMERCIAL SPECIES; FRESHWATER ENVIRONMENT; HABITAT TYPE; MACROECOLOGY; MARINE ENVIRONMENT; NEOTROPICAL REGION; RECONSTRUCTION; ZOOGEOGRAPHY;

ANIMAL; ARTICLE; BIOLOGY; CLASSIFICATION; FISH; GENETICS; PHYLOGEOGRAPHY;

ANIMALS; FISHES; HYDROBIOLOGY; PHYLOGEOGRAPHY;

SOUTH AMERICA;

ENGRAULIDAE; PISCES;

EID: 84858343487     PISSN: 1010061X     EISSN: 14209101     Source Type: Journal    
DOI: 10.1111/j.1420-9101.2012.02464.x     Document Type: Article

References (100)

1. Anderson, J.A. & Sues, H.D. 2007. Major Transitions in Vertebrate Evolution. Indiana University Press, Bloomington, IN.
2. Augusto, A., Pinheiro, A.S., Greene, L.J., Laure, H.J. & McNamara, J.C. 2009. Evolutionary transition to freshwater by ancestral marine palaemonids: evidence from osmoregulation in a tide pool shrimp. Aquatic Biology 7: 113-122.
3. Betancur-R, R. 2010. Molecular phylogenetics supports multiple evolutionary transitions from marine to freshwater habitats in ariid catfishes. Mol. Phylogenet. Evol. 55: 249-258.
4. Bloom, D.D. & Lovejoy, N.R. 2011. The biogeography of marine incursions in South America. In: Historical Biogeography of Neotropical Freshwater Fishes (J.S. Albert & R.E. Reis, eds), pp. 137-144. University of California Press, Berkeley.
5. Bornbusch, A.H. 1988. Gill raker morphologies of anchovies (Teleostei, Engraulidae) from the Rio Orinoco, Venezuela. Copeia 1: 174-182.
6. Brandley, M.C., Schmitz, A. & Reeder, T.W. 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54: 373-390.
7. Brown, J.M. & Lemmon, A.R. 2007. The importance of data partitioning and the utility of Bayes Factors in Bayesian phylogenetics. Syst. Biol. 56: 643-655.
8. Bruen, T., Philippe, H. & Bryant, D. 2006. A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665-2681.
9. Cassens, I., Vicario, S., Wadde, V.G., Balchowsky, H., Balle, D.V., Wang, D. et al. 2000. Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages. Proc. Natl Acad. Sci. USA 97: 11343-11347.
10. Crisp, M. 2006. Biome assembly: what we know and what we need to know. J. Biogeogr. 33: 1332-1333.
11. Crisp, M.D., Arroyo, M.T.K., Cook, L.G., Gandolfo, M.A., Jordan, G.J., McGlone, M.S. et al. 2009. Phylogenetic biome conservatism on a global scale. Nature 458: 754-U790.
12. Daeschler, E.B., Shubin, N.H. & Jenkins, F.A. 2006. A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature 440: 757-763.
13. Daniels, S.R., Cumberlidge, N., Perez-Losada, M., Marijnissen, S.A.E. & Crandall, K.A. 2006. Evolution of Afrotropical freshwater crab lineages obscured by morphological convergence. Mol. Phylogenet. Evol. 40: 227-235.
14. Di Dario, F. 2002. Evidence supporting a sister-group relationship between Clupeoidea and Engrauloidea (Clupeomorpha). Copeia 2002: 496-503.
15. Di Dario, F. 2009. Chirocentrids as engrauloids: evidence from suspensorium, branchial arches, and infraorbital bones (Clupeomorpha, Teleostei). Zool. J. Linn. Soc. 156: 363-383.
16. Donoghue, M.J. & Moore, B.R. 2002. Toward an integrative historical biogeography. Integr. Comp. Biol. 43: 261-270.
17. Gingerich, P.D., Haq, Mu., Zalmout, I.S., Khan, I.H. & Malkani, M.S. 2001. Origin of whales from early artiodactyls: hands and feet of Eocene Protocetidae from Pakistan. Science 293: 2239-2242.
18. Grande, L. 1985. Recent and fossil clupeomorph fishes with materials for revision of the subgroups of clupeoids. Bull. Am. Mus. Nat. His. 181: 231-372.
19. Grande, L. & Nelson, G. 1985. Interrelationships of fossil and recent anchovies (Teleostei: Engrauloidea) and description of a new species from the Miocene of Cyprus. Am. Mus. Novit. 2826: 1-16.
20. Grant, W.S. & Bowen, B.W. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J. Hered. 89: 415-426.
21. Grant, W.S. & Bowen, B.W. 2006. Living in a tilted world: climate change and geography limit speciation in Old World anchovies (Engraulis; Engraulidae). Biol. J. Linn. Soc. 88: 673-689.
22. Grant, W.S., Leslie, R.W. & Bowen, B.W. 2005. Molecular genetic assessment of bipolarity in the anchovy genus Engraulis. J. Fish Biol. 67: 1242-1265.
23. Grant, W.S., Lecomte, F. & Bowen, B.W. 2010. Biogeographical contingency and the evolution of tropical anchovies (genus Cetengraulis) from temperate anchovies (genus Engraulis). J. Biogeogr. 37: 1352-1362.
24. Gray, J. 1988. Evolution of the freshwater ecosystem: the fossil record. Palaeogeogr. Palaeoclimatol. Palaeoecol. 62: 1-214.
25. Griffith, R.W. 1987. Fresh-water or marine origin of the vertebrates. Comp. Biochem. Physiol. A Comp. Physiol. 87: 523-531.
26. Halstead, L.B. 1985. The vertebrate invasion of fresh water. Philos. Trans. R. Soc. B-Biol. Sci. 309: 243-258.
27. Hamilton, H., Caballero, S., Collins, A.G. & Brownell, R.L. 2001. Evolution of river dolphins. Proc. R. Soc. Lond. B Biol. Sci. 268: 549-556.
28. Harvey, P.H. & Pagel, M.D. 1991. The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford, UK.
29. Heger, T.J., Mitchell, E.A.D., Todorov, M., Golemansky, V., Lara, E., Leander, B.S. et al. 2010. Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent. Mol. Phylogenet. Evol. 55: 113-122.
30. Hendry, A.P., Lohmann, L.G., Conti, E., Cracraft, J., Crandall, K.A., Faith, D.P. et al. 2010. Evolutionary biology in biodiversity science, conservation, and policy: a call to action. Evolution 64: 1517-1528.
31. Hildebrand, S.F. 1943. A review of the American anchovies (family Engraulidae). Bull. Bingham oceanogr. Colln 8: 1-165.
32. Hoorn, C., Wesselingh, F.P., ter Steege, H., Bermudez, M.A., Mora, A., Sevink, J. et al. 2010. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330: 927-931.
33. Hou, Z., Sket, B., Fiser, C. & Li, S. 2011. Eocene habitat shift from saline to freshwater promoted Tethyan amphipod diversification. Proc. Natl Acad. Sci. USA 108: 14533-14538.
34. Kawahara, R., Miya, M., Mabuchi, K., Near, T.J. & Nishida, M. 2009. Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes. Mol. Phylogenet. Evol. 50: 401-404.
35. Lavoue, S., Miya, M., Saitoh, K., Ishiguro, N.B. & Nishida, M. 2007. Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences. Mol. Phylogenet. Evol. 43: 1096-1105.
36. Lavoue, S., Miya, M. & Nishida, M. 2009. Mitochondrial phylogenomics of anchovies (family Engraulidae) and recurrent origins of pronounced miniaturization in the order Clupeiformes. Mol. Phylogenet. Evol. 56: 480-485.
37. Lee, C.E. & Bell, M.A. 1999. Causes and consequences of recent freshwater invasions by saltwater animals. Trends Ecol. Evol. 14: 284-288.
38. Li, C.H. & Orti, G. 2007. Molecular phylogeny of clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences. Mol. Phylogenet. Evol. 44: 386-398.
39. Logares, R., Shalchian-Tabrizi, K., Boltovskoy, A. & Rengefors, K. 2007. Extensive dinoflagellate phylogenies indicate infrequent marine-freshwater transitions. Mol. Phylogenet. Evol. 45: 887-903.
40. Logares, R., Brate, J., Bertilsson, S., Clasen, J.L., Shalchian-Tabrizi, K. & Rengefors, K. 2009. Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol. 17: 414-422.
41. Logares, R., Brate, J., Heinrich, F., Shalchian-Tabrizi, K. & Bertilsson, S. 2010. Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). Mol. Biol. Evol. 27: 347-357.
42. Lopez, J.A., Chen, W.J. & Orti, G. 2004. Esociform phylogeny. Copeia 44: 9-464.
43. Losos, J.B., Leal, M., Glor, R.E., de Queiroz, K., Hertz, P.E., Schettino, L.R. et al. 2003. Niche lability in the evolution of a Caribbean lizard community. Nature 424: 542-545.
44. Lovejoy, N.R. 1996. Systematics of myliobatoid elasmobranchs: with emphasis on the phylogeny and historical biogeography of neotropical freshwater stingrays (Potamotrygonidae:Rajiformes). Zool. J. Linn. Soc. 117: 207-257.
45. Lovejoy, N.R. & Collette, B.B. 2001. Phylogenetic relationships of new world needlefishes (Teleostei: Belonidae) and the biogeography of transitions between marine and freshwater habitats. Copeia 32: 4-338.
46. Lovejoy, N.R., Bermingham, E. & Martin, A.P. 1998. Marine incursion into South America. Nature 396: 421-422.
47. Lovejoy, N.R., Albert, J.S. & Crampton, W.G.R. 2006. Miocene marine incursions and marine/freshwater transitions: evidence from Neotropical fishes. J. S. Am. Earth Sci. 21: 5-13.
48. Maddison, D.R. & Maddison, W.P. 2001. MacClade 4: analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland, MA.
49. Maddison, W.P. & Maddison, D.R. 2009. Mesquite: a modular system for evolutionary analysis.
50. Mank, J.E. & Avise, J.C. 2006. Supertree analyses of the roles of viviparity and habitat in the evolution of atherinomorph fishes. J. Evol. Biol. 19: 734-740.
51. Maynard-Smith, J. & Szathmary, E. 1997. The Major Transitions in Evolution. Oxford University Press, New York, NY.
52. Myers, G.S. 1949. Salt-tolerance of fresh-water fish groups in relation to zoogeographical problems. Bijdragen tot de Dierkunde 28: 315-364.
53. Nelson, G. 1970. The hyobranchial apparatus of teleostean fishes of the families Engraulidae and Chirocentridae. Am. Mus. Novit. 2410: 1-30.
54. Nelson, G. 1983. Anchoa-argentivittata, with notes on other Eastern Pacific anchovies and the Indo-Pacific genus Encrasicholina. Copeia 1983: 48-54.
55. Nelson, G. 1984. Identity of the anchovy Hildebrandichthys-setiger with notes on relationships and biogeography of the genera Engraulis and Cetengraulis. Copeia 1984: 422-427.
56. Nelson, G. 1986. Identity of the anchovy Engraulis-clarki with notes on the species-groups of Anchoa. Copeia 1986: 891-902.
57. Niedzwiedzki, G., Szrek, P., Narkiewicz, K., Narkiewicz, M. & Ahlberg, P.E. 2010. Tetrapod trackways from the early Middle Devonian period of Poland. Nature 463: 43-48.
58. Nielsen, R. & Yang, Z.H. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
59. Nylander, J.A.A., Ronquist, F., Huelsenbeck, J.P. & Nieves-Aldrey, J.L. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53: 47-67.
60. Nylander, J.A.A., Wilgenbusch, J.C., Warren, D.L. & Swofford, D.L. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24: 581-583.
61. Pagel, M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol. 48: 612-622.
62. Parry, G. 1966. Osmotic adaptation in fishes. Biol. Rev. Camb. Philos. Soc. 41: 392-444.
63. Pearse, A.S. 1927. The migration of animals from the ocean into freshwater and land habitats. Am. Nat. 61: 466-476.
64. Peng, Y.B. & Zhao, Z.R. 1988. A new genus and new species of Chinese anchovies. Journal of Fisheries of China 12: 355-358.
65. Ramon, M.L. & Knope, M.L. 2008. Molecular support for marine sculpin (Cottidae; Oligocottinae) diversification during the transition from the subtidal to intertidal habitat in the Northeastern Pacific Ocean. Mol. Phylogenet. Evol. 46: 475-483.
66. Rheindt, F.E., Christidis, L. & Norman, J.A. 2008. Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes. BMC Evol. Biol. 8: 1193.
67. Ribera, I. & Vogler, A.P. 2000. Habitat type as a determinant of species range sizes: the example of lotic-lentic differences in aquatic Coleoptera. Biol. J. Linn. Soc. 71: 33-52.
68. Ribera, I., Barraclough, T.G. & Vogler, A.P. 2001. The effect of habitat type on speciation rates and range movements in aquatic beetles: inferences from species-level phylogenies. Mol. Ecol. 10: 721-735.
69. Roberts, T.R. 1984. Amazonsprattus scintilla, a new genus and species from the Rio Nego, Brazil, the smallest known clupeomorph fish. Proc. Calif. Acad. Sci. 43: 317-321.
70. Robertson, J.D. 1957. The habitat of the early vertebrates. Biol. Rev. Camb. Philos. Soc. 32: 156-187.
71. Romer, A.S. & Grove, B.H. 1935. Environment of early vertebrates. Am. Midl. Nat. 16: 805-856.
72. Ronquist, F. & Huelsenbeck, J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
73. Schluter, D. 2000. The Ecology of Adaptive Radiations. Oxford University Press, Oxford.
74. Schluter, D., Price, T., Mooers, A.O. & Ludwig, D. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51: 1699-1711.
75. Shubin, N.H., Daeschler, E.B. & Jenkins, F.A. 2006. The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature 440: 764-771.
76. Stahl, D.A., Key, R., Flesher, B. & Smit, J. 1992. The phylogeny of marine and freshwater caulobacters reflects their habitat. J. Bacteriol. 174: 2193-2198.
77. Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
78. Sumida, S.S. & Martin, K.L.M., eds 1997. Amniote Origins: Completing the Transition to Land. Academic Press, San Diego, CA.
79. Swofford, D.L. 2002. PAUP* Phylogeny Analysis Using Parsimony (*and Other Methods), Version 40b10. Sinauer Association, Inc, Sunderland, MA.
80. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. 1997. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
81. Vermeij, G.J. 2005. Invasion as expectation: a historical fact of life. In: Species Invasions: Insights into Ecology, Evolution, and Biogeography (D.F. Sax, J.J. Stachowicz & S.D. Gaines, eds), pp. 315-339. Sinauer Associates, Sunderland, MA.
82. Vermeij, G.J. 2006. Historical contingency and the purported uniqueness of evolutionary innovations. Proc. Natl Acad. Sci. USA 103: 1804-1809.
83. Vermeij, G.J. & Dudley, R. 2000. Why are there so few evolutionary transitions between aquatic and terrestrial ecosystems? Biol. J. Linn. Soc. 70: 541-554.
84. Vermeij, G.J. & Wesselingh, F.P. 2002. Neogastropod molluscs from the Miocene of western Amazonia, with comments on marine to freshwater transitions in molluscs. J. Paleontol. 76: 265-270.
85. Weitzman, S.H. & Vari, R.P. 1988. Miniaturization in South American freshwater fishes; an overview and discussion. Proc. Biol. Soc. Wash. 101: 444-465.
86. Whitehead, P.J. 1973. The clupeoid fishes of the Guianas. Bull. Brit. Mus. Nat. His. 5: 1-227.
87. Whitehead, P.J.P. 1985. King Herring: his place amongst the clupeoids. Can. J. Fish. Aquat. Sci. 42: 3-20.
88. Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (Fundulus Sp.). Evolution 64: 2070-2085.
89. Whitehead, P.J.P., Nelson, G.J. & Wongratana, T. 1988. FAO Species Catalogue, Vol. 7. Clupeoid Fishes of the World (Suborder Clupeoidei). UNDP FAO, Rome.
90. Wiens, J.J. & Donoghue, M.J. 2004. Historical biogeography, ecology and species richness. Trends Ecol. Evol. 19: 639-644.
91. Wiens, J.J. & Graham, C.H. 2005. Niche conservatism: integrating evolution, ecology, and conservation biology. Ann. Rev. Ecol. Evol. Syst. 36: 519-539.
92. Wiens, J.J., Brandley, M.C. & Reeder, T.W. 2006. Why does a trait evolve multiple times within a clade? Repeated evolution of snakelike body form in squamate reptiles. Evolution 60: 123-141.
93. Wiens, J.J., Ackerly, D.D., Allen, A.P., Anacker, B.L., Buckley, L.B., Cornell, H.V. et al. 2010. Niche conservatism as an emerging principle in ecology and conservation biology. Ecol. Lett. 13: 1310-1324.
94. Wilson, A.B., Teugels, G.G. & Meyer, A. 2008. Marine incursion: the freshwater herring of Lake Tanganyika are the product of a marine invasion into West Africa. PLoS ONE 3: e1979.
95. Winemiller, K.O. & Leslie, M.A. 1992. Fish assemblages across a complex, tropical freshwater/marine ecotone. Environ. Biol. Fish 34: 29-50.
96. Yamanoue, Y., Miya, M., Doi, H., Mabuchi, K., Sakai, H. & Nishida, M. 2011. Multiple invasions into freshwater by pufferfishes (teleostei: tetraodontidae): a mitogenomic perspective. PLoS ONE 6: e17410.
97. Yang, Z.H. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586-1591.
98. Yang, Z.H., Nielsen, R., Goldman, N. & Pedersen, A.M.K. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.
99. Yoder, J.B., Clancey, E., Roches, S.D., Eastman, J.M., Gentry, L., Godsoe, W. et al. 2010. Ecological opportunity and the origin of adaptive radiations. J. Evol. Biol. 23: 1581-1596.
100. Yokoyama, R. & Goto, A. 2005. Evolutionary history of freshwater sculpins, genus Cottus (Teleostei: Cottidae) and related taxa, as inferred from mitochondrial DNA phylogeny. Mol. Phylogenet. Evol. 36: 654-668.