Phylogeographic and conservation genetic analysis of the Black Caiman (Melanosuchus niger)

Journal of Experimental Zoology Part A: Ecological Genetics and Physiology

Volumn 309, Issue 10, 2008, Pages 600-613

  Vasconcelos, William Rangel ^a   Hrbek, Tomas ^a,b   Da Silveira, Ronis ^a   De Thoisy, Benoit ^c   Dos Santos Ruffeil, Luis Augusto Araújo ^d   Farias, Izeni Pires ^a  

^a FEDERAL UNIVERSITY OF AMAZONAS   (Brazil)

^b UNIVERSITY OF PUERTO RICO RIO PIEDRAS   (Puerto Rico)

^c Association Kwata   (French Guiana)

^d Fundação Universidade Estadual Vale do Acaraú ^*  (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B;

ALLIGATOR; ANIMAL; CLASSIFICATION; CONFERENCE PAPER; ENVIRONMENTAL PROTECTION; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

ALLIGATORS AND CROCODILES; ANIMALS; BASE SEQUENCE; CONSERVATION OF NATURAL RESOURCES; CYTOCHROMES B; GENETIC VARIATION; GEOGRAPHY; HAPLOTYPES; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT;

ANIMALIA; MELANOSUCHUS NIGER;

EID: 57749203338     PISSN: 19325223     EISSN: None     Source Type: Journal    
DOI: 10.1002/jez.452     Document Type: Conference Paper

References (63)

1. Aleixo A. 2006. Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae). Biol J Linn Soc 89:383-395.
2. Bates HW. 1864. The naturalist on the River Amazon. New York, NY: Dutton. 427p.
3. Cantanhede AM, da Silva VMF, Farias IP, Hrbek T, Lazzarini SM, Alves-Gomes JA. 2005. Phylogeography and population genetics of the endangered Amazonian manatee, Trichechus inunguis Natterer, 1883 (Mammalia, Sirenia). Mol Ecol 14:401-413.
4. Cockerham CC, Weir BS. 1993. Estimation of gene flow from F-statistics. Evolution 47:855-863.
5. da Silva VMF. 2004. Conservação de golfinhos da Amazônia: ameaças e perspectivas. In: Cintra R, editor. História Natural, Ecologia e Conservação de Algumas Espécies de Plantas e Animais da Amazônia. Manaus, AM, Brazil: EDUA/INPA/FAPEAM. p 313-320.
6. Da Silveira R. 2002. Conservação e manejo do jacaré-açu (Melanosuchus niger) na Amazônia Brasileira. In: Verdade LM, Larriera A, editors. Conservação e Manejo de Jacarés e Crocodilos da América Latina. Piracicaba, SP: C.N. Editoria. p 61-78.
7. Da Silveira R, Thorbjarnarson J. 1999. Conservation implications of commercial hunting of black and spectacled caiman in the Mamirauá sustainable development reserve, Brazil. Biol Conserv 88:103-109.
8. Da Silveira R, Viana JP. 2003. Amazonian crocodilians: a keystone species for ecology and management or simply bait? Croc Spec Group Newsl 22:16-17.
9. Da Silveira R, Magnusson WE, Campos Z. 1997. Monitoring the distribution, abundance and breeding areas of Caiman crocodilus crocodilus and Melanosuchus niger in the Anavilhanas Archipelago, Central Amazon, Brazil. J Herpetol 31:514-520.
10. de Thoisy B. 2004. French Guiana regional report. Croc Spec Group Newsl 24:4-5.
11. de Thoisy B, Hrbek T, Farias IP, Vasconcelos WR, Lavergne A. 2006. Genetic structure and population dynamics of black caiman (Melanosuchus niger). Biol Conserv 133:474-482.
12. Dever JA, Strauss RE, Rainwater TR, McMurry ST, Densmore III LD. 2002. Genetic diversity, population subdivision, and gene flow in Morelet's crocodile (Crocodylus moreletii) from Belize, Central America. Copeia 2002:1078-1091.
13. 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.
14. Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47-50.
15. Farias IP, Da Silveira R, de Thoisy B, Monjeló LAdS, Thorbjarnarson J, Hrbek T. 2004. Genetic diversity and population structure of Amazonian crocodilians. Anim Conserv 7:265-272.
16. Fetzner Jr JW, Crandall KA. 2003. Linear habitats and the nested clade analysis: an empirical evaluation of geographic versus river distances using an Ozark crayfish (Decapoda: Cambaridae). Evolution 57:2101-2118.
17. Fittkau EJ. 1970. Role of caimans in the nutrient regime of mouth-lakes of Amazon affluents. Biotropica 2:138-142.
18. Frankham R, Ballou JR, Briscoe DA. 2002. Introduction to conservation genetics. Cambridge, UK: Cambridge University Press. 617p.
19. Fu Y-X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915-925.
20. Garrigan D, Marsh PC, Dowling TE. 2002. Long-term effective population size of three endangered Colorado River fishes. Anim Conserv 5:95-102.
21. Glenn TC, Stanton JL, Lu A, Davis LM, Alvardo Bremer JR, Rhodes WE, Brisbin Jr IL, Sawyer RH. 2002. Low mitochondrial DNA variation among American alligators and a novel non-coding region in crocodilians. J Exp Zool (Mol Dev Evol) 294:312-324.
22. Goulding M, Smith NJH, Mahar DJ. 2000. Floods of fortune: ecology and economy along the Amazon. New York, NY: Columbia University Press. 184p.
23. Goulding M, Barthem RB, Ferreira EJG. 2003. The Smithsonian Atlas of the Amazon. Washington, DC: Smithsonian Institution Press. 256p.
24. Grant WAS, Bowen BW. 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.
25. Hall T. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
26. Herron JC. 1994. Body size, spatial distribution, and microhabitat use in the caimans, Melanosuchus niger and Caiman crocodilus, in a Peruvian lake. J Herpetol 28:508-513.
27. Hilton-Taylor C. 2000. 2000 IUCN red list of threatened species. Gland, Switzerland: IUCN.
28. Hrbek T, Farias IP, Crossa M, Sampaio I, Porto JIR, Meyer A. 2005. Population genetic analysis of Arapaima gigas, one of the largest freshwater fishes of the Amazon basin: implications for its conservation. Anim Conserv 8:297-308.
29. King FW, Burke RL. 1981. Crocodilian, tuatara and turtle species of the world. A taxonomic and geographic reference. Washington, DC: Association of Systematic Collections. 216p.
30. Li W-H. 1997. Molecular evolution. Sunderland, MA: Sinauer Associates. 487p.
31. Lovery S, Moritz C, Fielder DR. 1996. Genetic patterns suggest exponential population growth in a declining species. Mol Biol Evol 13:1106-1113.
32. Magnusson WE. 1985. Habitat selection, parasites and injuries in Amazonian crocodilians. Amazoniana 9:193-204.
33. Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res 27:209-220.
34. Martínez-Cruz B, Godoy JA, Negro JJ. 2004. Population genetics after fragmentation: the case of the endangered Spanish imperial eagle (Aquila adalberti). Mol Ecol 13:2243-2255.
35. Medem F. 1983. Los Crocodylia de Sur America, Vol. 2. Bogota, Colombia: Ed. Carrera. 270p.
36. Nei M. 1987. Molecular evolutionary genetics. New York, NY: Columbia University Press. 512p.
37. Plotkin MJ, Medem F, Mittermeier RA, Constable IA. 1983. Distribution and conservation of the black caiman (Melanosuchus niger). In: Rhodin A, Mitaya K, editors. Advances in herpetology and evolutionary biology. Cambridge, MA: Harvard University Press.
38. Posada D, Crandall KA, Templeton AR. 2000. GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol Ecol 9:487-488.
39. Poulsen NA, Nielsen EE, Schierup MH, Loeschcke V, Gronkjaer P. 2006. Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua). Mol Ecol 15:321-331.
40. Ray DA, Dever JA, Platt SG, Rainwater TR, Finger AG, McMurry ST, Batzer MA, Barr B, Stafford PJ, McKnight J, Densmore III LD. 2004. Low levels of nucleotide diversity in Crocodylus moreletii and evidence of hybridization with C. acutus. Conserv Genet 5:449-462.
41. Raymond M, Rousset F. 1995. An exact test for population differentiation. Evolution 49:1280-1283.
42. Rebêlo GH, Lugli L. 2001. Distribution and abundance of four caiman species (Crocodylia: Alligatoridae) in Jaú National Park, Amazonas, Brazil. Rev Biol Trop 49:1095-1109.
43. Rebêlo GH, Magnusson WE. 1983. An analysis of the effect of hunting on Caiman crocodilus and Melanosuchus niger base on the sizes of confiscated skins. Biol Conserv 26:95-104.
44. Rice WR. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
45. Ross JP. 1998. Crocodiles. Status survey and conservation action plan, 2nd edition. Gland, Switzerland: IUCN-SSC. Crocodile Specialist Group. 167p.
46. Rozas J, Sánchez-DelBarrio JC, Messenguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
47. Ruzzante DE, Taggart CT, Doyle RW, Cook D. 2001. Stability in the historical pattern of genetic structure of Newfoundland cod (Gadus morhua) despite the catastrophic decline in population size from 1964 to 1994. Conserv Genet 2:257-269.
48. Ryberg WA, Fitzgerald LA, Honeycutt RL, Cathey JC. 2002. Genetic relationships of American alligator populations distributed across different ecological and geographic scales. J Exp Zool (Mol Dev Evol) 294:325-333.
49. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual. Cold Springs Harbor, NY: Cold Springs Harbor Laboratory Press.
50. Santos MdCF, Ruffino ML, Farias IP. 2007. High levels of genetic variability and panmixia of the tambaqui Colossoma macropomum (Cuvier, 1818) in the main channel of the Amazon River. J Fish Biol 71A:33-44.
51. Smith NJH. 1980. Caimans, capybaras, otters, manatees, and man in Amazônia. Biol Conserv 19:177-187.
52. Sumner J, Jessop T, Paetkau D, Moritz C. 2004. Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae. Mol Ecol 13:259-269.
53. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
54. Taplin LE, Grigg GG. 1989. Historical zoogeography of the eusuchian crocodylians: a physiological perspective. Am Zool 29:885-901.
55. Templeton AR. 2004. Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol Ecol 13:789-809.
56. Templeton AR, Sing CF. 1993. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping: IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134:659-669.
57. Templeton AR, Boerwinkle E, Sing CF. 1987. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics 117:343-351.
58. Thorbjarnarson JB. 1996. Reproductive characteristics of the order Crocodylia. Herpetologica 52:8-28.
59. Uruena E. 1990. Black caiman in Guyana. Croc Spec Group Newsl 9:24.
60. Vasconcelos WR, Hrbek T, Da Silveira R, De Thoisy B, Marioni B, Farias IP. 2006. Population genetic analysis of Caiman crocodilus (Linnaeus, 1758) from South America. Genet Mol Biol 21:220-230.
61. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256-276.
62. WWF_Colombia. 2005. Pink river dolphin. http://orinoco.wwf.org.co; accessed on 6/3/2007.
63. Zhang D-X, Hewitt GM. 1996. Nuclear integrations: challenges for mitochondrial DNA markers. Trends Ecol Evol 11:247-251.