Cryptic diversity and conservation units in the Bahama parrot

Conservation Genetics

Volumn 11, Issue 5, 2010, Pages 1809-1821

  Russello, M A ^a   Stahala, C ^b   Lalonde, D ^a   Schmidt, K L ^c   Amato, G ^c  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b FLORIDA STATE UNIVERSITY   (United States)

^c DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

Amazona leucocephala bahamensis; Cuban Amazon parrot; Historical DNA; Museum specimen; Phylogenetic species; Population genetic; Subspecies dilemma

Indexed keywords

ANTHROPOGENIC EFFECT; ARCHIPELAGO; BAYESIAN ANALYSIS; BIRD; CLUSTER ANALYSIS; CRYPSIS; MITOCHONDRIAL DNA; PERSISTENCE; PHYLOGENETICS; POPULATION DECLINE; POPULATION GENETICS; SPECIES CONSERVATION; SPECIES DIVERSITY; TAXONOMY;

BAHAMAS;

AMAZONA; AMAZONA LEUCOCEPHALA; AMAZONA LEUCOCEPHALA BAHAMENSIS; PSITTACIDAE;

EID: 77956879405     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-010-0074-z     Document Type: Article

References (81)

1. Attrill R (1980) The status and conservation of the Bahamas Amazon (Amazona leucocephala bahamensis). In: Pasquier RF (ed) Conservation of new world parrots. Smithsonian Institution Press, Washington, DC, pp 81-88.
2. Barrowclough GF, Flesness NR (1996) Species, subspecies, and races: the problem of units of management in conversation. In: Kleiman DG, Allen ME, Thompson KV, Lumpkin S, Harris H (eds) Wild mammals in captivity: principles and techniques. University of Chicago Press, Chicago, pp 247-254.
3. Beheregaray LB, Caccone A (2007) Cryptic biodiversity in a changing world. J Biol 6: 1-5.
4. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2001) Genetix, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UPR 9060, Université de Montpellier II, Montpellier, France.
5. Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker K, Ingram KK, Das I (2007) Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22: 148-155.
6. Brightsmith DJ (2005a) Competition, predation and nest niche shifts among tropical cavity nesters: phylogeny and natural history evolution of parrots (Psittaciformes) and trogons (Trogoniformes). J Avian Biol 36: 64-73.
7. Brightsmith DJ (2005b) Parrot nesting in southeastern Peru: seasonal patterns and keystone trees. Wilson Bull 117: 296-305.
8. Brown DM, Brenneman RA, Koepfli KP, Pollinger JP, Mila B, Georgiadis NJ, Louis EE, Grether GF, Jacobs DK, Wayne RK (2007) Extensive population genetic structure in the giraffe. BMC Biol 5: 57.
9. Brownstein MJ, Carpten JD, Smith JR (1996) Modulation of non-templated nucleotide addition by tag DNA polymerase: primer modifications that facilitate genotyping. Biotechniques 20: 1004-1010.
10. Ceballos G, Ehrlich PR (2009) Discoveries of new mammal species and their implications for conservation and ecosystem services. Proc Natl Acad Sci USA 106: 3841-3846.
11. Clark AH (1905) The West Indian parrots. Auk 22: 337-344.
12. Cory CB (1891) Descriptions of thirteen new species of birds from the island of Grand Cayman, West Indies. Auk 3: 497-501.
13. Cracraft J (1983) Species concepts and speciation analysis. Curr Ornithol 1: 159-187.
14. Davis JI, Nixon KC (1992) Populations, genetic-variation, and the delimitation of phylogenetic species. Syst Biol 41: 421-435.
15. Eberhard JR, Bermingham E (2004) Phylogeny and biogeography of the Amazona ochrocephala (Aves: Psittacidae) complex. Auk 121: 318-332.
16. Eberhard JR, Wright TF, Bermingham E (2001) Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona. Mol Biol Evol 18: 1330-1342.
17. Enkerlin-Hoeflich EC, Snyder NFR, Wiley JW (2006) Behavior of wild Amazona and Rhynchopsitta parrots, with comparative insights from other psittacines. In: Luescher AU (ed) Manual of parrot behavior. Blackwell Publishing, Oxford.
18. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
19. 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.
20. Frankham R (1995) Effective population size adult population size ratios in wildlife-a review. Genet Res 66: 95-107.
21. Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10: 305-318.
22. Gaunt AS, Oring LW (1997) Guidelines to the use of wild birds in research. The Ornithological Council, Washington, DC.
23. Gentile G, Fabiani A, Marquez C, Snell HL, Snell HM, Tapia W, Sbordoni V (2009) An overlooked pink species of land iguana in the Galápagos. Proc Natl Acad Sci USA 106: 507-511.
24. Gnam RS, Burchsted A (1991) Population estimates for the Bahamas Parrot on Abaco Island. Bahamas, J Field Ornithol, p 62.
25. Goldstein PZ, DeSalle R, Amato G, Vogler AP (2000) Conservation genetics at the species boundary. Conserv Biol 14: 120-131.
26. Guo SW, Thompson EA (1992) A Monte-Carlo method for combined segregation and linkage analysis. Am J Hum Genet 51: 1111-1126.
27. Haig SM, Beever EA, Chambers SM, Draheim HM, Dugger BD, Dunham S, Elliott-Smith E, Fontaine JB, Kesler DC, Knaus BJ, Lopes IF, Loschl P, Mullins TD, Sheffield LM (2006) Taxonomic considerations in listing subspecies under the US Endangered Species Act. Conserv Biol 20: 1584-1594.
28. Hale EE (1891) The life of Christopher Columbus: from his own letters and journals and other documents of his time. G. L. Howe and Co., Chicago.
29. Harpending HC (1994) Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol 66: 591-600.
30. Isaac NJB, Mallet J, Mace GM (2004) Taxonomic inflation: its influence on macroecology and conservation. Trends Ecol Evol 19: 464-469.
31. Johnson JA, Watson RT, Minde DP (2005) Prioritizing species conservation: does the Cape Verde kite exist? Proc R Soc B 272: 1365-1371.
32. Keegan WF (1992) Beachhead in the Bahamas-Columbus encounters a new world. Archaeology 45: 44-50.
33. Leite KCE, Seixas GHF, Berkunsky I, Collevatti RG, Caparroz R (2008) Population genetic structure of the blue-fronted Amazon (Amazona aestiva, Psittacidae: Aves) based on nuclear microsatellite loci: implications for conservation. Genet Mol Res 7: 819-829.
34. Li WH (1977) Distribution of nucleotide differences between 2 randomly chosen cistrons in a finite population. Genetics 85: 331-337.
35. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
36. Longmire JL, Maltbie M, Baker RJ (1997) Use of 'lysis buffer' in DNA isolation and its implication for museum collections. Occas Pap Mus Texas Tech Univ 163: 1-3.
37. Matuzak GD, Bezy MB, Brightsmith DJ (2008) Foraging ecology of parrots in a modified landscape: seasonal trends and introduced species. Wilson J Ornithol 120: 353-365.
38. Mayr E (1942) Systematics and the origin of species. Columbia University Press, New York.
39. Mayr E (1963) Animal species and evolution. Harvard University Press, Cambridge.
40. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York.
41. Ottens-Wainright P, Halanych KM, Eberhard JR, Burke RI, Wiley JW, Gnam RS, Aquilera XG (2004) Independent geographic origin of the genus Amazona in the West Indies. J Caribb Ornithol 17: 23-49.
42. Palstra FP, Ruzzante DE (2008) Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence? Mol Ecol 17: 3428-3447.
43. Peters J (1928) The races of Amazona leucocephala. Auk 45: 342-344.
44. Pfenninger M, Schwenk K (2007) Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BMC Evol Biol 7: 121.
45. Phillimore AB, Owens IPF (2006) Are subspecies useful in evolutionary and conservation biology? Proc R Soc B 273: 1049-1053.
46. Piry S, Luikart G, Cornuet JM (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90: 502-503.
47. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
48. Poulakakis N, Glaberman S, Russello MA, Beheregaray LB, Ciofi C, Powell JR, Caccone A (2008) Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise. Proc Natl Acad Sci USA 105: 15464-15469.
49. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
50. Raymond M, Rousset F (1995) Genepop (version-1. 2)-population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
51. Reynolds MBJ (2006) Conservation taxonomy of the Cuban parrot: morphological, plumage and flight call variation. Loma Linda University, Loma Linda.
52. Reynolds MBJ, Hayes WK (2009) Conservation taxonomy of the Cuban parrot (Amazona leucocephala): I. variation in morphology and plumage. J Caribb Ornithol 22: 1-18.
53. Ribas CC, Tavares ES, Yoshihara C, Miyaki CY (2007) Phylogeny and biogeography of Yellow-headed and Blue-fronted Parrots (Amazona ochrocephala and Amazona aestiva) with special reference to the South American taxa. Ibis 149: 564-574.
54. Rice WR (1989) Analysing tables of statistical tests. Evolution 43: 223-225.
55. Rivera-Milan FF, Collazo JA, Stahala C, Moore WJ, Davis A, Herring G, Pagliaro R, Thompson JL, Bracey W (2005) Estimation of density and population size and recommendations for monitoring trends of Bahama parrots on Great Abaco and Great Inagua. Wildl Soc Bull 33: 823-834.
56. Rogers AR (1995) Genetic evidence for a Pleistocene population explosion. Evolution 49: 608-615.
57. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9: 552-569.
58. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
59. Russello MA, Amato G (2004) A molecular phylogeny of Amazona: implications for Neotropical parrot biogeography, taxonomy, and conservation. Mol Phylogenet Evol 30: 421-437.
60. Russello M, Calcagnotto D, DeSalle R, Amato G (2001) Characterization of microsatellite loci in the endangered St. Vincent Parrot, Amazona guildingii. Mol Ecol Notes 1: 162-164.
61. Russello MA, Glaberman S, Gibbs JP, Marquez C, Powell JR, Caccone A (2005a) A cryptic taxon of Galápagos tortoise in conservation peril. Biol Lett 1: 287-290.
62. Russello MA, Lin K, Amato G, Caccone A (2005b) Additional microsatellite loci for the endangered St. Vincent Parrot, Amazona guildingii. Conserv Genet 6: 643-645.
63. Russello MA, Brazaitis P, Gratten J, Watkins-Colwell GJ, Caccone A (2007) Molecular assessment of the genetic integrity, distinctiveness and phylogeographic context of the Saltwater crocodile (Crocodylus porosus) on Palau. Conserv Genet 8: 777-787.
64. Ryder OA (1986) Species conservation and systematics-the dilemma of subspecies. Trends Ecol Evol 1: 9-10.
65. Schneider S, Excoffier L (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates very among sites: application to human mitochondrial DNA. Genetics 152: 1079-1089.
66. Schneider S, Roessli D, Excoffier L (2000) Arlequin v2. 000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Switerland.
67. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18: 233-234.
68. Snyder NFR, McGowan P, Gilardi J, Grajal A (eds) (2000) Parrots: status, survey, and conservation action plan 2000-2004. International Union for Conservation of Nature, Gland.
69. Swofford D (2002) PAUP*: phylogenetic analysis using parsimony, v. 4. 0b10. Illinois Natural History Survey, Champaign.
70. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526.
71. Trontelj P, Fiser C (2009) Cryptic species diversity should not be trivialised. System Biodivers 7: 1-3.
72. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4: 535-538.
73. Vogler AP, Desalle R (1994) Diagnosing units of conservation management. Conserv Biol 8: 354-363.
74. Wandeler P, Hoeck PEA, Keller LF (2007) Back to the future: museum specimens in population genetics. Trends Ecol Evol 22: 634-642.
75. Waples RS (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conserv Genet 7: 167-184.
76. Waples RS, Do C (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Resour 8: 753-756.
77. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
78. Wiley JW, Gnam RS, Koenig SE, Dornelly A, Galvez X, Bradley PE, White T, Zamore M, Reillo PR, Anthony D (2004) Status and conservation of the family Psittacidae in the West Indies. J Caribb Ornithol 17: 94-154.
79. Wilson E, Brown W (1953) The subspecies concept and its taxonomic application. Syst Zool 2: 97-111.
80. Wright TF, Dahlin CR, Salinas-Melgoza A (2008) Stability and change in vocal dialects of the yellow-naped Amazon. Anim Behav 76: 1017-1027.
81. Zink RM (2004) The role of subspecies in obscuring avian biological diversity and misleading conservation policy. Proc R Soc Lond B 271: 561-564.