On the phylogenetic position of a rare Iberian endemic mammal, the Pyrenean desman (Galemys pyrenaicus)

Gene

Volumn 375, Issue 1-2, 2006, Pages 1-13

  Cabria, María Teresa ^a,b   Rubines, Jonathan ^a,b   Gómez Moliner, Benjamín ^b   Zardoya, Rafael ^a  

^a MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

^b UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

Author keywords

Eulipotyphla; Laurasiatheria; Mitochondrial genome; Nuclear genes; Talpidae

Indexed keywords

AMINO ACID; CYTOCHROME B; NUCLEOTIDE;

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; BAT; BAYES THEOREM; CARNIVORA; CONTROLLED STUDY; DESMANA MOSCHATA; GALEMYS PYRENAICUS; GENETIC ANALYSIS; GENETIC LINE; GENOME; HEDGEHOG; INSECTIVORE; MAMMAL; MITOCHONDRION; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; PERISSODACTYLA; PHYLOGENY; PRIORITY JOURNAL; TAXONOMY; UNINDEXED SEQUENCE;

ANIMALS; BASE SEQUENCE; DNA; DNA PRIMERS; INSECTIVORA; PHYLOGENY; POLYMERASE CHAIN REACTION;

CARNIVORA; CETARTIODACTYLA; CHIROPTERA; DESMANA MOSCHATA; ERINACEIDAE; GALEMYS PYRENAICUS; LAURASIATHERIA; MAMMALIA; PERISSODACTYLA; PHOLIDOTA (MAMMAL); SORICIDAE; TALPIDAE;

EID: 33744508632     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.01.038     Document Type: Article

References (63)

1. Abascal F., Zardoya R., and Posada D. Prottest: selection of best-fit models of protein evolution. Bioinformatics 21 (2005) 2104-2105
2. Arnason U., Gullberg A., and Janke A. Phylogenetic analyses of mitochondrial DNA suggest a sister group relationship between Xenarthra (Edentata) and ferungulates. Mol. Biol. Evol. 14 (1997) 762-768
3. Arnason U., et al. Mammalian mitogenomic relationships and the root of the eutherian tree. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 8151-8156
4. Butler P.M. The Phylogeny and Classification of the Tetrapods (1988), Clarendon, Oxford
5. Campbell B. The shoulder anatomy of mole. A study in phylogeny adaptation. Am. J. Anat. 64 (1939) 1-39
6. Cao Y., Fujiwara M., Nikaido M., Okada N., and Hasegawa M. Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data. Gene 259 (2000) 149-158
7. Castien E., and Gosálbez J. Distribución geográfica y hábitats ocupados por Galemys pyrenaicus (Geoffroy,1811) (Insectivora: Talpidae) en los Pirineos Occidentales. Doñana, Acta Vertebr. 19 (1992) 37-44
8. Cornelli P.S., and Ward R.H. Mitochondrial genes and mammalian phylogenies: increasing the reliability of branch length estimation. Mol. Biol. Evol. 17 (2000) 224-234
9. Douady C.J., and Douzery E.J.P. Molecular estimation of Eulipotyphlan divergence times and the evolution of "Insectivora". Mol. Phylogenet. Evol. 28 (2003) 285-296
10. Douady C.J., Catzeflis F., Kao D.J., Springer M.S., and Stanhope M.J. Molecular evidence for the monophyly of Tenrecidae (Mammalia) and the timing of the colonization of Madagascar by Malagasy tenrecs. Mol. Phylogenet. Evol. 22 (2002) 357-363
11. Douady C.J., et al. Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews. Mol. Phylogenet. Evol. 25 (2002) 200-209
12. Douady C.J., Scally M., Springer M.S., and Stanhope M.J. "Lipotyphlan" phylogeny based on the growth hormone receptor gene: a reanalysis. Mol. Phylogenet. Evol. 30 (2004) 778-788
13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
14. Fitch W.M. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20 (1971) 406-416
15. Gonzalez-Esteban J., Villate I., Castien E., Rey I., and Gosálbez J. Age determination of Galemys pyrenaicus. Acta Theriol. 47 (2002) 107-112
16. Gregory W.K. The orders of mammals. Bull. Am. Mus. Nat. Hist. 27 (1910) 1-524
17. Grenyer R., and Purvis A. A composite species-level phylogeny of the 'Insectivora' (Mammalia: Order Lipotyphla Haeckel, 1866). J. Zool. Lond. 260 (2003) 245-247
18. Guindon S., and Gascuel O. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Syst. Biol. 52 (2003) 696-704
19. Huelsenbeck J.P., and Ronquist F.R. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
20. Huelsenbeck J.P., Ronquist F.R., Nielsen R., and Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294 (2001) 2310-2314
21. Hutchinson J.H. Fossil Talpidae (Insectivora, Mammalia) from the late Tertiary of Oregon. Bull. Mus. Nat. Hist. Univ. Oregon 11 (1968) 1-117
22. Hutterer R. Order insectivora. In: Wilson D.E., and Reeder D.M. (Eds). Mammal Species of the World (1993), Smithsonian Institution Press, Washington 69-130
23. Kocher T.D., et al. Dynamics of mitochondrial DNA evolution in animals. Proc. Natl. Acad. Sci. U. S. A. 86 (1989) 6196-6200
24. Krettek A., Gullberg A., and Arnason U. Sequence analysis of the complete mitochondrial DNA molecule of the hedgehog, Erinaceus europaeus, and the phylogenetic position of the Lipotyphla. J. Mol. Evol. 41 (1995)
25. Lin Y.-H., et al. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol. Biol. Evol. 19 (2002) 2060-2070
26. MacPhee R.D.E., and Novacek M.J. Definitions and relationships of Lipotyphla. In: Szalay F.S., Novacek M.J., and McKenna M.C. (Eds). Mammal Phylogeny: Placentals (1993), Springer-Verlag, New york 13-31
27. Madsen O., et al. Parallel adaptive radiations in two major clades of placental mammals. Nature 409 (2001) 610-614
28. McKenna M.C. Toward a phylogeny and classification of the Mammalia. In: Luckett W.P., and Szalay F.S. (Eds). Phylogeny of the Primates: a Multidisciplinary Approach (1975), Plenum Press, New York 21-46
29. McKenna M.C., and Bell S.K. Classification of Mammals Above the Species Level (1997), Columbia Univ. Press, New York
30. Miyamoto M., and Goodman M. Biomolecular systematics of eutherian mammals: phylogenetic patterns and classification. Syst. Zool. 35 (1986) 230-240
31. Motowaka M. Phylogenetic relationships within the family Talpidae (Mammalia: Insectivora). J. Zool. Lond. 263 (2004) 147-157
32. Mouchaty S.K., Catzeflis F., Janke A., and Arnason U. Molecular evidence of an African phiomorpha-South American caviomorpha clade and support for hystricognathi based on the complete mitochondrial genome of the cane rat (Thryonomys swinderianus). Mol. Phylogenet. Evol. 18 (2000) 127-135
33. Mouchaty S.K., Gullberg A., Janke A., and Arnason U. The phylogenetic position of the Talpidae within Eutheria based on analysis of complete mitochondrial sequences. Mol. Biol. Evol. 17 (2000) 60-67
34. Murphy W.J., Eizirik E., Johnson W.E., Zhang Y.P., Ryder O.A., and O'Brien S.J. Molecular phylogenetics and the origin of placental mammals. Nature 409 (2001) 614-618
35. Murphy W.J., et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294 (2001) 2348-2350
36. Narita Y., Oda S.-I., Takenaka O., and Kageyama T. Phylogenetic position of eulipotyphla inferred from the cDNA sequences of pepsinogens a and c. Mol. Phylogenet. Evol. 21 (2001) 32-42
37. Nikaido M., Harada M., Cao Y., Hasegawa M., and Okada N. Monophyletic origin of the order chiroptera and its phylogenetic position among mammalia, as inferred from the complete sequence of the mitochondrial DNA of a Japanese megabat, the Ryukyu flying fox (Pteropus dasymallus). J. Mol. Evol. 51 (2000) 318-328
38. Nikaido M., et al. Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevaluation of the phylogeny of bats and insectivores. J. Mol. Evol. 53 (2001) 508-516
39. Nikaido M., Cao Y., Harada M., Okada N., and Hasegawa M. Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla. Mol. Phylogenet. Evol. 28 (2003) 276-284
40. Ojala D., Montoya J., and Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature 290 (1981) 470-474
41. Palmeirim J.M., and Hoffman R.S. Galemys pyrenaicus. Mamm. Species 207 (1983) 1-5
42. Palumbi S.R., Martin A., Romano S., MacMillan W., Stice L., and Grabowski G. The Simple Fool's Guide to PCR (1991), Department of Zoology, University of Hawaii, Honolulu
43. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
44. Robinson-Rechavi M., and Graur D. Usage optimization of unevenly sampled data through the combination of quartet trees: a eutherian draft phylogeny based on 640 nuclear and mitochondrial proteins. Isr. J. Zool. 47 (2001) 259-270
45. Roca A.L., et al. Mesozoic origin for West Indian insectivores. Nature 429 (2004) 649-651
46. Ronquist F.R., and Huelsenbeck J.P. MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
47. Rzhetsky A., and Nei M. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9 (1992) 945-967
48. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning. A Laboratory Manual (1989) Cold Spring Harbor, NY
49. San Mauro D., Gower D.J., Oommen O.V., Wilkinson M., and Zardoya R. Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1. Mol. Phylogenet. Evol. 33 (2004) 413-427
50. Sbisa E., Tanzariello F., Reyes A., Pesole G., and Saccone C. Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205 (1997) 125-140
51. Shinohara A., Campbell K.L., and Suzuki H. Molecular phylogenetic relationships of moles, shrew moles, and desmans from the new and old worlds. Mol. Phylogenet. Evol. 27 (2003) 247-258
52. Shinohara A., et al. Evolution and biogeography of talpid moles from continental East Asia and the Japanese islands inferred from mitochondrial and nuclear gene sequences. Zoolog. Sci. 21 (2004) 1177-1185
53. Simmons M.P., Carr T.G., and O'Neill K. Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters. Mol. Phylogenet. Evol. 32 (2004) 913-926
54. Springer M.S., Amrine H.M., Burk A., and Stanhope M.J. Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogeneous base composition. Syst. Biol. 48 (1999) 65-75
55. Springer M.S., et al. A molecular classification for the living orders of placental mammals and the phylogenetic placement of primates. In: Dagosto M., and Ravosa M. (Eds). Primate Origins and Adaptations (2003), Plenum, New York 178-215
56. *and other methods), version 4.0b 10 (2002), Sinauer Associates, Inc., Sunderland, MA, US
57. Teeling E.C., Scally M., Kao D.J., Romagnoll M.L., Springer M.S., and Stanhope M.J. Molecular evidence regarding the origin of echolocation and flight in bats. Nature 403 (2000) 188-192
58. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin J., and Higgins D.G. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
59. Waddell P.J., Okada N., and Hasegawa M. Towards resolving the interordinal relationships of placental mammals. Syst. Biol. 48 (1999) 1-5
60. Waddell P.J., Kishino H., and Ota R. A phylogenetic foundation for comparative mammalian genomics. Genome Inform. 12 (2001) 141-154
61. Walberg M.W., and Clayton D.A. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9 (1981) 5411-5421
62. Whidden H.P. Comparative myology of moles and the phylogeny of the Talpidae (Mammalia, Lypotyphla). Am. Mus. Novit. 3294 (2000) 1-53
63. Yates T.L., and Moore D.W. Speciation and evolution in the family Talpidae (Mammalia: Insectivora). In: Nevo E., and Reig O.A. (Eds). Evolution of Subterranean Mammals at the Organismal and Molecular Levels (1990), Alan R. Liss, New York 1-22