Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape

Molecular Phylogenetics and Evolution

Volumn 62, Issue 1, 2012, Pages 87-96

  Bryson, Robert W ^a   García Vázquez, Uri Omar ^b   Riddle, Brett R ^a  

^a UNIVERSITY OF NEVADA   (United States)

^b UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

Biogeography; Divergence dating; Mexico; Mitochondrial DNA; Phrynosoma; Phylogeography

Indexed keywords

ADENOSINE TRIPHOSPHATASE; NADH DEHYDROGENASE SUBUNIT 4; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE; REPTILIAN PROTEIN;

ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; LIZARD; MEXICO; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; PHYLOGENY; PHYLOGEOGRAPHY; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

ADENOSINE TRIPHOSPHATASES; ANIMALS; BAYES THEOREM; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENETIC SPECIATION; GENETIC VARIATION; IGUANAS; LIKELIHOOD FUNCTIONS; MEXICO; NADH DEHYDROGENASE; PHYLOGENY; PHYLOGEOGRAPHY; REPTILIAN PROTEINS; SEQUENCE ANALYSIS, DNA;

PHRYNOSOMA; PHRYNOSOMA ORBICULARE; PHRYNOSOMATINAE; SQUAMATA;

EID: 83655191932     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.09.007     Document Type: Article

References (93)

1. Anducho-Reyes M.A., Cognato A.I., Hayes J.L., Zuñiga G. Phylogeography of the bark beetle Dendroctonus mexicanus Hopkins (Coleoptera: Curculionidae: Scolytinae). Mol. Phylogen. Evol. 2008, 49:930-940.
2. Arévalo E., Davis S.K., Sites J. Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in Central Mexico. Syst. Biol. 1994, 43:387-418.
3. Barrowclough G.F., Zink R.M. Funds enough, and time: mtDNA, nuDNA and the discovery of divergence. Mol. Ecol. 2009, 18:2934-2936.
4. Brower L.P., Castilleja G., Peralta A., Lopez-Garcia J., Bojorquez-Tapia L., Diaz S., Melgarejo D., Missrie M. Quantitative changes in forest quality in a principal overwintering area of the monarch butterfly in Mexico, 1971-1999. Conserv. Biol. 2002, 16:346-359.
5. Bryson R.W., Pastorini J., Burbrink F.T., Forstner M.R.J. A phylogeny of the Lampropeltis mexicana complex (Serpentes: Colubridae) based on mitochondrial DNA sequences suggests evidence for species-level polyphyly within Lampropeltis. Mol. Phylogen. Evol. 2007, 43:674-684.
6. Bryson R.W., Murphy R.W., Lathrop A., Lazcano-Villareal D. Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes. J. Biogeogr. 2011, 38:697-710.
7. Bryson R.W., García-Vázquez U.O., Riddle B.R. Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican transition zone. J. Biogeogr. 2011, 38:1570-1584.
8. Bryson R.W., Murphy R.W., Graham M.R., Lathrop A., Lazcano-Villareal D. Historical diversification of the Crotalus intermedius group and Pleistocene pine-oak woodland connections between Mexico's Sierra Madre Occidental and Sierra Madre Oriental. J. Biogeogr. 2011, 10.1111/j.1365-2699.2011.02565.x.
9. Burbrink F.T., Pyron R.A. The impact of gene-tree/species-tree discordance on diversification rate estimation. Evolution 2011, 65:1851-1861.
10. Burney C.W., Brumfield R.T. Ecology predicts levels of genetic differentiation in Neotropical birds. Am. Nat. 2009, 174:358-368.
11. Carreño A.L., Helenes J. Geology and ages of the islands. A New Island Biogeography of the Sea of Cortés 2002, 14-40. Oxford University Press, New York. T.J. Case, M.L. Cody, E. Ezcurra (Eds.).
12. Castoe T.A., Spencer C.L., Parkinson C.L. Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): a perspective on North American desert biogeography. Mol. Phylogen. Evol. 2007, 42:193-212.
13. Castoe T.A., Daza J.M., Smith E.N., Sasa M.M., Kuch U., Campbell J.A., Chippindale P.T., Parkinson C.L. Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography. J. Biogeogr. 2009, 36:88-103.
14. Challenger A. Utilización y Conservación de los Ecosistemas Terrestres de México. Pasado, Presenté y Yuturo 1998, CONABIO, México, DF.
15. Corona A.M., Toledo V.H., Morrone J.J. Does the trans-mexican volcanic belt represent a natural biogeographic unit? An analysis of the distributional patterns of Coleoptera. J. Biogeogr. 2007, 34:1008-1015.
16. Daza J.M., Castoe T.A., Parkinson C.L. Using regional comparative phylogeographic data from snake lineages to infer historical processes in Middle America. Ecography 2010, 33:343-354.
17. Dixon J.R., Lemos-Espinal J.A. Anfibios y Reptiles del Estado de Querétaro, México. Amphibians and Reptiles of the State of Querétaro, México 2010, México, CONABIO, México, DF.
18. Drummond A.J., Rambaut A. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
19. Edwards S.V., Beerli P. Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 2000, 54:1839-1854.
20. Edwards S., Bensch S. Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008. Mol. Ecol. 2009, 18:2930-2933.
21. Estes R. Sauria terrestria, Amphisbaenia. Handbuch der Paläoherpetologie 1983, 1-249. Gustav Fischer Verlag, NY. W.P. Stuttgart (Ed.).
22. Farjon A., Styles B.T. Flora Neotropica: Pinus (Pinaceae) 1997, New York Botanical Garden, New York, NY.
23. Felsenstein J. Inferring Phylogenies 2004, Sinauer Associates, Sunderland, MA.
24. Ferrusquía-Villafranca I., González-Guzmán L.I. Northern Mexico's landscape, Part II: the biotic setting across time. Biodiversity, Ecosystems, and Conservation in Northern Mexico 2005, 39-51. Oxford University Press, Oxford, NY. J.-L.E. Cartron, G. Ceballos, R.S. Felger (Eds.).
25. Galicia L., García-Romero A. Land use and land cover change in highland temperate forests in the Izta-Popo National Park, Central Mexico. Mountain Res. Dev. 2007, 27:48-57.
26. Godinho R., Crespo E.G., Ferrand N. The limits of mtDNA phylogeography: complex patterns of population history in a highly structured Iberian lizard are only revealed by the use of nuclear markers. Mol. Ecol. 2008, 17:4670-4683.
27. Gómez-Tuena A., Orozco-Esquivel Ma.T., Ferrari L. Igneous petrogenesis of the Trans-Mexican Volcanic Belt. Geol. Soc. America, Special Paper 2007, 422:129-181.
28. Gugger P.F., Gonzalez-Rodriguez A., Rodriguez-Correa H., Sugita S., Cavender-Bares J. Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of 'rear edge' populations. New Phytol. 2011, 189:1185-1199.
29. Hewitt G.M. Genetic consequences of climatic oscillations in the Quaternary. Philos. Trans. R. Soc. London, B 2004, 359:183-195.
30. Hillis D.M., Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 1993, 42:182-192.
31. Horowitz S.B. An arrangement of the subspecies of the horned toad, Phrynosoma orbiculare (Iguanidae). Am. Mid. Nat. 1955, 54:204-218.
32. Hudson R.R., Coyne J.A. Mathematical consequences of the genealogical species concept. Evolution 2002, 56:1557-1565.
33. Hulsey C.D., García de León F.J., Johnson Y.S., Hendrickson D.A., Near T.J. Temporal diversification of Mesoamerican cichlid fishes across a major biogeographic boundary. Mol. Phylogen. Evol. 2004, 31:754-764.
34. Jennings W.B., Edwards S.V. Speciational history of Australian grass finches (Poephila) inferred from 30 gene trees. Evolution 2005, 59:2033-2047.
35. Jones, K.B., 1995. Phylogeography of the desert horned lizard (Phrynosoma platyrhinos) and the short-horned lizard (Phrynosoma douglassi): patterns of divergence and diversity. PhD Thesis, University of Nevada, Las Vegas.
36. Kerhoulas N.J., Arbogast B.S. Molecular systematics and Pleistocene biogeography of Mesoamerican flying squirrels. J. Mammal. 2010, 91:654-667.
37. Kubatko L., Gibbs H.L., Bloomquist E.W. Inferring species-level phylogenies and taxonomic distinctiveness using multi-locus data in Sistrurus rattlesnakes. Syst. Biol. 2011, 60:393-409.
38. Lamb T., Avise J.C., Gibbons J.W. Phylogeographic patterns in mitochondrial DNA of the desert tortoise (Xerobates agassizi), and evolutionary relationships among the North American desert tortoises. Evolution 1989, 43:76-87.
39. Leaché A.D., McGuire J.A. Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree. Mol. Phylogen. Evol. 2006, 39:628-644.
40. Leaché A.D., Mulcahy D.G. Phylogeny, divergence times, and species limits of spiny lizards (Sceloporus magister species group) in western North American deserts and Baja California. Mol. Ecol. 2007, 16:5216-5233.
41. Lemos-Espinal J.A., Smith H.M. Anfibios y Reptiles del Estado de Chihuahua, México/Amphibians and Reptiles of the State of Chihuahua, México 2007, CONABIO, México, DF.
42. Lemos-Espinal J.A., Smith H.M. Anfibios y Reptiles del Estado de Coahuila, México/Amphibians and Reptiles of the State of Coahuila, México 2007, CONABIO, México, DF.
43. León-Paniagua L., Navarro-Sigüenza A.G., Hernández-Baños B.E., Morales J.C. Diversification of the arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) in the Mesoamerican highlands. Mol. Phylogen. Evol. 2007, 42:653-664.
44. Lindell J., Méndez-de la Cruz F.R., Murphy R.W. Deep biogeographical history and cytonuclear discordance in the black-tailed brush lizard (Urosaurus nigricaudus) of Baja California. Biol. J. Linnaean Soc. 2008, 94:89-104.
45. Luna-Vega I., Alcántara-Ayala O., Espinosa-Organista D., Morrone J.J. Historical relationships of the Mexican cloud forests: a preliminary vicariance model applying parsimony analysis of endemicity to vascular plant taxa. J. Biogeogr. 1999, 26:1299-1305.
46. Luxbacher A.M., Knouft J.H. Assessing concurrent patterns of environmental niche and morphological evolution among species of horned lizards (Phrynosoma). J. Evol. Biol. 2009, 22:1669-1678.
47. Macey J.R., Wang Y., Ananjeva N.B., Larson A., Papenfuss T.J. Vicariant patterns of fragmentation among gekkonid lizards of the genus Teratoscincus produced by the Indian Collision: a molecular phylogenetic perspective and an area cladogram for Central Asia. Mol. Phylogen. Evol. 1999, 12:320-332.
48. Marshall C.J., Liebherr J.K. Cladistic biogeography of the Mexican transition zone. J. Biogeogr. 2000, 27:203-216.
49. McCormack J.E., Peterson A.T., Bonaccorso E., Smith T.B. Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina). Mol. Ecol. 2008, 17:2505-2521.
50. McCormack J.E., Zellmer A.J., Knowles L.L. Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models. Evolution 2010, 64:1231-1244.
51. McCormack J.E., Heled J., Delaney K.S., Peterson A.T., Knowles L.L. Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays. Evolution 2011, 65:184-202.
52. McDiarmid R.W. A collection of reptiles and amphibians from the highland faunal assemblage of western Mexico. Contrib. Sci. Los Angeles Co. Mus. 1963, 68:1-15.
53. McDonald J.A. Phytogeography and history of the alpine-subalpine flora of northeastern Mexico. Biological Diversity of Mexico: Origins and Distribution 1993, 681-703. Oxford University Press, Oxford, NY. T.P. Ramamoorthy, R.A. Bye, A. Lot, J. Fa (Eds.).
54. Mendoza-Quijano, F., Vázquez Díaz, J., Quintero Díaz, G.E., 2007. Phrynosoma orbiculare. In: IUCN 2010. IUCN Red List of Threatened Species. Version 2010.4.
55. Mittermeier R.A., Gil P.R., Hoffman M., Pilgrim J., Brooks T., Mittermeier C.G., Lamoreux J., da Fonseca G.A.B. Hotspots Revisited: Earth's Biologically Richest and Most Endangered Terrestrial Ecoregions 2005, Conservation International, Washington, DC.
56. Montanucci R.R. Notes on systematics of homed lizards allied to Phrynosoma orbiculare (Lacertilia: Iguanidae). Herpetologica 1979, 35:116-124.
57. Montanucci R.R. A phylogenetic study of the horned lizards, genus Phrynosoma, based on skeletal and external morphology. Contrib. Sci. Nat. Hist. Mus. Los Angeles Co. 1987, 390:1-36.
58. Moore W.S. Inferring phylogenies from mtDNA variation: mitochondrial gene trees versus nuclear gene trees. Evolution 1995, 49:718-726.
59. Morafka D.J. A biogeographical analysis of the Chihuahuan Desert through its herpetofauna. Biogeographica 1977, 9:1-313.
60. Morando M., Avila L.J., Baker J., Sites J.W. Phylogeny and phylogeography of the Liolaemus darwinii complex (Squamata: Liolaemidae): evidence for introgression and incomplete lineage sorting. Evolution 2004, 58:842-876.
61. Mulcahy D.G., Mendelson J.R. Phylogeography and speciation of the morphologically variable, widespread species Bufo valliceps, based on molecular evidence from mtDNA. Mol. Phylogen. Evol. 2000, 17:173-189.
62. Mulcahy D.G., Spaulding A., Mendelson J.R., Brodie E.D. Phylogeography of the Flat-tailed Horned lizard (Phrynosoma mcallii) and systematics of the P. mcallii-platyrhinos mtDNA complex. Mol. Ecol. 2006, 15:1807-1826.
63. Murphy R.W., Trepanier T.L., Morafka D.J. Conservation genetics, evolution and distinct population segments of the Mojave fringe-toed lizard, Uma scoparia. J. Arid Environ. 2006, 67:226-247.
64. Nylander, J.A.A., 2004. MrModeltest v2. Program Distributed by the Author. Evolutionary Biology Centre, Uppsala University, Uppsala.
65. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (Are We There Yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Bioinformatics 2008, 24:581-583.
66. Paniagua L.L., Morrone J.J. Do the Oaxacan Highlands represent a natural biotic unit? A cladistic biogeographical test based on vertebrate taxa. J. Biogeogr. 2009, 36:1939-1944.
67. Pellmyr O., Segraves K.A. Pollinator divergence within an obligate mutualism: two yucca moth species (Lepidoptera; Prodoxidae: Tegeticula) on the Joshua tree (Yucca brevifolia; Agavaceae). Ann. Entomol. Soc. America 2003, 96:716-722.
68. Peterson A.T., Flores-Villela O.A., León-Paniagua L.S., Llorente-Bousquets J.E., Luis-Martinez M.A., Navarro-Siguenza A.G., Torres-Chavez M.G., Vargas-Fernandez I. Conservation priorities in northern Middle America: moving up in the world. Biodiversity Lett. 1993, 1:33-38.
69. Presch W. Evolutionary osteology and relationships of the horned lizard genus Phrynosoma (Family Iguanidae). Copeia 1969, 1969:250-275.
70. Pyron R.A., Burbrink F.T. Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula. Mol. Ecol. 2009, 18:3443-3457.
71. Pyron R.A., Burbrink F.T. Hard and soft allopatry: physically and ecologically mediated modes of geographic speciation. J. Biogeogr. 2010, 37:2005-2015.
72. Rabosky D.L. Likelihood methods for inferring temporal shifts in diversification rates. Evolution 2006, 60:1152-1164.
73. Rabosky D.L. LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol. Bioinf. Online 2006, 2:257-260.
74. Ramamoorthy T., Bye R., Lot A., Fa J. Biological Diversity of Mexico: Origins and Distribution 1993, Oxford University Press, Oxford.
75. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. http://beast.bio.ed.ac.uk/Tracer.
76. Riddle B.R., Hafner D.J., Alexander L.F., Jaeger J.R. Cryptic vicariance in the historical assembly of a Baja California peninsular desert biota. Proc. Natl Acad. Sci. USA 2000, 97:14438-14443.
77. Riddle B.R., Hafner D.J., Alexander L.F. Phylogeography and systematics of the Peromyscus eremicus species group and the historical biogeography of North American warm regional deserts. Mol. Phylogen. Evol. 2000, 17:145-160.
78. Robinson M.D., Van Devender T.R. Miocene lizards from Wyoming and Nebraska. Copeia 1973, 1973:698-704.
79. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
80. Salinas-Moreno Y., Mendoza-Correa G., Barrios M.A., Cisneros R., Macías-Sámano J., Zúñiga G. Areography of the genus Dendroctonus (Coleoptera: Curculionidae: Scolytinae) in México. J. Biogeogr. 2004, 31:1163-1177.
81. SEMARNAT, 2010. Norma Oficial Mexicana NOM-059-SEMARNAT-2010. Protección ambiental-Especies nativas de México de flora y fauna silvestres-Categorías de riesgo y especificaciones para su inclusión, exclusión o cambio-Lista de especies en riesgo, México. Jueves 30 de diciembre de 2010.
82. Sherbrooke W.C. Introduction to Horned Lizards of North America 2003, University of California Press, CA.
83. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
84. Sullivan J., Arellano E., Rogers D.S. Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to past climatic fluctuations. Am. Nat. 2000, 155:755-768.
85. Tennessen J.A., Zamudio K.R. Genetic differentiation among mountain island populations of the striped plateau lizard, Sceloporus virgatus (Squamata: Phrynosomatidae). Copeia 2008, 2008:558-564.
86. Upton D.E., Murphy R.W. Phylogeny of the side-blotched lizards (Phrynosomatidae: Uta) based on mtDNA sequences: support for a midpeninsular seaway in Baja California. Mol. Phylogen. Evol. 1997, 8:104-113.
87. Van Devender T.R., Eshelman R.E. Referral of the fossil lizard Sceloporus holmani (late Pliocene of north-central Kansas) to the genus Phrynosoma. Herpetologica 1979, 35:380-382.
88. Weir J.T., Bermingham E., Miller M.J., Klicka J., González M.A. Phylogeography of a morphologically diverse Neotropical montane species, the common bush-tanager (Chlorospingus ophthalmicus). Mol. Phylogen. Evol. 2008, 47:650-664.
89. Wiens J.J., Parra-Olea G., García-París M., Wake D.B. Phylogenetic history underlies elevational patterns of biodiversity in tropical salamanders. Proc. R. Soc. London 2007, 274:919-928.
90. Wiens J.J., Kuczynski C.A., Arif S., Reeder T.W. Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data, and a revised phylogeny for Sceloporus. Mol. Phylogen. Evol. 2010, 54:150-161.
91. Wood D.A., Vandergast A.G., Lemos-Espinal J.A., Fisher R.N., Holycross A.T. Refugial isolation and divergence in the narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data. Mol. Ecol. 2011, 10.1111/j.1365-294X.2011.05211.x.
92. Zaldivar-Riverón A., Nieto-Montes de Oca A., Laclette J.P. Phylogeny and evolution of dorsal pattern in the Mexican endemic lizard genus Barisia (Anguidae: Gerrhonotinae). J. Zool. Syst. Evol. Res. 2005, 43:243-257.
93. Zink R.M., Barrowclough G.F. Mitochondrial DNA under siege in avian phylogeography. Mol. Ecol. 2008, 17:2107-2121.