Multilocus phylogeny of the widely distributed South American lizard clade Eulaemus (Liolaemini, Liolaemus)

Zoologica Scripta

Volumn 43, Issue 4, 2014, Pages 323-337

  Olave, Melisa ^a   Avila, Luciano J ^a   Sites, Jack W ^b   Morando, Mariana ^a  

^a Centro Nacional Patagonico Consejo Nacional de Invest Cientificas y Tecnicas ^*  (Argentina)

^b BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIOLAEMUS; SQUAMATA;

EID: 84902317123     PISSN: 03003256     EISSN: 14636409     Source Type: Journal    
DOI: 10.1111/zsc.12053     Document Type: Article

References (56)

1. Abdala, C. S. (2007). Phylogeny of the boulengeri group (Iguania: Liolaemidae, Liolaemus). Zootaxa, 1538, 1-84.
2. Abdala, C. S. & Juarez Heredia, V. I. (2013). Taxonomía y filogenia de ungrupo de lagartosamenzados: El grupo de Liolaemus anomalus (Iguania: Liolaemidae). Cuadernos de Herpetología, 27, 109-153.
3. Aparicio, J. & Ocampo, M. (2010). Liolaemus grupo montanus Etheridge, 1995 (Iguania - Liolaemidae). Cuadernos de Herpetología, 24, 133-135.
4. Avila, L. J., Morando, M., Perez, C. H. F. & Sites, J. W., Jr (2004). Phylogenetic relationships of lizards of the Liolaemus petrophilus group (Squamata, Liolaemidae), with description of two new species from western Argentina. Herpetologica, 60, 187-203.
5. Avila, L. J., Morando, M. & Sites, J. W., Jr (2006). Congeneric phylogeography: hypothesizing species limits and evolutionary processes in Patagonian lizards of the Liolaemus boulengeri group (Squamata: Liolaemini). Biological Journal of the Linnean Society of London, 89, 241-275.
6. Avila, L. J., Morando, M., Perez, D. R. & Sites, J. W., Jr (2009). A new species of Liolaemus from Añelo sand dunes, Northern Patagonia, Neuquén, Argentina, and molecular phylogenetic relationships of the Liolaemus wiegmannii species group (Squamata, Iguania, Liolaemini). Zootaxa, 2234, 39-55.
7. Beheregaray, L. B. (2008). Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Molecular Ecology, 17, 3754-3774.
8. Breitman, M. F., Avila, L. J., Sites, J. W., Jr & Morando, M. (2011). Lizards from the end of the world: phylogenetic relationships of the Liolaemus lineomaculatus section (Squamata: Iguania: Liolaemini). Molecular Phylogenetics and Evolution, 59, 364-376.
9. Breitman, M. F., Avila, L. J., Sites, J. W., Jr & Morando, M. (2012). How lizards survived blizzards: phylogeography of the Liolaemus lineomaculatus group (Liolaemidae) reveals multiple breaks and refugia in southern Patagonia, and their concordance with other co-distributed taxa. Molecular Ecology, 25, 6068-6085.
10. Breitman, M. F., Morando, M. & Avila, L. J. (2013). Past and present taxonomy of Liolaemus lineomaculatus section (Liolaemidae): is the morpholocial arrangement hypothesis valid?. Zoological Journal of the Linnean Society, 168, 612-668.
11. Brito, P. H. & Edwards, S. V. (2009). Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica, 135, 439-455.
12. Camargo, A., Avila, L. J., Morando, M. & Sites, J. W., Jr (2012). Accuracy and precision of species trees: effects of locus, individual and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii Group (Squamata, Liolaemidae). Systematic Biology, 61, 272-288.
13. Cei, J. M. (1986). Reptiles del centro, centro-oeste y sur de la Argentina. Herpetofauna de las zonas áridas y semiáridas.
14. Cruz, F. B., Fitzgerald, L. A., Espinoza, R. E. & Schulte, J. A., II (2005). The importance of phylogenetic scale in tests of Bergmann's and Rapoport's rules: lessons from a clade of South American lizards. Journal of Evolutionary Biology, 18, 1559-1574.
15. Donoso-Barros, R. (1966). Reptiles de Chile. Santiago: Universidad de Chile.
16. Drummond, A. J. & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
17. Espinoza, R. E., Wiens, J. J. & Tracy, C. R. (2004). Recurrent evolution of herbivory in small, cold-climate lizards: breaking the ecophysiological rules of reptilian herbivory. Proceedings of the National Academy of Sciences, USA, 101, 16819-16824.
18. Etheridge, R. (1995). Redescription of Ctenoblepharys adspersa, Tschudi, 1845, and the taxonomy of Liolaeminae (Reptilia: Squamata: Tropiduridae). American Museum Novitates, 3142, 1-34.
19. Etheridge, R. (2000). A review of lizards of the Liolaemus wiegmannii Group (Squamata, Iguania, Tropiduridae). And a history of morphological change in the sand-dwelling species. Herpetological Monograph, 14, 293-352.
20. Etheridge, R. & de Queiroz, K. (1988) A phylogeny of Iguanidae. In R. Estes & G. Pregill (Eds) Phylogenetic Relationships of the Lizard Families, Essays Commemorating Charles L. Camp (pp. 283-368). Stanford: Stanford University Press.
21. Fontanella, F. M., Olave, M., Avila, L. J., Sites, J. W., Jr & Morando, M. (2012). Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences. Zoological Journal of the Linnean Society, 164, 825-835.
22. Funk, D. J. & Omland, K. E. (2003). Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology and Systematics, 34, 397-423.
23. Halloy, M., Etheridge, R. & Burghardt, G. M. (1998). To bury in sand Phylogenetic relationships among lizard species of the boulengeri Group, Liolaemus (Reptilia: Squamata: Tropiduridae), based on behavioral characters. Herpetological Monograph, 12, 1-37.
24. Heath, L., van der Walt, V., Varsani, A. & Martin, D. P. (2006). Recombination patterns in aphthoviruses mirror those found in other picornaviruses. Journal of Virology, 80, 11827-11832.
25. Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059-3066.
26. Knowles, L. L. (2009). Statistical Phylogeography. Annual Review of Ecology, Evolution and Systematics, 40, 593-612.
27. Knowles, L. L. & Kubatko, L. S. (2010). Estimating Species Trees: Practical and Theoretical Aspects. Hoboken, NJ: Wiley, Blackwell.
28. Knowles, L. L., Carstens, B. C. & Keat, M. L. (2007). Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence. Current Biology, 17, 1-7.
29. Kuhner, M. K. & Felsenstein, J. (1994). Simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution, 11, 459-468.
30. Leaché, A. D. & Rannala, B. (2011). The accuracy of species tree estimation under simulation: a comparison of methods. Systematic Biology, 60, 126-137.
31. Lobo, F. (2001). A phylogenetic analysis of lizards of the Liolaemus chiliensis group (Iguania: Tropiduridae). Herpetological Journal, 11, 137-150.
32. Lobo, F. (2005). Las relaciones filogenéticas dentro del grupo chiliensis (Iguania: Liolaemidae: Liolaemus): sumando nuevos caracteres y taxones. Acta Zoológica Lilloana, 49, 67-89.
33. Maddison, W. P. (1997). Gene trees in species trees. Systematic Biology, 46, 523-536.
34. Martin, D. & Rybicki, E. (2000). RDP: detection of recombination amongst aligned sequences. Bioinformatics, 16, 562-563.
35. Medina, C. D., Avila, L. J. & Morando, M. (2013). Hacia una taxonomía integral: poniendo a prueba especies candidatas relacionadas a Liolaemus buergeri Werner 1907 (Iguania: Liolaemini) mediante análisis morfológicos. Cuadernos de Herpetología, 27, 27-34.
36. Morando, M. (2004). Sistemática y filogenia de grupos de especies de los géneros Phymaturus y Liolaemus (Squamata: Tropiduridae: Liolaeminae) del oeste y sur de Argentina. Unpublished D. Phil. Thesis, Universidad Nacional de Tucumán, Argentina.
37. Morando, M., Avila, L. J. & Sites, J. W., Jr (2003). Sampling strategies for delimiting species: genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata: Liolaemidae) in Andean-Patagonian South America. Systematic Biology, 52, 159-185.
38. Morando, M., Avila, L. J., Baker, J. & Sites, J. W., Jr (2004). Phylogeny and phylogeography of the Liolaemus darwinii complex (Squamata: Liolaemidae): evidence for introgression and incomplete lineage sorting. Evolution, 58, 842-861.
39. Morando, M., Avila, L. J., Turner, C. & Sites, J. W., Jr (2007). Molecular evidence for species complex in the Patagonian lizard Liolaemus bibronii and phylogeography of the closely related Liolaemus gracilis (Squamata: Liolaemini). Molecular Phylogenetics and Evolution, 43, 952-973.
40. Morando, M., Avila, L. J., Turner, C. & Sites, J. W., Jr (2008). Phylogeography between valleys and mountains: the history of Liolaemus koslowskyi (Squeamata, Liolaemini). Zoologica Scripta, 37, 603-638.
41. Noonan, B. & Yoder, A. D. (2009). Anonymous nuclear markers for Malagasy plated lizards (Zonosaurus). Molecular Ecology Resources, 9, 402-404.
42. Olave, M., Avila, L. J., Sites, J. W., Jr & Morando, M. (2011). Evidence of hybridization in the Argentinean lizard Liolaemus gracilis and Liolaemus bibronii (Iguani:Liolaemini): an integrative approach based on genes and morphology. Molecular Phylogenetics and Evolution, 61, 381-391.
43. Olave, M., Avila, L. J., Sites, J. W. Jr & Morando, M. (2012) Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata). First Joint Congress in Evolutionary Biology, Ottawa, Canada.
44. Penny, D. & Hendy, M. D. (1985). The use of tree comparison metrics. Systematic Zoology, 34, 75-82.
45. Portik, D., Wood, P. L., Jr, Grismer, J. L., Stanley, E. L. & Jackman, T. R. (2012). Identification of 104 rapidly-evolving nuclear protein-coding markers for amplification across scaled reptiles using genomic resources. Conservation Genetic Resources, 4, 1-10.
46. Posada, D. (2008). jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
47. Pyron, R. A., Burbrink, F. T. & Wiens, J. J. (2013). A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology, 2013, 13-93.
48. Quinteros, S. A. & Abdala, C. S. (2011). A new species of Liolaemus of the Liolaemus montanus section (Iguania: Liolaemidae) from Northwestern Argentina. Zootaxa, 2789, 35-48.
49. Ronquist, F. & Huelsenbeck, J. P. (2003). MrBayes version 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
50. Schulte, J. A., II, Macey, J. R., Espinoza, R. E. & Larson, A. (2000). Phylogenetic relationships in the iguanid lizard genus Liolaemus: multiple origins of viviparous reproduction and evidence for recurring Andean vicariance and dispersal. Biological Journal of the Linnean Society of London, 69, 75-102.
51. Than, C. & Nakhleh, L. (2009). Species tree inference by minimizing deep coalescences. PLoS Computational Biology, 5, e1000501. doi:10.1371/journal.pcbi.1000501
52. Than, C. & Nakhleh, L. (2010). Inference of parsimonious species phylogenies from multi-locus data by minimizing deep coalescences. In L. L. Knowles & L. S. Kubatko (Eds) Estimating Species Trees: Practical and Theoretical Aspects (pp. 79-98). Hoboken, NJ: Wiley-VCH.
53. Townsend, T. M., Alegre, R. E., Kelley, S. T., Wiens, J. J. & Reeder, T. W. (2008). Rapid developmental of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles. Molecular Phylogenetics and Evolution, 47, 129-142.
54. Whitfield, J. B. & Lockhart, P. J. (2007). Deciphering ancient rapid radiations. Trends in Ecology and Evolution, 22, 258-265.
55. Wiens, J. J., Reeder, T. W. & Montes de Oca, A. N. (1999). Molecular phylogenetics and evolution in sexual dichromatism among population of the Yarrow's spiny lizard (Sceloporus jarrovii). Evolution, 53, 1884-1897.
56. Yang, Z. & Rannala, B. (2010). Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences, USA, 107, 9264-9269.