Biodiversity Literature Repository

Submit to community
Liberated Data
Published August 7, 2014 | Version v1
Journal article Restricted

The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs

Description

Bryson Jr, Robert W., Smith, Brian Tilston, Oca, Adrian Nieto-Montes De, García-Vázquez, Uri Omar, Riddle, Brett R. (2014): The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs. Zoological Journal of the Linnean Society 172 (1): 103-116, DOI: 10.1111/zoj.12169, URL: http://dx.doi.org/10.1111/zoj.12169

Files

Restricted

The record is publicly accessible, but files are restricted. Log in to check if you have access.

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:FF90D817FFD9FFA8AF754D0FB36EF514

Related works

Cites
Publication: 10.5061/dryad.3rc02 (DOI)
Publication: 10.1093/sysbio/syt041 (DOI)
Has part
Figure: 10.5281/zenodo.5313673 (DOI)
Figure: 10.5281/zenodo.5313675 (DOI)
Figure: 10.5281/zenodo.5313677 (DOI)

References

  • Acevedo M, Young B. 2004. Hyla bocourti. The IUCN Red List of Threatened Species, Version 2014.1. Available at: http:// www.iucnredlist.org.
  • Ballard JWO, Whitlock MC. 2004. The incomplete naturalhistory of mitochondria. Molecular Ecology 13: 729- 744.
  • Barber PH. 1999. Phylogeography of Hyla arenicolor (Cope) based on mitochondrial sequence data. Molecular Ecology 8: 547-562.
  • Bossu CM, Near TJ. 2009. Gene trees reveal repeated instances of mitochondrial DNA introgression in orangethroat darters (Percidae: Etheostoma). Systematic Biology 58: 114- 129.
  • Bossuyt F, Milinkovitch MC. 2000. Convergent adaptive radiations in Madagascan and Asian ranid frogs reveal covariation between larval and adult traits. Proceedings of the National Academy of Sciences, USA 97: 6585- 6590.
  • Bryson RW, Garcia-Vazquez UO, Riddle BR. 2011a. Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone. Journal of Biogeography 38: 1570-1584.
  • Bryson RW, Murphy RW, Graham MR, Lathrop A, Lazcano-Villareal D. 2011b. Ephemeral Pleistocene woodlands connect the dots for highland rattlesnakes of the Crotalus intermedius group. Journal of Biogeography 38: 2299- 2310.
  • Bryson RW, Murphy RW, Lathrop A, Lazcano-Villareal D. 2011c. Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes. Journal of Biogeography 38: 697-710.
  • Bryson RW, Nieto-Montes de Oca A, Jaeger JR, Riddle BR. 2010. Elucidation of cryptic diversity in a widespread Nearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamic landscape. Evolution 64: 2315-2330.
  • Bryson RW, Pastorini J, Burbrink FT, Forstner MRJ. 2007. A phylogeny of the Lampropeltis mexicana complex (Serpentes: Colubridae) based on mitochondrial DNA sequences suggests evidence for species-level polyphyly within Lampropeltis. Molecular Phylogenetics and Evolution 43: 674-684.
  • Bryson RW, Smith BT, Nieto-Montes de Oca A, Garcia- Vazquez UO, Riddle BR. 2014. Data from: The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs. Dryad Digital Repository. doi: 10.5061/dryad.3rc02.
  • Carling MD, Brumfield RT. 2008. Haldane's rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sex-linked loci across the Passerina bunting hybrid zone. Evolution 62: 2600-2615.
  • Carstens BC, Knowles LL. 2007. Estimating phylogeny from gene tree probabilities in Melanoplus grasshoppers despite incomplete lineage sorting. Systematic Biology 56: 400-411.
  • Chan KMA, Levin SA. 2005. Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherit- ed DNA. Evolution 59: 720-729.
  • Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
  • Duellman WE. 1970. The hylid frogs of Middle America. Monograph of the Museum of Natural History, The University of Kansas 1: 1-753.
  • Duellman WE. 2001. The hylid frogs of middle America, 2nd edn. Lawrence, KS: Society for the Study of Amphibians and Reptiles.
  • Durish ND, Halcomb KE, Kilpatrick CW, Bradley RD. 2004. Molecular systematics of the Peromyscus truei species group. Journal of Mammalogy 85: 1160-1169.
  • Eckert AJ, Carstens BC. 2008. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Molecular Phylogenetics and Evolution 49: 832-842.
  • Edwards SV, Bensch S. 2009. Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008. Molecular Ecology 18: 2930-2933.
  • Edwards SV, Liu L, Pearl DK. 2007. High resolution species trees without concatenation. Proceedings of the National Academy of Sciences, USA 104: 5936-5941.
  • Eliosa-Leon HR. 2002a. Variacion geografica en Hyla eximia (Anura: Hylidae). MSc Thesis, Universidad Nacional Autonoma de Mexico.
  • Eliosa-Leon HR. 2002b. Variacion geografica en Hyla eximia (Anura: Hylidae). Boletin de la Sociedad Herpetologica Mexicana 10: 59-60.
  • Fa JE, Morales LM. 1993. Patterns of mammalian diversity in Mexico. In: Ramamoorthy TP, Bye R, Lot A, Fa J, eds. Biological diversity in Mexico: origins and distribution. New York: Oxford University Press, 319-361.
  • Fouquet A, Noonan BP, Rodrigues MT, Pech N, Gilles A, Gemmell NJ. 2012. Multiple Quaternary refugia in the eastern Guiana Shield revealed by comparative phylogeography of 12 frog species. Systematic Biology 61: 461- 489.
  • Funk DJ, Omland KE. 2003. Species-level paraphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology and Systematics 34: 397-423.
  • Good JM, Hird S, Reid N, Demboski JR, Steppan SJ, Martin-Nims TR, Sullivan J. 2008. Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular Ecology 17: 1313-1327.
  • Gross JB. 2012. The complex origin of Astyanax cavefish. BMC Evolutionary Biology 12: 105.
  • Heled J, Drummond A. 2010. Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution 27: 570-580.
  • Holloway AK, Cannatella DC, Gerhardt HC, Hillis DM. 2006. Polyploids with different origins and ancestors form a single sexual polyploidy species. American Naturalist 167: E88-E101.
  • Hua X, Fu C, Li J, Nieto-Montes de Oca A, Wiens JJ. 2009. A revised phylogeny of Holarctic treefrogs (genus Hyla) based on nuclear and mitochondrial DNA sequences. Herpetologica 65: 246-259.
  • Jezkova T. 2010. Reconstructing species responses to past climatic changes using niche modeling and genetic data. PhD Thesis, University of Nevada Las Vegas.
  • Joly S. 2012. JML: testing hybridization from species trees. Molecular Ecology Resources 12: 179-184.
  • Joly S, McLenachan PA, Lockhart PJ. 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. American Naturalist 174: e54-e70.
  • Jones KB. 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.
  • 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.
  • Katoh K, Toh H. 2008. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 9: 212.
  • Klymus KE, Gerhardt HC. 2012. AFLPs resolve intraspecific relationship and infer genetic structure among lineages of the canyon treefrog, Hyla arenicolor. Molecular Phylogenetics and Evolution 65: 654-667.
  • Klymus KE, Humfeld SC, Gerhardt HC. 2012. Geographic variation in male advertisement calls and female preference of the wide-ranging canyon treefrog, Hyla arenicolor. Biological Journal of the Linnean Society 107: 219-232.
  • Klymus KE, Humfeld SC, Marshall VT, Cannatella D, Gerhardt HC. 2010. Molecular patterns of differentiation in canyon treefrogs (Hyla arenicolor): evidence for introgressive hybridization with the Arizona treefrog (H. wrightorum) and correlations with advertisement call differences. Journal of Evolutionary Biology 23: 1425-1435.
  • Leache AD. 2010. Species trees for spiny lizards (genus Sceloporus): identifying points of concordance and conflict between nuclear and mitochondrial data. Molecular Phylogenetics and Evolution 54: 162-171.
  • Leache AD, McGuire JA. 2006. Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree. Molecular Phylogenetics and Evolution 39: 628- 644.
  • Linnen CR, Farrell BD. 2007. Mitonuclear discordance is caused by rampant mitochondrial introgression in Neodiprion (Hymenoptera: Diprionidae) sawflies. Evolution 61: 1417- 1438.
  • Liu L, Pearl DK. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology 56: 504-514.
  • Luxbacher AM, Knouft JH. 2009. Assessing concurrent patterns of environmental niche and morphological evolution among species of horned lizards (Phrynosoma). Journal of Evolutionary Biology 22: 1669-1678.
  • Markova S, Dufresne F, Manca M, Kotlik P. 2013. Mitochondrial capture misleads about ecological speciation in the Daphnia pulex complex. PLoS ONE 8: e69497.
  • Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462- 2463.
  • Monaghan MT, Wild R, Elliot M, Fujisawa T, Balke M, Inward DJG, Lees DC, Ranaivosolo R, Eggleton P, Barraclough TG, Vogler AP. 2009. Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Systematic Biology 58: 298-311.
  • Moore WS. 1995. Inferring phylogenies from mtDNA variation: mitochondrial gene trees versus nuclear gene trees. Evolution 49: 718-726.
  • Mulcahy DG, Spaulding A, Mendelson JR, Brodie ED Jr. 2006. Phylogeography of the Flat-tailed Horned lizard (Phrynosoma mcallii) and systematics of the P. mcallii- platyrhinos mtDNA complex. Molecular Ecology 15: 1807- 1826.
  • Nevado B, Fazalova V, Backeljau T, Hanssens M, Verheyen E. 2011. Repeated unidirectional introgression of nuclear and mitochondrial DNA between four congeneric Tanganyikan cichlids. Molecular Biology and Evolution 28: 2253-2267.
  • Nylander JAA. 2004. MRMODELTEST v2. Program distributed by the author. Uppsala: Evolutionary Biology Centre, Uppsala University.
  • Paniagua LL, Morrone JJ. 2009. Do the Oaxacan Highlands represent a natural biotic unit? A cladistic biogeographical test based on vertebrate taxa. Journal of Biogeography 36: 1939-1944.
  • Parra-Olea G, Garcia-Paris M, Papenfuss TJ, Wake DB. 2005. Systematics of the Pseudoeurycea bellii (Caudata: Plethodontidae) species complex. Herpetologica 61: 145-158.
  • Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology 55: 595- 609.
  • Puebla-Olivares F, Bonaccorso E, Espinosa de los Monteros A, Omland KE, Llorente-Bousquets JE, Peterson AT, Navarro-Siguenza AG. 2008. Speciation in the emerald toucanet (Aulacorhynchus prasinus) complex. The Auk 125: 39-50.
  • Pyron RA, Wiens JJ. 2011. A large-scale phylogeny of Amphibia including over 2,800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution 61: 543-583.
  • R Development Core Team. 2011. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing. Available at: http://www.R-project.org
  • Rabosky DL, Talaba AL, Donnellan SC, Lovette IJ. 2009. Molecular evidence for hybridization between two Australian desert skinks, Ctenotus leonhardii and Ctenotus quattuordecimlineatus (Scincidae : Squamata). Molecular Phylogenetics and Evolution 53: 368-377.
  • Rambaut A, Drummond AJ. 2007. Tracer v1.5. Available at: http://beast.bio.ed.ac.uk/Tracer
  • Reid NM, Demboski JR, Sullivan J. 2012. Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes. Systematic Biology 61: 44-62.
  • Ronquist F, Huelsenbeck JP. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
  • Ruane S, Bryson RW, Pyron RA, Burbrink FT. 2014. Coalescent species delimitation in milksnakes (genus Lampropeltis) and impacts on phylogenetic comparative analyses. Systematic Biology 63: 231-250.
  • Rubinoff D, Holland BS. 2005. Between two extremes: mitochondrial DNA is neither the panacea nor the nemesis of phylogenetic and taxonomic inference. Systematic Biology 54: 952-961.
  • Ruiz-Sanchez E, Specht CD. 2013. Influence of the geological history of the Trans-Mexican Volcanic Belt on the diversification of Nolina parviflora (Asparagaceae: Nolinoideae). Journal of Biogeography 40: 1336-1347.
  • Satler JD, Carstens BC, Hedin M. 2013. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus). Systematic Biology 62: 805-823. doi:10.1093/sysbio/syt041.
  • Shields GF, Adams D, Garner G, Labelle M, Pietsch J, Ramsay M, Schwartz C, Titus K, Williamson S. 2000. Phylogeography of mitochondrial DNA variation in brown bears and polar bears. Molecular Phylogenetics and Evolution 15: 319-326.
  • Smith SA, Nieto Montes de Oca A, Reeder TW, Wiens JJ. 2007. A phylogenetic perspective on elevational species richness patterns in Middle American treefrogs: why so few species in lowland tropical rainforests? Evolution 61: 1188-1207.
  • Stephens M, Donnelly P. 2003. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics 73: 1162- 1169.
  • Takahata N, Slatkin M. 1984. Mitochondrial DNA gene flow. Proceedings of the National Academy of Sciences, USA 81: 1764-1767.
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739.
  • Tang Q-Y, Liu S-Q, Yu D, Liu H-Z, Danley PD. 2012. Mitochondrial capture and incomplete lineage sorting in the diversification of balitorine loaches (Cypriniformes, Balitoridae) revealed by mitochondrial and nuclear genes. Zoologica Scripta 41: 233-247.
  • Tanner WW, Dixon JR, Harris HS. 1972. A new subspecies of Crotalus lepidus from western Mexico. Great Basin Naturalist 32: 16-24.
  • Toews DPL, Brelsford A. 2012. The biogeography of mitochondrial and nuclear discordance in animals. Molecular Ecology 21: 3907-3930.
  • Webb RG. 1984. Herpetogeography in the Mazatlan-Durango region of the Sierra Madre Occidental, Mexico. In: Seigel RA, Hunt LE, Knight JL, Malaret L, Zuschlag NL, eds. Vertebrate ecology and systematics - a tribute to Henry S. Fitch. Lawrence: Museum of Natural History, University of Kansas, 217-241.
  • Willis SC, Farias IP, Orti G. 2014. Testing mitochondrial capture and deep coalescence in Amazonian cichlid fishes (Cichlidae: Cichla). Evolution 68: 256-268. doi:10.1111/ evo.12230.
  • Willis SC, Nunes MS, Montana CG, Farias IP, Lovejoy NR. 2007. Systematics, biogeography, and evolution of the Neotropical peacock basses Cichla (Perciformes: Cichlidae). Molecular Phylogenetics and Evolution 44: 291-307.
  • Zakharov EV, Lobo NF, Nowak C, Hellmann JJ. 2009. Introgression as a likely cause of mtDNA paraphyly in two allopatric skippers (Lepidoptera: Hesperiidae). Heredity 102: 590-599.