1.Avise JC: Phylogeography: The History and Formation of Species. Harvard University Press. Cambridge, Massachussetts; 2000.
2.Avise JC: Phylogeography: Retrospect and prospect. J Biogeogr 2008, 36: 3–15.
3.D’Amen M, Zimmermann NE, Pearman PB: Conservation of phylogeographic lineages under climate change. Glob Ecol Biogeogr 2012, 22: 93–104.
4.Hickerson MJ, Stahl E, Takebayashi N: msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation. BMC Bioinform 2007, 8, 268. doi: 10.1186/1471–2105–8–268
5.Barrera-Guzmán AO, Milá B, Sánchez-González LA, Navarro-Sigüenza AG: Speciation in an avian complex endemic to the mountains of Middle America (Ergaticus, Aves: Parulidae). Mol Phylogenet Evol 2012, 62(3): 907–920. doi: 10.1016/j.ympev.2011.11.020
6.Hewitt GM: The genetic legacy of the Quaternary ice ages. Nature 2000, 405: 907–913.
7.Navarro-Sigüenza AG, Peterson AT, Nyari A, García-Deras GM, García-Moreno J: Phylogeography of the Buarremon brush-finch complex (Aves, Emberizidae) in Mesoamerica. Mol Phylogenet Evol 2008, 47: 21–35.
8.Navarro-Sigüenza AG, García-Hernández MA, Peterson AT: A new species of brush-finch (Arremon; Emberizidae) from western Mexico. Wilson J Ornithol 2013, 125: 443–684.
9.Cicero C, Koo MS: The role of niche divergence and phenotypic adaptation in promoting lineage diversification in the Sage Sparrow (Artemisiospiza belli, Aves: Emberizidae). Biol J Linn Soc 2012, 107: 332–354.
10.González C, Ornelas JF, Gutiérrez-Rodríguez C: Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis). BMC Evol Biol 2011, 11:38. doi: 10.1186/1471–2148–11–38
11.Milá B, Wayne RK, Fitze P, Smith TB: Divergence with gene flow and fine-scale phylogeographical structure in the wedge-billed woodcreeper, Glyphorynchus spirurus, a Neotropical rainforest bird. Mol Ecol 2009, 18: 2979–2995. doi: 10.1111/j.1365–294X.2009.04251.x
12.Pérez-Emán JL, Mumme RL, Jabloński PG: Phylogeography and adaptive plumaje evolution in central american subspecies of the slate-throated redstart (Myioborus miniatus). Ornithol Monogr 2010, 67: 90–102.
13.Ortíz-Ramírez MF, Andersen MJ, Zaldívar-Riverón A, Ornelas JF, Navarro-Sigüenza AG: Geographic isolation drives divergence of uncorrelated genetic and song variation in the Ruddy-capped Nightingale-Thrush (Catharus frantzii; Aves: Turdidae). Mol Phylogenet Evol 2016, 94: 74–86. doi: 10.1016/j.ympev.2015.08.017
14.Arbeláez-Cortés E: Filogeografía comparada: conceptos, métodos y patrones generales en aves Neotropicales. Acta Biolo Colomb 2012, 17: 19–38.
15.Arbeláez-Cortés E, Milá B, Navarro-Sigüenza AG: Multilocus analysis of intraspecific differentiation in three endemic bird species from the northern Neotropical dry forest. Mol Phylogenet Evol 2014, 70: 236–377. doi: 10.1016//j.mpev.2013.10.006
16.Linder HP: On areas of endemism, with an example from the African Restionaceae. Syst Biol 2001, 50: 892–912. doi: 10.1080/106351501753462867
17.Sánchez-González LA, Navarro-Sigüenza AG: History meets ecology: a geographical analysis of ecological restriction in the Neotropical humid montane forest avifaunas. Divers Distrib 2009, 15: 1–11.
18.Harris D, Rogers DS, Sullivan J: Phylogeography of Peromyscus furvus (Rodentia; Muridae) based on cytochrome b sequence data. Mol Ecol 2000, 9: 2129–2135. doi: 10.1046/j.1365–294x.2000.01135.x
19.Muñoz-Villers LE, López-Blanco J: Land use/cover changes using Landsat TM/ETM images in a tropical and biodiverse montainous area of central-eastern Mexico. Int J Remote Sens 2007, 29: 71–93.
20.Hernández-Baños BE, Peterson AT, Navarro-Sigüenza AG, Escalante-Pliego P: Bird faunas of the humid montane forests of Mesoamerica. Biogeographic patterns and priorities for conservation. Bird Conserv Int 1995, 5: 251–277.
21.Luna-Vega I, Espinosa D, Contreras-Medina R: Biodiversidad de la Sierra Madre del Sur. Universidad Nacional Autónoma de México, Ciudad de México; 2016.
22.Morales R, Escalante T, Noguera-Urbano EA, Gámez N, Rodríguez-Tapia G: Conservation biogeography in the Mexican Mountain Component: bridging conservation and patterns of endemism. Therya 2016, 7(2): 215–229. doi: 10.12933/therya–16–329
23.Antonelli A, Kissling WD, Flantua SG, Bermúdez MA, Mulch A, Muellner-Riehl AN, Kreft H, Linder HP, Badgley C, Fjeldså J, Fritz SA, Rahbek C, Herman F, Hooghiemstra H, Hoorn C: Geological and climatic influences on mountain biodiversity. Nat Geosci 2018, 11: 718–725. doi: 10.1038/s41561–018–0236-z
24.Bertelli S, Szumik C, Goloboff PA, Giannini NP, Navarro-Sigüenza AG, Peterson AT, Cracraft J: Mexican land birds reveal complexity in fine-scale patterns of endemism. J Biogeogr 2017, 44(8): 1836–1846. doi: 10.1111/jbi.12987
25.Carnaval AC, Hickerson MJ, Haddad CFB, Rodrigues MT, Moritz C: Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot. Science 2009, 323(5915): 785–789. doi: 10.1126/science.1166955
26.García-Moreno J, Navarro-Sigüenza AG, Peterson AT, Sánchez-González LA: Genetic variation coincides with geographic structure in the common Bush-tanager (Chlorospingus ophthalmicus) complex from Mexico. Mol Phylogenet Evol 2004, 33: 186–196. doi: 10.1016/j.ympev.2004.05.007
27.Ornelas JF, Ruiz-Sánchez E, Sosa V: Phylogeography of Podocarpus matudae (Podocarpaceae): pre-Quaternary relicts in northern Mesoamerican cloud forests. J Biogeogr 2010, 37: 2384–2396. doi: 10.1111/j.1365–2699.2010.02372.x
28.Ornelas JF, Sosa V, Soltis DE, Daza JM, González C, Soltis PS, Gutiérrez-Rodríguez C, Espinosa de los Monteros A, Castoe TA, Bell C, Ruiz-Sánchez E: Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica. PLoS ONE 2013, 8:e56283
29.Halffter G, Llorente-Bousquets J, Morrone JJ: La perspectiva biogeográfica histórica. In Capital natural de México vol. I: Conocimiento actual de la biodiversidad. CONABIO, México; 2008: 67–86.
30.Campbell JA, Blancas-Hernández JC, Smith EN: A new species of stream-breeding treefrog of the genus Charadrahyla (Hylidae) from the Sierra Madre del Sur of Guerrero, Mexico. Copeia 2009, 2: 287–295.
31.Feria-Ortiz M, García-Vázquez UO: A new species of Plestiodon (Squamata: Scincidae) from Sierra Madre del Sur of Guerrero, México. Zootaxa 2012, 3339: 57–68.
32.González-Villarreal LM: Two new species of oak (Fagaceae, Quercus sect. Lobatae) from the Sierra Madre del Sur, Mexico. Brittonia 2003, 55(1): 49–60. doi: 10.1663/0007- 196X(2003)055[0049:TNSOOF]2.0.CO;2
33.Navarro-Sigüenza AG, Blancas-Calva E, Almazán-Núñez RC, Hernández-Baños BE, García-Trejo EA, Peterson AT: Diversidad y endemismo de las aves de la Sierra Madre del Sur. In Biodiversidad de la Sierra Madre del Sur. Edited by: Luna-Vega I, Espinosa D, Contreras-Medina R. Universidad Nacional Autónoma de México, Ciudad de México; 2016: 381–411.
34.Ordóñez-Garza N, Matson, JO, Strauss RE, Bradley RD, Salazar-Bravo J:. Patterns of phenotypic and genetic variation in three species of endemic Mesoamerican Peromyscus (Rodentia: Cricetidae). J Mammal 2010, 91(4): 848–859. doi: 10.1644/09-MAMM-A–167.1
35.Morrone JJ: Halffter’s Mexican transition zone (1962–2014), cenocrons and evolutionary biogeography. J Zool Syst Evol Res 2015, 53: 249–257. doi: 10.1111/jzs.12098
36.Barrier E, Velasquillo L, Chavez M, Gaulon R: Neotectonic evolution of the Isthmus of Tehuantepec (southeastern Mexico). Tetonophysics 1998, 287(1–4): 77–96. doi: 10.1016/s0040–1951(98)80062–0
37.Ferrari L, Orozco-Esquivel T, Manea V, Manea M: The dynamic history of the Trans-Mexican Volcanic Belt and the Mexico subduction zone. Tectonophysics 2012, 522: 122–149.
38.Morán-Zenteno DJ, Tolson G, Martínez-Serrano RG, Martiny B, Schaaf P, Silva-Romo G, Macías-Romo C, Alba-Aldave L, Hernández-Bernal MS, Solis-Pichardo GN: Tertiary arc-magnetism of the Sierra Madre del Sur, Mexico, and its transition of the volcanic activity of the Trans-Mexican Volcanic Belt. J S Am Earth Sci 1999, 12(6): 513–535.
39.Morán-Zenteno DJ, Martiny B, Tolson G, Solís-Pichardo G, Alba-Aldave L, Hernández-Bernal M del Sol, Macías-Romo C, Martínez-Serrano RG, Schaaf P, Silva-Romo G: Geocronología y características geoquímicas de las rocas magmáticas de la Sierra Madre del Sur. B Soc Geol Mex 2000, 53: 27–58.
40.Morrone JJ: Biogeographic regionalization of the Sierra Madre del Sur province, Mexico. Rev Mex Biodivers 2017, 88: 710–714. doi: 10.1016/j.rmb.2017.07.012
41.Arbeláez-Cortés E, Roldán-Piña D, Navarro-Sigüenza AG: Multilocus phylogeography and morphology give insights into the recent evolution of a Mexican endemic songbird: Vireo hypochryseus. J Avian Biol 2014, 45(3): 253–263. doi: 10.1111/j.1600–048X.2013.00335.x
42.Cortés-Rodríguez N, Hernández-Baños BE, Navarro-Sigüenza AG, Peterson AT, García-Moreno J: Phylogeography and population genetics of the Amethyst-throated Hummingbird (Lampornis amethystinus). Mol Phylogenet Evol 2008, 48: 1–11. doi: 10.1016/j.ympev.2008.02.005
43.Klicka J, Spellman GM, Winker K, Chua V, Smith BT: A phylogeographic and population genetic analysis of a widespread, sedentary North American bird: The Hairy Woodpecker (Picoides villosus). Auk 2011, 128(2): 346–362. doi: 10.1525/auk.2011.10264
44.Mason NA, Olvera-Vital A, Lovette IJ, Navarro-Sigüenza AG: Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White-collared Seedeater complex (Thraupidae: Sporophila torqueola). Ecol Evol 2018, 8(3): 1867–1881. doi: 10.1002/ece3.3799
45.Núñez-Zapata J, Peterson AT, Navarro-Sigüenza AG: Pleistocene diversification and speciation of White-throated Thrush (Turdus assimilis; Aves: Turdidae). J Ornithol 2016, 157(4): 1073–1085. doi: 10.1007/s10336–016–1350–6
46.Navarro-Sigüenza AG, Peterson AT: An alternative species taxonomy of the birds of Mexico. Biota Neotrop 2004, 4: 1–32.
47.Chan LM, Brown JL, Yoder AD: Integrating statistical genetic and geospatial methods bring new power to phylogeography. Mol Phylogenet Evol 2011, 59: 523–537.
48.Duennes MA, Lozier JD, Hines HM, Cameron SA: Geographical patterns of genetic divergence in the widespread Mesoamerican bumblebee Bombus ephippiatus (Hymenoptera: Apidae). Mol Phylogenet Evol 2012, 64(1): 219–231. doi: 10.1016/j.ympev.2012.03.018
49.Masta S: Phylogeography of the jumping spider Habronattus pugillis (Araneae: Salticidae): recent vicariance of sky island populations? Evolution 2000, 54: 1699–1711.
50.McCormack JE, Bowen BS, Smith TB: Integrating paleoecology and genetics of bird populations in two sky island archipelagos. BMC Biol 2008, 6: 28. doi: 10.1186/1441–7007–6–28
51.Tennessen JA, Zamudio KR: Genetic differentiation among mountain island populations of the Striped Plateau Lizard, Sceloporus virgatus (Squamata: Phrynosomatidae). Copeia 2008, 2008(3): 558–564. doi: 10.1643/CG–06–038
52.Endo Y, Nash M, Hoffmann AA, Slatyer R, Miller AD: Comparative phylogeography of alpine invertebrates indicates deep lineage diversification and historical refugia in the Australian Alps. J Biogeogr 2015, 42: 89–102. doi: 10.1111/jbi.12387
53.Ornelas JF, González C, Hernández-Baños BE, García-Moreno J: Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird. Ecol Evol 2016, 6(4): 1104–1127. doi: 10.1002/ece3.1950
54.Oswald JA, Overcast I, Mauck WM, Andersen MJ, Smith BT: Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds. Mol Ecol 2017, 26(5): 1386–1400. doi:10.1111/mec.14013
55.Qu Y, Lei F: Comparative phylogeography of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Hume’s ground tit (Pseudopodoces humilis). Mol Phylogenet Evol 2009, 51: 312–326. doi: 10.1016/j.ympev.2009.01.013
56.Qu Y, Lei F, Zhang R, Lu X: Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau. Mol Ecol 2010, 19: 338–351. doi: 10.1111/j.1365–294X.2009.04445.x
57.Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS: Comparative phylogeography of unglaciated Eastern North America. Mol Ecol 2006, 15: 4261–4293. doi: 10.1111/j.1365–294X.2006.03061.x
58.Frankham R: Challenges and opportunities of genetic approaches to biological conservation. Biol Conserv 2010, 143: 1919–1927 doi: 10.1016/j.biocon.2010.05.011
59.Frankham R, Bradshaw CJA, Brook BW: Genetics in conservation management: Revised recommendations for the 50/50 rules, Red List criteria and population viability analyses. Biol Conserv 2014, 170: 56–63 doi: 10.1016/j.biocon.2013.12.036
60.Gamble T, Colli GR, Rodrigues MT, Werneck FP, Simons AM: Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America’s open biomes. Mol Phylogenet Evol 2011, 62: 943–953. doi: 10.1016/j.ympev.2011.11.033
61.Moritz C, Faith DP: Comparative phylogeography and the identification of genetically divergent areas for conservation. Mol Ecol 1998, 7: 419–429.
62.Pearse DE, Crandall KA: Beyond FST: Analysis of population genetic data for conservation. Conserv Genet 2004, 5: 585–602.
63.Qu Y, Song G, Gao B, Quan Q, Ericson PGP, Lei F: The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography. J Biogeogr 2015, 42: 179–192.
64.Yannic, G, St-Laurent MH, Ortego J, Taillon J, Beauchemin A, Bernatchez L, Dussault C, Côté SD: Integrating ecological and genetic structure to define management units for caribou in Eastern Canada. Conserv Genet 2016, 17: 437–453. doi: 10.1007/s10592–015–0795–0
65.Avendaño JE, Stiles FG, Cadena CD: A new subspecies of Common Bush-Tanager (Chlorospingus flavopectus, Emberizidae) from the east slope of the Andes of Colombia. Ornitología Colombiana 2013, 13: 44–58.
66.Bonaccorso E, Navarro-Sigüenza AG, Sánchez-González LA, Peterson AT, García-Moreno J: Genetic differentiation of the Chlorospingus ophthalmicus complex in Mexico and Central America. J Avian Biol 2008, 39: 311–321. doi: 10.1111/j.2008.0908–8857.04233.x
67.Bonaccorso E, Guayasamin JM, Peterson AT, Navarro-Sigüenza AG: Molecular phylogeny and systematics of Neotropical toucanets in the genus Aulacorhynchus. Zool Scr 2011, 40: 336–349.
68.Hernández-Baños BE, Zamudio-Beltrán LE, García-Moreno J, Eguiarte LE: Phylogenetic relationships within the genus Eupherusa inferred from mtDNA sequences. Ornitol Neotrop 2012, 23: 55–62.
69.Lovette IJ, Pérez-Emán JL, Sullivan JP, Banks RC, Fiorentino I, Córdoba-Córdoba S, Echeverry-Galvis M, Barker FK, Burns KJ, Klicka J, Lanyon SM, Bermingham E: A comprehensive multilocus phylogeny for the Wood-warblers and a revised classification of the Parulidae (Aves). Mol Phylogenet Evol 2010, 57: 753–770. doi: 10.1016/j.ympev.2010.07.018
70.Maldonado-Sánchez D, Gutiérrez-Rodríguez C, Ornelas JF: Genetic divergence on the common bush-tanager Chlorospingus ophthalmicus (Aves: Emberizidae) throughout Mexican cloud forests: The role of geography, ecology and Pleistocene climatic fluctuations. Mol Phylogenet Evol 2016, 99: 76–88. doi: 10.1016/j.ympev.2016.03.014
71.McGuire JA, Witt CC, Altshuler DL, Remsen JV: Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Syst Biol 2007, 56(5): 837–856. doi: 10.1080/10635150701656360
72.McGuire JA, Witt CC, Remsen JV, Corl A, Rabosky DL, Altshuler DL, Dudley R: Molecular phylogenetics and the diversification of hummingbirds. Curr Biol 2014, 24(8): 910–916. doi: 10.1016/j.cub.2014.03.016
73.Navarro-Sigüenza AG, Peterson AT, López-Medrano E, Benítez-Díaz H: Species limits in Mesoamerican Aulacorhynchus toucanets. Wilson J Ornithol 2001, 113(4): 363–372. doi: 10.1676/0043–5643(2001)113[0363:SLIMAT]2.0.CO;2
74.Puebla-Olivares F, Bonaccorso E, Espinosa de los Monteros A, Omland KE, Llorente-Busquets JE, Peterson, AT, Navarro-Sigüenza AG: Speciation in the emerald toucanet (Aulacorhynchus prasinus) complex. Auk 2008, 125: 39–50.
75.Sánchez-González LA, Navarro-Sigüenza AG, Peterson AT, García-Moreno J: Taxonomy of Chlorospingus ophthalmicus in Mexico and northern Central America. Bull Br Ornithol Club 2007, 127(1): 34–49.
76.Schindel DE, Stoeckle MY, Milensky CM, Trizna M, Schmidt BK, Gebhard CA, Graves GR: Project Description: DNA barcodes of bird species in the National Museum of Natural History, Smithsonian Institution, USA. ZooKeys 2011, 152: 87–91. doi: 10.3897/zookeys.152.2473
77.Lanfear R, Calcott B, Ho SYW, Guindon S: PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses. Mol Biol Evol 2012, 29(6): 1695–1701.
78.Hunt JS, Bermingham E, Ricklefs RE: The molecular systematics and biogeography of Antillean thrashers, tremblers and mockingbirds (Aves: Mimidae). Auk 2001, 118(1): 35–55.
79.Lovette IJ: Molecular phylogeny and plumage signal evolution in a trans Andean and circum Amazonian avian species complex. Mol Phylogenet Evol 2005, 32: 512–523. doi: 10.1016/j.ympev.2004.01.007
80.Ronquist F, Huelsenbeck J, Teslenko M: MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 2011, 61(3): 539–542. doi: 10.1093/sysbio/sys029
81.Rambaut A, Suchard MA, Xie D, Drummond AJ: Tracer v1.6 (2014, available from http://beast.bio.ed.ac.uk/Tracer)
82.Silvestro D, Michalak I: raxmlGUI: a graphical front-end for RAxML. Org Divers Evol 2012, 12(4): 335–337. doi: 10.1007/s13127–011–0056–0
83.Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21): 2688–2690. doi: 10.1093/bioinformatics/btl446
84.Stamatakis A: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30(9): 1312–1313. doi: 10.1093/bioinformatics/btu033
85.Bandelt HJ, Forster P, Röhl A: Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999, 16(1): 37–48.
86.Crandall KA, Templeton AR: Applications of intraspecific phylogenetics. In New uses for new phylogenies. Edited by: Harvey PH, Leigh Brown AJ, Maynard Smith J, Nee, S. Oxford, UK: Oxford University Press; 1996: 81–99.
87.Guillot G, Estoup A, Mortier F, Cosson JF: A spatial statistical model for landscape genetics. Genetics 2005, 170: 1261–1280.
88.Guillot G, Mortier F, Estoup A: Geneland: A program for landscape genetics. Mol Ecol Notes 2005, 5: 712–715.
89. Wright S: Evolution in Mendelian populations. Genetics 1931, 16(2): 97–159.
90.Wright S: Evolution and genetics of populations. Vol. 4.Variability Within and Among Natural Populations. Univ. of Chicago Press, Chicago; 1978.
91.Hartl DL, Clark AG: Principles of population genetics (Vol. 116). Sunderland: Sinauer Associates; 1997
92.Fu YX: Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147: 915–925.
93.Tajima F: Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123: 585–595.
94.Excoffier L, Laval G, Schneider S: Arlequin ver 3.0: An integrated software package for population genetics data analysis. Evol Bioinform Online 2005, 1: 47–50.
95.Drummond AJ, Suchard MA, Xie D, Rambaut A: Bayesian phylogenetics with BEAUTi and the BEAST 1.7. Mol Biol Evol 2012, 29: 1969–1973.
96.Xie WG, Lewis PO, Fan Y, Kuo L, Chen MH: Improving marginal likelihood estimation for bayesian phylogenetic model selection. Syst Biol 2011, 60: 150–160.
97.Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253, 769–778. doi: 10.1016/j.jtbi.2008.04.005
98.Yule GU: A Mathematical theory of evolution based on the conclusions of Dr. J C Willis. Philos Trans Royal Soc B 1925, 213: 21–87. doi: 10.1098/rstb.1925.0002
99.Nabholz B, Lanfear R, Fuchs J: Body mass-corrected molecular rate for bird mitochondrial DNA. Mol Ecol 2016, 25: 4438–4449. doi: 10.1111/mec.13780
100.Drummond AJ, Ho SYW, Phillips MJ, Rambaut A: Relaxed phylogenetics and dating with confidence. PLoS Biol 2006, 4(5): e88. doi: 10.1371/journal.pbio.0040088
101.Pons J, Ribera I, Bertranpetit J, Balke M: Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera. Mol Phylogenet Evol 2010, 56: 796–807. doi: 10.1016/j.ympev.2010.02.007
102.Tong KJ, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW: A comparison of methods for estimating substitution rates from ancient sequence data. BMC Evol Biol 2018, 18:70. doi: 10.1186/s12862–018–1192–3
103.Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV: Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol 2012, 29(9): 2157–2167. doi: 10.1093/molbev/mss084
104.Baele G, Li WLS, Drummond AJ, Suchard MA, Lemey P: Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol Biol Evol 2013, 30(2): 239–243. doi: 10.1093/molbev/mss243
105.Raftery AE: Approximate Bayes factors and accounting for model uncertainty in generalized linear models. Biometrika 1996, 83: 251–266.
106.Cornuet JM, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois R, Martin JM, Estoup A: DIY ABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics 2014, 30(8): 1187–1189. doi: 10.1093/bioinformatics/btt763
107.Bertorelle G, Benazzo A, Mona S: ABC as a flexible framework to estimate demography over space and time: Some cons, many pros. Mol Ecol 2010, 19: 2609–2625.
108.Knowles LL, Alvarado-Serrano DF: Exploring the population genetic consequences of the colonization process with spatio-temporally explicit models: insights from coupled ecological, demographic and genetic models in montane grasshoppers. Mol Ecol 2010, 19(17): 3727–3745. doi: 10.1111/j.1365–294X.2010.04702.x
109.Lerner HRL, Meyer M, James HF, Hofreiter M, Fleischer RC: Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian Honeycreepers. Curr Biol 2011, 21: 1838–1844.
110.Lim HC, Sheldon FH: Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia. Mol Ecol 2011, 20: 3414–3438.
111.Manthey JD, Klicka J, Spellman GM: Isolation-driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae). Mol Ecol 2011, 20: 4371–4384.
112.Smith BT, Klicka J: The profound influence of the Late Pliocene Panamanian uplift on the exchange, diversification, and distribution of New World birds. Ecography 2010, 33: 333–342.
113.Weir JT, Schluter D: Calibrating the avian molecular clock. Mol Ecol 2008, 17: 2321–2328.
114.Cornuet JM, Ravigne V, Estoup A: Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). BMC Bioinform 2010, 11: 401. doi: 10.1186/1471–2105–11–401
115.Fontaine MC, Austerlitz F, Giraud T, Labbé F, Papura D, Richard-Cervera S, Delmotte F: Genetic signature of a range expansion and leap-frog event after the recent invasion of Europe by the grapevine downy mildew pathogen Plasmopara viticola. Mol Ecol 2013, 22(10): 2771–2786. doi: 10.1111/mec.12293
116.Licona-Vera Y, Ornelas JF, Wethington S, Bryan KB: Pleistocene range expansions promote divergence with gene flow between migratory and sedentary populations of Calothorax hummingbirds. Biol J Linn Soc 2018, 124: 645–667.
117.Darriba D, Taboada GL, Doallo R, Posada D: jModelTest2: more models, new heuristics and parallel computing. Nat Methods 2012, 9(8): 772.
118.Guindon S, Gascuel O: A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Syst Biol 2003, 52: 696–704.
119.Bagley JC, Hickerson M, Johnson JB: Testing hypotheses of diversification in Panamanian frogs and freshwater fishes using hierarchical approximate Bayesian computation with model averaging. Diversity 2018, 10(4): 120. doi: 10.3390/d10040120
120.Stone GN, Lohse K, Nicholls JA, Fuentes-Utrilla P, Sinclair F, Schoenrogge K, Csoka G, Melika G, Nieves-Aldrey JL, Pujade-Villar J, Tavakoli M, Askew RR, Hickerson MJ: Reconstructing community assembly in time and space reveals enemy scape in a western Paleartic insect community. Curr Biol 2012, 22(6): 532–537. doi: 10.1016/j.cub.2012.01.059
121.Zamudio-Beltrán LE, Hernández-Baños BE: Genetic and morphometric divergence in the Garnet-Throated Hummingbird Lamprolaima rhami (Aves: Trochilidae). Peer J 2018 6:e5733. doi: 10.7717/peerj.5733
122.Cabanne G, Dhorta F, Sari E, Santos F, Miyaki C: Nuclear and mitochondrial phylogeography of the Atlantic forest endemic Xiphorhynchus fuscus (Aves: Dendrocolaptidae): Biogeography and systematics implications. Mol Phylogenet Evol 2008, 49(3): 760–773. doi: 10.1016/j.ympev.2008.09.013
123.Sánchez-González LA, Morrone JJ, Navarro-Sigüenza AG: Distributional patterns of the Neotropical montane forest avifaunas. Biol J Linn Soc 2008, 94(1): 175–194. doi: 10.1111/j.1095–8312.2008.00979.x
124.Devitt TJ: Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Neartic-Neotropical transition. Mol Ecol 2006, 15(14): 4387–4407. doi: 10.1111/j.1365–294X.2006.03015.x
125.Hernández-Baños BE: Filogenia del género Eupherusa Gould (Aves: Trochilidae). Doctoral dissertation 1998, Facultad de Ciencias, Universidad Nacional Autónoma de México, México.
126.Vázquez-Miranda H, Navarro-Sigüenza AG, Omland KE: Phylogeography of the Rufous-Naped Wren (Campylorhynchus rufinucha): Speciation and Hybridization in Mesoamerica. Auk 2009, 126(4): 765–778. doi: 10.1525/auk.2009.07048
127.Flores-Villela O, Sánchez-H O: A new species of Abronia (Squamata:Anguidae) from the Sierra Madre del Sur of Guerrero, Mexico, with comments on Abronia deppii. Herpetologica 2003, 59(4): 524–531. doi: 10.1655/02–39
128.Nieto-Montes de Oca A, Campbell JA, Flores-Villela O: A new species of Xenosaurus (Squamata: Xenosauridae) from the Sierra Madre del Sur of Oaxaca, Mexico. Herpetologica 2001, 57(1): 32–47.
129.Zarza E, Reynoso VH, Emerson BC: Diversification in the northern neotropics: mitochondrial and nuclear DNA phylogeography of the iguana Ctenosaura pectinata and related species. Mol Ecol 2008, 17: 3259–3275. doi: 10.1111/j.1365–294X.2008.03826.x
130.Gibbard P, van Kolfschoten T: The Pleistocene and Holocene Epochs. In A Geologic Time Scale 2004. Edited by Gradstein FH, Ogg JG, Smith AG. Cambridge University Press; 2005: 441–452.
131.Lüthi D, Le Floch M, Bereiter B, Blunier T, Barnola JM, Siegenthaler U, Raynaud D, Jouzel J, Fischer H, Kawamura K, Stocker TF: High-resolution carbon dioxide concentration record 650,000–800,000 years before present. Nature 2008, 453(7193): 379–382. doi: 10.1038/nature06949
132.Grant WS, Bowen BW: Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. J Hered 1998, 89: 415–426.
133.Watterson GA: Allele frequencies after a bottleneck. Theor Popul Biol 1984, 26: 387–407.
134.Barber PH: Phylogeography of the canyon treefrog, Hyla arenicolor (Cope) based on mitochondrial DNA sequence data. Mol Ecol 1999, 8(4): 547–562. doi: 10.1046/j.1365–294X.1999.00593.x
135.Frankham R: Do island populations have less genetic variation than mainland populations? Heredity 1997, 78(3): 311–327.
136.Barker BS, Rodríguez-Robles JA, Aran VS, Montoya A, Waide RB, Cook JA: Sea level, topography, and island diversity: Phylogeography of the Puerto Rican Red-eyed Coquí, Eleutherodactylus antillensis. Mol Ecol 2012, 21(24): 6033–6052. doi: 10.1111/mec.12020
137.Gutiérrez-García TA, Vázquez-Domínguez E: Consensus between genes and stones in the biogeographic and evolutionary history of Central America. Quat Res 2013, 79(3): 311–324. doi: 10.1016/j.yqres.2012.12.007
138.Bryson RW, García-Vázquez UO, Riddle BR: Relative roles of Neogene vicariance and Quaternary climate change on the historical diversification of bunchgrass lizards (Sceloporus scalaris group) in Mexico. Mol Phylogenet Evol 2012, 62: 447–457. doi: 10.1016/j.ympev.2011.10.014
139.Verma SP, Carrasco-Núñez G: Reappraisal of the geology and geochemistry of Volcán Zamorano, Central Mexico: Implications for discriminating the Sierra Madre Occidental and the Mexican Volcanic Belt. Int Geol Rev 2003, 45: 724–752.
140.Smith BT, McCormack JE, Cuervo AM, Hickerson MJ, Aleixo A, Cadena CD, Pérez-Emán J, Burney CW, Xie X, Harvey MG, Faircloth BC, Glenn TC, Derryberry EP, Prejean J, Fields S, Brumfield RT: The drivers of tropical speciation. Nature 2014, 515(7527): 406–409. doi: 10.1038/nature13687
141.Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB: Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu RevEcol Evol Syst 2002, 33: 707–740. doi: 10.1146/annurev.ecolsys.33.010802.150500
142.Barber BR, Klicka J: Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna. Proc Royal Soc B 2010, 277(1694): 2675–2681. doi: 10.1098/rspb.2010.0343
143.Caballero M, Lozano-García S, Vázquez-Selem L, Ortega B: Evidencias de cambio climático y ambiental en registros glaciales y en cuencas del centro de México durante el último máximo glacial. B Soc Geol Mex 2010, 62: 359–377.
144.Lachniet MS, Vázquez-Selem L: Last Glacial Maximum equilibrium line altitudes in the circum-Caribbean (Mexico, Guatemala, Costa Rica, Colombia, and Venezuela). Quat Int 2005, 138: 129–144. doi: 10.1016/j.quaint.2005.02.010
145.Ramírez-Barahona S, Eguiarte LE: The role of glacial cycles in promoting genetic diversity in the Neotropics: the case of cloud forests during the last glacial maximum. Ecol Evol 2013, 3(3): 725–738. doi: 10.1002/ece3.483