Biogeographic calibrations for the molecular clock

Biology Letters

Volumn 11, Issue 9, 2015, Pages

  Ho, Simon Y W ^a   Tong, K Jun ^a   Foster, Charles S P ^a   Ritchie, Andrew M ^a   Lo, Nathan ^a   Crisp, Michael D ^b  

^a UNIVERSITY OF SYDNEY   (Australia)

^b AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Bayesian phylogenetics; Biogeography; Calibration; Divergence dating; Molecular clock

Indexed keywords

BAYESIAN ANALYSIS; BIOGEOGRAPHY; CALIBRATION; DIVERGENCE; EVOLUTIONARY BIOLOGY; FOSSIL; NUMERICAL MODEL; PHYLOGENETICS;

CALIBRATION; CLIMATE CHANGE; FOSSIL; GEOGRAPHIC AND GEOLOGICAL PHENOMENA; MOLECULAR EVOLUTION; PHYLOGENY; PHYLOGEOGRAPHY; PROCEDURES;

CALIBRATION; CLIMATE CHANGE; EVOLUTION, MOLECULAR; FOSSILS; GEOLOGICAL PHENOMENA; PHYLOGENY; PHYLOGEOGRAPHY;

EID: 84941591543     PISSN: 17449561     EISSN: 1744957X     Source Type: Journal    
DOI: 10.1098/rsbl.2015.0194     Document Type: Review

References (57)

1. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB. 2002 Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst. 33, 707-740. (doi:10.1146/annurev.ecolsys.33.010802.150500).
2. Zuckerkandl E, Pauling L. 1962 Molecular disease, evolution, and genic heterogeneity. In Horizons in biochemistry (eds M Kasha, B Pullman), pp. 189- 225. New York, NY: Academic Press.
3. Ho SYW, Duchene S. 2014 Molecular-clock methods for estimating evolutionary rates and timescales. Mol. Ecol. 23, 5947-5965. (doi:10.1111/mec.12953).
4. Donoghue PC, Benton MJ. 2007 Rocks and clocks: calibrating the tree of life using fossils and molecules. Trends Ecol. Evol. 22, 424-431. (doi:10.1016/j.tree.2007.05.005).
5. Heath TA, Huelsenbeck JP, Stadler T. 2014 The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc. Natl Acad. Sci. USA 111, E2957-E2966. (doi:10.1073/pnas.1319091111).
6. Hipsley CA, Muller J. 2014 Beyond fossil calibrations: Realities of molecular clock practices in evolutionary biology. Front. Genet. 5, 138. (doi:10.3389/fgene.2014.00138).
7. Shapiro B, Ho SYW. 2014 Ancient hyaenas highlight the old problem of estimating evolutionary rates. Mol. Ecol. 23, 499-501. (doi:10.1111/mec.12621).
8. Kodandaramaiah U. 2011 Tectonic calibrations in molecular dating. Curr. Zool. 57, 116-124.
9. Forest F. 2009 Calibrating the tree of life: fossils, molecules and evolutionary timescales. Ann. Bot. 104, 789-794. (doi:10.1093/aob/mcp192).
10. Marko PB. 2002 Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the Isthmus of Panama. Mol. Biol. Evol. 19, 2005-2021. (doi:10.1093/oxfordjournals.molbev.a004024).
11. Rabosky DL. 2014 Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS ONE 9, e89543. (doi:10.1371/journal.pone.0089543).
12. Excoffier L, Foll M, Petit RJ. 2009 Genetic consequences of range expansions. Annu. Rev. Ecol. Evol. Syst. 40, 481-501. (doi:10.1146/annurev.ecolsys.39.110707.173414).
13. Ho SYW, Shapiro B. 2011 Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol. Ecol. Res. 11, 423-434. (doi:10.1111/j.1755-0998.2011.02988.x).
14. Crandall ED, Sbrocco EJ, DeBoer TS, Barber PH, Carpenter KE. 2012 Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf following the Last Glacial Maximum. Mol. Biol. Evol. 29, 707-719. (doi:10.1093/molbev/msr227).
15. Heads M. 2005 Dating nodes on molecular phylogenies: A critique of molecular biogeography. Cladistics 21, 62-78. (doi:10.1111/j.1096-0031.2005.00052.x).
16. Upchurch P. 2008 Gondwanan break-up: legacies of a lost world? Trends Ecol. Evol. 23, 229-236. (doi:10.1016/j.tree.2007.11.006).
17. Grobys JWG, Gohl K, Eagles G. 2008 Quantitative tectonic reconstructions of Zealandia based on crustal thickness estimates. Geochem. Geophys. Geosyst. 9, 1. (doi:10.1029/2007GC001691).
18. Schellart WP, Lister GS, Toy VG. 2006 A Late Cretaceous and Cenozoic reconstruction of the Southwest Pacific region: Tectonics controlled by subduction and slab rollback processes. Earth-Sci. Rev. 76, 191-233. (doi:10.1016/j.earscirev.2006.01.002).
19. Ericson PG, Klopfstein S, Irestedt M, Nguyen JMT, Nylander JA. 2014 Dating the diversification of the major lineages of Passeriformes (Aves). BMC Evol. Biol. 14, 8. (doi:10.1186/1471-2148-14-8).
20. Hewitt G. 2000 The genetic legacy of the Quaternary ice ages. Nature 405, 907-913. (doi:10.1038/35016000).
21. Karl SA, Toonen RJ, Grant WS, Bowen BW. 2012 Common misconceptions in molecular ecology: Echoes of the modern synthesis. Mol. Ecol. 21, 4171-4189. (doi:10.1111/j.1365-294X.2012.05576.x).
22. Edwards SV, Beerli P. 2000 Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54, 1839-1854. (doi:10.1111/j.0014-3820.2000.tb01231.x).
23. Hickerson MJ, Gilchrist MA, Takebayashi N. 2003 Calibrating a molecular clock from phylogeographic data: moments and likelihood estimators. Evolution 57, 2216-2225. (doi:10.1111/j.0014-3820.2003.tb00234.x).
24. Wiley EO. 1988 Vicariance biogeography. Annu. Rev. Ecol. Syst. 19, 513-542. (doi:10.1146/annurev.es.19.110188.002501).
25. Kodandaramaiah U. 2009 Use of dispersal-vicariance analysis in biogeography: A critique. J. Biogeogr. 37, 3-11. (doi:10.1111/j.1365-2699.2009.02221.x).
26. Papadopoulou A, Anastasiou I, Vogler AP. 2010 Revisiting the insect mitochondrial molecular clock: The mid-Aegean trench calibration. Mol. Biol. Evol. 27, 1659-1672. (doi:10.1093/molbev/msq051).
27. Lieberman BS. 1997 Early Cambrian paleogeography and tectonic history: A biogeographic approach. Geology 25, 1039-1042. (doi:10.1130/0091-7613(1997)025, 1039:ECPATH.2.3.CO;2).
28. Baldwin BG, Sanderson MJ. 1998 Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc. Natl Acad. Sci. USA 95, 9402- 9406. (doi:10.1073/pnas.95.16.9402).
29. Woodburne MO. 2010 The Great American Biotic Interchange: dispersals, tectonics, climate, sea level and holding pens. J. Mammal Evol. 17, 245-264. (doi:10.1007/s10914-010-9144-8).
30. Leigh EG, O'Dea A, Vermeij GJ. 2014 Historical biogeography of the Isthmus of Panama. Biol. Rev. 89, 148-172. (doi:10.1111/brv.12048).
31. Montes C et al. 2015 Middle Miocene closure of the Central American Seaway. Science 348, 226-229. (doi:10.1126/science.aaa2815).
32. Crayn DM, Costion C, Harrington MG. 2015 The Sahul-Sunda floristic exchange: dated molecular phylogenies document Cenozoic intercontinental dispersal dynamics. J. Biogeogr. 42, 11-24. (doi:10.1111/jbi.12405).
33. Peng Z, Ho SYW, Zhang Y, He S. 2006 Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes. Mol. Phylogenet. Evol. 39, 568-572. (doi:10.1016/j.ympev.2005.10.016).
34. Genner MJ, Seehausen O, Lunt DH, Joyce DA, Shaw PW, Carvalho GR, Turner GF. 2007 Age of cichlids: new dates for ancient lake fish radiations. Mol. Biol. Evol. 24, 1269-1282. (doi:10.1093/molbev/msm050).
35. Waters JM, Rowe DL, Apte S, King TM, Wallis GP, Anderson L, Norris RJ, Craw D, Burridge CP. 2007 Geological dates and molecular rates: Rapid divergence of rivers and their biotas. Syst. Biol. 56, 271-282. (doi:10.1080/10635150701313855).
36. Stauffer B. 1999 Climate change: cornucopia of ice core results. Nature 399, 412-413. (doi:10.1038/20807).
37. Lambeck K, Esat TM, Potter EK. 2002 Links between climate and sea levels for the past three million years. Nature 419, 199-206. (doi:10.1038/nature01089).
38. He LJ, Zhang AB, Weese D, Li SF, Li JS, Zhang J. 2014 Demographic response of cutlassfish (Trichiurus japonicus and T. nanhaiensis) to fluctuating palaeo-climate and regional oceanographic conditions in the China seas. Sci. Rep. 4, 6380. (doi:10.1038/srep06380).
39. Cook LG, Crisp MD. 2005 Directional asymmetry of long-distance dispersal and colonization could mislead reconstructions of biogeography. J. Biogeogr. 32, 741-754. (doi:10.1111/j.1365-2699.2005.01261.x).
40. Fleischer RC, McIntosh CE, Tarr CL. 1998 Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates. Mol. Ecol. 7, 533-545. (doi:10.1046/j.1365-294x.1998.00364.x).
41. Price JP, Clague DA. 2002 How old is the Hawaiian biota? Geology and phylogeny suggest recent divergence. Proc. R. Soc. Lond. B 269, 2429-2435. (doi:10.1098/rspb.2002.2175).
42. Hennig W. 1966 Phylogenetic systematics. Urbana, IL: University of Illinois Press.
43. Haines WP, Schmitz P, Rubinoff D. 2014 Ancient diversification of Hyposmocoma moths in Hawaii. Nat. Commun. 5, 3502. (doi:10.1038/ncomms4502).
44. Mairal M, Pokorny L, Aldasoro JJ, Alarcón M, Sanmartín I. 2015 Ancient vicariance and climatedriven extinction continental-wide disjunctions in Africa: The case of the Rand Flora genus Canarina (Campanulaceae). Mol. Ecol. 24, 1335-1354. (doi:10.1111/mec.13114).
45. Heads M. 2011 Old taxa on young islands: A critique of the use of island age to date island-endemic clades and calibrate phylogenies. Syst. Biol. 60, 204-218. (doi:10.1093/sysbio/syq075).
46. Vences M, Vieites DR, Glaw F, Brinkmann H, Kosuch J, Veith M, Meyer A. 2003 Multiple overseas dispersal in amphibians. Proc. R. Soc. Lond. B 270, 2435-2442. (doi:10.1098/rspb.2003.2516).
47. Sanderson MJ. 2002 Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol. 19, 101-109. (doi:10.1093/oxfordjournals.molbev.a003974).
48. Ho SYW, Phillips MJ. 2009 Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 58, 367- 380. (doi:10.1093/sysbio/syp035).
49. Yang Z, Rannala B. 2006 Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23, 212-226. (doi:10.1093/molbev/msj024).
50. Ho SYW. 2007 Calibrating molecular estimates of substitution rates and divergence times in birds. J. Avian Biol. 38, 409-414. (doi:10.1111/j.0908-8857.2007.04168.x).
51. Nowak MD, Smith AB, Simpson C, Zwickl DJ. 2013 A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses. PLoS ONE 8, e66245. (doi:10.1371/journal.pone.0066245).
52. Heath TA. 2012 A hierarchical Bayesian model for calibrating estimates of species divergence times. Syst. Biol. 61, 793-809. (doi:10.1093/sysbio/sys032).
53. Inoue J, Donoghue PC, Yang Z. 2010 The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst. Biol. 59, 74-89. (doi:10.1093/sysbio/syp078).
54. Duchêne S, Lanfear R, Ho SYW. 2014 The impact of calibration and clock-model choice on molecular estimates of divergence times. Mol. Phylogenet. Evol. 78, 277-289. (doi:10.1016/j.ympev.2014.05.032).
55. Hope AG, Ho SYW, Malaney JL, Cook JA, Talbot SL. 2014 Accounting for rate variation among lineages in comparative demographic analyses. Evolution 68, 2689-2700. (doi:10.1111/evo.12469).
56. Rogers AR, Harpending H. 1992 Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9, 552-569.
57. Bertorelle G, Benazzo A, Mona S. 2010 ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol. Ecol. 19, 2609-2625. (doi:10.1111/j.1365-294X.2010.04690.x).