Price RA, Liston A, Strauss SH. Phylogeny and systematics of *Pinus*. In: Richardson DM, editor. Ecology and Biogeography of *Pinus*. Cambridge: Cambridge University Press; 2000. p. 49–68.

Google Scholar

Millar CI. Early evolution of pines. In: Richardson DM, editor. Ecology and Biogeography of *Pinus*. Cambridge: Cambridge University Press; 2000. p. 69–91.

Google Scholar

Ryberg PE, Rothwell GW, Stockey RA, Hilton J, Mapes G, Riding JB. Reconsidering relationships among stem and crown group Pinaceae: oldest record of the genus *Pinus* from the Early Cretaceous of Yorkshire, United Kingdom. Int J Plant Sci. 2012;173(8):917–32.

Article
Google Scholar

Falcon-Lang HJ, Mages V, Collinson M. The oldest *Pinus* and its preservation by fire. Geology. 2016;44(4):303–6.

Article
Google Scholar

Gernandt DS, Lopez GG, Garcia SO, Liston A. Phylogeny and classification of *Pinus*. Taxon. 2005;54(1):29–42.

Article
Google Scholar

Parks M, Cronn R, Liston A. Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from *Pinus* L. (Pinaceae). BMC Evol Biol. 2012;12(1):100.

Article
PubMed
PubMed Central
Google Scholar

Little ELJ, Critchfield WB. Subdivisions of the genus *Pinus* (pines). US Forest Services; 1969. Report No.: 1144.

Liston A, Robinson WA, Pinero D, Alvarez-Buylla ER. Phylogenetics of *Pinus* (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Mol Phylogenet Evol. 1999;11(1):95–109.

Article
CAS
PubMed
Google Scholar

Syring J, Willyard A, Cronn R, Liston A. Evolutionary relationships among *Pinus* (Pinaceae) subsections inferred from multiple low-copy nuclear loci. Am J Bot. 2005;92(12):2086–100.

Article
PubMed
Google Scholar

Krupkin AB, Liston A, Strauss SH. Phylogenetic analysis of the hard pines (*Pinus* subgenus Pinus, Pinaceae) from chloroplast DNA restriction site analysis. Am J Bot. 1996;83(4):489–98.

Article
Google Scholar

He TH, Pausas JG, Belcher CM, Schwilk DW, Lamont BB. Fire-adapted traits of *Pinus* arose in the fiery Cretaceous. New Phytol. 2012;194(3):751–9.

Article
PubMed
Google Scholar

Stevens GC, Enquist BJ. Macroecological limits to the abundance and distribution of *Pinus*. In: Richardson DM, editor. Ecology and Biogeography of *Pinus*. Cambridge: Cambridge University Press; 2000. p. 183–90.

Google Scholar

Hao ZZ, Liu YY, Nazaire M, Wei XX, Wang XQ. Molecular phylogenetics and evolutionary history of sect. Quinquefoliae (*Pinus*): Implications for Northern Hemisphere biogeography. Mol Phylogenet Evol. 2015;87:65–79.

Article
PubMed
Google Scholar

Eckert AJ, Hall BD. Phylogeny, historical biogeography, and patterns of diversification for *Pinus* (Pinaceae): Phylogenetic tests of fossil-based hypotheses. Mol Phylogenet Evol. 2006;40(1):166–82.

Article
CAS
PubMed
Google Scholar

Willyard A, Syring J, Gernandt DS, Liston A, Cronn R. Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for *Pinus*. Mol Biol Evol. 2007;24(1):90–101.

Article
PubMed
Google Scholar

Gernandt DS, Magallon S, Lopez GG, Flores OZ, Willyard A, Liston A. Use of simultaneous analyses to guide fossil-based calibrations of Pinaceae phylogeny. Int J Plant Sci. 2008;169(8):1086–99.

Article
Google Scholar

Gernandt DS, Hernandez-Leon S, Salgado-Hernandez E, de la Rosa JAP. Phylogenetic relationships of *Pinus* subsection Ponderosae inferred from rapidly evolving cpDNA regions. Syst Bot. 2009;34(3):481–91.

Article
Google Scholar

Hernandez-Leon S, Gernandt DS, de la Rosa JAP, Jardon-Barbolla L. Phylogenetic relationships and species delimitation in *Pinus* section Trifoliae inferrred from plastid DNA. PLoS One. 2013;8(7):e70501.

Ho SYW, Phillips MJ. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol. 2009;58(3):367–80.

Article
PubMed
Google Scholar

Benton MJ, Donoghue PCJ. Paleontological evidence to date the tree of life. Mol Biol Evol. 2007;24(1):26–53.

Article
CAS
PubMed
Google Scholar

Roquet C, Thuiller W, Lavergne S. Building megaphylogenies for macroecology: taking up the challenge. Ecography. 2013;36(1):13–26.

Article
PubMed
PubMed Central
Google Scholar

Lukoschek V, Keogh JS, Avise JC. Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches. Syst Biol. 2012;61(1):22–43.

Article
PubMed
Google Scholar

Alvin KL. Further conifers of the Pinaceae from the Wealden Formation of Belgium. Mém Inst R Sci Nat Belg. 1960;146:16–21.

Google Scholar

Stockey RA, Nishida M. *Pinus haboroensis* sp.nov. and the affinities of permineralized leaves from the Upper Cretaceous of Japan. Can J Bot. 1986;64(9):1856–66.

Article
Google Scholar

Robison CR. *Pinus triphylla* and *Pinus quinquefolia* from the Upper Cretaceous of Massachusetts. Am J Bot. 1977;64(6):726–32.

Article
Google Scholar

Meijer JJF. Fossil woods from the Late Cretaceous Aachen Formation. Rev Palaeobot Palyno. 2000;112(4):297–336.

Article
CAS
Google Scholar

Axelrod DI, Cota J. A further contribution to closed-cone pine (Oocarpae) history. Am J Bot. 1993;80(7):743–51.

Article
Google Scholar

Axelrod DI. Cenozoic history of some western American pines. Ann Mo Bot Gard. 1986;73(3):565–641.

Article
Google Scholar

Miller CN. Structurally preserved cones of *Pinus* from the Neogene of Idaho and Oregon. Int J Plant Sci. 1992;153(1):147–54.

Article
Google Scholar

Xing YW, Liu YS, Su T, Jacques FMB, Zhou ZK. *Pinus prekesiya* sp nov from the upper Miocene of Yunnan, southwestern China and its biogeographical implications. Rev Palaeobot Palyno. 2010;160(1–2):1–9.

Article
Google Scholar

Yamada T, Yamada M, Tsukagoshi M. Fossil records of subsection Pinus (genus *Pinus*, Pinaceae) from the Cenozoic in Japan. J Plant Res. 2014;127(2):193–208.

Article
PubMed
Google Scholar

Klaus W. Ein *Pinus canariensis* Smith-Zapfenfund aus dem Ober-Miozän (Pannon) des Wiener Beckens: A fossil cone of *Pinus canariensis* Smith from the Upper Miocene (Pannon) of the Vienna Basin (Austria). Ann Nat-hist Museum Wien. 1980;84:79–84.

Google Scholar

dos Reis M, Donoghue PCJ, Yang Z. Bayesian molecular clock dating of species divergences in the genomics era. Nature Rev Genet. 2016;17(2):71–80.

Article
PubMed
Google Scholar

Drummond AJ, Bouckaert RR. Bayesian evolutionary analysis with BEAST. Cambridge: Cambridge University Press; 2015.

Rutschmann F, Eriksson T, Abu Salim K, Conti E. Assessing calibration uncertainty in molecular dating: The assignment of fossils to alternative calibration points. Syst Biol. 2007;56(4):591–608.

Article
CAS
PubMed
Google Scholar

Ronquist F, Klopfstein S, Vilhelmsen L, Schulmeister S, Murray DL, Rasnitsyn AP. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst Biol. 2012;61(6):973–99.

Article
PubMed
PubMed Central
Google Scholar

Yang ZH, Rannala B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol Biol Evol. 2006;23(1):212–26.

Article
CAS
PubMed
Google Scholar

Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006;4(5):699–710.

Article
CAS
Google Scholar

Duchene S, Lanfear R, Ho SYW. The impact of calibration and clock-model choice on molecular estimates of divergence times. Mol Phylogenet Evol. 2014;78:277–89.

Article
PubMed
Google Scholar

Thorne JL, Kishino H, Painter IS. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol. 1998;15(12):1647–57.

Article
CAS
PubMed
Google Scholar

Heath TA, Huelsenbeck JP, Stadler T. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc Natl Acad Sci U S A. 2014;111(29):E2957–66.

Article
CAS
PubMed
PubMed Central
Google Scholar

Gavryushkina A, Welch D, Stadler T, Drummond AJ. Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput Biol. 2014;10(12):e1003919.

Condamine FL, Nagalingum NS, Marshall CR, Morlon H. Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating. BMC Evol Biol. 2015;15:65.

Arcila D, Pyron RA, Tyler JC, Orti G, Betancur-R R. An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Mol Phylogenet Evol. 2015;82:131–45.

Article
PubMed
Google Scholar

Grimm GW, Kapli P, Bomfleur B, McLoughlin S, Renner SS. Using more than the oldest fossils: dating Osmundaceae with three Bayesian clock approaches. Syst Biol. 2015;64(3):396–405.

Article
PubMed
Google Scholar

Gavryushkina A, Heath TA, Ksepka DT, Stadler T, Welch D, Drummond AJ. Bayesian total-evidence dating reveals the recent crown radiation of penguins. Syst Biol. 2016;66(1):57–73.

Google Scholar

Leslie AB, Beaulieu JM, Rai HS, Crane PR, Donoghue MJ, Mathews S. Hemisphere-scale differences in conifer evolutionary dynamics. Proc Natl Acad Sci U S A. 2012;109(40):16217–21.

Article
CAS
PubMed
PubMed Central
Google Scholar

Geada Lopez G, Kamiya K, Harada K. Phylogenetic relationships of Diploxylon pines (subgenus Pinus) based on plastid sequence data. Int J Plant Sci. 2002;163(5):737–47.

Article
Google Scholar

Hilton J, Riding JB, Rothwell GW. Age and identity of the oldest pine fossils: COMMENT. Geology. 2016;44(8):e400–1.

Article
Google Scholar

Gallien L, Saladin B, Boucher FC, Richardson DM, Zimmermann NE. Does the legacy of historical biogeography shape current invasiveness in pines? New Phytol. 2016;209(3):1096–105.

Article
PubMed
Google Scholar

Ho SYW, Duchene S. Molecular-clock methods for estimating evolutionary rates and timescales. Mol Ecol. 2014;23(24):5947–65.

Article
PubMed
Google Scholar

Linder HP, Hardy CR, Rutschmann F. Taxon sampling effects in molecular clock dating: An example from the African Restionaceae. Mol Phylogenet Evol. 2005;35(3):569–82.

Article
CAS
PubMed
Google Scholar

Soares AER, Schrago CG. The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages. J Theor Biol. 2015;364:31–9.

Article
PubMed
Google Scholar

Poux C, Madsen O, Glos J, de Jong WW, Vences M. Molecular phylogeny and divergence times of Malagasy tenrecs: influence of data partitioning and taxon sampling on dating analyses. BMC Evol Biol. 2008;8:102.

Yang ZH, Donoghue PCJ. Dating species divergences using rocks and clocks. Philos Trans R Soc B-Biol Sci. 2016;371:20150126.

Warnock RCM, Parham JF, Joyce WG, Lyson TR, Donoghue PCJ. Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors. Proc Roy Soc B-Biol Sci. 2015;282:20141013.

Warnock RC, Joyce WG, Parham JF, Lyson TR, Donoghue PC. Exploring uncertainty in the calibration of the molecular clock. J Vertebr Paleontol. 2012;32:190–1.

Google Scholar

Parham JF, Donoghue PCJ, Bell CJ, Calway TD, Head JJ, Holroyd PA, et al. Best practices for justifying fossil calibrations. Syst Biol. 2012;61(2):346–59.

Article
PubMed
Google Scholar

Donoghue PCJ, Yang ZH. The evolution of methods for establishing evolutionary timescales. Philos Trans R Soc B-Biol Sci. 2016;371:20160020.

Heled J, Drummond AJ. Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Syst Biol. 2012;61(1):138–49.

Article
PubMed
Google Scholar

Magallon SA. Dating lineages: molecular and paleontological approaches to the temporal framework of clades. Int J Plant Sci. 2004;165(4):S7–S21.

Sauquet H, Ho SYW, Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, et al. Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of *Nothofagus* (Fagales). Syst Biol. 2012;61(2):289–313.

Article
PubMed
Google Scholar

Magallon S, Gomez-Acevedo S, Sanchez-Reyes LL, Hernandez-Hernandez T. A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. New Phytol. 2015;207(2):437–53.

Article
PubMed
Google Scholar

Gernandt DS, Leon-Gomez C, Hernandez-Leon S, Olson ME. *Pinus nelsonii* and a cladistic analysis of Pinaceae ovulate cone characters. Syst Bot. 2011;36(3):583–94.

Article
Google Scholar

Smith SY, Stockey RA. A new species of *Pityostrobus* from the lower Cretaceous of California and its bearing on the evolution of Pinaceae. Int J Plant Sci. 2001;162(3):669–81.

Article
Google Scholar

Klymiuk AA, Stockey RA, Rothwell GW. The first organismal concept for an extinct species of Pinaceae: *Pinus arnoldii* Miller. Int J Plant Sci. 2011;172(2):294–313.

Article
Google Scholar

Farjon A. A Handbook of the World's Conifers, vol. 2. Leiden: BRILL; 2010.

Parks M, Cronn R, Liston A. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol. 2009;7:84.

Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 2008;36(19).

Gernandt DS, Liston A, Pinero D. Phylogenetics of *Pinus* subsections Cembroides and Nelsoniae inferred from cpDNA sequences. Syst Bot. 2003;28(4):657–73.

Google Scholar

Wang XR, Tsumura Y, Yoshimaru H, Nagasaka K, Szmidt AE. Phylogenetic relationships of Eurasian pines (*Pinus*, Pinaceae) based on chloroplast rbcL, matK, rpl20-rps18 spacer, and trnV intron sequences. Am J Bot. 1999;86(12):1742–53.

Article
CAS
PubMed
Google Scholar

Song BH, Wang XQ, Wang XR, Ding KY, Hong DY. Cytoplasmic composition in *Pinus densata* and population establishment of the diploid hybrid pine. Mol Ecol. 2003;12(11):2995–3001.

Article
PubMed
Google Scholar

Katoh K, Standley DM. MAFFT Multiple sequence alignment software Version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.

Article
CAS
PubMed
PubMed Central
Google Scholar

Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56(4):564–77.

Article
CAS
PubMed
Google Scholar

Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, et al. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Comput Biol. 2014;10(4):e1003537.

Saladin B, Leslie AB, Wüest RO, Litsios G, Conti E, Salamin N, et al. Data from: Fossils matter: improved estimates of divergence times in *Pinus* reveal older diversification. Dryad Digital Repository. 2017. doi:10.5061/dryad.74f2r.2.

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):1695–701.

Article
CAS
PubMed
Google Scholar

Heath TA: Divergence Time Estimation using BEAST v2.2.0. In. Source URL: http://treethinkers.org/tutorials/divergence-time-estimation-using-beast/: Tutorial written for workshop on applied phylogenetics and molecular evolution, Bodega Bay California; 2015: 1–44.

Hadfield JD. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J Stat Softw. 2010;33(2):1–22.

Article
Google Scholar

R Core Team. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2014. http://www.r-project.org.

Google Scholar

Heibl C. PHYLOCH: R language tree plotting tools and interfaces to diverse phylogenetic software packages. 2013. http://www.christophheibl.de/Rpackages.html. Accessed 28 Mar 2017.

Paradis E, Claude J, Strimmer K. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics. 2004;20(2):289–90.

Article
CAS
PubMed
Google Scholar

Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W. GEIGER: investigating evolutionary radiations. Bioinformatics. 2008;24(1):129–31.

Article
CAS
PubMed
Google Scholar

Hijmans RJ. Raster: Geographic Data Analysis and Modeling. R package version 2.3–33; 2016. http://cran.r-project.org/package=raster. Accessed 28 Mar 2017.

Blakey RC. Global Paleogeography; 2016 [updated June, 2016]. https://www2.nau.edu/rcb7/. Accessed 4 Mar 2017.