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A Review of Molecular-Clock Calibrations and Substitution Rates In Molecular Phylogenetics and Evolution 78 (2014) 25–35 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev A review of molecular-clock calibrations and substitution rates in liverworts, mosses, and hornworts, and a timeframe for a taxonomically cleaned-up genus Nothoceros ⇑ Juan Carlos Villarreal , Susanne S. Renner Systematic Botany and Mycology, University of Munich (LMU), Germany article info abstract Article history: Absolute times from calibrated DNA phylogenies can be used to infer lineage diversification, the origin of Received 31 January 2014 new ecological niches, or the role of long distance dispersal in shaping current distribution patterns. Revised 30 March 2014 Molecular-clock dating of non-vascular plants, however, has lagged behind flowering plant and animal Accepted 15 April 2014 dating. Here, we review dating studies that have focused on bryophytes with several goals in mind, (i) Available online 30 April 2014 to facilitate cross-validation by comparing rates and times obtained so far; (ii) to summarize rates that have yielded plausible results and that could be used in future studies; and (iii) to calibrate a species- Keywords: level phylogeny for Nothoceros, a model for plastid genome evolution in hornworts. Including the present Bryophyte fossils work, there have been 18 molecular clock studies of liverworts, mosses, or hornworts, the majority with Calibration approaches Cross validation fossil calibrations, a few with geological calibrations or dated with previously published plastid substitu- Nuclear ITS tion rates. Over half the studies cross-validated inferred divergence times by using alternative calibration Plastid DNA substitution rates approaches. Plastid substitution rates inferred for ‘‘bryophytes’’ are in line with those found in angio- Substitution rates sperm studies, implying that bryophyte clock models can be calibrated either with published substitution rates or with fossils, with the two approaches testing and cross-validating each other. Our phylogeny of Nothoceros is based on 44 accessions representing all suspected species and a matrix of six markers of nuclear, plastid, and mitochondrial DNA. The results show that Nothoceros comprises 10 species, nine in the Americas and one in New Zealand (N. giganteus), with the divergence between the New Zealand species and its Chilean sister species dated to the Miocene and therefore due to long-distance dispersal. Based on the new tree, we formally transfer two species of Megaceros into Nothoceros, resulting in the new combinations N. minarum (Nees) J.C. Villarreal and N. schizophyllus (Gottsche ex Steph.) J.C. Villarreal, and we also newly synonymize eight names described in Megaceros. Ó 2014 Elsevier Inc. All rights reserved. 1. Introduction studies. Part of the explanation may lie in the scarcity of liverwort, moss, or hornwort fossils suitable for calibration, although recent Molecular clock dating has become an indispensable tool in work has brought to light characteristic hornwort spores evolutionary biology and has utterly transformed the field of bio- (Chitaley and Yawale, 1980; Graham, 1987; Archangelsky and geography. Absolute times from calibrated phylogenies can be Villar de Seone, 1996) and many amber-preserved mosses used to infer the climate or geological context of lineage diversifi- (Heinrichs et al., 2013). The problem of a scarce fossil record, of cation (Schneider et al., 2004), the role of long distance dispersal in course, is not restricted to non-vascular plants. In other clades with shaping current distribution patterns (Renner, 2005; Heinrichs poor fossil records, researchers have overcome the difficulty by et al., 2009a; Schaefer et al., 2009; Linder et al., 2013), or the origin applying substitution rates taken from related plant groups, prefer- of new ecological niches (Schneider et al., 2004; Schuettpelz and ably with similar generation times. Substitution rates of plastid Pryer, 2009; Bytebier et al., 2011; Crisp et al., 2011). The use of and nuclear markers, especially of the internal transcribed spacer dated phylogenies in evolutionary studies of non-vascular plants, regions of ribosomal DNA (ITS1 and ITS2), are available from many however, has lagged behind flowering plant and animal dating fossil-calibrated phylogenies (e.g., Richardson et al., 2001; Kay et al., 2006). Alternatively, workers have used geological events as calibration points, usually the age of oceanic islands with ende- ⇑ Corresponding author. mic radiations, which obviously cannot be older than the island E-mail address: [email protected] (J.C. Villarreal). http://dx.doi.org/10.1016/j.ympev.2014.04.014 1055-7903/Ó 2014 Elsevier Inc. All rights reserved. 26 J.C. Villarreal, S.S. Renner / Molecular Phylogenetics and Evolution 78 (2014) 25–35 (e.g., Schaefer et al., 2009). Another way around a lack of calibra- and taxonomic authors, voucher details, and GenBank accession tion fossils is to use a two-tiered approach, in which the clade of numbers. We sequenced four plastid markers, viz. the rbcL gene, interest’s root node is assigned an age obtained in another data the trnL-F intron and spacer, the rps4-trnS spacer, and a portion of matrix, in which fossil calibration was possible because it con- matK; a fragment of the mitochondrial nad5–nad4 spacer; and the tained a different taxon sampling (as done in Heinrichs et al. 2007). nuclear 5.8S gene and ITS2 ribosomal RNA. Methods for DNA A combination of these approaches to calibrate branch lengths extraction, PCR protocols and sequencing are detailed in Villarreal (genetic distances) in phylogenies has been used to infer diver- et al. (2012) and Villarreal and Renner (2013); primer sequences gence times also in bryophytes. Here, we review such dating stud- are shown in Table S3. The first author identified all material based ies with several goals in mind. One is that a review will facilitate on his study of the types of most names published in Nothoceros and cross-validation by comparing rates and divergence times obtained Megaceros. The total alignment included 47 accessions and 5993 so far; another is that plastid or nuclear ITS rates that have yielded base pairs (bp). After excluding regions of ambiguous alignment plausible results could be used in future studies; a third is that we (exclusions sets available from TreeBase accession number wanted to calibrate a species-level phylogeny for Nothoceros, the 15666) the matrix consisted of 4660 aligned nucleotides. only hornwort genus with transcriptome data and a complete plastid genome (Villarreal et al., 2013; Li et al., 2014). 2.3. Phylogenetic analyses The genus Nothoceros contains approximately ten species, and together with Dendroceros, Megaceros, and Phaeomegaceros it makes Phylogenetic analyses were performed under likelihood (ML) up the family Dendrocerotoceae (Duff et al., 2007). Except for the optimization using RAxML 7.2.8 (Stamatakis et al., 2008) and the New Zealand species N. giganteus, Nothoceros is restricted to the GTR + C substitution model, with six unlinked partitions for the dif- Americas, where it occurs in southernmost South America (N. fuegi- ferent markers. Additional analyses were made with three unlinked ensis and N. endiviifolius), the foothills of the Andes, Central Ameri- partitions (one partition per genomic compartment). Statistical sup- can and Caribbean mountains above 400 m (N. vincentianus, N. port was assessed via 500 ML bootstrap replicates under the same canaliculatus, N. renzagliensis and N. superbus), high Andean páramos substitution model. Bayesian analyses were conducted in MrBayes and punas, and the Southern Appalachian Mts. in Eastern North 3.2 (Ronquist et al., 2012), using the default two runs and four chains America (N. aenigmaticus; Villarreal et al., 2010a, 2012). Its sister (one cold and three heated), with default priors on most parameters clade consists of Dendroceros, which has 43 species and a pantrop- except that we modified the prior on branch lengths using the ical and south temperate distribution, and Megaceros, which occurs approach of Brown et al. (2010) for branch length exponential priors in Africa, Australia, New Zealand, and South America, at least as tra- (k ¼lnð0:5Þ) where brl is the average branch length obtained from brl ditionally circumscribed. The sister to all three genera is Phaeome- the maximum likelihood tree. We again used six or three data parti- gaceros, with 9–10 species in tropical Asia, New Zealand, austral tions, applying best-fit models found with MrModel test v.2 and tropical America (Villarreal et al., 2010b). The placement of (Nylander, 2004; all are shown in Table S4). Model parameters for the New Zealand species of Nothoceros close to one of its two Chilean state frequencies, the rate matrix, and gamma shape were unlinked, species in a previous molecular phylogeny (Villarreal et al., 2012) and posterior probabilities of tree topologies were estimated from that included eight species of Nothoceros raised the question of the the partitions. Tracer 1.5 (Rambaut et al., 2013; part of the BEAST age of this disjunction. To answer this question, we generated package) was used to assess convergence and to judge the percent- sequence data from up to seven loci from the three plant genomic age of burn-in for tree constructions. Convergence was usually compartments and sampled all species of Nothoceros, mostly with achieved in MrBayes after 4 Â 106 generations, with trees sampled multiple representatives per species. every 1000th generation for a total length of 40 Â 106 generations; we discarded 10% of each run and then pooled runs. 2. Materials and methods 2.4. Molecular clock dating 2.1. Review and partial reanalysis of published bryophyte clock dating To convert genetic branch lengths to absolute times, we applied studies three approaches: (A) A strict clock calibrated with a plastid genome substitution rate of 5.0 Â 10À4 subst./site/my for land For all published molecular clock studies on bryophytes that we plants calculated for the entire single copy region and inverted are aware of, we summarized key aspects, such as size of the data repeats by Palmer (1991).
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