2015
DOI: 10.1016/j.ympev.2015.06.019
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Phylogeny and species delimitations in European Dicranum (Dicranaceae, Bryophyta) inferred from nuclear and plastid DNA

Abstract: DNA sequences have been widely used for taxonomy, inferring phylogenetic relationships and identifying species boundaries. Several specific methods to define species delimitations based on molecular phylogenies have appeared recently, with the generalized mixed Yule coalescent (GMYC) method being most popular. However, only few studies on land plants have been published so far and GMYC analyses of bryophytes are missing. Dicranum is a large genus of mosses whose (morpho-)species are partly ill-defined and freq… Show more

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Cited by 48 publications
(21 citation statements)
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“…Firstly, we used (a) a rate of 4.47 × 10 −3 subst./site/my (with 95% highest posterior density intervals (95HPD): 1.76 × 10 −3 −8.34 × 10 −3 subst./site/my), corresponding to the evolutionary rate estimated for ITS in Polytrichaceae mosses [Method I2a in (Biersma et al, 2017)]. We performed an additional dating analysis based on (b) a much slower nuclear substitution rate (1.35 × 10 −3 subst./site/my) originally derived from angiosperms (Les et al, 2003, and references therein), but previously used in molecular studies on bryophytes (Hartmann et al, 2006;Lang et al, 2015;Biersma et al, 2017). Apart from the differences in rate, all settings in both analyses remained the same.…”
Section: Molecular Datingmentioning
confidence: 99%
“…Firstly, we used (a) a rate of 4.47 × 10 −3 subst./site/my (with 95% highest posterior density intervals (95HPD): 1.76 × 10 −3 −8.34 × 10 −3 subst./site/my), corresponding to the evolutionary rate estimated for ITS in Polytrichaceae mosses [Method I2a in (Biersma et al, 2017)]. We performed an additional dating analysis based on (b) a much slower nuclear substitution rate (1.35 × 10 −3 subst./site/my) originally derived from angiosperms (Les et al, 2003, and references therein), but previously used in molecular studies on bryophytes (Hartmann et al, 2006;Lang et al, 2015;Biersma et al, 2017). Apart from the differences in rate, all settings in both analyses remained the same.…”
Section: Molecular Datingmentioning
confidence: 99%
“…Input trees were RAxML trees calculated on CIPRES Science Gateway (Miller et al 2010) under default parameters. Two analyses are provided: PTP_ML (maximum likelihood solution) which gives the most likely solution among the dataset, and PTP_sh (Bayesian solution) which considers the frequency of the nodes across the sampling (Lang et al 2015). We only retained molecular species with posterior delimitation probabilities higher than 0.91 (Zhang et al 2013).…”
Section: Molecular Species Delimitationmentioning
confidence: 99%
“…Molecular species delimitation using ABGD and PTP is sensitive to balanced sampling, especially in number of replicates per taxon (Puillandre et al 2012;Zhang et al 2013;Lang et al 2015). The initial dataset (Appendix) contained singletons and some taxa with more than ten samples (Riccardia chamedryfolia).…”
Section: Species Delimitationmentioning
confidence: 99%
“…Chloroplast markers (atpB-rbcL, trnT-F, atpI-atpH) provided little phylogenetic signal to delimit species (Stech, 2004), as also reported for other moss genera such as Dicranum Hedw. (Lang, Bocksberger, & Stech, 2015), and were partly difficult to sequence, especially at pB-rbcL, the slightly more variable of the cpDNA markers. In contrast, the nuclear ribosomal internal transcribed spacer (ITS1-5.8S-ITS2) region, the most widely used nuclear marker for plant phylogenetic inferences (Stech & Quandt, 2010), is highly variable in Campylopus.…”
Section: Introductionmentioning
confidence: 99%