TreeBASE Search-Analyses for study 15161

@ARTICLE{TreeBASE2Ref22715, author = {Justin Thomas Wynns and Conny B. Asmussen-Lange}, title = {A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales).}, year = {2014}, keywords = {barcoding; bryophytes; intergenic spacer; intron; ITS; molecular systematics; rbcL; trnK/matK}, doi = {10.3732/ajb.1300269}, url = {http://}, pmid = {}, journal = {American Journal of Botany}, volume = {101}, number = {4}, pages = {1--18}, abstract = {? Premise of the study: Within the Hypnales ? the most derived and species-rich order of pleurocarpous mosses ? phylogenies at or below the family level often show poor resolution. In preparation for a phylogeny of the genus Plagiothecium, we wished to identify the DNA markers best suited for evolutionary reconstruction in this group of hypnalean pleurocarps. ? Methods: For each of 25 collections of Plagiothecium and associated taxa, 16 DNA regions were sequenced: nuclear ITS and 26S, and plastid rps4, rps4?trnL, trnL?F, trnK(matK)?psbA, psbA?trnH, trnM?V, trnD?T, rbcL, atpB?rbcL, psbT?H, rpoC1 exon 2 (partial), the trnG intron, the rpl16 intron and the plastid ribosomal spacer DNA (cpITS). Each region was evaluated on the basis of its ability to resolve clades, the amount of homoplasy present in the data set, and the relative ease of obtaining the data. Descriptive statistics for each region are given. ? Key results: Under-utilized plastid markers for bryophytes like trnK?psbA, rps4?trnL and trnD?T outperformed more traditional markers like trnL?F and rps4. Individual plastid topologies were similar, suggesting that only a limited amount of plastid data are needed to recover a backbone phylogeny. Adding a small amount of nuclear ribosomal data to a large plastid matrix restructured the recovered topology, emphasizing the importance of sampling multiple genomes and the need for new low-copy nuclear markers in bryophyte systematics. ? Conclusions: Future genus-level phylogenies of pleurocarpous mosses should target under-utilized plastid markers like trnK?psbA and rps4?trnL in conjunction with low-copy nuclear markers. } }

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Analyses for Study 15161

Citation title: "A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales).".

Study name: "A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales).".

This study is part of submission 15161 (Status: Published).

Analyses

Analysis 1

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all plastid branch-and-bound --

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1 Output object(s)

Analysis 2

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1 Input object(s)

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all data branch-and-bound --

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2 Output object(s)

Analysis 3

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1 Input object(s)

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all nuclear branch-and-bound --

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1 Output object(s)

Analysis 4

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1 Input object(s)

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26S heuristic (1000 reps, max 10 trees/rep) --

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6 Output object(s)

Analysis 5

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1 Input object(s)

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atpB-rbcL branch-and-bound --

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24 Output object(s)

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Analysis 6

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1 Input object(s)

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cpITS branch-and-bound --

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30 Output object(s)

Analysis 7

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1 Input object(s)

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ITS branch-and-bound --

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1 Output object(s)

Analysis 8

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psbT-H branch-and-bound --

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30 Output object(s)

Analysis 9

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rbcL branch-and-bound --

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6 Output object(s)

Analysis 10

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1 Input object(s)

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rpl16 branch-and-bound --

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8 Output object(s)

Analysis 11

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1 Input object(s)

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rpoC1 branch-and-bound --

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30 Output object(s)

Analysis 12

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1 Input object(s)

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rps4 heuristic (1000 reps, max 10 trees/rep) --

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1 Output object(s)

Analysis 13

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1 Input object(s)

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rps4-trnL branch-and-bound --

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4 Output object(s)

Analysis 14

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1 Input object(s)

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trnD-T branch-and-bound --

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15 Output object(s)

Analysis 15

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trnG branch-and-bound --

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12 Output object(s)

Analysis 16

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1 Input object(s)

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psbA-trnH branch-and-bound --

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5 Output object(s)

Analysis 17

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1 Input object(s)

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trnK-psbA branch-and-bound --

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4 Output object(s)

Analysis 18

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trnL-F branch-and-bound --

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19 Output object(s)

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Analysis 19

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trnM-V branch-and-bound --

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