20,000 species and five key markers: The status of molecular bryophyte phylogenetics

Abstract

A number of reviews have accompanied and monitored the progress of molecular phylogenetic research on bryophytes, focusing on the publication record itself, bryophyte phylogeny and systematics in the molecular era, as well as the evolution and phylogenetic utility of markers from different genomes. However, none of the recent reviews include a detailed characterization of all molecular markers used in bryophyte phylogenetics. Here we provide an overview of the history and current state of marker utilization, including coding and non-coding sequence markers from all three genomes as well as fingerprinting approaches. The molecular architecture and evolutionary peculiarities, as well as practical aspects such as amplification and sequencing strategies, are outlined for the DNA sequence markers, with a focus on the most commonly employed regions. Their phylogenetic utility and potential for solving some of the remaining, pressing questions in bryophyte phylogeny, as well as their suitability for molecular species identification by DNA barcoding, are discussed.

New insights into the phylogeny and relationships within the worldwide genus Riccardia (Aneuraceae, Marchantiophytina)

“…The plastid markers rps4, trnL-F and psbA-trnH, classically used in phylogenetic reconstructions among bryophytes (Quandt & Stech 2004;Preuβing et al 2010;Carter 2012), were selected because of their small size (< 1000 bp) allowing good amplification success and their potential informative variability at the infra-generic level Stech & Quandt 2010). In total, 291 new sequences generated from 98 samples were used in this study: 95 rps4 sequences, 98 trnL-F sequences and 98 psbA-trnH sequences.…”

Molecular, morphological, and biogeographic perspectives on the classification of Acrobolboideae (Acrobolbaceae, Marchantiophyta)

“…Five plastid genome regions were amplified: rbcL gene, atpB-rbcL intergenic spacer, psbA-trnH intergenic spacer, the psbT-H region (psbT-psbN-psbH; Stech & Quandt, 2010), and the trnL-F region. Each PCR reaction contained 12 μl deionized (DI) water, 3 μl dNTPs, 1 μl MgCl 2 (50mM), 1 μl of each primer, 1 μl BSA (20mg/mL), 0.5 μl Taq polymerase, and 1.5 μl template DNA.…”

A special issue of Phytotaxa dedicated to Bryophytes: The closest living relatives of early land plants

“…Stech & Quandt (2010) provide an indispensable resource for bryologists engaged in phylogenetic research using DNA markers. Their paper reviews the history of the use of molecular markers (with an emphasis on DNA sequence data) in the reconstruction of bryophyte relationships.…”