Schneider, Harald , Pedersen, Niklas , Navarro Gomez, Adriana , Russell, Stephen J. , Ansell, Stephen , Grundmann, Michael , Vogel, Johannes C. .
Establishing nuclear markers to generate a comprehensive phylogeny of asplenioid ferns.
Current phylogenetic studies on ferns rely nearly exclusively on sequencing of chloroplast genome regions such as the coding regions atpB, rbcL and rps4 and non-coding region rps4-trnS IGS and trnL-trnF IGS. Chloroplast markers have several advantages but they have also disadvantages in studies requiring either information about both parents of the inferred specimens or more variation as usually displayed by chloroplast markers. In recent studies, randomly amplified markers e.g. AFLPs were explored to overcome some of these challenges. In contrast to other land plant lineages, sequencing of nuclear genes have been explored only in a handful of studies aiming to reconstruct the phylogenetic relationships of closely related ferns. In this study, we explore the utility of four nuclear markers in studies on the fern family Aspleniaceae. Asplenioid ferns are well known for the frequent occurrence of hybrids and polyploids. We designed, therefore, this study to address issues caused by multiplication and putative different phylogenetic history of nuclear genes. In the first step, we employed existing primers and protocols of each of the four regions 1) nrITS1 and nrITS2, 2) LEAFY intron II, 3) pgiC (Partial) and 4) gapC (partial). In the second step, we cloned the sequences obtained in the successful PCR reactions before sequencing. Special attention was given to the issue of obtaining non-fern sequences because this problem may have been overlooked in a previous study using nuclear markers. To evaluate the potential of each of the four markers, we 1) calculate the number of phylogenetic informative sites in datasets comparing more or less closely related lineages of asplenioid ferns, 2) consider issues concerning alignments, 3) explore the identification of orthologous respectively paralogous copies and identify putative pseudogenes.
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1 - Natural History Museum, Cromwell Road, London, SW7 5BD, UK
2 - Natural History Museum, Botany, Cromwell Road, London, SW7 5BD, united kingdom
3 - Natural History Museum, Department of Botany, Cromwell Road, London, SW7 5BD, England
Low-copy Nuclear Markers
Presentation Type: Oral Paper:Papers for Sections
Location: Lake Michigan/Hilton
Date: Monday, July 9th, 2007
Time: 11:00 AM