Barrington, David S. , Li, Chun-xiang .
Tracing hybrid ancestry with data from a set of single-copy nuclear genes retrieved by direct sequencing.
Sequence variation in single-copy nuclear genes and the internal transcribed spacer of three naturally occurring hybrids with known diploid progenitors demonstrates that direct sequencing of multiple nuclear genes is an effective tool for analysis of hybrids and their derived allopolyploids in the ferns. We tested three established origin hypotheses for hybrids using the single-copy nuclear gene sequences gapCp, PGIc, and LFY, plus ITS.
We used a direct-sequencing approach. In most cases we encountered a region near the 5’ end of our sequences where almost all positions had single peaks in the sequencing chromatograms. In most of the hybrids and few of the diploid progenitors there was a downstream region where each position had two (or sometimes more) peaks. Analysis of the component nucleotides revealed that the double peaks are the result of heterozygosity for indels at the 5’ end of the double-peak region, leading us to call these regions indel artifacts. Further analysis of the component nucleotides in these indel artifacts allows an expanded search for nucleotide summation in hybrids.
We sampled three hybrids: the endemic Costa Rican diploid hybrid Polystichum concinnum X P. speciosissimum, the widespread North American allotetraploid P. scopulinum, and the European allotetraploid Polystichum aculeatum. We found consistent summation of diagnostic nucleotides for the predicted progenitors across all four markers for all three hybrids.
This technique has substantial potential for the exploration of unresolved species complexes. Our exploratory analysis of the East-Asian Polystichum tsus-simense and allies reveals the reticulate relationships between a suite of three putative diploids (P. herbaceum, P. revolutum, and a third unrecognized lineage), and their two derivatives P. tsus-simense and P. xiphophyllum, with species delimitations that are at odds with traditional morphological circumscriptions. The utility of this approach lies in the corroboration of multiple nuclear sequences in testing hypotheses for hybrid origins.
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1 - University of Vermont, Plant Biology Department, Marsh Life Sciences Bldg, 109 Carrigan Drive, Burlington, Vermont, 05405-0086, USA
2 - State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, The Chinese Academy of Science, Nanjing, Jiangsu Pr., 210008, China
single copy nuclear genes.
Presentation Type: Oral Paper:Papers for BSA Sections
Location: Alpine B/Snowbird Center
Date: Monday, July 27th, 2009
Time: 9:00 AM