Introgression explains incongruence between nuclear and chloroplast DNA-based phylogenies in Allium section Cepa

Abstract

Phylogenetic relationships between species of Allium section Cepa and A. r q k (section Rhirirideum) have been inferred from nuclear DNA variation (RAPDs; nDNA dataset) and from morphological, pollen epidermis texture, chromosomal and chemical variation (supranuclear dataset). These sets were complemented with data, taken from the literature, on cpDNA variation and crossability. The trees produced with the supranuclear, nDNA and cpDNA datasets were compared by using the topology of the most parsimonious tree of one dataset as the constraint for the construction of a most parsimonious tree of another dataset. The accuracy of the trees were evaluated by calculating several Consistency and Incongruence Indices. The constrained tree of supranuclear-nDNA datasets showed the highest index values. The tree topologies of the supranuclear and cpDNA datasets were the least similar. The cpDNA tree and crossability dendrograms were identical. The most important difference between the nDNAsupranuclear trees and the cpDNA-crossability trees pertains to the position of Allium r q k , which is much closer to the clade A. cepa/A. uauilozii in the cpDNA tree than in the nDNA tree. This difference is considered to be the result of chloroplast capture from one species to another after an introgression event. A shorter distance between species inferred from a cpDNA tree than from a nDNA or comparable tree might be indicative for the level of crossability.

Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)

“…However, it has become increasingly clear that differences in phylogenetic reconstructions may result from differences in evolutionary history for different genomes or genes (MasonGamer and Kellogg 1996;Rieseberg et al 1996;Van Raamsdonck et al 1997;Baum et al 1998;Jackson et al 1999;Martinsen et al 2001;Chan and Levin 2005). Allelic sorting in the single-copy nuclear genes may account for some of the detected incongruence; e.g.…”

“…Strictly speaking, in chloroplast capture, only the chloroplast genome is shared between species (Wolfe and Elisens 1995;Van Raamsdonck et al 1997;Jackson et al 1999;Kornkven et al 1999). In some of these cases, other nuclear genomic regions may have been transferred between species, i.e.…”

Phylogeographic Patterns and High Levels of Chloroplast Dna Diversity in Four Packera (Asteraceae) Species in Southwestern Alberta

“…In addition, such variation has been used to infer hybridization and introgression (Rieseberg and Brunsfeld 1992;Liston and Kadereit 1995;Van Raamsdonk et al 1997) and to trace the ancestry of polyploids (Wendel and Albert 1992;Lowe and Abbott 1996).…”

Development of microsatellite markers in cultivated and wild species of sections Cepa and Phyllodolon in Allium

“…Nonetheless, most morphological characters differ remarkably from others in these sections and are much more similar to those of section Oreiprason (Fritsch and Friesen 2002). Further recent evidence indicates that A. roylei might have a hybrid origin, as its nuclear DNA profile is related to species of the sections Cepa and Phyllodolon but its chloroplast DNA profile to the section Schoenoprasum (van Raamsdonk et al 1997Raamsdonk et al , 2000.…”