Reconstructing patterns of reticulate evolution in plants

Abstract

Until recently, rigorously reconstructing the many hybrid speciation events in plants has not been practical because of the limited number of molecular markers available for plant phylogenetic reconstruction and the lack of good, biologically based methods for inferring reticulation (network) events. This situation should change rapidly with the development of multiple nuclear markers for phylogenetic reconstruction and new methods for reconstructing reticulate evolution. These developments will necessitate a much greater incorporation of population genetics into phylogenetic reconstruction than has been common. Population genetic events such as gene duplication coupled with lineage sorting and meiotic and sexual recombination have always had the potential to affect phylogenetic inference. For tree reconstruction, these problems are usually minimized by using uniparental markers and nuclear markers that undergo rapid concerted evolution. Because reconstruction of reticulate speciation events will require nuclear markers that lack these characteristics, effects of population genetics on phylogenetic inference will need to be addressed directly. Current models and methods that allow hybrid speciation to be detected and reconstructed are discussed, with a focus on how lineage sorting and meiotic and sexual recombination affect network reconstruction. Approaches that would allow inference of phylogenetic networks in their presence are suggested.

Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains

“…Observations of our phylogenies show that incongruence are primarily deep ones that affect the topological positions of major clades, not positions of species within clades. Such discordances between phylogenies based on nuclear and chloroplast markers are generally caused by convergent evolution, lineage sorting, or ancient hybridization and introgression (Rieseberg and Soltis, 1991;Mason-Gamer et al, 1995;Rieseberg et al, 1996;Wendel and Doyle, 1998;Sang and Zhong, 2000;Comes and Abbott, 2001;Linder and Rieseberg, 2004). Among these, hybridization and incomplete lineage sorting have gained considerable attention and are known to confound phylogenetic analyses (Sang and Zhong, 2000;Maddison and Knowles, 2006;Joly et al, 2009).…”

Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers

“…majalis S1 Fig. 3 (continued) and horizontal gene transfer) can cause these phylogenetic inconsistencies (Cronn and Wendel, 2004;Linder and Rieseberg, 2004;Maddison, 1997;Rieseberg and Soltis, 1991;Wendel and Doyle, 1998;Zou and Ge, 2008). Among these causes, introgression and incomplete lineage sorting have been frequently discussed as the prominent factors of phylogenetic incongruence at lower taxonomic levels (Cronn and Wendel, 2004;Joly et al, 2009;Maddison and Knowles, 2006).…”

“…Hybridization has long been recognized as an important driving force in plant evolution (Abbott, 1992;Mallet, 2007;Paun et al, 2009;Rieseberg, 1995Rieseberg, , 1997, which can lead to high intraspecific genetic diversity, creation of new species or ecotypes, and reticulate evolution (Anderson, 1948;Linder and Rieseberg, 2004;Whitham et al, 1994). As a result, it is particularly challenging to reconstruct species relationships for groups including hybrids.…”

Reconstruction of phylogenetic relationships in a highly reticulate group with deep coalescence and recent speciation (Hieracium, Asteraceae)

“…Since then, a large number of studies using many unlinked markers have been published, but gene tree incongruence has been found to be a common phenomenon (Degnan and Rosenberg, 2009), which seems to intensify as the number of markers increases (Rokas and Carroll, 2006). One cause of such incongruence is hybridization (for example, Linder and Rieseberg, 2004;Fehrer et al, 2007), which is one of the major processes in the evolution of vascular plants (Arnold, 1997) and is increasingly being recognized as important for animals as well. Allopolyploidy, which is merging genomes from different species, is frequently involved in hybrid speciation (Rieseberg and Willis, 2007) and can further complicate phylogenetic inference.…”

“…As LCNMs have not yet been used as frequently for phylogenetic and hybrid inference as other types of markers, their evolutionary dynamics are still less well understood and have to be assessed for each particular system to which they are applied. Their potential and drawbacks have been reviewed by Sang (2002), Linder and Rieseberg (2004), and Small et al (2004).…”