Interesting new method to study gene tree discordance.
Different genes tell different stories. When you construct phylogenetic trees for several genes, chances are that you end up with a collection of discordant gene trees. This discordance can be the result of several biological processes, including hybridization. [If you want to know more about gene tree discordance, check out these excellent papers by Maddison (1997) and Degnan & Rosenberg (2009).] A recent paper in Journal of Evolutionary Biology introduces a new method to study this phenomenon.
Melisa Olave and her colleagues explored the occurrence of hybridization in the South American lizard genus Liolaemus. This group of lizards comprises no less than 267 species and is distributed from southern Peru to southern Chile. Hybridization has been documented between numerous species. The current study focuses on hybridization between members of the boulengeri complex and the rothi complex.
Based on two mitochondrial genes and 12 nuclear loci, the researchers uncovered current and past hybridization between several species (check the paper if you are interested in which species exchanged genes). This hybrid history leads to high levels of gene tree discordance. To explore this phenomenon, they introduce a new statistic: the extra lineage contribution (XLC) statistic.
Exploring Gene Tree Discordance
Basically, the XLC quantifies the contribution of each sample (individual or allele) to the amount of gene tree discordance. Without going into technical details, the statistic calculates how many extra lineages are needed to reconcile a given gene tree with the species tree. The statistic ranges from 0 to 1, where 0 means no contribution and 1 indicates maximum contribution to gene tree discordance. If you want to try this approach on your own data, there is a R function available here.
This new statistic provides a useful tool to explore the contribution of particular individuals and genes to the discordance between gene trees and the species tree. A valuable resource in our quest to understand the evolutionary importance of hybridization.
Olave, M., Avila, L.J., Sites, J.W., Morando, M. (2018) Hybridization could be a common phenomenon within the highly diverse lizard genus Liolaemus. Journal of Evolutionary Biology, 31:893-903.