Alex Sumadijaya, HiluLab, Dept. of Biological Sciences, VirginiaTech.
Bothriochloa Kuntze, Capillipedium Stapf, and Dichanthium Willemet are three closely related genera in the tribe of Andropogoneae (Poaceae). Bothriochloa is the genus under investigation here with variable number of recognized 34 to 35 species worldwide (Clayton and Renvoize 1986, Clayton et al. 2002, The Plant List, Simon 2006). De Wet and Harlan (1970) introduced the compilospesies issue as the interbreeding phenomenon that involves several species of Bothriochloa as well as across closely related genera of Capillipedium and Dichanthium that later on refer as BCD. The core of the interbreeding is Bothriochloa intermedia, that presently known as Bothriochloa bladhii which serves as the main hub of the gene flow with different taxa on polyploid level.
The hypothesis of this research is ‘if the interbreeding happens, then some of the clade would not be monophyletic, because interbreeding blurs the demarcation among species in the compilospecies’. The main objective of this research is to establish a core of the phylogenetic relationship for the compilospecies. The focus was Australia, but I added few more accessions from outside of the continent to give a better picture on the evolutionary scheme of this compilospecies.
After succeed in amplifying seven regions in chloroplast genome, I focused on three regions of TrnTF, rpS16 intron, and 3'trnK. These regions have more nucleotides substitution and provide more information than the rest.
Partition Homogeneity Test (PHT) was conducted to assess whether or not these data sets compatible to each other to build robust phylogeny. Unfortunately, after running PHT on PAUP (Swofford 2003) for more than a week, I did not achieve result. In fact, the program was keep running and slowing down the whole workstation. I decided to stop PHT and suspected this thing happens due to the high level of homogeneity across these sequences. Two other software alternatives, TNT and NONA were not compatible with the latest operating system to run PHT in lab. Therefore, I proceed with all of the dataset available combined.
Furthermore, these three regions were subject to model testing by using JModelTest (Guindon and Gascuel 2003, Darriba et al. 2012) to select the best model for nucleotide substitution and site heterogeneity.
Later on, phylogenetic trees were reconstructed based on the combination of all data sets (trnTF, rpS 16 intron, or 3'trnK) as well as individually analyzed. Three different analyses conducted were Maximum Parsimony (MP), Randomized Accelerated Maximum Likelihood (RAxML), and Bayesian Inference (BI).
Comparison of three data sets shows that with more datasets, the resolution of the tree is resolved better with robust topology. Two data sets however, accommodate more taxa in the topology and present a better picture of the relationship among species in the compilospecies. The phenomena of Capillipedium and Dichanthium nested in Bothriochloa based on chloroplast genome is a new discovery that never expected due to the assumption of the maternal inheritance of the chloroplast does not cross across genera. This finding is adding more understanding as well as more questions on the compilospecies itself.
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