The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris

There are a huge number of phylogenetic studies based on mitochondrial DNA (mtDNA); however, these may represent gene trees that may not be congruent with the species tree. A solution to this problem is to include additional, independent, loci from the nuclear genome. At fine taxonomic levels, i.e. between populations and closely related species, previously suggested nucle ar markers such as intron sequence data may not be appropriate. In this stu dy we investigate the use of amplified fragment length polymorphisms (AFLP) to aid determination of the species tree for 24 specimens of a medically i mportant snake, Trimeresurus albolabris. This is of particular importance f or many venomous snakes as venom often varies intraspecifically. Five diffe rent primer combinations produced 434 bands and were analysed by constructi ng a phylogenetic tree using neighbour joining and principal component anal ysis. Results were similar across all methods and found distinct groupings. The results were compared with mtDNA data and a reconciled tree was constr ucted in order to determine the species tree for T. albolabris. We found th at T. albolabris (sensu lato) is not monophyletic. Specimens from the Indon esian islands (except West Java) form a distinct clade and we propose eleva tion to species level. A specimen from Nepal is also distinct and suggests that this population also deserves specific status. We suggest that AFLPs m ay prove a valuable aid in determining species trees as opposed to gene tre es at fine taxonomic levels and this should facilitate the incorporation of molecular data into such activities as antivenom production and conservati on management.