Nuclear and mtDNA phylogenies of the Trimeresurus complex: implications for the gene versus species tree debate.

Phylogenies based on mitochondrial DNA (mtDNA) may represent gene trees that may not be congruent with the equivalent species tree. One solution to this problem is to include additional, independent loci from the nuclear genome. Sequence data from the seventh intron of the beta-fibrinogen gene were generated for 25 specimens of vipers, including 8 nominal species of the Trimeresurus complex of Asian pit vipers. Phylogenetic trees were generated using maximum-parsimony and maximum-likelihood methods. The taxonomic level at which the intron provided significant phylogenetic information was examined and the trees were compared to those produced from previously obtained mtDNA cytochrome b sequences. A variety of different approaches (separate analyses, conditional data combination, and consensus) were used in an attempt to provide a sound organismal phylogeny based on both nuclear and mtDNA data sets. We discuss the implications for the gene tree-species tree debate and its particular relevance to medically important organisms.

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 nuclear markers such as intron sequence data may not be appropriate. In this study we investigate the use of amplified fragment length polymorphisms (AFLP) to aid determination of the species tree for 24 specimens of a medically important snake, Trimeresurus albolabris. This is of particular importance for many venomous snakes as venom often varies intraspecifically. Five different primer combinations produced 434 bands and were analysed by constructing a phylogenetic tree using neighbour joining and principal component analysis. Results were similar across all methods and found distinct groupings. The results were compared with mtDNA data and a reconciled tree was constructed in order to determine the species tree for T. albolabris. We found that T. albolabris (sensu lato) is not monophyletic. Specimens from the Indonesian islands (except West Java) form a distinct clade and we propose elevation to species level. A specimen from Nepal is also distinct and suggests that this population also deserves specific status. We suggest that AFLPs may prove a valuable aid in determining species trees as opposed to gene trees at fine taxonomic levels and this should facilitate the incorporation of molecular data into such activities as antivenom production and conservation management.

A phylogenetic analysis of body size evolution in the Anolis roquet group (Sauria: Iguanidae): character displacement or size assortment?

The important role that competition plays in structuring communities is well documented; however, the role of competition in an evolutionary context remains unclear. Evolutionary investigations into the role of competition have often focused on the process of character displacement, and a good example of this is the evolution of body size in the Anolis lizards of the Caribbean islands. Previous work on the A. roquet species group has taken a phylogenetic approach and concluded that patterns of body size differences are not caused by character displacement but are a result of size assortment. Using a phylogenetic reconstruction based on the sequence of the cytochrome b gene (cyt-b) and ancestral character-state reconstruction methods, we investigated the roles of character displacement and size assortment. Our results indicated that size assortment alone was insufficient to explain the observed patterns of body size differences. Furthermore, we found that change in body size was associated with a change in allopatry/sympatry, thus supporting the character-displacement hypothesis. We conclude that patterns of body size differences in the A. roquet species group appear to be the result of a combination of character displacement and size assortment because character displacement was only found to be possible on three occasions.