ABSTRACT
The phylogeny of the paper wasp genus Polistes is investigated using morphological and behavioural characters, as well as molecular data from six genes (COI, 12S, 16S, 28S, H3, and EF1-α). The results are used to investigate the following evolutionary hypotheses about the genus: (i) that Polistes first evolved in Southeast Asia, (ii) that dispersal to the New World occurred only once, and (iii) that long-term monogyny evolved as an adaptation to overwintering in a temperate climate. Optimization of distribution records on the recovered tree does not allow unambiguous reconstruction of the ancestral area of Polistes. While the results indicate that Polistes dispersed into the New World from Asia, South America is recovered as the ancestral area for all New World Polistes: Nearctic species groups evolved multiple times from this South American stock. The final tree topology suggests strongly that the genus first arose in a tropical environment, refuting the idea of monogyny as an overwintering adaptation.
ABSTRACT
Phylogenetic analyses that incorporate the most character information also provide the most explanatory power. Here I demonstrate the value of such an approach through a direct optimization sensitivity analysis of apid bee phylogeny. Whereas prior studies have relied solely on one class of data or the other, this analysis combines previously published molecular, morphological, and behavioural characters into a single supermatrix. The final dataset includes 191 ingroup and 30 outgroup taxa, and includes data from seven unaligned gene sequences (18S, 28S, wingless, EF1-α, polII, Nak, LW rhodopsin), 209 adult and larval morphological characters, and two behavioural characters. Nine different sets of transformation cost parameters are evaluated, along with their relative degrees of character incongruence. The preferred parameter set returns a strict consensus tree somewhat similar to, but more resolved than, a previous parsimony tree based on molecules alone. I also describe the effects of including EF1-α and LW rhodopsin intron sequences on the outcome of the direct optimization analysis. By accounting for more evidence, this study provides the most comprehensive treatment yet of apid phylogenetic relationships.
ABSTRACT
Lineage sorting has been suggested as a major force in generating incongruent phylogenetic signal when multiple gene partitions are examined. The degree of lineage sorting can be estimated using the coalescent process and simulation studies have also pointed to a major role for incomplete lineage sorting as a factor in phylogenetic inference. Some recent empirical studies point to an extreme role for this phenomenon with up to 50-60% of all informative genes showing incongruence as a result of lineage sorting. Here, we examine seven large multi-partition genome level data sets over a large range of taxonomic representation. We took the approach of examining outgroup choice and its impact on tree topology, by swapping outgroups into analyses with successively larger genetics distances to the ingroup. Our results indicate a linear relationship of outgroup distance with incongruence in the data sets we examined suggesting a strong random rooting effect. In addition, we attempted to estimate the degree of lineage sorting in several large genome level data sets by examining triads of very closely related taxa. This exercise resulted in much lower estimates of incongruent genes that could be the result of lineage sorting, with an overall estimate of around 10% of the total number of genes in a genome showing incongruence as a result of true lineage sorting. Finally we examined the behavior of likelihood and parsimony approaches on the random rooting phenomenon. Likelihood tends to stabilize incongruence as outgroups get further and further away from the ingroup. In one extreme case, likelihood overcompensates for sequence divergence but increases random rooting causing long branch repulsion.
