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Anthropologists and archaeologists increasingly use phylogenetic methods to test hypotheses involving cross-cultural traits, but the appropriateness of applying tree-based methods to analyze cultural traits is unclear. The authors developed a spatially explicit computer simulation model to investigate trait evolution in relation to phylogeny and geography and used the simulation to assess the sensitivity of two comparative methods (independent contrasts and partial Mantel tests) to different degrees of horizontal transmission. Simulation results show that (a) the method of independent contrasts is sensitive to even small amounts of horizontal transmission in cultural data sets, (b) Mantel tests fail to cleanly discriminate between datasets characterized by different levels of horizontal and vertical trait transmission, and (c) partial Mantel tests do not produce markedly improved statistical performance when testing for associations among traits (as compared to independent contrasts). The results highlight the need for empirical estimates of horizontal transmission and extinction rates in cross-cultural datasets.

To improve the accuracy of tree reconstruction, phylogeneticists are extracting increasingly large multigene data sets from sequence databases. Determining whether a database contains at least k genes sampled from at least m species is an NP-complete problem. However, the skewed distribution of sequences in these databases permits all such data sets to be obtained in reasonable computing times even for large numbers of sequences. We developed an exact algorithm for obtaining the largest multigene data sets from a collection of sequences. The algorithm was then tested on a set of 100,000 protein sequences of green plants and used to identify the largest multigene ortholog data sets having at least 3 genes and 6 species. The distribution of sizes of these data sets forms a hollow curve, and the largest are surprisingly small, ranging from 62 genes by 6 species, to 3 genes by 65 species, with more symmetrical data sets of around 15 taxa by 15 genes. These upper bounds to sequence concatenation have important implications for building the tree of life from large sequence databases.