The 10kTrees website: A new online resource for primate phylogeny

Abstract

Luke Matthews is an anthropologist and primatologist whose interests include the evolution of primate behavior, primate traditions, and human cultural evolution. He has conducted primatological fieldwork in Ecuador and Argentina. He employs phylogenetics, network analysis, and cluster analysis to study inheritance systems that range from DNA sequences to primate foraging traditions and human material culture. Importantly, the 10,000 trees that we provide are not random, but instead use recent systematic methods to create a plausible set of topologies that reflect our certainty about some nodes on the tree and uncertainty about other nodes given the dataset.The trees also reflect uncertainty about branch lengths.The comparative method has undergone a revolution in the past 20 years. 2,[14][15][16] Specifically, new phylogenetic methods provide a way to incorporate evolutionary history directly into comparative research. Phylogeny is essential to comparative research because related species tend to resemble one another, resulting in non-independent data points. 2,[17][18] Phylogenetic comparative methods can be used to investigate whether two traits change in tandem through time, while also providing the historical scaffolding to identify independent evolutionary origins of the traits of interest. More recently, phylogenetic methods have provided a toolkit to investigate the tempo and mode of evolution, [19][20] to quantify phylogenetic signal in comparative data, [21][22] and to study the factors that influence diversification rates. [23][24] Computer simulations have revealed that it is usually preferable to conduct comparative tests with some form of phylogenetic method because this reduces false positives (Type I errors) and increases statistical power. [17][18][25][26] This latter point is often under-appreciated, but it is a logical outcome of phylogenetic comparative analyses that reduce error associated with the estimation of statistics and thus enhance the probability of detecting real effects. 26Researchers generally want to include as many species as possible in a comparative analysis. To incorporate phylogeny in comparative studies of primates, previous researchers have used either published primate-wide "supertrees" such as the Purvis phylogeny, 27 or they compiled smaller trees from the literature, often patching these together from among existing phylogenies based on morphology or genetics. 28-29More recently, Bininda-Emonds et al. [30][31] produced a new supertree of mammals, and researchers have begun to use the primate portion of this tree in comparative studies of primates. 32-34The actual tree topology and timing of speciation events is, however, never known with certainty. In addition, phylogenetic relationships should be continually proportion to their posterior probability (see Box 1). The set of trees obtained reflects uncertainty in the phylogeny given the substitution model and data; more certain nodes are found across a greater proportion of the sample of trees, while less certain nodes ...

Coevolution of cultural intelligence, extended life history, sociality, and brain size in primates

“…Reproductive lifespan was calculated as age of sexual maturity subtracted from maximum longevity. Comparative datasets were matched to a dated consensus phylogeny for 301 primate species (10kTrees version 3, using GenBank taxonomy) (65). Taxonomic mismatches were resolved using the 10kTrees Translation table and the International Union for Conservation of Nature (IUCN) Red List website (66).…”

Centrality in primate–parasite networks reveals the potential for the transmission of emerging infectious diseases to humans

“…Several traits have been found to affect parasitism, such as population density, geographic range size, group size, body mass, and diet (19). We explored whether these traits also covary with centrality of the primates using phylogenetic generalized least squares (PGLS) models (26) with the primate consensus dated tree from the 10kTrees Project (27). In a model with multiple predictor variables, we found that primates with denser populations living in larger groups and having broad distributions were more central [population density: estimate ± 1 SE = 0.32 ± 0.15, t = 2.10, P = 0.04; geographic range size: estimate ± 1 SE = 0.28 ± 0.14, t = 1.95, P = 0.05; group size: estimate ± 1 SE = 0.36 ± 0.17, t = 2.08, P = 0.04, R 2 = 0.490; PGLS with phylogenetic signal (λ) = 0.138, P = 0.06 compared to a model with λ = 0, n = 122 primates].…”

Phylogenetic signal in primate behaviour, ecology and life history

“…We used the 10kTrees dated phylogeny v. 3 with the associated taxonomy from GenBank [57]. We estimated phylogenetic signal in each trait using Blomberg's K and Pagel's l (see §1), with the picante [28] and phytools packages [31], respectively, in R [58].…”