Ecological requirements and environmental conditions can influence diversification across temporal and spatial scales. Understanding the role of ecological niche evolution under phylogenetic contexts provides insights on speciation mechanisms and possible responses to future climatic change. Large-scale phyloclimatic studies on the megadiverse Neotropics, where biomes with contrasting vegetation types occur in narrow contact, are rare. We integrate ecological and biogeographic data with phylogenetic comparative methods, to investigate the relative roles of biogeographic events and niche divergence and conservatism on the diversification of the lizard genus Kentropyx Spix, 1825 (Squamata: Teiidae), distributed in South American rainforests and savannas. Using five molecular markers, we estimated a dated species tree, which recovered three clades coincident with previously proposed species groups diverging during the mid-Miocene. Biogeography reconstruction indicates a role of successive dispersal events from an ancestral range in the Brazilian Shield and western Amazonia. Ancestral reconstruction of climatic tolerances and niche overlap metrics indicate a trend of conservatism during the diversification of groups from the Amazon Basin and Guiana Shield, and a strong signal of niche divergence in the Brazilian Shield savannas. Our results suggest that climatic-driven divergence at dynamic forest-savanna borders might have resulted in adaptation to new environmental niches, promoting habitat shifts and shaping speciation patterns of Neotropical lizards. Dispersal and ecological divergence could have a more important role in Neotropical diversification than previously thought.

We integrate ecological and biogeographic data with phylogenetic comparative methods (based on five molecualr markers), to investigate the relative roles of biogeographic events and niche divergence and conservatism on the diversification of the lizard genus Kentropyx Spix, 1825 (Squamata: Teiidae), distributed in South American rainforests and savannas.

Supporting Information for the paper ‘The combined role of dispersal and niche evolution in the diversification of Neotropical lizards’ by Sheu, Y., J. P. Zurano, M. A. Ribeiro-Junior, T. C. S. Avila-Pires, M. T. Rodrigues, G. R. Colli, and F. P. Werneck.

Table S1. Details of the samples used for molecular data collecting, with locality data for sequenced samples, identification number, longitude and latitude.

Table S2. Primers used for amplification and sequencing of the six loci used in this study.

Table S3. Complete set of Genbank accession numbers (Excel File).

Table S4. Complete set of geographical records used for ecological niche modeling (Excel File).

Table S5. Occurrence points sample sizes and predictors (bioclimatic, vegetation, and aridity index) used to construct niche models for nine species of the lizard genus Kentropyx. Parameters selected for each species and model performance are also depicted.

Table S6. Molecular markers used at this study for Kentropyx spp. H = number of haplotypes; Hd = haplotype diversity; Pi = Nucleotide diversity (per site).

Fig S1. Nuclear gene tree generated by Bayesian inference from the concatenated nuclear markers SNCAIP, DNH3, RP40 and R35.

Fig S2. Gene trees generated by Bayesian inference using the markers (a) SNCAIP, (b) DNH3; (c) RP40 and (d) R35.

Fig S3. Species tree and biogeographic reconstruction with all possible ancestral areas inferred under the DEC + J model presented as pie charts on each node.

Fig S4. Predicted niche occupancy profiles (PNO) for the nine species of Kentropyx.

Fig S5. Ancestral reconstruction of the 12 variables used to construct the niche models for Kentropyx.