The Cerrado is a wide Neotropical savanna with tremendously high endemic diversity. Yet, it is not clear what the prevalent processes leading to such diversification are. We used the Cerrado-endemic lizard Norops meridionalis to investigate the main abiotic factors that promoted genetic divergence, the timings of these divergence events, and how these relate to cryptic diversity in the group. We sequenced mitochondrial and nuclear genes from 21 sites of N. meridionalis to generate species tree, divergence time estimations, and estimate species limits. We also performed population-level analysis and estimated distribution models to test the roles of niche conservatism and divergence in the group diversification. We found that N. meridionalis is composed by at least five cryptic species. Divergence time estimations suggest that the deepest branches split back into the early-mid Miocene, when most of the geophysical activity of the Cerrado took place. The deep divergences found in N. meridionalis suggest that beta anoles invaded South America much earlier than previously thought. Recent published evidence supports this view, indicating that the Panama gap closed as early as 15 mya, allowing for an early invasion of Norops into South America. The spatial pattern of diversification within N. meridionalis follows a northwest-southeast direction, which is consistent across several species of vertebrates endemic to the Cerrado. Also, we found evidence for non-stationary isolation by distance, which occurs when genetic differentiation depends on space. Our preliminary data in two out of five lineages suggest that niche conservatism is an important mechanism that promoted geographic fragmentation in the group.

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Aim Our aims were to investigate the spatial genetic structure of Micrablepharus atticolus and to assess the relative importance of differentiation in plateaus versus depressions, in areas of historical stability versus instability, and in central versus peripheral regions. Location The Brazilian Cerrado. Methods We compared the elevational range of M. atticolus with that of its sister species, Micrablepharus maximiliani, to investigate their putative elevational segregation. We identified past (6, 21 and 130 ka) and current variables associated with the distribution of M. atticolus. Based on cytochrome b sequences, we compared genetic diversity indexes and neutrality statistics between plateau/depression, stable/unstable and core/periphery populations. We identified geographically homogeneous and maximally differentiated groups of populations and tested the association between genetic and geographical distances. Finally, we traced elevational range on the phylogeny and tested for a significant phylogenetic signal associated with elevation. Results We found no elevational segregation between M. atticolus and M. maximiliani. There is high genetic diversity and structuring among populations, with the primary differentiation occurring between north‐eastern and south‐western Cerrado localities. We recognized three main groups of populations that roughly correspond to the southern, central‐northern and north‐western portions of the Cerrado, which diverged between 3.5 and 1.5 Ma. Genetic diversity indices indicated no differences between plateaus and depressions or stable and unstable areas, but samples from peripheral isolates in south‐western Amazonia exhibited low haplotype and nucleotide diversity and signs of population expansion. Main conclusions The diversification of M. atticolus in the Cerrado was primarily affected by events in the late Neogene. We found no support for the plateau/depression and stability/instability hypotheses, but we did find support for the core/periphery hypothesis. The spatial patterns seemingly resulted from a combination of shifting environmental conditions during climatic cycles, with repeated colonizations of plateaus and depressions, isolation by distance, and divergence in and recolonization of peripheral isolates within Amazonia.

A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, and other data types. Gene-tree discordance is often caused by incomplete lineage sorting, lateral gene transfer, and gene duplication. Multispecies-coalescent methods can account for incomplete lineage sorting and are believed by many to be more accurate than concatenation. However, simulation studies and empirical data have demonstrated that concatenation and species tree methods often recover similar topologies. We use three popular methods of phylogenetic reconstruction (one concatenation, two species tree) to evaluate relationships within Teiidae. These lizards are distributed across the United States to Argentina and the West Indies, and their classification has been controversial due to incomplete sampling and the discordance among various character types (chromosomes, DNA, musculature, osteology, etc.) used to reconstruct phylogenetic relationships. Recent morphological and molecular analyses of the group resurrected three genera and created five new genera to resolve non-monophyly in three historically ill-defined genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the phylogenetic relationships of the Teiidae using "next-generation" anchored-phylogenomics sequencing. Our final alignment includes 316 loci (488,656bp DNA) for 244 individuals (56 species of teiids, representing all currently recognized genera) and all three methods (ExaML, MP-EST, and ASTRAL-II) recovered essentially identical topologies. Our results are basically in agreement with recent results from morphology and smaller molecular datasets, showing support for monophyly of the eight new genera. Interestingly, even with hundreds of loci, the relationships among some genera in Tupinambinae remain ambiguous (i.e. low nodal support for the position of Salvator and Dracaena).

The lizard genus Kentropyx (Squamata: Teiidae) comprises nine species, which have been placed in three species groups (calcarata group, associated to forests ecosystems; paulensis and striata groups, associated to open ecosystems). We reconstructed phylogenetic relationships of Kentropyx based on morphology (pholidosis and coloration) and mitochondrial DNA data (12S and 16S), using maximum parsimony and Bayesian methods, and evaluated biogeographic scenarios based on ancestral areas analyses and molecular dating by Bayesian methods. Additionally, we tested the life-history hypothesis that species of Kentropyx inhabiting open ecosystems (under seasonal environments) produce larger clutches with smaller eggs and that species inhabiting forest ecosystems (under aseasonal conditions) produce clutches with fewer and larger eggs, using Stearns' phylogenetic-subtraction method and canonical phylogenetic ordination to take in to account the effects of phylogeny. Our results showed that Kentropyx comprises three monophyletic groups, with K. striata occupying a basal position in opposition to previous suggestions of relationships. Additionally, Bayesian analysis of divergence time showed that Kentropyx may have originated at the Tertiary (Eocene/Oligocene) and the 'Pleistocene Refuge Hypothesis' may not explain the species diversification. Based on ancestral reconstruction and molecular dating, we argued that a savanna ancestor is more likely and that historical events during the Tertiary of South America promoted the differentiation of the genus, coupled with recent Quaternary events that were important as dispersion routes and for the diversification at populational levels. Clutch size and egg volume were not significantly different between major clades and ecosystems of occurrence, even accounting for the phylogenetic effects. Finally, we argue that phylogenetic constraints and phylogenetic inertia might be playing essential roles in life history evolution of Kentropyx.