Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genome-wide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.

While traditionally species recognition has been based solely on morphological differences either typological or quantitative, several newly developed methods can be used for a more objective and integrative approach on species delimitation. This may be especially relevant when dealing with cryptic species or species complexes, where high overall resemblance between species is coupled with comparatively high morphological variation within populations. Rock lizards, genus Darevskia, are such an example, as many of its members offer few diagnostic morphological features. Herein, we use a combination of genetic, morphological and ecological criteria to delimit cryptic species within two species complexes, D. chlorogaster and D. defilippii, both distributed in northern Iran. Our analyses are based on molecular information from two nuclear and two mitochondrial genes, morphological data (15 morphometric, 16 meristic and four categorical characters) and eleven newly calculated spatial environmental predictors. The phylogeny inferred for Darevskia confirmed monophyly of each species complex, with each of them comprising several highly divergent clades, especially when compared to other congeners. We identified seven candidate species within each complex, of which three and four species were supported by Bayesian species delimitation within D. chlorogaster and D. defilippii, respectively. Trained with genetically determined clades, Ecological Niche Modeling provided additional support for these cryptic species. Especially those within the D. defilippii-complex exhibit well-differentiated niches. Due to overall morphological resemblance, in a first approach PCA with mixed variables only showed the separation between the two complexes. However, MANCOVA and subsequent Discriminant Analysis performed separately for both complexes allowed for distinction of the species when sample size was large enough, namely within the D. chlorogaster-complex. In conclusion, the results support four new species, which are described herein.

The climatic cycles of the Quaternary, during which global mean annual temperatures have regularly changed by 5–10°C, provide a special opportunity for studying the rate, magnitude, and effects of geographic responses to changing climates. During the Quaternary, high- and mid-latitude species were extirpated from regions that were covered by ice or otherwise became unsuitable, persisting in refugial retreats where the environment was compatible with their tolerances. In this study we combine modern geographic range data, phylogeny, Pleistocene paleoclimatic models, and isotopic records of changes in global mean annual temperature, to produce a temporally continuous model of geographic changes in potential habitat for 59 species of North American turtles over the past 320 Ka (three full glacial-interglacial cycles). These paleophylogeographic models indicate the areas where past climates were compatible with the modern ranges of the species and serve as hypotheses for how their geographic ranges would have changed in response to Quaternary climate cycles. We test these hypotheses against physiological, genetic, taxonomic and fossil evidence, and we then use them to measure the effects of Quaternary climate cycles on species distributions. Patterns of range expansion, contraction, and fragmentation in the models are strongly congruent with (i) phylogeographic differentiation; (ii) morphological variation; (iii) physiological tolerances; and (iv) intraspecific genetic variability. Modern species with significant interspecific differentiation have geographic ranges that strongly fluctuated and repeatedly fragmented throughout the Quaternary. Modern species with low genetic diversity have geographic distributions that were highly variable and at times exceedingly small in the past. Our results reveal the potential for paleophylogeographic models to (i) reconstruct past geographic range modifications, (ii) identify geographic processes that result in genetic bottlenecks; and (iii) predict threats due to anthropogenic climate change in the future.

Aim We explored the phylogenetic relationships of species of Mesalina, using one nuclear and two mitochondrial loci. This genus of lacertid lizards is widely distributed in North Africa and the Middle East and our goal was to develop a scenario capable of explaining the current distribution and evolutionary patterns within the genus in the context of the wider historical biogeography of the region.Location North Africa and the Middle East. MethodsThe assembled dataset consisted of 193 Mesalina individuals, representing 12 species distributed across the geographical range of the genus. Bayesian and maximum likelihood methods were used to support phylogenetic inferences on two mitochondrial (cytochrome b and 16S ribosomal RNA) and one nuclear (beta-fibrinogen intron 7) markers. Palaeogeographical and palaeoclimatic data were used to support the inferred phylogeographical patterns. ResultsMesalina lizards exhibit high genetic diversity and complex phylogenetic patterns, leading to an unsatisfactory systematic hypothesis of one paraphyletic and three polyphyletic traditional species. The estimated divergence times place the origin of the genus in the early Miocene (c. 22 Ma) and the divergence of most currently recognized species in the middle to late Miocene. The inferred ancestral distribution suggests that the genus and most of its species originated somewhere in Arabia or the Middle East, with the exception of the Mesalina olivieri complex, which may be of African origin.Main conclusions Phylogenetic reconstruction based on the three loci studied suggests a higher than expected cryptic diversity of Mesalina in North Africa and the Middle East. We suggest that the tectonic movements of the Arabian plate, coupled with the climatic changes occurring since the Miocene, may be responsible for the phylogeographical patterns of North African and Middle Eastern Mesalina.