Intragenomic variation in ITS1 and ITS2 is known to exist but is widely ignored in phylogenetic studies using these gene regions. The amount of variation in seven crayfish species, including three populations of Orconectes luteus and two of Procambarus clarkii, was assessed by sequencing 3, 5, or 10 clones from the same individuals, for a total of 77 sequences. The ITS1 and ITS2 sequences reported here are some of the longest known, with aligned lengths of 760 and 1,300 bp, respectively. They contain multiple microsatellite insertions, all of which show considerable intragenomic variation in the number of repeat elements. This variation is enough to obscure phylogenetic relationships at the population level, although relationships between species can be estimated. Given the hybridization techniques used to locate microsatellites, multiple-copy regions like ITS1 and ITS2 will be preferentially found if they contain microsatellites, and in these cases the microsatellites will not behave as typical Mendelian markers and could give spurious results.

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.

DNA sequences from parts of the 12S, 16S and cytochrome b mitochondrial genes, which totalled 1049 aligned base pairs, were used to estimate the relationships of 49 species of Lacertidae, including representatives of 19 out of the 23 recognized genera and 23 species of the paraphyletic genus Lacerta. These data were used, together with morphological information, to estimate the relationships within the family. Molecular evidence corroborates the monophyletic status of many genera and species groups originally based on morphology. It indicates that Psammodromus forms a clade with Gallotia, which is the sister taxon of all other lacertids. These comprise three units: the primarily Afrotropical armatured group; the largely Oriental Takydromus; and the west Palaearctic Lacerta and its derivatives, Podarcis and Algyroides. Morphology also supports the first three assemblages, but suggests that they are derived from a paraphyletic Lacerta. Within Lacerta and its allies, DNA sequence analysis corroborates the affinity of some members of each of the subgenera Lacerta s. str. and Timon, and of the L. saxicola group. It also supports the relationship of L. monticola, L. bonnali and L. horvathi, and suggests that the L. parva–L. fraasi clade and L. brandti are not related to Psammodromus–Gallotia, as morphology indicates, but instead are associated respectively with the L. danfordi and L. saxicola groups. DNA sequence data provide additional evidence that the eastern Arabian ‘Lacerta’ jayakari and ‘L.’ cyanura are members of the armatured clade and also sister species. Our analysis supports an origin for present lacertids in west Eurasia. The armatured clade invaded Africa, probably in the mid–Miocene, spreading widely and evolving increasingly xeric–adapted forms, one lineage of which later moved back into the Palaearctic. ‘Lacerta’ jayakari and ‘L.’ cyanura are assigned to Omanosaura, Lutz and Mayer 1986. The name Gallotiinae Cano, Baez, Lopez–Jurado and Ortega, 1984 is available for the Gallotia–Psammodromus clade, Eremiainae Shcherbak 1975 for the armatured clade and Lacertinae for Lacerta, Podarcis and Algyroides. Two new subgenera of Lacerta are proposed here: Caucasilacerta for L. saxicola and its allies, and Parvilacerta for L. parva and L. fraasi.