Genomic heterogeneity of historical gene flow between two species of newts inferred from transcriptome data

The role of gene flow in species formation is a major unresolved issue in speciation biology. Progress in this area requires information on the long‐term patterns of gene flow between diverging species. Here, we used thousands of single‐nucleotide polymorphisms derived from transcriptome resequencing and a method modeling the joint frequency spectrum of these polymorphisms to reconstruct patterns of historical gene flow between two Lissotriton newts: L. vulgaris (Lv) and L. montandoni (Lm). We tested several models of divergence including complete isolation and various scenarios of historical gene flow. The model of secondary contact received the highest support. According to this model, the species split from their common ancestor ca. 5.5 million years (MY) ago, evolved in isolation for ca. 2 MY, and have been exchanging genes for the last 3.5 MY Demographic changes have been inferred in both species, with the current effective population size of ca. 0.7 million in Lv and 0.2 million in Lm. The postdivergence gene flow resulted in two‐directional introgression which affected the genomes of both species, but was more pronounced from Lv to Lm. Interestingly, we found evidence for genomic heterogeneity of interspecific gene flow. This study demonstrates the complexity of long‐term gene flow between distinct but incompletely reproductively isolated taxa which divergence was initiated millions of years ago

A new species of Varanus (Anguimorpha: Varanidae) from the early Miocene of the Czech Republic, and its relationships and palaeoecology

Skeletal remains of a new early Miocene (Ottnangian, MN 4 mammal zone) monitor lizard, Varanus mokrensis sp. nov., are described from two karst fissures in the Mokrá-Western Quarry (1/2001 Turtle Joint; 2/2003 Reptile Joint), Czech Republic, providing the first documented example of a European varanid for which osteological data permit a well-supported assignment to the genus Varanus. The new species is morphologically similar to the Recent Indo-Asiatic varanids of the Varanus bengalensis group. It differs from all other Varanus species on the basis of a single autapomorphy and a combination of 11 characters. As a distinguishing feature of V. mokrensis, the parietal and squamosal processes of the postorbitofrontal form a narrowly acute angle. The teeth show distinct, smooth cutting edges along the mesial and distal margins of the apical portion of their crowns. This feature is not observed in most extant Asiatic Varanus species and may represent a plesiomorphic condition. The results of parsimony phylogenetic analyses, with and without character reweighting, reveal poor resolution within Varanus. A Bayesian analysis shows V. mokrensis to be closely related to extant representatives of the Indo-Asiatic Varanus clade, with close affinities to the V. bengalensis species group. The topology of the Bayesian tree supports the hypothesis that Miocene monitors from Mokrá are representatives of a lineage that is ancestral to the well-defined clade of extant African varanids, including the early Miocene V. rusingensis. In addition, our results support a Eurasian origin for the varanid clade. The extant African Varanus species probably originated in the late Oligocene. The radiation of African varanids probably occurred during the late Oligocene to early Miocene time interval. The occurrence of Varanus in the early Miocene of Mokrá-Western Quarry corresponds to the warm phase of the Miocene Climatic Optimum. Remains of a diverse aquatic and heliophobe amphibian fauna at the 2/2003 Reptile Joint site indicate more humid conditions than those at the 1/2001 Turtle Joint site