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Highlights
• Genomes for all five Natrix species, two represented by two distinct subspecies each, were sequenced.
• Two genomes were de-novo assembled to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp.
• Evidence for interspecific hybridization, both between allopatric and widely sympatric species.
• Fossil-calibrated molecular clock using genomes indicates that species are ancient several million-year-old lineages.
• Our findings imply that speciation took place despite continued gene flow.
Abstract
Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.
This review lists Agama smithii Boulenger 1896 as a synonym of Agama agama (Linnaeus 1758), Agama trachypleura Peters 1982 as a synonym of Acanthocercus phillipsii (Boulenger 1895) and describes for the first time Acanthocercus guentherpetersi n. sp. Without more convincing evidence, Chamaeleon ruspolii Boettger 1893 cannot be accepted as specifically distinct from Chamaeleo dilepis Leach 1819, nor Chamaeleo calcaricarens Böhme 1985 from C. africanus Laurenti 1768. Consequently, 101 species of lizard are currently recognised in Ethiopia, of which some 40% appear to be denizens of the Somali-arid zone. This significant proportion is attributable in part to the importance of the Horn of Africa as a centre for reptilian diversification and endemicity, in part to the fact that this lowland fauna was rather extensively sampled during the 1930s, but also to the conspicuous neglect of lizards in other regions of the country. Mountain and forested habitats are widespread in Ethiopia, so it seems extraordinary to record only five saurian species which are believed to be endemic in such environments. The inference that there are many more still to be discovered has important implications for conservation, because montane forest is known to be among the most threatened of Ethiopian biomes and there is clearly an urgent need for its herpetofauna to be more thoroughly researched and documented.