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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.
Genomic sequencing and analysis of worldwide skipper butterfly (Lepidoptera: Hesperiidae) fauna points to imperfections in their current classification. Some tribes, subtribes and genera as they are circumscribed today are not monophyletic. Rationalizing genomic results from the perspective of phenotypic characters suggests two new tribes, two new subtribes and 50 new genera that are named here: Ceratrichiini Grishin, trib. n., Gretnini Grishin, trib. n., Falgina Grishin, subtr. n., Apaustina Grishin, subtr. n., Flattoides Grishin, gen. n., Aurivittia Grishin, gen. n., Viuria Grishin, gen. n., Clytius Grishin, gen. n., Incisus Grishin, gen. n., Perus Grishin, gen. n., Livida Grishin, gen. n., Festivia Grishin, gen. n., Hoodus Grishin, gen. n., Anaxas Grishin, gen. n., Chiothion Grishin, gen. n., Crenda Grishin, gen. n., Santa Grishin, gen. n., Canesia Grishin, gen. n., Bralus Grishin, gen. n., Ladda Grishin, gen. n., Willema Grishin, gen. n., Argemma Grishin, gen. n., Nervia Grishin, gen. n., Dotta Grishin, gen. n., Lissia Grishin, gen. n., Xanthonymus Grishin, gen. n., Cerba Grishin, gen. n., Avestia Grishin, gen. n., Zetka Grishin, gen. n., Turmosa Grishin, gen. n., Mielkeus Grishin, gen. n., Coolus Grishin, gen. n., Daron Grishin, gen. n., Barrolla Grishin, gen. n., Brownus Grishin, gen. n., Tava Grishin, gen. n., Rigga Grishin, gen. n., Haza Grishin, gen. n., Dubia Grishin, gen. n., Pares Grishin, gen. n., Chitta Grishin, gen. n., Artonia Grishin, gen. n., Lurida Grishin, gen. n., Corra Grishin, gen. n., Fidius Grishin, gen. n., Veadda Grishin, gen. n., Tricrista Grishin, gen. n., Viridina Grishin, gen. n., Alychna Grishin, gen. n., Ralis Grishin, gen. n., Testia Grishin, gen. n., Buzella Grishin, gen. n., Vernia Grishin, gen. n., and Lon Grishin, gen. n. In addition, the following taxonomic changes are suggested. Prada Evans is transferred from Hesperiinae to Trapezitinae. Echelatus Godman and Salvin, Systaspes Weeks, and Oenides Mabille are removed from synonymy and are treated as valid genera. The following genera are new junior subjective synonyms: Tosta Evans of Eantis Boisduval; Turmada Evans of Neoxeniades Hayward, Arita Evans of Tigasis Godman, and Alera Mabille of Perichares Scudder. Eantis pallida (R. Felder) (not Achlyodes Hübner), Gindanes kelso (Evans) (not Onenses Godman and Salvin), Isoteinon abjecta (Snellen) (not Astictopterus C. and R. Felder), Neoxeniades ethoda (Hewitson) (not Xeniades Godman), Moeris anna (Mabille) (not Vidius Evans), and Molo pelta Evans (not Lychnuchus Hübner) are new genus-species combinations. The following are species-level taxa: Livida assecla (Mabille) (not a subspecies of Livida grandis (Mabille), formerly Pythonides Hübner) and Alychna zenus (E. Bell) (not a junior subjective synonym of Alychna exclamationis (Mabille), formerly Psoralis Mabille); and Barrolla molla E. Bell (formerly Vacerra Godman) is a junior subjective synonym of Barrolla barroni Evans (formerly Paratrytone Godman). All these changes to taxonomic status of names are propagated to all names currently treated as subspecies (for species), subgenera (for genera) and synonyms of these taxa. Finally, taxa not mentioned in this work are considered to remain at the ranks and in taxonomic groups they have been previously assigned to.