Phylogenomics of Anguis and Pseudopus (Squamata, Anguidae) indicates Balkan-Apennine mitochondrial capture associated with the Messinian event.

A dated phylogenetic hypothesis on the evolutionary history of the extant taxa of the Western Palearctic lizards Anguis and Pseudopus is revised using genome-wide nuclear DNA and mitogenomes. We found overall concordance between nuclear and mitochondrial DNA phylogenies, with one significant exception - the Apennine A. veronensis. In mitochondrial DNA, this species forms a common clade with the earliest diverging lineage, the southern Balkan endemic A. cephallonica, while it clusters together with A. fragilis in nuclear DNA. The nuclear phylogeny conforms to the morphology, which is relatively similar between A. veronensis and A. fragilis. The most plausible explanation for the mitonuclear discordance is ancient mitochondrial capture from the Balkan ancestor of A. cephallonica to the Apennine population of the A. fragilis-veronensis ancestor. We hypothesize that this capture occurred only in a geographically restricted population. The dating of this presumed mitochondrial introgression and capture coincides with the Messinian event, when the Balkan and Apennine Peninsulas were presumably largely connected. The dated nuclear phylogenomic reconstruction estimated the divergence of A. cephallonica around 12 Mya, while the sister clade representing the A. fragilis species complex consisting of the sister species A. fragilis-A. veronensis and A. colchica-A. graeca further diversified around 7 Mya. The depth of nuclear divergence among the evolutionary lineages of Pseudopus (0.5-1.2 Mya) supports their subspecies status.

Phylogenetic relationships and divergence dating in the Glass Lizards (Anguinae).

The Glass Lizards are a subfamily (Anguinae) of Anguid Lizards with an elongated limbless body plan that occur throughout the Northern Hemisphere primarily in North America, Europe, and Asia, but also have a presence in North Africa and Indonesia. We used twenty-five nuclear loci (15,191 bp) and 2090 bp of the mtDNA genome to generate a phylogeny containing all known species groups to explore species relationships within the group as well as divergence dating. We also examined the group in the context of a coalescent species tree analysis and species delimitation. All major lineages were found to be monophyletic with potential cryptic diversity in some. The Anguinae first appeared in the Eocene and most lineages were present by the beginning of the Miocene. The Anguinae originated in Europe from an Anguidae ancestor that crossed the Thulean land bridge, spreading to Asia after the drying of the Turgai Sea, then across Beringia as the climate permitted. A species tree analyses found support for the major Anguinae lineages and species delimitation supported accepted species.

DNA barcoding reveals distinct population of Dopasia gracilis (Squamata: Anguidae) in Mizoram, Northeast India.

The DNA barcode data of Asian Glass Lizard, Dopasia gracilis, is limited in the global database, especially from India. The present study aimed to generate a barcode sequence of morphologically identified D. gracilis from the Mizoram state in northeast India and compared with other Anguidae species. The studied species showed monophyletic clustering in the Bayesian analysis (BA) phylogeny with strong posterior probability support and also discriminated sufficient Kimura 2 parameter genetic distances. The barcode data of D. gracilis revealed high intra-species genetic variability and formed two clusters in BA phylogeny. The Templeton, Crandall, and Sing network also depicted four different haplotypes within the barcode sequences of D. gracilis. The DNA sequences generated from northeast India showed 6.5-6.6% and 7.3% genetic distances with the sequences generated from Yunnan Province and Tibetan Plateau, respectively. Considering the high genetic distances, multiple clustering, and distinct haplotypes, the present study assumed the presence of possible cryptic diversity of D. gracilis in the Indochina sub-region and a distinct population in northeast India. We recommended the generation of more DNA information from different localities to elucidate the actual diversity of D. gracilis within the known range distribution.

Next-generation sequencing yields a complete mitochondrial genome of the Asian Glass Lizard (Dopasia gracillis) from the Yungui Plateau in Southwest China.

The Asian Glass Lizard, Dopasia gracillis, has wide distribution in North India, Nepal, South China, and Indochina. In this study, a complete mitochondrial genome of D. gracillis from the Yungui Plateau in Southwest China was determined by next-generation sequencing. Similar to the typical mtDNA of vertebrates, the mitogenome was 17,133 bp in length and comprised the standard set of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 control region. The concatenated PCGs were used to conduct Bayesian phylogenetic analyses together with mitogenome data of Anguidae and related taxa in GenBank. The resulting phylogenetic tree confirmed the monophyly of Anguidae and Aguinae as well as D. gracillis, respectively. The mitogenome reported here will contribute to the examination of phylogeographic structure for D. gracillis and understanding of mitochondrial DNA evolution in Anguidae.

The complete mitochondrial genome of the Hainan Glass Lizard (Dopasia hainanensis) determined by next-generation sequencing.

The complete mitochondrial genome of the Hainan Glass Lizard (Dopasia hainanensis) from its type locality (Diaoluo Mountain in Hainan Island, China) was determined using next-generation sequencing. The mitogenome was 17,000 bp in length and comprised the standard set of 1 control region, 2 rRNAs, 22 tRNAs, plus 13 protein-coding genes (PCGs). The PCGs were used to perform Bayesian phylogenetic analysis together with other Anguidae and Helodermatidae as well as Shinisauridae lizards with mitogenome in GenBank. The resulting phylogenetic tree recovered D. hainanensis as the sister-taxon to Dopasia harti. The mitogenome of D. hainanensis will provide a valuable resource for various study areas such as species delimitation, molecular evolution, and phylogenetic inference.

The complete mitochondrial genome of Chinese glass lizard Ophisaurus harti (Squamata: Anguidae).

The complete mitochondrial genome of Ophisaurus harti is a circular molecule of 17,163 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The A + T content of the overall base composition of H-strand is 54.9% (T: 23.4%; C: 30.8%; A: 31.5%; G: 14.3%). COI gene begins with GTG as start codon, while other 12 protein-coding genes start with a typical ATG initiation codon. ND1. COI. ATP8. ATP6. ND4L and ND5 genes are terminated with TAA as stop codon, ND2. ND6 and Cyt b end with TAG, COIII ends with TA, COII and ND3 end with T and ND4 ends with TG.