Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection

Abstract

We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini), based on complete mitochondrial genome analysis. Nextgeneration sequencing (NGS) of genomic DNA was used to obtain 16 new mitogenomes of Darevskia. These, along with 35 sequences downloaded from GenBank: genera Darevskia, Zootoca, Podarcis, Phoenicolacerta, Takydromus, Lacerta, and Eremias-were used in the analysis. All four analytical methods (Bayesian Inference, BI; Maximum Likelihood, ML; Maximum Parsimony, MP; and Neighbor-Joining, NJ) showed almost congruent intrageneric topologies for Darevskia and other lizard genera. However, ML and NJ methods on one side, and BI and MP methods on the other harvested conflicting phylogenies. The ML/ NJ topology supports earlier published separation of Darevskia into three mitochondrial clades (Murphy, Fu, Macculloch, Darevsky, and Kupinova, 2000), but BI and MP topologies support that the basal branching occurred between D. parvula from the western Lesser Caucasus and the rest of Darevskia. All topologies altered the phylogenetic position of some individual species, including D. daghestanica, D. derjugini, and D. chlorogaster. Reanalysis after excluding four saturated genes from the data set, and excluding genus Eremias gives fully convergent topologies. The most basal branching for true lizards was between Far Eastern Takydromus and the Western Eurasian genera (BI). Comparing phylogenetic performance of individual genes relative to whole mitogenome data, concatenated 16S RNA (the least saturated gene in our analyses) and Cytochrome b genes generate a robust phylogeny that is fully congruent with that based on the complete mitogenome.

The more you search, the more you find: Cryptic diversity and admixture within the Anatolian rock lizards (Squamata, Darevskia)

“…The estimated timing of divergence obtained here is slightly older than that reported in previous studies (Mid‐Pleistocene in Tarkhnishvili, 2012; Tarkhnishvili et al., 2013), but similar to the estimates in Murtskhvaladze et al. (2020) (1 Mya) and Garcia‐Porta et al. (2019) (1.34 Mya).…”

“…However, the proposed estimates of relationships among these taxa seem to be as many as the studies investigating them. For instance, in some studies, D. portschinskii and D. rudis appear as sister taxa, with D. valentini in a basal position (Freitas, Rocha, et al., 2016; Freitas, Vavakou, et al., 2016), while in others D. portschinskii clusters with D. valentini , and D. rudis is their sister taxon (Freitas, 2017; Murtskhvaladze et al., 2020). Although the support of D. portschinskii as sister taxon to D. rudis and D. valentini is strong in our study, the same cannot be said concerning the remaining clades (Figure 4).…”

“…Very recently, Murtskhvaladze et al. (2020) analysed the phylogeny of Darevskia rock lizards using mitogenomes, concluding that D. portschinskii and D. valentini are sister taxa, with D. rudis as their sister clade. The estimated divergence time among these groups was 1 Mya.…”

Meiotic synapsis of homeologous chromosomes and mismatch repair protein detection in the parthenogenetic rock lizard Darevskia unisexualis

“…According to the recent study species divergence of D. raddei s.l. and D. valentini occured about 18, 5 million years ago (Murtskhvaladze et al, 2020). Meiotic prophase I progression in D. unisexualis traced using immuno‐FISH technique, revealed that all studied oocyte I nuclei demonstrated non‐distorted meiotic prophase I.…”

Mitogenome analyses elucidate the evolutionary relationships of a probable Eocene wet tropics relic in the xerophilic lizard genus Acanthodactylus

“…The nearly complete newly assembled mitogenomes of A. guineensis and A. schmidti as well as the twelve additional taxa of Gallotiinae and Eremiadini each consist of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes typical for vertebrates. Gene order was the same as in other known lacertid mitogenomes 29 – 31 . We also recovered partial sequences of the control region for all mitogenomes.…”