A. A. Bannikova

Molecular phylogeny of the genus Alticola (Cricetidae, Rodentia) as inferred from the sequence of the cytochrome b gene

Central Asian mountain voles Alticola is one of the least known groups of voles both in evolution and life history. This genus includes three subgenera Alticola s.str., Aschizomys and Platycranius, and belongs to the tribe Clethrionomyini comprising also red‐backed voles Clethrionomys and oriental voles Eothenomys. In order to elucidate the phylogenetic relationships within Alticola and to examine its position within the tribe, mitochondrial cytochrome b (cyt b) gene variation was estimated, and the results were compared with morphological and palaeontological data. Maximum likelihood (ML), neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian phylogenetic analyses show that the genus Alticola does not appear to be a monophyletic group since the representatives of Aschizomys branch within Clethrionomys, whereas two other subgenera (Alticola and Platycranius) form a separate monophyletic clade. Flat‐headed vole Alticola (Platycranius) strelzowi is nested within the nominative subgenus showing close association with A. (Alticola) semicanus. Surprisingly, the two species of Aschizomys do not form a monophyletic group. The results of the relaxed‐clock analysis suggest that the Alticola clade splits from the Clethrionomys stem in early Middle Pliocene while basal cladogenetic events within Alticola s.str. dates back to the late Middle to early Late Pliocene. A scenario of evolution in Clethrionomyini is put forward implying rapid parallel morphological changes in different lineages leading to the formation of Alticola‐like biomorphs adapted to mountain and arid petrophilous habitats.

Supraspecies relationships in the subfamily Arvicolinae (Rodentia, Cricetidae): An unexpected result of nuclear gene analysis

Phylogenetic analysis of the supraspecies relationships was carried out using partial sequences of two nuclear genes in the subfamily Arvicolinae, which is one of the youngest and species-rich groups of myomorph rodents. The analysis with the new data resolved the majority of polytomy nodes in the phylogenetic trees reported for Arvicolinae, suggesting a gradual, rather than a saltatory, mode for their evolution. Mole voles Ellobiusini, steppe voles Lagurini, and gray voles Arvicolini were fount to be a monophyletic group that corresponds to the latest third wave of radiation within the subfamily. Red-back voles Myodini (=Clethrionomini) are a sister clade to this group and correspond to the second radiation wave. The order of divergence remained unresolved for the earliest radiation wave (Ondatrini, Prometheomyini, Dicrostonychini, and Lemmini). The close relationships observed for mole, gray, and steppe voles are unexpected and contradict the conventional views that Ellobiusini are an ancient group and are separate from all other voles on evidence of the extreme simplicity of their rooted molars and the peculiar structure of their skull and postcranial skeleton. It was assumed that many of these morphological characters indicate adaptation to subterranean life and provide no phylogenetic signal.

Molecular systematics and evolutionary biogeography of the genus Talpa (Soricomorpha: Talpidae).

The range of the genus Talpa covers almost all Europe up to Western Asia. This genus has never been the object of comprehensive systematic studies using molecular and genetic techniques, such that the evolutionary relationships among species remain unclear. Talpa shows high levels of endemism, and the influence of past glaciation cycles on the distribution pattern of several species has been hypothesized. In this work, we assessed the molecular systematics of the genus using the mitochondrial gene cytochrome b from eight of the nine extant species of Talpa moles. Furthermore, molecular clock estimations were used to hypothesize a biogeographic scenario in concordance with fossil data. Results suggest a monophyletic origin of the genus and a common ancestor for the western European moles T. europaea, T. caeca, T. romana and T. occidentalis. The eastern species T. altaica and T. caucasica are basally divergent. The estimated ages of divergence among lineages are in accordance with a Miocene origin of the extant moles. The genus likely originated in Asia, spreading into Europe during the Pliocene. The evolution of moles appears to have been driven by changes in moisture levels that influenced extinction and speciation events during the Miocene and the Pliocene. Pleistocene climatic oscillations likely caused the range shrinkages and expansions that led to the current distribution pattern of most Talpa species.

Molecular phylogeny and systematics of Dipodoidea: a test of morphology‐based hypotheses

Lebedev, V.S., Bannikova, A.A., Pagès, M., Pisano, J., Michaux, J.R. & Shenbrot, G.I. (2012). Molecular phylogeny and systematics of Dipodoidea: a test of morphology‐based hypotheses. —Zoologica Scripta, 42, 231–249.

Using Inter-SINE-PCR to Study Mammalian Phylogeny

Results of the use of the fingerprinting method related to short interspersed elements (SINEs), inter-SINE–PCR, in the study of phylogenetic and taxonomic relationship in mammals from orders Chiroptera (family Vespertilionidae) and Lipotyphla (family Erinaceidae) are reported. The inter-SINE–PCR method is based on the amplification of fragments situated between copies of SINEs, which are short retroposons spaced 100 to 1000 bp apart. Specifically selected primers were used, which are complementary to consensus sequences of two short retroposons: the mammalian interspersed repeat (MIR), which is typical of all mammals and some other vertebrates, was used in the cases of bats and Erinaceidae, and the ERI-1 element recently isolated from the genome of the Daurian hedgehog was used in the case of Erinaceidae. The results support the current view on phylogenetic relationship between hedgehogs belonging to genera Erinaceus, Hemiechinus, and Paraechinus (but not the genus Atelerix). In bats, the phylogenetic reconstruction revealed a statistically valid topology only at lower taxonomic levels, whereas the topology for the genus and supragenus ranks was unresolved and fan-shaped. The benefits and limitations of the inter-SINE–PCR method are discussed.

Molecular differentiation and taxonomy of the sunwatcher toad-headed agama species complex Phrynocephalus superspecies helioscopus (Pallas 1771) (Reptilia: Agamidae)

Lizards of the sunwatcher toad-headed agama species complex Phrynocephalus superspecies helioscopus, mostly distributed in Central Asia and Middle East, were examined using analysis of variation at the mitochondrial cytochrome oxidase c subunit I gene fragment and fingerprint analysis of nuclear DNA (inter-SINE PCR technique). A total of 86 individual tissue samples from 53 populations, to the full extent representing different parts of the species complex range, were subjected to molecular genetic examination, and surprisingly deep differentiation was revealed. The populations analyzed split into 12 isolated phylogroups, many of which were characterized by a narrow range and genetic isolation. Monophyly of sunwatcher (Ph. helioscopus) and Persian (Ph. persicus) toad-headed agamas was confirmed. However, both of these species probably represent the species complexes. Zoogeography of Central Asiais discussed.

Variable and Invariable DNA Repeat Characters Revealed by Taxonprint Approach are Useful for Molecular Systematics

Abstract. A specially optimized restriction analysis of highly repetitive DNA elements, called DNA taxonprint, was applied for phylogenetic study of primates and lizards. It was shown that electrophoretic bands of DNA repeats revealed by the taxonprint technique have valuable properties for molecular systematics. Approximately half of taxonprint bands (TB) are invariable and do not disappear from the genomes during evolution or change spontaneously. Presumably these invariable bands are restriction fragments of dispersed DNA repeats. Another group represents variable taxonprint bands that differ even between closely related species. These variable bands are probably represented by tandem DNA repeats and could be used as species-specific markers. It was shown that taxonprint bands are independent characters since the appearance of a new taxonprint band does not change the previous band pattern. Phylogenetic reconstruction carried out on taxonprint data demonstrated that this approach could be of general utility for molecular systematics and species identification.

Radiation Events in the Subfamily Arvicolinae (Rodentia): Evidence from Nuclear Genes

Voles and lemmings (subfamily Arvicolinae) areone of the youngest and speciesrich groups of myomorphic rodents prevailing in different landscapezones of the northern hemisphere. Because of unprecedented fossil records, as well as rapid and continuingmorphogenesis, they became leading forms in correlation and biostratigraphy of late Cenozoic continentaldeposits. For the same reasons, they are an almostideal model group for testing various evolutionary scenarios and phylogenetic hypotheses on the one hand,and for comparison of the possibilities and limitationsof different methodical approaches to phylogeny analysis and system generation, on the other hand.This study consisted in analysis of two nuclear genevariation, which demonstrated that mole lemmings(Ellobuisini), steppe lemmings (Lagurini) and grayvoles (Arvicolini) were sister groups. This divergencewas the latest, third step of subfamily radiation. Thenew data on close sister relationships of mole lemmings, gray voles, and steppe lemmings and on the latemole lemming radiation are unexpected and contradictory to traditional views.Originally, system generation and relationshipanalysis within the subfamily were based on comparatively studying the morphological traits in the modernand extinct forms; the most important results werereported in summary monographs and articles [1–4].As new approaches (karyological, allozyme analysis, molecular methods) appeared, modified schemeswere developed based on the new data [5–12]. Comprehensively studying the group revealed some distincthigher categories of the tribal rank in all summariesand systems, including the latest ones [11]. At thesame time, their composition, relationships, and thetime of divergence still remain obscure. Morphological approaches fail to reconstruct the evolutionary history and relationships of such a young and rapidlyevolving group because of a few available traits andnumerous parallelisms.The study of Arvicolinae molecular phylogeny hasbeen so far based on the mitochondrial cytochrome

Taxonomic position of Afghan vole (Subgenus Blanfordimys) by the sequence of the mitochondrial cytb gene

It is rather difficult to construct a system of gray voles of the tribe Microtini by a set of morphological and karyological characters because form generation is mosaic at these organization levels. The sequence of the mitochondrial cytochrome b gene was used to study the phylogenetic relationships and taxonomic position of the Central Asian subgenus Blanfordimys. Afghan vole Microtus (Blanfordimys) afghanus and Bucharian vole M. (Blanfordimys) bucharensis clustered with Pamir vole M. (Neodon) juldaschi, which is conventionally assigned to another subgenus. The last two species proved to be significantly closer to each other than either of them was to M. (Blanfordimys) afghanus, which disagrees with the monophyletic origin accepted for Blanfordimys. The genetic distances between the species of the subgenus Blanfordmys and M. juldaschi were comparable with the distances between the sister subgenera Microtus s. str. and Sumeriomys or Pallasiinus and Alexandromys and with the basal divergence of supraspecific clades in the subgenus Terricola. It was assumed that a special Central Asian group of species exists within the tribe Microtini and includes species of the subgenus Blanfordimys and M. juldaschi and that the subgenera Neodon and Blanfordimys should be revised.

Molecular genetic diversification of the lizard complex Darevskia raddei (Sauria: Lacertidae): Early stages of speciation

To characterize the molecular genetic diversity of the genus Darevskia, several populations were examined by the inter-SINE-PCR method, reporting the number and sizes of the spacers between individual copies of SINE-like interspersed repeats. Examination of 17 D. raddei geographical populations and several reference species revealed unequal genetic differences, measured as Nei and Li’s genetic distances (DNL), for different groups of samples. The highest homogeneity was observed for the apparently panmictic D. raddei nairensis population from the basin of the Hrazdan River: genetic differences within each of the five samples and between them were similarly low (less than 0.1). The difference between ten samples of D. raddei raddei from Armenia and Karabakh (0.2–0.3) was somewhat higher than the interindividual difference within each sample (0.1–0.2), indicating that the samples belonged to different populations. The assumption was supported by the phylogenetic tree topology and multidimensional scaling. The differences between samples from the morphological subspecies D. raddei raddei and D. raddei nairensis ranged 0.3–0.4. The difference of two D. raddei raddei samples of Talysh (Azerbaijan) from other samples of the same subspecies corresponded to the subspecific level. The genetic distances between the good species D. raddei and D. rudis was 0.6–0.7. In terms of DNL, a questionable population from northwestern Turkey (“D. tristis”) was closer to D. rudis (DNL = 0.45), probably representing its subspecies. The phylogeography of D. raddei is discussed.