Phylogeny and Phylogeography of the Holarctic

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (10 March 2023) | Viewed by 10300

Special Issue Editor

Institute of Cytology and Genetics SB RAS, Pr.Lavrientieva 10, 630090 Novosibirsk, Russia
Interests: phylogeography; phylogeny; transcriptomics; Paleartic; earthworms; amphibians; hypoxia tolerance; freeze tolerance

Special Issue Information

Dear Colleagues,

Advances in DNA sequencing technology, in recent decades, have revolutionized our knowledge on the patterns of interspecific and intraspecific relationships. The phylogeny of various groups of living organisms and the geographic patterns of the genetic diversity of individual species have been extensively studied, which has provided us with insights into the formation and histories of biotas of various regions and their relationships. The Holarctic is the largest of the biogeographic realms, but it is relatively poor in species, especially in its boreal and arctic regions. Within the Holarctic, North America and Europe have been studied particularly intensely; however, the rest of Eurasia lags behind these regions in terms of the number of studies and of the groups covered by them. The aim of this Special Issue is to contribute to the phylogeny and phylogeography of various organism groups of the Holarctic, and to summarize the knowledge on different regions within this area. Submissions are not restricted to any particular taxonomic group or spatial scale.

Dr. Sergey Shekhovtsov
Guest Editor

Manuscript Submission Information

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Keywords

  • phylogeography
  • phylogenetics
  • Holarctic
  • Eurasia
  • North America
  • migration
  • dispersal

Published Papers (6 papers)

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Research

15 pages, 3479 KiB  
Article
An Invisible Boundary between Geographic Ranges of Cryptic Species of Narrow-Headed Voles (Stenocranius, Lasiopodomys, Cricetidae) in Transbaikalia
by Tatyana V. Petrova, Ivan A. Dvoyashov, Yury A. Bazhenov, Ekaterina V. Obolenskaya and Andrey A. Lissovsky
Diversity 2023, 15(3), 439; https://doi.org/10.3390/d15030439 - 16 Mar 2023
Cited by 1 | Viewed by 1225
Abstract
The narrow-headed vole species complex is represented by Lasiopodomys gregalis and L. raddei, which probably diverged at the beginning of the Middle Pleistocene and came into secondary contact in the Transbaikal region. The current study analyzed mitochondrial gene cytochrome b, nuclear [...] Read more.
The narrow-headed vole species complex is represented by Lasiopodomys gregalis and L. raddei, which probably diverged at the beginning of the Middle Pleistocene and came into secondary contact in the Transbaikal region. The current study analyzed mitochondrial gene cytochrome b, nuclear gene BRCA1, and microsatellite data and was aimed at clarifying geographic ranges of these species and searching for hybrid zones between them. It turned out that the geographic range of L. raddei is almost surrounded by that of L. gregalis; these species are strictly parapatric without a single detected sympatry zone. Although in none of the tested populations did the BRCA1 genotyping contradict the pattern revealed by mitochondrial cytb, microsatellite loci showed traces of hybridization in several populations. Results of species distribution modeling indicated that these species are characterized by quite similar (caused by the same environmental factors), but nevertheless significantly different, ecological preferences. Full article
(This article belongs to the Special Issue Phylogeny and Phylogeography of the Holarctic)
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9 pages, 3758 KiB  
Article
Formica picea and F. candida (Hymenoptera: Formicidae): Synonyms or Two Species?
by Zoya A. Zhigulskaya, Sergei V. Shekhovtsov, Tatiana V. Poluboyarova and Daniil I. Berman
Diversity 2022, 14(8), 613; https://doi.org/10.3390/d14080613 - 29 Jul 2022
Cited by 2 | Viewed by 1719
Abstract
Ants of the «Formica piceaF. candida» complex are widespread across Eurasia. However, it is still a matter of debate if it constitutes one or two species. In this study, we collected a sample of specimens from different parts of [...] Read more.
Ants of the «Formica piceaF. candida» complex are widespread across Eurasia. However, it is still a matter of debate if it constitutes one or two species. In this study, we collected a sample of specimens from different parts of Eurasia, sequenced the mitochondrial cox1 and cytb genes, as well as three nuclear loci—wg, Top1, and ITS2—and analyzed the available published data. We found this complex to contain a new, yet undescribed, taxon that has a large distribution in Siberia and East Asia. Thus, the «Formica piceaF. candida» complex consists of at least three taxa with distinct distributions. Full article
(This article belongs to the Special Issue Phylogeny and Phylogeography of the Holarctic)
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7 pages, 1188 KiB  
Communication
Molecular Characterization of Ctenotaenia marmotae (Frölich, 1802) Railliet, 1893 (Cyclophyllidea: Anoplocephalidae) Parasitizing Rodents of the Genus Marmota and Spermophilus from Eurasia
by Anton Krivopalov, Sergey Abramov, Lyudmila Akimova, Alina Barkhatova, Anton Gromov, Sergey Konyaev, Natalia Lopatina, Anna Sidorovich, Egor Vlasov, Pavel Vlasenko and Vadim Zinchenko
Diversity 2022, 14(7), 531; https://doi.org/10.3390/d14070531 - 30 Jun 2022
Cited by 1 | Viewed by 1372
Abstract
Cestodes Ctenotaenia marmotae are a widespread parasite of Eurasian ground squirrels. Being the only valid species of its genus, it has been recorded in ten host species from the genera Marmota and Spermophilus. Its definitive hosts live in similar ecological conditions and [...] Read more.
Cestodes Ctenotaenia marmotae are a widespread parasite of Eurasian ground squirrels. Being the only valid species of its genus, it has been recorded in ten host species from the genera Marmota and Spermophilus. Its definitive hosts live in similar ecological conditions and their area covers a wide geographical territory. Therefore, it remained unclear whether C. marmotae is a single species and how high the level of its genetic variability is. The present study analyzed the variability of two mitochondrial cestode genes from four host species from geographically distant localities. Phylogenetic analysis revealed that the newly obtained sequences form a species-level clade with already known sequences from the GenBank. Small genetic distances between the studied sequences indicate low intraspecific genetic variability within the C. marmotae, which may be a consequence of rapid expansion of the cestodes in ground squirrel species inhabiting the flat and mountain steppe landscapes in the past. Full article
(This article belongs to the Special Issue Phylogeny and Phylogeography of the Holarctic)
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16 pages, 2596 KiB  
Article
Narrow-Headed Voles Species Complex (Cricetidae, Rodentia): Evidence for Species Differentiation Inferred from Transcriptome Data
by Tatyana Petrova, Maria Skazina, Aleksander Kuksin, Olga Bondareva and Natalia Abramson
Diversity 2022, 14(7), 512; https://doi.org/10.3390/d14070512 - 24 Jun 2022
Cited by 2 | Viewed by 1599
Abstract
The narrow-headed vole complex includes two cryptic species, Lasiopodomys raddei and L. gregalis, and three allopatrically-distributed lineages with obscure taxonomic ranks within the latter. Based on the RNA-seq data of 12 specimens, the current study aims to find the molecular mechanisms of intraspecies [...] Read more.
The narrow-headed vole complex includes two cryptic species, Lasiopodomys raddei and L. gregalis, and three allopatrically-distributed lineages with obscure taxonomic ranks within the latter. Based on the RNA-seq data of 12 specimens, the current study aims to find the molecular mechanisms of intraspecies differentiation and, in particular, reproductive isolation between analyzed groups. According to the results of the GO-enrichment analysis, about a hundred biological processes associated with genes with contrasting SNPs for L. gregalis and L. raddei were identified. Among them, processes of interspecific interactions, defense responses, responses to external stimuli, and the perception of chemical stimuli and smell were identified, indicating the likely existence of pre-copulatory behavioral and physiological mechanisms that contribute to reproductive isolation between cryptic species. An evaluation of the ratio of non-synonymous substitutions to synonymous ones showed evidence of selection in L. raddei compared to L. gregalis for a large part of the analyzed genes. Among the analyzed genes, genes with both weakening and intensifying selection were found. Full article
(This article belongs to the Special Issue Phylogeny and Phylogeography of the Holarctic)
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6 pages, 972 KiB  
Communication
Distribution and Molecular Diversity of Paranoplocephala kalelai (Tenora, Haukisalmi & Henttonen, 1985) Tenora, Murai & Vaucher, 1986 in Voles (Rodentia: Myodes) in Eurasia
by Anton Krivopalov, Pavel Vlasenko, Sergey Abramov, Lyudmila Akimova, Alina Barkhatova, Nikolai Dokuchaev, Anton Gromov, Sergey Konyaev, Natalia Lopatina, Egor Vlasov and Eugeny Zakharov
Diversity 2022, 14(6), 472; https://doi.org/10.3390/d14060472 - 12 Jun 2022
Cited by 1 | Viewed by 1754
Abstract
Cestodes Paranoplocephala kalelai, which parasitizes in the small intestine of Myodes voles and is distributed in northern Fennoscandia, was found in six habitats in the Asian part of Russia and eastern Kazakhstan, which indicates a wider distribution of P. kalelai on the [...] Read more.
Cestodes Paranoplocephala kalelai, which parasitizes in the small intestine of Myodes voles and is distributed in northern Fennoscandia, was found in six habitats in the Asian part of Russia and eastern Kazakhstan, which indicates a wider distribution of P. kalelai on the continent. Analysis of mtDNA showed that P. kalelai is characterized by significant molecular variability in Eurasia. This study complements the data on the distribution of P. kalelai and provides the first molecular data from the territory of Russia and Kazakhstan. The sequence variability of two mitochondrial genes cox1 and nad1 of P. kalelai was studied in two species of voles: gray red-backed Myodes rufocanus and northern red-backed vole Myodes rutilus. Five haplotype groups in the cox1 and nad1 gene networks were identified, and the existence of two mtDNA lines in P. kalelai outside northern Fennoscandia was confirmed. The geographical distribution of the identified haplotypes suggests that the foothills of the Altai-Sayan mountains and southern West Siberia may serve as a refugium for P. kalelai during repeated glaciations. Full article
(This article belongs to the Special Issue Phylogeny and Phylogeography of the Holarctic)
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8 pages, 1111 KiB  
Article
Genotyping-by-Sequencing Analysis Shows That Siberian Lindens Are Nested within Tilia cordata Mill
by Sergei V. Shekhovtsov, Irina N. Shekhovtsova and Oleg E. Kosterin
Diversity 2022, 14(4), 256; https://doi.org/10.3390/d14040256 - 30 Mar 2022
Cited by 1 | Viewed by 1902
Abstract
Tilia sibirica and T. nasczokinii are considered to be endemic Siberian linden species. They have very small distributions located hundreds to thousands of kilometers away from other lindens. It is unclear how closely these species are related to the widespread Tilia cordata: [...] Read more.
Tilia sibirica and T. nasczokinii are considered to be endemic Siberian linden species. They have very small distributions located hundreds to thousands of kilometers away from other lindens. It is unclear how closely these species are related to the widespread Tilia cordata: according to the current hypotheses, they could be pre-Pleistocene relicts or remnants of the recent continuous range of T. cordata that existed during the Holocene climatic optimum. Earlier studies detected significant differences between T. sibirica, T. nasczokinii, and T. cordata in microsatellite loci, but not in plastid sequences. Here we performed a phylogenetic analysis of several linden species based on GBS data. The obtained GBS sequences were assembled to create phylogenetic trees based on 16,000–294,000 variable sites. We found that T. cordata and the two putative Siberian species formed a monophyletic group. It consisted of three clades: the basal clade containing specimens from the Caucasus, and two sister clades representing populations from the East European Plains+the Urals and Siberia, respectively. Neither of the Siberian species was related to the Far Eastern T. amurensis, as was hypothesized earlier. Our study suggests that the colonization of Europe and Siberia after the Last Glacial Maximum occurred from different glacial refugia. Full article
(This article belongs to the Special Issue Phylogeny and Phylogeography of the Holarctic)
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