Nuclear variation and phylogeography of the chromosomally highly polymorphic common shrew (Sorex araneus) represent a subject of considerable interest for understanding microevolutionary processes in wide-ranging mammals. In the present study, we addressed this issue using SNP data generated via the ddRADseq approach and based on extensive geographic sampling. Our results are consistent with the hypothesis of a recent range expansion from a refugium located in the Balkan-Danubian region, followed by subsequent colonization of Eastern Europe and, later, Siberia. This scenario had previously been proposed on the basis of mitochondrial DNA data. On the contrary, genetic relatedness of shrews from southern Karelia and central Siberia, as suggested previously from mtDNA variation, is not supported by our SNP dataset. Nuclear data reveal substantial gene flow across the boundaries between chromosomal races and racial groups.

Using the example of multiple species groups and species complexes, it is empirically shown that the resolving power of a set of 10–20 nuclear loci is insufficient for the study of their genetic differentiation. For an adequate analysis of phylogenetic relationships (including reticulation events) and assessment of divergence levels within such groups of closely related species, it is necessary to multiply the number of nuclear loci and transit to high-throughput next-generation deep sequencing. However, the question of the genomic coverage required for the purposes of such study remains open. In other words, exactly how many genes in a set are needed to measure the genetic distance resolving the relationships between branches on the phylogenetic tree reconstruction of a complex of closely related species? We chose protein-coding sequences as a standard set of markers. Distances of 160–180 genes with a combined length of 270 000–300 000 bp were used to estimate the divergence levels of closely related mammalian species. In most cases, the interspecific distances are within the range of 0.15–0.75

The taxonomy of the stripe-backed shrew complex ( Sorex cylindricauda species group), distributed in mountains of western China, appears challenging due to remarkable variation in morphological traits and relatively recent times of diversification. According to classical points of view only two or three species of the stripe-backed shrews can be distinguished. However, previous molecular reconstructions revealed at least 14 genetic lineages including a number of undescribed cryptic species. In the current study we revise the taxonomic status of large-sized stripe-backed shrews occurring in high mountain areas in south Gansu, north-western Sichuan and western Qinghai that were previously treated as S. aff. cylindricauda or S. sinalis. The available molecular data place them in a separate species-level lineage of the stripe-backed shrew complex. Our morphological analysis indicate that shrews of this lineage are distinct from the two other large-sized Chinese species, S. cylindricauda and S. sinalis , based on both cranial and external traits. Therefore, we here describe it as a species new to science, the karyotype of which is characterized by 2n = 26 with an additional B chromosome and NFa = 44. Our molecular phylogenetic analysis demonstrates multiple instances of mitonuclear discordance among lineages within the S. cylindricauda complex, which is likely a result of mtDNA introgression, thus highlighting the important role of reticulation events in the evolution of the group.

A new species of gymnure of the genus Neohylomys is described from northern Vietnam based on morphological and molecular differences. The species Neohylomys vietnamensis sp. nov. differs from the closely related species N. hainanensis from Hainan Island, China, previously the only species of the genus Neohylomys, by morphological and morphometric traits and by the mitochondrial cytb (8% of divergence) and nuclear BRCA1 genes. To date, the new species is known to exist only in northern Vietnam.

Multilocus analysis was for the first time used to study the phylogeny of the Crocidura suaveolens s. l. species complex. Sequencing data for 16 nuclear genes indicated that several distinct forms exist within the species complex. The structure of the complex did generally not contradict its mitochondrial phylogeny. Siberian shrew showed certain specificity of the nuclear genome, but the degree of its genetic differentiation did not correspond to the species level. Relationships of Crocidura aff. suaveolens from South Gansu and Sichuan with other forms of the species complex were clarified. Shrews from Buryatia and Khentei also belong to this form, but their mtDNA apparently introgressed from C. shantungensis in the past. Hybridization of C. suaveolens s. str. with C. aff. suaveolens and C. güeldenstaedtii occurred recently. Due to multiple introgression events in the history of C. suaveolens s. l., a far larger set of loci is necessary for the analysis of the phylogenetic relationships between its forms.

Within the most speciose genus of extant mammals -Crocidura, the pergrisea species complex distributed in South West Asia remains the least studied, largely due to the rarity of its representatives. We examined the phylogenetic position of two putative species of the pergrisea species complex (C. serezkyensis and C. arispa) using historical DNA isolated from museum specimens. On the basis of sequence data for two nuclear and one mitochondrial genes we have come to the following conclusions: C. serezkyensis and C. arispa are rather close to each other and belong to a separate lineage of white-toothed shrews for which C. ramona from Israel is the relatively close sister branch. The pergrisea species complex does not include C. zarudnyi, which was previously shown to be close to C. suaveolens. The clade including C. pergrisea species complex and C. ramona likely belongs to a large Afro-Mediterranean clade, which includes also the Afromontane clade, the Mediterranean clade and C. leucodon. The problems of systematics within the pergrisea species complex are discussed.

In the present study, we reconstruct phylogenetic relationships within the chromosomally variable Sorex araneus species group based on 20 nuclear loci and the mitochondrial cyt b gene. In the species tree, Nearctic S. arcticus represents the earliest offshoot of the group followed by Holarctic S. tundrensis and Siberian S. daphaenodon . Five other species distributed mostly in Europe form a well‐supported clade. Coding regions showed stronger phylogenetic signal than introns. The results suggest a high incidence of reticulation in the evolution of the group. The authentic mitochondrial lineage of the Iberian shrew S. granarius was found to be close phylogenetically to S. coronatus , which confirms that some populations of the Iberian shrew S. granarius were introgressed from S. araneus. Footprints of deeper reticulations are revealed for the first time, indicating the potential hybrid origin of the S. arcticus and S. coronatus lineages. Ancient hybridisations are hypothesised to be the source of discordance between molecular‐ and karyotype‐based phylogenetic reconstructions.

The northern three-toed jerboa Dipus sagitta had long been considered to be a single polytypic species. High genetic diversity of D. sagitta was earlier revealed on the basis of several mitochondrial and nuclear genes, and several separate species were hypothesized to occur within the taxon. However, the relationships between phylogenetic lineages have not been established because of the small sample size of nuclear genes. In the present work, a far larger set of nuclear DNA loci was used, and thus, a higher resolution of the phylogenetic tree was achieved for ten D. sagitta forms. The structure revealed for the species mainly confirmed the topology and relationships of the mtDNA lineages. Yet the mitochondrial and nuclear phylogenies were not completely consistent. Some of the D. sagitta genetic lineages were therefore assumed to be a product of reticular evolutionary processes. The taxon was concluded to be the diverse species complex D. sagitta sensu lato, in which long-diverged lineages are not always reproductively isolated.

A range-wide phylogenetic/phylogeographic study of the three-toed jerboas of the genus Stylodipus is conducted using the mitochondrial cytb gene and fragments of several nuclear genes. The genus has been believed to include three species: S. telum (W Central Asia, SE Europe), S. andrewsi (E Central Asia), and S. sungorus (Dzungar basin). Our data support the dichotomy between S. andrewsi and the other taxa forming S. telum species group. Within the latter, both mtDNA and nuclear loci indicate a species-level divergence between S. telum and the S. t. birulae lineage (Zaisan depression, NE Kazakhstan), previously considered a subspecies of S. telum and here elevated to full species. S. sungorus is recovered as a close sister group to S. birulae on the basis of nuclear data but clustered with S. telum in the mitochondrial tree. The latter taxon is the most variable and includes two closely related eastern and western sublineages, separated by the Volga-Ural sands and joined by a more divergent S. t. karelini lineage (E Kazakhstan). The observed mitonuclear discordance is hypothesized to occur due to mtDNA introgression resulting from hybridization between S. sungorus and S. t. karelini, which highlights the important role of reticulations in the evolution of Dipodidae.

Five-toed jerboas of the subfamily Allactaginae comprise several complex taxa occurring over a wide distribution range covering a large part of the Eurasian arid belt. In this study, we employed current methods of molecular phylogenetics based on 15 nuclear genes and the mitochondrial gene cytb to revise relations and systematics within Allactaginae. We also applied species distribution modelling projected on paleo-environmental data to reconstruct the geographic patterns of speciation in Allactaginae. We elucidated the intergeneric relationships within this subfamily and clarified interspecies relations within the genus Scarturus. Moreover, our results demonstrate the species status of S. caprimulga; outline the currently understudied diversity within Orientallactaga, Allactaga, and Pygeretmus; and improve the divergence estimates of these taxa. Based on our results from modelling of geographic range fragmentation in allactagines, we suggest the dating and location of speciation events and present hypotheses regarding general habitat niche conservatism in small mammals.

The genus Chionomys includes two supraspecific groups: "nivalis" and "gud-roberti".For a long time, it has been thought that the nivalis group includes only C. nivalis.Here, molecular phylogenetic analysis of nine specimens from Turkey, Armenia, and Iran was performed using the Cytb gene and two nuclear genes: BRCA1 and GHR.In the results on Cytb, two specimens from central Taurus Mountains (Turkey), morphologically similar to C. nivalis, stood apart from all studied C. nivalis geographic forms at the species level (9-12%).Meanwhile, 38 km southwest from our collection site, there is known C. nivalis of the Caucasian-Asia Minor molecular-genetic clade.Hence, the form from central Taurus and common Asia Minor C. nivalis seem sympatric.Therefore, they are most likely genetically isolated from each other as separate species.A morphometric comparison of the Taurus specimens and C. nivalis from the eastern part of the geographic range was carried out by principal component analysis of 12 craniometric characteristics.In some craniometric characteristics, the type specimens of the new species are clearly larger than all subspecies of C. nivalis from the eastern part of the range, except C. n. layi.That is why we consider those two central-Taurus specimens a holotype and paratype of a new cryptic species: C. stekolnikovi sp.nov.In addition to the morphological diagnosis, we used data on amino acid substitutions in Cytb and nucleotide substitutions in BRCA1 and GHR.

Taxonomic status of gliding squirrels belonging to the "northern" form of Petinomys setosus known from N. Burma and Thailand has been controversial. Earlier it was assigned to a distinct genus Olisthomys, however, currently it is synonymized with P. setosus s. str. from Sumatra and Borneo Islands, and Malay Peninsula. A squirrel collected in Song Hinh forest (Phu Yen Province, south central Vietnam) was examined genetically using sequence data on three mitochondrial genes (cytb, 12S, 16S) and one nuclear (IRBP) gene. The molecular results demonstrated that this squirrel is significantly divergent from the other examined specimens of Petinomys and belongs to a separate genetic lineage within the Glaucomyina clade. The obtained phylogenetic pattern supports recognition of Olisthomys as a valid genus; however, to confirm this conclusion a comprehensive taxonomic revision of Petinomys and related genera is required. The reconsideration of taxonomic position of the "northern" P. setosus also raises the question of the conservation status of this taxon.

Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the Erinaceus hedgehogs species complex, offering a unique comparison of two secondary contact zones between Erinaceus europaeus and E. roumanicus. Results confirmed diversification of the genus during the Pleistocene period, and detected a new refugial lineage of E. roumanicus outside the Mediterranean basin, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from E. europaeus to E. roumanicus suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different age and thus of the different stage of evolution of reproductive isolating mechanisms in each hybrid zone.

Background: High-dose chemotherapy (HDCT) followed by autologous transplantation of hematopoietic stem cells (ASCT) is the gold standard of treatment for patients with primary-refractory and relapsed forms of Hodgkin’s lymphoma (R/R HL).There are several most commonly used conditioning regimens for HDCT followed ASCT.However, there are currently no data on the conduct of randomized studies that would compare the effectiveness and toxicity of different regimens. Aims: Comparison HDCT (CLV, LEAM, BeEAC) as a conditioning regimen before ASCT for the treatment of R/R HL. Methods: In retrospective study were included 279 patients with HL, median age 30 years;121 men and 158 women. All patients received HDCT and ASCT in NMSC named after N.I.Pirogov (2006 - 2018). Conditioning regimens: CLV (cyclophosphamide, lomustine, etoposide) – 78 patients, LEAM (lomustin, etoposide, cytarabine, melphalan) – 129 patients, BeEAC (bendamustine, cytarabine, etoposide, cyclophosphamide) – 72 patients. Results: Hematologic toxicity of different regimens (CLV, LEAM, BeEAC). All patients developed grade IV neutropenia, anemia with/without transfusion necessity, severe thrombocytopenia with transfusion requirements in most cases. Duration of neutropenia was the same – 9 days. Duration of thrombocytopenia in CLV regimen – 9 days, LEAM and BeEAC -11 days. Anemia Grade II (median) was identified in CLV, Grade III (median) in LEAM and BeEAC regimens. Non-hematologic toxicity. Presented in Table 1. Table 1. - Toxicity of different regimens. Transplant-related mortality (until D + 30) was: CLV -1,3 %, LEAM- 3,1 %, BeEAC – 2,8%. Efficiency of condition regimens. Comparison of OS and PFS of different regimens pretended in figure 1,2. Characteristic CLV LEAM BeEAC Oral mucositis 34,6% (n=27) 56,6% (n=72) 40,3 % (n=29) Enteropathy 16,2 % (n=13) 60,4% (n=78) 39% (n=28) Cardiotoxic effects 1,38 % (n=1) 2,3% (n=3) 6,9% (n=5) Pulmonary toxicity 1,3% (n=1) 0% (n=0) 4,1% (n=3) Hepatic toxicity 15,4% (n=12) 17,0% (n=22) 27,8 % (n=18) Infection 68% (n=53) 76% (n=98) 69,4%(n=50) Image:Summary/Conclusion: HDCT followed ASCT is the best therapeutic approach for a R/R HL. HDCT is of utmost importance, with BeEAC, LEAM and CLV conditioning regimens being considered as viable alternatives. Our results suggest a comparable efficacy of BeEAC, LEAM and CLV conditioning in terms of survival and disease control for HL patients treated with HDCT and ASCT. However, we also observed higher rates of gastrointestinal and cardiac toxicities in patients transplanted after LEAM and BeEAC. The worst OS in patients received LEAM can be explained by the fact that the regimen was used in our hospital earlier than others, when such drugs as Nivolumab and Brentuximab vedotin were not available to the patients with relapse after HDCT and ASCT.

We studied the polymorphism of the cytb gene in two forms of the Lesser White-toothed Shrew species complex: Crocidura suaveolens s. stricto and C. sibirica. The haplotypes of C. sibirica are found to be very similar to those of Crocidura suaveolens. They do not belong to a distinct haplogroup. The molecular diversity of the populations in the Asian part of the range is higher than in Eastern Europe. For the combined sample from Asia and Europe together, we revealed a significant signal of population expansion. Analysis of the expansion time showed that the Asian territory was colonized earlier (before the last glacial maximum) than the Eastern Europe (at the very end of the Late Pleistocene and in the early Holocene). The results of the ancestral area reconstruction are consistent with the hypothesis of a Middle Asian origin of the C. suaveolens/C. sibirica group, recent colonization of Inner Asia and later penetration into Eastern Europe.

Phylogeography of the steppe bat, Myotis davidii in the eastern part of its broad range, was explored for the first time using mitochondrial genetic markers. The presence of two main intraspecific clades, Eastern and Western, was confirmed. Definite inner structure inside the Eastern group was shown. We discovered genetic diversity hotspot in northwestern Mongolia and neighboring regions, where highly divergent haplotypes are found. Presumably, this can be explained by Pleistocene refugial structure shaped by the ridges of the Mongolian Altai. The haplogroups from the southeast of Mongolia and Transbaikalia found to be related, while populations of the Kerulen valley located between these regions carry more distant haplotypes.

Almost 60 years have passed since the degree of DNA difference between two species was discovered to be a function of the time since their divergence. Later, it became clear that there is no universal molecular clock and the rate of molecular evolution varies greatly depending on the gene and phylogenetic lineage, correlating with biological characteristics (generation length, body size, and fertility) and features of the genome. The development of the molecular clock concept is associated with progress in methods that allow the degree of inconstancy of the rate of molecular evolution to be taken into account and measured. Currently, dating is mostly performed using Relaxed Clock methods, which rely on various models of the evolution rate (for example, with or without autocorrelation of rates in adjacent branches). Another relevant factor that allows reduction of the errors of molecular dating is the increase in the amount of data up to the genomic level, which enhances the requirements for computationally efficient algorithms and the methods of data partitioning. A separate problem is the time dependence of evolutionary rate estimates (the phenomenon of rate decay), which is especially important for the analysis of recent history. In the absence of an adequate sequence evolution model, time estimates can be significantly biased, which often affects the results obtained with mtDNA. One of the most important trends is the development of methods for obtaining calibration information: the more complete use of the constantly and rapidly growing volume of paleontological data, the analysis of paleoDNA, and other variants of heterochronous data. Despite the fact that the accuracy of estimates of the levels of molecular divergences continues to grow, the uncertainty in dating persists, largely due to the ambiguity of calibrations and the shortcomings of existing models of DNA sequence evolution.

The phylogeographic structure of the endemic white-toothed shrews of Vietnam, which belong to the Crocidura kegoensis–C. zaitsevi group, was assessed using mitochondrial and nuclear data. Specimens from 12 localities across Vietnam, including the holotypes of C. kegoensis and C. zaitsevi , were evaluated according to the complete mitochondrial cytochrome b ( cytb ) gene and fragments of eight independent nuclear loci. The results of molecular analyses revealed the conspecificity of C. kegoensis and C. zaitsevi . Therefore, the name Crocidura zaitsevi Jenkins et al., 2007, can be considered as a synonym of C. kegoensis Lunde et al., 2004, which has a complex phylogeographical structure. The analysis of cytb proved the existence of distinct mtDNA lineages in C. kegoensis : lineage A, which is distributed in the northern and central parts of the Annamite Range; and lineage B, which is only found in the south parts of the species range. Nuclear data support the differentiation between northern and southern populations, with the position of the central populations remaining unresolved. The estimated divergence times of the main mitochondrial lineages indicate that the Vietnamese endemic group, C. kegoensis−C. zaitsevi , represents a young taxon, with all radiation events occurring in the cooling periods of the Pleistocene.