Genotyping and Phylogenetic Analysis of Yersinia pestis by MLVA: Insights into the Worldwide Expansion of Central Asia Plague Foci

BACKGROUND: The species Yersinia pestis is commonly divided into three classical biovars, Antiqua, Medievalis, and Orientalis, belonging to subspecies pestis pathogenic for human and the (atypical) non-human pathogenic biovar Microtus (alias Pestoides) including several non-pestis subspecies. Recent progress in molecular typing methods enables large-scale investigations in the population structure of this species. It is now possible to test hypotheses about its evolution which were proposed decades ago. For instance the three classical biovars of different geographical distributions were suggested to originate from Central Asia. Most investigations so far have focused on the typical pestis subspecies representatives found outside of China, whereas the understanding of the emergence of this human pathogen requires the investigation of strains belonging to subspecies pestis from China and to the Microtus biovar. METHODOLOGY/PRINCIPAL FINDINGS: Multi-locus VNTR analysis (MLVA) with 25 loci was performed on a collection of Y. pestis isolates originating from the majority of the known foci worldwide and including typical rhamnose-negative subspecies pestis as well as rhamnose-positive subspecies pestis and biovar Microtus. More than 500 isolates from China, the Former Soviet Union (FSU), Mongolia and a number of other foci around the world were characterized and resolved into 350 different genotypes. The data revealed very close relationships existing between some isolates from widely separated foci as well as very high diversity which can conversely be observed between nearby foci. CONCLUSIONS/SIGNIFICANCE: The results obtained are in full agreement with the view that the Y. pestis subsp. pestis pathogenic for humans emerged in the Central Asia region between China, Kazakhstan, Russia and Mongolia, only three clones of which spread out of Central Asia. The relationships among the strains in China, Central Asia and the rest of the world based on the MLVA25 assay provide an unprecedented view on the expansion and microevolution of Y. pestis

Genome-Wide Mycobacterium tuberculosis Variation (GMTV) Database: A New Tool for Integrating Sequence Variations and Epidemiology

Background Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. Description Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. Conclusions Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains

Genotyping of Capreolus pygargus Fossil DNA from Denisova Cave Reveals Phylogenetic Relationships between Ancient and Modern Populations

BACKGROUND: The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples. CONCLUSION/SIGNIFICANCE: Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect

Insight into Microevolution of Yersinia pestis by Clustered Regularly Interspaced Short Palindromic Repeats

BACKGROUND: Yersinia pestis, the pathogen of plague, has greatly influenced human history on a global scale. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), an element participating in immunity against phages' invasion, is composed of short repeated sequences separated by unique spacers and provides the basis of the spoligotyping technology. In the present research, three CRISPR loci were analyzed in 125 strains of Y. pestis from 26 natural plague foci of China, the former Soviet Union and Mongolia were analyzed, for validating CRISPR-based genotyping method and better understanding adaptive microevolution of Y. pestis. METHODOLOGY/PRINCIPAL FINDINGS: Using PCR amplification, sequencing and online data processing, a high degree of genetic diversity was revealed in all three CRISPR elements. The distribution of spacers and their arrays in Y. pestis strains is strongly region and focus-specific, allowing the construction of a hypothetic evolutionary model of Y. pestis. This model suggests transmission route of microtus strains that encircled Takla Makan Desert and ZhunGer Basin. Starting from Tadjikistan, one branch passed through the Kunlun Mountains, and moved to the Qinghai-Tibet Plateau. Another branch went north via the Pamirs Plateau, the Tianshan Mountains, the Altai Mountains and the Inner Mongolian Plateau. Other Y. pestis lineages might be originated from certain areas along those routes. CONCLUSIONS/SIGNIFICANCE: CRISPR can provide important information for genotyping and evolutionary research of bacteria, which will help to trace the source of outbreaks. The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate

Eustenancistrocerus (Eustenancistrocerus) jerichoensis

Eustenancistrocerus (Eustenancistrocerus) jerichoensis (von Schulthess, 1928) Odynerus jerichoensis von Schulthess, 1928: 73 –74, ♀ ♂ (type locality: “Jericho” [Israel]). Eustenancistrocerus aemulus Giordani Soika, 1952: 35–36, ♂ (type locality: “ Persia sud-occidentale” [Iran]). Material examined. Russia. Dagestan: Derbent District, Kamyshchay River Valley (41°54′N, 48°13′E), 10. VI.2017, 4 ♂, 11. VI.2017, 6 ♂, 12. VI.2017, 1 ♂, leg. M.V. Mokrousov, 12. VI.2017, 1 ♂, leg. V. Gromenko; ibid., on Tamarix hohenackeri, 13. VI.2018, 3 ♂, leg. A.V. Fateryga; Tarumovka District, 20 km SSE Kochubey (44°15′N, 46°40′E), 6. VII.2018, 1 ♂, leg. Yu.V. Astafurova, K.I. Fadeev, V.M. Loktionov, M.V. Mokrousov, M.Yu. Proshchalykin [CAFK]. Distribution. * Russia: European part (North Caucasus).— Azerbaijan, Turkey, Syria, Jordan, Israel, Iran. Remarks. This species was misidentified as E. tegularis Morawitz, 1885 in our previous report (Fateryga et al. 2017).Published as part of Fateryga, Alexander V. & Mokrousov, Mikhail V., 2019, New records of eumenine wasps (Hymenoptera: Vespidae: Eumeninae) from Russia with description of a new species of Leptochilus de Saussure, 1853, pp. 412-422 in Zootaxa 4612 (3) on page 415, DOI: 10.11646/zootaxa.4612.3.7, http://zenodo.org/record/323520

Euodynerus (Euodynerus) hellenicus Bluthgen 1942

Euodynerus (Euodynerus) hellenicus Blüthgen, 1942 Euodynerus dantici hellenicus Blüthgen, 1942: 301, ♀ ♂ (type locality: “Kykladen-Insel Amorgos” [Greece]). Euodynerus hellenicus vechti Gusenleitner, 1972: 77–78, ♀ ♂ (type locality: “ Spanien, Badajoz, Merida” [Spain]). Material examined. Russia. Dagestan: Kumtorkalinskiy District, Barkhan Sarykum (43°00′N, 47°14′E), 24. VI.2018, 1 ♀, leg. K.I. Fadeev [CAFK]. Georgia. Tiflis [currently Tbilisi, 41°44′N, 44°50′E], 2 ♂, coll. F. Morawitz. Azerbaijan. Helendorf [currently Goygol, 40°35′N, 46°20′E], 1 ♀, coll. F. Morawitz [ZISP]. Distribution. * Russia: European part (North Caucasus).—* Georgia, * Azerbaijan, S Europe, Turkey, Afghanistan.Published as part of Fateryga, Alexander V. & Mokrousov, Mikhail V., 2019, New records of eumenine wasps (Hymenoptera: Vespidae: Eumeninae) from Russia with description of a new species of Leptochilus de Saussure, 1853, pp. 412-422 in Zootaxa 4612 (3) on page 414, DOI: 10.11646/zootaxa.4612.3.7, http://zenodo.org/record/323520

Stenodynerus xanthomelas

Stenodynerus xanthomelas (Herrich-Schäffer, 1839) Material examined. Russia. Krasnoyarsk Territory: Minusinsk District, vicinity of Minusinsk [52°42′N, 91°42′E], 2–9. V.1924, 1 ♂, leg. N. Filippov [ZISP]. Distribution. Russia: European part (Central, East, South, North Caucasus, Crimea), Western Siberia (Altai), *Eastern Siberia (Krasnoyarsk Terr.).—W, S, and E Europe, Georgia, Armenia, Turkey, Iran, China.Published as part of Fateryga, Alexander V. & Mokrousov, Mikhail V., 2019, New records of eumenine wasps (Hymenoptera: Vespidae: Eumeninae) from Russia with description of a new species of Leptochilus de Saussure, 1853, pp. 412-422 in Zootaxa 4612 (3) on page 419, DOI: 10.11646/zootaxa.4612.3.7, http://zenodo.org/record/323520

Eustenancistrocerus (Eustenancistrocerus) tegularis

Eustenancistrocerus (Eustenancistrocerus) tegularis (Morawitz, 1885) Distribution. S and E Europe, Armenia, Azerbaijan, Turkey, Syria, Israel, Iran, Central Asia, Kazakhstan.Published as part of Fateryga, Alexander V. & Mokrousov, Mikhail V., 2019, New records of eumenine wasps (Hymenoptera: Vespidae: Eumeninae) from Russia with description of a new species of Leptochilus de Saussure, 1853, pp. 412-422 in Zootaxa 4612 (3) on page 420, DOI: 10.11646/zootaxa.4612.3.7, http://zenodo.org/record/323520

Stenodynerus punctifrons

Stenodynerus punctifrons (Thomson, 1874) Material examined. Russia. Astrakhan Province: Akhtubinsk District, Bogdo-Baskunchak Nature Reserve, 1 km W former settlement of “NIAGLOS” [48°04′N, 46°53′E], Merike’s trap, 29. V.2014, 1 ♀, leg. K.A. Grebennikov [CAFK]. Distribution. Russia: European part (Central, *South), Urals, Western Siberia (Omsk Prov., Novosibirsk Prov., Altai), Eastern Siberia (Tyva, Irkutsk Prov., Buryatia, Yakutia, Zabaikalskiy Terr.), Far East (Amurskaya Prov., Primorskiy Terr.).—W, S, and E Europe, Caucasus, Turkey,? Iran, Kyrgyzstan, Kazakhstan, Mongolia.Published as part of Fateryga, Alexander V. & Mokrousov, Mikhail V., 2019, New records of eumenine wasps (Hymenoptera: Vespidae: Eumeninae) from Russia with description of a new species of Leptochilus de Saussure, 1853, pp. 412-422 in Zootaxa 4612 (3) on page 419, DOI: 10.11646/zootaxa.4612.3.7, http://zenodo.org/record/323520