scholarly journals High genetic diversity of ancient horses from the Ukok Plateau

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241997
Author(s):  
Nadezhda V. Vorobieva ◽  
Alexey I. Makunin ◽  
Anna S. Druzhkova ◽  
Mariya A. Kusliy ◽  
Vladimir A. Trifonov ◽  
...  
Keyword(s):  
Mitochondrial Haplotype ◽  
Altai Mountains ◽  
Sequencing Data ◽  
Migration Routes ◽  
High Genetic Diversity ◽  
Wild Horse ◽  
Domestic Horses ◽  
Ukok Plateau ◽  
Horse Domestication ◽  
Complete Mitochondrial Genomes

A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area.

scholarly journals Comparative Genetic Analysis of Yersinia pestis Strains Isolated on the Ukok Plateau and other Territories of the Altai Mountains

2021 ◽  
pp. 59-69
Author(s):  
G. A. Eroshenko ◽  
A. N. Balykova ◽  
Ya. M. Krasnov ◽  
E. A. Naryshkina ◽  
E. N. Rozhdestvensky ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
De Novo ◽  
Molecular Genetic ◽  
Genetic Identification ◽  
Likelihood Method ◽  
High Mountain ◽  
Altai Mountains ◽  
Natural Foci ◽  
Ukok Plateau ◽  
Average Size

The aim of the study was molecular-genetic identification and analysis of the phylogenetic relationship of Yersinia pestis strains isolated on the Ukok Plateau in 2020, in order to establish the current boundaries of the natural mega focus of plague in the Altai Mountains in Russia and Mongolia.Materials and methods. 37 strains of Y. pestis of the main subspecies isolated in the Tuva mountain and Gorno-Altai high-mountain plague foci and adjacent territories of Mongolia in 1971–2020 were studied. The whole genome sequencing of the strains was performed using the Ion S5 XL System (Thermo Fischer Scientific). Ion Torrent Suite software package 5.12 and Newbler gsAssembler 2.6 were used to process the data and assemble de novo the sequences of raw reads. The average size of the collected genome was 4.55 million base pairs. Core SNPs were detected by aligning the contigs of Y. pestis strains on the CO92 genome using the Snippy 4.6 program, then 28 SNP homoplasies were removed. The resulting set of SNPs contained only the core region of the genome (955 SNPs). The dendrogram was constructed using the Maximum Likelihood method applying the PhyML 3.1 program.Results and discussion. The current population structure of Y. pestis of the main subspecies, antique biovar, phylogenetic line 4.ANT, endemic to the foci of the Altai Mountains in Russia and Mongolia has been determined. The presence of 4.ANT-21 clone, which became widespread in the territory of these natural foci of plague at the begining of the XXI century, was revealed. It is shown that three strains isolated on the Ukok Plateau in 2020 belong to clone 4.ANT-21. According to phylogenetic analysis, evidence of 4.ANT circulation on the Ukok Plateau before 2018 was obtained. The lesson that has been learned is that it is necessary to study the territories of Mongolia, Kazakhstan and China bordering the Ukok Plateau in order to establish the current boundaries of the 4.ANT mega focus. 

A first comparison of bone histomorphometry in extant domestic horses ( Equus caballus ) and a Pleistocene Indian wild horse ( Equus namadicus )

2020 ◽  
Vol 15 (6) ◽  
pp. 448-460
Author(s):  
Marco ZEDDA ◽  
Vijay SATHE ◽  
Prateek CHAKRABORTY ◽  
Maria Rita PALOMBO ◽  
Vittorio FARINA
Keyword(s):  
Bone Histomorphometry ◽  
Equus Caballus ◽  
Wild Horse ◽  
Domestic Horses

Genetic diversity of the relict moss Rhytidium rugosum (Hypnales) in Europe inferred from the ITS region (nrDNA)

Biologia ◽  
2011 ◽  
Vol 66 (1) ◽  
Author(s):  
Marko Sabovljević ◽  
Jan-Peter Frahm
Keyword(s):  
Genetic Diversity ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Data Sampling ◽  
Migration Routes ◽  
High Genetic Diversity ◽  
Moss Species ◽  
Asian Populations ◽  
Survival Potential

AbstractPost-glacial survival, potential migration routes, genetic diversity and phylogeography of the boreal moss species Rhytidium rugosum have been studied. This species is considered to be one of glacial relics of the wide but scattered Holarctic range. According to molecular data sampling from the selected European, American and Asian populations high genetic diversity of this species is present, even if this species is mostly sterile and produced sex organs extremely rarely and spread mostly asexually. Analysing the internal transcribed spacer (ITS) of the nuclear ribosomal DNA, it can be concluded that the populations of this species survived glaciations in various places in Europe and settled and re-settled present range space in various times from various refuges.

scholarly journals The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets

2019 ◽  
Vol 37 (1) ◽  
pp. 183-194 ◽  
Author(s):  
Tom van der Valk ◽  
Catalina M Gonda ◽  
Henri Silegowa ◽  
Sandra Almanza ◽  
Itzel Sifuentes-Romero ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genomic Data ◽  
Congo Basin ◽  
Whole Genome Sequencing Data ◽  
Sources Of Information ◽  
Sequencing Data ◽  
High Genetic Diversity ◽  
Term Survival ◽  
Congo River ◽  
Elusive Species

Abstract Genomic data can be a powerful tool for inferring ecology, behavior, and conservation needs of highly elusive species, particularly, when other sources of information are hard to come by. Here, we focus on the Dryas monkey (Cercopithecus dryas), an endangered primate endemic to the Congo Basin with cryptic behavior and possibly <250 remaining adult individuals. Using whole-genome sequencing data, we show that the Dryas monkey represents a sister lineage to the vervets (Chlorocebus sp.) and has diverged from them ∼1.4 Ma with additional bidirectional gene flow ∼750,000–∼500,000 years ago that has likely involved the crossing of the Congo River. Together with evidence of gene flow across the Congo River in bonobos and okapis, our results suggest that the fluvial topology of the Congo River might have been more dynamic than previously recognized. Despite the presence of several homozygous loss-of-function mutations in genes associated with sperm mobility and immunity, we find high genetic diversity and low levels of inbreeding and genetic load in the studied Dryas monkey individual. This suggests that the current population carries sufficient genetic variability for long-term survival and might be larger than currently recognized. We thus provide an example of how genomic data can directly improve our understanding of highly elusive species.

scholarly journals Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation

2020 ◽  
Author(s):  
Jiangbin Fan ◽  
Johannes A Jehle ◽  
Jörg T Wennmann
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Insect Pests ◽  
Consensus Sequence ◽  
Cydia Pomonella ◽  
Next Generation Sequencing Data ◽  
Snp Analysis ◽  
Sequencing Data ◽  
High Genetic Diversity ◽  
Cydia Pomonella Granulovirus

Abstract Genetic diversity of viruses is driven by genomic mutations and selection through its host, resulting in differences in virulence as well as host responses. For baculoviruses, which are naturally occurring pathogens of insects and which are frequently sprayed on hundred thousands to millions of hectares as biocontrol agents of insect pests, the phenomenon of virus–host co-evolution is of particular scientific interest and economic importance because high virulence of baculovirus products is essential and emergence of host resistance needs to be avoided as much as possible. In the present study, the population structure of twenty isolates of the Cydia pomonella granulovirus (CpGV), including twelve isolates from different geographic origins and eight commercial formulations, were studied on the basis of next-generation sequencing data and by analyzing the distribution of single nucleotide polymorphisms (SNPs). An entirely consensus sequence-free quantitative SNP analysis was applied for the identification of 753 variant SNP sites being specific for single as well as groups of CpGV isolates. Based on the quantitative SNP analysis, homogenous, heterogenous as well as mixed isolates were identified and their proportions of genotypes were deciphered, revealing a high genetic diversity of CpGV isolates from around the world. Based on hierarchical clustering on principal components (HCPC), six distinct isolate/group clusters were identified, representing the proposed main phylogenetic lineages of CpGV but comprising full genome information from virus mixtures. The relative location of different isolates in HCPC reflected the proportion of variable compositions of different genotypes. The established methods provide novel analysis tools to decipher the molecular complexity of genotype mixtures in baculovirus isolates, thus depicting the population structure of baculovirus isolates in a more adequate form than consensus based analyses.

scholarly journals Analysis of Segregation Ratio Distortion and Linkage Mapping in Two Switchgrass F1 Populations: Lowland-lowland and Lowland-upland Using Genotyping by Sequencing Data

2019 ◽  
Author(s):  
Rasyidah Razar ◽  
Katrien Devos ◽  
Ali Missaoui
Keyword(s):  
Genetic Diversity ◽  
Segregation Distortion ◽  
Biomass Yield ◽  
Genotyping By Sequencing ◽  
Segregation Ratio ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Sequencing Data ◽  
Target Number ◽  
High Genetic Diversity

Abstract Background: Switchgrass is an emerging bioenergy crop due to its perennial nature, high biomass yield, and ability to grow in marginal land. The high genetic diversity in switchgrass germplasm can be exploited to capture favorable traits that increase the range of adaptation and biomass yield. Genetic diversity can be explored using single nucleotide polymorphisms (SNPs) that next-generation sequencing has made possible for high-throughput genotyping. We used genotyping-by-sequencing (GBS) of genomic fragments resulting from two methylation sensitive restriction enzymes: PstI and MspI . Two bi-parental F1 populations were developed from crosses between lowland B6 and lowland AP13 (AB population), and lowland B6 with upland VS16 genotypes (BV population), with a target number of 298 progenies in each population. Pseudo-testcross strategy was adopted to perform linkage analysis in these populations that are segregating for winter dormancy using single dose markers (SDA): heterozygous in one parent and homozygous in the other parent. We compared the amount of polymorphisms between the two crosses and examined the pattern of segregation distortion based on the SNPs data generated. Results: Two genetic maps were generated for each population, with 2772 markers in AB and 3766 markers in BV. The higher number of markers in the BV population was expected for since the parents originated from different ecotypes and verified to have the highest genetic distance. More segregation distortion was observed in markers located in the telomeric regions where more genes reside. More markers from the AB population exhibited segregation distortion compared to the BV, and the proportion of heterozygous alleles were significantly higher than homozygous alleles in AB population. The linkage maps showed strong collinearity with P. virgatum V5.1 reference genome with a very minimal number of markers originating from different chromosomes. Conclusion: Understanding the extent of segregation distortion in switchgrass crosses is important for the correct inclusion of markers based on their segregation ratio when constructing a linkage map. Switchgrass linkage maps should be a useful resource to dissect beneficial biomass traits linked to SNP markers.

The Russian-Japanese "Pazyryk" Programme the First Year of Joint Studies

1995 ◽  
Vol 1 (3) ◽  
pp. 307-311
Author(s):  
V.I. Molodin ◽  
A.P. Derevyanko
Keyword(s):  
Iron Age ◽  
Field Research ◽  
First Year ◽  
Altai Mountains ◽  
Adequate Funding ◽  
Unique Material ◽  
Ukok Plateau ◽  
Joint Study ◽  
Scythian Period ◽  
Do So

AbstractThe early Iron Age tumuli of the Altai mountains are unique in preserving largely intact frozen corpses, horses, textiles, leather and wood of the Scythian period. Further such burials exist: in 1991 a reconnaissance excavation of a frozen tumulus at Ak-Alakh again yielded a fabulous inventory. However the conditions of their preservation require their rapid rescue and conservation and adequate funding to do so. In 1991 the USSR and Japan signed an agreement for the joint study of the tumuli of the Pazyryk culture, which included provisions for the conduct of field research on the Ukok plateau, the restoration and conservation of materials from the tumuli (Japan has made Yens 100 m available for this purpose), and the transport of the excavated tumuli to musea. A large tumulus of the 5th-3rd c. B.C. at Kurtuguntas has since been excavated, the unique material recovered was conserved on site and the burial construction transported to the museum at Akademgorodok. In the Bertok valley 60 sites were surveyed and 15 excavated (only one tulumus had been disturbed in antiquity). A monograph is in preparation.

scholarly journals Increased Difficulties to Control Late Blight in Tunisia Are Caused by a Genetically Diverse Phytophthora infestans Population Next to the Clonal Lineage NA-01

Plant Disease ◽  
2014 ◽  
Vol 98 (7) ◽  
pp. 898-908 ◽  
Author(s):  
Kalthoum Harbaoui ◽  
Walid Hamada ◽  
Ying Li ◽  
Vivianne G. A. A. Vleeshouwers ◽  
Theo van der Lee
Keyword(s):  
Genetic Diversity ◽  
Late Blight ◽  
Phytophthora Infestans ◽  
Agricultural Practices ◽  
Weather Conditions ◽  
Genotypic Diversity ◽  
Mitochondrial Haplotype ◽  
Potato Seed ◽  
Clonal Lineage ◽  
High Genetic Diversity

In Tunisia, late blight caused by Phytophthora infestans is a serious threat to potato and tomato. The Mediterranean weather conditions can be conducive to infection in all seasons and the host crops, tomato and potato, are grown year round. Potato is planted and harvested in two to four overlapping intervals from August to June and tomato is grown both in open fields and in greenhouses. The consequences of these agricultural practices and the massive import of seed potato on the genetic variation of P. infestans are largely unknown. We conducted a survey in which 165 P. infestans isolates, collected from five subregions in Tunisia between 2006 and 2008, on which we studied genotypic diversity through nuclear (simple-sequence repeat [SSR]) markers and combined this with a previous study on their mitochondrial haplotypes (mtDNA). The phylogenetic analysis revealed the presence of a major clonal lineage (NA-01, A1 mating type, mitochondrial haplotype Ia). Isolates belonging to this clonal lineage were found in all regions and showed a relatively simple virulence pattern on a potato differential set carrying different Solanum demissum resistance genes. Apart from isolates belonging to this NA-01 clonal lineage, a group of isolates was found that showed a high genetic diversity, comprising both mating types and a more complex race structure that was found in the regions where late blight on potato was more difficult to control. The population on potato and tomato seems to be under different selection pressures. Isolates collected from tomato showed a low genetic diversity even though potato isolates collected simultaneously from the same location showed a high genetic diversity. Based on the SSR profile comparison, we could demonstrate that the four major clonal lineages found in the Netherlands and also in other European countries could not be found in Tunisia. Despite the massive import of potato seed from Europe, the P. infestans population in Tunisia was found to be clearly distinct.

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