scholarly journals GENETIC DIVERSITY OF ECHINOCOCCUS MULTILOCULARIS CESTODES IN EUROPE AS DETERMINED BY MITOCHONDRIAL AND NUCLEAR SEQUENCES

2019 ◽  
pp. 754-758
Author(s):  
Viliam Šnábel ◽  
Tamás Sréter ◽  
Bruno Gottstein ◽  
Jakub Gawor ◽  
Thomas Romig ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Central Europe ◽  
Echinococcus Multilocularis ◽  
Nuclear Dna ◽  
Mountain Range ◽  
Nucleotide Polymorphisms ◽  
Arctic Regions ◽  
European Distribution ◽  
And Migration ◽  
S Model

Alveolar echinococcosis caused by metacestode stage of the tapeworm Echinococcus multilocularis is considered as one of the most pathogenic zoonoses in temperate and arctic regions. To more thoroughly ascertain genetic diversity in E. multilocularis tapeworms from Europe and to indicate transmission patterns of parasite, 25 isolates from a contiguous territory of eight European countries were subjected to sequencing of mitochondrial and nuclear DNA. A total of 2 715 nucleotide sequences in nad1, cox1, rrnS, atp6 and actII genes were screened in the current study. Whereas in 24 isolates profiles belonging to a previously described European clade were identified, the interesting feature was related to the detection of the form being close to North American strain N1 (that appeared to have lower zoonotic potential) in Austrian patient. The known occurrence of this variant has thus extended from the St. Lawrence Island in the Bering Sea and Russian isolates in Yakutia to central Europe. The finding indicates that N1 genotype has not only circumpolar trans-Beringian distribution, but during glacial events in Pleistocene a more southerly fox dispersal has likely transmitted N1 into central Europe. Further distinguished genotype was confined to four isolates from southern Germany (mountain range of Swabian Jura) and had five substitutions compared to the main European form. One Latvian isolate had two mutations in cox1, one of which was identical to German isolates from Feldstetten. Single nucleotide polymorphisms were detected in single isolates from Slovakia, Hungary and France in cox1 and actIIgenes. Lower genetic diversity detected in the examined isolates in more peripheral zones of its European distribution has supported Knapp ́s model (2009) suggesting that parasite focus in Europe is governed by “mainland-island” transmission where ancestral foci supply hitherto non-endemic areas by dispersal generated by fox mobility and migration.

scholarly journals Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach

2021 ◽  
Vol 12 ◽  
Author(s):  
Sanjaya Gyawali ◽  
Gehendra Bhattarai ◽  
Ainong Shi ◽  
Chris Kik ◽  
Lindsey J. du Toit
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Selective Sweep ◽  
Spinacia Oleracea ◽  
Genomic Region ◽  
Day Length ◽  
Mountain Range ◽  
Nucleotide Polymorphisms ◽  
Selective Sweeps ◽  
Genetic Diversity And Structure

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica group. Likewise, the S. oleracea Q1 group had a smaller Fst (0.008) with the Q2 group than with the Q3 group (Fst = 0.012), and a greater gene flow (Nm = 30.13) with the Q2 group than with the Q3 group (Nm = 21.83). The Q2 accessions originated primarily from Uzbekistan while the Q3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q2 and Q3 groups of S. turkestanica. Accessions with admixtures of Q2 and Q3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.

scholarly journals Cryptic speciation in the Warbling Vireo (Vireo gilvus)

The Auk ◽  
2021 ◽  
Author(s):  
Scott F Lovell ◽  
M Ross Lein ◽  
Sean M Rogers
Keyword(s):  
Contact Zone ◽  
Nuclear Dna ◽  
Biological Species ◽  
Valid Species ◽  
Migration Routes ◽  
Dna Evidence ◽  
Show Evidence ◽  
And Migration ◽  
Surrounding Areas ◽  
Taxonomic Groups

Abstract Eastern (Vireo gilvus gilvus) and western (V. g. swainsoni) forms of the Warbling Vireo have essentially allopatric breeding ranges across north-central North America, but come into contact in central Alberta, Canada. In 1986, Jon Barlow presented preliminary morphological and song evidence suggesting that the Warbling Vireo complex might comprise more than one valid species. However, to date, Barlow’s suggestion is supported by only limited DNA evidence, demonstration of molt and migration differences between the taxa, and anecdotal accounts of differences in song, morphology, plumage, and ecology. We analyzed variation in both mitochondrial and nuclear DNA in birds from Alberta and surrounding areas to determine the levels of genetic differentiation and hybridization occurring in the contact zone, and whether the two taxa warrant recognition as separate biological species. Our analyses reveal that Warbling Vireos in Alberta and the surrounding areas are separated into two well-defined, genetically differentiated, and monophyletic clades corresponding to previously recognized taxonomic groups. The two taxa come into contact in a narrow (~85 km) zone in Barrhead County, northwest of Edmonton, Alberta. They show evidence of limited hybridization. The distinct genetic differences are maintained in the contact zone, where individuals of the two taxa may occupy neighboring territories. Differences in spring arrival dates, molt schedules, and migration routes indicate that a migratory divide may play an important role in reproductive isolation. We suggest that the two taxa are distinct cryptic species: an eastern form, Vireo gilvus, and a western form, Vireo swainsoni.

scholarly journals Revised distribution and phytosociological data of Orobanche coerulescens Stephan in Willd. (Orobanchaceae): Poland in relation to Central Europe

2012 ◽  
Vol 26 (1) ◽  
pp. 61-72 ◽  
Author(s):  
Renata Piwowarczyk
Keyword(s):  
Eastern Europe ◽  
Central Europe ◽  
Plant Communities ◽  
Field Research ◽  
Range Limits ◽  
Migration Routes ◽  
Original Field ◽  
Critical Revision ◽  
And Migration ◽  
North Western

Abstract Orobanche coerulescens has a Eurasian distribution. The species is classified as extinct at most of its localities at the western limit of its range. Its populations are very scarce and critically endangered in Central Europe. This work presents the current distribution of O.coerulescens in Poland, based on a critical revision of herbarium and literature data as well as results of original field research, and reviews its distribution in Central Europe (partly in Eastern Europe). Habitats, plant communities, and migration routes of O.coerulescens in Central Europe are discussed. The species was initially known in Poland from now historical localities in Pomerania and the valley of the lower Vistula. In 2000-2011 it was recorded at 9 localities in Podlasie, the Małopolska Upland (Wyżyna Małopolska), and the Łódź Hills (Wzniesienia Łódzkie). Its abundance at the localities ranged from a few to over 1000 shoots. These are the largest populations of O.coerulescens at its western and north-western range limits.

scholarly journals Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

2014 ◽  
Vol 80 (14) ◽  
pp. 4398-4413 ◽  
Author(s):  
Sam Crauwels ◽  
Bo Zhu ◽  
Jan Steensels ◽  
Pieter Busschaert ◽  
Gorik De Samblanx ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Fingerprinting ◽  
Wine Industry ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
Spoilage Yeasts ◽  
Off Flavors ◽  
Carbon And Nitrogen Metabolism

ABSTRACTBrettanomycesyeasts, with the speciesBrettanomyces(Dekkera)bruxellensisbeing the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However,B. bruxellensisis also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance,Brettanomycesyeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50Brettanomycesstrains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between theB. bruxellensisfingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate ofB. bruxellensis(VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminateBrettanomycesstrains and provides a first glimpse at the genetic diversity and genome plasticity ofB. bruxellensis.

GENETIC VARIATION IN RARE AND WIDESPREAD LOMATIUM SPECIES (APIACEAE): A COMPARISON OF AFLP AND SSCP DATA

2001 ◽  
Vol 58 (2) ◽  
pp. 347-356 ◽  
Author(s):  
M. A. GITZENDANNER ◽  
P. S. SOLTIS
Keyword(s):  
Rare Species ◽  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Allelic Variation ◽  
Plant Conservation ◽  
Single Copy ◽  
Small Populations ◽  
Nucleotide Polymorphisms ◽  
Widespread Species ◽  
Low Levels

Plant conservation genetics has been hampered by a lack of markers for studies of levels and patterns of variation in rare species. We investigated the levels of variation in several rare and widespread species of the western North American genus Lomatium Raf. (Apiaceae) using two relatively new molecular markers: AFLPs and single-strand conformation polymorphisms (SSCPs). For each species, approximately 150 AFLP loci have been scored, yielding estimates of species-level percent polymorphic loci in rare species ranging from near zero to over 80%. Levels of AFLP diversity were similar in two of the rare species, L. bradshawii (Rose ex Mathias) Mathas & Constance and L. ochocense Helliwell & Constance, and the widespread species. The third rare species, L. cookii Kagan, which has small populations, has low levels of diversity based on AFLPs. We also examined nucleotide diversity at the single-copy nuclear-DNA locus glyceraldehyde 3-phosphate dehydrogenase (Gap-C). PCR-amplified segments were analysed for allelic variation using SSCPs, and intrapopulational nucleotide polymorphisms were identified in both L. bradshawii and L. cookii. In the 211bp segment of Gap-C analysed, five nucleotide sites were segregating within populations of L. bradshawii and two in L. cookii.

scholarly journals Genetic diversity and dispersal potential of the stonefly Dinocras cephalotes in a central European low mountain range

2014 ◽  
Vol 33 (1) ◽  
pp. 181-192 ◽  
Author(s):  
Vasco Elbrecht ◽  
Christian K. Feld ◽  
Maria Gies ◽  
Daniel Hering ◽  
Martin Sondermann ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mountain Range ◽  
Central European ◽  
Dispersal Potential ◽  
Low Mountain Range

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

2017 ◽  
Author(s):  
Marina Pais ◽  
Kentaro Yoshida ◽  
Artemis Giannakopoulou ◽  
Mathieu A. Pel ◽  
Liliana M. Cano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
South American ◽  
Nucleotide Polymorphisms ◽  
Natural Ecosystems ◽  
Asexual Lineage ◽  
Irish Famine ◽  
Eukaryotic Microbes ◽  
And Migration ◽  
Potato Famine

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012,Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Cooke et al. 2012, Yoshida et al. 2013,Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.

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