scholarly journals Selection Pressure and Founder Effects Constrain Genetic Variation in Differentiated Populations of Soilborne Bymovirus Wheat yellow mosaic virus (Potyviridae) in China

2013 ◽  
Vol 103 (9) ◽  
pp. 949-959 ◽  
Author(s):  
B.-J. Sun ◽  
L.-Y. Sun ◽  
A. K. Tugume ◽  
M. J. Adams ◽  
J. Yang ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Mosaic Virus ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Phylogenetic Trees ◽  
Population Diversity ◽  
Yellow Mosaic Virus ◽  
Founder Effects ◽  
Wheat Yellow Mosaic Virus ◽  
Recent Emergence

To study the population genetic structure and forces driving the evolution of Wheat yellow mosaic virus (WYMV), the nucleotide sequences encoding the coat protein (CP) (297 sequences) or the genome-linked virion protein (VPg) (87 sequences) were determined from wheat plants growing at 11 different locations distributed in five provinces in China. There were close phylogenetic relationships between all sequences but clustering on the phylogenetic trees was congruent with their provenance, suggesting an origin-dependent population genetic structure. There were low levels of genetic diversity, ranging from 0.00035 ± 0.00019 to 0.01536 ± 0.00043 (CP), and 0.00086 ± 0.00039 to 0.00573 ± 0.00111 (VPg), indicating genetic stability or recent emergence of WYMV in China. The results may suggest that founder effects play a role in shaping the genetic structure of WYMV. Between-population diversity was consistently higher than within-population diversity, suggesting limited gene flow between subpopulations (average FST 0.6241 for the CP and 0.7981 for the VPg). Consistent amino acid substitutions correlated with the provenance of the sequences were observed at nine positions in the CP (but none in the VPg), indicating an advanced stage in population structuring. Strong negative (purifying) selection was implicated on both the CP and VPg but positive selection on a few codons in the CP, indicating an ongoing molecular adaptation.

scholarly journals Population genetic structure of pedunculate oak (Quercus robur L.) in Belarus according to the analysis of chloroplast DNA

2021 ◽  
pp. 59-70
Author(s):  
Vladimir E. Padutov
Keyword(s):  
Genetic Structure ◽  
Chloroplast Dna ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Quercus Robur ◽  
Phylogenetic Trees ◽  
Rflp Analysis ◽  
Pedunculate Oak ◽  
Maximum Likelihood Methods ◽  
The Republic

Pedunculate oak (Quercus robur L.) is one of the main forest forming species in the Republic of Belarus. Its population genetic structure was formed under the influence of various migration processes. Six chloroplast DNA loci (µdt1, µdt3, µdt4, µcd4, µcd5 and µkk4) were used for the genogeographic study. The material for the analysis was collected in 100 oak forest stands (2325 samples); 18 allelic variants were identified, which are grouped into 17 different combinations (haplotypes). Five of them are widespread (the proportion of occurrence varies from 7 to 48 %, totalling 85 %). The remaining 12 are rare (the proportion of occurrence varies from 1 to 3 %, totalling 15 %). Phylogenetic trees constructed using the nearest neighbour and maximum likelihood methods show the presence of two groups (branches) of haplotypes. One of it comprises 8 variants including 2 dominant haplotypes and the other comprises 9 variants including 3 dominant haplotypes. PCR-RFLP analysis of chloroplast DNA showed that the pedunculate oak in Belarus originates from the Balkan refugium. Haplotype No. 1 (µdt189, µdt3123, µdt4142, µcd494, µcd574, µkk4109) is found almost everywhere in Belarus with the exception of the southwest and northeast, while haplotype No. 8 (µdt189, µdt3121, µdt4142, µcd494, µcd574, µkk4109) is mainly localised in the southwest and northeast. Haplotypes No. 3 (µdt189, µdt3120, µdt4141, µcd494, µcd575, µkk4109) and No. 7 (µdt189, µdt3122, µdt4142, µcd494, µcd574, µkk4109) predominantly found in the west of the country. Haplotype No. 2 (µdt190, µdt3120, µdt4141, µcd495, µcd574, µkk4109) is typical for the southeast.

scholarly journals Population genetic structure and gene flow in Alcea aucheri (Boiss.) Alef.: A potential medicinal plant

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 867-882
Author(s):  
Liu Hang ◽  
Li Pan ◽  
Tang Yong ◽  
Luo Jianguo ◽  
Xu Xingmin ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Genetic Difference ◽  
Morphological Variability ◽  
Molecular Data ◽  
Mantel Test ◽  
Population Diversity ◽  
Population Genetic Differentiation

The genus Alcea, a member of Malvaceae family consists of approximately 75 species worldwide distributing mainly in South-West Asia. Among these, 33 species grow in Iran. Plants of the Alcea (or Althaea) are among important medicinal plants in Iranian traditional medicine. They have long been used in the treatment of health problems and diseases. Alcea aucheri (Boiss.) Alef. species are distributed in different habitats of Iran. There is no information on its population genetic structure, genetic diversity, and morphological variability in Iran. Therefore, due to the importance of these plant species, we performed a combination of morphological and molecular data for this species. For this study, we used 118 randomly collected plants from 10 geographical populations in 5 provinces. AMOVA test revealed significant genetic difference among the studied populations and also revealed that, 74% of total genetic variability was due to within population diversity while, 26% was due to among population genetic differentiation. Mantel test showed positive significant correlation between genetic distance and geographical distance of the studied populations. Networking, STRUCTURE analyses revealed some degree of gene flow among these populations.

scholarly journals Population Genetic Structure of the Staphylococcus intermedius Group: Insights into agr Diversification and the Emergence of Methicillin-Resistant Strains

2007 ◽  
Vol 189 (23) ◽  
pp. 8685-8692 ◽  
Author(s):  
Jeanette Bannoehr ◽  
Nouri L. Ben Zakour ◽  
Andrew S. Waller ◽  
Luca Guardabassi ◽  
Keith L. Thoday ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Quorum Sensing ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Ecological Niches ◽  
Methicillin Resistant ◽  
Zoonotic Infections ◽  
Staphylococcus Intermedius ◽  
Recent Emergence ◽  
Resistant Strains

ABSTRACT The population genetic structure of the animal pathogen Staphylococcus intermedius is poorly understood. We carried out a multilocus sequence phylogenetic analysis of isolates from broad host and geographic origins to investigate inter- and intraspecies diversity. We found that isolates phenotypically identified as S. intermedius are differentiated into three closely related species, S. intermedius, Staphylococcus pseudintermedius, and Staphylococcus delphini. S. pseudintermedius, not S. intermedius, is the common cause of canine pyoderma and occasionally causes zoonotic infections of humans. Over 60 extant STs were identified among the S. pseudintermedius isolates examined, including several that were distributed on different continents. As the agr quorum-sensing system of staphylococci is thought to have evolved along lines of speciation within the genus, we examined the allelic variation of agrD, which encodes the autoinducing peptide (AIP). Four AIP variants were encoded by S. pseudintermedius isolates, and identical AIP variants were shared among the three species, suggesting that a common quorum-sensing capacity has been conserved in spite of species differentiation in largely distinct ecological niches. A lack of clonal association of agr alleles suggests that assortive recombination may have contributed to the distribution of agr diversity. Finally, we discovered that the recent emergence of methicillin-resistant strains was due to multiple acquisitions of the mecA gene by different S. pseudintermedius clones found on different continents. Taken together, these data have resolved the population genetic structure of the S. intermedius group, resulting in new insights into its ancient and recent evolution.

Sign in / Sign up

Export Citation Format

Share Document