scholarly journals Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri.

2022 ◽  
Author(s):  
Pablo Villarreal ◽  
Carlos Villarroel ◽  
Samuel O’Donnell ◽  
Nicolas Agier ◽  
Julian Quintero-Galvis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Diversity ◽  
Divergence Time ◽  
Glacial Refugia ◽  
Ecological Niches ◽  
Natural Environments ◽  
South American ◽  
The South ◽  
Adaptive Genetic Variation ◽  
High Genetic Diversity

Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles, which explains its ecological versatility. The yeast Lachancea cidri is an ideal model for exploring the interplay between genetics, ecological function and evolution. L. cidri is a species that diverged from the Saccharomyces lineage before the whole-genome duplication and exhibits a broad distribution across the South Hemisphere, thus displaying an important ecological success. Here, we applied phylogenomics to investigate the adaptive genetic variation of L. cidri isolates obtained from natural environments in Australia and South America. Our approach revealed the presence of two main lineages according to their geographic distribution (Aus and SoAm). Estimation of the divergence time suggest that South American and Australian lineages diverged near the last glacial maximum event during the Pleistocene (64-8 KYA), consistent with the presence of multiple glacial refugia. Interestingly, we found that the French reference strain belongs to the Australian lineage, with a recent divergence (405-51 YA), likely associated to human movements. Additionally, species delimitation analysis identified different evolutionary units within the South American lineage and, together with parameters like Pi (π) and FST, revealed that Patagonia contains most of the genetic diversity of this species. These results agree with phenotypic characterizations, demonstrating a greater phenotypic diversity in the South American lineage. These findings support the idea of a Pleistocene-dated divergence between South Hemisphere lineages, where the Nothofagus and Araucaria ecological niches likely favored the extensive distribution of L. cidri in Patagonia.

scholarly journals Genetic diversity of Geophagus brasiliensis from the South American Atlantic Rainforest

2017 ◽  
Vol 6 ◽  
pp. e433-e434 ◽  
Author(s):  
R.S. Azevedo ◽  
A. Bitencourt ◽  
D.A. Silva ◽  
A. Amorim ◽  
R. Mazzoni ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Atlantic Rainforest ◽  
South American ◽  
The South ◽  
Geophagus Brasiliensis

scholarly journals Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
James A. Schulte
Keyword(s):  
Divergence Time ◽  
Penalized Likelihood ◽  
Molecular Data ◽  
Molecular Dating ◽  
Taxon Sampling ◽  
South American ◽  
The South ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Age Estimates

Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.

scholarly journals Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

2021 ◽  
Vol 15 (2) ◽  
pp. e0009207
Author(s):  
Veronica Bravo ◽  
Assaf Katz ◽  
Lorena Porte ◽  
Thomas Weitzel ◽  
Carmen Varela ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Epidemiological Data ◽  
Diagnostic Methods ◽  
Campylobacter Coli ◽  
South American ◽  
Differential Distribution ◽  
High Genetic Diversity ◽  
A Genome

Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n = 81), collected in 2017–2019 in Santiago, Chile. This culture collection accounts for more than one third of the available genome sequences from South American clinical strains. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.

scholarly journals Genetic diversity in the Andes: variation within and between the South American species of Oreobolus R. Br. (Cyperaceae)

Alpine Botany ◽  
2017 ◽  
Vol 127 (2) ◽  
pp. 155-170 ◽  
Author(s):  
María Camila Gómez-Gutiérrez ◽  
R. Toby Pennington ◽  
Linda E. Neaves ◽  
Richard I. Milne ◽  
Santiago Madriñán ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
South American ◽  
The South ◽  
South American Species ◽  
The Andes

scholarly journals Genetic Diversity and Population Structure of Llamas (Lama glama) from the Camelid Germplasm Bank—Quimsachata

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 541
Author(s):  
Gabriela F. Paredes ◽  
Claudia E. Yalta-Macedo ◽  
Gustavo A. Gutierrez ◽  
Eudosio A. Veli-Rivera
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
South American ◽  
Germplasm Bank ◽  
Genetic Stock ◽  
High Genetic Diversity ◽  
Lama Glama ◽  
Global Population

Llamas (Lama glama) are invaluable resources of Peru. Despite their importance, their population is decreasing. The Camelid Germplasm Bank—Quimsachata was created as a guardian of this South American camelid (SAC) species and established a bank of llamas from their two types, Ch’aku and Q’ara. However, these populations need to present high genetic diversity to be considered suitable conservation stocks. Thus, in the present study, 13 microsatellites specific for the SAC were used to assess the current genetic variability and differentiation of the llama population from the Bank. The global population showed high genetic diversity with a total of 157 different alleles, with an average of 12.08 alleles per microsatellite, an expected and observed heterozygosity of 0.758 and 0.707, respectively, and an average polymorphic information content (PIC) of 0.723. Although considered as two different breeds and managed separately, the genetic differentiation between Ch’aku and Q’ara was low (FST = 0.01). Accordingly, the gene flow value was high (Nm = 30.5). Overall, our results indicate the existence of high genetic variation among individuals, and thus, this llama population could be considered a suitable genetic stock for their conservation and for sustainability programs. Additionally, the 13 microsatellites can be used to study other Peruvian llama populations and monitor the genetic variability of llamas from the Camelid Germplasm Bank—Quimsachata.

scholarly journals High genetic diversity of the symbiotic dinoflagellates in the coral Pocillopora meandrina from the South Pacific

2005 ◽  
Vol 148 (5) ◽  
pp. 913-922 ◽  
Author(s):  
H. Magalon ◽  
E. Baudry ◽  
A. Husté ◽  
M. Adjeroud ◽  
M. Veuille
Keyword(s):  
Genetic Diversity ◽  
South Pacific ◽  
The South ◽  
High Genetic Diversity ◽  
Symbiotic Dinoflagellates

scholarly journals Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan

2014 ◽  
Vol 95 (9) ◽  
pp. 1945-1957 ◽  
Author(s):  
Asif Naeem ◽  
Takushi Hosomi ◽  
Yorihiro Nishimura ◽  
Muhammad Masroor Alam ◽  
Tomoichiro Oka ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Diversity ◽  
Amino Acid Sequences ◽  
Pairwise Distance ◽  
Full Genome Sequence ◽  
Emerging Viruses ◽  
High Genetic Diversity ◽  
Genotype Assignment ◽  
Pcr Targeting

Human cardioviruses or Saffold viruses (SAFVs) of the family Picornaviridae are newly emerging viruses whose genetic and phenotypic diversity are poorly understood. We report here the full genome sequence of 11 SAFV genotypes from Pakistan and Afghanistan, along with a re-evaluation of their genetic diversity and recombination. We detected 88 SAFV from stool samples of 943 acute flaccid paralysis cases using reverse transcriptase-PCR targeting the 5′ untranslated region (UTR). Further characterization based on complete VP1 analysis revealed 71 SAFVs belonging to 11 genotypes, including three previously unidentified genotypes. SAFV showed high genetic diversity and recombination based on phylogenetic, pairwise distance distributions and recombination mapping analyses performed herein. Phylogenies based on non-structural and UTRs were highly incongruent indicating frequent recombination events among SAFVs. We improved the SAFV genotyping classification criteria by determining new VP1 thresholds based on the principles used for the classification of enteroviruses. For genotype assignment, we propose a threshold of 23 and 10 % divergence for VP1 nucleotide and amino acid sequences, respectively. Other members of the species Theilovirus, such as Thera virus and Theiler’s murine encephalomyelitis virus, are difficult to classify in the same species as SAFV, because they are genetically distinct from SAFV, with 41–56 % aa pairwise distances. The new genetic information obtained in this study will improve our understanding of the evolution and classification of SAFV.

scholarly journals Genetic and chemical differentiation ofCampylobacter coliandCampylobacter jejunilipooligosaccharide pathways

2016 ◽  
Author(s):  
Alejandra Culebro ◽  
Joana Revez ◽  
Ben Pascoe ◽  
Yasmin Friedmann ◽  
Matthew D Hitchings ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lipid A ◽  
Phenotypic Diversity ◽  
Outer Core ◽  
Mass Spectrometry Analysis ◽  
High Genetic Diversity ◽  
Spectrometry Analysis ◽  
Structure Heterogeneity ◽  
Species Specific ◽  
First Time

ABSTRACTDespite the importance of lipooligosaccharides (LOS) in the pathogenicity of campylobacteriosis, little is known about the genetic and phenotypic diversity of LOS inC. coli. In this study, we investigated the distribution of LOS locus classes among a large collection of unrelatedC. coliisolates sampled from several different host species. Furthermore, we pairedC. coligenomic information and LOS chemical composition for the first time to identify mechanisms consistent with the generation of LOS phenotypic heterogeneity. After classifying three new LOS locus classes, only 85% of the 144 isolates tested were assigned to a class, suggesting higher genetic diversity than previously thought. This genetic diversity is at the basis of a completely unexplored LOS structure heterogeneity. Mass spectrometry analysis of the LOS of nine isolates, representing four different LOS classes, identified two features distinguishingC. coliLOS fromC. jejuni’s. GlcN-GlcN disaccharides were present in the lipid A backbone in contrast to the GlcN3N-GlcN backbone observed inC. jejuni. Moreover, despite that many of the genes putatively involved in Qui3pNAcyl were absence in the genomes of various isolates, this rare sugar was found in the outer core of allC. coli. Therefore, regardless the high genetic diversity of LOS biosynthes is locus inC. coli, we identified species-specific phenotypic features ofC. coliLOS which might explain differences betweenC. jejuniandC. coliin terms of population dynamics and host adaptation.Depositories (where applicable)The whole genome sequences ofC. coliare publicly available on the RAST server (http://rast.nmpdr.org) with guest account (login and password ‘guest’) under IDs: 195.91, 195.96-195.119, 195.124-195.126, 195.128-195.130, 195.133, 195.134, 6666666.94320

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