scholarly journals Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated

2019 ◽  
Author(s):  
Devani Romero Picazo ◽  
Tal Dagan ◽  
Rebecca Ansorge ◽  
Jillian M. Petersen ◽  
Nicole Dubilier ◽  
...  
Keyword(s):  
Bacterial Colonization ◽  
Gill Tissue ◽  
Genetic Isolation ◽  
Isolated Populations ◽  
Genome Wide ◽  
Colonization Dynamics ◽  
Symbiont Transmission ◽  
Environmental Bacteria ◽  
Host Life ◽  
High Degree

AbstractEukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated populations. The reconstruction of core genome-wide strain sequences from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel lifespan and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life-cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.

scholarly journals Study of the current vegetation of the historical lava flows of the Arafo Volcano, Tenerife, Canary Islands, Spain

2020 ◽  
Vol 41 (2) ◽  
pp. 193-212
Author(s):  
Victoria Eugenia Martín Osorio ◽  
Wolf Hermann Wildpret Martín ◽  
Rocío González Negrín ◽  
Wolfredo Wildpret De la Torre
Keyword(s):  
Canary Islands ◽  
Nutrient Deficiency ◽  
Lava Flows ◽  
Pinus Canariensis ◽  
Healthy Tree ◽  
New Associations ◽  
Colonization Dynamics ◽  
Vegetation Complex ◽  
High Degree ◽  
Two Populations

Vegetation research on the lava flows of the historic volcanic eruption of 1705 in Arafo, Tenerife, Canary Islands, is presented. The study area located in the 830000-year-old valley of Güímar was created after a massive landslide 47 km3 in volume. The research is divided into three parts, which cover an altitudinal range from around 35 to 1583 m a.s.l. from the Lower-semiarid Inframediterranean up to the Lower-dry lower-Mesomediterranean bioclimatic belts. First, a phytosociological study of the vegetation present in the area was made and concluded that richness in pioneer communities form a vegetation complex with a high degree of endemicity. Two new associations and four pioneer communities are proposed. Especially notable are the communities of Stereocauletum vesuviani and the pioneer communities of Pinus canariensis. The second part of the research was a field sampling study of 450 individuals of Pinus canariensis, which were measured at different altitudes to obtain data about the colonization dynamics of this species on this 300 years old substrate. We found that stem diameter seems to be a good indicator for healthy tree development at a range between 700 to 1300 m asl, which corresponds to the pine forest as potential vegetation and that many individuals show signs of nutrient deficiency. The third part consists of the publication of two new populations of the Canarian endemism Himantoglossum metlesicsianum, a highly endangered orchid. The monitoring of these two populations has recently begun, and further research will be conducted on all three aspects of this publication, which will be presented and expanded upon in the future.

scholarly journals Allelic variation contributes to bacterial host specificity

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Min Yue ◽  
Xiangan Han ◽  
Leon De Masi ◽  
Chunhong Zhu ◽  
Xun Ma ◽  
...  
Keyword(s):  
Allelic Variation ◽  
Multinomial Logistic Regression ◽  
Gene Gain ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Serovar Typhimurium ◽  
Functional Analyses ◽  
High Degree

Abstract Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

scholarly journals Bacterial colonization dynamics associated with respiratory syncytial virus during early childhood

2020 ◽  
Vol 55 (5) ◽  
pp. 1237-1245 ◽  
Author(s):  
Jaelle C. Brealey ◽  
Paul R. Young ◽  
Theo P. Sloots ◽  
Robert S. Ware ◽  
Stephen B. Lambert ◽  
...  
Keyword(s):  
Early Childhood ◽  
Respiratory Syncytial Virus ◽  
Bacterial Colonization ◽  
Colonization Dynamics ◽  
Syncytial Virus

scholarly journals Associative Overdominance and Negative Epistasis Shape Genome-Wide Ancestry Landscape in Supplemented Fish Populations

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 524
Author(s):  
Maeva Leitwein ◽  
Hugo Cayuela ◽  
Louis Bernatchez
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Recombination Rate ◽  
Management Strategies ◽  
Population Level ◽  
Negative Effects ◽  
Isolated Populations ◽  
Positive Effects ◽  
Genome Wide ◽  
Negative Epistasis

The interplay between recombination rate, genetic drift and selection modulates variation in genome-wide ancestry. Understanding the selective processes at play is of prime importance toward predicting potential beneficial or negative effects of supplementation with domestic strains (i.e., human-introduced strains). In a system of lacustrine populations supplemented with a single domestic strain, we documented how population genetic diversity and stocking intensity produced lake-specific patterns of domestic ancestry by taking the species’ local recombination rate into consideration. We used 552 Brook Charr (Salvelinus fontinalis) from 22 small lacustrine populations, genotyped at ~32,400 mapped SNPs. We observed highly variable patterns of domestic ancestry between each of the 22 populations without any consistency in introgression patterns of the domestic ancestry. Our results suggest that such lake-specific ancestry patterns were mainly due to variable associative overdominance (AOD) effects among populations (i.e., potential positive effects due to the masking of possible deleterious alleles in low recombining regions). Signatures of AOD effects were also emphasized by highly variable patterns of genetic diversity among and within lakes, potentially driven by predominant genetic drift in those small isolated populations. Local negative effects such as negative epistasis (i.e., potential genetic incompatibilities between the native and the introduced population) potentially reflecting precursory signs of outbreeding depression were also observed at a chromosomal scale. Consequently, in order to improve conservation practices and management strategies, it became necessary to assess the consequences of supplementation at the population level by taking into account both genetic diversity and stocking intensity when available.

scholarly journals A Genome-Wide Association Scan of RR and QT Interval Duration in 3 European Genetically Isolated Populations

2009 ◽  
Vol 2 (4) ◽  
pp. 322-328 ◽  
Author(s):  
Fabio Marroni ◽  
Arne Pfeufer ◽  
Yurii S. Aulchenko ◽  
Christopher S. Franklin ◽  
Aaron Isaacs ◽  
...  
Keyword(s):  
Qt Interval ◽  
Genome Wide Association ◽  
Interval Duration ◽  
Isolated Populations ◽  
Genome Wide ◽  
A Genome ◽  
Qt Interval Duration

scholarly journals Genome-wide identification of candidate genes associated with β-glucan trait in a hulled and hulless barley (Hordeum vulgare L.) population

2020 ◽  
Author(s):  
Longhua Zhou ◽  
Ting He ◽  
Guimei Guo ◽  
Jing Li ◽  
Ruiju Lu ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
R Package ◽  
Snp Markers ◽  
Genetic Loci ◽  
Hordeum Vulgare L ◽  
Reduced Representation ◽  
Sequencing Platform ◽  
Genome Wide ◽  
Degree Of Confidence ◽  
High Degree

Abstract Background: To date, excavating the genomic sites based on the whole barley assembled genome sequences associated with β-glucan trait remains blank, resulting in omission of several genetic loci or existence of false positive. Results: Here, of 87 barley resources (39 hulled and 48 hulless) collected from China, the β-glucan content ranged from 2.07% to 6.56%. GWAS (genome-wide association study) was carried out using 191,098 SNP markers by RRGS (Reduced-Representation Genome Sequencing) platform in FarmCPU model excuted in rMVP R package. Four subpopulations (POP1～POP4) were identified. GWAS showed one SNP, in chromosome 7 (chr7), negatively mapped and for two genes HORVU7Hr1G000320, HORVU7Hr1G000040, which are from nucleotide triphosphates hydrolases superfamily; previous study had proved the superfamily could inhibit β-glucan synthase activities. GWAS also showed that five SNPs for β-glucan trait were separately mapped in chr2, chr3, chr4, chr5 and chr6 non-coding regions and one SNP mapped for HORVU1Hr1G000010 in chr1, which is for plant sugar response. Conclusions: Through the highest density of SNP markers to date, this study identifys several SNP genetic loci with high degree of confidence for β-glucan trait, and has a certain value for β-glucan regulatory mechanism research in furture.

scholarly journals The genomic impact of European colonization of the Americas

2019 ◽  
Author(s):  
Linda Ongaro ◽  
Marilia O. Scliar ◽  
Rodrigo Flores ◽  
Alessandro Raveane ◽  
Davide Marnetto ◽  
...  
Keyword(s):  
Gene Flow ◽  
Demographic History ◽  
Colonial Era ◽  
Genome Wide ◽  
A Genome ◽  
European Colonization ◽  
High Degree ◽  
The Impact ◽  
North And South America ◽  
North And South

AbstractThe human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored.Here we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected i) the genetic structure, ii) the admixture profile, iii) the demographic history and iv) sex-biased gene-flow dynamics, of the Americas.We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East and to specific regions of Africa.

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