Aude Gilabert

Aude Gilabert
Cirad - La recherche agronomique pour le développement | CIRAD · Département Scientifique Systèmes Biologiques (BIOS)

PhD in Biology and Agronomy

About

48
Publications
4,456
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690
Citations
Citations since 2016
32 Research Items
552 Citations
2016201720182019202020212022020406080
2016201720182019202020212022020406080
2016201720182019202020212022020406080
2016201720182019202020212022020406080
Additional affiliations
April 2012 - April 2014
The University of Calgary
Position
  • PostDoc Position

Publications

Publications (48)
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark l...
Article
Full-text available
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, P. vivax-like, was discovered in African great apes and is hypothesized to have given rise to P. vivax in humans. To unravel the evolutionary history and adaptation...
Data
Overview of the P. vivax-like and P. vivax samples. Plasmodium species, sample ID, accession number, geographic location, year of collection, Plasmodium co-infections, host species infected by this Plasmodium parasite, bibliographic reference, and usage are indicated. For multispecies co-infections, a sample was considered infected with a Plasmodiu...
Data
Overview of the dating analyses under the JTT model of evolution. (A) Influence of the choice of the species pair of reference for the divergence dating method of Silva and colleagues [29]. The slopes of the regressions α of the protein divergence between each species pair and the protein divergence between the reference species pairs (representing...
Data
P. vivax PvP01 genome-wide signatures of selection. The branch-site test of positive selection for orthologous genes product, gene length, and dN/dS ratio for PvP01, as well as the P value for this test, are indicated. Only significant tests are reported. The test was considered significant when the P value was below 0.05. In orange are indicated g...
Data
Genome synteny between P. vivax reference genome PvP01 and P. vivax-like genome Pvl06. Top: reference chromosome from Plasmodium vivax PvP01; bottom: Pvl06 genome. Orange = forward strand gene; blue = reverse strand gene; green = missing core gene; black = singleton gene; yellow = gap. Genome annotation stored as embl files, one for each chromosome...
Data
RAF distributions in the 11 P. vivax-like samples sequenced in this study. This graph represents, for each sample, the density distribution of the frequency of the reference alleles in the sequenced reads across all sites (x-axis). A U-shape of the RAF distribution, meaning that almost all positions carry either the reference or a single alternate...
Data
Alignment and tree files of the clag sequences analyzed in S4 Fig. clag, Cytoadherence-linked asexual gene. (GZ)
Data
Data used to generate S5 Fig. The table gives the estimations of α, the slopes of the TLS regressions of the divergence of the proteins between every possible species pairs and the reference species pair. We performed the analyses considering 3 different pairs of reference species (column entitled "ref") and 4 different amino acid models of substit...
Data
Alignment of the 100,616 SNVs detected among the 11 chimpanzee P. vivax-like and 19 human P. vivax samples analyzed in this study. Sample code are the ones used in S1 Table. SNV, single nucleotide variant. (FASTA)
Data
Overview of the SNV calling of the P. vivax-like samples. *p1, p5, p10, and p20 refer to the percentage of positions covered by at least 1, 5, 10, or 20 reads, after filtering to select high-quality positions (quality phred score ≥30 and a P value for strand bias, mapping quality, or tail distance bias >0.001; see Materials and methods section for...
Data
P. vivax-like PVL01 genome-wide signatures of selection. The branch-site test of positive selection for orthologous genes product, gene length, dN/dS ratio for PVL01 as well as the P value for this test are indicated. Only significant tests are reported. The test was considered significant when the P value was below 0.05. In orange are indicated ge...
Data
P. vivax and P. falciparum genome-wide signatures of selection. The list of the 10 orthologous genes showing a signature of selection in both P. vivax PvP01 and P. falciparum 3D7 is indicated, based on the branch-site tests of positive selection. The branch-site tests of selection for PF3D7 genes were performed by Otto and colleagues [13] (see Supp...
Data
Phylogenetic tree, inferred using RAxML program, of clag genes in P. vivax PvP01 (in green), P. vivax-like Pvl01 (in blue), P. cynomolgi (B, Berok strain) and P. knowlesi (H strain). Bootstrap values are indicated. Pictograms represent the host species (human, gorilla, chimpanzee, Asian monkey). The black star indicates a pseudogene detected in pvC...
Data
Influence of the model of substitution on the estimates of the relative divergence times obtained using the method from Silva and colleagues [29]. The values of α, the estimations of the divergence time of every species pair relative to that of the species pair of reference (i.e., P. knowlesi–P. vivax [Pkn–Pv], P. malariae–P. malariae-like [Pm–Pml]...
Data
Alignment used to generate the ML phylogenetic tree of the 13 Plasmodium species considered for the dating analyses and the resulting tree file. ML, maximum likelihood. (GZ)
Data
Dataset used to generate S6 Fig. Both the complete alignment of the mitochondrial portion used to reconstruct the phylogenetic tree and the alignment of the 127 variable positions used to perform the reticulate network are given, as well as the resulting tree and network files. (GZ)
Data
Sequencing and Plasmodium multispecies co-infections information. Host contamination was estimated by mapping the reads against the human genome from the Genome Reference Consortium GRCh37 (Genbank accession: GCA_000001405) for all samples but Pvl09, for which reads were mapped against the reference genome of An. gambiae str. PEST (Genbank accessio...
Data
Genome synteny between P. vivax reference genome PvP01 and P. vivax-like genome Pvl01. Top: reference chromosome from P. vivax PvP01; bottom: Pvl01 genome. Orange = forward strand gene; blue = reverse strand gene; green = missing core gene; black = singleton gene; yellow = gap. Genome annotation stored as embl files, one for each chromosome is avai...
Data
Relationships between P. vivax and P. vivax-like samples based on a portion of the mitochondrial genome. (A) Phylogenetic tree based on an alignment of 2,530 bp of the mitochondrial genome and performed using FastTree 2.1.5 implemented in Geneious [55]. FastTree support values >0.7 are given. (B) Reticulate network built with SplitsTree4 on 126 var...
Data
Relationships between P. vivax and P. vivax-like samples using phylogenetic trees based on 100, 200, 300, 400, 500, 600, 800, 1,000, or 5,000 SNVs. Data can be found in S7 Data. SNV, single nucleotide variant. (PDF)
Data
Dataset used to produce S7 Fig. For each analysis with a different number of SNVs considered, the alignment and the resulting tree file are available. SNV, single nucleotide variant. (ZIP)
Data
Alignment and phylogenetic tree files of the rbp gene sequences analyzed in Fig 1. rbp, reticulocyte-binding protein. (GZ)
Article
Full-text available
Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite Plasmodium praefalciparum. Little is known about the other gorilla- and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum, but none of them are capable of establishing repeated infection and transmi...
Preprint
Full-text available
Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite P. praefalciparum. Little is known about the other gorilla and chimpanzee-infecting species in the same ( Laverania ) subgenus as P. falciparum but none of them are capable of establishing repeated infection and transmission in...
Chapter
Frequent bottlenecks and recent diversification result in relatively low levels of genetic diversity and population structure in modern humans, making inferences of their history difficult from classical genetic markers. To get around this drawback, pathogens, which have coevolved with humans and generally present a higher genetic diversity, can il...
Article
Full-text available
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, Plasmodium vivax-like , was discovered in African great apes and is hypothesized to have given rise to P. vivax in humans. To unravel the evolutionary history and ad...
Article
Full-text available
Ecological control has often focused on factors enhancing control of pests by their natural enemies, while factors reducing the colonization rate of crops by pests have been comparatively neglected. We present an approach to assess landscape influence on the intensity of wheat colonization by a major crop pest, the aphid Rhopalosiphum padi. We used...
Article
Full-text available
Background Signalling pathways underlie development, behaviour and pathology. To understand patterns in the evolution of signalling pathways, we undertook a comprehensive investigation of the pathways that control the switch between growth and developmentally quiescent dauer in 24 species of nematodes spanning the phylum. Results Our analysis of 4...
Article
Full-text available
Re-examination, using molecular tools, of the diversity of haemosporidian parasites (among which the agents of human malaria are the best known) has generally led to rearrangements of traditional classifications. In this study, we explored the diversity of haemosporidian parasites infecting vertebrate species (particularly mammals, birds and reptil...
Data
Full-text available
The trees give the relationship between our sequences and others sequences of genbank. Phylogenetic tree was rooted using Leucocytozoon spp (Figure A). Phylogenetic tree was rooted using Eimeria spp (Figure B). And one table gives all accession numbers of sequences used in our study (Table A)
Article
Parthenogenesis is the main mode of reproduction of aphids. Their populations are therefore composed of clones whose frequency distribution varies in space and time. Previous population genetic studies on aphids have highlighted the existence of highly abundant clones (‘super-clones’), distributed over large geographic areas and persisting over tim...
Article
According to environmental-based theories on the maintenance of sexual reproduction, sexual and asexual populations may coexist if they occupy different ecological niches. The aphid Rhopalosiphum padi offers a good opportunity to test this hypothesis since sexual and asexual lineages show local coexistence during a large part of their respective li...
Article
Full-text available
Hybridization, the interbreeding of diagnosably divergent species, is a major focus in evolutionary studies. Eels, both from North America and Europe migrate through the Atlantic to mate in a vast, overlapping area in the Sargasso Sea. Due to the lack of direct observation, it is unknown how these species remain reproductively isolated. The detecti...
Article
Full-text available
The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass dr...
Article
The health and economic importance of parasitic nematodes cannot be overstated. Moreover, they offer a complex and diverse array of life strategies, raising a multitude of evolutionary questions. Researchers are applying population genetics to parasitic nematodes in order to disentangle some aspects of their life strategies, improve our knowledge a...
Article
Only few studies are available dealing with the relation between winter host density and spatial distribution and spring colonization of winter cereals by the host-alternating cereal aphid species Rhopalosiphum padi and Metopolophium dirhodum. Large-scale studies in climatically different agroecosystems in Germany from 2004 to 2006 revealed for R.p...
Poster
E-poster communication at the 6th World Fisheries Congress: Multi-loci Bayesian inference and computational simulations of population size history in different eel species (Edinburgh, Scotland);
Chapter
Full-text available
Frequent bottlenecks and divergences that are too recent result in human in relatively low levels of genetic diversity and structure populations, making inferences of their history difficult from genetic markers. To get around this drawback, pathogens, which have coevolved with humans and generally present a higher genetic diversity, can illuminate...
Article
In aphids, reproductive mode is generally assumed to be selected for by winter climate. Sexual lineages produce frost-resistant eggs, conferring an advantage in regions with cold winters, while asexual lineages predominate in regions with mild winters. However, habitat and resource heterogeneities are known to exert a strong influence on sex mainte...
Article
Full-text available
The genetic structure of reservoir populations is a key characteristic in understanding the persistence of infectious diseases in natural systems. In the Highlands of Madagascar, where plague has persisted since 1920, the black rat, Rattus rattus (L., 1758), is the sole species acting as a reservoir of the disease. Ecological surveys have shown a c...

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