Hervé Philippe's research while affiliated with Station d’Ecologie Expérimentale à Moulis and other places
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Publications (272)
Plant adaptation to a terrestrial life 450 million years ago played a major role in the evolution of life on Earth. This shift from an aquatic environment has been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the non-vascular plants Marchantia polymorpha and studied its intraspecific diversity...
The extent of intraspecific genomic variation is key to understanding species evolutionary history, including recent adaptive shifts. Intraspecific genomic variation remains poorly explored in eukaryotic microorganisms, especially in the nuclear dimorphic ciliates, despite their fundamental role as laboratory model systems and their ecological impo...
The colonization of novel environments requires a favorable response to conditions never, or rarely, encountered in recent evolutionary history. For example, populations colonizing upslope habitats must cope with lower atmospheric pressure at elevation, and thus reduced oxygen availability. The embryo stage in oviparous organisms is particularly su...
Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species' response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally induced phenotypic variation across generations, and can influence adaptation. To date, t...
Objectives
Identifying orthology relationships among sequences is essential to understand evolution, diversity of life and ancestry among organisms. To build alignments of orthologous sequences, phylogenomic pipelines often start with all-vs-all similarity searches, followed by a clustering step. For the protein clusters (orthogroups) to be as accu...
Objectives
Complex algae are photosynthetic organisms resulting from eukaryote-to-eukaryote endosymbiotic-like interactions. Yet the specific lineages and mechanisms are still under debate. That is why large scale phylogenomic studies are needed. Whereas available proteomes provide a limited diversity of complex algae, MMETSP (Marine Microbial Euka...
It is commonly assumed that increasing the number of characters has the potential to resolve evolutionary radiations. Here, we studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous origin mitochondrion, plastid and nucleus). Surprisingly while statistical support for the relationships between the six major Ochrophyta l...
Dispersal is the movement of organisms from one habitat to another that potentially results in gene flow. It is often plastic, allowing organisms to adjust dispersal movements depending on environmental conditions. A fundamental aim in ecology is to understand the determinants underlying dispersal and its plasticity. We utilized 22 strains of the c...
Ciliates have an extraordinary genetic system in which each cell harbors two distinct kinds of nucleus, a transcriptionally active somatic nucleus and a quiescent germline nucleus. The latter undergoes classical, heritable genetic adaptation, while adaptation of the somatic nucleus is only short-term and thus disposable. The ecological and evolutio...
Dispersal is the movement of organisms from one habitat to another that potentially results in gene flow. It is often found to be plastic, allowing organisms to adjust dispersal movements depending on environmental conditions. A fundamental aim in ecology is to understand the determinants underlying dispersal and its plasticity. We utilized 22 stra...
The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomi...
It is commonly assumed that increasing the number of characters has the potential to resolving radiations. We studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous size and origin (6,762 sites for mitochondrion, 21,692 sites for plastid and 209,105 sites for nucleus). While statistical support for the relationships bet...
Climate change is generating range shifts in many organisms, notably along the altitudinal gradient. However, moving up in altitude exposes organisms to lower oxygen availability, which may negatively affect development and fitness, especially at high temperatures. To test this possibility in a potentially upward-colonizing species, we artificially...
Climate change is generating range shifts in many organisms, notably along the altitudinal gradient. However, moving up in altitude exposes organisms to lower oxygen availability, which may negatively affect development and fitness, especially at high temperatures. To test this possibility in a potentially upward-colonizing species, we artificially...
Hybridization can leave genealogical signatures in an organism's genome, originating from the parental lineages and persisting over time. This potentially confounds phylogenetic inference methods that aim to represent evolution as a strictly bifurcating tree. We apply a phylotranscriptomic approach to study the evolutionary history of, and test for...
Climate change is generating range shifts in many organisms, notably along the elevational gradient in mountainous environments. However, moving up in elevation exposes organisms to lower oxygen availability, which may reduce the successful reproduction and development of oviparous organisms. To test this possibility in an upward‐colonizing species...
The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia and Deuterostomia. Protostomia contains the Ecdysozoa and the Lophotrochozoa; Deuterostomia contains the Chordata and the Xenambulacraria (Hemichordata, Echinodermata and Xenacoelomorpha). Their names refer to a supposed distinct origin of...
Orthology assignment is a key step of comparative genomic studies, for which many bioinformatic tools have been developed. However, all gene clustering pipelines are based on the analysis of protein distances, which are subject to many artefacts. In this paper we introduce Broccoli, a user-friendly pipeline designed to infer, with high precision, o...
Orthology assignment is a key step of comparative genomic studies, for which many bioinformatic tools have been developed. However, all gene clustering pipelines are based on the analysis of protein distances, which are subject to many artefacts. In this paper we introduce Broccoli, a user-friendly pipeline designed to infer, with high precision, o...
Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria-related organelles (MROs). There has been debate regarding the...
Background
Multiple Sequence Alignments (MSAs) are the starting point of molecular evolutionary analyses. Errors in MSAs generate a non-historical signal that can lead to incorrect inferences. Therefore, numerous efforts have been made to reduce the impact of alignment errors, by improving alignment algorithms and by developing methods to filter ou...
Our planet is teeming with an astounding diversity of plants. In a mere single group of closely related species, tremendous diversity can be observed in their form and function — the colour of petals in flowering plants, the shape of the fronds in ferns, and the branching pattern of the gametophyte in mosses. Diversity can also be found in subtler...
Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species’ response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, t...
Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was acco...
Xenoturbella and the acoelomorph worms (Xenacoelomorpha) are simple marine animals with controversial affinities. They have been placed as the sister group of all other bilaterian animals (Nephrozoa hypothesis), implying their simplicity is an ancient characteristic [1, 2]; alternatively, they have been linked to the complex Ambulacraria (echinoder...
A key question in molecular evolutionary biology concerns the relative roles of mutation and selection in shaping genomic data. Moreover, features of mutation and selection are heterogeneous along the genome and over time. Mechanistic codon substitution models based on the mutation-selection framework are promising approaches to separating these ef...
Optimization of Kraken database.
(PDF)
Sensitivity of Kraken according to kmer size and confidence threshold.
The classified fractions of the 440 cyanobacterial genomes (expressed in %) are summarized as one box-and-whiskers plot for every combination of Kraken parameters. Boxes correspond to interquartile ranges (IQR = Q3–Q1), whereas medians (Q2) are shown as thick horizontal black li...
Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no dat...
Taxonomic distribution of contaminating sequences in all cyanobacterial genome assemblies, based on DIAMOND blastx estimates.
The 440 assemblies (in the global ranking order of S2 Table) were analyzed with DIAMOND blastx, as explained in the main text (using a LCA approach against a protein version of our curated Ensembl 30 database). Taxonomic cla...
Sensitivity of Kraken and DIAMOND blastx as a function of the distance to reference genomes using two different databases.
For each of the 343 cyanobacterial genome assemblies, the classified fraction using Kraken (at a kmer size of 21, expressed in %) (a,b) or DIAMOND blastx (c) is plotted against its evolutionary distance (expressed in substituti...
Global ranking of the cyanobacterial genome assemblies.
The table gives the accession, the name (binomial incl. strain), the main assembly properties (as determined by QUAST), and the ranking results of the 440 assemblies surveyed. Assemblies are sorted from the most contaminated to the less contaminated. (*) indicates assemblies for which raw read...
List of the public cyanobacterial genome assemblies used in this study.
The table gives the accession, the name (binomial incl. strain), the taxonomy (order, NCBI lineage), the ecology (morphology and habitat), and the assembly properties (as determined by QUAST) of the 440 assemblies surveyed. Assemblies are sorted by NCBI lineage. (*) indicates a...
Taxonomic overview of the contaminant genera of the assemblies in the top-21 ranking.
Only contaminants that could be identified at least at the genus level are considered. Redundant assemblies were only analyzed once. Absolute counts are in pseudo-reads, whereas relative counts are expressed with respect to the total number of pseudo-reads indenti...
Correlation of all six methods with the global ranking.
Spearman rank correlations were computed for all six methods and the global ranking, considering either all 440 assemblies, or only the 343 typical assemblies, or only the 50 top-ranking assemblies out of the 440.
(XLSX)
Summary of the optimization of the “42” analyses.
The table gives the number of ribosomal proteins added to each MSA using different combinations of “42” parameters. The final combination is highlighted on a red background.
(XLSX)
Taxonomic analysis of the scaffolds of the assemblies in the top-21 ranking.
The table gives the DIAMOND blastx taxonomic classifications (in %, at the phylum level) of each scaffold of the top-21 assemblies (one sheet per assembly). For each scaffold, the GC-content (in %) and the scaffold length (in nt) are also reported.
(XLSX)
Overview of public cyanobacterial genome assemblies.
The 440 strains were classified into the eight orders defined in Komarek et al. 2014 [Syn: Synechococcales, Nos: Nostocales, Osc: Oscillatoriales, Chc: Chroococcales, Pleu: Pleurocapsales, Spi: Spirulinales, Glb: Gloeobacterales, Chd: Chroococcidiopsidales (and Glm: Gloeoemargaritales)], and furt...
Validation of our methods for detecting contaminants.
The top-21 ranking assemblies were split into segments of 10,000 nt for detailed analysis. On the X axis, segment-containing scaffolds were sorted by increasing average GC-content, with vertical thin lines representing scaffold boundaries. Segments were classified as either cyanobacterial (green...
BACKGROUND
Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific inter...
Background:
Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood, and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolu...
Background
Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutio...
Detecting selection on codon usage (CU) is a difficult task, since CU can be shaped by both the mutational process and selective constraints operating at the DNA, RNA and protein levels. Yang and Nielsen (2008) developed a test (which we call CUYN) for detecting selection on CU using two competing mutation-selection models of codon substitution. Th...
Background:
Multiple RNA samples are frequently processed together and often mixed before multiplex sequencing in the same sequencing run. While different samples can be separated post sequencing using sample barcodes, the possibility of cross contamination between biological samples from different species that have been processed or sequenced in...
The relationships at the root of the animal tree have proven difficult to resolve, with the current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum Ctenophora) are the sister group of all other animals [1–5]. The choice of evolu- tionary models seems to be at the core of the prob- lem because Porifera tends to emerge as...
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on "standards" for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full...
The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduce the risk of being misinterpreted by high node support values influenced by unevenly distributed missing data or unrealistic model assumptions. Here, we use three largely inde...
Resolving the early diversification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera) are the sister group to all other animals (“Porifera-sister” hypothesis), consistent with a single origin of the gut, nerve cells, and muscle ce...
In the mid-2000s, molecular phylogenetics turned into phylogenomics, a development that improved the resolution of phylogenetic trees through a dramatic reduction in stochastic error. While some then predicted “the end of incongruence”, it soon appeared that analysing large amounts of sequence data without an adequate model of sequence evolution am...
The DNA barcoding concept (Woese et al.; Hebert et al.) has considerably boosted taxonomy research by facilitating the identification of specimens and discovery of new species. Used alone or in combination with DNA metabarcoding on environmental samples (Taberlet et al.), the approach is becoming a standard for basic and applied research in ecology...
Significance
Clarifying the phylogeny of animals is fundamental to understanding their evolution. Traditionally, sponges have been considered the sister group of all other extant animals, but recent genomic studies have suggested comb jellies occupy that position instead. Here, we analyzed the current genomic evidence from comb jellies and found no...
Animals make up only a small fraction of the eukaryotic tree of life, yet, from our vantage point as members of the animal kingdom, the evolution of the bewildering diversity of animal forms is endlessly fascinating. In the century following the publication of Darwin's Origin of Species, hypotheses regarding the evolution of the major branches of t...
This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, whic...
Reconstructing the origin and evolution of land plants and their
algal relatives is a fundamental problem in plant phylogenetics, and
is essential for understanding how critical adaptations arose, including
the embryo, vascular tissue, seeds, and flowers. Despite
advances inmolecular systematics, some hypotheses of relationships
remain weakly resol...
Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly reso...
The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how t...
The intention of this editorial is to steer researchers through methodological choices in molecular evolution, drawing on the combined expertise of the authors. Our aim is not to review the most advanced methods for a specific task. Rather, we define several general guidelines to help with methodology choices at different stages of a typical phylog...
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked...
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked...
Figure S6. Alignment AliMG. Alignments AliMG (3485 positions, 106 taxa) created using the combination MUSCLE + Gblocks.
Figure S5. Composition of the amino acid alignment used in this study. Principal component analysis of the amino acid composition per species for the amino acid alignment AliMG used in this study. Species have been color-coded per group corresponding to each of the main cnidarian clades (Coronatae, Cubozoa, Discomedusa, Hexacorallia, Hydrozoa, Octo...
Background
Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically...
Figure S1. Cnidarian phylogeny of mitochondrial protein genes using the reduced alignment AliMGred with 103 species. Phylogenetic analyses of cnidarian protein coding genes under the GTR model and CAT approximation with RAxML for the reduced AliMG alignment (AliMGred), where the coronate Linuche unguiculata, the tube anemone Ceriantheopsis american...
Figure S4. The use of several statistical tests verifying the validity of some groups in cnidarians for the reduced alignment AliMGred. Probability values for the AU, KH and SH tests and BI values for several clades traditionally recognized in Cnidaria for the reduced alignment AliMGred containing 103 species, where the coronate Linuche unguiculata...
Figure S3. Cnidarian phylogeny of mitochondrial protein genes using the codon alignment CodAliM75tx-ser3. Phylogenetic analyses of cnidarian protein coding genes under the QMM + Γ model with PhyloBayes for the CodAliM75tx-ser3 alignments (5318 parsimony-informative characters). Support values correspond to the posterior probabilities for QMM and GT...
Figure S7. Table of morphological characters mapped on the best tree. Mapping of morphological characters under DELTRAN and ACCTRAN models differed only for characters (5) and (7). (1) symmetry: medusozoan taxa have been scored radial, but Marques and Collins (2004) subdivided it into radial, biradial, or radial tetramerous; Octocorallia, Zoanthari...
Figure S2. Cnidarian phylogeny of mitochondrial protein genes using the codon alignment CodAliM75tx-argleuser3. Phylogenetic analyses of cnidarian protein coding genes under the QMM + Γ model with PhyloBayes for the CodAliM75tx-argleuser3 alignments (4785 parsimony-informative characters). Support values correspond to the posterior probabilities fo...
