Benoît Perez-Lamarque

Benoît Perez-Lamarque
Ecole Normale Supérieure de Paris | ENS · Département de Biologie

PhD

About

22
Publications
3,050
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92
Citations
Citations since 2016
22 Research Items
92 Citations
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20162017201820192020202120220102030405060
Introduction
I am currently a PostDoc in Evolutionary biology at IBENS. I did my PhD co-advised by Hélène Morlon (IBENS, PSL University, Paris), Marc-André Selosse and Florent Martos (ISYEB, Museum of Natural History). I am working on host-microbiota evolution, from the development of modeling approaches to empirical applications especially on mycorrhizal networks.

Publications

Publications (22)
Article
Full-text available
Background The root mycobiome plays a fundamental role in plant nutrition and protection against biotic and abiotic stresses. In temperate forests or meadows dominated by angiosperms, the numerous fungi involved in root symbioses are often shared between neighboring plants, thus forming complex plant-fungus interaction networks of weak specializati...
Article
Full-text available
MacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on predicting...
Article
Full-text available
Lycopodiaceae species form an early-diverging plant family, characterized by achlorophyllous and subterranean gametophytes that rely on mycorrhizal fungi for their nutrition. Lycopodiaceae often emerge after a disturbance, like in the Hochfeld reserve (Alsace, France) where seven lycopod species appeared on new ski trails following a forest cut. He...
Preprint
Full-text available
Background and Aims Epiphytism has evolved repeatedly in plants and has resulted in a considerable number of species with original characteristics. Succulent forms in particular are thought to have evolved as an adaptation to the epiphytic environment, because the water supply is generally erratic compared to soils'. However, succulent organs also...
Article
Full-text available
Long‐term vertical transmissions of gut bacteria are thought to be frequent and functionally important in mammals. Several phylogenetic‐based approaches have been proposed to detect, among species‐rich microbiota, the bacteria that have been vertically transmitted during a host clade radiation. Applied to mammal microbiota, these methods have somet...
Preprint
Full-text available
Long-term vertical transmissions of gut bacteria are thought to be frequent and functionally important in mammals. Several phylogenetic-based approaches have been proposed to detect, among species-rich microbiota, the bacteria that have been vertically transmitted during a host clade radiation. Applied to mammal microbiota, these methods have somet...
Article
Full-text available
1. In soils, plants and fungi can form complex mycorrhizal networks allowing nutrient transfers between plant individuals and species. It is less clear, however, whether such networks exist on the bark of trees where epiphytic plant communities thrive in rainforests. Previous work showed that tropical epiphytic orchids especially, harbor symbiotic...
Preprint
Full-text available
Background The root mycobiome plays a fundamental role in plant nutrition and protection against biotic and abiotic stresses. In temperate forests or meadows dominated by angiosperms, the numerous fungi involved in root symbioses are often shared between neighboring plants, thus forming complex plant-fungus interaction networks of weak specializati...
Preprint
Full-text available
The main hypotheses about the evolution of animal cognition emphasise the role of conspecifics. Yet, space is often simultaneously occupied by multiple species from the same ecological guild. These sympatric species can compete for food, which may thereby stimulate or hamper cognition. Considering brain size as a proxy for cognition, we tested whet...
Article
Full-text available
Analyzing diversification dynamics is key to understanding the past evolutionary history of clades that led to present‐day biodiversity patterns. While such analyses are widespread in well‐characterized groups of species, they are much more challenging in groups which diversity is mostly known through molecular techniques. Here, we use the largest...
Article
Full-text available
The degree of similarity between the microbiotas of host species often mirrors the phylogenetic proximity of the hosts. This pattern, referred to as phylosymbio- sis, is widespread in animals and plants. While phylosymbiosis was initially interpreted as the signal of symbiotic transmission and coevolution between microbes and their hosts, it is now...
Article
The diversification of a host lineage can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to investigate how their associated microbial communities have changed as the spiders colonized new locations. Us...
Article
Full-text available
Background As in most land plants, the roots of orchids (Orchidaceae) associate with soil fungi. Recent studies have highlighted the diversity of fungal partners involved, mostly within Basidiomycotas. The association with a polyphyletic group of fungi collectively called rhizoctonias (Ceratobasidiaceae, Tulasnellaceae and Serendipitaceae) is the m...
Preprint
Full-text available
A bstract Whether interactions between species are conserved on evolutionary time-scales has spurred the development of both correlative and process-based approaches for testing phylogenetic signal in interspecific interactions: do closely related species interact with similar partners? Here we use simulations to test the statistical performances o...
Thesis
Full-text available
A plethora of recent studies have characterized the composition and functional role of microbial communities hosted by animals and plants, called microbiota. The overall goal of my PhD is to advance our understanding of how microbiota evolve with their host species, using data comprised of the phylogenetic relationships between host species and met...
Article
Significance The ochrophytes are an ancient and important group of eukaryotic algae, including diatoms, the most important photosynthesisers in the modern ocean, and a wide range of other species. Throughout their history, ochrophytes have exchanged genes with bacteria and eukaryotes through horizontal gene transfer (HGT), diversifying their cell b...
Preprint
Full-text available
The diversification of a host organism can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to determine the evolutionary history of a host and its associated microbial communities, altogether forming the...
Preprint
Full-text available
Arbuscular mycorrhizal fungi (AMF) are widespread microfungi that provide mineral nutrients to most land plants and form one of the oldest terrestrial symbioses. They have often been referred to as an "evolutionary cul-de-sac" for their limited ecological and species diversity. Here we use a global database of AMF to analyze their diversification d...
Article
Full-text available
While mutualistic interactions are widespread and essential in ecosystem functioning, the emergence of uncooperative cheaters threatens their stability, unless there are some physiological or ecological mechanisms limiting interactions with cheaters. In this framework, we investigated the patterns of specialization and phylogenetic distribution of...
Article
Full-text available
Microbiota play a central role in the functioning of multicellular life, yet understanding their inheritance during host evolutionary history remains an important challenge. Symbiotic microorganisms are either acquired from the environment during the life of the host (i.e. environmental acquisition), transmitted across generations with a faithful a...
Preprint
Full-text available
While mutualisms are widespread and essential in ecosystem functioning, the emergence of uncooperative cheaters threatens their stability, unless there are functional or evolutionary mechanisms limiting cheaters interactions. Here, we evaluated the constraints upon mycoheterotrophic (MH) cheating plants in the mutualistic interaction network of aut...

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Project (1)
Project
Informed by high throughput sequencing data, recent studies on the microbiota - microbial communities associated with a multicellular host - have highlighted the major roles played by these microorganisms in the functioning and evolution of their plant and animal hosts. These bacteria, fungi, viruses and other microbes are durably associated with their hosts, greatly influencing the host nutrition, development, protection, or even behavior. In humans for example, microbiota perturbations are correlated with pathological syndromes such as obesity or autism. Given the importance of microbiota composition on the host, it is essential to study to what extent host-microbiota interactions are conserved. Host-microbiota associations range from labile and poorly specific interactions, to highly conserved and ultra-specific associations; the latter type of interactions are particularly favorable to coevolution. The gradient of specificity in host-microbiota interactions results mainly from the transmission mode of the symbionts to the offspring; yet, the analytical tools needed to analyze these transmission modes from molecular data are lacking. The aim of this PhD project is twofold: i) develop the tools for processing the increasing amount of molecular biota data in order to unravel the dynamics of host-microbiota interactions across evolutionary timescales, and ii) quantify, within large empirical microbiota datasets, the importance of the different transmission modes and study their evolutionary consequences. The first part of the project proposes to develop probabilistic models to infer, via maximum likelihood inference, the evolutionary history of each microbial species considered independently. The model inputs will be the host phylogeny and a nucleotidic alignment of the microbial sequences associated with each host. We will consider a model in which the microbial sequences evolve by mutation along the branches of the host phylogeny, are vertically transmitted during host speciation events, and experiment horizontal host transfers. Finally, we will try to relax the hypothesis of independence between microbial taxa in order to take into account the interactions between symbionts (competitive inhibition, functional replacement…). We will compute the likelihoods associated with the microbial alignments under different evolution models, which will enable us to estimate the models' parameters (e.g. the horizontal host transfer frequency between host lineages). The second part will consist in the improvement of statistical approaches to better characterize the host-microbiota interaction networks, and in the development of models to test precise hypotheses about network evolution. These very large networks (huge number of microbial taxa) will require the development of tools to detect local patterns and structures. The model-based approaches will consist in probabilistic models for the evolution of interactions and will be paired with statistical inferences of the associated parameters via maximum likelihood. Applying the approaches developed in Part 1) and 2) to a set of available empirical microbiota dataset, including the microbiota of great apes and plant-fungi mycorrhizal networks, we will unravel the transmission dynamics and test precise hypotheses about the assembly and evolution of the microbiota.