Francois Bonhomme

Francois Bonhomme
Université de Montpellier | UM1 · Institut des Sciences de l’Évolution Montpellier (ISEM)

D. Sci.

About

616
Publications
67,891
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21,993
Citations
Additional affiliations
October 1978 - September 2020
Université de Montpellier
Position
  • Directeur de Recherches CNRS
October 1978 - November 2012
July 1976 - December 2012
Université de Montpellier

Publications

Publications (616)
Article
How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure...
Preprint
The speciation of ecotypes can unfold in diverse ways and likely depends on multiple processes. The variants involved in ecotype divergence can include new mutations as well as older allelic variation that evolved in different contexts. Among the different types of variants that can contribute to reproductive isolation between ecotypes, structural...
Preprint
Full-text available
How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure...
Preprint
Full-text available
The house mouse, Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such inve...
Article
Full-text available
Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site...
Article
House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details h...
Article
Full-text available
Deep hydrothermal vents are highly fragmented and unstable habitats at all temporal and spatial scales. Such environmental dynamics likely play a non-negligible role in speciation. Little is, however, known about the evolutionary processes that drive population-level differentiation and vent species isolation and, more specifically, how geography a...
Article
Hydrothermal vents form archipelagos of ephemeral deep-sea habitats that raise interesting questions about the evolution and dynamics of the associated endemic fauna, constantly subject to extinction-recolonization processes. These metal-rich environments are coveted for the mineral resources they harbor, thus raising recent conservation concerns....
Article
Full-text available
Here we report the discovery of a high-temperature hydrothermal vent field on the Woodlark Ridge, using ship-borne multibeam echosounding and Remotely Operated Vehicle (ROV) exploration. La Scala Vent Field comprises two main active areas and several inactive zones dominated by variably altered basaltic rocks, indicating that an active and stable h...
Preprint
Full-text available
House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely-used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details h...
Article
Full-text available
Ecosystems worldwide are suffering from climate change. Coral reef ecosystems are globally threatened by increasing sea surface temperatures. However, gene expression plasticity provides the potential for organisms to respond rapidly and effectively to environmental changes, and would be favored in variable environments. In this study, we investiga...
Article
Full-text available
Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pre-tested by selection in the species of origin. While introgressed alleles are generally deleterious, several studies have reported introgression as the...
Article
Full-text available
Reports of morphological differences between European anchovy (Engraulis cf. encrasicolus) from coastal and marine habitats have long existed in the ichthyologic literature and have given rise to a long‐standing debate on their taxonomic status. More recently, molecular studies have confirmed the existence of genetic differentiation between the two...
Preprint
Full-text available
Scleractinian corals are of great ecological interest as ecosystem engineer species. Accordingly, there is a wealth of studies on their adaptive abilities facing climate change. Such studies should rely on precise species and population delimitation. Nevertheless species delimitation in corals can be hindered by the lack of adequate genetic markers...
Data
Supporting Information Table S1. Sample locations and number of generations mouse strains that were kept in the lab. Table S2. Location and genes associated with sequenced fragments in the MKK7 region on mouse chromosome 8. Table S3. Primer sequences and amplification conditions for sequencing of 2.6 kb of 5 ' upstream sequence of the MKK7 gene...
Article
Full-text available
The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. to track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeol...
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Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstruc...
Article
Full-text available
Understanding the genetic underpinnings of fitness trade-offs across spatially variable environments remains a major challenge in evolutionary biology. In Mediterranean gilthead sea bream, first-year juveniles use various marine and brackish lagoon nursery habitats characterized by a trade-off between food availability and environmental disturbance...
Article
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Evaluating species dispersal across the landscape is essential to design appropriate management and conservation actions. However, technical difficulties often preclude direct measures of individual movement, while indirect genetic approaches rely on assumptions that sometimes limit their application. Here, we show that the temporal decay of admixt...
Preprint
Full-text available
Understanding how new species arise through the progressive establishment of reproductive isolation barriers between diverging populations is a major goal in Evolutionary Biology. One important result of speciation genomics studies is that the genomic regions involved in reproductive isolation frequently harbor anciently diverged haplotypes that pr...
Article
Full-text available
Aim The distribution of the western house mouse (Mus musculus domesticus) around the world has been strongly influenced by the movement of humans. The close association between the house mouse and human phylogeography has been primarily studied in the peripheral distribution of the species. Here, we inferred the complex colonization history of Cypr...
Preprint
Full-text available
Ecosystems worldwide are suffering from climate change. For example, the coral reef ecosystems are globally threatened by increasing sea surface temperatures. However gene expression plasticity provides the potential for organisms to respond rapidly and effectively to environmental change, and would be favored in variable environments. In this stud...
Article
Full-text available
The originally published version of this Article contained errors in Figure 5, whereby the sign for Spearman's rho was incorrect in panels b and c. These errors have now been corrected in both the PDF and HTML versions of the Article.
Article
Full-text available
Speciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive...
Article
North Africa is now recognized as a major area for the emergence and dispersal of anatomically modern humans from at least 315 kya. The Mediterranean Basin is thus particularly suited to study the role of climate versus human-mediated changes on the evolutionary history of species. The Algerian mouse (Mus spretus Lataste) is an endemic species from...
Article
Investigating gene flow between closely related species and its variation across the genome is important to understand how reproductive barriers shape genome divergence before speciation is complete. An efficient way to characterize differential gene flow is to study how the genetic interactions that take place in hybrid zones selectively filter ge...
Article
Full-text available
Abstract Background Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evalu...
Preprint
Full-text available
Investigating variation in gene flow across the genome between closely related species is important to understand how reproductive isolation builds up during the speciation process. An efficient way to characterize differential gene flow is to study how the genetic interactions that take place in hybrid zones selectively filter gene exchange betwee...
Preprint
Full-text available
Speciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive...
Article
Full-text available
The house mouse is a powerful model to dissect the genetic basis of phenotypic variation, and serves as a model to study human diseases. Despite a wealth of discoveries, most classical laboratory strains have captured only a small fraction of genetic variation known to segregate in their wild progenitors, and existing strains are often related to e...
Article
Seven microsatellite markers were used to investigate the population structure of the offshore ecotype of the European anchovy (Engraulis encrasicolus) by comparing 12 marine samples collected off the Moroccan coast with an inshore sample taken as a reference for the lagoonal ecotype. F-statistics, correspondence analysis and Bayesian assignment al...
Article
Full-text available
Hybrid zones provide natural experiments where new combinations of genotypes and phenotypes are produced. Studying the reshuffling of genotypes and remodeling of phenotypes in these zones is of particular interest to document the building of reproductive isolation and the possible emergence of transgressive phenotypes that can be a source of evolut...
Article
Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by pop...
Article
Full-text available
The phylogeography of the house mouse (Mus musculus L.), an emblematic species for genetic and biomedical studies, is only partly understood, essentially because of a sampling bias towards its most peripheral populations in Europe, Asia and the Americas. Moreover, the present-day phylogeographic hypotheses stem mostly from the study of mitochondria...
Article
Full-text available
Similar to seemingly maladaptive genes in general, the persistence of inherited cancer-causing mutant alleles in populations remains a challenging question for evolutionary biologists. In addition to traditional explanations like senescence or antagonistic pleiotropy, here we put forward a new hypothesis to explain the retention of oncogenic mutati...
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Background: Carcinogenesis affects not only humans but almost all metazoan species. Understanding the rules driving the occurrence of cancers in the wild is currently expected to provide crucial insights into identifying how some species may have evolved efficient cancer resistance mechanisms. Recently the absence of correlation across species bet...
Article
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The whitemouth croaker (Micropogonias furnieri) is the main fish species of the demersal fisheries along the Atlantic coast of South America. There has been much debate regarding the number of stocks of this heavily exploited fish off the Brazilian coast between latitudes 23 • S and 33 • S. Analyses of morphometric and meristic data suggest that tw...
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Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers...
Article
The freshwater blenny (Salaria fluviatilis), an endemic fish to the tributaries of the Mediterranean and Black seas, is considered endangered in five of the nine Mediterranean-European countries. Substantial effort has recently been made to improve our understanding of its biology (i.e., habitat modelling, morphology, behaviour), but developing a c...
Article
Full-text available
The euryhaline European sea bass Dicentrarchus labrax L., inhabiting the coasts of the eastern Atlantic Ocean and Mediterranean Sea, has had many opportunities for differentiation throughout its large natural range. However, evidence for this has been incompletely documented geographically and with an insufficient number of markers. Therefore, its...
Article
Scientists are increasingly coming to realize that oncogenic phenomena are both frequent and detrimental for animals, and must therefore be taken into account when studying the biology of wildlife species and ecosystem functioning. Here, we argue that several behaviours that are routine in an individual's life can be associated with cancer risks, o...
Article
Scientists are increasingly coming to realize that oncogenic phenomena are both frequent and detrimental for animals, and must therefore be taken into account when studying the biology of wildlife species and ecosystem functioning. Here, we argue that several behaviours that are routine in an individual's life can be associated with cancer risks, o...
Article
Full-text available
Convincing evidence reporting adaptive variation for physiologically and/or ecologically important traits in marine taxa is often derived from studies comparing field and laboratory observations and based on candidate-gene markers, mainly allozymes, responding to habitat selection. Likewise, patterns of genetic differentiation between sea and lagoo...
Article
Full-text available
The existence of cryptic salinity-related phenotypes has been hypothesized in the “euryhaline” sea bass (Dicentrarchus labrax). How differential osmoregulation costs between freshwater and saltwater environments affect fitness and phenotypic variation is misunderstood in this species. During an experiment lasting around five months, we investigated...
Article
Full-text available
The European sea bass (Dicentrarchus labrax) is a temperate zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here, we provide a high-quality chromosome-scale as...
Article
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For an increasing number of biologists, cancer is viewed as a dynamic system governed by evolutionary and ecological principles. Throughout most of human history, cancer was an uncommon cause of death and it is generally accepted that common components of modern culture, including increased physiological stresses and caloric intake, favor cancer de...
Article
Full-text available
Melicertus kerathurus represents an economically important resource for fisheries and aquaculture. Seven microsatellite loci from 373 specimens of M. kerathurus collected in different parts of the Mediterranean and NE Atlantic were identified. Four of these microsatellites showed a moderate level of polymorphism, with 2 to 14 alleles per locus, whe...
Article
Full-text available
We investigated genetic transitions in European anchovies (Engraulidae) by analysing one mitochondrial and six nuclear microsatellite loci in samples from 28 geographical locations, primarily in the Western Mediterranean with external samples from the Black Sea in the East, and the Gulf of Biscay in the West. Four samples were collected from lagoon...
Article
Full-text available
Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important...
Data
Transcaucasia comprises a key region for understanding the history of both the hybrid zone between house mouse lineages and the dispersal of the Neolithic way of life outside its Near Eastern cradle. The opportunity to document the colonization history of both men and mice in Transcaucasia was made possible by the discovery of mouse remains accumul...
Chapter
The House Mouse Mus musculus is now seen as a polytypic species where three main branches have differentiated in isolation within the past 500. 000 years and have come to contact again on several occasions. It is almost invariably considered as being constituted of three subspecies, Mus musculus castaneus being considered as more polymorphic, with...
Chapter
The western Mediterranean short-tailed mouse Mus spretus is, besides the house mouse M. musculus and its various subspecies from which it has diverged more than 1 million years ago, the second species from the genus Mus to have been established as a laboratory model. Indeed, its intercrossability with the latter has rendered this species very instr...
Chapter
Mus musculus (L) encompasses all the subspecies and geographical or chromosomal races of the house mouse. It is also the species which has paid the largest tribute to modern science, because the historical laboratory strains (the old inbreds) stem from this species through the old tradition of fancy mice which were bred in Europe and Asia for their...
Chapter
Archaeological and historical records indicate that mice were already bred as pets three millennia ago: it was then logical that these small mammals should be used by early scientists for performing their experiments. Even if this choice may retrospectively appear relatively opportunistic, it nevertheless turned out to be an excellent one in the mo...
Article
Full-text available
The population genetic structure of sea bass (Dicentrarchus labrax) along a transect from the Atlantic Ocean (AO) to the Eastern Mediterranean (EM) Sea differs from that of most other marine taxa in this area. Three populations (AO, Western Mediterranean [WM], EM) are recognized today, which were originally two allopatric populations. How two ances...
Article
Full-text available
Transcaucasia comprises a key region for understanding the history of both the hybrid zone between house mouse lineages and the dispersal of the Neolithic way of life outside its Near Eastern cradle. The opportunity to document the colonization history of both men and mice in Transcaucasia was made possible by the discovery of mouse remains accumul...