Replaying the tape of life in the twenty-first century

International audienceShould the tape of life be replayed, would it produce similar living beings? A classical answer has long been ‘no’, but accumulating data are now challenging this view. Repeatability in experimental evolution, in phenotypic evolution of diverse species and in the genes underlying phenotypic evolution indicates that despite unpredictability at the level of basic evolutionary processes (such as apparition of mutations), a certain kind of predictability can emerge at higher levels over long time periods. For instance, a survey of the alleles described in the literature that cause non-deleterious phenotypic differences among animals, plants and yeasts indicates that similar phenotypes have often evolved in distinct taxa through independent mutations in the same genes. Does this mean that the range of possibilities for evolution is limited? Does this mean that we can predict the outcomes of a replayed tape of life? Imagining other possible paths for evolution runs into four important issues: (i) resolving the influence of contingency, (ii) imagining living organisms that are different from the ones we know, (iii) finding the relevant concepts for predicting evolution, and (iv) estimating the probability of occurrence for complex evolutionary events that occurred only once during the evolution of life on earth

FlyPNS, a database of the Drosophila embryonic and larval peripheral nervous system

BACKGROUND: The embryonic and larval peripheral nervous system of Drosophila melanogaster is extensively studied as a very powerful model of developmental biology. One main advantage of this system is the ability to study the origin and development of individual sensory cells. However, there remain several discrepancies regarding the organization of sensory organs in each abdominal segment A1-A7. DESCRIPTION: We have constructed a web site called FlyPNS (for Fly Peripheral Nervous System) that consolidates a wide range of published and unpublished information about the embryonic and larval sensory organs. It communicates (1) a PNS pattern that solves the discrepancies that have been found in the recent literature, (2) the correspondence between the different nomenclatures that have been used so far, (3) a comprehensive description of each sensory organ, and (4) a list of both published and unpublished markers to reliably identify each PNS cell. CONCLUSIONS: The FlyPNS database integrates disparate data and nomenclature and thus helps understanding the conflicting observations that have been published recently. Furthermore, it is designed to provide assistance in the identification and study of individual sensory cells. We think it will be a useful resource for any researcher with interest in Drosophila sensory organs

The Coding Loci of Evolution and Domestication: Current Knowledge and Implications for Bio-Inspired Genome Editing

International audienceOne promising application of CRISPR/Cas9 is to create targeted mutations to introduce traits of interest into domesticated organisms. However, a major current limitation for crop and livestock improvement is to identify the precise genes and genetic changes that must be engineered to obtain traits of interest. Here we discuss the advantages of bio-inspired genome editing, i.e. the engineered introduction of natural mutations that have already been associated with traits of interest in other lineages (breeds, populations, or species). To get a landscape view of potential targets for genome editing, we used Gephebase (www.gephebase.org), a manually-curated database compiling published data about the genes responsible for evolutionary and domesticated changes across Eukaryotes, and examined the >1,200 mutations that have been identified in the coding regions of more than 700 genes in animals, plants and yeasts. We observe that our genetic knowledge is relatively important for certain traits, such as xenobiotic resistance, and poor for others. We also note that protein-null alleles, often due to nonsense and frameshift mutations, represent a large fraction of the known loci of domestication (42% of identified coding mutations), compared to intraspecific (27%) and interspecific evolution (11%). While this trend may be subject to detection, publication, and curation biases, it is consistent with the idea that breeders have selected large-effect mutations underlying adaptive traits in specific settings, but that these mutations and associated phenotypes would not survive the vagaries of changing external and internal environments. Our compilation of the loci of evolution and domestication uncovers interesting options for bio-inspired and transgene-free genome editing

The differential view of genotype–phenotype relationships

International audienceAn integrative view of diversity and singularity in the living world requires a better understanding of the intricate link between genotypes and phenotypes. Here we re-emphasize the old standpoint that the genotype–phenotype (GP) relationship is best viewed as a connection between two differences, one at the genetic level and one at the phenotypic level. As of today, predominant thinking in biology research is that multiple genes interact with multiple environmental variables (such as abiotic factors, culture, or symbionts) to produce the phenotype. Often, the problem of linking genotypes and phenotypes is framed in terms of genotype and phenotype maps, and such graphical representations implicitly bring us away from the differential view of GP relationships. Here we show that the differential view of GP relationships is a useful explanatory framework in the context of pervasive pleiotropy, epistasis, and environmental effects. In such cases, it is relevant to view GP relationships as differences embedded into differences. Thinking in terms of differences clarifies the comparison between environmental and genetic effects on phenotypes and helps to further understand the connection between genotypes and phenotypes

Gene drive and its applications

Le forçage génétique est une nouvelle technique de manipulation génétique qui a été développée ces cinq dernières années et qui permet de propager rapidement des modifications génétiques dans les populations naturelles. Les applications potentielles sont nombreuses, à la fois en santé publique, en agriculture et en biologie de la conservation. Cet article présente les développements actuels de cette biotechnologie, ainsi que les enjeux et les risques qui y sont associés.Gene drive is a new genetic engineering technology that has been developed over the past five years and that allows genetic modifications to spread rapidly in natural populations. Potential applications are numerous, for public health issues, agriculture and conservation biology. This article presents the current developments in this biotechnology, as well as the issues and risks associated with it

Gephebase, a database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes

International audienceGephebase is a manually-curated database compiling our accumulated knowledge of the genes and mutations that underlie natural, domesticated and experimental phenotypic variation in all Eukaryotes-mostly animals, plants and yeasts. Gephebase aims to compile studies where the genotype-phenotype association (based on linkage mapping, association mapping or a candidate gene approach) is relatively well supported. Human clinical traits and aberrant mutant phenotypes in laboratory organisms are not included and can be found in other databases (e.g. OMIM, OMIA, Monarch Initiative). Gephebase contains more than 1700 entries. Each entry corresponds to an allelic difference at a given gene and its associated phenotypic change(s) between two species or two individuals of the same species, and is enriched with molecular details , taxonomic information, and bibliographic information. Users can easily browse entries and perform searches at various levels using boolean operators (e.g. transposable elements, snakes, carotenoid content , Doebley). Data is exportable in spreadsheet format. This database allows to perform meta-analyses to extract global trends about the living world and the research fields. Gephebase should also help breeders , conservationists and others to identify promising target genes for crop improvement, parasite/pest control, bioconservation and genetic diagnostic. It is freely available at www.gephebase.org

A Major Locus Controls a Genital Shape Difference Involved in Reproductive Isolation Between Drosophila yakuba and Drosophila santomea

International audienceRapid evolution of genitalia shape, a widespread phenomenon in animals with internal fertilization, offers the opportunity to dissect the genetic architecture of morphological evolution linked to sexual selection and speciation. Most quantitative trait loci (QTL) mapping studies of genitalia divergence have focused on Drosophila melanogaster and its three most closely related species, D. simulans, D. mauritiana, and D. sechellia, and have suggested that the genetic basis of genitalia evolution involves many loci. We report the first genetic study of male genitalia evolution between D. yakuba and D. santomea, two species of the D. melanogaster species subgroup. We focus on male ventral branches, which harm females during interspecific copulation. Using landmark-based geometric morphometrics, we characterized shape variation in parental species, F1 hybrids, and backcross progeny and show that the main axis of shape variation within the backcross population matches the interspecific variation between parental species. For genotyping, we developed a new molecular method to perform multiplexed shotgun genotyping (MSG), which allowed us to prepare genomic DNA libraries from 365 backcross individuals in a few days using little DNA. We detected only three QTL, one of which spans 2.7 Mb and exhibits a highly significant effect on shape variation that can be linked to the harmfulness of the ventral branches. We conclude that the genetic architecture of genitalia morphology divergence may not always be as complex as suggested by previous studies

Data from: The loci of repeated evolution: a catalogue of genetic hotspots of phenotypic variation

What is the nature of the genetic changes underlying phenotypic evolution? We have catalogued 1008 alleles described in the literature that cause phenotypic differences among animals, plants and yeasts. Surprisingly, evolution of similar traits in distinct lineages often involves mutations in the same gene (“gene reuse”). This compilation yields three important qualitative implications about repeated evolution. First, the apparent evolution of similar traits by gene reuse can be traced back to two alternatives, either several independent causative mutations or a single original mutational event followed by sorting processes. Second, hotspots of evolution – defined as the repeated occurrence of de novo mutations at orthologous loci and causing similar phenotypic variation – are omnipresent in the literature with more than 100 examples covering various levels of analysis, including numerous gain-of-function events. Third, several alleles of large effect have been shown to result from the aggregation of multiple small-effect mutations at the same hotspot locus, thus reconciling micro-mutationist theories of adaptation with the empirical observation of large-effect variants. While data heterogeneity and experimental biases prevented us from extracting quantitative trends, our synthesis highlights the existence of genetic paths of least resistance leading to viable evolutionary change

Data from: Distinct copulation positions in Drosophila pachea males with symmetric or asymmetric external genitalia

Left-right asymmetric genitalia have appeared multiple times independently in insects and have been associated with changes in mating positions. However, there is little experimental data on how the evolution of genital asymmetries may have affected the evolution of mating positions or vice versa. As opposed to its closely-related species, Drosophila pachea has a conspicuous asymmetry in its male genitalia external lobes, with the left lobe being 1.49 ± 0.08 (SD) times longer and thinner than the right lobe. In a laboratory stock, we found that 20% of the males possess fully symmetric lobes. To better understand how asymmetric genitalia may affect mating, we compared D. pachea copulation behaviour between these mutant males and wild-type males. We found that D. pachea wild-type males adopt a one-sided mating posture with the male always one-sided 8.55° ± 1.79° (SD) towards the female’s right side. Within 45-min recordings, all wild-type males did mate whereas 39% of symmetric mutants failed to form a stable mating complex and did not mate. In successful copulations, symmetric mutants also adopted a right-sided mating posture but the angle between male and female bodies was significantly more variable compared to wild-type males. Our results suggest that lobe size asymmetry is required for the formation of a stable mating complex and for the positioning of the male according to a precise angle on the female. However, lobe size asymmetry is not required for D. pachea right-sided mating posture

Formation des organes sensoriels chez D. melanogaster (lignages cellulaires, apoptose et évolution)

PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF