Stéphane R . Prigent | Muséum National d'Histoire Naturelle (original) (raw)

Papers by Stéphane R . Prigent

Zenodo (CERN European Organization for Nuclear Research), Dec 31, 2008

bioRxiv (Cold Spring Harbor Laboratory), Dec 23, 2020

Animals can be permanently attached to a substrate for several days, weeks or months in aerial en... more Animals can be permanently attached to a substrate for several days, weeks or months in aerial environments at certain stages of their development such as eggs and pupae. Pupa adhesion has evolved multiple times in insects and is thought to maintain the animal in a place where it is not detectable by predators. Here, we investigate whether pupa adhesion in Drosophila could also protect the animal by preventing potential predators from detaching the pupa. We measured the adhesion of Drosophila species originating from the same area and found that pupa adhesion varies among species, which can be explained by different glue production strategies. Then, we compared attached and manually detached pupae in both field and laboratory assays to investigate the role of pupa adhesion to prevent predation. First, we found that attached pupae remain on site 30 % more than detached pupae in the field after three days, probably because they are less predated. Second, we observed that attached pupae are less efficiently predated by ants in the laboratory, because they are not carried back to the ant nest and because more ants are needed to consume them onsite. Our results show that pupa adhesion is a crucial mechanical trait for Drosophila fly survival that can prevent the animal from being taken away by predators.

F1000Research, Apr 9, 2019

Gephebase is a manually-curated database compiling our accumulated knowledge of the genes and mut... more Gephebase 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 or understood. Human disease and aberrant mutant phenotypes in laboratory model organisms are not included in Gephebase and can be found in other databases (eg. 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 between two individuals of the same species, and is enriched with molecular details, taxonomic information, and bibliographic information. Users can easily browse entries for their topic of interest and perform searches at various levels, whether phenotypic, genetic, taxonomic or bibliographic (eg. transposable elements, cis-regulatory mutations, snakes, carotenoid content, an author name). Data can be searched using keywords and boolean operators and is exportable in spreadsheet format. This database allows to perform meta-analysis to extract general information and global trends about evolution, genetics, and the field of evolutionary genetics itself. Gephebase should also help breeders, conservationists and others to identify the most promising target genes for traits of interest, with potential applications such as crop improvement, parasite and pest control, bioconservation, and genetic diagnostic. It is freely available at www.gephebase.org.

During the early stages of local adaptation and speciation, genetic differences tend to accumulat... more During the early stages of local adaptation and speciation, genetic differences tend to accumulate at certain regions of the genome leading to the formation of genomic islands of divergence (GIDs). This pattern may be due to selection and/or difference in the rate of recombination. Here, we investigate the possible causes of GIDs inDrosophila yakuba mayottensis, and reconfirm using field collection its association with toxic noni (Morinda citrifolia) fruits on the Mayotte island. Population genomics revealed lack of genetic structure on the island and identified 20 GIDs distinguishingD. y. mayottensisfrom generalist mainland populations ofD. y. yakuba. The GIDs were enriched with gene families involved in the metabolism of lipids, sugars, peptides and xenobiotics, suggesting a role in host shift. We assembled a new genome forD. y. mayottensisand identified five novel chromosomal inversions. Twelve GIDs (∼72% of outlier windows) fell close to or within subspecies-specific inversions....

Zootaxa, 2008

Nine species of the genus Phortica are found from Kenya, African, including two known and seven n... more Nine species of the genus Phortica are found from Kenya, African, including two known and seven new species: Phortica (Allophortica) sexpunctata (Séguy, 1938), P. (Phortica) sobodo Burla, 1954, P. (P.) angulata sp. nov., P. (P.) curvispina sp. nov., P. (P.) machoruka sp. nov., P. (P.) manjano sp. nov., P. (P.) melanopous sp. nov., P. (P.) vinywelea sp. nov. and P. (P.) unispina sp. nov. The seven new species belong to the foliiseta species complex that is early found from the Oriental Region. A key to all Kenyan species is provided.

A revision of the Zygothrica samoaensis species group (Diptera: Drosophilidae), with division int... more A revision of the Zygothrica samoaensis species group (Diptera: Drosophilidae), with division into three species subgroups and description of five new species

African Entomology, 2020

Drosophila suzukii (Matsumura, 1931) is an Asian pest of grapes and other soft fruits that has in... more Drosophila suzukii (Matsumura, 1931) is an Asian pest of grapes and other soft fruits that has invaded North America and Europe during the last decade. Here we report its recent occurrence in two islands of the Comoros archipelago in the Mozambique Channel, namely Mayotte and Ngazidja (Grande Comore), in April 2017 and November 2018, respectively. We also document its absence from other African islands of the Mozambique Channel and the Western Indian Ocean including Mayotte until 2013. Drosophila ashburneri Tsacas, 1984 is the only member of the suzukii species subgroup known from the Comoros, but it is morphologically distinct and likely distantly related to D. suzukii. Drosophila suzukii has likely been recently introduced to the Comoros archipelago, perhaps from La Réunion island where it first appeared in November 2013. In all these tropical islands, D. suzukii was found in high-altitude habitats in agreement with its adaptation to cold environments. These results suggest the high susceptibility of highlands in Eastern and Southern Africa to be infested by this pest in a near future.

Annales de la Société entomologique de France (N.S.), 2020

Accepté le 4 décembre 2019) Summary. The Drosophilid fauna has been less investigated in the Atla... more Accepté le 4 décembre 2019) Summary. The Drosophilid fauna has been less investigated in the Atlantic Afrotropical islands than in the Indian Ocean. Located about 250 km from the continent, the volcanic island of São Tomé has been colonized mostly by natural means, probably by the wind, since the emergence of the island about 15 million years ago, and presumably also by anthropogenic transportation of invasive and domestic species. To date, 37 different Drosophilid species have been mentioned from São Tomé. The present work extends this list to 80 species. The genera Zygothrica, Phorticella and Hypselothyrea are newly recorded from the island. Among these 80 species, only 12 are putatively introduced by human activities, suggesting the preponderance of natural arrivals. Compared to other islands, São Tomé harbours a high diversity of drosophilids. At least 14 species are supposed to be endemic. Future molecular comparisons between the island flies and their continental relatives will probably help to identify other endemic species. The high diversity observed in São Tomé is certainly due to the large size of the island, and to the presence of vast natural altitudinal forests offering a variety of possible habitats. Further collections are likely to lead to an increase of the species list. From now, São Tomé island appears as an excellent laboratory for studying the ecology and evolution of the Drosophila model. Résumé. Des collectes de terrain révèlent que São Tomé est l'île afrotropicale avec la plus grande diversité de drosophiles (Diptères : Drosophilidae). La faune de Drosophilidae a été moins étudiée dans les îles afrotropicales de l'Atlantique que dans l'océan Indien. Située à environ 250 km du continent, l'île volcanique de São Tomé a été colonisée principalement de façon naturelle, probablement à l'aide du vent, depuis l'émergence de l'île il y a environ 15 millions d'années, et par le transport supposé d'espèces domestiques et invasives par l'activité humaine. Jusqu'à présent, 37 espèces de Drosophilidae étaient mentionnées à São Tomé. Le présent travail accroît cette liste à 80 espèces. Les genres Zygothrica, Phorticella et Hypselothyrea sont nouvellement cités de l'île. Parmi ces 80 espèces, seulement 12 pourraient avoir été introduites par les activités humaines, révélant la prépondérance des colonisations naturelles. Comparée à d'autres îles, São Tomé abrite une plus grande diversité de drosophiles. Au moins 14 espèces sont supposées être endémiques. Il est probable que d'autres espèces endémiques seront identifiées lorsque les études moléculaires permettront de comparer les individus de São Tomé avec les espèces apparentées du continent africain. La diversité observée à São Tomé est certainement due à la grande taille de l'île et à la présence d'une vaste forêt d'altitude offrant une grande variété d'habitats. De futures collectes permettront d'accroître la liste d'espèces. L'île de São Tomé apparaît comme un excellent territoire pour l'étude de l'écologie et de l'évolution du modèle drosophile.

Nucleic Acids Research, 2019

Molecular Phylogenetics and Evolution, 2019

The subgenus Sophophora of Drosophila, which includes D. melanogaster, is an important model for ... more The subgenus Sophophora of Drosophila, which includes D. melanogaster, is an important model for the study of molecular evolution, comparative genomics, and evolutionary developmental biology. Numerous phylogenetic studies have examined species relationships in the well-known melanogaster, obscura, willistoni, and saltans species groups, as well as the relationships among these clades. In contrast, other species groups of Sophophora have been relatively neglected and have not been subjected to molecular phylogenetic analysis. Here, we focus on the endemic African Drosophila fima and dentissima lineages. We find that both these clades fall within the broadly defined melanogaster species group, but are otherwise distantly related to each other. The new phylogeny supports pervasive divergent and convergent evolution of male-specific grasping structures (sex combs). We discuss the implications of these results for defining the boundaries of the melanogaster species group, and weigh the relative merits of "splitting" and "lumping" approaches to the taxonomy of this key model system.

Molecular Phylogenetics and Evolution, 2011

Phylogenetic relationships of 26 Phortica species were investigated based on DNA sequence data of... more Phylogenetic relationships of 26 Phortica species were investigated based on DNA sequence data of two mitochondrial (ND2, COI) and one nuclear (28S rRNA) genes. Five monophyletic groups were recovered in the genus Phortica, of which three were established as new subgenera, Alloparadisa, Ashima, and Shangrila. The subgenus Allophortica was suggested as the most basal lineage in Phortica, followed by the lineage of P. helva + P. sobodo + P. varipes. The remaining Phortica species, most of Oriental distribution, formed a monophyletic group, and were subdivided into three lineages (i.e., the subgenera Ashima, Phortica, and Shangrila). The subgenera Shangrila and Phortica were suggested as sister taxa, and four clades were recovered in the subgenus Ashima. The result of reconstruction of ancestral distribution and estimation of divergence times indicates that, the ancestor of the genus Phortica restricted to Africa, its initial diversification was dated back to ca. 23 Mya (coinciding with the Oligocene/Miocene boundary); sympatric speciation and an Africa-to-Asia dispersal was proposed to account for the current distribution of Allophortica and the rest Phortica; most of the rest diversification of Phortica occurred in southern China, and the divergence between the African clade and its Oriental counterpart was suggested as a result of vicariance following a dispersal of their ancestral species from southern China to Africa.

Molecular Phylogenetics and Evolution, 2010

The Zaprionus genus group comprises three drosophilid genera (Zaprionus, Phorticella and Samoaia)... more The Zaprionus genus group comprises three drosophilid genera (Zaprionus, Phorticella and Samoaia) that are thought to be related to the Drosophila immigrans species group. We revised the phylogenetic relationships among the three genera and their placement within the subfamily Drosophilinae using one mitochondrial (COII) and one nuclear (Amyrel) gene. The Bayesian tree inferred from concatenated amino acid sequences of the two genes strongly suggests the polyphyly of the Zaprionus genus group and of each of the genera Zaprionus and Phorticella. Paraphyly of the D. immigrans species group was also shown here; the quadrilineata subgroup formed the sister clade to the genus Samoaia. These results suggest the necessity of taxonomic revisions for some relevant genera and species groups included within the genus Drosophila.

Fig. 3. Phylogenetic analysis of the genus Zaprionus and Microdrosophila aff. mamaru (Burla, 1954... more Fig. 3. Phylogenetic analysis of the genus Zaprionus and Microdrosophila aff. mamaru (Burla, 1954). This tree is the neighbor-joining tree. The maximum likelihood tree gives the same topology. Nodes with a bootstrap value lower than 50% were merged. Bootstrap values were calculated over 1000 repeats. Above nodes: bootstrap values for maximum likelihood using a GTR + G + I model. Below nodes: bootstrap values for neighbor-joining using the Kimura-2p distance.

Fig. 4. Phylogenetic analysis of the subgenus Sophophora and Lissocephala aff. diola Tsacas & Lac... more Fig. 4. Phylogenetic analysis of the subgenus Sophophora and Lissocephala aff. diola Tsacas & Lachaise, 1979. Conventions as for Fig. 3.

Fig. 1. Percent success and failure in obtaining a COI sequence from specimens. A. Total number o... more Fig. 1. Percent success and failure in obtaining a COI sequence from specimens. A. Total number of flies in the sample. B. Date of field collection (month indicated in lowercase Roman numerals). n = number of specimens used.

Fig. 2. Percent divergence of the morphospecies DNA barcode from the closest neighbor found in th... more Fig. 2. Percent divergence of the morphospecies DNA barcode from the closest neighbor found in the barcode database.

L'amylase hydrolyse les polysaccharides tels que l'amidon et le glycogene. Elle est donc ... more L'amylase hydrolyse les polysaccharides tels que l'amidon et le glycogene. Elle est donc essentielle dans la digestion des organismes qui utilisent ces substrats comme la principale ressource energetique. La variabilite electrophoretique des amylases qui est considerable chez les drosophiles, notamment chez drosophila melanogaster, est generalement consideree comme neutre vis-a-vis de la selection. Nous montrons dans cette etude qu'au contraire, les variations electrophoretiques des amylases de plus d'une centaine d'especes de drosophiles sont correlees a des facteurs environnementaux. L'evolution des amylases apparait controlee par les pressions de selection exercees, a la fois, par les conditions climatiques et les regimes alimentaires. Les especes mycophages, exploitant les champignons dont le principal polysaccharide de reserve est le glycogene, presentent des amylases tres particulieres qui migrent vers la cathode (type mycophage) contrairement a la situ...

The Drosophilidae is well known for the model species in genetics. But beyond Drosophila melanoga... more The Drosophilidae is well known for the model species in genetics. But beyond Drosophila melanogaster a huge diversity of species exists within the family. This diversity takes different aspects, including the morphology, the behavior and the ecology. Diversity is not only observed at a worldwide scale but also at the smaller scale of an island like Taiwan. Taiwan is an island of about 35 000 km (0.024% of emerged lands) lying in the West part of the Pacific ocean close to the Asian continent and located on the Fire Belt between the Japanese archipelago and the Philippines. The island shows a variety of relief with mountains culminating at 3952 m and is bathed in a tropical to subtropical climate. The first drosophilid species recorded specifically from Taiwan were described by Hendel in 1914. Up to now 309 species have been recorded in Taiwan (nearly 8% of world species). Taiwanese drosophilids are distributed in 31 genera (41% of world genera) with the dominance of the Drosophila ...

The proposition of Van der Linde et al. (BZN 64: 238–242) to maintain the name of Drosophila mela... more The proposition of Van der Linde et al. (BZN 64: 238–242) to maintain the name of Drosophila melanogaster has two consequences. The first is the loss of the name ‘Sophophora’ through synonymy with Drosophila. The second is the loss of identity of the current genus Drosophila (s.s.). To justify their proposition Van der Linde et al. (BZN 64: 238–242) emphasized the role of D. melanogaster in science and weakened the taxonomical significance of Drosophila (s.l.) and Drosophila (s.s.) that they proposed to split. In my opinion their arguments are oversimplified or not justified. The species of Drosophila (s.s.) have also played a major role in science and the classification is not as messy as it is suggested. I think the proposed nomenclatural change would be more detrimental for science than the simple elevation of Sophophora to the genus rank.

The proposition of Van der Linde et al. (BZN 64: 238-242) to maintain the name of Drosophila mela... more The proposition of Van der Linde et al. (BZN 64: 238-242) to maintain the name of Drosophila melanogaster has two consequences. The first is the loss of the name 'Sophophora' through synonymy with Drosophila. The second is the loss of identity of the current genus Drosophila (s.s.). To justify their proposition Van der Linde et al. (BZN 64: 238-242) emphasized the role of D. melanogaster in science and weakened the taxonomical significance of Drosophila (s.l.) and Drosophila (s.s.) that they proposed to split. In my opinion their arguments are oversimplified or not justified. The species of Drosophila (s.s.) have also played a major role in science and the classification is not as messy as it is suggested. I think the proposed nomenclatural change would be more detrimental for science than the simple elevation of Sophophora to the genus rank. What is the colloquial meaning of Drosophila? As indicated in the application, the genus Drosophila was established by Fallén (1823) to include twelve species. But the scientific renown of Drosophila was acquired later, at the beginning of the 20th century, when several species became study material for biological research and particularly for genetics. It is worth noting that the Drosophila model has never been restricted to only one species and more than 200 species of Drosophila have been cultured for laboratory research. Today most of the species under study are provided by stock centres, the Tucson and the Ehime centres being the two most important. Despite the name 'Drosophila stock centres' both provide species of other genera. The Tucson Drosophila Species Stock Center (http://stockcenter.arl.arizona.edu/) provides subcultures of approximately 240 different Drosophila species. These include species of Chymomyza, Hirtodrosophila, Samoaia, Scaptodrosophila, Scaptomyza, Zaprionus as well as the Hawaiian 'Drosophila'. The Ehime Drosophila stock centre (http://kyotofly.kit.jp/cgi-bin/ ehime/index.cgi) maintains 400 strains of 50 species and distributes these genetic resources to Drosophila researchers worldwide. These too include Colocasiomyia, Chymomyza, Hirtodrosophila, Scaptodrosophila and Zaprionus. Thus it is clear that, for geneticists, the name 'Drosophila' does not mean specifically D. melanogaster but the family DROSOPHILIDAE (and so includes D. melanogaster). Fly geneticists used to refer to the model species as 'melanogaster' instead of 'Drosophila' because the research community is aware that many species are used as study material. Research is also carried out on albomicans, ananassae, immigrans, indianus, kikkawai, mojavensis, virilis and, whichever genus individual species belong to, all are considered to be 'Drosophila'. This usage suggests that, even under the name of Sophophora melanogaster, the species will still be considered as a 'Drosophila' and the term can be used in the titles and keywords of future publications. We should also note 137 Bulletin of Zoological Nomenclature 65(2) June 2008 that 'drosophila' (without initial upper case and not italicized) would be more appropriate. The extent of paraphyly in Drosophila The paraphyly of the voluminous genus Drosophila has been recognized for decades, and by numerous authors, for example Throckmorton (1975) in his phylogenetic analysis. Nonetheless, the only work to really address the question was the cladistic study by Grimaldi (1990). This contribution was so important that the classification it established for drosophilid species has remained fundamentally unchanged ever since. However, he admitted that a definitive, comprehensive study of relationships between subgenera and species groups in Drosophila remained to be done. Van der Linde et al. (BZN 64: 238-242) mentioned Hawaiian 'Drosophila' as a clade within Drosophila (s.s.), however this situation has not been fully accepted. Grimaldi (1990) grouped those species in the genus Idiomyia Grimshaw, 1901 and he suggested that calling Idiomyia (s.l.) 'Drosophila', despite the morphological evidence to the contrary, would be 'diluting the diagnosis of the genus Drosophila, as a monophyletic group, of biological meaning.' Moreover the Hawaiian 'Drosophila' are generally recognized to be the sister group of the genus Scaptomyza. Therefore it would be illogical to downgrade the Hawaiian 'Drosophila' but not Scaptomyza under the genus Drosophila. Despite some unfounded contestation the Hawaiian 'Drosophila' were considered to belong to Idiomyia by Grimaldi (1990) and are still classified in this way in Bachli's database (http://taxodros.unizh.ch/). Therefore, the monophyletic genus Drosophila, as defined by Grimaldi (1990), consists of only three major clades: Sophophora and the immigrans-tripunctata and virilis-repleta radiations of the subgenus Drosophila. Today there are good arguments to upgrade Sophophora to generic status, particularly thanks to the meticulous work of M.J. Toda and his team (e.g. Hu & Toda, 2001). Moreover, the results of their morphological analyses are also supported by molecular data. Nevertheless, this does not justify disruption of the subgenus Drosophila as there is no morphological analysis indicating its paraphyly and most molecular analyses fail to resolve the branch order in this part of the phylogeny. Van der Linde et al. (BZN 64, pp. 238-242) argue that various genera are positioned within Drosophila (s.l.). In fact these genera are positioned between Sophophora and Drosophila (s.s.), or between the Hawaiian 'Drosophila' and the radiations of Drosophila (s.s.), but there is no strong evidence that any such genera intercalate between the immigrans-tripunctata and virilis-repleta radiations. If molecular analysis eventually suggests the paraphyly of Drosophila (s.s.) it would be necessary to study the morphology more deeply. As far as is known, however, the genus Drosophila is monophyletic once the subgenus Sophophora is removed (Grimaldi, 1990; Hu & Toda, 2001). Additional references Grimaldi, D.A. 1990. A phylogenetic, revised classification of the genera in the Drosophilidae (Diptera).