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The sequences generated in this study were deposited in GenBank (Accession number: MW021146–MW021160).; International audience; The Asian citrus psyllid, Diaphorina citri, is a major threat to citrus production worldwide, as it transmits 'Candidatus Liberibacter asiaticus', the pathogen associated with the devastating Asian form of huanglongbing. The psyllid has spread widely from its native South Asia during the past 300 years, most recently to Africa. We report the first population genomic analyses of D. citri in Kenya and La Reunion based on next-generation sequencing of their mitochondrial genomes. We analyzed mitochondrial sequences of 264 D. citri individuals to establish genetic relationships among accessions from D. citri populations from Asia, North America and Africa. Haplotype network analysis indicated that the psyllids from Kenya were genetically close to an accession from Cambodia, and distinctly different to those from La Reunion. These findings revealed populations in southern Indochina would be the likely source of the D. citri introduction into East Africa through human-mediated transfer of psyllid-infested plants.

International audience; The fast development of aquaculture over the past decades has made it the main source of fish protein and led to its integration into the global food system. Mostly originating from inland production systems, aquaculture has emerged as strategy to decrease malnutrition in low-income countries. The Nile tilapia (Oreochromis niloticus) was introduced to Madagascar in the 1950s, and is now produced nationally at various scales. Aquaculture mostly relies on fry harvested from wild populations and grow-out in ponds for decades. It has recently been diversified by the introduction of several fast-growing strains. Little is known how local genetic diversity compares to recently introduced strains, although high and comparable levels of genetic diversity have previously been observed for both wild populations and local stocks. Our study compares DNA barcode genetic diversity among eight farms and several strains belonging to three species sampled. DNA-based lineage delimitation methods were applied and resulted in the detection of six well differentiated and highly divergent lineages. A comparison of DNA barcode records to sequences on the Barcode of Life Data System (BOLD) helped to trace the origin of several of them. Both haplotype and nucleotide diversity indices highlight high levels of mitochondrial genetic diversity, with several local strains displaying higher diversity than recently introduced strains. This allows for multiple options to maintain high levels of genetic diversity in broodstock and provides more options for selective breeding programs.

Elaeidobius kamerunicus Faust (Coleoptera, Curculionidae) is one of the specific pollinators on inflorescences of the African oil palm Elaeis guineensis Jacquin. This derelomine weevil is native to tropical Africa. During the late 20th century, it was introduced into all tropical regions where E. guineensis is grown, in order to improve its pollination and fruit set. Despite an overall success, a decline in pollination efficiency has been documented in several regions. In this study, we reconstructed a multilocus phylogeography of the world populations of E. kamerunicus, in order to explore its genetic diversity in its native and introduced ranges. Our results showed that African populations of E. kamerunicus are forming two differentiated mitochondrial clusters in West and central Africa, forming a contact zone along the Cameroon Volcanic Line. The existence of this sharp contact zone along this weak altitudinal barrier suggests that other parameters, such as climate, may be driving the distribution of populations. A differential genetic structure between mitochondrial and nuclear genes, and the strong level of genetic structure of the mitochondrial gene, also suggest sex-biased dispersal in this species, with males dispersing more than females. The genetic structure inferred from Asian and South American populations suggests that they originate from populations of both western and central tropical Africa and that a bottleneck has probably been experienced by these populations.

International audience; Phlyctinus callosus (Schoenherr, 1826) (Curculionidae, Entiminae, Oosomini) is a species native to the Western Cape province of the Republic of South Africa. It is regarded as a key pest of orchards and vineyards. Detailed observations of its morphology and ecology have shown this species to be a complex of closely related species. In this study we describe the species of this complex, provide morphological and molecular diagnostic tools to distinguish between species, and review their distribution and host plant associations. In all, six species are recognized in the P. callosus complex and five are described as new (P. grootbosensis Haran sp. nov., P. xerophilus Haran sp. nov., P. planithorax Haran sp. nov., P. littoralis Haran sp. nov., P. aloevorus Haran sp. nov.). Sequences of the mitochondrial gene used (cytochrome oxidase I, COI) indicated that P. xerophilus Haran sp. nov. might comprise several cryptic species for which stable morphological features could not be identified at this stage. The species of the genus Phlyctinus appear to be primarily associated with various Asteraceae found in humid, sandy and disturbed habitats.

The genus Elaeidobius Kuschel, 1952 (Curculionidae, Curculioniae, Derelomini) is an Afrotropical genus associated with the male inflorescences of the oil palm Elaeis guineensis Jacq. The activity of species in this genus is critical for pollen transportation and for the fruit set of this economically important palm. In this study, the genus Elaeidobius was revised using an integrative taxonomic approach, combining traditional taxonomic treatment of species and an analysis of sequences of mitochondrial genes (COI and COII). A total of eight species is now recognized: five now formally included within it [E. bilineatus Hustache, 1924) comb. nov., E. kamerunicus (Faust, 1898) comb. nov., E. plagiatus (Fåhraeus, 1844) comb. nov., E. singularis (Faust, 1898) comb. nov., E. subvittatus Faust, 1898)], one transferred here from the genus Prosoestus to the genus Elaeidobius, E. spatulifer (Marshall, 1950) comb. nov., and two newly described species (E. pilimargo Haran & Kuschel sp. nov., E. piliventris Haran & Kuschel sp. nov.). The following new synonymies are proposed: Prosoestus armatus Voss, 1956 = E. bilineatus (Hustache, 1924) comb. nov. and Derelomus uelensis Hustache = E. singularis (Faust, 1898). An illustrated key to the species is provided with photographs of the adult habitus and male genitalia.

International audience; Recent phylogenetic studies and taxonomic reviews have led to nearly complete resolution of the phylogenetic divisions within the old world rats and mice (Muridae, Murinae). The Micromys division and Pithecheir division are two notable exceptions where groupings of species into these divisions based on morphology and arboreal lifestyle have not been supported by phylogenetic evidence. Several enigmatic species from these divisions have been missing from molecular studies, preventing a rigorous revision of phylogenetic relationships. In this study, we sequenced for the first time one mitochondrial and three nuclear genes from South-East Asian keystone species of these two arboreal divisions: Hapalomys delacouri (Micromys division), Lenothrix canus and Pithecheir parvus (Pithecheir division). We also complemented the molecular data already available for the two divisions with new data from Sundaic Chiropodomys, Indian Vandeleuria oleracea and the recently described Sulawesian Margaretamys christinae. Using this new phylogenetic framework and molecular dating methodologies, our study allows some more detailed classification of the former Micromys and Pithecheir divisions, while confirming their polyphyletic status. Specifically, the former Micromys division should now be split into four monotypic divisions: Chiropodomys, Hapalomys, Micromys and Vandeleuria divisions. The former Pithecheir division is likely to be refined and restricted to Pithecheir and probably Pithecheirops, whereas Lenothrix and Margaretamys should now be recognized as representatives of the Dacnomys division. Our findings have profound implications with regard to the systematics of Murinae, as well as to the early evolution of murine morphology and dental characters.

WOS: 000393307200217, PubMed ID: 26540489, The bank vole, Myodes glareolus, lives in deciduous forests throughout the Palearctic region. In Turkey, this species is distributed only in northern Anatolia (the Black Sea region) where these forests exist. This study reveals genetic differentiation among bank vole populations based on two regions of mitochondrial DNA (cytochrome b and D-loop). Populations in northern Anatolia are divided into two genetic lineages (the "eastern" and "western Black Sea" lineages) by the Kizilirmak Valley. While the western Black Sea lineage is close to the Balkan lineage, in accordance with their geographical proximities, surprisingly, the Uludag lineage, also situated in Western Turkey appears related to the eastern Black Sea population. The divergence time analyses suggest a separation between the Balkan and Turkish groups around 0.26 Mya, whereas the split between the eastern and western Black sea lineages appeared a little bit later (0.20 Mya). Our results suggest that regional refuges existed for this species in Turkey and that small-scale habitat fragmentations led to genetic differentiations between Myodes populations., Scientific Research Projects Office of the Ankara University-BAPRO [09B4240001], This study was sponsored by the Scientific Research Projects Office of the Ankara University-BAPRO (Project: 09B4240001).

Correspondence and present address: Benjamin Pélissié, CIRAD, BIOS,UR-106, TA A-50/D, Campus de Baillarguet, 34398 Montpellier Cedex 5, France. E-mail: benjamin.pelissie@gmail.com; International audience; Specifying species boundaries is often tricky, because advanced biomolecular analyses can reveal that morphologically similar individuals in fact belong to distinct species. This is frequently the case when populations previously considered as a single polyphagous taxon prove to consist of several genetically distinct taxa using different resources, e.g., among insect parasitoids. Macrocentrus cingulum Brischke (Hymenoptera: Braconidae), a parasitoid of the genus Ostrinia (Lepidoptera: Crambidae) feeding on various host plants across the world, is one of them. In Western Europe, M. cingulum has never been found in Ostrinia nubilalis (Hubner) populations feeding on maize, although it heavily parasitizes sympatric Ostrinia scapulalis Walker populations feeding on mugwort. In contrast, it contributes to pest control of Ostrinia furnacalis Guenee feeding on maize in Asia and O. nubilalis feeding on maize in America, suggesting that European and Asian M. cingulum populations might form two distinct taxa. We tested this hypothesis by conducting phylogenetic and population genetic analyses based on two mitochondrial and two nuclear genes, on 97 M. cingulum individuals sampled in Asia, USA, and Europe. Our analyses not only suggest that all sampled M. cingulum probably belong to the same species, but also show a significant genetic differentiation between individuals originating from Europe on the one hand and Asia/USA on the other, which correlates with infestation patterns. Moreover, they show that American specimens are closely related to Asian ones, consistent with historical records about M. cingulum introductions into the USA in the 1920s and 1930s to control expanding O. nubilalis populations. Combining these results with what is known about the evolutionary history within the genus Ostrinia, we offer a candidate evolutionary scenario that is amenable to future empirical testing.

[Background] The European mink (Mustela lutreola, L. 1761) is a critically endangered mustelid, which inhabits several main river drainages in Europe. Here, we assess the genetic variation of existing populations of this species, including new sampling sites and additional molecular markers (newly developed microsatellite loci specific to European mink) as compared to previous studies. Probabilistic analyses were used to examine genetic structure within and between existing populations, and to infer phylogeographic processes and past demography., [Results] According to both mitochondrial and nuclear microsatellite markers, Northeastern (Russia, Estonia and Belarus) and Southeastern (Romania) European populations showed the highest intraspecific diversity. In contrast, Western European (France and Spain) populations were the least polymorphic, featuring a unique mitochondrial DNA haplotype. The high differentiation values detected between Eastern and Western European populations could be the result of genetic drift in the latter due to population isolation and reduction. Genetic differences among populations were further supported by Bayesian clustering and two main groups were confirmed (Eastern vs. Western Europe) along with two contained subgroups at a more local scale (Northeastern vs. Southeastern Europe; France vs. Spain)., [Conclusions] Genetic data and performed analyses support a historical scenario of stable European mink populations, not affected by Quaternary climate oscillations in the Late Pleistocene, and posterior expansion events following river connections in both North- and Southeastern European populations. This suggests an eastern refuge during glacial maxima (as already proposed for boreal and continental species). In contrast, Western Europe was colonised more recently following either natural expansions or putative human introductions. Low levels of genetic diversity observed within each studied population suggest recent bottleneck events and stress the urgent need for conservation measures to counteract the demographic decline experienced by the European mink., This work was partially funded by three LIFE projects (“Conservación del visón europeo (Mustela lutreola) en “Castilla León” LIFE 00/NAT/E7229, La Rioja” LIFE 00/NAT/E7331 and “Álava” LIFE 00/NAT/E7335), and grants from the Diputación Foral de Álava and the University of the Basque Country (GIU 06/09) awarded to BJGM. The Basque Government (BG) also financed this study (project numbers IT317-10; IT575-13)., We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

Numbers of substitutions per site for 15 protein-coding genes and six introns of the plant mitochondria were estimated to compare modes and tempos of evolution between exons and introns, and numbers of insertions–deletions per site also were investigated in introns. Intra-gene homogeneity of numbers of substitutions per site was assessed further among different taxa and between mitochondrial and nuclear paralogs translocated from the mitochondrial genome. Gene-to-gene differences in numbers of substitutions per site were found to be higher for nonsynonymous than synonymous sites, and this could be due to differential selection if mutation rate is assumed constant for the genome. Some mitochondrial genes have evolved as fast as chloroplast genes, thus faster than previously thought. For cox I, relative rate tests showed that woody taxa evolved slower than annuals at synonymous sites. Generation time, population size, and speciation rate are likely factors involved in this rate heterogeneity. Introns were less constrained than their adjacent exons for both overall numbers of substitutions per site and indels, but, on average, overall numbers of substitutions per site for introns were similar to numbers of synonymous substitutions per site for exons. Correlations were generally high between numbers of substitutions and numbers of indels per site for the same intron. Mitochondrial genes transferred to the nucleus had an accelerated rate of substitution per site, which was most significant at synonymous sites. These differences between paralogs in two different genomes are likely the result of different mutation rates.

The melon fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae) is an agricultural pest of major significance worldwide that primarily attacks cucurbit crops. In Reunion Island, it represents the main tephritid pest on cucurbits. In this paper, we provide a genetic characterization of populations of B. cucurbitae from Reunion Island and investigate their geographical origin using ten microsatellite loci at two mitochondrial gene fragments. Microsatellites reveal the occurrence of three different genetic clusters of B. cucurbitae in Reunion Island, all clearly distinguishable from their African and Asian relatives. These three clusters are sympatric and show no signs of recent bottlenecks. Levels of gene flow among clusters are relatively high, yet gene flow also occurs with populations from the African continent and, to a lesser extent, from Asia. The B. cucurbitae clusters show distinct distributions across eastern and western locations in Reunion Island (but not at different altitudes or between wild and cultivated host plants or between sampling periods), and their abundance is also correlated with the average amount of rainfall. Microsatellite and sequence analyses suggest Africa as the most probable source area for populations of B. cucurbitae in Reunion Island.

A survey on 148 clones of the aphid Rhopalosiphum padi from 11 widespread localities has been carried out to study the genetic structure of populations of this species as revealed by mitochondrial DNA restriction site and length polymorphisms as well as by restriction site analysis of a maternally inherited plasmid carried by the aphid eubacterial endosymbiont Buchnera aphidicola. Our results support the existence in the area under study of two main aphid maternal lineages strikingly coincidental with the two main reproductive categories displayed by this species. Those aphid clones possessing an incomplete life cycle that lacks the sexual phase (anholocyclic or androcyclic clones) show mitochondrial DNA (mtDNA) haplotype I and plasmid haplotype I, whereas those clones displaying the complete life cycle (holocyclic clones) posses some other distinct mtDNA haplotypes closely related to each other and plasmid haplotype II. While restriction-site analysis of maternally inherited markers points to a relatively ancient origin of anholocycly/androcycly (between 460 000 and 1 400 000 years) followed by interrupted gene flow with respect to the ancestral holocyclic population, mtDNA size variation also suggests that historical stochastic processes have a different effect on the evolution of both main aphid lineages. Evidence of occasional nuclear gene flow between lineages and its consequences on the correspondence between maternally inherited haplotypes and life cycle are also presented and discussed.

9th International Congress on Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases OCT 30-NOV 01, 2008 Irvine, CA; International audience; The tropical and subtropical parthenogenetic plant-parasitic nematodes Meloidogyne are polyphagous major agricultural pests. Implementing proper pest management approaches requires a good understanding of mechanisms, population structure, evolutionary patterns and species identification. A comparative analysis of the mitochondrial vs nuclear diversity was conducted on a selected set of Meloidogyne lines from various geographic origins. Mitochondrial co2-16S sequences and AFLP markers of total DNA were applied because of their ability to evidence discrete genetic variation between closely related isolates. Several distinct maternal lineages were present, now associated with different genetic backgrounds. Relative discordances were found when comparing mitochondrial and nuclear diversity patterns. These patterns are most likely related to crosses within one ancestral genetic pool, followed by the establishment of parthenogenesis. In this case, they mirror the genetic backgrounds of the original individuals. Another aspect could be that species emergence was recent or on process from this original genetic pool and that the relatively short time elapsed since then and before parthenogenesis settlement did not allow for lineage sorting. This could also be compatible with the hypothesis of hybrids between closely related species. This genetic pool would correspond to a species as defined by the species interbreeding concept, but also including the grey area of species boundaries. This complex process has implications on the way genotypic and phenotypic diversity should be addressed. The phenotype of parthenogenetic lines is at least for part determined by the ancestral amphimictic genetic background. A direct consequence is, therefore, in terms of risk management, the limited confidence one can have on the direct association of an agronomic threat to a simple typing or species delineation. Risk management strategies and tools must thus consider this complexity when designing quarantine implementation, resistance breeding programmes or molecular diagnostic

In southern Europe, orbiviral diseases such as bluetongue (BT) have been assumed to have been largely transmitted by the classical Afro-Asian vector Culicoides imicola Kieffer (Diptera: Ceratopogonidae). Recent outbreaks have occurred in regions where C. imicola is normally absent, supporting the theory that other species belonging to the Obsoletus or Pulicaris complexes may play a role in BT virus transmission. Investigations of the ecology of the species within the former group are hampered by females of member species being extremely difficult to separate by classical morphology. To allow straightforward separation of these species in France, a multiplex polymerase chain reaction-based on internal transcribed spacer (ITS)-1 rDNA was developed to distinguish between Culicoides chiopterus Meigen, Culicoides dewulfi Goetghebuer, Culicoides montanus Shakirjanova, Culicoides obsoletus Meigen, and Culicoides scoticus Downes & Kettle. This tool will be useful in defining both the vector role and larval biotopes of these species in Europe.

In the Americas and Caribbean, the lethal yellowing (LY) phytoplasma causes a disease of palms transmitted by the leafhopper Myndus crudus (family, Cixiidae), which may not be the sole vector. In Vanuatu and Ghana LY-like diseases also are rampant in coconut palm but M. taffini is thought to be a vector. Recently, high mortality in disease-resistant palms has occurred widely. The availability of a molecular marker would make possible the tracking of distribution and dispersal behaviors of Myndus species in relation to epidemic and non-epidemic areas. We employed PCR and mtCOI primers [F-C1-J-2195, R-L2-N-3014] to amplify from DNA extracts a 780 bp fragment. Phylogenetic analysis sorted putative Myndus spp. into three main clades: adiopodoumeensis (Ghana), crudus (Caribbean), and taffinii (Vanuvatu), the latter which comprised two sister groups. A fourth Myndus spp. from Oaxaca MEX grouped uniquely from other New World collections and herein has been identified as a new, putative vector species. (Texte intégral)

International audience

A PCR analysis of mitochondrial (mt) genomes of cybrid rapeseed plants revealed substoichiometric concentrations of molecules bearing different configurations of the gene (orf138) responsible for Ogura cytoplasmic male sterility (CMS). These substoichiometric molecules are also present in plants bearing the unmodified Ogura cytoplasm. In one cybrid family, which shows reversion of the male sterile phenotype, we observed changes in the respective proportions of these molecules. The phenotypic (sterility-fertility) reversion occurs as a result of a modification of the equilibrium state between the different forms of the orf138 gene and is very probably determined by the level of expression of this gene. Stable situations are always characterized by one predominant form; the others, when present, exist in substoichiometric amounts. We report results indicating that the different forms of the orf138 gene are continuously interconverted by recombination and that an active mechanism is involved in the maintenance of some substoichiometric molecules.

International audience

A method is presented for the estimation of nucleotide diversity and genetic structure of populations from RAPD (random amplified polymorphic DNA) data. It involves a modification of the technique developed by Lynch and Crease (1990) for the case of restriction sites as survey data. As new elements the method incorporates (i) dominance correction, (ii) values of asexual reproduction of the populations sampled, and (iii) an analytical variance of the number of nucleotide substitutions per site. Sampling was carried out at two geographic scales for three aphid species. At a macrogeographic scale, populations of Rhopalosiphum padi did not show statistical genetic differentiation. Aphis gossypii and Myzus persicae, which were sampled at a microgeographic scale, showed a higher genetic differentiation than R. padi, it being statistically significant in M. persicae. The major sources of sampling variance within- and between-populations were found to be nucleotide (i.e., the number of alleles used as a function of the number of primers used) and population (i.e., sample size) sampling. Extremely low estimates of nucleotide diversity were obtained for the species studied here. This result is consistent with previous reports on genetic diversity for the same or other aphid species which were based on allozyme polymorphism, mitochondrial DNA variation and qualitative analyses of RAPDs.