Population genomics revealed cryptic species within host-specific zombie-ant fungi (Ophiocordyceps unilateralis)

International audienceThe identification and delimitation of species boundaries are essential for understanding speciation and adaptation processes and for the management of biodiversity as well as development for applications. Ophiocordyceps unilateralis sensu lato is a complex of fungal pathogens parasitizing Formicine ants, inducing zombie behaviors in their hosts. Previous taxonomic works with limited numbers of samples and markers led to the "one ant-one fun-gus" paradigm, resulting in the use of ant species as a proxy for fungal identification. Here, a population genomics study with sampling on three ant species across Thailand supported the existence of host-specific species in O. unilateralis s.l. with no footprints of long term introgression despite occasional host shifts and first-generation hybrids. We further detected genetic clusters within the previously delimited fungal species, with each little footprints of recombination, suggesting high levels of inbreeding. The clusters within each of O. camponoti-leonardi and O. camponoti-saundersi were supported by differentiation throughout the genome, suggesting they may constitute further cryptic species parasitizing the same host, challenging the one ant-one fungus paradigm. These genetic clusters had different geographical ranges, supporting different biogeographic influences between the north/center and the south of Thailand, reinforcing the scenario in which Thailand endured compartmentation during the latest Pleistocene glacial cycles

Comprehensive treatise of Hevansia and three new genera Jenniferia, Parahevansia and Polystromomyces on spiders in Cordycipitaceae from Thailand

Collections of pathogenic fungi found on spiders from Thailand were selected for a detailed taxonomic study. Morphological comparison and phylogenetic analyses of the combined ITS, LSU, tef1, rpb1 and rpb2 sequence data indicated that these specimens formed new independent lineages within the Cordycipitaceae, containing two new genera occurring on spiders, i.e. Jenniferia gen. nov. and Polystromomyces gen. nov. Two new species in Jenniferia, J. griseocinerea sp. nov. and J. thomisidarum sp. nov., are described. Two strains, NHJ 03510 and BCC 2191, initially named as Akanthomyces cinereus (Hevansia cinerea), were shown to be part of Jenniferia. By including sequences of putative Hevansia species from GenBank, we also revealed Parahevansia as a new genus with the ex-type strain NHJ 666.01 of Pa. koratensis, accommodating specimens previously named as Akanthomyces koratensis (Hevansia koratensis). One species of Polystromomyces, Po. araneae sp. nov., is described. We established an asexual-sexual morph connection for Hevansia novoguineensis (Cordycipitaceae) with ex-type CBS 610.80 and proposed a new species, H. minuta sp. nov. Based on characteristics of the sexual morph, Hevansia and Polystromomyces share phenotypic traits by producing stipitate ascoma with fertile terminal heads; however, they differ in the shape and colour of the stipes. Meanwhile, Jenniferia produces non-stipitate ascoma with aggregated superficial perithecia forming a cushion. A new morphology of ascospores in Jenniferia is described, illustrated and compared with other species in Cordycipitaceae

Phylogeny and evolution of life-history strategies in the Sycophaginae non-pollinating fig wasps (Hymenoptera, Chalcidoidea)

<p>Abstract</p> <p>Background</p> <p>Non-pollinating Sycophaginae (Hymenoptera, Chalcidoidea) form small communities within <it>Urostigma </it>and <it>Sycomorus </it>fig trees. The species show differences in galling habits and exhibit apterous, winged or dimorphic males. The large gall inducers oviposit early in syconium development and lay few eggs; the small gall inducers lay more eggs soon after pollination; the ostiolar gall-inducers enter the syconium to oviposit and the cleptoparasites oviposit in galls induced by other fig wasps. The systematics of the group remains unclear and only one phylogeny based on limited sampling has been published to date. Here we present an expanded phylogeny for sycophagine fig wasps including about 1.5 times the number of described species. We sequenced mitochondrial and nuclear markers (4.2 kb) on 73 species and 145 individuals and conducted maximum likelihood and Bayesian phylogenetic analyses. We then used this phylogeny to reconstruct the evolution of Sycophaginae life-history strategies and test if the presence of winged males and small brood size may be correlated.</p> <p>Results</p> <p>The resulting trees are well resolved and strongly supported. With the exception of <it>Apocrytophagus</it>, which is paraphyletic with respect to <it>Sycophaga</it>, all genera are monophyletic. The Sycophaginae are divided into three clades: (i) <it>Eukoebelea</it>; (ii) <it>Pseudidarnes</it>, <it>Anidarnes </it>and <it>Conidarnes </it>and (iii) <it>Apocryptophagus</it>, <it>Sycophaga </it>and <it>Idarnes</it>. The ancestral states for galling habits and male morphology remain ambiguous and our reconstructions show that the two traits are evolutionary labile.</p> <p>Conclusions</p> <p>The three main clades could be considered as tribes and we list some morphological characters that define them. The same biologies re-evolved several times independently, which make Sycophaginae an interesting model to test predictions on what factors will canalize the evolution of a particular biology. The ostiolar gall-inducers are the only monophyletic group. In 15 Myr, they evolved several morphological adaptations to enter the syconia that make them strongly divergent from their sister taxa. Sycophaginae appears to be another example where sexual selection on male mating opportunities favored winged males in species with small broods and wingless males in species with large broods. However, some species are exceptional in that they lay few eggs but exhibit apterous males, which we hypothesize could be due to other selective pressures selecting against the re-appearance of winged morphs.</p

Contributions à l'étude des patrons de spéciation et de diversification chez les Ficus et les Chalcidiens mutualistes/parasites associés

Les plantes du genre Ficus entretiennent une relation de mutualisme avec des Chalcidiens pollinisateurs spécifiques Agaonidae, Hymenoptera). Cette relation est exploitée par des Chalcidiens parasites présentant des stratégies écologiques diverses (galligène, inquilins et parasitoïdes). Les relations Ficus-Chalcidiens comportent alors aussi bien des relations plantes-phytophages (Ficus-pollinisateurs, Ficus-galligènes) que des relations à multiples niveaux trophiques caractéristiques de communautés d insectes parasites (Ficusgalligènes, galligènes-inquilins et parasitoïdes). Grâce à des marqueurs moléculaires, nous mettons en évidence les patrons divers de spéciation et de diversification dans trois cas d études. En premier lieu, nous avons mis en évidence une différentiation génétique importante pour Ceratosolen fusciceps, le pollinisateur spécifique de Ficus racemosa, largement réparti de l Inde jusqu à l Australie tropicale. Les différentiations sont très importantes entre différentes régions biogéographiques, suggérant l existence de plusieurs espèce résultant de processus de spéciation allopatrique. En deuxième lieu, nous avons analysé la structuration génétique au sein d un complexe d espèces de Ficus sympatriques à statut taxonomique ambiguë, Ficus oligodon Ficus auriculata Ficus hainanensis. Nous mettons en évidene des traces d hybridation et d introgression locale et des histoires phylogéographiques probablement différentes, ce qui suggère une spéciation en cours, d apparence sympatrique mais qui pourrait avoir été à l origine allopatrique. Enfin, nous avons étudié la diversification dans deux genres africains de la famille Sycophaginae (une famille de Chalcidiens parasites présentant des stratégies écologiques diversifiées) en mettant en relation phylogénie moléculaire avec variations morphologiques. Ces trois cas d étude montrent une large diversité de patrons de spéciation et de diversification dans les relations Ficus-Chalcidiens.Plants of genus Ficus are pollinated by specific pollinating chalcid wasps (Agaonidae, Hymenoptera). This mutualism is exploited by parasitic chalcid wasps presenting a variety of ecological strategies (gallers, inquilines and parasitoids). The Ficus-Chalcid wasp relationships thus comprise plant-phytophagous insect interactions (Ficus-pollinator, icusgaller) as well as complex interactions organized into hierarchical communities of parasitic insects (Ficus-gallers, gallers-inquilines and parasitoids). Using molecular markers, we illustrate a diversity of patterns of speciation and diversification in three study cases. First, we found substantial genetic differentiation between populations of Ceratosolen fusciceps, the specific pollinator of Ficus racemosa which is largely distributed from India to tropical Australia. The differentiation corresponds to biogeographic regions, suggesting the occurrence of more than one species that could have emerged through a process of allopatric speciation. Second, we shed light on the taxonomic status of the sympatric species complex of Ficus oligodon Ficus auriculata Ficus hainanensis by analysing the genetic differentiation between morphotypes. These species show traces of hybridisation and introgression, and present a complex phylogeographic history, suggesting an ongoing process of speciation that could have originated through allopatric differentiation despite coexistence in sympatry. Finally, we studied the diversification pattern in two African genera of the family Sycophaginae (a family of parasitic chalcid wasps presenting diverse ecological strategies) by plotting morphological variation on a molecular phylogeny. These three study cases show the diversity of speciation and diversification patterns in the Ficus-chalcid wasp interaction.MONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Experimental infection of the ant Polyrhachis furcata with Ophiocordyceps reveals specificity of behavioural manipulation

International audienc

Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species

While recent sequencing technologies (third generation sequencing) can successfully sequence all copies of nuclear ribosomal DNA (rDNA) markers present within a genome and offer insights into the intragenomic variation of these markers, high intragenomic variation can be a source of confusion for high-throughput species identification using such technologies. High-throughput (HT) amplicon sequencing via PacBio SEQUEL I was used to evaluate the intragenomic variation of the ITS region and D1–D2 LSU domains in nine Cordyceps species, and the accuracy of such technology to identify these species based on molecular phylogenies was also assessed. PacBio sequences within strains showed variable level of intragenomic variation among the studied Cordyceps species with C. blackwelliae showing greater variation than the others. Some variants from a mix of species clustered together outside their respective species of origin, indicative of intragenomic variation that escaped concerted evolution shared between species. Proper selection of consensus sequences from HT amplicon sequencing is a challenge for interpretation of correct species identification. PacBio consensus sequences with the highest number of reads represent the major variants within a genome and gave the best results in terms of species identification

Tables S1-S3 : Ficus genotypes

Table S1 Genotypes of parents and offspring in controlled crosses. Table S2 Parent and offspring probability of assignation to genetic cluster using Structure. Table S3 Genotypes at the 7 retained loci of 355 individuals used for the global analysis

TreeML_EF

ML tree from the analysis of EF sequence

TreeML_Cytb

ML tree from the analysis of Cytb sequence

Genetic structure and hybridization in the species group of <em>Ficus auriculata</em>: can closely related sympatric <em>Ficus</em> species retain their genetic identity while sharing pollinators?: Genetic structure and hybridization in the species group of Ficus auriculata: can closely related sympatric Ficus species retain their genetic identity while sharing pollinators?

Times Cited: 1 0 1International audienceObligate mutualistic nursery pollination systems between insects and plants have led to substantial codiversification involving at least some parallel cladogenesis, as documented in Yucca, Ficus and Phyllanthaceae. In such systems, pollinators are generally species specific thus limiting hybridization and introgression among interfertile host species. Nevertheless, in the three systems, cases of one insect pollinating several plant species are reported. In most cases, host plants sharing pollinators are allopatric. However, in the case of the species group of Ficus auriculata, forms may co-occur over large parts of their range. We show here that the species group of F. auriculata is constituted by four well-defined genetic entities that share pollinators. We detected hybrids in nature mainly when both parental forms were growing nearby. Controlled crosses showed that F1 offspring could be successfully backcrossed. Hence, despite sharing pollinators and despite hybrid viability, the different forms have preserved their genetic and morphological identity. We propose that ecological differentiation among forms coupled with limited overlap of reproductive season has facilitated the maintenance of these interfertile forms. As such, establishment of pollinator host specificity may not be a prerequisite for sympatric diversification in Ficus