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

Conserved community structure and simultaneous divergence events in the fig wasps associated with Ficus benjamina in Australia and China

Localised patterns of species diversity can be influenced by many factors, including regional species pools, biogeographic features and interspecific interactions. Despite recognition of these issues, we still know surprisingly little about how invertebrate biodiversity is structured across geographic scales. In particular, there have been few studies of how insect communities vary geographically while using the same plant host. We compared the composition (species, genera) and functional structure (guilds) of the chalcid wasp communities associated with the widespread fig tree, Ficus benjamina, towards the northern (Hainan province, China) and southern (Queensland, Australia) edges of its natural range. Sequence data were generated for nuclear and mtDNA markers and used to delimit species, and Bayesian divergence analyses were used to test patterns of community cohesion through evolutionary time. Both communities host at least 14 fig wasp species, but no species are shared across continents. Community composition is similar at the genus level, with six genera shared although some differ in species diversity between China and Australia; a further three genera occur in only China or Australia. Community functional structure remains very similar in terms of numbers of species in each ecological guild despite community composition differing a little (genera) or a lot (species), depending on taxonomic level. Bayesian clustering analyses favour a single community divergence event across continents over multiple events for different ecological guilds. Molecular dating estimates of lineage splits between nearest inter-continental species pairs are broadly consistent with a scenario of synchronous community divergence from a shared "ancestral community". Fig wasp community structure and genus-level composition are largely conserved in a wide geographic comparison between China and Australia. Moreover, dating analyses suggest that the functional community structure has remained stable for long periods during historic range expansions. This suggests that ecological interactions between species may play a persistent role in shaping these communities, in contrast to findings in some comparable temperate systems

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

Single Nucleotide Polymorphisms (SNPs) of Beauveria species

Fungi are rich in complexes of sibling species that need combinations of approaches to be delimited, including with genomic information. Beauveria (Cordycipitaceae, Hypocreales) is a well-known genus of entomopathogenic fungi, used as a biocontrol agent. We present in this study a polyphasic taxonomy regarding two widely distributed complexes of Beauveria: B. asiatica and B. bassiana sensu lato. Some of the genetic groups as previously detected within both taxa were either confirmed or fused using population genomics. High levels of divergence were found between two clades in B. asiatica and between three clades in B. bassiana, supporting their subdivision as distinct species. Fungal culture and DNA extraction.Seventy-eight strains of presumably 12 Beauveria species from BIOTEC culture collection (BCC) and ARS collection of entomopathogenic fungal cultures (ARSEF), including the type strains of known species and strains previously identified as B. bassiana or B. asiatica as well as some unidentified strains. The strains were cultured in 50 ml of potato dextrose broth and incubated at 25 °C for a week. Fungal mycelia were harvested by filtering with a sterilized nylon mesh and washed with ethylene diamine tetraacetic acid (EDTA) and distilled water. DNA extraction was done using a cetrimonium bromide (CTAB)-based method; the DNAs were purified using the high pure PCR template preparation kit (Roche). DNA library construction and sequencingFor whole genome shotgun sequencing of 78 strains, approximately 300 ng of each DNA sample was used for a library construction following the protocol in the MGIEazy FS library prep kit (MGI Tech, Shenzhen, China). The samples were pooled and sequenced in a single lane. Paired-end (150 bp) sequencing was performed on the MGISEQ-2000RS (MGI Tech, Shenzhen, China) according to the manufacturer’s instructions. Data processing and detection of single nucleotide polymorphisms (SNPs) Using the MegaBOLT V1.5.6.11 software package, raw reads were de-multiplexed according to their barcodes and the adapter/barcode sequences were removed. After removing the low-quality regions, clean reads were mapped to the B. bassiana reference genome ARSEF8028 (Valero-Jiménez et al. 2016) using the MegaBOLT V1.5.6.11 alignment software (Minimap2 version 2.11-r797-v03) and the variants were called using GATK HaplotypeCaller version 3.8. SNP markers with poor quality data were filtered out using the following criteria: (a) a minor allele frequency &lt;0.1; (b) depth coverage less than 10x; (c) more than 20% missing data. The ploidy was set as haploid as all the strains were collected from asexual mycelia, i.e. putatively haploid for this ascomycete fungus.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

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

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

VCF files of the final sets of single nucleotice polymorphisms (SNPs) inferred from the common genome reference of Ophiocordyceps polyrhachis-furcata for all samples (file NK_jointSNPs_All-on-OPF_final_NoDel_bi.vcf), from the genome reference of O. camponoti-leonardi for the samples belonging to this species (OCL_jointSNPs_passed_bi.vcf), and from the genome reference of O. camponoti-saundersi (OCS_jointSNPs_passed_bi.vcf).THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

PacBio amplicon sequencing of Cordyceps species

Data of high-throughput ITS-D1/D2 LSU amplicon sequencing, using double barcodes.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

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

International audienc