Y. Y. Che and J. , Large-scale phylogenetic analyses provide insights into unrecognized diversity and historical biogeography of Asian leaf-litter frogs, genus Leptolalax (Anura: Megophryidae), Mol. Phylogenet. Evol, vol.124, pp.162-171, 2018.

,

C. De-bekker, R. A. Ohm, H. C. Evans, A. Brachmann, and D. P. Hughes, Ant-infecting Ophiocordyceps genomes reveal a high diversity of potential behavioral manipulation genes and a possible major role for enterotoxins, Sci. Rep, vol.7, pp.1-13, 2017.

D. M. De-vienne, G. Refrégier, M. López-villavicencio, A. Tellier, M. E. Hood et al., Cospeciation vs host-shift speciation: Methods for testing, evidence from natural associations and relation to coevolution, New Phytol, vol.198, pp.347-385, 2013.

A. L. Delcher, Fast algorithms for large-scale genome alignment and comparison, Nucleic Acids Res, vol.30, pp.2478-2483, 2002.

C. Fi?er, C. T. Robinson, and F. Malard, Cryptic species as a window into the paradigm shift of the species concept, Mol. Ecol, vol.27, pp.613-635, 2018.

E. Fournier and T. Giraud, Sympatric genetic differentiation of a generalist pathogenic fungus, Botrytis cinerea, on two different host plants, grapevine and bramble, J. Evol. Biol, vol.21, pp.122-132, 2008.

F. Gao, C. Ming, W. Hu, and H. Li, New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era, G3 Genes|Genomes|Genetics, vol.6, pp.1563-1571, 2016.

N. M. Gerardo, S. R. Jacobs, C. R. Currie, and U. G. Mueller, Ancient host-pathogen associations maintained by specificity of chemotaxis and antibiosis, PLoS Biol, vol.4, pp.1358-1363, 2006.

N. M. Gerardo, U. G. Mueller, S. L. Price, and C. R. Currie, Exploiting a mutualism: Parasite specialization on cultivars within the fungus-growing ant symbiosis, Proc. R. Soc. B Biol. Sci, vol.271, pp.1791-1798, 2004.

T. Giraud, R. Yockteng, M. López-villavicencio, G. Refrégier, and M. E. Hood, Mating system of the anther smut fungus Microbotryum violaceum: Selfing under heterothallism, Eukaryot. Cell, 2008.

G. M. Hewitt, Quaternary Genetic consequences of climatic oscillations in the Genetic consequences of climatic oscillations in the Quaternary, 2012.

D. P. Hughes, S. B. Andersen, N. L. Hywel-jones, W. Himaman, J. Billen et al., Behavioral mechanisms and morphological symptoms of zombie ants dying from fungal infection, BMC Ecol, vol.11, 2011.

N. Kobmoo, D. Wichadakul, N. Arnamnart, . Rodríguez-de-la, R. C. Vega et al., A genome scan of diversifying selection in Ophiocordyceps zombie-ant fungi suggests a role for enterotoxins in co-evolution and host specificity, Mol. Ecol, vol.27, pp.3582-3598, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01921814

S. Kurtz, A. Phillippy, A. L. Delcher, M. Smoot, M. Shumway et al., Versatile and open software for comparing large genomes, Genome Biol, vol.5, 2004.

A. Laciny, I. S. Druzhinina, L. Lim, A. Kopchinskiy, H. Zettel et al., Colobopsis explodens sp. n., model species for studies on "exploding ants" (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group, Zookeys, vol.751, pp.1-40, 2018.

B. R. Larget, S. K. Kotha, C. N. Dewey, and C. Ané, BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis Bret, Bioinformatics, vol.26, pp.2910-2911, 2010.

H. Li, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, 2013.

J. T. Lifjeld, When taxonomy meets genomiocs: lessons from a common songbird, Mol. Ecol, pp.2901-2903, 2015.

R. G. Loreto, S. L. Elliot, M. L. Freitas, T. M. Pereira, and D. P. Hughes, Long-term disease dynamics for a specialized parasite of ant societies: A field study, PLoS One, vol.9, 2014.

J. J. Luangsa-ard, R. Ridkaew, K. Tasanathai, D. Thanakitpipattana, and N. Hywel-jones, Ophiocordyceps halabalaensis: A new species of Ophiocordyceps pathogenic to Camponotus gigas in Hala Bala Wildlife Sanctuary, Southern Thailand, Fungal Biol, vol.115, pp.608-614, 2011.

D. R. Matute and V. E. Sepúlveda, Fungal species boundaries in the genomics era, Fungal Genet. Biol, vol.103249, 2019.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010.

A. Miraldo, S. Li, M. K. Borregaard, A. Flórez-rodríguez, S. Gopalakrishnan et al., An Anthropocene map of genetic diversity, Science, vol.353, pp.1532-1535, 2016.

M. C. Molina, R. Del-prado, P. K. Divakar, D. Sánchez-mata, and A. Crespo, Another example of cryptic diversity in lichen-forming fungi: The new species Parmelia mayi (Ascomycota: Parmeliaceae), Org. Divers. Evol, vol.11, pp.331-342, 2011.

S. Mongkolsamrit, N. Kobmoo, K. Tasanathai, A. Khonsanit, W. Noisripoom et al., Life cycle, host range and temporal variation of Ophiocordyceps unilateralis/Hirsutella formicarum on Formicine ants, J. Invertebr. Pathol, vol.111, 2012.

S. Mongkolsamrit, W. Noisripoom, D. Thanakitpipattana, T. Wutikhun, J. W. Spatafora et al., Disentangling cryptic species with isaria-like morphs in Cordycipitaceae, Mycologia, vol.110, pp.230-257, 2018.

B. Pfeifer, U. Wittelsbürger, S. E. Ramos-onsins, and M. J. Lercher, PopGenome: An efficient swiss army knife for population genomic analyses in R, Mol. Biol. Evol, 2014.

J. K. Pickrell and J. K. Pritchard, Inference of Population Splits and Mixtures from GenomeWide Allele Frequency Data, PLoS Genet, vol.8, 2012.

P. Pramual, C. Kuvangkadilok, V. Baimai, and C. Walton, Phylogeography of the black fly Simulium tani (Diptera: Simuliidae) from Thailand as inferred from mtDNA sequences, 2005.

. Ecol, , vol.14, pp.3989-4001

S. Purcell, B. Neale, K. Todd-brown, L. Thomas, M. A. Ferreira et al., PLINK: a tool set for whole-genome association and population-based linkage analyses, Am. J. Hum. Genet, vol.81, pp.559-575, 2007.

A. Raj, M. Stephens, and J. K. Pritchard, fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets, Genetics, vol.197, pp.573-589, 2014.

,

F. Ronquist, M. Teslenko, P. Van-der-mark, D. L. Ayres, A. Darling et al., MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Syst. Biol, vol.61, pp.539-542, 2012.

F. Rousset, Genetic Differentiation and Estimation of Gene Flow from F-Statistics Under Isolation by Distance, Genetics, vol.145, pp.1219-1228, 1997.

R. Savary, F. G. Masclaux, T. Wyss, G. Droh, J. Cruz-corella et al., A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis, ISME J, vol.12, pp.17-30, 2018.

L. Scrucca, M. Fop, T. B. Murphy, and A. E. Raftery, mclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models, R J, vol.8, pp.289-317, 2016.

V. E. Sepúlveda, R. Marquez, D. A. Turissini, W. E. Goldman, and D. R. Matute, Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum, vol.8, pp.1339-1356, 2017.

S. Sittipraneed, D. Sihanuntavong, and S. Klinbunga, Genetic differentiation of the honey bee (Apis cerana) in Thailand revealed by polymorphism of a large subunit of mitochondrial ribosomal DNA, Insectes Sociaux, vol.48, pp.266-272, 2001.

B. T. Smith, G. F. Seeholzer, M. G. Harvey, A. M. Cuervo, and R. T. Brumfield, A latitudinal phylogeographic diversity gradient in birds, PLoS Biol, vol.15, pp.1-24, 2017.

,

T. H. Struck, J. L. Feder, M. Bendiksby, S. Birkeland, J. Cerca et al., Finding Evolutionary Processes Hidden in Cryptic Species, Trends Ecol. Evol, vol.33, pp.153-163, 2018.

E. H. Stukenbrock and J. Y. Dutheil, Fine-Scale Recombination Maps of Fungal Plant, vol.208, pp.1209-1229, 2018.

J. W. Taylor, C. Hann-soden, S. Branco, I. Sylvain, and C. E. Ellison, Clonal reproduction in fungi, Proc. Natl. Acad. Sci, vol.112, pp.8901-8908, 2015.

J. W. Taylor, D. J. Jacobson, S. Kroken, T. Kasuga, D. M. Geiser et al., Phylogenetic Species Recognition and Species Concepts in Fungi, Fungal Genet. Biol, vol.31, pp.21-32, 2000.

I. J. Tsai, D. Bensasson, A. Burt, and V. Koufopanou, Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle, Proc. Natl. Acad. Sci. 105, pp.4957-4962, 2008.

V. T. Tu, G. Csorba, M. Ruedi, N. M. Furey, N. T. Son et al., Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia, Eur. J. Taxon, pp.1-38, 2017.

E. Vercken, M. C. Fontaine, P. Gladieux, M. E. Hood, O. Jonot et al., Glacial refugia in pathogens: European genetic structure of anther smut pathogens on Silene latifolia and Silene dioica, PLoS Pathog, vol.6, 2010.

L. Vincenot, F. Popa, F. Laso, K. Donges, K. H. Rexer et al., Out of Asia: Biogeography of fungal populations reveals Asian origin of diversification of the Laccaria amethystina complex, and two new species of violet Laccaria, Fungal Biol, vol.121, pp.939-955, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02180986

P. S. Ward, B. B. Blaimer, and B. L. Fisher, A revised phylogenetic classification of the ant subfamily Formicinae (Hymenoptera: Formicidae), with resurrection of the genera Colobopsis and Dinomyrmex, Zootaxa, vol.4072, pp.343-357, 2016.

. Fig, S11 Neighbor-net phylogenetic networks for a) Ophiocordyceps camponoti-leonardi, b) O. polyrhachis-furcata and c) O. camponoti-saundersi