Evolutionary histories of symbioses between microsporidia and their amphipod hosts : contribution of studying two hosts over their geographic ranges. Adrien Quiles To cite this version: Adrien Quiles. Evolutionary histories of symbioses between microsporidia and their amphipod hosts : contribution of studying two hosts over their geographic ranges.. Biodiversity and Ecology. Univer- sité Bourgogne Franche-Comté; Uniwersytet lódzki, 2019. English. NNT : 2019UBFCK094. tel- 02878707 HAL Id: tel-02878707 https://tel.archives-ouvertes.fr/tel-02878707 Submitted on 23 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE BOURGOGNE FRANCHE-COMTÉ, France - UMR CNRS 6282 Biogéosciences, Equipe Ecologie Evolutive. UNIVERSITY OF LODZ, Poland - Department of Invertebrate Zoology and Hydrobiology. Philosophiæ doctor in Life Sciences, Ecology and Evolution Adrien QUILES Evolutionary histories of symbioses between microsporidia and their amphipod hosts : contribution of studying two hosts over their geographic ranges. Ph.D defense will be held the 12/13/2019 amphitheatre Monge, 6 boulevard Gabriel, 21000 Dijon, 13/12/2019 Jury : Didier BOUCHON, Professor Poitiers University Reviewer Łukasz KAJTOCH, Doctor Polish Academy of Sciences (Kraków) Reviewer habilitated Isabelle FLORENT,Professor National Museum of Natural History Examiner (Paris) Jerzy BANBURA, Professor Lodz University Examiner, Président Thierry RIGAUD, Research Scientific Research National Center Supervisor director Rémi WATTIER, Doctor Burgundy University Co-supervisor Karolina BACELA, Doctor Lodz University Co-Supervisor habilitated "Imagination is more important than knowledge. For knowledge is limited, whereas imagination embraces the entire world, stimulating progress, giving birth to evolution." Albert Einstein As quoted in "What Life Means to Einstein: An Interview by George Sylvester Viereck" in The Saturday Evening Post (26 October 1929) ACKNOWLEDGMENT Special thanks to; All the people who helped me during the development of my thesis and especially my directors, Thierry RIGAUD, Rémi WATTIER and Karolina BACELA- SPYCHALSKA how trusted me to carry this project, their great availability and all their advices during those 3 years of team work. I would like, to thank the members of my jury to accept the evaluation of this thesis work: Didier BOUCHON, Łukasz KAJTOCH, Isabelle FLORENT, Jerzy BANBURA. I know your time is precious and I am grateful for the comments, criticisms and advice you will give me and I will make the best use of it to improve my work. This work would not have been possible without the support of the Agence Nationale de la Recherche (ANR-15-CE32-0006), and the Polish ministry of science and education (N N303 579439 and N N304 350139), which allowed me, thanks to those research allocation and various financial support, to devote myself serenely to the development of my thesis. Michal GRABOWSKI who help me improving articles and part of the thesis. Tomasz REWICZ, Tomasz MAMOS which provided me inestimable valuable materials of Gammarids samples from all across Europe, to advance this research. Sébastien DUPERRON and Richard CORDEAU for their help and many advise during thesis supervisory committee. This work could not have been carried out without the availability and friendship of Maria TEIXEIRA which showed me the molecular biological lab and help me doing experiences. Manon CHOGNE, Camille SABARLY, Sebastien MOTREUIL and Alexandre BAUER for their friendship in the laboratory and outside. Aleksandra JABLONSKA for her friendship when I was in cold winter time in Poland. The help of tree hard worker third degree student, Nicolas LAMBIN, Vincent GARDET, Laurène CHEVALIER for dissecting, extracting DNA and screening thousands of individuals for microsporidia with me. At the end of this journey, I finally thank those who are dear to me and that I have somewhat neglected during those tree year to complete this thesis. Their attentions and encouragements have accompanied me throughout these years. To my parents, Muriel and Jean-Marc QUILES my brother Robin QUILES. I have a particular thought for my grandmothers, Daisy CAMIER and Nadine QUILES. I would like to thanks all my friends for their support and trust. CONTENTS GENERAL BACKGROUND................................................................................................ 1 SYMBIOSES AND THEIR EVOLUTIONARY CONSEQUENCES ............................. 1 Co-evolutionary patterns and processes ........................................................................ 1 Parasitism ....................................................................................................................... 4 MICROSPORIDIA: the ultimate parasites? ...................................................................... 7 General characteristics and cycle ................................................................................... 7 Phylogeny ...................................................................................................................... 8 GAMMARIDS ................................................................................................................. 13 Distribution and Ecological role .................................................................................. 13 Phylogeny and cryptic diversity .................................................................................. 16 MICROSPORIDIA – AMPHIPODA ASSOCIATIONS ................................................ 19 Ph.D AIMS ...................................................................................................................... 29 REFERENCES ................................................................................................................ 31 CHAPTER I. MICROSPORIDIAN INFECTIONS IN THE SPECIES COMPLEX GAMMARUS ROESELII (AMPHIPODA) OVER ITS GEOGRAPHICAL RANGE: EVIDENCE FOR BOTH HOST–PARASITE CO- DIVERSIFICATION AND RECENT HOST SHIFTS ................................. 47 I.1 ABSTRACT ............................................................................................................ 48 I.2 BACKGROUND ..................................................................................................... 49 I.3 METHODS .............................................................................................................. 51 I.3.1 Sampling .......................................................................................................... 51 I.3.2 Host dissection and total DNA extraction ....................................................... 51 I.3.3 Molecular screening for microsporidians ........................................................ 51 I.3.4 Sequencing of the microsporidian SSU rDNA ................................................ 52 I.3.5 Phylogeny reconstruction for microsporidians ................................................ 52 I.3.6 Geographical distribution of parasites and potential host specificity .............. 53 I.3.7 Host phylogeny and distribution versus microsporidia prevalence and phylogeny ......................................................................................................... 53 I.4 RESULTS ................................................................................................................ 53 I.4.1 Overall prevalence and broad geographical distribution of microsporidian infections in G. roeselii .................................................................................... 53 I.4.2 Microsporidian diversity and phylogenetic position ........................................ 53 I.4.3 Rare infections (i.e. infections not ascribed to the genera Nosema, Cucumispora and Dictyocoela) .............................................................................................. 53 I.4.4 Infections ascribed to the genus Nosema ......................................................... 55 I.4.5 Infections ascribed to the genus Cucumispora ................................................ 57 I.4.6 Infections ascribed to the genus Dictyocoela ................................................... 57 I.4.7 Parasite infections across G. roeselii phylogeny ............................................. 57 I.5 DISCUSSION ......................................................................................................... 60 I.5.1 Diversity of microsporidian infections in Gammarus roeselii across its entire range ................................................................................................................. 60 I.5.2 Infections ascribed to the genus Nosema ......................................................... 61 I.5.3 Infections ascribed to the genus Cucumispora ................................................ 62 I.5.4 Infections ascribed to the genus Dictyocoela ................................................... 62 I.5.5 Comparison of microsporidian diversity in G. roeselii with other gammarid hosts ................................................................................................................