Université Pierre et Marie Curie Ecole doctorale Complexité du Vivant Evolution Paris Seine - UMR CNRS 7138 Equipe Adaptation, Intégration, Réticulation et Evolution Study of modularity in molecular, morphological and linguistic evolution using networks methods Par Jananan PATHMANATHAN Thèse de doctorat en Biologie Evolutive Dirigée par Eric BAPTESTE et Philippe LOPEZ Présentée et soutenue publiquement le 23 Octobre 2017 Devant un jury composé de : Dr Eric BAPTESTE (DR CNRS, Université Pierre et Marie Curie, France) Encadrant Pr Didier CASANE (PR, Université Paris Diderot, France) Rapporteur Pr Tal DAGAN (PR, Université de Kiel, Allemagne) Examinatrice Pr Christophe DESSIMOZ (PR, Université de Lausanne, Suisse) Rapporteur Pr Michel MORANGE (PR, Université Pierre et Marie Curie, France) Examinateur Pr Philippe LOPEZ (PR, Université Pierre et Marie Curie, France) Encadrant Pr Mark RAGAN (PR, Université du Queensland, Australie) Examinateur Dr Hélène TOUZET (DR CNRS, Université Lille 1, France) Examinatrice கற்ற ைகமண் அள) , கல்லாத# உலகள) ! ("Kattrathu Kai Mann Alavu, Kallathathu Ulagalavu") One of my favorite Tamil proverbs ! "What you have learned is a mere handful; What you haven't learned is the size of the world" "Known is a drop unknown is an ocean" Reconstruction of Hallucigenia sparsa by Danielle Dufault. Acknowledgements I think writing the acknowledgments should be the hardest part of the thesis. Especially for me who grown up in the Tamil culture, I need to be careful not to forget anybody and the main problem is deciding which person to thank first! One thing that I have learned during my PhD is that "Networks are cool". So I decided to construct an undirected network of acknowledgments just behind this page. With this network, people can start reading from any node. Nodes are linked randomly ! ERIC PHILIPPE Thank you very much for this great Many thanks for this unforgettable experience! opportunity! You are an amazing evolutionist I still remember our interview, I was a bit EDUARDO and also a wonderful human being. I really afraid the first time I met you. But then few You are an human encyclopedia! enjoyed all our discussions on sciences and daysda ys after the PhD started, I realized how You know almost everything. personal life maters. I like the way you have humblehu mb and friendly person you are. You are I am happy that you are now a explained main aspects of the evolution using oneon e of the person that I admire and who will be permanent member of the team! simple examples. I learned so many things foreverfo re in my memories. from you! I hope we will be still have opportunities to work together. ROMAIN MY FAMILY You are a friendly person. I think the I thank you for your support. I thank my dad for beer smuggling in Jussieu with Gabriel his good words. I thank my mom for her will be one the memorable moments ;) delicious food which were important during my J Be confident, you will do great things down periods with Eric and Philippe ! RAPHAEL I thank my brother to have take the leaderader We spent so many good position during my thesis. I thank my sisterer to J times! You are an excellent let me stay in here house to write my thesis young scientist. For sure one day, you will become as ETIENNE famous as your god Koonin. I enjoyed to work with you and also CHLOE our trip in Montréal I am quite jealous of your dedication ! You with Raphaël. have such a tight time table with all your extra activities. I really like your ability to listen and sleep during talks :) ALEX, RAY & ROB DANIELLE Nice to have collaborated You are a lovely secretary. with you. Your feedbacks I will never forget you. were very useful to improve Thanks for everything ! my programs. PhD EXAMINATION JURY MEMBERS Thanks a lot to have accepted to be in my PhD examination panel. I hope you will like my work ! MARY & JAMES Thanks for your hospitality during our meeting in Manchester. I hope to collaborate with you in more projects ! LATIFA & PAULA FRANÇOIS Thanks for your help It was a great pleasure to during all the events ! have worked with you. I thank you to be part of my PhD committee. ANNESO,ANNE ARNAUD, GABRIEL,GABR JUILIETTE, MARGUERITTEMA & THOMAS ANDREW GUILLAUME Thanks for all the nice You are a people magnet. I am impressed by You are a nice person. I moment that we had ( SCEP, your talent to mesmerize people, most of the will never forget our Journée de doctorants and time women, at the bar. "Désolé mon français trainings at gym. We had parties) est très mauvais ..." these are your hypnotizing nice time with the other lab TO ALL PEOPLE words. I like your habit to take the shower mate especially during FROM IBPS playing with tool kits. after each party J Raph's party J Thanks for everything ! MATTIS You are such a great person. I am always amazed EDU by your multiple talents from juggling to Viva Catalunya ! DOMINIQUE programming and in linguistic. It was a real We had great time together. Thanks for having spent pleasure to have worked with you and spent time time on reading my ERC with you near the Seine during your detox days ;) lab book and signed it on all pages ! UPMC, DOCTORAL SCHOOL & ERC Thank you for everything ! INAKIAK I PhD COMMITTEE MEMBERS Thanks for your helplp on our project ! TO ALL MY Great to have met you.you. Thanks to have been part of my PhD COLLABORATORS committee and for your useful comments Thanks for your collaboration ! about my works. TABLE OF CONTENTS I. INTRODUCTION .................................................................................................................. 1 I.1 MODULARITY ................................................................................................................ 3 I.2 NETWORKS AND BIG DATA ....................................................................................... 5 I.2.1 Data avalanche ........................................................................................................... 6 I.2.2 Sequence Similarity Networks ................................................................................... 9 I.2.3 Computational bottleneck of SSN ........................................................................... 10 I.3 AIMS OF THE THESIS ................................................................................................. 12 II. NETWORK-THINKING IN EVOLUTION ....................................................................... 15 II.1 NETWORKS: A COMPLEMENTARY METHOD TO PHYLOGENETIC ANALYSIS OF EVOLUTION ............................................................................................ 17 Article n°1 .................................................................................................................... 21 II.2 MULTI-LEVEL NETWORKS TO STUDY EVOLUTION ......................................... 59 Article n°2 .................................................................................................................... 63 II.3 APPLICATION OF BIPARTITE GRAPHS FOR THE ANALYSIS OF INTERDOMAIN LGT BETWEEN ULTRASMALL AND LARGER PROKARYOTES. 81 Article n°3 .................................................................................................................... 83 III. MODULARITY IN EVOLUTION .................................................................................... 99 III.1 MOLECULAR EVOLUTION ................................................................................... 101 III.1.1 CompositeSearch: A new tool for studying modularity in molecular evolution . 106 Article n°4 .................................................................................................................. 107 III.1.2 Impact of genomic structure and mobility on gene remodeling in plasmids, allowing the evolution of new dependency systems. ..................................................... 133 Article n°5 .................................................................................................................. 135 III.1.3 Evolution of genes and rules of gene remodeling during the transition and stabilization of animal multicellularity. ......................................................................... 151 Article n°6 .................................................................................................................. 153 III.2 MORPHOLOGICAL EVOLUTION ......................................................................... 169 Article n°7 .................................................................................................................. 171 III.3 LINGUISTIC EVOLUTION ..................................................................................... 201 Article n°8 .................................................................................................................. 205 Article n°9 .................................................................................................................. 225 IV. CONCLUSION ................................................................................................................ 243 V. REFERENCES .................................................................................................................. 249 ANNEX 1 ............................................................................................................................... 259 Article n°10 ................................................................................................................ 261 ANNEX 2 ..............................................................................................................................