Using big data to understand evolutionary patterns in Geometridae and Erebidae, the two most diverse families of Lepidoptera HAMID REZA GHANAVI DEPARTMENT OF BIOLOGY | FACULTY OF SCIENCE | LUND UNIVERSITY List of papers I. Murillo-Ramos L, Brehm G, Sihvonen P, Hausmann A, Holm S, Ghanavi HR, Õunap E, Truuverk A, Staude H, Friedrich E, Tammaru T, Wahlberg N. 2019. A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies. PeerJ 7:e7386 DOI 10.7717/peerj.7386 II. Ghanavi HR, Chazot N, Sanmartín I, Murillo-Ramos L, Duchêne S, Sihvonen P, Brehm G, Wahlberg N. 2020. Biogeography and Diversification Dynamics of the Moth Family Geometridae (Lepidoptera). Manuscript. III. Ghanavi HR, Twort V, Zahiri R, Wahlberg N. 2020. Phylogenomics of Erebidae (Lepidoptera): using old DNA extracts to resolve old phylogenetic questions with whole genome sequencing. Manuscript. IV. Ghanavi HR, Twort V, Hartman T, Zahiri R, Wahlberg N. 2020. The accuracy of mitochondrial genomes for family level phylogenies, the case of erebid moths (Lepidoptera; Erebidae). Manuscript. V. Ghanavi HR, Twort V, Duplouy A. 2020. Exploring nonspecific/bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera). Manuscript. Faculty of Science 956425 Department of Biology 789178 ISBN 978-91-7895-642-5 9 Using big data to understand evolutionary patterns in Geometridae and Erebidae, the two most diverse families of Lepidoptera Hamid Reza Ghanavi DOCTORAL DISSERTATION by due permission of the Faculty of Science, Lund University, Sweden. To be defended at Blå hallen, Ekologihuset, Sölvegatan 37, Lund. On Friday 9th October 2020, at 13h00. Faculty opponent Dr Dimitar Dimitrov Uviversity Museum of Bergen, Norway Organization Document name Doctoral Dissertation LUND UNIVERSITY Date of issue October 2020 Department of Biology Systematic Biology Group Ecology Building SE-22362, Lund. Author: Hamid Reza Ghanavi Sponsoring organization: This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Slodowska-Curie grant agreement No. 6422141 Title and subtitle Using big data to understand evolutionary patterns in Geometridae and Erebidae, the two most diverse families of Lepidoptera Abstract Lepidoptera (moths and butterflies) are one of the most diverse groups of organisms on earth. They have conquered all the continents apart from Antarctica. The reasons of such high diversity are still not clear. One of the first steps to study the causes of such evolutionary success is to have a clear idea of their phylogenetic relationships. In this thesis I focus on the diversity of two of the most diverse families of Lepidoptera, Geometridae with over 23,000 described species and Erebidae with over 24,000 species. In the case of Geometridae I focus in obtaining a robust phylogenetic hypothesis and then study the diversification dynamics and the biogeographical history which have shaped their actual diversity and distribution. In this project I used the most complete dataset of the family in order to study their evolutionary patterns. In the case of the Erebidae family, obtaining a robust phylogenetic hypothesis was more challenging. In the most complete study of the group up to date, using a multi locus Sanger based approach, it was not possible to resolve the deep phylogeny of the family. Therefore, I used high throughput sequencing (HTS) approaches to resolve the complex deep phylogenetic history of the group. In this project I used old DNA extracts of over 10 years old to explore the possibility of using this genetic resource for genomic studies. In addition, I evaluated the accuracy and range of resolution of the mitochondrial genomes in this family. And finally, I explored the alternative possibilities which the HTS approaches offer us to study the presence of symbiotic interactions using genomic data. Key words Lepidoptera, Megadiverse, Diversification, Biogeography, Phylogenomics, Geometridae, Erebidae Classification system and/or index terms (if any) Supplementary bibliographical information Language English ISSN and key title ISBN 978-91-7895-642-5 Recipient’s notes Number of pages 174 Price Security classification I, the undersigned, being the copyright owner of the abstract of the above-mentioned dissertation, hereby grant to all reference sources permission to publish and disseminate the abstract of the above-mentioned dissertation. Signature Date 2020-09-01 Using big data to understand evolutionary patterns in Geometridae and Erebidae, the two most diverse families of Lepidoptera Hamid Reza Ghanavi Cover design by Zahra Saberi Copyright pp 1-xx Hamid Reza Ghanavi Paper 1 © by the Authors (Published) Paper 2 © by the Authors (Manuscript unpublished) Paper 3 © by the Authors (Manuscript unpublished) Paper 4 © by the Authors (Manuscript unpublished) Paper 5 © by the Authors (Manuscript unpublished) Faculty of Science Department of Biology ISBN 978-91-7895-642-5 (print) ISBN 978-91-7895-643-2 (pdf) Printed in Sweden by Media-Tryck, Lund University, Lund 2020 To everyone who taught me something. Table of Contents List of papers........................................................................................................... 8 Autor contribution.................................................................................................. 9 Introduction .......................................................................................................... 11 Background .................................................................................................. 11 Big data and phylogenomics ........................................................................ 12 Diversification analyses ............................................................................... 14 Historical Biogeography .............................................................................. 18 Study System ......................................................................................................... 20 Aims of the Thesis ................................................................................................. 23 Brief Methodology ................................................................................................ 25 Results and Discussion ......................................................................................... 27 Conclusions ........................................................................................................... 32 Acknowledgements ............................................................................................... 34 References ............................................................................................................. 34 List of papers I. Murillo-Ramos L, Brehm G, Sihvonen P, Hausmann A, Holm S, Ghanavi HR, Õunap E, Truuverk A, Staude H, Friedrich E, Tammaru T, Wahlberg N. 2019. A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies. PeerJ 7:e7386 DOI 10.7717/peerj.7386 II. Ghanavi HR, Chazot N, Sanmartín I, Murillo-Ramos L, Duchêne S, Sihvonen P, Brehm G, Wahlberg N. 2020. Biogeography and Diversification Dynamics of the Moth Family Geometridae (Lepidoptera). Manuscript. III. Ghanavi HR, Twort V, Zahiri R, Wahlberg N. 2020. Phylogenomics of Erebidae (Lepidoptera): using old DNA extracts to resolve old phylogenetic questions with whole genome sequencing. Manuscript. IV. Ghanavi HR, Twort V, Hartman T, Zahiri R, Wahlberg N. 2020. The accuracy of mitochondrial genomes for family level phylogenies, the case of erebid moths (Lepidoptera; Erebidae). Manuscript. V. Ghanavi HR, Twort V, Duplouy A. 2020. Exploring non- specific/bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera). Manuscript. 8 Autor contribution I. Contributed in the study conception. Contributed in the study design. Contributed to the data collection. Limited contribution to the analyses. Limited contribution to the manuscript preparation. II. Contributed in the study conception. Contributed in the study design. Collected the data. Performed majority of the analyses. Took the lead in manuscript preparation. III. Contributed in the study conception. Contributed in the study design. Collected the data. Performed all the analyses. Took the lead in manuscript preparation. IV. Contributed in the study conception. Contributed in the study design. Collected the data. Performed all the analyses. Took the lead in manuscript preparation. V. Contributed in the study conception. Contributed in the study design. Collected the data. Limited contribution to the analyses. Took the lead in manuscript preparation. 9 10 Introduction Background Many biologists throughout history have reflected over the diversity of organisms on Earth and the processes which have shaped the actual diversity (Hooker 1854; Darwin 1859; Wallace 1869). Some groups of organisms are very species rich, while others contain only a few representatives. Of course, the amount of time passed since the last most recent common ancestor of a group plays a big role in the diversity. Some smaller groups appeared only very recently. But there are also many cases where different groups of the same age have very different diversities in reality. The process during which the diversity of a group changes is called diversification. Diversification comprises both the proliferation (i.e. speciation) and decline (i.e. extinction) of diversity. The actual observed