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Speciation in the Cladophorales Species Flock of Ancient Lake Baikal

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Speciation in the Cladophorales Species Flock of Ancient Lake Baikal SPECIATION IN THE CLADOPHORALES SPECIES FLOCK OF ANCIENT LAKE BAIKAL by Sergio Diaz Martinez A thesis submitted to the Victoria University of Wellington in fulfilment of the requirements for the degree of Doctor of Philosophy in Marine Biology School of Biological Sciences Victoria University of Wellington Te Whare Wānanga o te Ūpoko o te Ika a Māui 2019 I Front page image: Cladophora compacta from Boedeker et al. (2018) II Abstract Understanding speciation is one of the great challenges in evolutionary biology as many of the processes involved in speciation, as well as the forces leading to morphological and genetic differentiation, are not fully understood. Three main modes of speciation have been described: allopatric, parapatric and sympatric. Sympatric speciation is the most enigmatic mode because in the absence of physical barriers, disruptive selection, assortative mating and hybridization play central roles in reproductive isolation. Although it is accepted that sympatric speciation is possible, only a few examples of this process exist to date. Another common method of speciation in plants and algae is via polyploidization. Recently, a promising system to study speciation in sympatry was discovered: the endemic Cladophorales species flock in ancient Lake Baikal, Russia. The flock consists of sixteen taxa grouped in four genera: Chaetocladiella, Chaetomorpha, Cladophora and Gemmiphora. In spite of their morphological diversity, recent molecular analyses have shown that this is a monophyletic group with low genetic variation and nested within the morphologically simple genus Rhizoclonium. Due to their high number of species, endemism and sympatric distribution, many interesting questions have arisen such as what processes are involved in speciation, and whether this group might be a novel example of sympatric speciation. In this study, we analysed the population genetics of the endemic Baikalian Cladophorales to infer the processes shaping the evolution of the group. First, a set of microsatellites was designed using high-throughput sequencing data. Second, species delimitation methods based on genetic clustering were performed. Third, the population genetics of three widely distributed species was analysed looking for evidence of panmixia, a common criteria to support sympatric speciation. A total of 11 microsatellites that mostly cross-amplify between most species were obtained. The genotyping revealed that most loci had more than two alleles per individual indicating polyploidy. As such, the analyses required a different approach which consisted in coding the genotypes as ‘allelic phenotypes’, allowing the use of individuals of different ploidy levels in the same data set. The species delimitation of 15 operative morphotaxa and 727 individuals supported reproductive isolation of five morphotaxa and two hypotheses of conspecificity. However, some morphotaxa showed unclear assignments revealing the need of further research to clarify their reproductive limits. Finally, the population genetics of III Chaetomorpha moniliformis, Cladophora compacta and Cl. kursanovii revealed patterns of genetic variation and structure that suggest different reproductive strategies and dispersal abilities. This demonstrates that contrasting biological characteristics may arise in closely related lineages: Chaetomorpha moniliformis with dominant asexual reproduction and long dispersal abilities; Cladophora compacta with high genetic diversity, no population structure and likely to reproduce sexually; Cl. kursanovii with a structure congruent with geographic distribution and more restricted dispersal. The results suggest that polyploidy, rather than speciation with gene flow, is the force driving the reproductive isolation and evolution of this flock. Although many questions remain to be studied, this research provides the first insights into the diversification of this Cladophorales species flock and contributes to the understanding of speciation in freshwater algae. IV My science to the mankind My faith to the nature My loyalty to life Dedicated to Edith Calixto Pérez Dedicado a Edith Calixto Pérez V Acknowledgments I would like to thank Victoria University of Wellington for the opportunity to study my PhD and the Doctoral Scholarship. The main research funds for this study were given by Christian Boedeker´s Marsden Fund FastStart grant (Royal Society of New Zealand). This study used samples collected by Christian Boedeker, O. A. Timoshkin, A. Kupchinsky and the crews of the research vessels Titov, Papanin and Koptyug (Limnological Institute of the Russian Academy of Sciences, Irkutsk). The work could not have been conducted without these important samples. To the Australasian Society for Phycology and Aquatic Botany for grants to attend the conferences and present the progress of this work. I would like to thank to Dr. Joe Zuccarello for accepting me as a student, his guidance, patience and motivation helped me to improve my skills and my knowledge in science and phycology. To Christian Boedeker, his support and comments helped to see things from a different angle. I could not have had better supervisors and I am proud of had been their student. To the examiners of this thesis, Dr. Peter Ritchie, Dr. Stacy Krueger-Hadfield and Dr. Chrissen Gemmill, their suggestions and comments helped me to improve this manuscript. To Edith, who walked by me during this journey. There are no words to express how grateful I feel for her support and love. Without her this would be only a dream, thank you. To my family in Mexico, thanks for all the support in spite of the distance. To my mother Juana, my father Alejandro, my brother Alejandro, my sister Diana and her husband Francisco, my uncle Javier and my grandfather Jorge. Finally, to all the people and friends that I meet in New Zealand, for their friendship and all the time we spent together. (Andrea, Ruben “Boris”, Tania, Johanna, Balam, Kim, Olivia, Maren, Sven), phycology colleagues (Wendy Nelson, Roberta D'Archino, Judy Sutherland) and Patricia Stein, for her help with the tons of questions I had during this time. VI Table of contents Chapter One ................................................................................................................................ 1 GENERAL INTRODUCTION .................................................................................................. 1 1.1 Introduction ........................................................................................................................... 2 1.2 Species and speciation ........................................................................................................... 2 1.2.1 Modes of speciation .......................................................................................................... 2 1.2.2 Hybrid speciation ............................................................................................................. 3 1.2.3 Polyploidy as a mechanism of speciation......................................................................... 4 1.2.4 Polyploidy in algae........................................................................................................... 5 1.3 Species concepts and species delimitation ........................................................................... 6 1.3.1 Species and the inference of their boundaries .................................................................. 6 1.3.2 Population genetics for species delimitation and genetic structure of species ................ 7 1.3.3 Population genetics on algae ........................................................................................... 8 1.4 Ancient Lake Baikal as system for the study of speciation ................................................ 9 1.5 Cladophorales of Lake Baikal, a case of sympatric speciation? ..................................... 12 1.5.1 Characteristics of the order Cladophorales ................................................................... 12 1.5.2 The endemic Cladophorales of Lake Baikal................................................................... 15 1.6 Goals of this research .......................................................................................................... 17 Chapter Two .............................................................................................................................. 21 MICROSATELLITE DESIGN AND INSIGHTS INTO PLOIDY FOR THE LAKE BAIKAL CLADOPHORALES SPECIES FLOCK ............................................................... 21 2.1 Abstract ................................................................................................................................ 22 2.2 Introduction ......................................................................................................................... 23 2.3 Materials and Methods ....................................................................................................... 26 2.3.1 HTS data and assembly .................................................................................................. 26 2.3.2 Microsatellite detection and primers development ........................................................ 27 2.3.3 Microsatellite testing ...................................................................................................... 27 2.4 Results .................................................................................................................................. 29 2.4.1 HTS data ........................................................................................................................
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