Diversity, Phylogenesis and Evolutionary Mechanisms in the Genus Rubus

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Diversity, Phylogenesis and Evolutionary Mechanisms in the Genus Rubus Palacký University Olomouc Faculty of Science Department of Botany Diversity, phylogenesis and evolutionary mechanisms in the genus Rubus PhD. Thesis Mgr. Michal Sochor Supervisor: Doc. RNDr. Bohumil Trávníček, Ph.D. Consultant: RNDr. Radim J. Vašut, PhD. Olomouc 2016 Bibliografická identifikace Jméno a příjmení autora: Michal Sochor Název práce: Diverzita, fylogeneze a evoluční mechanismy v rodu Rubus Typ práce: doktorská Pracoviště: Katedra botaniky PřF UP Vedoucí práce: doc. RNDr. Bohumil Trávníček, PhD. Rok obhajoby: 2016 Abstrakt: Rod ostružiník (Rubus), zejména jeho nejbohatší podrod (subgenus Rubus), představuje v Evropě a na Jižním Kavkazu jednu z taxonomicky nejkomplikovanějších skupin rostlin. Jen v Evropě je uznáváno více než 750 druhů ostružiníků, z nichž naprostá většina je polyploidních s různou mírou asexuálního rozmnožování pomocí semen (apomixe, agamospermie). Pouze málo druhů je diploidních, a tedy striktně sexuálních. Ostružiníková flóra Jižního Kavkazu je prozkoumaná jen velmi sporadicky, ačkoliv nepochybně představuje jedno z evolučních center podrodu Rubus. Předložená práce se zabývá třemi dílčími tématy: 1.) fylogeneze evropských ostružiníků s důrazem na nalezení vztahů a vazeb mezi diploidními a polyploidními taxony; 2.) fylogeografie diploidního okruhu R. ulmifolius/sanctus agg. a její vztah k evoluci polyploidního komplexu série Discolores; 3.) cytotypová, reprodukční a haplotypová diverzita kolchidských ostružiníků. Práce ukazuje, že celý polyploidní komplex i přes svou bohatost a rozmanitost vznikl z genofondů pouhých 7 ancestrálních diploidních druhů nebo druhových okruhů, z nichž tři jsou pravděpodobně vyhynulé. Naopak některé diploidní druhy jižní Evropy a Makaronézie se na evoluci polyploidů zřejmě nepodílely. Jeden z předků, R. ulmifolius/sanctus agg., prodělal během posledního glaciálu redukci svého rozšíření a efekt hrdla lahve ve východních částech areálu. To vedlo ke snížení genetické diverzity a snad i ke snížení kompetiční schopnosti, což mohlo usnadnit expanzivní šíření nově vzniklých polyploidních apomiktů v severozápadní Evropě a na Jižním Kavkazu. Dále se ukázalo, že tito apomikti nezřídka kombinují preglaciálních genetickou divezitu diploidních předků s genofondem recentních sexuálů ze svého regionu. Ačkoliv většina recentních apomiktů vznikla až v průběhu holocénu, agamický komplex jako celek je mnohem starší, sahající přinejmenším do předchozího interglaciálu. Apomixe by tedy neměla být vnímána jako slepá ulička evoluce, ale jako způsob uchování a šíření genetické diverzity v prostoru a čase. Kromě výhod samotné apomixe a (allo)polyploidie tak současní apomikti mohou těžit jak z genetické diverzity svých vyhynulých (nebo geneticky značně pozměněných) předků, tak i z lokálně adaptovaných genových komplexů recentních diploidů. Jedna z kapitol práce podává první vhled do evoluce ostružiníků západního Kavkazu – Kolchidy. Ukazuje, že v Kolchidě dominují tetraploidní linie, které jsou buď striktně sexuální (morphoser. Glandulosi a Radula), nebo apomiktické s minimální reziduální sexualitou (morphoser. Discolores a Micantes). Variabilita v plastidové DNA odhalila izolovanost kolchidských ostružiníků od recentní evropské batoflóry a omezenou účast recentních diploidů na evoluci polyploidního komplexu. Klíčová slova: apomixe, evoluce, geografická parthenogeneze, hybridizace, ostružiník, polyploidie, Rubus Počet stran: 119 Jazyk: anglický 1 Bibliographical identification Author's first name and surname: Michal Sochor Title: Diversity, phylogenesis and evolutionary mechanisms in genus Rubus Type of thesis: PhD. thesis Department: Department of Botany, Faculty of Science, Palacky University Supervisor: doc. RNDr. Bohumil Trávníček, PhD. Year of defence: 2016 Abstract: Genus Rubus, especially its richest subgenus – Rubus, is one of the taxonomically most complicated plant groups in Europe and the Southern Caucasus. In Europe, more than 750 species are recognised, most of which are polyploids with varied degree of asexual reproduction via seeds (apomixis, agamospermy). Only few species are diploid and thus strictly sexual. The Caucasian bramble flora is only poorly explored, although it undoubtedly represents one of the evolutionary centres of the subgenus. The thesis covers three topics: 1. Phylogenesis of European brambles with special focus on relationships among diploid and polyploid taxa; 2. Phylogeography of diploid R. ulmifolius/sanctus agg. and its relation to the evolution of polyploids from series Discolores; 3. cytotype, haplotype and reproduction diversity of Colchic brambles. The study shows that the rich and diverse polyploid complex originated from only seven diploid species or species aggregates, of which three are probably extinct today. On contrary, some South European and Macaronesian diploids did not contribute to the evolution of polyploids. One of the diploid ancestors, R. ulmifolius/sancus agg., experienced a reduction in its distribution and significant bottlenecks in eastern parts of its distribution area. This led to the decrease in the genetic diversity and subsequently possibly to lower competition abilities which may have enabled an expansion of newly arisen polyploids in Northwest Europe and the Southern Caucasus. It is further shown that apomicts combine pre-glacial gene-pools of the diploid ancestors and genetic diversity of recent sexuals from their region. Although most of the recent apomicts were formed in the Holocene, the whole agamic complex is much older, its history stretching at least to the last interglacial period. Therefore, apomixis should not be seen as an evolutionary dead end, but as a way of preservation and spread of genetic diversity in space and time. In addition to the advantages of asexuality and (allo)polyploidy, apomicts can use both genetic diversity of their extinct (or markedly changed) ancestors and the locally adapted gene complexes of contemporary diploids. One of the chapters provide the first insight into evolution of west Caucasian brambles. It shows that tetraploid accessions are prevalent and exhibit either strict sexuality (morphoser. Glandulosi and Radula), or apomixis with rare residual sexuality (morphoser. Discolores and Micantes). Plastid DNA variation revealed isolation of Colchic and European brambles and limited involvement of contemporary diploids on evolution of the polyploid complex. Keywords: apomixis, evolution, geographic parthenogenesis, hybridization, brambles, polyploidy, Rubus Number of pages: 119 Language: English 2 Contents Acknowledgements ......................................................................................................... 4 Declaration ...................................................................................................................... 5 Author Contributions..................................................................................................... 5 CHAPTER 1: Introduction and aims of the thesis.......................................................... 6 Asexuality and its role in plant evolution ..................................................................... 7 Systematics of apomictic complexes ............................................................................ 8 Geographic patterns in agamic complexes ................................................................... 9 Eurasian blackberries as a model system.................................................................... 11 Aims of the thesis ....................................................................................................... 12 CHAPTER 2: How just a few makes a lot: Speciation via reticulation and apomixis on example of European brambles (Rubus subgen. Rubus, Rosaceae).................... 13 Abstract....................................................................................................................... 14 Introduction................................................................................................................. 14 Materials and methods ................................................................................................ 17 Results......................................................................................................................... 19 Discussion................................................................................................................... 24 Conclusion .................................................................................................................. 35 CHAPTER 3: Origin of apomicts as a result of the sexual ancestor's phylogeography: a model case of European and Caucasian brambles (Rubus, Rosaceae) ....................................................................................................................... 36 Abstract....................................................................................................................... 37 Introduction................................................................................................................. 37 Materials and methods ................................................................................................ 39 Results......................................................................................................................... 41 Discussion................................................................................................................... 46 Conclusion .................................................................................................................
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