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Macaronesian Fern Diplazium Caudatum (Athyriaceae)

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Macaronesian Fern Diplazium Caudatum (Athyriaceae) Departamento de Botánica Tesis Doctoral Ph.D. Thesis Diversidad genética y modelo filogeográfico de cuatro especies de helechos relictos del Terciario: Vandenboschia speciosa (Willd.) G. Kunkel, Diplazium caudatum (Cav.) Jermy, Pteris incompleta Cav. y Culcita macrocarpa C. Presl. Genetic diversity and phylogeographic pattern of four Tertiary-relict fern species: Vandenboschia speciosa (Willd.) G. Kunkel, Diplazium caudatum (Cav.) Jermy, Pteris incompleta Cav. and Culcita macrocarpa C. Presl. Samira Ben-Menni Schuler Granada, 2019 Programa de Doctorado Biología Fundamental y de Sistemas Editor: Universidad de Granada. Tesis Doctorales Autor: Samira Ben-Menni Schuler ISBN: 978-84-1306-402-4 URI: http://hdl.handle.net/10481/58616 2 3 4 Contents Summary 1 Resumen 5 Introducción (General introduction; in Spanish) - La Geoflora Paleotropical 9 - El uso de marcadores moleculares para investigar procesos históricos y 11 contemporáneos en poblaciones vegetales - Especies objeto de estudio 15 - Referencias 20 Chapters Chapter 1. Genetic diversity and population history of the Killarney fern, 25 Vandenboschia speciosa (Hymenophyllaceae), at its southern distribution limit in continental Europe. Chapter 2. Phylogeographical analyses of a relict fern of palaeotropical geoflora 51 (Vandenboschia speciosa): distribution and diversity model in relation to the geological and climate events of the late Miocene and early Pliocene. Chapter 3. Genetic diversity and phylogeography of the relict fern Culcita 109 macrocarpa: influence of clonality and reproduction system on genetic structure. Chapter 4. Population variability and differentiation and phylogeographic 153 history in the endemic Ibero-Macaronesian fern Diplazium caudatum (Athyriaceae). Chapter 5. Development of polymorphic microsatellite markers for the 193 Iberian-Macaronesian endemic Laurisilva Brake (Pteris incompleta, Pteridaceae). Discusión (General discussion; in Spanish) 201 Conclusions 207 Conclusiones 209 6 Summary One of the main challenges of the evolutionary biology is to know the causes and processes that at level of species have caused the different patterns of diversity, distribution, and diversification of populations and gene lineages. The development and improvement of population genetics and phylogeographic analyses in relation to the advance in molecular biology techniques over the last decades has allowed these challenges to be overcome. However, there is still a large number of groups of organisms in which the phylogeographic and diversity pattern of many of its species has not been studied in depth, such as ferns and lycophytes. Fern and lycophyte species belong to ancestral lineages between the vascular plants, being the ferns the second most abundant group after angiosperms, with about 10,578 species. This doctoral thesis is developed with the objective of elucidating the patterns of genetic diversity and phylogeography of four species of Tertiary relict ferns: Culcita macrocarpa, Diplazium caudatum, Pteris incompleta, and Vandenboschia speciosa. These four ferns have a common history, having hypothetized their past belonging to the Paleotropical geoflora that populated the middle and lower latitudes of Eurasia and the western America from the late Cretaceous to the Upper Miocene. Currently, they share their distribution area and ecological niche, living toghether in most locations, in disjunct areas considered glacial refugia. Various molecular markers, of nuclear and/or chloroplast DNA origin, have been used to accomplish this objective. In Chapter 1 we investigate the genetic diversity and structure of Vandenboschia speciosa, at its southernmost distribution limit in continental Europe (S Iberian Peninsula: Andalusia, Spain). We analysed sporophyte populations using ten microsatellite loci. The results indicated moderate genetic diversity at the regional scale but low diversity at the population level and a significant genetic differentiation between populations. Population history in Andalusia is characterized by a migration- drift equilibrium with historical dispersals as the main factors influencing population structure. In Chapter 2 we reconstruct the evolutionary history of Vandenboschia speciosa, hypothesised to be of Tertiary Palaeotropical geoflora with a peculiar perennial gametophyte. We sequenced 40 populations across the species range in one plastid 1 region and two paralogues of the nuclear gapCp gene and conducted time-calibrated phylogenetic, phylogeographical, and species-distribution modelling analyses. Vandenboschia speciosa had a Tertiary origin. Late Miocene aridification possibly caused the long persistence in independent refugia on Eurosiberian Atlantic and Mediterranean coasts, with the independent evolution of gene pools resulting in two evolutionary units. Our results support the idea that the geological and climate events of the late Miocene/early Pliocene shifted Tertiary fern distribution patterns in Europe. In Chapter 3 we infer the phylogeographic history of C. macrocarpa, and evaluate the importance and effect of breeding system and clonality on the genetic variability of the species. We provided genetic data from eight microsatellite nuclear loci and one plastid DNA region for 17 populations covering the distribution range of the species, and species-distribution modelling data. The global phylogeography of C. macrocarpa is characterized by the differentiation of populations in two main groups, which coincide with the geographical distribution of the species in the North of the Iberian Peninsula and in the Macaronesian archipelagos and southern Iberian Peninsula. The differentiation of the gene lineages that characterize each group began during que Early Miocene (19.5 Ma). Within each group of populations we have detected, based on the levels of diversity, prevalence of clonality and interpopulation differentiation, relict populations (in Azores and several of the Cantabrian Cornice) and populations of recent origin. This population structure responds to a dynamic of colonization in which recent populations have originated from one or a few genets, from relictual populations, which have been established by intragametophytic selfing and vegetatively expanded. Current Andalusian populations have appeared by multiple colonizing events from Azores and the Cantabrian Cornice. In Chapter 4 we characterize the genetic diversity and the phylogeographic pattern of Diplazium caudatum throughout its distribution area. We analysed 12 populations using eight microsatellite loci, sequence one plastid region, and carry out species-distribution modelling analyses. We confirmed the Tertiary origin of these species. It seems that D. caudatum took refuge in the Macaronesian archipelagos when the coldest and driest climate began during the Pliocene-Pleistocene transition, and subsequently recolonized the continent, being present only in Andalusia. The model that best explains the pattern 2 of distribution and diversity observed in this species is long-distance dispersion with restriction of gene flow and genetic drift. In Chapter 5 we characterize eight microsatellite loci in Pteris incompleta, enabling future studies on the population genetic of this Iberian-Macaronesian species. The eight primer sets were tested on a total of 47 individuals from one Azorean and one Madeiran population, resulting in medium-high levels of diversity. 3 4 Resumen Uno de los principales desafíos de la biología evolutiva es conocer las causas y procesos que a nivel de especies han causado los diferentes patrones de diversidad, distribución y diversificación de poblaciones y linajes genéticos. El desarrollo y la mejora de la genética de poblaciones y los análisis filogeográficos en relación con el avance de las técnicas de biología molecular en las últimas décadas ha permitido superar estos desafíos. Sin embargo, todavía hay una gran cantidad de grupos de organismos en los que el patrón filogeográfico y de diversidad de muchas de sus especies no se ha estudiado en profundidad, como los helechos y los licófitos. Las especies de helechos y licófitos pertenecen a linajes ancestrales entre las plantas vasculares, siendo los helechos el segundo grupo más abundante después de las angiospermas, con aproximadamente 10.578 especies. Esta tesis doctoral se desarrolla con el objetivo de dilucidar los patrones de diversidad genética y filogeografía de cuatro especies de helechos relictos terciarios: Culcita macrocarpa, Diplazium caudatum, Pteris incompleta y Vandenboschia speciosa. Estos cuatro helechos tienen una historia común, habiendo hipotetizado su pasado perteneciente a la geoflora paleotropical que pobló las latitudes medias y bajas de Eurasia y el oeste de América desde el Cretácico tardío hasta el Mioceno superior. Actualmente, comparten su área de distribución y su nicho ecológico, viviendo juntos en la mayoría de los lugares, en áreas disyuntas consideradas refugios glaciales. Se han utilizado diversos marcadores moleculares, de ADN de origen nuclear y/o cloroplastidial, para lograr este objetivo. En el Capítulo 1 investigamos la diversidad genética y la estructura de Vandenboschia speciosa, en su límite de distribución más meridional en Europa continental (S Península Ibérica: Andalucía, España). Analizamos las poblaciones de esporofitos utilizando diez loci microsatélites. Los resultados indicaron una diversidad genética moderada a escala regional pero una diversidad baja a nivel de la población y una diferenciación genética significativa entre las poblaciones.
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