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Genetic Diversity of the Endemic Canary Island Pine Tree, Pinus Canariensis Miguel Navascués

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Genetic Diversity of the Endemic Canary Island Pine Tree, Pinus Canariensis Miguel Navascués Genetic Diversity of the Endemic Canary Island Pine Tree, Pinus canariensis Miguel Navascués To cite this version: Miguel Navascués. Genetic Diversity of the Endemic Canary Island Pine Tree, Pinus canariensis. Ecology, environment. University of East Anglia, Norwich, 2005. English. tel-00250082 HAL Id: tel-00250082 https://tel.archives-ouvertes.fr/tel-00250082 Submitted on 9 Feb 2008 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Genetic Diversity of the Endemic Canary Island Pine Tree, Pinus canariensis Miguel de Navascu´esMelero Thesis submitted for the degree of Doctor of Philosophy School of Biological Sciences University of East Anglia Supervisor: Dr. Brent C. Emerson September 2005 © This copy of the thesis has been supplied on condition that anyone who consults it is un- derstood to recognise that its copyright rests with the author and that no quotation from the thesis, nor any information derived therefrom, may be published without the author’s prior, written consent. “A perfect piece of DNA Caught in a flashing ray” This is the Place Red Hot Chili Peppers A Concetta A mis padres y a mis hermanos ABSTRACT The Canary Island pine, Pinus canariensis, is an endemic tree that forms one of the main forest ecosystems within the archipelago, and whose distribution has been reduced in the last five centuries by clear cutting for the extraction of timber and tar. It was in the XXth century that exploitation declined and reforestation programs were brought forward for the restoration of an ecosystem that harbours a number of endangered endemic species of plants and animals. In addition to reforestation efforts, an understanding of population genetic processes is also necessary for the successful conservation management of the Canarian pine forest, particularly in light of gathering evidence for local adaptation. In this thesis historical and contemporary gene flow within P. canariensis was studied with nuclear and chloroplast microsatellite markers. High immigration rates (0.68–0.75) were estimated as expected for an outcrossing wind-pollinated tree. Nevertheless, significant population differentiation (θ = 0.019, RST = 0.044) was detectable for sites separated by only a few kilometres. Within the context of reforestation programs the high levels of gene flow detected would appear to have a positive effect, by facilitating the immigration of local alleles from natural stands into potentially genetically depauperate first generation gene pools of reforested stands. Historical population growth was revealed with chloroplast microsatellites for most populations of P. canariensis. Population expansions for the pine parasite weevil Brachyderes rugatus were also detected, broadly coinciding with the pop- ulation expansions within the Canary Island pine forests. Given the estimated times of expansion, these population demographic increases would seem likely related to the process of colonisation of newly emerged islands or local patches after volcanic disturbance. Detection and dating of these expansions from chloro- plast microsatellites was, to some degree, negatively affected by homoplasy (i.e. parallel and back mutations). Coalescent simulations of the evolution of chloroplast microsatellites were ap- Abstract iii plied to study the effects of homoplasy in the statistical analysis of population structuring. Measures of genetic diversity based on number of haplotypes and measures based on genetic distances were differently affected. Genetic distances were underestimated but were proportional to the actual value. These effects help to explain the lower performance of statistical analyses for the detection and dat- ing of population expansions. Further research on the effects of homoplasy in the analysis of population differentiation using chloroplast microsatellites is essential. RESUMEN El pino canario, Pinus canariensis, es un endemismo que forma uno de los prin- cipales ecosistemas forestales de las Islas Canarias y cuya distribuci´onse ha re- ducido progresivamente en los ´ultimoscinco siglos a causa de las actividades extractoras de madera y pez. A partir del siglo XX la explotaci´on de los pinares canarios entra en declive y comienzan los programas de reforestaci´onde este eco- sistema, que alberga un cierto n´umerode endemismos de plantas y animales, algunos de ellos amenazados. Adem´asde las actividades de reforestaci´on, el conocimiento de los procesos gen´eticospoblacionales es fundamental para el de- sarrollo de planes de gesti´ony conservaci´onde los pinares canarios; especialmente importante es la investigaci´on concerniente al estudio de adaptaciones locales. En la presente tesis se han utilizado microsat´elitesnucleares y cloropl´asticos como marcadores moleculares para el estudio del flujo gen´eticohist´oricoy con- tempor´aneo en P. canariensis. Como era de esperar en una especie anem´ofilay al´ogama, se estimaron altas tasas de inmigraci´on (0.68–0.75). Sin embargo, la diferenciaci´ongen´eticaentre poblaciones separadas por pocos kil´ometros result´o significativa (θ = 0.019, RST = 0.044). Dentro del contexto de las programas de reforestaci´on,estos altos niveles de flujo gen´eticopodr´ıan tener un efecto positivo, al favorecer la inmigraci´on de alelos locales desde las masas naturales, increment´andose as´ıel acervo gen´eticode las repoblaciones, potencialmente em- pobrecidas en su primera generaci´on. Mediante el an´alisisde microsat´elitesde cloroplasto, se han detectado expan- siones demogr´aficas en el tiempos geol´ogicos de la mayor´ıade las poblaciones de P. canariensis. Tambi´ense han detectado crecimientos poblacionales del gorgojo par´asitodel pino canario, Brachyderes rugatus, aproximadamente coincidentes con las expansiones demogr´aficas del pinar. Considerando las dataciones de los momentos de expansi´on, estas explosiones demogr´aficas parecen relacionadas con la colonizaci´on de islas tras su emersi´ony la colonizaci´onde ´areas m´as restringidas tras los efectos destructores de erupciones volc´anicas. La detecci´ony dataci´on Abstract v de estas expansiones con microsat´elites de cloroplasto fueron, en cierta medida, afectadas negativamente por homoplasia (es decir, por mutaciones que revierten al estado ancestral o por mutaciones iguales adquiridas independientemente). Para estudiar los efectos de la homoplasia en los an´alisis de gen´eticade pobla- ciones, se han empleado simulaciones (basadas en la coalescencia) de la evoluci´on de los microsat´elitesde cloroplasto. Las medidas de diversidad gen´eticabasadas en el n´umerode haplotipos y las basadas en estimaciones de distancias gen´eticas se vieron afectadas de forma distinta. Aunque las distancias gen´eticasfueron subes- timadas ten´ıanvalores proporcionales a las distancias gen´eticasverdaderas. Estos efectos ayudan a explicar la reducci´on de precisi´on de los an´alisis de detecci´on y dataci´on de expansiones demogr´aficas. Investigaciones adicionales ser´ıanesen- ciales para revelar los efectos de la homoplasia en el an´alisis de la diferenciaci´on gen´eticaentre poblaciones mediante microsat´elitesde cloroplasto. CONTENTS Abstract ..................................... ii Resumen .................................... iv List of figures .................................. x List of tables .................................. xii List of abbreviations .............................. xiv Glossary ..................................... xv Acknowledgements ............................... xvi Part I Introduction 1 Foreword .................................... 2 On forestry, forest genetics and pines ................... 2 Aims and organisation of this work .................... 3 1. Canary Islands ............................... 5 1.1 Geography ............................... 5 1.2 Geology ................................ 6 1.2.1 Origin ............................. 6 1.2.2 Evolution ........................... 10 1.3 Climate and vegetation ........................ 13 1.3.1 Climate ............................ 13 1.3.2 Vegetation ........................... 15 1.4 Biogeography ............................. 17 1.4.1 Colonisation and dispersion ................. 17 1.4.2 Disharmony or attenuation .................. 20 1.4.3 Speciation ........................... 20 1.4.4 Endemicity .......................... 21 1.4.5 Species number ........................ 22 Contents vii 1.5 Summary ............................... 24 2. Canary Island pine ............................. 25 2.1 Description .............................. 25 2.2 Ecology ................................ 25 2.2.1 Distribution .......................... 25 2.2.2 Phytosociology ........................ 26 2.2.3 Reproductive system ..................... 28 2.2.4 Fire adaptation ........................ 28 2.3 Evolution and biogeography ..................... 29 2.4 Canarian pine and humans ...................... 32 2.4.1 Uses of the Canary Island pine forest ............ 32 2.4.2 Reforestation and conservation ............... 34 2.4.3 Pinus canariensis outside the archipelago ......... 36 2.5 Summary and further reading ...................
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