Junco: Evolutionary history and diversi�ication mechanisms in the avian genus a multidisciplinary approach using phenotypic, ecological, phylogeographic and phylogenomic data TESIS DOCTORAL GUILLERMO TORGEIR FRIIS MONTOYA Universidad Autónoma de Madrid Museo Natural de Ciencias Naturales Madrid, 2017 Thomas Nuttall, 1903 Museo Nacional de Ciencias Naturales Universidad Autónoma de Madrid (Consejo Superior de Investigaciones Dpto. De Biología Científicas) Dpto. De Biodiversidad y Biología Evolutiva Evolutionary history and diversification mechanisms in the avian genus Junco: a multidisciplinary approach using phenotypic, ecological, phylogeographic and phylogenomic data Memoria presentada por el licenciado Guillermo Torgeir Friis Montoya para optar al grado de Doctor en Biología por la Universidad Autónoma de Madrid DIRECTOR: TUTOR: Dr. Borja Milá Valcárcel Dr. José Luis Bella Sombría Museo Nacional de Ciencias Naturales Universidad Autónoma de Madrid Dpto. de Biodiversidad y Biología Dpto. de Biología Evolutiva TESIS DOCTORAL Madrid, 2017 Cover: Slate-colored junco illustration from “A popular handbook of the birds of United States and Canada” by Thomas Nuttall and Montague Chamberlain, 1903 “Depuis sa naissance, dans les îles ioniennes, il y a près de trois mille ans, la pensée occidentale a été partagée entre deux attitudes en apparence opposes. Selon l’une de ces philosophies la réalité authentique et ultime de l'univers ne peut résider qu’en des formes parfaitement immuables, invariantes par essence. Selon l’autre, au contraire, c’est dans le movement et l’évolution que réside la seule réalité de l’univers.” Jacques Monod, Le Hasard et la Nécessité (1970) “We shall never fully understand nature (or ourselves), and certainly never respect it, until we dissociate the wild from the notion of usability.” John Fowles, The Tree (1979). CONTENTS Agradecimientos .................................................................................................................15 Foreword ...............................................................................................................................17 Presentación .........................................................................................................................19 INTRODUCTION: ..................................................................................................................21 The field of speciation research ..................................................................23 Speciation in birds ........................................................................................24 High-throughput sequencing and the power of multidisciplinary approaches in speciation research .............................................................29 Study system ..................................................................................................32 General Objectives .................................................................................................37 General Methods: ...................................................................................................38 Population sampling ....................................................................................38 Phenotypic data and analysis .....................................................................38 Whole genome sequencing and assembly .................................................39 Genotyping-by-sequencing .........................................................................40 Alignment and variant calling ....................................................................41 References ................................................................................................................42 CHAPTER I: ...........................................................................................................................57 Abstract .....................................................................................................................59 Introduction .............................................................................................................61 Materials and methods: ........................................................................................64 Sequencing of mitochondrial and nuclear markers ................................64 Genotyping of genome-wide SNP loci ........................................................65 Phylogenetic analysis and molecular dating ............................................65 Genome-wide structure from SNP data .....................................................68 Phylogenomic analyses with SNP data ......................................................69 Phenotypic data and analysis .....................................................................70 Phenotypic versus genetic distance ...........................................................70 Results: ......................................................................................................................72 Phylogeography and divergence times .....................................................73 Genetic diversity and historical demography ..........................................76 Genome-wide structure from principal components analysis ...............77 Phylogenomic reconstruction .....................................................................77 Phenotypic differentiation and correlations with genetic distance ......79 Discussion: ...............................................................................................................82 Young and old junco clades: rapid diversification vs. long-term stasis ...............................................................................................................82 Rapid postglacial speciation along a latitudinal environmental gradient A potential role for sexual selection ...........................................................89 Taxonomic implications ..............................................................................90 Conclusions ..............................................................................................................91 References ................................................................................................................92 CHAPTER II: .......................................................................................................................101 Abstract ...................................................................................................................105 Introduction ..........................................................................................................105 Materials and methods: .....................................................................................108 Genotyping-by-sequencing .......................................................................108 Genetic structure analyses ........................................................................108 Phenotypic data and analysis ...................................................................110 Adaptive variation association tests .......................................................112 Results: ....................................................................................................................112 Neutral genetic structure among northern Junco forms .....................112 Patterns of phenotypic differentiation and sexual dichromatism .......114 Adaptive variation association tests .......................................................116 Discussion: .............................................................................................................118 Sexual dichromatism correlates with plumage coloration divergence and latitude .................................................................................................118 Interactions between sexual and natural selection ...............................120 The role of sexual selection in the early stages of speciation in the Junco complex ........................................................................................................123 Conclusions ............................................................................................................126 References .............................................................................................................128 CHAPTER III: .....................................................................................................................137 Abstract ...................................................................................................................139 Introduction ..........................................................................................................141 Materials and methods: .....................................................................................147 Genotyping-by-sequencing .......................................................................147 Genetic structure analyses ........................................................................148 Redundancy analysis and variance partition .........................................150 Niche divergence tests ...............................................................................152 Genome scans ..............................................................................................153 Results: ....................................................................................................................154 Neutral genetic structure ..........................................................................154