PHYLOGENETICS AND INTROGRESSION OF HABRONATTUS JUMPING SPIDERS USING TRANSCRIPTOMES (ARANEAE: SALTICIDAE) by Geneviève Leduc-Robert B.Sc., The University of British Columbia, 2011 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in The Faculty of Graduate and Postdoctoral Studies (Zoology) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) December 2015 ! Geneviève Leduc-Robert, 2015 Abstract Habronattus is a diverse genus of jumping spiders with complex courtship displays and colourful ornaments in males. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved because of conflicting signals from the few genes available. While such discordant gene trees could be the result of deep coalescence in the recently diverged group, there are many indications that hybridization may have occurred and could be the source of conflict. To infer Habronattus phylogenetic relationships and to investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. We conducted a concatenated phylogenetic analysis using Maximum Likelihood for 2.41 Mb of nuclear data and for 12.33 kb of mitochondrial data. The concatenated nuclear phylogeny was resolved with high bootstrap support (95-100%) at most nodes with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, and H. oregonensis, and Pellenes cf. levii. There are several nodes of the mitochondrial phylogeny that are incongruent to the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus group, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the extent of incomplete lineage sorting (ILS) and introgression, we analyzed gene tree discordance for loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the viridipes/clypeatus/coecatus (VCC) group (517 loci) and found high levels of genetic discordance, especially in VCC group. Finally, we tested specifically for nuclear introgression in the concatenated nuclear matrix with Patterson’s D statistics and DFOIL. We found nuclear introgression resulting in substantial admixture between americanus group species, and between H. sp. (ROBRT) and the clypeatus group, and more ! ""! minimal nuclear introgression between the clypeatus group and the coecatus group, and between the americanus group and several distant species. Our results indicate that hybridization may have been historically common between phylogenetically distant species of Habronattus, and that reproductive isolation is yet to be complete across the Habronattus phylogeny. ! """! Preface The collection of specimens was conducted as a team led by W.P. Maddison in Arizona and Mexico. Other specimens were already collected by David Maddison, Junxia Zhang, Damian Elias, and Marshal Hedin. I designed the study with the help of W.P. Maddison. I completed all the lab work and data analysis, except for the Bioanalyzer step completed by Joanne Denny, the cDNA library preparation completed by Debbie Adams and Anastasia Kuzmin and the Illumina sequencing step competed by Anastasia Kuzmin. There were steps in alignment and sequence processing completed with custom modules, designed by W.P. Maddison, in the Mesquite Gataga package. I prepared the manuscript with input from W.P. Maddison. ! "#! Table of contents Abstract .......................................................................................................................................... ii Preface .......................................................................................................................................... iv Table of contents ............................................................................................................................ v List of tables ..........................................................................................................................….. vii List of figures .............................................................................................................................. viii Acknowledgements ....................................................................................................................... ix 1. Introduction ................................................................................................................................ 1 2. Methods ...................................................................................................................................... 6 2.1 Taxon sampling ............................................................................................................ 6 2.2 Molecular extractions and sequencing ......................................................................... 7 2.3 Sequence read filtering and trimming .......................................................................... 8 2.4 Reference transcriptome .............................................................................................. 9 2.5 Reference-based assembly of transcriptomes ............................................................ 10 2.6 Sequence alignments .................................................................................................. 11 2.7 Phylogenetic analyses ................................................................................................ 13 2.7.1 Nuclear and mitochondrial matrices matrices ............................................. 13 2.7.2 16SND1 and Ef1-a phylogenies with broader species sample ................... 15 2.8 Introgression .............................................................................................................. 15 2.8.1 Bayesian concordance analysis ................................................................... 15 2.8.2 Patterson’s D statistic and DFOIL .................................................................. 17 3. Results ...................................................................................................................................... 21 3.1 Transcriptome assemblies .......................................................................................... 21 3.1.1 Reference transcriptome ............................................................................. 21 3.1.2 Reference-based transcriptomes assemblies ............................................... 22 3.2 Substitution model selection ...................................................................................... 22 3.3 Nuclear phylogenetic analyses ................................................................................... 23 3.4 Mitochondrial phylogenetic analyses ........................................................................ 26 3.5 16SND1 and Ef1-a phylogenies (broader species sample) ........................................ 27 3.6. Introgression ............................................................................................................. 28 3.6.1 Bayesian concordance analysis ................................................................... 28 3.6.2 Patterson’s D statistic and DFOIL .................................................................. 30 4. Discussion ................................................................................................................................ 33 4.1 Habronattus phylogeny ............................................................................................. 33 4.2 Introgression in Habronattus ..................................................................................... 35 4.2.1 Introgression within species groups ............................................................ 38 4.2.2 Distant introgression ................................................................................... 41 4.2.3 Potential drivers of hybridization ................................................................ 46 4.2.4 Evolutionary consequences of introgression .............................................. 49 4.2.5 Future research ............................................................................................ 51 5. Conclusions .............................................................................................................................. 53 Tables and figures ........................................................................................................................ 54 Bibliography ................................................................................................................................ 69 Appendices ................................................................................................................................... 76 1 List of specimens............................................................................................................76 ! #! 2 Summary of sequencing and read assemblies ............................................................... 81 3 Concordance factors and their credibility intervals for the americanus group ............. 86 4 Concordance factors and their credibility intervals for the VCC clade ........................ 87 5 Counts of biallelic patterns for DFOIL ............................................................................. 90 6 Counts of biallelic patterns for Patterson’s D statistics ...............................................