Diversification of Afrobatrachian Frogs and the Herpetofauna of the Arabian Peninsula By Daniel Portik A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Dr. Jimmy A. McGuire, Chair Dr. Rauri Bowie Dr. David Blackburn Dr. Rosemary Gillespie Fall 2015 Abstract Diversification of Afrobatrachian Frogs and the Herpetofauna of the Arabian Peninsula by Daniel Portik Doctor of Philosophy in Biology University of California, Berkeley Dr. Jimmy A. McGuire, Chair The identification of biotic and abiotic factors that promote the diversification of clades across Africa and the Arabian Peninsula remains a difficult challenge. A variety of ecological and evolutionary processes can be driving such patterns, and clade-specific traits may also play a role in the evolution of these groups. Comparative evolutionary studies of particular clades, relying on a phylogenetic framework, can be used to investigate many of these topics. Beyond these mechanisms there are abiotic factors, such as geological events, that can drive vicariance and dispersal events for large sets of taxa. The investigation of historical biogeography in a comparative phylogenetic framework can be used to detect such patterns. My dissertation explores these topics using reptiles and amphibians as study systems, and I rely on the generation of molecular sequence data, phylogenetics, and the use of comparative phylogenetic methods to address a variety of questions. I provide the abstract for each chapter below. Chapter 1: The reproductive modes of anurans (frogs and toads) are the most diverse among all the terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies, in which breeding is partially or completely independent of water, have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process which is thought to occur through a series of intermediate reproductive stages. A number of selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co-evolution with particular ecomorphologies have not been investigated in a comparative phylogenetic framework. We examined these topics and the evolution of reproductive mode in Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (~400 species). We find that direct development evolved twice independently from terrestrialized reproductive modes involving protected eggs or larvae, supporting the intermediate stages hypothesis. We detected correlated evolution in specific derived ecomorphologies and reproductive traits, including arboreality and arboreal oviposition, and fossoriality and subterranean oviposition. There is support for a link between lotic water systems and terrestrial 1 oviposition, and between arboreal ecomorphology and the use of lentic water systems for reproduction. Our findings indicate clade-specific processes driving the evolution of reproductive modes in the Afrobatrachia, and suggest that other processes such as habitat filtering and co-evolution with ecomorphology may generate global patterns of anuran reproductive modes. Chapter 2: Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers with targeted levels of informativeness in non-model organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, often with the aid of a reference genome to identify intron-exon boundaries and exclude shorter exons (< 200 bp). Here, we test an alternative approach that directly uses transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Based on a selection of 1,260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic scales for frogs, including species up to ~100 million years divergent from the focal group. After several conservative filtering steps, we recovered a large phylogenomic data set consisting of sequence alignments for 1,047 of the 1,260 transcriptome-based loci (~630,000 bp) and a large quantity of highly variable regions flanking the exons in transcripts (~70,000 bp). We recovered high numbers of both shorter (< 100 bp) and longer exons (> 200 bp), with no major reduction in coverage towards the ends of exons. We observed significant differences in the performance of blocking oligos for target enrichment and non-target depletion during captures, and observed differences in PCR duplication rates that can be attributed to the number of individuals pooled for capture reactions. We explicitly tested the effects of phylogenetic distance on capture sensitivity, specificity, and missing data, and provide a baseline estimate of expectations for these metrics based on nuclear pairwise differences among samples. We provide recommendations for transcriptome- based exon capture design based on our results, and describe multiple pipelines for data assembly and analysis. Chapter 3: The anuran family Hyperoliidae is Africa’s most diverse group of frogs, with a distribution across sub-Saharan Africa (16 genera, over 200 species), Madagascar (1 genus, 11 species), and the Seychelles Islands (1 monotypic genus). Hyperoliids are found in a variety of habitats and altitudes, but exhibit the highest species richness and co-occurring species in forested regions, including lowland rainforests and montane forests. As many as 14 hyperoliid species have been recorded in near sympatry, and species show high turnover based on both elevational and habitat gradients. Hyperoliids exhibit extensive morphological diversity, ranging from semi-terrestrial forms, to walker- climbers, to largely arboreal forms, and display considerable variation in body size across species and between the sexes. A striking and unique feature of many hyperoliid species is their bright coloration and patterning, which can be highly variable and driven by the presence of color polymorphism or sexual dichromatism. Using phylogenomic data, I reconstructed the evolutionary relationships of the family and investigated the evolution of sexual size dimorphism and sexual dichromatism. My examination of the body sizes of hyperoliid species revealed this family largely exhibits female-biased SSD, and I find evidence for an isometric scaling relationship between body sizes of the sexes. Within the genus Hyperolius I found significant differences in the evolutionary trend of male and 2 female body sizes, namely selection for a single optimal female body size and strong directional selection for males occurring in different subclades. I propose the functional relationship between female body size and arboreal oviposition may be opposing the selection for increased fecundity associated with larger female sizes. The body sizes of males may be the result of a combination of interspecific resource partitioning, division of acoustic space, and reproductive character displacement. Sexual dichromatism has evolved independently in two main clades of hyperoliids: 1) the common ancestor of the Malagasy and Seychelles Islands species ( Heterixalus , Tachycnemis ), and 2) the common ancestor of Hyperolius, Morerella , and Cryptothylax . A number of subsequent reversals to monochromatism occur in the genus Hyperolius and Heterixalus , with some cases of secondarily derived dichromatism. Chapter 4: The Red Sea has had a profound biogeographic effect on organisms with Afro-Asian distributions, resulting in complex patterns of admixture on the Arabian Peninsula. We investigate the phylogenetic affinities of a monitor lizard ( Varanus yemenensis ) restricted to the southwestern Arabian Peninsula by sequencing all African monitor species and several Asian monitor species for the mitochondrial gene ND2 and the nuclear marker RAG-1. We find evidence that V. yemenensis is of African origin, being most closely related to the white-throat monitor, V. albigularis , an African species complex distributed from the Horn of Africa to southern Africa. Using divergence-dating analyses, we investigate several biogeographic hypotheses to infer the likely mechanism of colonization of the Arabian Peninsula by this species. Our results reveal that both dispersal across a southern landbridge and overwater dispersal are potential explanations. The patterns observed in V. yemenensis are contrasted with other taxa having similar Afro-Arabian disjunct distributions to better understand the complex biogeographic history of this region. Chapter 5: The Arabian Peninsula is home to a unique fauna that has assembled and evolved throughout the course of major geophysical events, including the separation of the Arabian Plate from Africa and subsequent collision with Eurasia. Opportunities for faunal exchanges with particular continents occurred in temporally distinct periods, and the presence of African, Western Eurasian, and South Asian derived taxa on the Arabian Peninsula signifies the complexity of these historical biogeographic events. The six true toad species (family Bufonidae) endemic to Arabian Peninsula present a considerable taxonomic and biogeographic challenge because they are part of a global bufonid radiation, including several genera surrounding