UC Berkeley

The focus of this research is phylogenetic relationships within vertebrates, with a special emphasis on turtles. Despite a substantial amount of previous research, there are still several outstanding questions regarding relationships within vertebrates. By studying the phylogeny at several hierarchical levels (class, order, family, species), we can begin to understand the processes that produce the biodiversity around us. In addition, turtles provide a good system for phylogenetics, as there is relatively low species diversity allowing for more complete sampling, a rich fossil record to calibrate the phylogeny, and applications to conservation. For this research, I take a genomics/bioinformatics approach to assess vertebrate phylogeny. Using a combination of expressed sequence tags (ESTs) and targeted amplification of cDNA, I developed 75 single-copy, nuclear markers conserved across vertebrates (Chapter 1). I also analyze the use of different data types for higher-level phylogenetics. Comparing NUCL (nucleotides), N12 (1st and 2nd codon positions), DEGEN1 (modified sequences to account for codon degeneracy), and AA (amino acids), I find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL (Chapter 1). I use these molecular markers to build a vertebrate phylogeny to answer questions of relationships between and within major groups. In Chapter 2, I address the phylogenetic position of turtles within the amniote phylogeny. Despite over a century of morphological and molecular research, we still do not know where turtles reside in the vertebrate evolutionary tree. I also analyze different partitioning schemes, the effect of missing data, identifying unstable taxa in a phylogeny (rogue taxa), and the use of different data-types (Chapter 2). For the phylogenetic placement of turtles, different analyses and datasets produce different results. However, after performing topological and statistical tests, the weight of the evidence supports the grouping of turtles with archosaurs (birds and crocodiles), either with turtles being the sister group to Archosauria or Crocodylia. The focus of Chapter 3 is the phylogenetic relationships within turtles, with divergence dating analyses. Within turtles, a basal Pleurodira-Cryptodira was recovered and within Cryptodira, a basal Trionychia (soft-shell turtles) was recovered, with Chelonioidea next (sea turtles). A novel relationship recovered is the sister relationship between Platysternon and Testuguria (Testudinidae and Geoemydidae). Divergence dating analyses using new fossil evidence re-classifying stem cryptodires to be stem turtles find the origin of turtles to be much younger than previously believed (~153mya). For Amphibians, data point towards the diphyletic origin of the group (Chapter 5). Most of the recovered relationships within Squamata are consistent with the currently molecular phylogeny, with my data recovering a basal Dibamidae+Gekkonidae, but these results are in sharp contrast to recent morphological studies (Chapter 5). Mammal relationships in this phylogeny also mirror the current mammal phylogeny, favoring the Theria hypothesis (marsupial-placental sister groups) and a basal Afrotheria group (Chapter 5). For the problematic Scandentia (Tupaia) clade, there is phylogenetic signal allying Tupaia with Glires and Primates, but the signal with primates is stronger (Chapter 5). The last two groups, Actinopterygii (ray-finned fish) and Aves (birds), had relatively poor internal taxon sampling (Chapter 5). Although my results do not provide any new information, these new markers hold promise in helping to resolve relationships for fish and birds. Lastly, a species-level study was performed on turtles in Taiwan to identify the parental species of hybrid individuals found in the wild (Chapter 4). Through molecular methods, the parental species were identified as Mauremys sinensis and Mauremys reevesii. Presence of M. reevesii alleles on the main island of Taiwan indicates that this species may have been introduced. If so, then M. reevesii is non-native and conservation efforts should not be wasted protecting this species.