Investigating Evolutionary History Using Phylogenomics

Reconstructing the Tree of Life is one of the principal aims of evolutionary biology. The development of molecular phylogenetics to elucidate evolutionary history has complemented palaeontology, biogeography, and archaeology in elucidating biological history. The development of molecular-clock analyses allowed evolutionary timescales to be estimated using nucleotide sequences and other products of the evolutionary process Until recently, the twin challenges of molecular dating were in obtaining sufficient data and developing robust methods. The former concern is now less important as high–throughput sequencing technology allows entire genomes to be sampled. Genome–scale data enhances statistical power, but accompanying this wealth of data is a new suite of analytical challenges. One of these key challenges is analysing these data in synthesis with the paleontological record without statistical overparameterisation. There are also aspects of the evolutionary process, such as among–lineage rate variation, that can affect the precision and accuracy of current methods. In this thesis, I first use the richest nucleotide sequence data set of insects available to estimate an authoritative insect evolutionary timescale that dates the origins and diversification of every major insect order. I then focus on molecular-clock methods by testing their performance in inferring evolutionary rates from time–structured data, common in the study of ancient DNA. I find that among–rate lineage variation and phylo–temporal clustering affect rate estimates. I also study data partitioning, a common technique used to optimise the analysis of multilocus data where independent parameters are applied across different subsets of the data. New data from the genomic revolution gifts biologists new opportunities to re-examine enduring questions about the evolutionary process. Here, I use phylogenetic tools to show that evolution leaves figurative fingerprints on genomes over millions of years

Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches

Almost all examined cockroaches harbor an obligate intracellular endosymbiont, Blattabacterium cuenoti. On the basis of genome content, Blattabacterium has been inferred to recycle nitrogen wastes and provide amino acids and cofactors for its hosts. Most Blattabacterium strains sequenced to date harbor a genome of approximately 630 kbp, with the exception of the termite Mastotermes darwiniensis ( approximately 590 kbp) and Cryptocercus punctulatus ( approximately 614 kbp), a representative of the sister group of termites. Such genome reduction may have led to the ultimate loss of Blattabacterium in all termites other than Mastotermes. In this study, we sequenced 11 new Blattabacterium genomes from three species of Cryptocercus in order to shed light on the genomic evolution of Blattabacterium in termites and Cryptocercus. All genomes of Cryptocercus-derived Blattabacterium genomes were reduced ( approximately 614 kbp), except for that associated with Cryptocercus kyebangensis, which comprised 637 kbp. Phylogenetic analysis of these genomes and their content indicates that Blattabacterium experienced parallel genome reduction in Mastotermes and Cryptocercus, possibly due to similar selective forces. We found evidence of ongoing genome reduction in Blattabacterium from three lineages of the C. punctulatus species complex, which independently lost one cysteine biosynthetic gene. We also sequenced the genome of the Blattabacterium associated with Salganea taiwanensis, a subsocial xylophagous cockroach that does not vertically transmit gut symbionts via proctodeal trophallaxis. This genome was 632 kbp, typical of that of nonsubsocial cockroaches. Overall, our results show that genome reduction occurred on multiple occasions in Blattabacterium, and is still ongoing, possibly because of new associations with gut symbionts in some lineages