Peptide hormones are critical modulators of physiology and development in humans and have been well characterized for their effects on humans and other mammals. The question of the origin of the many families of peptide hormones in mammals is pressing, as it gives us a window into the evolution of important systems in all extant animals and their common ancestors. The focus of this thesis was to examine the origin of a select group of peptide hormone families including the secretin superfamily, reproductive neuropeptides, insulin and the insulin-like peptides, and stanniocalcin. The evolution of the secretin superfamily was found to have originated with the vertebrates, and new information from the genomes of basal vertebrates like the lamprey Petromyon marinus and elephant shark Callorhinchus milii allows us to better piece together the gene duplications that produced the current hormone family in humans and fish. The reproductive hormones, including gonadotropin-releasing hormone (GnRH), vasopressin/oxytocin, and kisspeptin were examined, with a focus on the evolution of their G protein-coupled receptors. GnRH was found to have originated in the early bilaterians, and its receptors clearly belong to a superfamily also containing receptors of the related neuropeptides adipokinetic hormone and corazonin, which have only been found in protostome invertebrates. Vasopressin/oxytocin receptors share a common ancestor with the GnRH receptors, although their peptides are not structurally related, and evolved at a similar time. Kisspeptin evolved later, within the vertebrates, however its receptors are closely related to an orphan receptor in protostome invertebrates, GPR54, with an unknown ligand. Insulin family members from the tunicate Ciona intestinalis and the amphioxus Branchiostoma floridae were identified, isolated and characterized to determine the nature of the insulin superfamily at the origin of the chordates, and it appears this family was well-developed already. Finally, the calcium-regulator stanniocalcin was identified, isolated and characterized in C. intestinalis and compared with the vertebrate and amphioxus stanniocalcins. A group of stanniocalcins were also discovered in a wide range of both protostomes and unicellular eukaryotes, indicating this ancient group of neurohormones appeared early in eukaryotic evolution. / Graduate

Phylogenetics is the study of the evolutionary relationship between species. Inference of phylogeny relies heavily on statistical models that have been extended and refined tremendously over the past years into very complex hierarchical models. Paper I introduces probabilistic graphical models to statistical phylogenetics and elaborates on the potential advantages a unified graphical model representation could have for the community, e.g., by facilitating communication and improving reproducibility of statistical analyses of phylogeny and evolution. Once the phylogeny is reconstructed it is possible to infer the rates of diversification (speciation and extinction). In this thesis I extend the birth-death process model, so that it can be applied to incompletely sampled phylogenies, that is, phylogenies of only a subsample of the presently living species from one group. Previous work only considered the case when every species had the same probability to be included and here I examine two alternative sampling schemes: diversified taxon sampling and cluster sampling. Paper II introduces these sampling schemes under a constant rate birth-death process and gives the probability density for reconstructed phylogenies. These models are extended in Paper IV to time-dependent diversification rates, again, under different sampling schemes and applied to empirical phylogenies. Paper III focuses on fast and unbiased simulations of reconstructed phylogenies. The efficiency is achieved by deriving the analytical distribution and density function of the speciation times in the reconstructed phylogeny. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Accepted.</p>

The signalling cascade of rods and cones use different but related protein components. Rods and cones, emerged in the common ancestor of vertebrates around 500 million years ago around when two whole genome duplications took place, named 1R and 2R. These generated a large number of additional genes that could evolve new or more specialised functions. A third event, 3R, occurred in the ancestor of teleost fish.  This thesis describes extensive phylogenetic and comparative synteny analyses of the opsins, transducin and phosphodiesterase (PDE6) of this cascade by including data from a wide selection of vertebrates. The expression of the zebrafish genes was also investigated. The results show that genes for these proteins duplicated in 1R and 2R as well as some in 3R. Expression analyses of the zebrafish genes revealed additional specialisations for the 3R gene duplicates. The transducin beta subunit genes, gnb1a and gnb1b, show co-localisation in rods but are expressed at different levels. Gnb3a and gnb3b show different expression in the adult retina with low expression of gnb3a and expression of gnb3b in cones of the dorso-medial retina. The transducin gamma subunit genes gngt2a and gngt2b are expressed in the ventral and dorso-medial retina respectively. The both of PDE6 gamma subunit genes, pde6ga and pde6gb are both expressed in rods but pde6ga shows rhythmic changes of expression with low daytime levels. Pde6ha and pde6hb are expressed in cones however pde6ha show high daytime expression. All investigated transducin and PDE6 subunit genes, but gnb1b, were also expressed in the adult pineal complex or at some point during development. These results provide compelling evidence that the 1R and 2R genome duplications facilitated the evolution of rods and cones by generating gene duplicates that could evolve distinct expression and function. This supports existence of colour vision before the origin of vertebrates, elaboration of this in the early vertebrate ancestor, along with origin of the black-and-white dim-light vision of rods. Furthermore, the different expression patterns observed in the zebrafish retina for teleost 3R duplicates demonstrate multiple additional specialisations.

tRNA genes have the fundamental role of translating the genetic code during protein synthesis. Beyond solely a passive decoding role, the tRNA pool exerts selection pressures on the codon usage of organisms and the viruses that infect them because processing codons read by rare tRNAs can be slow or even erroneous. To better understand the interactions of codons and anticodons in eukaryotic species, we first investigated whether tRNAs packaged into HIV-1 particles may relate to the poor codon usage of HIV-1 genes. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding poorly adapted codons are overrepresented in HIV-1 virions. Because the affinity of Gag-Pol for all tRNAs is non-specific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Moreover, differences that we found in the codon usage between early and late genes suggest alterations in the tRNA pool are induced late in viral infection. Next, we tested whether a reduced tRNA anticodon pattern, which was called into question by predicted tRNA datasets, is maintained across eukaryotes. tRNA prediction methods are prone to falsely identifying tRNA-derived repetitive sequences as functional tRNA genes. Thus, we proposed and tested a novel approach to identify falsely predicted tRNA genes using phylogenetics. Phylogenetic analysis removed nearly all the genes deviating from the anticodon pattern, therefore the anticodon pattern is reaffirmed across eukaryotes.

The Rhodophyta (red algae) are an ancient crown group of the Eukarya (ca. 1400-1500 million years), comprised of 5000 - 6000 species. Gametophytes of taxa excluding the speciose Class Florideophyceae are typically of very simple unicellular, filamentous or foliose morphologies. These simple morphologies are often homoplasious (resulting from convergent or parallel evolution) and can be indistinguishable among distinct taxa, leading to cryptic species. As a result, historical morphology-based taxonomy is often not congruent with evolutionary history. Intraspecific genetic variation is not yet characterized for non-Florideophyceae taxa. Here the intraspecific genetic variation was characterized for a locally endemic, morphologically distinct bangiophyte red alga, Bangia maxima Gardner using inter simple sequence repeat (ISSR) patterns from 91 individual filaments across seven local populations. A high degree of genetic variation was observed over very small distances (< 25 cm) and very little genetic exchange was observed between populations. It is possible that B. maxima is a true endemic species and its population dynamics may differ from other Bangia species. Metrics of sequence-based identification rely on genetic divergence among isolates to distinguish taxonomic units independent of morphology. Such metrics are especially useful for morphologically simple or cryptic species. The mitochondrial cytochrome oxidase c subunit 1 gene has been proposed for the Florideophyceae. An evaluation of this gene as a metric for non-Florideophyceae taxa was undertaken and limited utility was demonstrated in most lineages of Rhodophyta due to poor or inconsistent amplification and conflicts with nuclear and plastid phylogenies. Patterns of genetic divergence among taxa are used to infer evolutionary relationships. The nuclear ribosomal small subunit (nSSU rRNA) is the taxonomically broadest pool of gene sequence data for the Rhodophyta. The use of stochastic models of nucleotide evolution is the most common approach to inferring phylogenies using this gene, ignoring much of its evolutionary information as different characters that contribute to secondary structure (e.g. paired nucleotides) are treated independently. The incorporation of structural information leads to more biologically realistic evolutionary models increasing phylogenetic resolution. Parametric models incorporating structural information were used here to more fully resolve phylogenies for all known Rhodophyta lineages. Novel phylogenetic topologies were observed and well supported for each Class within the Rhodophyta resulting in a number of formally proposed or suggested taxonomic revisions. These include phylogenetic resolution of Rhodophyta Classes, support for the introduction of 11 genera within the Bangiales and support for various taxonomic revisions within the Florideophyceae previously proposed but not yet fully adopted. As structure evolves more slowly than its constituent sequence, secondary structure elements can further resolve evolutionary relationships, especially in lineages as old as the Rhodophyta. A novel encoding of secondary structure elements and subsequent multivariate analysis was performed for all known Rhodophyta nSSU rRNA gene sequences, reinforcing phylogenetic results. Computer programs developed for these analyses are publicly available. The analyses presented here significantly advanced understanding of the evolutionary distribution of cryptic species within the Rhodophyta. Furthermore, useful methods for the characterization of such species are presented, as is a demonstration of the utility of biologically realistic sequence models parameterizing nSSU rRNA structure in resolving ambiguous phylogenetic relationships. Most importantly, this work also represents a significant improvement toward taxonomy congruent with evolutionary history for the Rhodophyta.

Biodiversity in the tropics is disproportionately high compared to other habitats, and also under disproportionate threat from human impact. It is necessary to understand how this diversity evolved and how it is partitioned across space in order to preserve it. In this thesis I construct phylogenies of tropical forest dependent vertebrates from Southeast Asia and the islands of the Sunda shelf, a region referred to as Sundaland. I focus on the tree squirrels (genus Sundasciurus) and Asian barbets (Aves: Family Megalaimidae), two taxa with similar ecological characteristics. I use these phylogenies to test hypotheses that have been put forward to explain high levels of tropical diversity including the Pleistocene pump and museum hypotheses. I also use phylogenies to elucidate phylogeographic patterns within the region. I find no evidence for an increase in speciation in the Pleistocene, but I do find within species structure that dates to this period. Common phylogeographic patterns were identified between many forest dependent vertebrates that suggest that populations on the island of Sumatra are generally more closely related to Malay Peninsula populations than to populations on Borneo. From a methodological viewpoint we propose careful usage of universal primers in ancient DNA studies because of our finding of increased risk of amplifying pseudogenes of the mtDNA.

The Capsalidae is a diverse family of ectoparasites of marine fish (Platyhelminthes: Monogenea). It is a large family with approximately 180 described species and many more yet to be discovered. Capsalids have a global distribution and parasitise a diversity of hosts from the Chondrichthyes to bony fishes. A morphological classification exists for the family based on a few key characters such as testes number, their arrangement and morphology of the posterior attachment organ (haptor). Phylogenetic relationships within the family and its position within the Monogenea are largely unexplored. I have used various molecular phylogenetic techniques to resolve relationships and explore the evolution and radiation of this family. Specimens from the Capsalidae and other monogenean families (outgroups) were obtained through fresh collections and generous donations by other parasitologists. Specimens were stored in 95% undenatured ethanol. Three unlinked nuclear genes (28S ribosomal RNA, Histone 3 and Elongation Factor 1 α) and two mitochondrial genes (Cytochrome Oxidase 3 and Cytochrome B) were amplified for 78 capsalid taxa in 28 genera representing all nine subfamilies and 30 outgroup taxa (eight Polyopisthocotylea and 22 Monopisthocotylea). Analyses showed the Capsalidae is monophyletic, with the sister group remaining unresolved. Some analyses supported Gyrodactylidae and Udonellidae as the sister group but in other analyses, it was unresolved with the Monocotylidae and Microbothriidae also possible sister groups. The Capsalinae, Encotyllabinae and Nitzschiinae are monophyletic, but analyses did not support monophyly for the Benedeniinae, Entobdellinae and Trochopodinae. Monophyly was supported for Capsala, Capsaloides, Encotyllabe, Entobdella, Listrocephalos, Neobenedenia, Nitzschia and Tristoma, but Metabenedeniella is paraphyletic and Benedenia and Neoentobdella are polyphyletic. Comparisons of the distribution of character states for the small number of morphological characters on a molecular phylogeny show a high frequency of apparent homoplasy. Consequently the current morphological classification for the Capsalidae shows little correspondence with the phylogenetic hypotheses I present. I also sequenced the first complete mitochondrial (mt) genome for a capsalid species, Benedenia seriolae. The mt genome of B. seriolae shows some tRNA rearrangements in comparison to three Gyrodactylus spp. (Gyrodactylidae), the only other complete monopisthocotylean mt genomes sequenced. It also lacks the duplicated, conserved non-coding regions present in Gyrodactylus spp. making the genome smaller in size. I combined this genome with other available platyhelminth mt genomes to investigate the monophyly of Monogenea and the evolution of diet across the Neodermata. Results confirm paraphyly for the Monogenea and also suggest paraphyly for the epidermal feeding Monopisthocotylea. I hypothesise that the Monopisthocotylea represent the first shift to parasitism in the Neodermata from a free living ancestor and following this, there was a dietary shift to blood feeding (Polyopisthocotylea). The Digenea and Cestoda independently evolved dietary specialisations to suit their diverse microhabitats and broad range of vertebrate final hosts. Using Elongation Factor 1 α I have estimated molecular divergence dates for the Neodermata, Monogenea and Capsalidae. Molecular clock analyses estimate the Neodermata diverged from the free living platyhelminths 513 million years ago (mya) (95% HPD [highest posterior density]: 473–605) before the appearance of vertebrates in the fossil record. The Monogenea diverged from the other neodermatan classes 441 mya (95% HPD: 420–547) coinciding with the appearance of fish in the fossil record. The most recent common ancestor of the Capsalidae arose approximately 235 million years ago (95% HPD: 200–274) following the Permian/Triassic extinction event and coinciding with the diversification of bony fishes in the marine environment. I compared the capsalid phylogeny to a phylogeny of fishes that I generated using eight nuclear and three mt genes to explore the evolution and the radiation of the Capsalidae across fishes. There is no significant global signal of coevolution with only five parasite-host associations that may be a result of coevolution. Estimated molecular divergence dates are also compared and do not reveal temporal congruence. Radiation of the family may have been driven by host switching constrained by shared host ecology, biology, behaviour and plasticity in morphological adaptations by the parasites. This study advances our understanding of the evolution of this monogenean family and provides insights into the evolution of the Neodermata and the complicated realities of reconstructing the evolutionary history of parasitic groups. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1522353 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

Haplothrips victoriensis Bagnall (Thysanoptera: Phlaeothripidae) is an indigenous thrips of southern Australia. It is known as a predator of two-spotted mite. This project investigated various biological characteristics of H. victoriensis as a precursor to its potential use in biological control. In addition, H. victoriensis is very difficult to distinguish from other Haplothrips species in terms of morphology, especially as there are no keys to larvae. DNA barcoding and morphology of the larval stages are used to address these issues. The thesis is divided into seven chapters comprising an introduction, four main research chapters, conclusion and reference chapters. Chapter 2 covers the culturing techniques for H. victoriensis. Some new cases and rearing processes were designed to culture H. victoriensis and its prey. These were following series of rearing techniques investigated including rearing H. victoriensis for egg collection, H. victoriensis larvae and adults for biological and morphological observations, mass rearing of H. victoriensis, WFT and Tyrophagus mites, and rearing WFT for egg collection. Predatory H. victoriensis was reared in the laboratory with various diets of honey, pollen, Tyrophagus mites and western flower thrips (WFT). Chapter 3 investigates the biological development of H. victoriensis, including egg, larva, prepupa, pupa and adult stages. Haplothrips victoriensis fed with 10% honey solution, mixed pollen and Tyrophagus eggs took about 16-22 days to develop from eggs to adults at 25 oC. Developmental times of immature H. victoriensis varied when fed on different food sources. The longevity of H. victoriensis was significantly different with different diets. Chapter 4 examines predatory and cannibalistic characteristics and consumption of H. victoriensis on various prey. Haplothrips victoriensis was found to feed on many kinds of common prey; Two spotted mite (TSM), Tyrophagus mite, WFT, spotted alfalfa aphid, greenhouse whitefly and diamond back moth but not on ash whitefly. Importantly, H. victoriensis was also found to be cannibalistic which might affect population fluctuations in the laboratory and in the field. Chapter 5 examines the ecology and hosts of H. victoriensis in South Australia and taxonomy of H. victoriensis and some other Haplothrips species being similar to H. victoriensis. Haplothrips victoriensis was found to live on flowers from a range of different plant families. Morphological characteristics of the immature stages of H. victoriensis and a key developed to separate common Haplothrips in S.A. As well, COI was used to possibly identify H. victoriensis and its morphologically similar taxa and investigate whether H. victoriensis is a single species or perhaps contains cryptic species. None of the specimens of H. victoriensis included in the analyses showed any variation in COI indicating a single species for horticultural areas in S.A. Chapter 6 provides an overall discussion of the main results and indicates areas of future research. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1522174 / Thesis (M.Sc.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

There are over 18,500 living species of acanthomorph (spiny-rayed fishes), and they represent half of all living fish species and a third of extant vertebrates. They inhabit countless ecological niches, they are incredibly diverse, and they have developed a number of specialised morphological innovations. The earliest acanthomorphs are known from the Cenomanian, but they were neither diverse not abundant during the Cretaceous period. Following the end-Cretaceous extinction event, the acanthomorphs radiated, and by the Eocene they were anatomically modern. However, our understanding of the relationships between most fossil and living acanthomorphs, and the macroevolutionary processes behind their rise to dominance in the Recent, are poorly known. In this thesis, I aimed to develop our understanding of the evolution of the acanthomorphs by combining palaeontological and neontological data. I undertook three separate projects to accomplish this. First, I studied the anatomy two fossil representatives (†Aipichthys pretiosus and †'Aipichthys' nuchalis) of a primitive acanthomorph lineage, the lampridomorphs. I then placed these taxa in a phylogenetic analysis to reveal the pattern of character evolution leading to the crown-group. Second, I aimed to understand the morpho- logical condition at the base of the acanthomorph tree by studying the relationships between two extinct groups (†Ctenothrissiformes and †Pattersonichthyiformes) that may have branched from the acanthomorph stem. Phylogenetic analyses utilising morphological and molecular data support a stem ctenosquamate placement for these taxa. Third, using a timescaled supertree, I studied the evolution of one of the major acanthomorph innovations, the protrusile upper jaw. The combination of palaeontological and neontological data provided deep insight into the evolution of the acanthomorphs, and allowed for the identification of patterns and processes that could not be identified from studying extant taxa in isolation.

abstract: Leprosy and tuberculosis are age-old diseases that have tormented mankind and left behind a legacy of fear, mutilation, and social stigmatization. Today, leprosy is considered a Neglected Tropical Disease due to its high prevalence in developing countries, while tuberculosis is highly endemic in developing countries and rapidly re-emerging in several developed countries. In order to eradicate these diseases effectively, it is necessary to understand how they first originated in humans and whether they are prevalent in nonhuman hosts which can serve as a source of zoonotic transmission. This dissertation uses a phylogenomics approach to elucidate the evolutionary histories of the pathogens that cause leprosy and tuberculosis, Mycobacterium leprae and the M. tuberculosis complex, respectively, through three related studies. In the first study, genomes of M. leprae strains that infect nonhuman primates were sequenced and compared to human M. leprae strains to determine their genetic relationships. This study assesses whether nonhuman primates serve as a reservoir for M. leprae and whether there is potential for transmission of M. leprae between humans and nonhuman primates. In the second study, the genome of M. lepraemurium (which causes leprosy in mice, rats, and cats) was sequenced to clarify its genetic relationship to M. leprae and other mycobacterial species. This study is the first to sequence the M. lepraemurium genome and also describes genes that may be important for virulence in this pathogen. In the third study, an ancient DNA approach was used to recover M. tuberculosis genomes from human skeletal remains from the North American archaeological record. This study informs us about the types of M. tuberculosis strains present in post-contact era North America. Overall, this dissertation informs us about the evolutionary histories of these pathogens and their prevalence in nonhuman hosts, which is not only important in an anthropological context but also has significant implications for disease eradication and wildlife conservation. / Dissertation/Thesis / Appendix_A / Appendix_B / Appendix_F / Doctoral Dissertation Evolutionary Biology 2017