Human species display complex intraspecies population structure and unparalleled behavioral and cultural diversity. In order to elucidate human population history and pattern of evolutionary change of socio-cultural and ecological traits, the first composite phylogenetic tree of 574 human populations (ethno-linguistic groups) was created on the basis of 129 recently published phylogenetic hypotheses based on genomic, genetic and linguistic data, utilizing supertree method matrix representation with parsimony. Subsequently, 56 selected socio-cultural and ecological characters based on ethnographic cross-cultural data were optimized on topology of obtained supertrees in order to reconstruct patterns of evolutionary change and states present in ancestral populations. The results are discussed in the light of recent studies of human phylogeography and cultural phylogenetic studies.

abstract: Vertebrate genomes demonstrate a remarkable range of sizes from 0.3 to 133 gigabase pairs. The proliferation of repeat elements are a major genomic expansion. In particular, long interspersed nuclear elements (LINES) are autonomous retrotransposons that have the ability to "cut and paste" themselves into a host genome through a mechanism called target-primed reverse transcription. LINES have been called "junk DNA," "viral DNA," and "selfish" DNA, and were once thought to be parasitic elements. However, LINES, which diversified before the emergence of many early vertebrates, has strongly shaped the evolution of eukaryotic genomes. This thesis will evaluate LINE abundance, diversity and activity in four anole lizards. An intrageneric analysis will be conducted using comparative phylogenetics and bioinformatics. Comparisons within the Anolis genus, which derives from a single lineage of an adaptive radiation, will be conducted to explore the relationship between LINE retrotransposon activity and causal changes in genomic size and composition. / Dissertation/Thesis / M.S. Biology 2013

abstract: Studies of ancient pathogens are moving beyond simple confirmatory analysis of diseased bone; bioarchaeologists and ancient geneticists are posing nuanced questions and utilizing novel methods capable of confronting the debates surrounding pathogen origins and evolution, and the relationships between humans and disease in the past. This dissertation examines two ancient human diseases through molecular and bioarchaeological lines of evidence, relying on techniques in paleogenetics and phylogenetics to detect, isolate, sequence and analyze ancient and modern pathogen DNA within an evolutionary framework. Specifically this research addresses outstanding issues regarding a) the evolution, origin and phylogenetic placement of the pathogen causing skeletal tuberculosis in New World prior to European contact, and b) the phylogeny and origins of the parasite causing the human leishmaniasis disease complex. An additional chapter presents a review of the major technological and theoretical advances in ancient pathogen genomics to frame the contributions of this work within a rapidly developing field. This overview emphasizes that understanding the evolution of human disease is critical to contextualizing relationships between humans and pathogens, and the epidemiological shifts observed both in the past and in the present era of (re)emerging infectious diseases. These questions continue to be at the forefront of not only pathogen research, but also bioarchaeological and paleopathological scholarship. / Dissertation/Thesis / Doctoral Dissertation Anthropology 2014

Esta tese de doutorado versa sobre relações filogenéticas, evolução e biogeografia das espécies do gênero Ramphastos, representado pelos tucanos. / This PhD thesis is about phylogenetics, evolution and biogeography of the species of the genus Ramphastos (toucans).

O presente trabalho trata da revisão taxonômica e análise filogenética do gênero Armitermes Wasman, 1897 (Termitidae, Nasutitermitinae), que até esta revisão contava com 12 espécies: A. armiger, A. cerradoensis, A. euamignathus, A. gnomus, A grandidens, A. holmgreni, A. lane, A. manni, A. minutus, A. peruanus, A. projectidens e A. teevani, ocorrendo em toda Região Neotropical. Nesse trabalho, além da proposta de quatro espécies novas e duas sinonímias (A. cerradoensis com A. euamignathus e A. projectidens com A. manni), também se realizou uma análise filogenética e o resultado corrobora a criação de quatro novos gêneros, propostos com base no estudo da morfologia. Todos os soldados foram descritos e ilustrados, além das mandíbulas e tubo digestivo do operário e da casta do alado, quando disponível. Também foram incluídas chaves dicotômicas, baseadas na casta do soldado, para identificação das espécies dos gêneros propostos, além de mapas com a distribuição geográfica das espécies. / The present work deals with the taxonomic revision of the genus Armitermes Wasman, 1897 (Termitidae, Nasutitermitinae), which counts 12 species at the moment: A. armiger, A. cerradoensis, A. euamignathus, A. gnomus, A. grandidens, A. holmgreni, A. lanei, A. manni, A. minutus, A. peruanus, A. projectidens and A. teevani, occurring in all Neotropics. In this work, besides the proposal of four new species and two new synonymies (A. cerradoensis with A. euamignathus and A. projectidens with A. manni), a phylogenetic analysis was accomplished and its results used to support the proposal of four new genera based on morphology. All soldiers were described and illustrated, the mandibles and digestive tract of the worker and the imago caste, when available. Dichotomous keys based on soldiers were also included, for identifying the species of the genera proposed, as well as maps with the geographical distribution of species.

The Bemisia tabaci (Gennadius) sibling species group is known to comprise several morphologically undistinguishable mitotypes which can be separated into seven major phylogeographic clades using the 3' half of the mitochondrial cytochrome oxidase I gene. B. tabaci is the only vector of begomoviruses; it transmits the complex of viruses that cause the cotton leaf curl disease, which has rapidly spread from Pakistan to the Philippines, at southeast of Asia, in the last decade. The study of B. tabaci mitotypes has been limited to variants of worldwide distribution and those associated to agroecosystems, however, the study of indigenous mitotypes has been scarce. This dissertation provides a comprehensive study of the phylogeography and population biology of mitotypes belonging to two major phylogeographic clades, the Asia II and the Americas. The Asia II major clade contains the highest number of mitotypes, in contrast, there is a large gap in knowledge about mitotypes associated to highly endemistic niches in the Americas. To study the population biology of mitotypes belonging to the Asia II major phylogeographic clade, two fragments of the mtCOI gene were amplified by polymerase chain reaction (PCR) for adult whiteflies sampled from mono and multi-cropping systems in the provinces of Punjab and Sindh in Pakistan. Phylogenetic analyses suggested that three indigenous mitotypes were distinctively distributed across ecosystems of Pakistan. The Asia II-5 and II-7 were found restricted to multi-cropping systems of Lahore, while the Asia II-1 was found widespread throughout the cotton growing region of Pakistan. Moreover, population analyses suggested the Asia II-1 is undergoing demographic expansion following a recent selective sweep or bottleneck. This event explains the predominance of Asia II-1 in Pakistan and its spread towards the southern province of Sindh. Additionally, differences in DNA polymorphism and diversity between mtCOI fragments derived in dissimilar evolutionary pairwise distances, suggestive of future implications in the “species” delimitation at a global scale when choosing one fragment over the other. The endosymbiotic bacteria assemblages associated to indigenous mitotypes Asia II-1, II-5 and II-7 were studied by analysis of 16S rRNA profiles. Besides the primary symbiont Portiera, Arsenophonus was detected almost fixed in the studied populations and several unique strains of Arsenophonus were detected in Asia II-5 and II-7, suggesting possible unique environmental adaptation capacities of these mitotypes. Hierarchical clustering of 16S rRNA profiles, proposed host-based and environmental-related differentiation. Additionally, the disruption of parallel cladogenesis between the primary symbiont and B. tabaci, disallows rejection of the hypothesis that gene flow among B. tabaci mitotypes occurs. To study the population biology of indigenous mitotypes belonging to the Americas major clade, adult whiteflies were sampled from ecosystems of nine provinces in Ecuador. Based on phylogenetic analyses, three indigenous and one invasive mitotype were detected. Among the indigenous, a previously unrecognized mitotype, named ECU3, was found. Moreover, mitotypes were found coexisting in five locations, and the invasive B is thought to have displaced endemic mitotypes to the northern and eastern coastal habitats of Ecuador.

Philosophiae Doctor - PhD / The Ruschieae is the most diverse and speciose tribe within the large subfamily Ruschioideae (Aizoaceae), with approximately 71 genera and a distribution centred in the arid parts of the Greater Cape Floristic Region (GCFR) of South Africa. Recent phylogenetic analyses provided the first insights into generic relationships within the tribe, with a number of novel generic relationships discovered. The tribal phylogeny recovered 12 large clades, of which the Conophytum-clade was one the most morphologically diverse based on leaf and capsule characters. The Conophytum-clade is an early-diverging lineage of the Ruschieae and includes the following 10 genera: Cheiridopsis N.E.Br., Conophytum N.E.Br., Enarganthe N.E.Br., Ihlenfeldtia H.E.K.Hartmann, Jensenobotrya A.G.J.Herre, Namaquanthus L.Bolus, Octopoma N.E.Br., Odontophorus N.E.Br., Ruschianthus L.Bolus and Schlechteranthus Schwantes. The present study presents an expanded phylogenetic analysis of the Conophytum-clade, with the sampling of the majority of species in the genera and a representative sampling (56% of species) of the speciose genus Conophytum. Phylogenetic data for up to nine plastid gene regions (atpB–rbcL, matK, psbJ–petA, rpl16, rps16, trnD– trnT, trnL–F, trnQᶷᶷᶢ–rps16, trnS–trnG) were produced for each of the sampled species. The produced plastid data was analyses using maximum parsimony, maximum likelihood and Bayesian inference. The combined plastid phylogenetic analyses were used in combination with morphological, anatomical and palynological data to assess generic and subgeneric circumscriptions within the clade. Upon assessment of generic circumscriptions in the Conophytum-clade, the number of recognised genera in the clade decreased from ten to seven. Arenifera A.G.J.Herre, which had not been sampled in any phylogeny of the Ruschieae, and Octopoma were recovered as polyphyletic, with species placed in the Conophytum-clade, while the type species was placed in the xeromorphic clade of the tribal phylogeny. The species of Arenifera and Octopoma placed in the Conophytum-clade were subsequently included in Schlechteranthus upon assessment of generic circumscriptions between the taxa. Two morphological groupings were recognised within Schlechteranthus, one including the species of Schlechteranthus and the other including species previously recognised as Arenifera and Octopoma. These two morphological groupings were treated as subgenera, with the erection of the new subgenus Microphyllus R.F.Powell. A detailed taxonomic revision of subgenus Microphyllus is presented with a key to species, descriptions of the species (including a new species: S. parvus R.F.Powell & Klak), known geographical distributions and illustrations of the species. In addition to the changes mentioned above, the expanded sampling and phylogenetic analyses of the Conophytum-clade recovered Ihlenfeldtia and Odontophorus embedded in Cheiridopsis. The species of Ihlenfeldtia were recovered with species of heiridopsis subgenus Aequifoliae H.E.K.Hartmann, while the species of Odontophorus were recovered as polyphyletic within the Cheiridopsis subgenus Odontophoroides H.E.K.Hartmann clade. Cheiridopsis was subsequently expanded to include the species of Ihlenfeldtia and Odontophorus, with these species accommodated in the subgenera of Cheiridopsis. The phylogenetic placement and relationship of these species was supported by the shared capsule morphology. The expanded sampling of the clade did not resolve the phylogenetic relationship of the monotypic genera Enarganthe, Jensenobotrya, Namaquanthus and Ruschianthus, with these genera unresolved in the Conophytum-clade. These genera however, exhibit a unique combination of morphological characters, such as a glabrous leaf epidermis and variation in pollen exine and colpi structure, in contrast to the other genera of the clade. The assessment of the generic circumscription of these genera, based on the molecular, morphological, anatomical and palynological data suggested that the generic statuses of these monotypic genera should be maintained. The expanded phylogenetic sampling of the morphologically diverse and speciose genus Conophytum recovered the genus as monophyletic. This monophyly was supported by the unique floral type in Conophytum, with the fused petaloid staminodes forming a tube. None of the sectional classifications were recovered as monophyletic but the phylogenetic analyses did recover a few clades which more or less corresponded to the current sectional classification of the genus. A number of clades were also recovered which included species from a range of different sections. Diverse leaf and floral traits were shown to have evolved numerous times across the genus. This was particularly interesting with regards to the selected floral traits, as the phylogeny indicated a number of switches in floral morphologies across the genus. The floral diversity was assessed in complex species communities of Conophytum across the GCFR, where up to 11 species of Conophytum are found occurring sympatrically, and floral traits were shown to be different across the species within the communities. Pollination competition and adaptation were suggested as possible drivers of floral diversity in the genus, with differences in phenology, anthesis and floral morphology within the species complex communities. The unique floral type of Conophytum has enabled the species to develop a diverse range of specialised flowers, with a variety of structures, scents and colours, resulting in the diverse floral morphologies found across the genus. The complex Conophytum species communities included both closely as well as distantly related species, suggesting the soft papery capsules of Conophytum are wind dispersed. This adaptation to long distance seed dispersal resulted in a significantly higher phylogenetic diversity in Conophytum when compared to its sister genus, Cheiridopsis. A population genetics study of Conophytum also suggested that the capsules may be wind dispersed, with an indication of genetic connectivity between the geographically isolated populations of C. marginatum Lavis across the Bushmanland Inselberg Region. Although the capsules are dispersed by wind, the seeds are released from the hygrochastic capsules by runoff during rainfall events. The relationship between seed dispersal and runoff is evident from the genetic structure of populations of C. maughanii N.E.Br. and C. ratum S.A.Hammer that occur on the tops and the surrounding bases of the inselbergs, as the drainage pattern was found to directly influence population structure in these species. In addition, the AFLP analyses provided insight into the conservation of the flagship species C. ratum. The summit populations of this species were shown to sustain the populations at the base of the Gamsberg. This finding is especially important, as the distribution of the species is restricted to the Gamsberg inselberg, where mining has already commenced as of this year. / National Research Foundation (NRF)

The fish order Pleuronectiformes (flatfishes) include over 800 fish species, and are generally considered to be monophyletic. Phylogenetic relationships within the order remain largely unresolved, particularly for the Paralichthyidae, a very poorly defined family. In addition to the lack of consensus on intrarelationships within this order, flatfish diversification patterns are still poorly understood. Here we want to test the hypothesis that (i) a densely sampled phylogenetic tree will help to unravel the phylogenetic relationships within flatfish, and (ii) that the formation of the Isthmus of Panama has played a role in the diversification of flatfish, following their distribution in both oceans, Atlantic and Pacific. Maximum likelihood and Bayesian analyzes were performed on a dataset consisting of nine mitochondrial and nuclear loci on a set of 309 flatfish species. The heterogeneity of substitution rates, known to cause phylogenetic errors in large multigene alignments, can be corrected by data partitioning, or by using heterogeneous site models. Very few studies have compared the effects of using these approaches. We present a robust phylogenetic tree with different heterogeneous and well-supported models, and the intraordinal relationships of flatfish are discussed in light of these results. We present evidence for three new suborders within the flatfishes. The monophyletic status of most families is corroborated. The family Paralichthyidae and the family Poecilopsettidae were found to be polyphyletic. Heterogeneous models have not been able to solve the deeper relationships between flatfish. We also show that flatfish diversification occurred in a few families in at least two stages, related to distinct geological events.

The rate that HIV-infected individuals progress to AIDS and death varies greatly. Viral load taken during the asymptomatic phase of the disease is one of the best-known predictors of HIV progression rate and transmission risk, and is known to be in uenced by both host and environmental factors. However, the role that the virus itself plays in determining the viral load is less clear. Previous studies have attempted to quantify the amount the viral genome in uences viral load, or the heritability of viral load, using transmission pairs and phylogenetic signal in small sample sizes, but have produced highly disparate estimates. E cient and accurate methods to estimate heritability have been utilised by quantitative geneticists for years, but are rarely applied to non-pedigree data. Here, I present a novel application of a population-scale method based in quantitative genetics to estimate the heritability of viral load in HIV using a viral phylogeny. This new phylogenetic method allows the inclusion of more samples than ever previously used, and avoids confounding e ects associated with transmission pair studies. This new method was applied to the two largest HIV subtypes found in the UK, subtypes B and C, using sequences and clinical data from UK-wide HIV databases. For subtype B (n=8,483) and C (n=1,821), I estimated that 5.7% (CI 2.8{8.6%) and 29.7% (CI 14.8{44.7%) of the variance in viral load is determined by the viral genome, respectively. These estimates suggest that viral in uence on viral load varies greatly between subtypes, with subtype C having much larger viral control over viral load than subtype B. I expanded the phylogenetic method to test whether the component of the viral load determined by the virus has changed over time. In subtype B, I foundevidence of a small but signi cant decrease in the viral component of viral load of -0.05 log10 copies/mL/yr. I built a stochastic, individual-based model capable of simulating a realistic HIV epidemic, with heritable viral loads that in uence transmission and disease progression, capable of generating data sets to assess the accuracy of phylogenetic methods. This was successfully used to generate epidemics approximating those in a small African village and a Western `men who have sex with men' community under a variety of conditions. To test the accuracy of the new phylogenetic heritability estimation method, simulated datasets were generated with the heritability of viral load set at values of 30%, 50%, 70%, and 90%. Unfortunately, complications in the heritability equation used prevented full assessment of the new phylogenetic method on the simulated data. Future development of the model will enable simulation of realistic viral loads under varying heritability values, enabling simulation of data sets that can be used to test this and other heritability estimation methods. This new phylogenetic method allows accurate estimation of heritability in large datasets, and has provided valuable insight into the viral in uence on viral load in HIV.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol) / The guttural toad, Amietophrynus gutturalis, Power 1927, is a common toad with a broad geographic range through much of temperate, sub-tropical and tropical southern and central Africa. Introduced to the islands of Mauritius and Reunion in the 1960’s, and subsequently to Cape Town in the 1990’s, the species has become invasive in its extra-limital ranges. Determining the invasion history of a species provides valuable information for conservation biologists and managers and it is fundamentally important for improving our understanding of the underlying processes of biological invasions. This study aimed to determine the source populations of the extra-limital populations from Mauritius and Cape Town. Furthermore, studies investigating genetic diversity and demographics of African Bufonidae are largely absent from the literature. Understanding the evolutionary history of the species may also assist with determining their invasive ability and identifying similar features in other bufonids such as Amietophrynus regularis and A. xeros. Using mtDNA sequence data from the 16S and ND2 markers four geographically distinct clades were identified through Bayesian phylogenies and haplotype networks. However, a spatial analysis of molecular variance (SAMOVA) indicated a grouping structure of three clades. A total of 16 haplotypes were identified from 53 samples for the 16S marker and 22 haplotypes were identified from 43 samples for the ND2 marker. Both the Mauritius and Cape Town invasive populations were found to have originated from the eastern clade. However, they matched the common haplotype from this region which was found across a vast area that spans the KwaZulu-Natal province and into the Mpumulanga and Limpopo provinces. This did not allow for identifying a more precise region for the origin of the founder populations. The presence of haplotypes unique to the Cape Town invasive population, which group with the eastern clade, indicates that there has potentially been more than one introduction event. Demographic analysis revealed a recent population expansion in both the northern (Fs = -2.92) and the eastern clades (Fs = -5.03). Significant genetic variation was found among groups (93.92%), with low variation among populations and among populations within groups. Population pairwise differences were found to be significantly different between all clades except between the central and the southern clade. There was a negligible difference in the genetic diversity of the invasive populations when compared to the eastern clade. The eastern clades’ genetic diversity was low compared to the two other clades and demographic analysis revealed that this region has undergone the most recent population expansion. The negligible difference between the eastern clades’ genetic diversity and both invasive populations indicate that founder effects and genetic bottlenecking should have no impact on the invasive populations. / National Research Foundation (NRF)