Trypanosoma brucei gambiense group 1 is distinguished by a unique amino acid substitution in the HpHb receptor implicated in human serum resistance

Trypanosoma brucei rhodesiense (Tbr) and T. b. gambiense (Tbg), causative agents of Human African Trypanosomiasis (sleeping sickness) in Africa, have evolved alternative mechanisms of resisting the activity of trypanosome lytic factors (TLFs), components of innate immunity in human serum that protect against infection by other African trypanosomes. In Tbr, lytic activity is suppressed by the Tbr-specific serum-resistance associated (SRA) protein. The mechanism in Tbg is less well understood but has been hypothesized to involve altered activity and expression of haptoglobin haemoglobin receptor (HpHbR). HpHbR has been shown to facilitate internalization of TLF-1 in T.b. brucei (Tbb), a member of the T. brucei species complex that is susceptible to human serum. By evaluating the genetic variability of HpHbR in a comprehensive geographical and taxonomic context, we show that a single substitution that replaces leucine with serine at position 210 is conserved in the most widespread form of Tbg (Tbg group 1) and not found in related taxa, which are either human serum susceptible (Tbb) or known to resist lysis via an alternative mechanism (Tbr and Tbg group 2). We hypothesize that this single substitution contributes to reduced uptake of TLF and thus may play a key role in conferring serum resistance to Tbg group 1. In contrast, similarity in HpHbR sequence among isolates of Tbg group 2 and Tbb/Tbr provides further evidence that human serum resistance in Tbg group 2 is likely independent of HpHbR functio

Population genomics reveals the origin and asexual evolution of human infective trypanosomes

Evolutionary theory predicts that the lack of recombination and chromosomal re assortment in strictly asexual organisms results in homologous chromosomes irreversibly accumulating mutations and thus evolving independently of each other, a phenomenon termed the Meselson effect. We apply a population genomics approach to examine this effect in an important human pathogen, Trypanosoma brucei gambiense. We determine that T.b. gambiense is evolving strictly asexually and is derived from a single progenitor, which emerged within the last 10,000 years. We demonstrate the Meselson effect for the first time at the genome-wide level in any organism and show large regions of loss of heterozygosity, which we hypothesise to be a short-term compensatory mechanism for counteracting deleterious mutations. Our study sheds new light on the genomic and evolutionary consequences of strict asexuality, which this pathogen uses as it exploits a new biological niche, the human population

Examining the patterns and processes of speciation and species diversity in Australian Gehyra gecko lizards.

Understanding the process of speciation and the nature of relationships between species is one of the fundamental aims of evolutionary biology. These processes are integral to the study of species delimitation and taxonomy, phylogenetic reconstruction and evolutionary history and the study of speciation processes. Under this premise I evaluate a recently evolved and taxonomically challenging group– the Gehyra geckos of Australia, to gain a better understanding of how the process of speciation and species relationships have developed in this genus. My research has three main aims: 1) Explore the adequacy of current taxonomy in accounting for species diversity in the group and improve it where necessary: Gehyra have proven taxonomically troublesome historically, with extensive and geographically complex arrangements of genetic diversity apparently not associated with patterns of morphological diversity. I explored species delimitation and the taxonomic status of lineages within the arid-adapted Gehyra variegata species complex using multi-locus (mtDNA, nuclear loci, karyotypes) genetic, distribution and morphological data, generating the first comprehensive phylogenetic framework for the genus. I describe one new species and identify an additional five putative species. I support previously hypothesized high levels of cryptic diversity in the group and present a concentrated effort in taxonomically resolving the genus. 2) Evaluate previously proposed evolutionary scenarios for the diversification of the Australian Gehyra and propose a comprehensive evolutionary history of the group: Using a multi-locus dataset (one mtDNA locus, six nuclear loci), I generated a calibrated species tree of the group, which showed support for a late-Eocene to mid Miocene introduction of the genus to Australia from Asia and for the division of the Australian Gehyra into a tropically-adapted Gehyra australis species complex and a generally arid-adapted Gehyra variegata species complex containing morphologically transitionary species in the Kimberley region. My analyses did not support a previously suggested model of chromosomally driven speciation in Australian Gehyra and assert that diversification of both species complexes occurred simultaneously from the late Micoene through to the present. I undertook a quantitative evaluation of gene tree discordance in Gehyra, showing a high degree of discordance between genes for the group, further supporting the recent diversification of the group. 3) Examine possible processes of speciation in Australian Gehyra: I investigated a case study in which a geographically constrained, distinct population of Gehyra was shown to be morphologically and ecologically distinct but genetically indistinguishable from a comparatively widespread, geographically parapatric species. This indicates a scenario of emergent, ecological speciation and presents a model system in which the process of ecological speciation could be observed. It also contrasts previous studies highlighting allopatric speciation driving the Australian Gehyra radiation, showing ecological speciation may play an important role. In carrying out these studies, I have both explored the use of emergent methods for delimiting species and evaluating relationships between species, and significantly increased our understanding of the Australian Gehyra radiation. This body of work represents an ideal framework for rapid and effective evaluation of novel Gehyra species and will greatly assist in discovering and documenting the diversity of this problematic radiation in the future.Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 201

Data from: Delimiting species in recent radiations with low levels of morphological divergence: a case study in Australian Gehyra geckos

Recent conceptual and methodological advances have increased the ability to apply multifaceted approaches to species delimitation, which is particularly useful in delimiting recently diversified species where single lines of evidence lead to incorrect species delimitation or assignment of individuals to species (e.g. cryptic, morphological species and paraphyletic, hybridizing species). Species of the Australian Gehyra gecko radiation have historically proven difficult to delimit due the group’s uniform, almost continent-wide geographic distribution and conservative morphology, contrasting high chromosomal and genetic diversity. Using an integrated approach to species delimitation taking advantage of morphological, geographic distributional and multi-locus genetic data, we investigate the diversity within three Gehyra species from the Australian arid zone. Our results show that these species represent eight distinct phylogenetic lineages, which display different patterns of morphological distinction and reproductive isolation. Using a recently developed Bayesian species delimitation method, we also find different levels of support for putative species dependent on priors for population size and timing of diversification assumed. Our results show that the current taxonomy does not adequately account for the diversity of the group. Discrepancies between lines of evidence indicate that diversification of the group is recent and ongoing, thus posing challenges for both species concepts and delimitation

Data from: Morphological differentiation correlates with ecological but not genetic divergence in a Gehyra gecko.

Body size affects life history, the ecological niche of an organism and its interactions with other organisms. Resultantly, marked differences in body size between related organisms are often an indication of a species boundary. This is particularly evident in the Gehyra variegata species complex of geckos, which displays differential body sizes between genetically divergent species, but high levels of intra-specific morphological conservatism. We report on a Gehyra population that displays extraordinary body size differentiation in comparison with other G. variegata species. We used morphological and environmental data to show this population is phenotypically and ecologically distinct from its parapatric congener G. lazelli and that morphology and ecology are significantly correlated. Contrastingly, mtDNA analysis indicates paraphyly between the two groups and allele frequencies at six microsatellite loci show no population structure concordant with morpho/eco-type. These results suggest either ecological speciation or environmentally induced phenotypic polymorphism, in an otherwise morphologically conservative group

Comparative genomics of Japanese encephalitis virus shows low rates of recombination and a small subset of codon positions under episodic diversifying selection.

Orthoflavivirus japonicum (JEV) is the dominant cause of viral encephalitis in the Asian region with 100,000 cases and 25,000 deaths reported annually. The genome is comprised of a single polyprotein that encodes three structural and seven non-structural proteins. We collated a dataset of 349 complete genomes from a number of public databases, and analysed the data for recombination, evolutionary selection and phylogenetic structure. There are low rates of recombination in JEV, subsequently recombination is not a major evolutionary force shaping JEV. We found a strong overall signal of purifying selection in the genome, which is the main force affecting the evolutionary dynamics in JEV. There are also a small number of genomic sites under episodic diversifying selection, especially in the envelope protein and non-structural proteins 3 and 5. Overall, these results support previous analyses of JEV evolutionary genomics and provide additional insight into the evolutionary processes shaping the distribution and adaptation of this important pathogenic arbovirus

H3 alignment

H3 histone alignmen

PRL-R alignment

PRL-R alignmen