Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils.

Devil facial tumour 1 (DFT1) is a transmissible cancer clone endangering the Tasmanian devil. The expansion of DFT1 across Tasmania has been documented, but little is known of its evolutionary history. We analysed genomes of 648 DFT1 tumours collected throughout the disease range between 2003 and 2018. DFT1 diverged early into five clades, three spreading widely and two failing to persist. One clade has replaced others at several sites, and rates of DFT1 co-infection are high. DFT1 gradually accumulates copy number variants (CNVs) and its telomere lengths are short but constant. Recurrent CNVs reveal genes under positive selection, sites of genome instability and repeated loss of a small derived chromosome. Cultured DFT1 cell lines have increased CNV frequency and undergo highly reproducible convergent evolution. Overall, DFT1 is a remarkably stable lineage whose genome illustrates how cancer cells adapt to diverse environments and persist in a parasitic niche.This work was supported by grants from Wellcome (102942/Z/13/A), the National Science Foundation (DEB-1316549), the University of Tasmania Foundation (Eric Guiler Tasmanian Devil Research Grants), the Australian Research Council (DE 170101116) and a Philip Leverhulme Prize from the Leverhulme Trust. YMK was supported by a Herchel Smith Postgraduate Fellowship

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

Devil facial tumour 1 (DFT1) is a transmissible cancer clone endangering the Tasmanian devil. The expansion of DFT1 across Tasmania has been documented, but little is known of its evolutionary history. We analysed genomes of 648 DFT1 tumours collected throughout the disease range between 2003 and 2018. DFT1 diverged early into five clades, three spreading widely and two failing to persist. One clade has replaced others at several sites, and rates of DFT1 coinfection are high. DFT1 gradually accumulates copy number variants (CNVs), and its telomere lengths are short but constant. Recurrent CNVs reveal genes under positive selection, sites of genome instability, and repeated loss of a small derived chromosome. Cultured DFT1 cell lines have increased CNV frequency and undergo highly reproducible convergent evolution. Overall, DFT1 is a remarkably stable lineage whose genome illustrates how cancer cells adapt to diverse environments and persist in a parasitic niche

'A tragedy as old as history':Medical responses to infertility and artificial insemination by donor in 1950s Britain

This chapter will explore how the infertile patient was characterized, perceived, and treated by the medical profession in 1950s England and Scotland. Such was the concern that this subject engendered in postwar Britain that a Departmental Committee was appointed in 1958 (known as the Feversham Committee) to investigate infertility and its treatment through artificial insemination. The written and oral evidence submitted by medical witnesses to that Committee offers rich insights into medical thinking and practice, and into the complex sociomedical politics and ethical anxieties which surrounded the topic. The testimony of legal and religious witnesses will also be explored to a more limited extent in order to offer some context to medical understandings and treatments of infertility. It will be considered how women’s bodies, personalities, and even agency in proactively seeking motherhood through artificial insemination were heavily pathologized in medical and religious discourses, but also how the men involved – husbands, sperm donors and even doctors – did not escape this tendency to pathologize

Investigation of early-diverging land plant metabolism

The terrestrialisation of embryophytes was preceded by, and precipitated, the evolution of diverse metabolic capabilities to aid growth and survival on land. A broad understanding of metabolism across all land plants is important for the discovery of novel metabolic enzymes and pathways which may be used commercially and to design metabolic engineering strategies for crop improvement. However, metabolic research has mainly focused on a small number of angiosperm crops and model plants. The research described in this thesis was carried out with the goal of correcting this knowledge bias, using bioinformatic and computational techniques to characterise metabolism, and its associated evolutionary processes, in early-diverging land plants. The work is presented as three manuscripts. In the first I used metabolic modelling to investigate central metabolic fluxes in the liverwort Marchantia polymorpha, which exhibits extremely low carbon assimilation rates as a consequence of the low mesophyll conductance characteristic of bryophytes. I found that my constrained stoichiometric model of Marchantia was unable to achieve experimentally-defined growth rates without increasing carbon conversion efficiency by requiring either a very low cell maintenance cost, or some form of nocturnal carbon recycling. In the second manuscript I carried out a comparative analysis of secondary metabolism across the Chloroplastida, using homologous relationships between metabolic genes in 72 land plants and algae. The findings, supported by gene absences/presences in a further 305 plant and algal transcriptomes, elucidate details of the evolution of several phytohormone and biopolymer biosynthetic pathways. Finally, I used phylogenetic profiling and co-expression analysis to identify candidate genes associated with the previously discussed biosynthetic pathways. The results were validated by the identification of several known gene associations, and additional genes with various potential functional relationships with the pathways in question were detected

Low Incubation Temperature Induces DNA Hypomethylation in Lizard Brains

Developmental stress can have organizational effects on suites of physiological, morphological, and behavioral characteristics. In lizards, incubation temperature is perhaps the most significant environmental variable affecting embryonic development. Wall lizards (Podarcis muralis) recently introduced by humans from Italy to England experience stressfully cool incubation conditions, which we here show reduce growth and increase the incidence of scale malformations. Using a methylation-sensitive AFLP protocol optimized for vertebrates, we demonstrate that this low incubation temperature also causes hypomethylation of DNA in brain tissue. A consistent pattern across methylation-susceptible AFLP loci suggests that hypomethylation is a general response and not limited to certain CpG sites. The functional consequences of hypomethylation are unknown, but it could contribute to genome stability and regulation of gene expression. Further studies of the effects of incubation temperature on DNA methylation in ectotherm vertebrates may reveal mechanisms that explain why the embryonic thermal environment often has physiological and behavioral consequences for offspring

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

Devil facial tumour 1 (DFT1) is a transmissible cancer clone endangering the Tasmanian devil. The expansion of DFT1 across Tasmania has been documented, but little is known of its evolutionary history. We analysed genomes of 648 DFT1 tumours collected throughout the disease range between 2003 and 2018. DFT1 diverged early into five clades, three spreading widely and two failing to persist. One clade has replaced others at several sites, and rates of DFT1 coinfection are high. DFT1 gradually accumulates copy number variants (CNVs), and its telomere lengths are short but constant. Recurrent CNVs reveal genes under positive selection, sites of genome instability, and repeated loss of a small derived chromosome. Cultured DFT1 cell lines have increased CNV frequency and undergo highly reproducible convergent evolution. Overall, DFT1 is a remarkably stable lineage whose genome illustrates how cancer cells adapt to diverse environments and persist in a parasitic niche