Comparative genomic approaches to human evolutionary history

Understanding the success of the human species is central to evolutionary anthropology. While we share many traits with our relatives the great apes, only humans migrated to all corners of the earth and domesticated other species, leading to the emergence of complex societies. Investigations into human genomes have shown that they are a rich source of information for insights into our past. However, for a complete understanding of human evolution it is necessary to look beyond our own genomes. This thesis is about using comparative genomics to place human evolution within a wider context by studying adaptation in our closest living relatives and in the species that we domesticated. In the first study, I investigate the genetic changes involved in the earliest stages of dog domestication. Using a global sample of dog and wolf genomes I identify regions that are highly diverged between these species. I find that selection in the initial stages of dog domestication likely involved genes involved in the fight-or-flight response, advancing our understanding of this process. In the second study, I look for commonalities in the genetic changes that occurred during animal domestication across species. I compare genome sequences from experimentally and historically domesticated species. I identify genes and variants that may underlie the phenotypic changes that occurred during domestication. I find evidence of biological pathways that appear to always be involved in the domestication process. In the third study, I characterise the signatures of natural selection in all major Hominidae lineages using population genomic data. I find that most signatures of positive selection are species specific, although some loci appear to be selected across several lineages. I determine that the efficacy of selection varies between species and is significantly correlated with long-term effective population size. These results contribute to a more complete understanding of human evolution. i This thesis is based on the following manuscripts: 1. Cagan A & Blass T. (2016) Identification of genomic variants putatively targeted by selection during dog domestication. BMC Evolutionary Biology,16:1. 2. Cagan A, Albert FW, Plyusnina I, Trut L, Renaud G, Romagné F, Wiebe V, Kozhemjakina R, Gulevich R, Trapezov O, Yudin N, Alekhina T, Aitnazarov R, Trapezova L, Herbeck Y, Schöneberg T, Pääbo S. Genes and pathways selected during animal domestication. Submitted to eLife. 3. Cagan A, Theunert C, Laayouni H, Santpere G, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J, Andrés AM. (2016). Natural Selection in the Great Apes. Molecular Biology and Evolution, 33:3268-3283.:Summary 1 Zusammenfassung 8 Chapter 1 Identification of genomic variants putatively targeted by selection during dog domestication 16 Chapter 2 Genes and pathways selected during animal domestication 38 Chapter 3 Natural Selection in the Great Apes 73 References 149 Acknowledgments 152 Curriculum Vitae 153 Declaration of Independence 156 Author Contribution Statements 15

Bayesian localization of CNV candidates in WGS data within minutes

Background: Full Bayesian inference for detecting copy number variants (CNV) from whole-genome sequencing (WGS) data is still largely infeasible due to computational demands. A recently introduced approach to perform Forward-Backward Gibbs sampling using dynamic Haar wavelet compression has alleviated issues of convergence and, to some extent, speed. Yet, the problem remains challenging in practice. Results: In this paper, we propose an improved algorithmic framework for this approach. We provide new space-efficient data structures to query sufficient statistics in logarithmic time, based on a linear-Time, in-place transform of the data, which also improves on the compression ratio. We also propose a new approach to efficiently store and update marginal state counts obtained from the Gibbs sampler. Conclusions: Using this approach, we discover several CNV candidates in two rat populations divergently selected for tame and aggressive behavior, consistent with earlier results concerning the domestication syndrome as well as experimental observations. Computationally, we observe a 29.5-fold decrease in memory, an average 5.8-fold speedup, as well as a 191-fold decrease in minor page faults. We also observe that metrics varied greatly in the old implementation, but not the new one. We conjecture that this is due to the better compression scheme. The fully Bayesian segmentation of the entire WGS data set required 3.5 min and 1.24 GB of memory, and can hence be performed on a commodity laptop

Multireference Description of Nickel-Aryl Homolytic Bond Dissociation Processes in Photoredox Catalysis

Multireference electronic structure calculations consistent with known experimental data have elucidated a novel mechanism for photo-triggered Ni(II)–C homolytic bond dissociation in Ni 2,2′-bipyridine (bpy) photoredox catalysts. Previously, a thermally assisted dissociation from the lowest energy triplet ligand field excited state was proposed and supported by density functional theory (DFT) calculations that reveal a barrier of ∼30 kcal mol⁻¹. In contrast, multireference ab initio calculations suggest that this process is disfavored, with barrier heights of ∼70 kcal mol⁻¹, and highlight important ligand noninnocent and multiconfigurational contributions to excited state relaxation and bond dissociation processes that are not captured with DFT. In the multireference description, photo-triggered Ni(II)–C homolytic bond dissociation occurs via initial population of a singlet Ni(II)-to-bpy metal-to-ligand charge transfer (¹MLCT) excited state, followed by intersystem crossing and aryl-to-Ni(III) charge transfer, overall a formal two-electron transfer process driven by a single photon. This results in repulsive triplet excited states from which spontaneous homolytic bond dissociation can occur, effectively competing with relaxation to the lowest energy nondissociative triplet Ni(II) ligand field excited state. These findings guide important electronic structure considerations for the experimental and computational elucidation of the mechanisms of ground and excited state cross-coupling catalysis mediated by Ni heteroaromatic complexes

Functional exploration of colorectal cancer genomes using Drosophila

The multigenic nature of human tumours presents a fundamental challenge for cancer drug discovery. Here we use Drosophila to generate 32 multigenic models of colon cancer using patient data from The Cancer Genome Atlas. These models recapitulate key features of human cancer, often as emergent properties of multigenic combinations. Multigenic models such as ras p53 pten apc exhibit emergent resistance to a panel of cancer-relevant drugs. Exploring one drug in detail, we identify a mechanism of resistance for the PI3K pathway inhibitor BEZ235. We use this data to identify a combinatorial therapy that circumvents this resistance through a two-step process of emergent pathway dependence and sensitivity we term ‘induced dependence’. This approach is effective in cultured human tumour cells, xenografts and mouse models of colorectal cancer. These data demonstrate how multigenic animal models that reference cancer genomes can provide an effective approach for developing novel targeted therapies

Genetic Influences on Brain Gene Expression in Rats Selected for Tameness and Aggression

Inter-individual differences in many behaviors are partly due to genetic differences, but the identification of the genes and variants that influence behavior remains challenging. Here, we studied an F2 intercross of two outbred lines of rats selected for tame and aggressive behavior towards humans for more than 64 generations. By using a mapping approach that is able to identify genetic loci segregating within the lines, we identified four times more loci influencing tameness and aggression than by an approach that assumes fixation of causative alleles, suggesting that many causative loci were not driven to fixation by the selection. We used RNA sequencing in 150 F2 animals to identify hundreds of loci that influence brain gene expression. Several of these loci colocalize with tameness loci and may reflect the same genetic variants. Through analyses of correlations between allele effects on behavior and gene expression, differential expression between the tame and aggressive rat selection lines, and correlations between gene expression and tameness in F2 animals, we identify the genes Gltscr2, Lgi4, Zfp40 and Slc17a7 as candidate contributors to the strikingly different behavior of the tame and aggressive animals

A personalized platform identifies trametinib plus zoledronate for a patient with KRAS-mutant metastatic colorectal cancer

Colorectal cancer remains a leading source of cancer mortality worldwide. Initial response is often followed by emergent resistance that is poorly responsive to targeted therapies, reflecting currently undruggable cancer drivers such as KRAS and overall genomic complexity. Here, we report a novel approach to developing a personalized therapy for a patient with treatment-resistant metastatic KRAS-mutant colorectal cancer. An extensive genomic analysis of the tumor's genomic landscape identified nine key drivers. A transgenic model that altered orthologs of these nine genes in the Drosophila hindgut was developed; a robotics-based screen using this platform identified trametinib plus zoledronate as a candidate treatment combination. Treating the patient led to a significant response: Target and nontarget lesions displayed a strong partial response and remained stable for 11 months. By addressing a disease's genomic complexity, this personalized approach may provide an alternative treatment option for recalcitrant disease such as KRAS-mutant colorectal cancer

Priming of protective T cell responses against virus-induced tumors in mice with human immune system components

Many pathogens that cause human disease infect only humans. To identify the mechanisms of immune protection against these pathogens and also to evaluate promising vaccine candidates, a small animal model would be desirable. We demonstrate that primary T cell responses in mice with reconstituted human immune system components control infection with the oncogenic and persistent Epstein-Barr virus (EBV). These cytotoxic and interferon-γ–producing T cell responses were human leukocyte antigen (HLA) restricted and specific for EBV-derived peptides. In HLA-A2 transgenic animals and similar to human EBV carriers, T cell responses against lytic EBV antigens dominated over recognition of latent EBV antigens. T cell depletion resulted in elevated viral loads and emergence of EBV-associated lymphoproliferative disease. Both loss of CD4+ and CD8+ T cells abolished immune control. Therefore, this mouse model recapitulates features of symptomatic primary EBV infection and generates T cell–mediated immune control that resists oncogenic transformation

Astrocytic transporters in Alzheimer's disease

Astrocytes play a fundamental role in maintaining the health and function of the central nervous system. Increasing evidence indicates that astrocytes undergo both cellular and molecular changes at an early stage in neurological diseases, including Alzheimer’s disease. These changes may reflect a change from a neuroprotective to a neurotoxic phenotype. Given the lack of current disease modifying therapies for Alzheimer’s disease, astrocytes have become an interesting and viable target for therapeutic intervention. The astrocyte transport system covers a diverse array of proteins involved in metabolic support, neurotransmission and synaptic architecture. Therefore, specific targeting of individual transporter families has the potential to suppress neurodegeneration, a characteristic hallmark of Alzheimer’s disease. A small number of the four hundred transporter superfamilies’ are expressed in astrocytes, with evidence highlighting a fraction of these are implicated in Alzheimer’s disease. Here we review the current evidence for six astrocytic transporter subfamilies involved in Alzheimer’s disease, as reported in both animal and human studies. This review confirms that astrocytes are indeed a viable target, highlights the complexities of studying astrocytes and provides future directives to exploit the potential of astrocytes in tackling Alzheimer’s disease

The time scale of recombination rate evolution in great apes

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- And between-species genome-wide recombination rate variation in several close relatives