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Monday, 27 January 2020
Time Speaker Title Resources
09:30 to 11:00 Aneil Agrawal Drift, Inbreeding, and Ne

TBA

11:30 to 13:00 Guy Sella Introduction to quantitative genetics and GWAS

TBA

14:00 to 15:30 Poster Session Poster Session

TBA

16:00 to 17:30 Christian Schlotterer Introduction to experimental evolution

TBA

Tuesday, 28 January 2020
Time Speaker Title Resources
09:30 to 11:00 Christian Schlotterer Experimental evolution in asexual microbes

TBA

11:30 to 13:00 Aneil Agrawal Coalescence I: basic theory and connection to mol pop gen statistics

TBA

14:00 to 14:45 Christian Schlotterer Tutorial

TBA

14:45 to 15:30 Supreet Saini Research talk: Studies in allopatric and sympatric speciation using Saccharomyces cerevisiae as a model organism

In nature, organisms evolve to best fit their ecological niches, and while doing so, arrange themselves into discrete, reproductively isolated groups called species. While the evolutionary response of an organism is shaped by adaptive mutations, random genetic drift, and bottlenecks, the fundamental forces driving speciation events are largely unknown. In fact, speciation is, at times, characterized to be simply a by-product of an adaptive process. However, the reasons why an adaptive process defined by interaction between a genome and an environment, should dictate a process which is defined by interaction of two distinct genomes are not clear. While a number of theoretical and conceptual ideas and models have been proposed to explain speciation, no model systems or systematic experimental characterization of speciation events exists. This lack of understanding of speciation events forms the basis of our work. In this context, a study of factors that contribute to the process of speciation is of interest to us. Towards this end, we use Saccharomyces cerevisiae and the melibiose utilization system as the model system to study dynamics of speciation in allopatry and sympatry.

 

16:00 to 17:30 Guy Sella Preliminary considerations to modeling the evolution of complex traits

TBA

Wednesday, 29 January 2020
Time Speaker Title Resources
09:30 to 11:00 Aneil Agrawal Coalescence II: structured coalescent including pop structure, selfing, and background/balancing selection

TBA

11:30 to 13:00 Christian Schlotterer Experimental evolution in sexual eukaryotes

TBA

14:00 to 14:45 Aneil Agrawal Tutorial

TBA

14:45 to 15:30 Ranajit Das Research talk: Ancestry determination: more than just a homing tool

My current research focuses on tracing the ancestral origin and biogeographical affiliation of various human and endangered animal populations and deducing Ancestry Informative Markers (AIMs) for the same. There is an eternal quest to uncover our roots and our ancestral
origin to answer the primal questions ‘who am I?’ and ‘where am I from?’. Our DNA determines not only who we are but holds the key to uncovering our true ancestral past. A plethora of information stored inside the genome reflects our uniqueness and proximity to
different ancestral and modern-day populations. Given high correspondence between our genetic make-up and the geographical origin of our forefathers, it is possible to glean into precise ancestral origin using the genetic information. While genetically all humans are >99% identical, there are variations in our DNA that makes us unique. The most common type of variation is a single base pair change in the DNA known as Single Nucleotide Polymorphisms (SNPs). A collection of SNPs, commonly known as Ancestry Informative
Markers (AIMs), exhibit large differences among ancestral populations. These AIMs panels can help in tracing one’s ancestry with high precision. Understanding our ancestry is not only a ‘homing’ tool bringing you closer to your evolutionary past but also holds the key to detect ancestry specific disorders, develop ancestry-specific medicine and identify potential suspects by shortlisting individuals based on their ancestry. Further, the knowledge of ancestry can greatly aid in the preservation of biological diversity by maximizing genetic diversity through outbreeding and genomic admixture and preventing inbreeding among genetically related individuals. Thus determination of ancestry and AIMs can be monumental in the conservation of endangered wild animals.

16:00 to 17:30 Guy Sella Quantitative genetic variation and relating predictions to GWAS findings

TBA

Thursday, 30 January 2020
Time Speaker Title Resources
09:30 to 11:00 Christian Schlotterer Towards improved design of Evolve and Resequence studies

TBA

11:30 to 13:00 Guy Sella Polygenic adaptation

TBA

14:00 to 14:45 Guy Sella Tutorial

TBA

14:45 to 15:30 Maanasa Raghavan Research talk: In search of our molecular past: Reconstructing human population histories using ancient DNA

Technological advances in sequencing have propelled ancient DNA research into the ‘paleogenomics’ era, accompanied by a tremendous increase in the amount of generated data. Additionally, continued efforts towards optimizing laboratory pipelines, including sampling, DNA extraction, and library preparation techniques, have resulted in increased DNA yield from ancient samples. These genome-wide datasets are being used to reconstruct past population structures and understand how processes such as ancient migrations, admixture, selection, environmental changes, and epidemics have shaped present-day human gene pools. My talk will focus on the contributions of ancient DNA research to the emerging picture of modern human dispersals and provide perspectives on how collaborative efforts with the fields of archaeology and anthropology are providing a new dimension to our understanding of the human past.

16:00 to 17:30 Aneil Agrawal Sexually antagonistic selection - theory

TBA

Friday, 31 January 2020
Time Speaker Title Resources
09:30 to 11:00 Christian Schlotterer Understanding polygenic adaptation with experimental evolution

TBA

11:30 to 13:00 Guy Sella How selection on complex traits affects neutral diversity at linked loci

TBA

14:00 to 14:45 Imroze Khan Research talk: Cannibalism rescues fitness impacts of skewed sex-ratios in beetle Tribolium castaneum

Theory and experiments predict that cannibalism increases fitness under stressful conditions (e.g. resource limitation) in many animal species. However, empirical evidence where cannibalism directly manipulates fitness by providing added nutrition under resource competition is limiting. Our recent work highlights an example where skewed sex-ratios altered resource competition in populations of beetle Tribolium castaneum. Females living in female-biased (FB) groups dramatically suppressed each other’s fecundity by using toxin quinones and hydrocarbons secreted from their stink glands, demonstrating a form of nonsexual resource interference competition. Can cannibalism rescue such negative fitness impacts of female density by relaxing the resource competition in FB groups? In a proof-of-principle study, we tested this possibility by adding larvae as potential victims to adult beetles under different sex-ratio groups. We found that the opportunity to cannibalize quickly relaxed the competition in FB groups, with a rapid decline in quinone content and an increase in female fitness. Conversely, can secreted stink gland contents provide cues to increase cannibalism? To test this, we reconstituted the quinone and hydrocarbon- rich environment by supplementing the food with commercially available methyl-benzoquinone and pentadecene and showed that stink gland contents alone can increase female cannibalism behavior with immediate fitness advantage. Finally, we show that cannibalism merely acts as a source of protein acquisition for FB females since similar fitness gain was also observed with food supplemented with live yeast (source of protein), but not with excess wheat flour (beetle’s staple diet). We thus propose a general mechanism of chemical-driven fitness recovery in flour beetles where female-female competition triggers the release of chemical cues to modulate protein acquisition by cannibalism and increase fitness.

14:45 to 15:30 Deepa Agashe Research talk: The evolutionary consequences of cellular mistakes

TBA

16:00 to 17:30 Aneil Agrawal Sexually antagonistic selection - data

TBA

Monday, 03 February 2020
Time Speaker Title Resources
09:30 to 11:00 Lindi Wahl Fate of rare mutations: branching processes

An introduction to probability generating functions will be given, including an exploration of their properties, with particular emphasis on their use in modelling branching processes. PGFs for common probability mass functions, and the fixed point expression for the extinction probability of a branching process will be derived. Extensions to multitype and continuous time PGFs will be outlined. No prior knowledge of generating functions will be assumed.

Suggested reading: Freeman 2014, Deslauriers 2019, Fewster lecture notes (4.1 – 4.7)

11:30 to 13:00 Chris Marx Horizontal gene transfer

TBA

14:00 to 15:30 Poster Session Poster Session

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16:00 to 17:30 Vaishali Katju Mutation in evolution and the design of mutation accumulation experiments

TBA

Tuesday, 04 February 2020
Time Speaker Title Resources
09:30 to 11:00 Chris Marx Tradeoffs

TBA

11:30 to 13:00 Vaishali Katju Rate and spectrum of spontaneous mitochondrial mutations

TBA

14:00 to 14:45 Chris Marx Single rate-limiting steps can exist (Tutorial)

TBA

14:45 to 15:30 Krishna Swamy Research talk: Genes and Speciation: What can we learn about evolution using yeast?

How do new species arise? This is one of the fundamental problems of evolutionary biology. Although considerable effort has been devoted to understanding the underlying mechanisms of speciation, it is far from complete. Speciation in eukaryotes is due to reproductive isolation (i.e., pre-zygotic or post-zygotic) and mechanisms of post-zygotic reproductive isolation are better understood than that of pre-zygotic isolation. Dobzhansky-Muller incompatibilities represent a major driver of post-zygotic reproductive isolation between species. They are caused by two or more interacting components that cannot function properly when mixed with alleles from different species. At incipient stages of speciation, complex incompatibilities involving multiple genetic loci with weak effects are frequently observed, but their underlying mechanism remains elusive. We observed perturbed proteostasis manifesting as proteotoxic stress in introgressed hybrids of the yeast Saccharomyces cerevisiae carrying one or two chromosomes from its close relative Saccharomyces bayanus. Proteotoxicity in these introgressed yeast hybrids caused compromised fitness (mitosis) and sporulation (meiosis). The level of proteotoxicity was correlated with the number of multi-protein complexes encoded on replaced chromosomes and could be alleviated or aggravated by up- or down-regulating ubiquitin-proteasome degradation machinery. Using proteomic approaches, we detected destabilized multi-protein complexes in introgressed hybrids, providing evidence that proteotoxicity is due to improper interactions between the complex-subunits encoded by different genomes. Our results reveal the general role played by impaired protein complex assembly in complex incompatibilities.

16:00 to 17:30 Lindi Wahl Fate of rare mutations: diffusion approximations

We will cover an overview of the fixation or loss of a rare allele, and the advantages and disadvantages of using either a branching process or diffusion approximation to estimate these probabilities. Using the techniques covered in the previous lecture, we will derive Haldane’s classic approximation for the fixation probability. We will then derive the diffusion approximation for changes in allele frequency over time and demonstrate the solution to this equation for the fixation probability.
We will also demonstrate the use of the diffusion approximation in a simple model.

Suggested reading: Patwa 2008 (sections 1, 2)

Wednesday, 05 February 2020
Time Speaker Title Resources
09:30 to 11:00 Vaishali Katju Rate and spectrum of nuclear SNP and small indel mutations

TBA

11:30 to 13:00 Lindi Wahl Modelling adaptation

This lecture will begin with a historical overview of thinking and mathematical modelling of adaptation (Fisher, Kimura, Maynard Smith). We will then derive some basic results from Fisher’s
Geometric Model and discuss their implications. Finally, we will give an overview of the three regimes of adaptation: the single sweep, clonal interference and multiple mutation regimes.

Suggested reading: Orr 2005, Tenaillon 2014 (pp 1-8)

14:00 to 14:45 Vaishali Katju Tutorial

TBA

14:45 to 15:30 Kavita Jain Research talk: Fixation Probability in static and Dynamic Environments

TBA

16:00 to 17:30 Chris Marx Metabolic pathways

TBA

Thursday, 06 February 2020
Time Speaker Title Resources
09:30 to 11:00 Christopher Marx Purely Lamarckian “Evolution” can permit bacterial survival to a lethal stressor

TBA

11:30 to 13:00 Vaishali Katju Copy-number changes in evolution under drift versus selection

TBA

14:00 to 14:45 Lindi Wahl Tutorial

TBA

14:45 to 15:30 Krushnamegh Kunte Research talk: Haldane’s sieve and the evolution of novel polymorphisms in mimetic swallowtail butterflies 

Morphologically complex polymorphisms may be governed by simple genetic principles. Novel adaptive mutations that are genetically dominant over wild-type are able to rapidly advance through populations under strong selection (Haldane’s sieve). Supergene-like architecture should protect these mutations responsible for ecological morphs that occupy distinct adaptive peaks, but occasional recombination may fuel diversification of adaptive phenotypes. We demonstrate these principles in the female-limited, polymorphic Batesian mimicry in Papilio polytes. This polymorphic mimicry is complex but we found that it was fully governed in all mimetic forms by allelic variation of doublesex, a single switch-locus. Phylogenetic analysis revealed that the evolution of novel mimetic forms followed Haldane’s sieve, the most recently evolved mimetic form being universally dominant. The supergene-like genetic architecture of mimetic polymorphism was attributed to a large inversion around doublesex, but mimetic female forms shared the precise breakpoints of the inversion. Surprisingly, phenotypic intermediates due to recombination within this inversion were exceedingly rare. However, recombinations between exon 1 of the universally dominant female form and remaining exons of a recessive female form produced a novel, stable intermediate phenotype combining wing patterns of different mimetic forms, which is highly unusual for Batesian mimetic wing patterns with complete dominance. We thus show how an interaction of Haldane’s sieve, a strong genetic architecture and recombination may stabilize balanced polymorphisms but simultaneously facilitate the evolution novel forms.​

16:00 to 17:30 Lindi Wahl Modelling microbial evolution

This lecture focusses on mathematical models of microbial evolution experiments. We will start by outlining some of the key features of these experiments that are not addressed in classic population genetics theory. We will then give an overview of early work modelling experimental evolution in microbes. The lecture will highlight open questions and areas for new contributions.

Suggested reading: Miller 2011 (Introduction, Figure 1)

Friday, 07 February 2020
Time Speaker Title Resources
09:30 to 11:00 Lindi Wahl Research talk: How different is the flu you pass on from the flu you receive?

In this research talk, I will discuss work from my research group that estimates the probability that a de novo mutation occurs during a single influenza infection in a human, and is ultimately passed on to the next individual in the transmission chain. This research project makes use of many of the tools introduced in Lecture 1, in particular. Time permitting, we will also discuss some recent estimates of the probability of an H5N1 influenza pandemic.

Suggested reading: Sigal 2018

11:30 to 13:00 Vaishali Katju Transcriptional consequences of spontaneous mutations

TBA

14:00 to 15:30 Christopher Marx Research talk: A purely Lamarckian ‘evolution’ permits survival of a bacterium to a lethal stressor

We tend to appreciate microbes for their simplicity and predictability: a population of genetically identical cells inhabiting a uniform environment is expected to behave in a uniform way. However, counter-examples to this assumption are frequently being discovered, forcing a re-examination of the relationship between genotype and phenotype. In most such examples, bacterial cells are found to split into two discrete populations, for instance growing and non-growing. Here, we report the discovery of a novel example of microbial phenotypic heterogeneity in which cells are distributed along a gradient of phenotypes, ranging from low to high tolerance of a toxic chemical. Furthermore, we demonstrate that the distribution of phenotypes changes in different growth conditions, and we use mathematical modeling to show that cells may change their phenotype either randomly or in a particular direction in response to the environment. Our work expands our understanding of how a bacterial cell’s genome, family history, and environment all contribute to its behavior, with implications for the diverse situations in which we care to understand the growth of any single-celled populations.

16:00 to 17:30 Open discussions Open discussions

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