ICTS

Nearly 4 billion years ago, a series of remarkable incidents led to bunch of chemicals coming together to produce a self-sustaining chemical system that eventually became capable of undergoing Darwinian evolution. What were the possible evolutionary pathways that may have eventually culminated in the emergence of the first living organism and what did evolution look like before the emergence of LUCA, the Last Universal Common Ancestor of all known living organisms? The RNA world hypothesis suggests that the first living organisms were made up of RNA molecules and preceded the DNA-protein-based life that eventually emerged and proliferated. The hypothesis confers a central role to RNA molecules in both information encoding through RNA sequences and catalysis using RNA enzymes called ribozymes. Even though circumstantial evidence can be found for the existence of an RNA world, many questions remain to be answered before we can understand the origin of life in an RNA world and the transition from an RNA world to a DNA-protein world. In this talk, I will highlight the key issues pertaining to origin of life. By using mathematical and computational models that are guided by experiments, I will explore some of the plausible evolutionary pathways that may have led to the emergence of RNA-based “life” and the subsequent transition from the RNA world to the world where heritable genetic information is encoded in DNA sequences.

Intra-specific genetic diversity is an important component of biodiversity, as it informs on ecological and evolutionary processes shaping populations. We investigated its drivers in centipedes, an ancient group of soil arthropods with low dispersal ability, showing variation in species traits and biogeography. We assembled a database of 1245 mitochondrial cytochrome c oxidase subunit I sequences representing 128 centipede species from all five orders of Chilopoda. This sequence dataset was used to estimate genetic diversity for centipede species and compare its distribution with estimates from other arthropod groups. We studied the variation in centipede genetic diversity with species traits and biogeography using a beta regression framework, controlling for the effect of shared evolutionary history within a family. A wide variation in genetic diversity across centipede species (0 to 0.1713) falls towards the higher end of values among arthropods. Overall, 27.57% of the variation in mitochondrial COI genetic diversity in centipedes was explained by a combination of predictors related to life history and biogeography. Genetic diversity decreased with body size and latitudinal position of sampled localities, was greater in species showing maternal care and increased with geographic distance among conspecifics. Centipedes fall towards the higher end of genetic diversity among arthropods, which may be related to their long evolutionary history and low dispersal ability. In centipedes, the negative association of body size with genetic diversity may be mediated by its influence on local abundance or the influence of ecological strategy on long-term population history. Species with maternal care had higher genetic diversity, which goes against expectations and needs further scrutiny. Hemispheric differences in genetic diversity can be due to historic climatic stability and lower seasonality in the southern hemisphere. Overall, we find that despite the differences in mean genetic diversity among animals, similar processes related to life history strategy and biogeography are associated with the variation within them.

Examples of challenges to assumptions: selection on synonymous mutations, drift in MA experiments, genetic basis of tradeoffs, rarity of beneficial mutations

Genomic data science integrates genetics and computational biology research, employing statistical data analysis and computer science. It is crucial to study population genetics and evolutionary history using genomic data. Through the analysis of human genome data, researchers gain valuable insights into human migration patterns and population development. Technological advancements now enable scientists to sequence an individual's complete genome, yielding unprecedented information. Despite this progress, interpreting genomic data, especially in the case of humans, remains a more significant challenge than generating and curating it. While autosomal data is generally considered more robust than haploid data (mtDNA or Y chromosome) for ancestry information, there are instances where different markers reveal distinct population histories. This talk would discuss such cases and bring the most parsimonious interpretation.

Epistasis and its role in adaptation and speciation, fitness landscape models and experiments

Epistasis and its role in adaptation and speciation, fitness landscape models and experiments

We will study QTL mapping, GWAS, selective sweep, and iHS.

Simulation tools, determining what to simulate, simulating in discrete and continuous time

Female-limited polymorphisms (e. g. colour polymorphisms) are increasingly documented in many taxa, including insects, but also in vertebrates like lizards and birds. How and why such female-limited polymorphisms have evolved, their adaptive significance, genomic basis and phylogenetic history is gaining increased attention. Here, I will provide an overview of the evolution of such female-limited polymorphisms, with a focus on damselflies of the genus Ischnura, illustrating with research from my own lab and from other groups. Female-limited colour polymorphisms occur in several species of Ischnura and have evolved independently up to five times. One of the female morphs is male-limited in colouration (“andromorph females”) and benefits from male mimicry and reduced male mating harassment. Male search images are plastic, as revealed by opsin gene expression profiles that vary with local female morph frequencies. Plastic male mate preferences drive negative frequency-dependent selection (NFDS) that preserves these female polymorphisms over both micro- and macroevolutionary time scales. Our recent phylogenetic and genomic research revealed that these trans-species polymorphisms are at least 5 million years old, are shared between closely related species and arise from a major effect locus on chromosome 13, which shows chromosome-level reduced recombination and a high density of Transposable Elements (TE:s). Male-mimicking females arose in a background of female monomorphism and sexual dimorphism through a chromosomal inversion, followed by genomic expansion of the nascent morph locus, accumulation of TE:s and reduced recombination. The morph locus shows molecular signatures of long-term balancing selection (Tajima’s D). I will synthesize these findings from ecology, phylogenetics and genomics that have jointly uncovered the microevolutionary processes and macroevolutionary history of these polymorphisms.

Concept, models, and empirical cases of evolutionary rescue

We will study genomic signatures of speciation, molecular mechanisms of speciation, and chromosome evolution.

Eco-evolutionary models and open questions

We will study how to identify causative mutations of adaptation in natural populations and what we can learn from them.