Community Assembly and Habitat Specialization of Tropical Tree Species along Moisture Gradients in the Western Ghats Biodiversity Hotspot in India

The interactions between ecological and evolutionary processes mediated through functional traits that confer habitat specialization have been proposed to explain the spatial assembly of plant communities both across space and in different habitats. However, the scale at which these mechanisms operate and their relative importance in dominance and assembly of tree communities in different habitat types distributed across spatially-varying environmental gradients in tropical forests have been rarely tested. Here, I elucidate patterns of functional trait and phylogenetic variation and evolutionary history of key functional traits conferring habitat specialization to understand community assembly mechanisms operating within in tropical tree communities distributed across spatially varying environmental gradients and in different habitat types in Western Ghats biodiversity hotspot, India. The chapter 2 focuses on patterns of functional trait and phylogenetic co-variation among a community of tropical canopy trees distributed across spatially varying moisture gradient. I find that tree communities in plots that experience lower precipitation and longer duration of dry period show clustering of both functional traits and phylogenetic relationship suggesting environmental filtering play a key role in the assembly of tree communities in these forests. The chapter 3 explores the relationship between key functional traits, phylogenetic relationship and abundance of 210 co-occurring tree species distributed across contrasting extremes of seasonal flooding gradient i.e. flooded forest and terra-firme forest (non-flooded). I found that repeated evolution of key functional traits together with strong environmental filtering play a key role in determining the ecological success (dominance) and assembly of tree communities in flooded habitat. The chapter 4 focuses on climatic niche evolution and evolutionary history of flooded habitat specialization in global and endemic Myristicaceae members in the Western Ghats. I found that, repeated gain of swamp habitat specialization and associated morphological traits in global and Western Ghats Myristicaceae implying seasonal flooding gradient is an important driver of ecological speciation. I also found that local habitat specialization promotes range-wide niche evolution among sister taxa. By elucidating the pattern functional traits and phylogenetic relationship across flooding and spatially varying moisture gradient and analysis of climatic niche evolution and habitat specialization among co-occurring sister taxa, this thesis contributes to our understanding of the determinants of assembly, dominance and diversification of tropical tree communities across diverse habitat types in tropical forest biomes

Efficient Bayesian Inference of General Gaussian Models on Large Phylogenetic Trees

Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To incorporate such uncertainty, we present a scalable Bayesian inference framework under a general Gaussian trait evolution model that exploits Hamiltonian Monte Carlo (HMC). HMC enables efficient sampling of the constrained model parameters and takes advantage of the tree structure for fast likelihood and gradient computations, yielding algorithmic complexity linear in the number of observations. This approach encompasses a wide family of stochastic processes, including the general Ornstein-Uhlenbeck (OU) process, with possible missing data and measurement errors. We implement inference tools for a biologically relevant subset of all these models into the BEAST phylogenetic software package and develop model comparison through marginal likelihood estimation. We apply our approach to study the morphological evolution in the superfamilly of Musteloidea (including weasels and allies) as well as the heritability of HIV virulence. This second problem furnishes a new measure of evolutionary heritability that demonstrates its utility through a targeted simulation study

Genome Evolution and the Emergence of Fruiting Body Development in Myxococcus xanthus

BACKGROUND: Lateral gene transfer (LGT) is thought to promote speciation in bacteria, though well-defined examples have not been put forward. METHODOLOGY/PRINCIPLE FINDINGS: We examined the evolutionary history of the genes essential for a trait that defines a phylogenetic order, namely fruiting body development of the Myxococcales. Seventy-eight genes that are essential for Myxococcus xanthus development were examined for LGT. About 73% of the genes exhibit a phylogeny similar to that of the 16S rDNA gene and a codon bias consistent with other M. xanthus genes suggesting vertical transmission. About 22% have an altered codon bias and/or phylogeny suggestive of LGT. The remaining 5% are unique. Genes encoding signal production and sensory transduction were more likely to be transmitted vertically with clear examples of duplication and divergence into multigene families. Genes encoding metabolic enzymes were frequently acquired by LGT. Myxobacteria exhibit aerobic respiration unlike most of the delta Proteobacteria. M. xanthus contains a unique electron transport pathway shaped by LGT of genes for succinate dehydrogenase and three cytochrome oxidase complexes. CONCLUSIONS/SIGNIFICANCE: Fruiting body development depends on genes acquired by LGT, particularly those involved in polysaccharide production. We suggest that aerobic growth fostered innovation necessary for development by allowing myxobacteria access to a different gene pool from anaerobic members of the delta Proteobacteria. Habitat destruction and loss of species diversity could restrict the evolution of new bacterial groups by limiting the size of the prospective gene pool

Integrated analysis of epidemiological and phylogenetic data to elucidate viral transmission dynamics

While infectious disease outbreaks are often summarised by population averages such as the reproductive number, variation between individuals in terms of onwards transmissions modulates the degree of unpredictability of an epidemic, and it needs to be accounted for in models of infection control. This heterogeneity among individuals can be quantified by the dispersion parameter k of the offspring distribution, a distribution that defines the number of secondary infections per infected individual. I have developed an inference framework to estimate k and other epidemiological parameters by fitting stochastic transmission models to both incidence time series and the pathogen phylogeny. Applying the framework to simulated data, I found that more accurate, less biased and more precise estimates of the reproductive number and k were obtained by combining epidemiologic and phylogenetic analyses. Accurately estimating k was necessary for unbiased estimates of the reproductive number, but it did not affect the accurate estimation of epidemic start date and the probability of sampling an infection. I further demonstrated that inference was possible in the presence of phylogenetic uncertainty by sampling from the posterior distribution of phylogenies. In addition to methodological contributions, I found that the inclusion of sequences in statistical inference for polio improved the precision of parameter estimates. Based on sequences collected from patients during a poliovirus outbreak, the estimated values of k were high regardless of the data used. On the other hand, the k estimates were low when a transmission model was fit to environmental sequences collected in Pakistan, which is still endemic for wild poliovirus. Furthermore, analysis of environmental sequences was informative of seasonality parameters whereas inference from incidence time series alone was not. This type of analysis using environmental sequences would be useful as polio eradication draws to a close as the number of symptomatic cases approaches zero.Open Acces

THE EVOLUTION OF MORPHOLOGICAL DIVERSITY AND SEXUAL DIMORPHISM IN STICK AND LEAF INSECTS

How has the diversity of life forms come to be? This question is at the core of evolutionary biology and can be addressed at different scales: by studying the processes that drive modifications within populations of organisms generation after generation (microevolution), or by investigating patterns of changes on the tree of life over long periods of time (macroevolution). Understanding the ultimate drivers of morphological diversity eventually entails connecting microevolutionary processes with macroevolutionary patterns. My dissertation investigates the diversification of body and egg form and its drivers in a relatively small but particularly diverse insect order: the stick and leaf insects (Phasmatodea). As masters of camouflage, the 3,400 described species of phasmids are an ideal system to study morphological evolution as they vary tremendously in body morphology, going from long slender branch mimics to wide, flat animals that look exactly like leaves. This remarkable diversity of forms enables phasmids to avoid detection by visually-hunting predators. Even their remarkably diverse hardshelled eggs resemble a wide variety of plant seeds. In addition, males and females of the same species often look very different from each other, with females in extreme cases more than ten times the size of the males. In chapters one, two and three, I investigate the patterns of variation of female body morphology, sexual dimorphism and egg morphology respectively, and potential ecological, life history and biomechanical correlates in a phylogenetic context. I describe repeated convergence towards multiple body forms associated with habitat transitions but find substantial variation in the strength of convergence and underlying evolutionary paths. Then, I show that variation in the extent of sexual dimorphism is best explained by variation in selective pressures acting on males, namely locomotor (flight) performance and male competition (sexual selection). Finally, I show that variation in egg size and shape is driven by variation in life history strategies, mechanical constraints and oviposition strategy. In chapters four, five and six, I investigate the microevolutionary processes behind the primary macroevolutionary forces driving variation in sexual dimorphism. In chapter four, I show in leaf insects (Phyllium philippinicum) that larger males are poor flyers, suggesting that selection for flight performance favors smaller male body sizes in this species, and reinforcing the broader taxonomic findings of chapter two. In chapters five and six, I describe how a change in the mating system of thorny devil stick insects (Eurycantha calcarata) switched the direction of sexual selection and led to the evolution of exceptionally large male body sizes and exaggerated hindleg weapons, confirming the pervasive role of sexual selection in driving variation in male size and sexual dimorphism. Collectively, my research contributes to our understanding of the forces that shape the evolution of morphology in animals and their eggs

Molecular evolution of biological sequences

Evolution is an ubiquitous feature of living systems. The genetic composition of a population changes in response to the primary evolutionary forces: mutation, selection and genetic drift. Organisms undergoing rapid adaptation acquire multiple mutations that are physically linked in the genome, so their fates are mutually dependent and selection only acts on these loci in their entirety. This aspect has been largely overlooked in the study of asexual or somatic evolution and plays a major role in the evolution of bacterial and viral infections and cancer. In this thesis, we put forward a theoretical description for a minimal model of evolutionary dynamics to identify driver mutations, which carry a large positive fitness effect, among passenger mutations that hitchhike on successful genomes. We examine the effect this mode of selection has on genomic patterns of variation to infer the location of driver mutations and estimate their selection coefficient from time series of mutation frequencies. We then present a probabilistic model to reconstruct genotypically distinct lineages in mixed cell populations from DNA sequencing. This method uses Hidden Markov Models for the deconvolution of genetically diverse populations and can be applied to clonal admixtures of genomes in any asexual population, from evolving pathogens to the somatic evolution of cancer. To understand the effects of selection on rapidly adapting populations, we constructed sequence ensembles in a recombinant library of budding yeast ($\textit{S. cerevisiae}$). Using DNA sequencing, we characterised the directed evolution of these populations under selective inhibition of rate-limiting steps of the cell cycle. We observed recurrent patterns of adaptive mutations and characterised common mutational processes, but the spectrum of mutations at the molecular level remained stochastic. Finally, we investigated the effect of genetic variation on the fate of new mutations, which gives rise to complex evolutionary dynamics. We demonstrate that the fitness variance of the population can set a selective threshold on new mutations, setting a limit to the efficiency of selection. In summary, we combined statistical analyses of genomic sequences, mathematical models of evolutionary dynamics and experiments in molecular evolution to advance our understanding of rapid adaptation. Our results open new avenues in our understanding of population dynamics that can be translated to a range of biological systems.The work presented in this thesis has been supported by the Wellcome Trust as part of the PhD programme in Mathematical Genomics and Medicine at the University of Cambridge, by the Sanger Early Career Innovation Award, by Fundación Ibercaja, and partially supported by the National Science Foundation during a research stay at the Kavli Institute for Theoretical Physics (University of California, Santa Barbara)

A Genomic Investigation of Divergence Between Tuna Species

Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and applied as a reference for population genomic analysis of specimens from 9 localities spanning most of the Blackfin tuna range. Analysis suggested the presence of four weakly differentiated units corresponding to the northwestern Atlantic Ocean, Gulf of Mexico, Caribbean Sea, and southwestern Atlantic Ocean, respectively. Significant spatial autocorrelation of genotypes was observed for specimens collected within 800 km of each other. A high-quality genome assembly generated for the Yellowfin tuna using PacBio and Illumina sequences was scaffolded by a linkage map developed through analysis of the segregation of genome wide Single Nucleotide Polymorphisms in 164 larvae offspring from a single pair produced by controlled breeding. The genome assembly was used as a reference for population genomic analysis of juvenile specimens from the 4 main nursery areas hypothesized in the Atlantic Ocean basin. Analyses corroborated previously reported population subdivision between the east and west Atlantic Ocean, but also suggested subdivision associated with individual nursery areas within the east and west regions. Draft reference assemblies were generated for Albacore, Bigeye and Longtail tunas and used in combination with the Yellowfin and Blackfin tuna genomes obtained in this work and existing assemblies for bluefin tunas in preliminary analyses of genome wide variation between species of the Thunnus genus. Whole-genome derived SNP-based phylogenetic analysis of the Thunnus genus suggests phylogenetic relationships may be more complex than suggested in earlier work based on Restriction-site Associated DNA sequencing or muscle transcriptome sequencing and prompt for further analysis of the genus using a more comprehensive sampling of taxa in each oceanic basin

Population Structure and Comparative Genome Hybridization of European Flor Yeast Reveal a Unique Group of Saccharomyces cerevisiae Strains with Few Gene Duplications in Their Genome

Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four countries, with that of three wine strains did not reveal any large segmental amplification. Nonetheless, some genes, including YKL221W/MCH2 and YKL222C, were amplified in the genome of four out of six flor strains. Finally, we correlated ICR1 ncRNA and FLO11 polymorphisms with flor yeast population structure, and associate the presence of wild type ICR1 and a long Flo11p with thin velum formation in a cluster of Jura strains. These results provide new insight into the diversity of flor yeast and show that combinations of different adaptive changes can lead to an increase of hydrophobicity and affect velum formation