Yule’s 1925 paper introducing the branching model that bears his name was a landmark contribution to biodiversity sciences. In paper, Yule developed stochastic models explain observed distribution of species across genera and test hypotheses about relationship between clade age, diversity geographic range. Here, we discuss intellectual context in which produced this work, highlight key mathematical conceptual contributions using both more modern derivations critically examine some...

Parallel evolution is often assumed to result from repeated adaptation novel, yet ecologically similar, environments. Here, we develop and analyse a mathematical model that predicts the probability of parallel genetic standing variation as function strength phenotypic selection constraints imposed by architecture. Our results show increases with natural effective population size particularly likely occur for genes large effects. Building on these results, Bayesian framework estimating data....

Viral phylogenies provide crucial information on the spread of infectious diseases, and many studies fit mathematical models to phylogenetic data estimate epidemiological parameters such as effective reproduction ratio (Re) over time. Such phylodynamic inferences often complement or even substitute for conventional surveillance data, particularly when sampling is poor delayed. It remains generally unknown, however, how robust are, especially there uncertainty regarding pathogen prevalence...

Abstract COVID-19 has become endemic, with dynamics that reflect the waning of immunity and re-exposure, by contrast to epidemic phase driven exposure in immunologically naïve populations. Endemic does not, however, mean constant. Further evolution SARS-CoV-2, as well changes behavior public health policy, continue play a major role endemic load disease mortality. In this article, we analyze evolutionary models explore impact newly arising variant can have on short-term longer-term load,...

Birth-death stochastic processes are the foundations of many phylogenetic models and widely used to make inferences about epidemiological macroevolutionary dynamics. There a large number birth-death model variants that have been developed; these impose different assumptions temporal dynamics parameters sampling process. As each was individually derived, it has difficult understand relationships between them as well their precise biological mathematical assumptions. Without common foundation,...

Genomic epidemiology plays an ever-increasing role in our understanding of and response to the spread infectious pathogens. Phylogeography, reconstruction historical location movement pathogens from evolutionary relationships among sampled pathogen sequences, can inform policy decisions related viral jurisdictions. However, phylogeographic is impacted by fact that sampling virus sequencing policies differ jurisdictions, these differences cause bias reconstructions. Here we assess potential...

Populations are often spread across a spatially heterogeneous landscape, connected by migration. Consequently, the question arises whether divergent selective forces created spatial heterogeneity can overcome homogenising force of migration and loss diversity through genetic drift to favour different traits space. Such in population due selection is known as local adaptation. While adaptation has been studied variety settings, it remains unclear certain life-history arise. Life-history...

Population genomic analysis of hybrid zones is instrumental to our understanding the evolution reproductive isolation. Many temperate are formed by secondary contact between two parental populations that have undergone postglacial range expansion. Here, we show explicitly accounting for historical isolation followed expansion prior fundamental explaining genetic and fitness patterns in these zones. Specifically, ancestral population can result allele surfing, where neutral or slightly...

Sex chromosomes play a special role in the evolution of reproductive barriers between species. Here we describe conflicting roles nascent sex on patterns introgression an experimental hybrid swarm. Drosophila nasuta and albomicans are recently diverged, fully fertile sister species that have different chromosome systems. The fusion autosome (Muller CD) with ancestral X Y gave rise to neo-sex D. albomicans, while Muller CD remains unfused nasuta. We found large block containing overlapping...

All species are locked in a continual struggle to adapt local ecological conditions. In cases where fail locally adapt, they face reduced population growth rates, or even extinction. Traditional explanations for limited adaptation focus on maladaptive gene flow homogeneous environmental These classical have, however, failed explain variation the magnitude of observed across taxa. Here we show that variable levels better explained by trait dimensionality. First, develop and analyse...

Abstract The results of genome-wide association studies are known to be affected by epistasis and gene-by-environment interactions. Using a statistical model.... Genome-wide widely used identify “disease genes” conferring resistance/susceptibility infectious diseases. combination mathematical models simulations, we demonstrate that genetic interactions between hosts parasites [genotype-by-genotype (G × G) interactions] can drastically affect the these scans hamper our ability detect...

Abstract Genetic architecture plays an important role in the process of adaptation to novel environments. One example is allelic dominance, where advantageous recessive mutations have a lower probability fixation than dominant mutations. This classic observation, termed ‘Haldane's sieve’, has been well explored theoretically for single isolated populations adapting new selective regimes. However, dominance less understood peripheral environments face recurrent and maladaptive gene flow....

Abstract Birth-death stochastic processes are the foundation of many phylogenetic models and widely used to make inferences about epidemiological macroevolutionary dynamics. There a large number birth-death model variants that have been developed; these impose different assumptions temporal dynamics parameters sampling process. As each was individually derived, it has difficult understand relationships between them as well their precise biological mathematical assumptions. Without common...

Abstract Genomic epidemiology plays an ever-increasing role in our understanding of and response to the spread infectious pathogens. Phylogeography, reconstruction historical location movement pathogens from evolutionary relationships among sampled pathogen sequences, can inform policy decisions related viral jurisdictions. However, phylogeographic is impacted by fact that sampling virus sequencing policies differ jurisdictions, these differences cause bias reconstructions. Here we assess...

With the rising frequency of pathogen spillover worldwide, wildlife disease dynamics have received increased attention. There are many possible pathway a can invade and spread through host population, assumed transmission model used to capture propagation influence predictions net reproductive success (R0), determining outbreak dynamics. We synthesize comprehensive overview these models overarching implications, using bovine Tuberculosis (Mycobacterium bovis) as case study. unify sub-models...

Abstract As a corollary to the Red Queen hypothesis, host–parasite coevolution has been hypothesized maintain genetic variation in both species. Recent theoretical work, however, suggests that reciprocal natural selection alone is insufficient at individual loci. highlighted by our brief review of literature, models often vary along multiple axes (e.g. inclusion ecological feedbacks or abiotic mosaics), complicating comprehensive understanding effects interacting evolutionary processes on...

Antagonistic coevolution has long been suggested to help maintain host genetic variation. Although ecological and epidemiological feedbacks are known have important consequences on coevolutionary allele-frequency dynamics, their effects the maintenance of variation remains poorly understood. Here, we extend previous work in a classic matching alleles model by exploring feedbacks, where both allele frequencies population sizes allowed vary over time. We find that rarely maintains more than...

Abstract Population genomic analysis of hybrid zones is instrumental to our understanding the evolution reproductive isolation. Many temperate are formed by secondary contact between two parental populations that have undergone post-glacial range expansion. Here we show explicitly accounting for historical isolation followed expansion prior fundamental explaining genetic and fitness patterns in these zones. Specifically, ancestral population can result allele surfing where neutral or...

Abstract A phylogenetic tree has three types of attributes: size, shape (topology), and branch lengths. Phylody-namic studies are often motivated by questions regarding the size clades, nevertheless, nearly all inference methods only make use other two attributes. In this paper, we ask whether there is additional information if consider more explicitly in phylodynamic methods. To address question, first needed to be able compute expected distribution under a specified model; perhaps...

Disease transmission in wildlife is linked to ecosystem and human health, host community structure can mediate pathogen spread. Here, we decompose the well-known susceptible-infected (SI) compartmental models of disease for multi-host communities explore disease-biodiversity relationship. We examine parameters involved interspecific link them outbreak potential, R0. partition R0 into its separate elements that be associated with either recipient or donating host, show how this allows us...

Yule's 1925 paper introducing the branching model that bears his name was a landmark contribution to biodiversity sciences. In paper, Yule developed stochastic models explain observed distribution of species across genera and test hypotheses about relationship between clade age, diversity, geographic range. Here we discuss intellectual context in which produced this work, highlight key mathematical conceptual contributions using both more modern derivations, critically examine some...