Consider the diffusion process defined by the forward equation u(t,x)=12{xu(t,x)}-α{xu(t,x)} for t,x≥0 and -∞<α<∞, with an initial condition u(0,x)=δ(x-x). This equation was introduced and solved by Feller to model the growth of a population of independently reproducing individuals. We explore important coalescent processes related to Feller's solution. For any α and x>0 we calculate the distribution of the random variable A(s;t), defined as the finite number of ancestors at a time s in the past of a sample of size n taken from the infinite population of a Feller diffusion at a time t since its initiation. In a subcritical diffusion we find the distribution of population and sample coalescent trees from time t back, conditional on non-extinction as t→∞. In a supercritical diffusion we construct a coalescent tree which has a single founder and derive the distribution of coalescent times.
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http://dx.doi.org/10.1016/j.tpb.2023.12.001 | DOI Listing |
Genetics
January 2025
Interfaculty Bioinformatics Unit, University of Bern, Bern 3012, Switzerland.
Purifying selection is a critical factor in shaping genetic diversity. Current theoretical models mostly address scenarios of either very weak or strong selection, leaving a significant gap in our knowledge. The effects of purifying selection on patterns of genomic diversity remain poorly understood when selection against deleterious mutations is weak to moderate, particularly when recombination is limited or absent.
View Article and Find Full Text PDFMol Phylogenet Evol
January 2025
Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China. Electronic address:
Phylogenomic analyses have shown that reticulate evolution greatly affects the accuracy of phylogenetic inferences, and thus may challenge the authority of bifurcating phylogenetic trees. In this study, we re-evaluated the phylogenetic backbone of the genus Corylus based on complete taxon sampling and genomic data. We assembled 581 single-copy nuclear genes and whole plastomes from 64 genome resequencing datasets to elucidate the reticulate relationships within Corylus.
View Article and Find Full Text PDFThe worst-case runtime complexity to simulate haplotype segments identical by descent (IBD) is quadratic in sample size. We propose two main techniques to reduce the compute time, both of which are motivated by coalescent and recombination processes. We provide mathematical results that explain why our algorithm should outperform a naive implementation with high probability.
View Article and Find Full Text PDFSyst Biol
January 2025
School of Life Sciences and Department of Statistics, University of Warwick, UK.
The vast majority of pathogen phylogenetic studies do not consider the possibility of multiple merger events being present, where a single node of the tree leads to more than two descendent branches. These events are however likely to occur when studying a relatively small population or if there is high variability in the reproductive chances. Here we consider the problem of detecting the presence of multiple mergers in the context of dating a phylogeny, that is determining the date of each of the nodes.
View Article and Find Full Text PDFAnn Bot
January 2025
Département de Biologie, Université Laval, Canada.
Background And Aims: Resolving the phylogeny of hornworts is critical in understanding the evolution of key morphological characters that are unique to the group, including the pyrenoid. Extensive phylogenomic analyses have revealed unexpected complexities in the placement of Leiosporoceros, the previously identified sister taxon to other hornworts. We explore the role of incomplete lineage sorting (ILS) and ancient reticulation in resolving interrelationships and comprehending the diversification and evolutionary processes within hornworts.
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