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Divergence time estimation requires the reconciliation of two major sources of data. These are fossil and/or biogeographic evidence that give estimates of the absolute age of nodes (ancestors) and molecular estimates that give us estimates…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide the first deep investigation of the predictive potential of machine…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
Genetic robustness, the preservation of an optimal phenotype in the face of mutations, is critical to the understanding of evolution as phenotypically expressed genetic variation is the fuel of natural selection. The origin of genetic…
Branching architecture characterizes numerous systems, ranging from synthetic (hyper)branched polymers and biomolecules such as lignin, amylopectin, and nucleic acids to tracheal and neuronal networks. Its ubiquity reflects the many…
Y-chromosomal and mitochondrial DNA profiles have been used as evidence in courts for decades, yet the problem of evaluating the weight of evidence has not been adequately resolved. Both are lineage markers (inherited from just one parent),…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
We consider a fitness-structured population model with competition and migration between nearest neighbors. Under a combination of large population and rare migration limits we are particularly interested in the asymptotic behavior of the…
Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
Statistical averaging and asynchronous population dynamics as portfolio mechanisms are considered as the most important processes with which biodiversity contributes to ecosystem stability. However, portfolio theories usually regard…
The majority of cancer treatments end in failure due to Intra-Tumor Heterogeneity (ITH). ITH in cancer is represented by clonal evolution where different sub-clones compete with each other for resources under conditions of Darwinian natural…
Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to…
Ecological selection is a major driver of community assembly. Selection is classified as stabilizing when species with intermediate trait values gain the highest reproductive success, whereas selection is considered directional when fitness…
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a…
Background: Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequences that satisfy the base pairing constraints of a given RNA…
Cancer is a complex genetic disease involving uncontrolled cell growth and proliferation, and necessitates effective targeting of dysregulated cellular pathways underlying cancer progression. Multiple genetic and epigenetic alterations…
Polygenic risk scores (PRSs) can significantly enhance breast cancer risk prediction when combined with clinical risk factor data. While many studies have explored the value-add of PRSs, little is known about the potential impact of…