相关论文: Extended Distance-based Phylogenetic Analyses Appl…

Analyses of a set of 47 fossil and 4 modern skulls using phylogenetic geometric morphometric methods corroborate and refine earlier results. These include evidence that the African Iwo Eleru skull, only about 12,000 years old, indeed…

Estimating the phylogeny of the genus Homo is entering a new phase of vastly improved data and methodology. There is increasing evidence of 6 to 10 competing species/lineages at any point in the last half million years, making the…

A range of a priori hypotheses about the evolution of modern and archaic genomes are further evaluated and tested. In addition to the well-known splits/introgressions involving Neanderthal genes into out-of- Africa people, or Denisovan…

Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…

Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…

Although there has been much interest in estimating divergence and admixture from genomic data, it has proven difficult to distinguish gene flow after divergence from alternative histories involving structure in the ancestral population.…

Recent studies have shown that hybridization between modern and archaic humans was commonplace in the history of our species. After admixture, some individuals with admixed autosomes carried the modern Homo Sapiens uniparental DNAs, while…

Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…

We consider a large population of asexually reproducing individuals in absence of selective pressure. The population size is maintained constant by the environment. We find out that distances between individuals (time from the last common…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…

Phylogenetic analysis traditionally relies on labor-intensive manual extraction of morphological traits, limiting its scalability for large datasets. Recent advances in deep learning offer the potential to automate this process, but the…

As a variant of standard convolution, a dilated convolution can control effective receptive fields and handle large scale variance of objects without introducing additional computational costs. To fully explore the potential of dilated…

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…

As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient,…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular the fossilized…

Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…

A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…