相关论文: Bayesian phylogenetic estimation of fossil ages

In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004)…

Reproductive phenology, growth and mortality rates are key ecological parameters that determine population dynamics and are therefore of vital importance to stock assessment models for fisheries management. In many fish species, the…

Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and…

Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), many contact surveys have been conducted to measure changes in human interactions in the face of the pandemic and non-pharmaceutical interventions. These…

Degradation data are considered for assessing reliability in highly reliable systems. The usual assumption is that degradation units come from a homogeneous population. But in presence of high variability in the manufacturing process, this…

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…

I propose an approach to identify, among several strategies of phylogenetic analysis, those producing the most accurate results. This approach is based on the hypothesis that the more a result is reproduced from independent data, the more…

Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…

Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive sequentially in time and one is interested in performing…

It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…

The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such…

Context. Local young stellar associations (LYSAs <50 Myr and <150 pc) are important laboratories to test predictions from star-formation theories. Estimating their ages through various dating techniques with minimal biases is thus of…

We investigate the performance of grid-based techniques in estimating the age of stars in detached eclipsing binary systems. We evaluate the precision of the estimates due to the uncertainty in the observational constraints, and the…

In this article the results of Waddell and Azad (2009) are extended. In particular, the geometric percentage mean standard deviation measure of the fit of distances to a phylogenetic tree is adjusted for the number of parameters fitted to…

Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…

Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity with a main objective: disentangling the processes that drive species distributions from local to broad…

Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper,…

There has been concern in the literature about the methodology of using secondary calibration timepoints when estimating evolutionary divergence dates. Such timepoints are divergence time estimates that have been derived from one molecular…

We present a robust Bayesian method to analyze forestry data when samples are selected with probability proportional to length from a finite population of unknown size. Specifically, we use Bayesian predictive inference to estimate the…