相关论文: Expected Anomalies in the Fossil Record

Unbiased models are foundational in the archaeological study of cultural transmission. Applications have as- sumed that archaeological data represent synchronic samples, despite the accretional nature of the archaeological record. I…

Deamination has historically been important for authenticating ancient biomolecules. However, expanding paleogenomic datasets indicate that damage patterns are more influenced by burial hydrology and microstructural context than by…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

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…

Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…

Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing…

Irregularly sampled time series data arise naturally in many application domains including biology, ecology, climate science, astronomy, and health. Such data represent fundamental challenges to many classical models from machine learning…

In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…

Phylogenetic comparative methods are new in our field and are shrouded, for most linguists, in at least a little mystery. Yet the path that led to their discovery in comparative biology is so similar to the methodological history of…

Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans…

The origin of fluctuations in the average number of intermediate mass fragments seen in experiments in small projectile like fragments is discussed. We argue that these can be explained on the basis of a recently proposed model of…

We consider a recently-proposed alternative explanation of the CV period gap in terms of a revised mass-radius relation for the lower main sequence. We show that no such thermal-equilibrium relation is likely to produce a true gap. Using…

An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both…

To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…

With unprecedented advances in genetic engineering we are starting to see progressively more original examples of synthetic life. As such organisms become more common it is desirable to be able to distinguish between natural and artificial…

The large number of observed exoplanets ($\gtrsim $ 700) provides important constraints on their origin as deduced from the mass-period diagram of planets. The most surprising features in the diagram are 1) the (apparent) pile up of gas…

Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is…

Some practical results are derived for population inference based on a sample, under the two qualitative conditions of 'ignorability' and exchangeability. These are the 'Histogram Theorem', for predicting the outcome of a non-sampled member…

Comparing paleoclimate time series is complicated by a variety of typical features, including irregular sampling, age model uncertainty (e.g., errors due to interpolation between radiocarbon sampling points) and time uncertainty…

Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer…