Related papers: Inference for changes in biodiversity
The assessment of diversity and similarity is relevant in monitoring the status of ecosystems. The respective indicators are based on the taxonomic composition of biological communities of interest, currently estimated through the…
If predictions for species extinctions hold, then the `tree of life' today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely to contribute to future biodiversity, as…
Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…
The maintenance of diversity, the `commonness of rarity', and compositional turnover are ubiquitous features of species-rich communities. Through a minimal model, we consider how these features reflect the interplay between environmental…
Identifying which taxa in our microbiota are associated with traits of interest is important for advancing science and health. However, the identification is challenging because the measured vector of taxa counts (by amplicon sequencing) is…
Entropy measures of probability distributions are widely used measures in ecology, biology, genetics, and in other fields, to quantify species diversity of a community. Unfortunately, entropy-based diversity indices, or diversity indices…
A robust estimator is proposed for the parameters that characterize the linear regression problem. It is based on the notion of shrinkages, often used in Finance and previously studied for outlier detection in multivariate data. A thorough…
Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depend on the context and…
We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of…
Quantitative methods for studying biodiversity have been traditionally rooted in the classical theory of finite frequency tables analysis. However, with the help of modern experimental tools, like high throughput sequencing, we now begin to…
Phenotypic heterogeneity is a strategy commonly used by bacteria to rapidly adapt to changing environmental conditions. Here, we study the interplay between phenotypic heterogeneity and genetic diversity in spatially extended populations.…
How diversity is maintained in natural ecosystems is a long-standing question in Theoretical Ecology. By studying a system that combines ecological dynamics, heterogeneous interactions and spatial structure, we uncover a new mechanism for…
A refinement of the multinomial distribution is presented where the number of inversions in the sequence of outcomes is tallied. This refinement of the multinomial distribution is its joint distribution with the number of inversions in the…
Until recently, much of the microbial world was hidden from view. A global research effort has changed this, unveiling and quantifying microbial diversity across enormous range of critically-important contexts, from the human microbiome, to…
Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution…
How to estimate heterogeneity, e.g. the effect of some variable differing across observations, is a key question in political science. Methods for doing so make simplifying assumptions about the underlying nature of the heterogeneity to…
Several theoretical frameworks have been proposed to explain observed biodiversity patterns, ranging from the classical niche-based theories, mainly employing a continuous formalism, to neutral theories, based on statistical mechanics of…
Understanding the behaviors of ecological systems is challenging given their multi-faceted complexity. To proceed, theoretical models such as Lotka-Volterra dynamics with random interactions have been investigated by the dynamical…
1. Species distribution models and maps from large-scale biodiversity data are necessary for conservation management. One current issue is that biodiversity data are prone to taxonomic misclassifications. Methods to account for these…
In microbial communities, each species often has multiple, distinct phenotypes, but studies of ecological stability have largely ignored this subpopulation structure. Here, we show that such implicit averaging over phenotypes leads to…