Related papers: Robust estimation of microbial diversity in theory…
Challenges of assessing complexity and clonality in populations of mixed species arise in diverse areas of modern biology, including estimating diversity and clonality in microbiome populations, measuring patterns of T and B cell clonality,…
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…
Diversity measurement underpins the study of biological systems, but measures used vary across disciplines. Despite their common use and broad utility, no unified framework has emerged for measuring, comparing and partitioning diversity.…
This is a preliminary article stating and proving a new maximum entropy theorem. The entropies that we consider can be used as measures of biodiversity. In that context, the question is: for a given collection of species, which frequency…
We consider the classic problem of estimating T, the total number of species in a population, from repeated counts in a simple random sample. We look first at the Chao-Lee estimator: we initially show that such estimator can be obtained by…
One of the central questions of metacommunity theory is how dispersal of organisms affects species diversity. Here we show that the diversity-dispersal relationship should not be studied in isolation of other abiotic and biotic flows in the…
We propose to estimate the number of communities in degree-corrected stochastic block models based on a pseudo likelihood ratio statistic. To this end, we introduce a method that combines spectral clustering with binary segmentation. This…
Multilevel selection and the evolution of cooperation are fundamental to the formation of higher-level organisation and the evolution of biocomplexity, but such notions are controversial and poorly understood in natural populations. The…
Predicting species persistence within ecological communities is a fundamental challenge for both empirical and theoretical ecology. Existing methods span from mechanistic models, whose parameters are difficult to estimate from data, to…
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…
The population size ("abundance") of wildlife species has central interest in ecological research and management. Distance sampling is a dominant approach to the estimation of wildlife abundance for many vertebrate animal species. One…
When analyzing communities of microorganisms from their sequenced DNA, an important task is taxonomic profiling: enumerating the presence and relative abundance of all organisms, or merely of all taxa, contained in the sample. This task can…
High throughput sequencing (HTS) continues to expand our understanding of microbial communities, despite insufficient sequencing depths to detect all rare taxa. These low abundance taxa are not accounted for in existing methods for…
The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…
We introduce the first analytical model of asymmetric community dynamics to yield Hubbell's neutral theory in the limit of functional equivalence among all species. Our focus centers on an asymmetric extension of Hubbell's local community…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…
Dynamics of species' abundances in ecological communities are often described using models that only account for a few species. It is not clear when and why this would be possible, as most species form part of diverse ecological…
Phylogenetic diversity (PD) depends on sampling intensity, which complicates the comparison of PD between samples of different depth. One approach to dealing with differing sample depth for a given diversity statistic is to rarefy, which…
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with…
Recent attacks of various viruses with having deep and extensive impact at a global scale has warranted that microbiome be studied extensively and in a robust analytic framework. Microbiome typically refers to the collective genomes of such…