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Miller, Z. R.

Publications and source records attributed to Miller, Z. R..

21 records · Page 2Linked to original sources

Effects of phylogeny on coexistence in model communities

A species traits influence the way in which it interacts with the environment. Thus, we expect traits to play a role in determining whether a given set of species coexists. Traits are, in turn, the outcome of an eco-evolutionary process summarized by a phylogenetic tree. Therefore, the phylogenetic tree associated with a set of species should encode information about the assembly properties of the community. Many studies have high-lighted the potentially complex ways in which phylogenetic information is translated into species ecological properties. However, much less emphasis has been placed on developing expectations for community properties under a particular hypothesis. In this work, we couple a simple model of trait evolution on a phylogenetic tree with local community dynamics governed by Lotka-Volterra equations. This allows us to derive properties of the community of coexisting species as a function of the number of traits, tree topology and the size of the species pool. Our results highlight how phylogenies and traits, in concert, affect the coexistence of a set of species. In this way, our work provides new baseline expectations for the ways in which phylogenetic information is reflected in the structure of and coexistence within local communities.

ecology↗

A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

As a result of millions of years of transposon activity, multiple rounds of ancient polyploidization, and large populations that preserve diversity, maize has an extremely structurally diverse genome, evidenced by high-quality genome assemblies that capture substantial levels of both tropical and temperate diversity. We generated a pangenome representation (the Practical Haplotype Graph, PHG) of these assemblies in a database, representing the pangenome haplotype diversity and providing an initial estimate of structural diversity. We leveraged the pangenome to accurately impute haplotypes and genotypes of taxa using various kinds of sequence data, ranging from WGS to extremely-low coverage GBS. We imputed the genotypes of the recombinant inbred lines of the NAM population with over 99% mean accuracy, while unrelated germplasm attained a mean imputation accuracy of 92 or 95% when using GBS or WGS data, respectively. Most of the imputation errors occur in haplotypes within European or tropical germplasm, which have yet to be represented in the maize PHG database. Also, the PHG stores the imputation data in a 30,000-fold more space-efficient manner than a standard genotype file, which is a key improvement when dealing with large scale data.

genomics↗

Predicting coexistence in experimental ecologicalcommunities

The study of experimental communities is fundamental to the development of ecology. Yet, for most ecological systems, the number of experiments required to build, model, or analyze the community vastly exceeds what is feasible using current methods. Here, we address this challenge by presenting a statistical approach that uses the results of a limited number of experiments to predict the outcomes (coexistence and species abundances) of all possible assemblages that can be formed from a given pool of species. Using three well-studied experimental systems--encompassing plants, protists, and algae with grazers--we show that this method predicts with high accuracy the results of unobserved experiments, while making no assumptions about the dynamics of the systems. These results suggest a fundamentally different study design for building and quantifying experimental systems, requiring a small number of experiments relative to traditional approaches. By providing a scalable method for navigating large systems, this work provides an efficient way to study highly diverse experimental communities.

ecology↗