Ecotype Simulation 2: An improved algorithm for efficiently demarcating microbial species from large sequence datasets

Abstract

BackgroundMicrobial systematists have used molecular cutoffs to classify the vast diversity present within a natural microbial community without invoking ecological theory. The use of ecological theory is needed to identify whether or not demarcated groups are the ecologically distinct, fundamental units (ecotypes), necessary for understanding the system. Ecotype Simulation, a Monte-Carlo approach to modeling the evolutionary dynamics of a microbial population based on the Stable Ecotype Model of microbial speciation, has proven useful for finding these fundamental units. For instance, predicted ecotypes of Synechococcus forming microbial mats in Yellowstone National Park hot springs, which were previously considered to be a single species based on phenotype, have been shown to be ecologically distinct, with specialization to different temperature and light levels. Unfortunately, development of high-throughput DNA sequencing methods has outpaced the ability of the program to analyze all of the sequence data produced. ResultsWe developed an improved version of the program called Ecotype Simulation 2, which can rapidly analyze alignments of very large sequence datasets. For instance, while the older version takes days to analyze 200 sequences, the new version can analyze 1.92×10 5 sequences in about six hours. The faster simulation identified similar ecotypes as found with the slower version, but from larger amounts of sequence data. ConclusionsBased on ecological theory, Ecotype Simulation 2 provides a much-needed approach that will help guide microbial ecologists and systematists to the natural, fundamental units of bacterial diversity.

Biogeography of American Northwest Hot Spring A/B′-Lineage Synechococcus Populations

“…This allowed us to restrict most analyses to sequences that were frequently detected. Also, analyses of HFS10s have proven valuable by increasing the sampling of variants within putative ecotypes, thereby enhancing our ability to demonstrate that sequence diversity within a putative ecotype is ecologically homogeneous (Becraft et al, 2015;Wood et al, 2020). However, we still used all sequences with >1 representative to analyze dispersal (see below).…”

“…To analyze the distribution of HFS10 variation within ecological populations among chemically similar springs and regions, Ecotype Simulation 2 (ES2) was used to predict putative ecotypes (PEs) from the variation sampled. ES2 uses evolutionary simulation analysis to predict ecologically distinct or geographically isolated clusters in a phylogeny (Wood et al, 2020). Directions for download and instructions for the use of ES2 are freely available at https://github.com/sandain/ecosim.…”

“…Frontiers in Microbiology | www.frontiersin.org sample to provide the data matrix analyzed by CCA. The plotting function used by Wood et al (2020) was used here to display the distribution of HFS10 variants and predominant PEs in the CCA ordination space. This plotting function reports a p-value for each PE demarcation that represents the probability that the observed distribution of the PE in ordination space is in a tighter cluster than a randomly produced distribution of the same size in the same ordination space.…”

“…In this study, we reanalyzed American Northwest samples collected by Papke et al (2003) using high-throughput sequencing of amplicons of a segment of a more highlyresolving, protein-encoding locus (psaA) (Becraft et al, 2011(Becraft et al, , 2015. We have used Ecotype Simulation 2 (Wood et al, 2020) to identify the most newly divergent psaA segment sequence clusters that can coexist indefinitely because they are either ecologically distinct (ecotypes) or geographically isolated populations (geotypes), or both (Cohan and Perry, 2007). This permitted rigorous analysis of the distribution of A-and B ′ -like Synechococcus genetic diversity in hot springs that are separated by <1 to > 800 km, with the aim of gaining a better understanding of the role of allopatric processes in the diversification of Synechococcus.…”

A Genomic Perspective on Ecological Diversification in Bacillus in Death Valley National Park

“…In previous studies, sequence clusters identified by Ecotype Simulation have all been shown to be ecologically distinct from one another (Connor et al, 2010;Ward et al, 2005;Koeppel et al, 2008). The Ecotype Simulation 2 (ES2) algorithm was used to demarcate putative ecotypes in the foundational study for this thesis (DelGaudio, 2018;Wood et al, 2018).…”