Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process

Harris, Keith, Parsons, Todd L., Ijaz, Umer Z., Lahti, Leo, Holmes, Ian and Quince, Christopher (2017) Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process. Proceedings of the IEEE, 105 (3). pp. 516-529. ISSN 0018-9219

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Neutral models which assume ecological equivalence between species provide null models for community assembly. In Hubbell's unified neutral theory of biodiversity (UNTB), many local communities are connected to a single metacommunity through differing immigration rates. Our ability to fit the full multisite UNTB has hitherto been limited by the lack of a computationally tractable and accurate algorithm. We show that a large class of neutral models with this mainland-island structure but differing local community dynamics converge in the large population limit to the hierarchical Dirichlet process. Using this approximation we developed an efficient Bayesian fitting strategy for the multisite UNTB. We can also use this approach to distinguish between neutral local community assembly given a nonneutral metacommunity distribution and the full UNTB where the metacommunity too assembles neutrally. We applied this fitting strategy to both tropical trees and a data set comprising 570 851 sequences from 278 human gut microbiomes. The tropical tree data set was consistent with the UNTB but for the human gut neutrality was rejected at the whole community level. However, when we applied the algorithm to gut microbial species within the same taxon at different levels of taxonomic resolution, we found that species abundances within some genera were almost consistent with local community assembly. This was not true at higher taxonomic ranks. This suggests that the gut microbiota is more strongly niche constrained than macroscopic organisms, with different groups adopting different functional roles, but within those groups diversity may at least partially be maintained by neutrality. We also observed a negative correlation between body mass index and immigration rates within the family Ruminococcaceae. This provides a novel interpretation of the impact of obesity on the human microbiome as a relative increase in the importance of local growth versus external immigration within this key group of carbohydrate degrading organisms.

Item Type: Article
Additional Information: Funding Information: The work of K. Harris was supported by a Unilever Research Grant. The work of T. L. Parsons was supported by the CNRS, and was also supported in part by the Fondation Sciences Mathématiques de Paris. The work of U. Z. Ijaz was supported by NERC IRF NE/L011956/1. The work of L. Lahti was supported by the Academy of Finland (Decision 256950). The work of I. Holmes was supported by NIH R01 Grant HG004483. The work C. Quince was supported by an MRC Fellowship MR/M50161X/1 as part of the CLIMB consortium MR/L015080/1. Publisher Copyright: © 1963-2012 IEEE.
Uncontrolled Keywords: diversity,ecological modelling,hierarchical dirichlet process,hubbell's unified neutral theory of biodiversity,microbial communities,computer science(all),electrical and electronic engineering,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1700
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 09 Sep 2022 08:30
Last Modified: 04 Jul 2023 10:31
DOI: 10.1109/JPROC.2015.2428213

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