Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process Article Swipe
Keith Harris
,
Todd L. Parsons
,
Umer Zeeshan Ijaz
,
Leo Lahti
,
Ian Holmes
,
Christopher Quince
·
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1109/jproc.2015.2428213
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1109/jproc.2015.2428213
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.
Related Topics
Concepts
Metacommunity
Neutral theory of molecular evolution
Hierarchical Dirichlet process
Ecology
Relative abundance distribution
Population
Biodiversity
Null model
Community
Dirichlet process
Biology
Bayesian probability
Relative species abundance
Mathematics
Computer science
Abundance (ecology)
Statistics
Ecosystem
Artificial intelligence
Biological dispersal
Latent Dirichlet allocation
Topic model
Sociology
Demography
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1109/jproc.2015.2428213
- OA Status
- green
- Cited By
- 75
- References
- 52
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W1494269785
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W1494269785Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1109/jproc.2015.2428213Digital Object Identifier
- Title
-
Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet ProcessWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2015Year of publication
- Publication date
-
2015-08-14Full publication date if available
- Authors
-
Keith Harris, Todd L. Parsons, Umer Zeeshan Ijaz, Leo Lahti, Ian Holmes, Christopher QuinceList of authors in order
- Landing page
-
https://doi.org/10.1109/jproc.2015.2428213Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://arxiv.org/pdf/1410.4038Direct OA link when available
- Concepts
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Metacommunity, Neutral theory of molecular evolution, Hierarchical Dirichlet process, Ecology, Relative abundance distribution, Population, Biodiversity, Null model, Community, Dirichlet process, Biology, Bayesian probability, Relative species abundance, Mathematics, Computer science, Abundance (ecology), Statistics, Ecosystem, Artificial intelligence, Biological dispersal, Latent Dirichlet allocation, Topic model, Sociology, DemographyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
75Total citation count in OpenAlex
- Citations by year (recent)
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2025: 6, 2024: 5, 2023: 9, 2022: 9, 2021: 9Per-year citation counts (last 5 years)
- References (count)
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52Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.organisms. | 301 |
| abstract_inverted_index.population | 79 |
| abstract_inverted_index.communities | 24 |
| abstract_inverted_index.constrained | 226 |
| abstract_inverted_index.correlation | 255 |
| abstract_inverted_index.distinguish | 107 |
| abstract_inverted_index.equivalence | 5 |
| abstract_inverted_index.immigration | 33, 261, 293 |
| abstract_inverted_index.macroscopic | 228 |
| abstract_inverted_index.neutrality. | 249 |
| abstract_inverted_index.resolution, | 192 |
| abstract_inverted_index.biodiversity | 20 |
| abstract_inverted_index.carbohydrate | 299 |
| abstract_inverted_index.distribution | 117 |
| abstract_inverted_index.hierarchical | 83 |
| abstract_inverted_index.microbiomes. | 149 |
| abstract_inverted_index.approximation | 88 |
| abstract_inverted_index.metacommunity | 30, 116, 124 |
| abstract_inverted_index.interpretation | 271 |
| abstract_inverted_index.computationally | 52 |
| abstract_inverted_index.mainland-island | 68 |
| abstract_inverted_index.Ruminococcaceae. | 266 |
| cited_by_percentile_year.max | 99 |
| cited_by_percentile_year.min | 94 |
| countries_distinct_count | 4 |
| institutions_distinct_count | 6 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/15 |
| sustainable_development_goals[0].score | 0.5699999928474426 |
| sustainable_development_goals[0].display_name | Life in Land |
| citation_normalized_percentile.value | 0.87184853 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |