Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson’s index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weig...
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| Format: | Article |
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PeerJ Inc.
2013-09-01
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| Online Access: | https://peerj.com/articles/157.pdf |
| _version_ | 1797420495338995712 |
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| author | Connor O. McCoy Frederick A. Matsen IV |
| author_facet | Connor O. McCoy Frederick A. Matsen IV |
| author_sort | Connor O. McCoy |
| collection | DOAJ |
| description | In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson’s index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, they are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different datasets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPDθ, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. On the three datasets, a phylogenetic measure always performed best, and two abundance-weighted phylogenetic diversity measures were the only measures ranking in the top four across all datasets. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult. |
| first_indexed | 2024-03-09T07:03:18Z |
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| id | doaj.art-7a239d9f51ea46c3bd4f12c6d6bc168f |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:03:18Z |
| publishDate | 2013-09-01 |
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| spelling | doaj.art-7a239d9f51ea46c3bd4f12c6d6bc168f2023-12-03T09:47:28ZengPeerJ Inc.PeerJ2167-83592013-09-011e15710.7717/peerj.157157Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depthConnor O. McCoy0Frederick A. Matsen IV1Fred Hutchinson Cancer Research Center, Seattle, WA, United StatesFred Hutchinson Cancer Research Center, Seattle, WA, United StatesIn microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson’s index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, they are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different datasets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPDθ, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. On the three datasets, a phylogenetic measure always performed best, and two abundance-weighted phylogenetic diversity measures were the only measures ranking in the top four across all datasets. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult.https://peerj.com/articles/157.pdfAlpha diversityDiversity indicesPhylogenetic diversityMicrobial ecologyHuman microbiome |
| spellingShingle | Connor O. McCoy Frederick A. Matsen IV Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth PeerJ Alpha diversity Diversity indices Phylogenetic diversity Microbial ecology Human microbiome |
| title | Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth |
| title_full | Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth |
| title_fullStr | Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth |
| title_full_unstemmed | Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth |
| title_short | Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth |
| title_sort | abundance weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth |
| topic | Alpha diversity Diversity indices Phylogenetic diversity Microbial ecology Human microbiome |
| url | https://peerj.com/articles/157.pdf |
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