Diversity time-period and diversity-time-area relationships exemplified by the human microbiome

Abstract We extend the ecological laws of species-time relationship (STR) and species-time-area relationship (STAR) to general diversity time-period relationship (DTR) and diversity-time-area relationship (DTAR), and test the extensions with the human vaginal microbiome datasets by building 1460 DTR...

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Autor principal:	Zhanshan (Sam) Ma
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3d98cf5450994bbaa5752fc490f52247
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spelling	oai:doaj.org-article:3d98cf5450994bbaa5752fc490f522472021-12-02T12:32:48ZDiversity time-period and diversity-time-area relationships exemplified by the human microbiome10.1038/s41598-018-24881-32045-2322https://doaj.org/article/3d98cf5450994bbaa5752fc490f522472018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-24881-3https://doaj.org/toc/2045-2322Abstract We extend the ecological laws of species-time relationship (STR) and species-time-area relationship (STAR) to general diversity time-period relationship (DTR) and diversity-time-area relationship (DTAR), and test the extensions with the human vaginal microbiome datasets by building 1460 DTR/DTAR models. Our extensions were inspired by the observation that Hill numbers, well regarded as the most appropriate measure of alpha-diversity and also particularly suitable for multiplicative beta-diversity partitioning, are actually in the units of effective species, and therefore, should be able to substitute for species in the STR and STAR. We found that the traditional power law (PL) model is only applicable for DTR at diversity order zero (i.e., species richness); at higher diversity orders (q = 1–4), the power law with exponent cutoff (PLEC) and power law with inverse exponent cutoff (PLIEC) are more appropriate. In particular, PLEC has an advantage over PLIEC in predicting maximal accumulation diversity (MAD) over time. In fact, with the DTR extensions, we can construct DTR and MAD profiles. To the best of our knowledge, this is the first comprehensive investigation of the DTR/DTAR in human microbiome. Methodologically, our DTR/DTAR profiles can characterize general diversity scaling beyond species richness, covering both alpha- and beta-diversity regimes across different diversity orders.Zhanshan (Sam) MaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-16 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zhanshan (Sam) Ma Diversity time-period and diversity-time-area relationships exemplified by the human microbiome
description	Abstract We extend the ecological laws of species-time relationship (STR) and species-time-area relationship (STAR) to general diversity time-period relationship (DTR) and diversity-time-area relationship (DTAR), and test the extensions with the human vaginal microbiome datasets by building 1460 DTR/DTAR models. Our extensions were inspired by the observation that Hill numbers, well regarded as the most appropriate measure of alpha-diversity and also particularly suitable for multiplicative beta-diversity partitioning, are actually in the units of effective species, and therefore, should be able to substitute for species in the STR and STAR. We found that the traditional power law (PL) model is only applicable for DTR at diversity order zero (i.e., species richness); at higher diversity orders (q = 1–4), the power law with exponent cutoff (PLEC) and power law with inverse exponent cutoff (PLIEC) are more appropriate. In particular, PLEC has an advantage over PLIEC in predicting maximal accumulation diversity (MAD) over time. In fact, with the DTR extensions, we can construct DTR and MAD profiles. To the best of our knowledge, this is the first comprehensive investigation of the DTR/DTAR in human microbiome. Methodologically, our DTR/DTAR profiles can characterize general diversity scaling beyond species richness, covering both alpha- and beta-diversity regimes across different diversity orders.
format	article
author	Zhanshan (Sam) Ma
author_facet	Zhanshan (Sam) Ma
author_sort	Zhanshan (Sam) Ma
title	Diversity time-period and diversity-time-area relationships exemplified by the human microbiome
title_short	Diversity time-period and diversity-time-area relationships exemplified by the human microbiome
title_full	Diversity time-period and diversity-time-area relationships exemplified by the human microbiome
title_fullStr	Diversity time-period and diversity-time-area relationships exemplified by the human microbiome
title_full_unstemmed	Diversity time-period and diversity-time-area relationships exemplified by the human microbiome
title_sort	diversity time-period and diversity-time-area relationships exemplified by the human microbiome
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/3d98cf5450994bbaa5752fc490f52247
work_keys_str_mv	AT zhanshansamma diversitytimeperiodanddiversitytimearearelationshipsexemplifiedbythehumanmicrobiome
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Diversity time-period and diversity-time-area relationships exemplified by the human microbiome

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