Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities

High-throughput sequencing (HTS) is rapidly becoming a popular and robust tool to characterize biodiversity of complex communities, especially for those dominated by microscopic species such as zooplankton. The popular use of HTS-based methods has prompted a possible method of inferring relative spe...

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Autores principales:	C Sun, Y Zhao, H Li, Y Dong, HJ MacIsaac, A Zhan
Formato:	article
Lenguaje:	EN
Publicado:	Inter-Research 2015
Materias:	Biology (General) QH301-705.5 Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/0f544684acf240c5a471cf9493ea122c
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spelling	oai:doaj.org-article:0f544684acf240c5a471cf9493ea122c2021-11-18T09:16:49ZUnreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities1864-77821864-779010.3354/ab00629https://doaj.org/article/0f544684acf240c5a471cf9493ea122c2015-05-01T00:00:00Zhttps://www.int-res.com/abstracts/ab/v24/n1/p9-15/https://doaj.org/toc/1864-7782https://doaj.org/toc/1864-7790High-throughput sequencing (HTS) is rapidly becoming a popular and robust tool to characterize biodiversity of complex communities, especially for those dominated by microscopic species such as zooplankton. The popular use of HTS-based methods has prompted a possible method of inferring relative species abundance from sequencing data. However, these methods remain largely untested in many communities as to whether sequence data can reliably quantify relative species abundance. Here we tested the relationship between species abundance and sequence abundance in zooplankton using 2 methods: (1) spiking known amounts of indicator species into existing zooplankton communities, and (2) comparing results obtained from parallel replicates for the same natural zooplankton communities. Although we detected a general trend that low-abundance species usually corresponded to low-abundance sequence reads, further statistical analyses revealed that sequencing data could not reliably quantify relative species abundance, even for the same indicator species spiked into different zooplankton communities. The distribution of sequence reads statistically varied even between parallel replicates of the same natural zooplankton communities. Our study reveals that sequence abundance may generally qualitatively reflect species abundance as the general trend between these 2 variables exists; however, extra caution is required when using HTS-based approaches to make quantitative inferences regarding zooplankton communities.C SunY ZhaoH LiY DongHJ MacIsaacA ZhanInter-ResearcharticleBiology (General)QH301-705.5MicrobiologyQR1-502ENAquatic Biology, Vol 24, Iss 1, Pp 9-15 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5 Microbiology QR1-502
spellingShingle	Biology (General) QH301-705.5 Microbiology QR1-502 C Sun Y Zhao H Li Y Dong HJ MacIsaac A Zhan Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities
description	High-throughput sequencing (HTS) is rapidly becoming a popular and robust tool to characterize biodiversity of complex communities, especially for those dominated by microscopic species such as zooplankton. The popular use of HTS-based methods has prompted a possible method of inferring relative species abundance from sequencing data. However, these methods remain largely untested in many communities as to whether sequence data can reliably quantify relative species abundance. Here we tested the relationship between species abundance and sequence abundance in zooplankton using 2 methods: (1) spiking known amounts of indicator species into existing zooplankton communities, and (2) comparing results obtained from parallel replicates for the same natural zooplankton communities. Although we detected a general trend that low-abundance species usually corresponded to low-abundance sequence reads, further statistical analyses revealed that sequencing data could not reliably quantify relative species abundance, even for the same indicator species spiked into different zooplankton communities. The distribution of sequence reads statistically varied even between parallel replicates of the same natural zooplankton communities. Our study reveals that sequence abundance may generally qualitatively reflect species abundance as the general trend between these 2 variables exists; however, extra caution is required when using HTS-based approaches to make quantitative inferences regarding zooplankton communities.
format	article
author	C Sun Y Zhao H Li Y Dong HJ MacIsaac A Zhan
author_facet	C Sun Y Zhao H Li Y Dong HJ MacIsaac A Zhan
author_sort	C Sun
title	Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities
title_short	Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities
title_full	Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities
title_fullStr	Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities
title_full_unstemmed	Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities
title_sort	unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities
publisher	Inter-Research
publishDate	2015
url	https://doaj.org/article/0f544684acf240c5a471cf9493ea122c
work_keys_str_mv	AT csun unreliablequantitationofspeciesabundancebasedonhighthroughputsequencingdataofzooplanktoncommunities AT yzhao unreliablequantitationofspeciesabundancebasedonhighthroughputsequencingdataofzooplanktoncommunities AT hli unreliablequantitationofspeciesabundancebasedonhighthroughputsequencingdataofzooplanktoncommunities AT ydong unreliablequantitationofspeciesabundancebasedonhighthroughputsequencingdataofzooplanktoncommunities AT hjmacisaac unreliablequantitationofspeciesabundancebasedonhighthroughputsequencingdataofzooplanktoncommunities AT azhan unreliablequantitationofspeciesabundancebasedonhighthroughputsequencingdataofzooplanktoncommunities
_version_	1718420886202089472

Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities

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