Predicting microbial traits with phylogenies
Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the 'macrobial' world, microbial ecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogenies and limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists.
Main Authors: | , |
---|---|
Other Authors: | |
Format: | artículo biblioteca |
Published: |
Nature Publishing Group
2016
|
Online Access: | http://hdl.handle.net/10261/141154 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100004837 |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-cide-es-10261-141154 |
---|---|
record_format |
koha |
spelling |
dig-cide-es-10261-1411542021-11-22T12:54:46Z Predicting microbial traits with phylogenies Goberna, M. Verdú, Miguel Ministerio de Economía y Competitividad (España) Ministerio de Ciencia e Innovación (España) Goberna, M. [0000-0001-5303-3429] Verdú, Miguel [0000-0002-9778-7692] Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the 'macrobial' world, microbial ecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogenies and limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists. Financial support was provided by the Spanish Ministry of Science and Innovation (R+D Projects CGL2011-29585-C02-01 and CGL2014-58333-P). MG acknowledges support by the Ramón y Cajal Programme (Spanish Ministry of Economy and Competitiveness). Peer Reviewed 2016-12-05T10:10:30Z 2016-12-05T10:10:30Z 2016 2016-12-05T10:10:30Z artículo http://purl.org/coar/resource_type/c_6501 issn: 1751-7370 ISME Journal 10: 959-967 (2016) http://hdl.handle.net/10261/141154 10.1038/ismej.2015.171 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100004837 26371406 Postprint https://doi.org/10.1038/ismej.2015.171 Sí none Nature Publishing Group |
institution |
CIDE ES |
collection |
DSpace |
country |
España |
countrycode |
ES |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cide-es |
tag |
biblioteca |
region |
Europa del Sur |
libraryname |
Biblioteca del CIDE España |
description |
Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the 'macrobial' world, microbial ecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogenies and limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists. |
author2 |
Ministerio de Economía y Competitividad (España) |
author_facet |
Ministerio de Economía y Competitividad (España) Goberna, M. Verdú, Miguel |
format |
artículo |
author |
Goberna, M. Verdú, Miguel |
spellingShingle |
Goberna, M. Verdú, Miguel Predicting microbial traits with phylogenies |
author_sort |
Goberna, M. |
title |
Predicting microbial traits with phylogenies |
title_short |
Predicting microbial traits with phylogenies |
title_full |
Predicting microbial traits with phylogenies |
title_fullStr |
Predicting microbial traits with phylogenies |
title_full_unstemmed |
Predicting microbial traits with phylogenies |
title_sort |
predicting microbial traits with phylogenies |
publisher |
Nature Publishing Group |
publishDate |
2016 |
url |
http://hdl.handle.net/10261/141154 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100004837 |
work_keys_str_mv |
AT gobernam predictingmicrobialtraitswithphylogenies AT verdumiguel predictingmicrobialtraitswithphylogenies |
_version_ |
1777665537761869824 |