Cargando…
Phylogenetic diversity statistics for all clades in a phylogeny
The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10311342/ https://www.ncbi.nlm.nih.gov/pubmed/37387175 http://dx.doi.org/10.1093/bioinformatics/btad263 |
_version_ | 1785066723375841280 |
---|---|
author | Grover, Siddhant Markin, Alexey Anderson, Tavis K Eulenstein, Oliver |
author_facet | Grover, Siddhant Markin, Alexey Anderson, Tavis K Eulenstein, Oliver |
author_sort | Grover, Siddhant |
collection | PubMed |
description | The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats. |
format | Online Article Text |
id | pubmed-10311342 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-103113422023-07-01 Phylogenetic diversity statistics for all clades in a phylogeny Grover, Siddhant Markin, Alexey Anderson, Tavis K Eulenstein, Oliver Bioinformatics Evolutionary, Comparative and Population Genomics The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats. Oxford University Press 2023-06-30 /pmc/articles/PMC10311342/ /pubmed/37387175 http://dx.doi.org/10.1093/bioinformatics/btad263 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Evolutionary, Comparative and Population Genomics Grover, Siddhant Markin, Alexey Anderson, Tavis K Eulenstein, Oliver Phylogenetic diversity statistics for all clades in a phylogeny |
title | Phylogenetic diversity statistics for all clades in a phylogeny |
title_full | Phylogenetic diversity statistics for all clades in a phylogeny |
title_fullStr | Phylogenetic diversity statistics for all clades in a phylogeny |
title_full_unstemmed | Phylogenetic diversity statistics for all clades in a phylogeny |
title_short | Phylogenetic diversity statistics for all clades in a phylogeny |
title_sort | phylogenetic diversity statistics for all clades in a phylogeny |
topic | Evolutionary, Comparative and Population Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10311342/ https://www.ncbi.nlm.nih.gov/pubmed/37387175 http://dx.doi.org/10.1093/bioinformatics/btad263 |
work_keys_str_mv | AT groversiddhant phylogeneticdiversitystatisticsforallcladesinaphylogeny AT markinalexey phylogeneticdiversitystatisticsforallcladesinaphylogeny AT andersontavisk phylogeneticdiversitystatisticsforallcladesinaphylogeny AT eulensteinoliver phylogeneticdiversitystatisticsforallcladesinaphylogeny |