Effects of discordance between species and gene trees on phylogenetic diversity conservation

DOI10.1007/S00285-022-01845-WMaRDI QIDQ2103384zbMATH OpenOpenAlexFDO

Authors Kristina Wicke, Mareike Fischer, Laura Salter Kubatko

Publication date 13 December 2022

Published in Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2112.10717

zbMATH Keywords

biodiversity conservationfair proportion indexgene treemultispecies coalescentphylogenetic diversityspecies tree

Mathematics Subject Classification ID

Coalescent processes (60J90) Problems related to evolution (92D15)

Abstract: Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into account the unique and shared evolutionary history of each species as indicated by its placement in an underlying phylogenetic tree. Traditionally, phylogenetic trees were inferred from single genes and the resulting gene trees were assumed to be a valid estimate for the species tree, i.e., the "true" evolutionary history of the species under consideration. However, nowadays it is common to sequence whole genomes of hundreds or thousands of genes, and it is often the case that conflicting genealogical histories exist in different genes throughout the genome, resulting in discordance between individual gene trees and the species tree. Here, we analyze the effects of gene and species tree discordance on prioritization decisions based on the FP index. In particular, we consider the ranking order of taxa induced by (i) the FP index on a species tree, and (ii) the expected FP index across all gene tree histories associated with the species tree. On one hand, we show that for particular tree shapes, the two rankings always coincide. On the other hand, we show that for all leaf numbers greater than or equal to five, there exist species trees for which the two rankings differ. Finally, we illustrate the variability in the rankings obtained from the FP index across different gene tree and species tree estimates for an empirical multilocus mammal data set.

Recommendations

• Phylogenetic diversity and biodiversity indices on phylogenetic networks
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• The equivalence of two phylogenetic biodiversity measures: the Shapley value and fair proportion index

Cites work

• Equality of Shapley value and fair proportion index in phylogenetic trees
• Evolutionarily distinctive species often capture more phylogenetic diversity than expected
• scientific article; zbMATH DE number 3078997 (Why is no real title available?)
• The probability distribution of ranked gene trees on a species tree
• The Shapley value of phylogenetic trees

Cited in

(5)

• Phylogenetic diversity and biodiversity indices on phylogenetic networks
• Evolutionarily distinctive species often capture more phylogenetic diversity than expected
• Biodiversity, Shapley value and phylogenetic trees: some remarks
• A genome evolution-based framework for measures of originality for clades
• Spaces of phylogenetic diversity indices: combinatorial and geometric properties

Describes a project that uses

Uses Software

• Mathematica
• RAxML
• PAUP*

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