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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?
Carlo Ricotta1, Giovanni Bacaro, Michela Marignani
1Department of Environmental Biology, University of Rome La Sapienza, Rome, Italy.
Oecologia
|April 25, 2012
Summary
Dated phylogenies are crucial for ecology, but often unavailable. Using taxonomic hierarchies as proxies for dated phylogenies provides surprisingly accurate diversity estimates, outperforming undated phylogenies.
Area of Science:
- Ecology
- Phylogenetics
- Conservation Biology
Background:
- Dated phylogenies are increasingly vital for ecological studies, community structure analysis, and conservation planning.
- A significant challenge is the lack of reliable, time-calibrated phylogenies for many taxonomic groups, hindering systematic phylogenetic methods in ecology.
- Using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies is a potential solution, but the information loss is not well understood.
Purpose of the Study:
- To investigate how using undated phylogenies and taxonomic hierarchies biases diversity measures, specifically mean pairwise phylogenetic distance.
- To compare diversity estimates derived from undated phylogenies and taxonomic hierarchies against those from dated phylogenies generated using Phylomatic software.
- To assess the reliability of these proxy methods in ecological and conservation contexts.
Main Methods:
- Employed three distinct plant species datasets sampled at various ecological scales.
- Utilized the freely available software Phylomatic to generate dated phylogenies.
- Calculated mean pairwise phylogenetic distances for communities using dated phylogenies, undated phylogenies, and taxonomic hierarchies for comparison.
Main Results:
- Diversity estimates from dated phylogenies (Phylomatic) showed a stronger relationship with estimates from taxonomic hierarchies than with those from undated phylogenies.
- The correlation between dated phylogenies and taxonomic hierarchies strengthened when analyses were restricted to angiosperm species.
- Undated phylogenies appeared to be less reliable proxies for estimating community phylogenetic diversity compared to taxonomic hierarchies.
Conclusions:
- Taxonomic hierarchies can serve as a more effective proxy for estimating community phylogenetic diversity than undated phylogenies, especially when dated phylogenies are unavailable.
- The use of Phylomatic-generated dated phylogenies provides a robust baseline for comparison, highlighting the utility of taxonomic data in ecological assessments.
- Findings suggest that taxonomic hierarchies offer a valuable and accessible alternative for ecological studies and conservation planning where time-calibrated phylogenies are lacking, particularly within angiosperms.
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