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Published on: October 23, 2019
Understanding phylogenetic incongruence: lessons from phyllostomid bats
Liliana M Dávalos1, Andrea L Cirranello, Jonathan H Geisler
1Department of Ecology and Evolution, State University of New York at Stony Brook, 11794, USA.
Biological Reviews of the Cambridge Philosophical Society
|August 16, 2012
Summary
Phylogenetic conflict in Phyllostomidae bats arises from both methodological issues and biological factors like sequence saturation and convergent evolution. Addressing these requires improved models and more comprehensive genomic data for accurate evolutionary history reconstruction.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Genomics
Background:
- Phylogenetic conflict, where evolutionary trees from different data types or subsets disagree, is common in evolutionary studies.
- The New World bat family Phyllostomidae has shown persistent conflict between morphological and molecular phylogenies for over a decade.
- Understanding the drivers of this conflict is crucial to avoid drawing incorrect evolutionary conclusions.
Purpose of the Study:
- To develop and apply methods to resolve phylogenetic conflict in Phyllostomidae bats.
- To identify and minimize methodological and biological sources of incongruence in evolutionary trees.
- To guide future data collection for robust phylogenomic and morphological analyses.
Main Methods:
- Incorporated new morphological data and expanded molecular analyses for Phyllostomidae and outgroups.
- Addressed methodological conflicts by standardizing taxonomic sampling, character sampling, and phylogenetic algorithms.
- Evaluated biological conflict sources including saturation, convergent evolution, paralogy, lateral gene transfer, and lineage sorting.
Main Results:
- Methodological issues contribute to phylogenetic conflict but can be mitigated through data standardization.
- Biological factors such as saturation in morphological and molecular data, and adaptive convergence in nectar-feeding lineages, are significant drivers of conflict.
- While accounting for sequence saturation reduced conflict, it did not fully resolve it, indicating other biological processes are at play.
- Paralogy, lateral gene transfer, and poor taxon sampling were ruled out as primary causes of incongruent gene trees.
Conclusions:
- Phylogenetic conflict in Phyllostomidae is driven by a combination of methodological and biological factors, including saturation and convergence.
- Overcoming incongruence necessitates advanced phylogenetic models and extensive genomic and allelic sequencing.
- Adaptive molecular evolution leading to convergence was observed in mitochondrial proteins of nectar-feeding phyllostomids.
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