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Working through polytomies: auklets revisited.

Elizabeth M Humphries¹, Kevin Winker

¹University of Alaska Museum, Department of Biology & Wildlife, Institute of Arctic Biology, Fairbanks, AK 99775, USA. ftemh@uaf.edu

Molecular Phylogenetics and Evolution

|August 1, 2009

Summary

Resolving phylogenetic polytomies in Aethia auklets was successful using mitochondrial DNA (mtDNA) gene sequences, particularly NADH dehydrogenase subunit 2 (ND2). Amplified fragment length polymorphism (AFLP) data did not effectively resolve these evolutionary relationships.

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Area of Science:

Evolutionary Biology
Phylogenetics
Molecular Evolution

Background:

Polytomies, or unresolved branching patterns in evolutionary trees, pose challenges in phylogenetic reconstruction.
These 'bushes' can arise from rapid evolutionary divergence or excessive homoplasy in the data.
The Aethia auklet radiation serves as a model system to investigate methods for resolving such phylogenetic uncertainties.

Purpose of the Study:

To evaluate the efficacy of different approaches for resolving polytomies within the Aethia auklet genus.
To compare the performance of mitochondrial DNA (mtDNA) gene choice, intraspecific sampling depth, molecular evolution models, and Amplified Fragment Length Polymorphism (AFLP) markers.

Main Methods:

Phylogenetic analyses were conducted using various mitochondrial DNA genes, including NADH dehydrogenase subunit 2 (ND2).
Different Bayesian models of molecular evolution were applied to assess their impact on phylogenetic resolution.
The study involved varying the number of individuals sampled per species and utilized AFLP markers for comparison.

Main Results:

A fully resolved phylogeny was achieved using ND2 sequence data under two Bayesian models.
This resolution was corroborated with an expanded mtDNA dataset under one of the models.
AFLP data failed to resolve the phylogeny, exhibiting significant conflict and low confidence support for relationships, suggesting potential homoplasy or incomplete lineage sorting.

Conclusions:

Mitochondrial DNA, specifically the ND2 gene, is effective for resolving polytomies in the Aethia auklet radiation.
The choice of molecular evolution model and adequate intraspecific sampling are crucial for accurate phylogenetic inference.
AFLP markers appear less suitable for resolving shallow divergences like that observed in Aethia auklets due to high homoplasy or incomplete lineage sorting.