Data from: Phylogenomics and biogeography of honeyeaters in the genus Myzomela (Meliphagidae)
Data files
Jun 02, 2026 version files 228.56 MB
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astral.zip
5.24 KB
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beast.zip
116.26 KB
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biogeobears.zip
2.77 KB
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contigs_myzomela.zip
130.88 MB
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iqtree.zip
97.55 MB
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README.md
1.90 KB
Abstract
Myzomela (Aves: Meliphagidae) is a diverse group of small, colorful honeyeaters found throughout the Australo-Papuan region, including nearly every island from Wallacea to Samoa. While the genus has played an important role in the development of biogeographic and speciation theory, the evolutionary history of this radiation remains poorly understood. Here, we present the first comprehensive phylogenomic tree that encompasses nearly all recognized taxonomic diversity within the group. Our phylogenetic hypothesis, based on ultraconserved elements and multi-locus sequence data, reveals several novel relationships and helps clarify species boundaries. Specifically, we find that three polytypic species complexes are not monophyletic, warranting taxonomic revision. Additionally, ancestral range estimation supports multiple waves of colonization into Wallacea and the South Pacific, highlighting the extraordinary dispersal abilities of the genus. These dispersal events were followed by rapid diversification—especially in the South Pacific—where some lineages have spurred further radiations. Our findings provide new insights into the complex diversification history of Myzomela and offer a robust taxonomic framework, which is crucial for informing conservation decisions in the face of ongoing and pervasive biodiversity loss.
Dataset DOI: 10.5061/dryad.5mkkwh7j7
Description of the data and file structure
contigs_myzomela.zip - contains UCE contigs for each of the 115 samples used in the study. Each filename begins with the first three letters of the species epithet (or genus for outgroup samples), followed by the museum number listed in Table S1 and the missing-data threshold value (0.3). Each file contains UCE consensus sequences (see the Bioinformatics section of the Methods for a description of how these sequences were generated).
iqtree.zip - IQ-TREE input alignments and tree files
- myzo_UCEs_ML_115tips.tre = UCE ML tree
- myzo_UCEs_alignment.fasta = UCE alignment in fasta format (75% complete matrix)
- myzo_mtDNA_alignment.nex = mtDNA alignment for backbone constraint tree search
- myzo_mtDNA_ML_unconstrained_136tips.tre = mtDNA ML backbone unconstrained tree
- myzo_mtDNA_ML_constrained_136tips.tre = mtDNA ML backbone constraint tree
beast.zip - BEAST tree files
- myzo_mtDNA_BEAST_constrained_136tips.nex = chronogram
- myzo_multi-locus_BEAST_89tips.nex = introns + mtDNA Bayesian tree
- myzo_multi-locus_alignment.nex = introns + mtDNA alignment
astral.zip - ASTRAL coalescent species tree files
- myzo_tissue_only_ASTRAL.tre = UCE species tree based on tissue only
- myzo_cladeI_ASTRAL.tre = UCE species tree based on tissue and toepads for Clade I
- myzo_cladeII_ASTRAL.tre = UCE species tree based on tissue and toepads for Clade II
- myzo_cladeIII_ASTRAL.tre = UCE species tree based on tissue and toepads for Clade III
biogeobears.zip - BioGeoBEARS input tree and geographic range data
- myzo_5_areas.txt = geographic areas used for ancestral range estimation
- myzo_47tips.tre = Myzomela species-level tree with outgroups
