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The phylogenetic position of the extinct Hawaiian honeyeaters: Overcoming the limitations of antique DNA

https://doi.org/10.1101/2025.06.02.657453

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Trimmomatic: a flexible trimmer for Illumina sequence data

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Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction

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Sequence capture of ultraconserved elements from bird museum specimens

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MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

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inferredcites →https://doi.org/10.1126/science.aat7244openalex-snapshot

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inferredcites →https://doi.org/10.1126/science.aaz6970openalex-snapshot

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Genetic Analyses from Ancient DNA

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Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

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DNA damage in preserved specimens and tissue samples: a molecular assessment

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Assessing the efficiency of multiple sequence alignment programs

inferredcites →https://doi.org/10.1186/s12915-018-0581-9openalex-snapshot

Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

inferredcites →https://doi.org/10.1186/s13104-015-1689-4openalex-snapshot

Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error

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inferredcites →https://doi.org/10.1371/journal.pone.0104579openalex-snapshot

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inferredcites →https://doi.org/10.2173/bow.bombyc1.01openalex-snapshot

Waxwings (Bombycillidae)

inferredcites →https://doi.org/10.2173/bow.dulida1.01openalex-snapshot

Palmchat (Dulidae)

inferredcites →https://doi.org/10.2173/bow.mohoid1.01openalex-snapshot

Hawaiian Honeyeaters (Mohoidae)

inferredcites →https://doi.org/10.2173/bow.ptilio1.01openalex-snapshot

Silky-flycatchers (Ptiliogonatidae)

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Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root

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Very few sites can reshape the inferred phylogenetic tree

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