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The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation

https://doi.org/10.1093/sysbio/syac012
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.cub.2018.03.020openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.tree.2007.05.005openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.tree.2009.01.009openalex-snapshot
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inferredcites →https://doi.org/10.1038/nature12130openalex-snapshot
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inferred← citeshttps://doi.org/10.11646/zootaxa.5849.4.3zenodo-depositor-declared
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inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108472openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108633openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108642openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108735openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41467-024-45289-wopenalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41586-024-07324-0openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/aob/mcaf128openalex-snapshot
Resolving relationships in the radiation of Australia’s largest pea clade (Fabaceae tribe Mirbelieae) with target-capture sequencing
inferred← citeshttps://doi.org/10.1093/botlinnean/boae050openalex-snapshot
Estimation of divergence time and comparative plastid genomics of Orchis species (Orchidaceae)
inferred← citeshttps://doi.org/10.1093/cz/zoag014openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/evolinnean/kzae026openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/gbe/evaf025openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/molbev/msae214openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syae057openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syae065openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syaf050openalex-snapshot
Practical Guide and Review of Fossil Tip-Dating in Phylogenetics
inferred← citeshttps://doi.org/10.1101/2024.11.29.625936openalex-snapshot
Bayesian Least-Squares Supertrees (BLeSS): Flexible Inference of Large Time-Calibrated Phylogenies
inferred← citeshttps://doi.org/10.1101/2025.09.19.677265openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/2041-210x.14404openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jbi.70098openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.20263openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.71469openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.71521openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/syen.12614openalex-snapshot
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inferred← citeshttps://doi.org/10.24072/pcjournal.556openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ani13142246openalex-snapshot
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