Extended Data Fig. 4: Best-scoring maximum likelihood tree using Polarization-Free Damage Weighting consensus. | Nature Ecology & Evolution

Extended Data Fig. 4: Best-scoring maximum likelihood tree using Polarization-Free Damage Weighting consensus.

From: Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen

Extended Data Fig. 4

Tree constructed in IQ-TREE2 using ModelFinder, which selected the K3Pu+F + R4 substitution model. The tree is based on an alignment with 91% partial deletion applied in MEGA, including all 146 previously published and two newly reported pre-Holocene horse mitochondrial genomes. Branch supports are tested using 1000 bootstrap iterations. SCEN reconstructions have the Polarization-Free Damage Weighting method applied.

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