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Scripts used for the UCE based phylogeny of Indian Owlets

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[Published in Ibis] Re-assessing the phylogenetic status and evolutionary relationship of Forest Owlet [Athene blewitti (Hume 1873)] using genomic data

ABSTRACT

Phylogenetic relationships are often challenging to resolve in recent/younger lineage when only a few loci are used. Ultra Conserved Elements (UCE) are highly conserved regions across taxa that help resolve shallow and deep divergences. We utilized UCEs harvested from whole genomes to assess the phylogenetic position and taxonomic affiliation of an endangered endemic owlet in the family Strigidae – the Forest Owlet Athene blewitti. The taxonomic placement of this species has been revised multiple times. A multigene study attempted to address the question but showed a discrepancy across datasets in its placement of the species within genus Athene. We assembled a dataset of 5018 nuclear UCE loci with increased taxon sampling. Forest Owlet was found to be an early split from the Athene clade but sister to other Athene; and consistent across three approaches - maximum likelihood, bayesian, and the multispecies coalescence. Divergence dating using fossil calibrations suggest that the Athene lineage split from its ancestor about 7.6Mya, and the Forest Owlet diverged about 5.2Mya, consistent with previous multigene approaches. Despite osteological differences from other Athene, we suggest the placement of the Forest Owlet as a member of the Athene to emphasize its evolutionary relationship.

HIGHLIGHTS

* Phylogenomics using genome-wide nuclear markers yielded a well-supported topology for Athene and Glaucidium lineages.

* Three different methods of phylogenetic tree construction showed that Forest Owlet is an early split from all other Athene species.

* Divergence dating in the bayesian framework puts the Forest Owlet age between 5.0my to 5.5my.

Data used for this study can be found on Open Science Framework (OSF) (https://osf.io/ed9s2/).

Graphical_Abstract_2

How to cite : K. L., V., Natesh, M., Mehta, P., Jayapal, R., Mukherjee, S. and Robin, V.V. (2022), Re-assessing the phylogenetic status and evolutionary relationship of Forest Owlet (Athene blewitti (Hume 1873)) using genomic data. Ibis. https://doi.org/10.1111/ibi.13097

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