Ancient proteins resolve controversy over the identity of Genyornis eggshell

Data for Demarchi et al. in <i>PNAS</i> (2022):<b>Ancient proteins resolve controversy over the identity of <i>Genyornis</i> eggshell</b><br>The repository contains data used in<b>A) </b>Phylogenetic analyses of two eggshell protein sequences of an undetermined ootaxon and bird reference proteinsPhylogenetic analyses on eggshell proteins were conducted by Josefin Stiller (contact: [e-mail])<br><br><b>B) </b>Phylogenetic analyses for the minibarcodes for 3 undetermined ootaxa and bird reference mitochondrial sequences.Phylogenetic analyses on minibarcodes were conducted by Alicia Grealy (contact: [e-mail])<br><br><b>C)</b> AlphaFold models of <i>Genyornis</i> XCA-1 structures. Analyses were conducted by Thomas Sicheritz-Pontén and Matthew Collins (contact: [e-mail], [e-mail])<br>----------------------------------------------------------------------------<br><br><b>Contents of the repository</b><b>:</b><b><br></b><b>A) Phylogenetics - palaeoproteomics </b><b><br></b><b>- CLEC1.zip </b>Analysis of XCA-1 (CLEC1) protein sequences<b>concatenation.zip </b>Analysis of concatenated CLEC1 and lactadherin protein sequences<b>- concatenation_with_tree_constraint.zip </b>Analysis of concatenated CLEC1 and lactadherin protein sequences using a topological constraint for living bird species while the undetermined ootaxon can be placed freely during tree search<b>- lactadherin.zip</b> Analysis of lactadherin-MFGE8 (lactadherin) protein sequences<b>- noOU-amino_acid.zip </b>Analysis of concatenated CLEC1 and lactadherin protein sequences without the sequence of the undetermined ootaxon (UO)<b>- noOU-cds_DNA.zip</b> Analysis of concatenated CLEC1 and lactadherin DNA sequences without the sequence of the undetermined ootaxon (UO)<b>- subset-Australasian_taxa.zip </b>Analysis of concatenated CLEC1 and lactadherin protein sequences for a subset of the bird species that inhabit Australia and adjacent islands<br><b>- subset-Palaeognathae_and_Galloanseres.zip</b> Analysis of concatenated CLEC1 and lactadherin protein sequences for a subset of the bird species that are part of Palaeognathae and Galloanseres<b>- subset-taxa_with_both_genes.zip</b> Analysis of concatenated CLEC1 and lactadherin protein sequences for a subset of the bird species that have both protein sequences<b>- Undetermined_ootaxon.CLEC1.fa </b>Consensus protein sequence for the undetermined ootaxon (UO)<b>- Undetermined_ootaxon.lactadherin.fa</b> Consensus protein sequence for the undetermined ootaxon (UO)<br>----------------------------------------------------------------------------<br><br><b>B) Palaeogenetics - phylogenetics dataset:</b><b><br></b><b>palaeogenetics_with_minibarcodes.zip</b> Sequence data and phylogenetic analyses for minibarcodes obtained from 3 ootaxa together with mitochondrial sequences from birds<br>Contains 4 directories with subdirectories:<b>1) concatenated_alignment: </b>- /alignments: .phy files containing the partitioned, concatenated mitochondrial sequence data for one ootaxon alongside modern bird taxa. There are two alignments for each of the three ootaxa—one where the mitochondrion was reconstructed using all avian reads (aves), and the other where the mitochondrion was reconstructed excluding chicken reads (nogallus). - /iqtree_log: iqtree log files for running the ML phylogenetic inference in Iqtree- partition_file: .nex files defining the partitions for each .phy file in /concatened_alignment/alignments- /trees: ML consensus for each .phy file in /concatened_alignment/alignments <b>2) consensus_sequences: </b>mitochondrial consensus sequence for each of the three ootaxa—there are two for each ootaxa—one where the mitochondrion was reconstructed using all avian reads (aves), and the other where the mitochondrion was reconstructed excluding chicken reads (nogallus). <br><b>3) partitions:</b> .phy alignments of each partition (m1, m2, m3, stems, loops) prior to concatenation for each of the three ootaxa. There are two alignments per partition for each of the three ootaxa—one where the mitochondrion was reconstructed using all avian reads (aves), and the other where the mitochondrion was reconstructed excluding chicken reads (nogallus). <b>4) sequence_data</b>: - /12S_amplicon_barcode# the 12SAC mini barcode amplified from one ootaxon (see Supplementary Information)- /capture_data: demultiplexed and trimmed .fastq raw sequence capture data from the three ootaxa and controls; quality filtered data is provided as .fasta files for each. <br><b>C) AlphaFold models of <i>Genyornis</i> XCA-1:</b><b><br></b>Directory contains 14 files in Protein Data Bank (pdb) file format (.pbd files), in which the missing variable region of XCA-1 (76-83) was replaced by the sequence (here termed cassette) found in found in each of the following species: <br><i>Apteryx australis/Apteryx owenii/Apteryx rowi</i><i>Nothoprocta ornata</i><i>Numida meleagris</i><i>Nothoprocta perdicaria</i><i>Anas platyrhynchos/Asarcornis scutulata/Cairina moschata/Oxyura jamaicensis</i><i>Struthio camelus</i><i>Cygnus atratus</i><i>Nothocercus ulius</i><i>Chauna torquata</i><i>Dromaius novaehollandiae</i><i>Rhea americana/Rhea pennata</i><i>Eudromia elegans</i><i>Anseranas semipalmata</i>