Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae)

Different genomic regions may reflect conflicting phylogenetic topologies on account of incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Phylogenetic analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal that the northern and southern populations of E. godlewskii are each sister to E. cioides and E. cia, respectively. In contrast, phylogenetic analysis based on genome-wide data support the monophyly of E. godlewskii with the following tree topology: (((E. godlewskii, E. cia), E. cioides), E. jankowskii). Using D-sta..., Dataset and supporting information from the manuscript of Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae)., , These files contains original fasta or vcf file for phylogenetic analyses in the manuscript USYB-2023-045

File \"Concatenated_NRW.fas\" contains aligned NRW sequences;
File \"Dsuite_output_data.txt\" contains output data of Dsuite analysis; huimei, liban, sandaomei, south and north represent E. cia, E. jankowskii, E. cioides, southern E. godlewskii and northern E. godlewskii, respectively; BBAA, ABBA and BABA represents the counts conform to the corresponding site patterns; for other parameters, please refer to Dsuite tutorial;
File \"ldfil.recode.vcf.gz\" contains linkage disequilibrium pruned vcf file;
File \"mitochondrial_cytb.fas\" contains aligned mitochondrial cytb sequences;
File \"mitochondrial_other_sequences.fas\" contains aligned mitochondrial sequences without cytb gene
File \"MP-EST_input_20000 trees.rar\" contains 20000 sliding window trees for the input to MP-EST analysis;
File \"ALSTRAL_input_trees_of_Z_chromosome.trees\" contains 3583 sliding window trees from chromosome Z for the i...