Table 1 Summary of phylogenomic datasets and associated analyses.

From: Genome-scale data reveal the role of hybridization in lichen-forming fungi

Dataset

Alignment length

Missing data

Analyses

nuclear REALPHY

18,457,947

6.0%

Concatenated ML (IQ-TREE)

mtDNA REALPHY

63,877

12.4%

Concatenated ML (IQ-TREE)

BUSCO 1 kb + SNPs

142,437

7.0%

Species tree inferred using quartet amalgamation (SVDquartets) & ABBA/BABA test of introgression (HyDe)

407 CEG trees

NA

0%

Summary species tree (ASTRAL-III)/network approach incorporating both incomplete lineage sorting and hybridization (MPL, PhyloNet)

  1. The nuclear REALPHY dataset was generated using contigs >5 kb from a draft genome assembly of R. melanophthalma as the reference; the mitochondrial REALPHY dataset was generated using the longest assembled mitochondrial contig; the ‘BUSCO 1 kb + SNPs’ dataset represents all polymorphic sites from concatenated alignments of all BUSCO gene regions >1 kb; and the ‘407 CEG trees’ are gene topologies inferred from 407 core eukaryotic gene regions passing quality filters. Alignment lengths and percentage of missing data are given for each alignment.
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