Table 2 Comparisons of coalescent-based ASTRAL species phylogenies with and without collapsing poorly supported bipartitions in replicate gene trees.

Data set	Program	Without collapsing branches		With collapsing branches
Data set	Program	Conflicting bipartitions (%)^a	Highly conflicting bipartitions (%)^b	Conflicting bipartitions (%)^a	Highly conflicting bipartitions (%)^b
Animal: Bees	IQ-TREE	22.46	1.87	18.18	1.60
Animal: Birds	IQ-TREE	6.09	0	6.60	0
Animal: Butterflies	IQ-TREE	7.35	0.49	5.39	0.74
Animal: Lizards	IQ-TREE	7.69	0	0	0
Animal: Marine fishes	IQ-TREE	7.69	0	13.68	0
Animal: Rodents	IQ-TREE	0	0	0	0
Plant: Cardueae	IQ-TREE	12.20	0	12.20	0
Plant: Caryophyllales	IQ-TREE	0	0	0	0
Plant: Green plants	IQ-TREE	5.70	0.38	5.53	0.55
Plant: Jaltomata	IQ-TREE	8.33	0	0	0
Plant: Protea	IQ-TREE	14.52	0	3.23	0
Fungi: Aspergillaceae	IQ-TREE	0	0	0	0
Fungi: Budding yeasts	IQ-TREE	0.29	0	0.29	0
Fungi: Hanseniaspora	IQ-TREE	0	0	0	0
Fungi: Rhizoplaca	IQ-TREE	3.57	0	0	0
Animal: Bees	RAxML-NG	27.27	1.87	8.02	0
Animal: Birds	RAxML-NG	4.06	0	0	0
Animal: Butterflies	RAxML-NG	6.86	0.49	6.86	0
Animal: Lizards	RAxML-NG	19.23	0	0	0
Animal: Marine fishes	RAxML-NG	3.42	0	5.98	0
Animal: Rodents	RAxML-NG	0	0	0	0
Plant: Cardueae	RAxML-NG	12.20	0	3.66	0
Plant: Caryophyllales	RAxML-NG	0	0	0	0
Plant: Green plants	RAxML-NG	0.26	0	1.02	0.09
Plant: Jaltomata	RAxML-NG	8.33	0	0	0
Plant: Protea	RAxML-NG	14.52	0	8.06	0
Fungi: Aspergillaceae	RAxML-NG	0	0	0	0
Fungi: Budding yeasts	RAxML-NG	0.29	0	0.59	0
Fungi: Hanseniaspora	RAxML-NG	0	0	0	0
Fungi: Rhizoplaca	RAxML-NG	3.57	0	0	0

Since running all 19,414 gene alignments from 15 phylogenomic data sets was computationally intractable, we sampled the first 100 genes from each data set. For each data set, coalescent-based ASTRAL trees were reconstructed from the Run1 and Run2 sets of 100 individual gene trees without and with collapsing branches with low bootstrap support values (≤50%); both Run1 and Run2 used identical settings, including substitution model, random starting seed number, number of threads of execution, number of independent tree searches, number of bootstrap replicates, and ML program.
^aPercentage of conflicting bipartitions between coalescent-based ASTRAL species phylogenies inferred using Run1 and Run2 gene trees.
^bPercentage of highly conflicting bipartitions (LPP ≥ 90%) between coalescent-based ASTRAL species phylogenies inferred using Run1 and Run2 gene trees.

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