Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics

Bayless, Keith M.; Trautwein, Michelle D.; Meusemann, Karen; Shin, Seunggwan; Petersen, Malte; Donath, Alexander; Podsiadlowski, Lars; Mayer, Christoph; Niehuis, Oliver; Peters, Ralph S.; Meier, Rudolf; Kutty, Sujatha Narayanan; Liu, Shanlin; Zhou, Xin; Misof, Bernhard; Yeates, David K.; Wiegmann, Brian M.

doi:10.1186/s12915-020-00944-8

Table 1 Schizophora phylogenetic analysis strategies exploring different datasets

From: Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics

Analysis	No. of taxa	Type of data	Matrix reduction	Partitioning	Substitution model selection	Phylogenetic program	No. of genes	No. of positions
1	70	Amino acids	All genes	By gene	WAG+G	Concatenation: ExaML	3145	1,671,428
2	70	Amino acids	MARE SOS	PartitionFinder 132 metapartitions	Selected by PartitionFinder for each gene	Concatenation: ExaML	1130	520,259
3	70	Amino acids	MARE SOS	ModelFinder 132 metapartitions	Selected by ModelFinder for each gene including LG4X	Concatenation: RAxML-light	1130	520,259
4	70	Amino acids	MARE SOS	ModelFinder 132 metapartitions	LG4X	Concatenation: RAxML-light	1130	520,259
5	70	Amino acids	MARE + AliStat 80% site coverage	Unpartitioned	WAG+G	Concatenation: ExaML	1061	168,544
6	64	Amino acids	MARE SOS	PartitionFinder 132 metapartitions	Selected by PartitionFinder for each gene	Concatenation: RAxML	1130	520,259
7	70	Nucleotides 1+2	All genes	Unpartitioned	GTR+I+G	Concatenation: ExaML	3145	5,014,547
8	70	Nucleotides 1+2	MARE SOS	PartitionFinder 738 metapartitions	Selected by PartitionFinder for each gene	Concatenation: ExaML	1130	1,040,518
9	70	Amino acids	Information cutoff from MARE	n/a	n/a	MSC: ASTRAL-III on ML gene trees with bootstraps	600	n/a
10	70	Nucleotides 1+2	Information cutoff from MARE	n/a	n/a	MSC: ASTRAL-III on ML gene trees with bootstraps	600	n/a
11	70	Amino acids	Minimum alignment length > 600 aa	n/a	n/a	MSC: ASTRAL-III on ML gene trees with bootstraps	276	n/a
12	70	Amino acids	MARE SOS	n/a	n/a	MSC: ASTRAL-III on ML gene trees	1130	n/a
13	70	Nucleotides 1+2	MARE SOS	n/a	n/a	MSC: ASTRAL-III on ML gene trees	1130	n/a
14	70	Amino acids	Information cutoff from MARE	n/a	n/a	MSC: ASTRAL-III on ML gene trees	600	n/a

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