Comparative Genomics Datasets Across Taxa

We use six multi-gene datasets and a single-gene HIV dataset, and each dataset includes one or more outgroup species defined by the original papers (Table 1).

Table 1

Summary of the biological datasets

Dataset	Species	Genes	Outgroups	Download
Plants [23 ]	104	852	Monomastix opisthostigma,	DOI 10.1186/2047-217X-3-17
			Uronema sp.,
			Nephroselmis pyriformis,
			Pyramimonas parkeae
Mammals [36 ]	37	424	Chicken	DOI 10.13012/C5BG2KWG
Insects [31 (link)]	144	1478	IXODES SCAPULARIS,	http://esayyari.github.io/InsectsData
			Symphylella vulgaris,
			Glomeris pustulata,
			Lepeophtheirus salmonis,
			DAPHNIA PULEX,
			Cypridininae sp,
			Sarsinebalia urgorii,
			Celuca puligator,
			Litopenaeus vannamei
Cannon [32 (link)]	78	213	Salpingoeca rosetta,	DOI 10.5061/dryad.493b7
			Monosiga brevicollis
			Mnemiopsis leidyi,
			Pleurobrachia bachei,
			Euplokamis dunlapae
Rouse [33 (link)]	26	393	Mnemiopsis leidyi,	DOI 10.5061/dryad.79dq1
			Amphimedon queenslandica,
			Trichoplax adhaerens,
			Nematostella vectensis
Frogs [39 ]	164	95	Latimeria chalumnae,	DOI 10.5061/dryad.12546.2
			Protopterus annectens,
			Homo sapiens,
			Crocodylus siamensis,
			Gallus gallus,
			Ichthyophis bannanicus,
			Batrachuperus yenyuanensis,
			Andrias davidianus

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Mai U, & Mirarab S. (2018). TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genomics, 19(Suppl 5), 272.

Publication 2018

Biological Daphnia Gallus gallus Gene Homo sapiens Lepeophtheirus salmonis Litopenaeus Multi gene Trichoplax

Corresponding Organization : University of California, San Diego

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Variable analysis

independent variables

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dependent variables

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control variables

Use of outgroup species to serve as a reference for the analysis

controls

Positive controls: None specified
Negative controls: None specified

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