Split-inducing indels in phylogenomic analysis

Donath, Alexander; Stadler, Peter F.

doi:10.1186/s13015-018-0130-7

Algorithms for Molecular Biology

Table 2 Detailed comparision of the differences between the ENCODE guide tree and the best maximum likelihood trees calculated from splid data derived from various alignment tools

From: Split-inducing indels in phylogenomic analysis

	ClustalW	Dialign-TX	Mafft	Mafft G-INS-i	Mafft L-INS-i	Muscle	Prank	ProbConsRNA	T-Coffee	TBA/Multiz
Afrotheria	×	×	–	×	×	×	×	×	×	×
Afrotheria	Sister group to Boreoeutheria	Sister group to Boreoeutheria		Sister group to Boreoeutheria	Sister group to Boreoeutheria	Within Boreoeutheria	Sister group to Xenarthra	Sister group to (Laurasiatheria, Xenarthra)	Sister group to (Laurasiatheria, Xenarthra)	Sister group to Euarchontoglires
((elephant, rock hyrax), tenrec)	×	×	–	×	×	×	×	×	×	×
Xenarthra (Armadillo)	Sister taxon to Epitheria	Sister taxon to Epitheria	Sister taxon to part of the paraphyletic Epitheria	Sister taxon to Epitheria	Sister taxon to Epitheria	Sister taxon to Epitheria	Sister taxon to Afrotheria	Sister taxon to Laurasiatheria	Sister taxon to Laurasiatheria	Sister group to Epitheria
Boreoeutheria	×	×	×	×	×	–	–	–	–	–
Laurasiatheria	×	×	×	×	×	×	×	×	×	×
Insectivora	×	×	×	×	×	×	×	×	×	×
Chiroptera	×	×	×	×	×	×	×	×	×	×
((rfbat, flying fox), sbbat)	×	×	×	×	×	×	×	–	×	–
Carnivora	×	×	×	×	×	×	×	×	×	×
Horse	(bats, horse)	(Carn., horse)	(Carn., horse)	(Carn., horse)	(cow, horse)	((bats, cow), horse)	((bats, cow), horse)	(((bats, cow), Carn.), horse)	(cow, horse)	(Carn., horse)
Cow	((bats, horse), cow)	(((Carn., horse), bats), cow)	(((Carn., horse), bats), cow)	(bats, cow)	(cow, horse)	(bats, cow)	(bats, cow)	(bats, cow)	(cow, horse)	(((Carn., horse), bats), cow)
Euarchontoglires	×	×	×	×	×	–	×	×	–	×
Glires	×	–	–	–	–	–	×	×	–	×
Rodentia	–	–	–	×	×	–	×	×	–	×
Muroidea	×	×	×	×	×	× Basal within Epitheria	×	×	×	×
Rabbit	Sister taxon to Muroidea	Sister taxon to tree shrew; both sister group to Primata	Basal within Euarchontoglires	Sister taxon to tree shrew; both sister group to Rodentia	Sister taxon to tree shrew; both sister group to Rodentia	Sister taxon to Euarchontoglires	Sister taxon to Rodentia	Sister taxon to Rodentia	Sister taxon to Primata	Sister taxon to Rodentia
Primata	×	×	×	×	×	×	×	–	×	×
Strepsirrhini	×	×	×	×	×	×	×	×	×	×
Platyrrhini	×	×	×	×	×	×	×	×	×	×
(((squirrel monkey, marmoset), owl monkey), dusky titi)	–	–	–	–	–	–	–	–	×	–
Catarrhini	×	×	×	×	×	×	×	×	×	×
Cercopithecidae	×	×	×	×	×	×	×	×	×	×
(((baboon, macaque), vervet), colobus)	–	–	–	×	×	×	×	–	×	–
Hominoidea	×	×	×	×	×	×	×	×	×	×
(((chimp, human), orangutan), gibbon)	×	×	×	×	×	×	–	–	×	–
Tree shrew	In Glires; sister taxon to (Hystricomorpha, Sciuromorpha)	Sister taxon to rabbit; both sister group to Primata	Sister taxon to Rodentia	Sister taxon to rabbit; both sister group to Rodentia	Sister taxon to rabbit; both sister group to Rodentia	Sister taxon to (Hystricomorpha, Sciuromorpha)	Basal within Euarchontoglires	Sister taxon to Strepsirrhini	Sister taxon to remaining (Epitheria, Xenarthra)	Sister taxon to Glires
\(d_{RF}\)	20	18	18	14	16	22	16	20	20	14
\(d'_{RF}\)	0.3030	0.2727	0.2727	0.2121	0.2424	0.3333	0.2424	0.3030	0.3030	0.2121
\(d_{Q}\)	2347	2980	2748	1892	2043	6376	4164	6951	9458	3932
\(d'_{Q}\)	0.0398	0.0506	0.0467	0.0321	0.0347	0.1082	0.0707	0.1180	0.1606	0.0668

Splids (gap length \(\ge\) 2 bp) were extracted from the ENCODE regions containing sequence information for all taxa. For each tree the symmetric difference (Robinson–Foulds distance, \(d_{RF}\)), the normalized RF distance (\(d'_{RF}\)), the quartet distance (\(d_{Q}\), at most 58,905), and the normalized quartet distance (\(d'_{Q}\)) to the ENCODE guide tree is shown. rfbat = Rhinolophus ferrumequinum, sbbat = Myotis lucifugus, Carn. = Carnivora. “×” = monophyly/position recovered, “–” = monophyly/position not recovered. See text for details

Back to article page

ISSN: 1748-7188

Contact us

General enquiries: journalsubmissions@springernature.com