. Author manuscript; available in PMC: 2015 Jun 1.

Published in final edited form as: Mol Phylogenet Evol. 2014 Feb 28;75:165–183. doi: 10.1016/j.ympev.2014.02.023

Table 1.

Sequences used in this study.

Scientific name	Common name	NCBI Accession No	Reference
Primates
Strepsirrhini
Lorisiformes
Lorisidae
Loris tardigradus	Slender loris	NC_012763	Matsui et al., 2009
Nycticebus coucang	Slow loris	NC_002765	Arnason et al., 2000
Perodicticus potto	Potto	NC_012764	Matsui et al., 2009
Galagidae
Galago senegalensis	Senegal galago	NC_012761	Matsui et al., 2009
*Otolemur crassicaudatus*^a	Thick-tailed galago	KJ434961	This study
Chiromyiformes
Daubentoniidae
*Daubentonia madagascariensis*^a	Aye-aye	KJ158462	This study
Lemuriformes
Lemuridae
Eulemur mongoz	Mongoose lemur	NC_010300	Arnason et al., 2008
Eulemur fulvus fulvus	Brown lemur	NC_012766	Matsui et al., 2009
Eulemur fulvus mayottensis	Brown lemur	NC_012769	Matsui et al., 2009
Eulemur macaco macaco	Black lemur	NC_012771	Matsui et al., 2009
Lemur catta	Ring-tailed lemur	NC_004025	Arnason et al., 2002
Varecia variegata	Black and white ruffled lemur	NC_012773	Matsui et al., 2009
Cheirogaleidae
*Mirza coquereli*^a	Coquereli’s giant mouse lemur	KJ158463	This study
Lepilemuridae
Lepilemur hubbardorum	Hubbard’s sportive lemur	NC_014453	Lei at al., 2010
Indridae
Propithecus coquereli	Coquerel’s sifaka	AB286049	Matsui et al., 2007
Haplorrhini
Tarsiformes
Tarsiidae
Tarsius bancanus	Horsfield’s tarsier	NC_002811	Schmitz et al., 2002b
Tarsius syrichta	Philippine tarsier	NC_012774	Matsui et al., 2009
Anthropoidea
Platyrrhini
Cebidae
Aotus lemurinus	Lemurine night monkey	FJ785421	Hodgson et al., 2009
Cebus albifrons	White-fronted capuchin	AJ309866	Arnason et al., 2000
Saimiri sciureus	Common squirrel monkey	FJ785425	Hodgson et al., 2009
Saguinus oedipus	Cotton-top tamarin	FJ785424	Hodgson et al., 2009
Pithecidae
Callicebus donacophilus	Bolivian titi	FJ785423	Hodgson et al., 2009
Atelidae
Ateles belzebuth	White-bellied spider monkey	FJ785422	Hodgson et al., 2009
Catarrhini
Cercopithecoidea
Colobinae
Colobus guereza	Guereza	AY863427	Raaum et al., 2005
Nasalis larvatus	Proboscis monkey	DQ355298	Sterner et al., 2006
Pilocolobus badius	Western red colobus	DQ355301	Sterner et al., 2006
Presbytis melalophos	Mitred leaf monkey	DQ355299	Sterner et al., 2006
Pygathrix nemaeus	Douc langur	DQ355302	Sterner et al., 2006
Rhinopithecus roxellana	Golden snub-nosed monkey	DQ355300	Sterner et al., 2006
Semnopithecus entellus	Hanuman langur	DQ355297	Sterner et al., 2006
Trachypithecus obscurus	Dusky leaf monkey	NC_006900	Raaum et al., 2005
Cercopithecinae
*Allenopithecus nigroviridis*^a	Allen’s swamp monkey	KJ434962	This study
*Cercocebus torquatus*^a	Collared mangabey	KJ434959	This study
*Cercopithecus diana*^a	Diana monkey	KJ434958	This study
*Cercopithecus lhoesti*^a	L’Hoest’s monkey	KJ434957	This study
*Cercopithecus mitis*^a	Blue monkey	KJ434956	This study
Chlorocebus aethiops	Grivet	NC_007009	Raaum et al., 2005
Chlorocebus pygerythrus	Vervet monkey	NC_009747	Wertheim & Worobey, 2007
Chlorocebus sabaeus	Green monkey	EF597503	Wertheim & Worobey, 2007
Chlorocebus tantalus	Tantalus monkey	NC_009748	Wertheim & Worobey, 2007
*Erythrocebus patas*^a	Patas monkey	KJ434955	This study
*Lophocebus aterrimus*^a	Black crested mangabey	KJ434960	This study
Macaca sylvanus	Barbary ape	NC 002764	Arnason et al., 2000
Macaca mulatta	Rhesus monkey	NC_005943	Gokey et al., 2004
Macaca fascicularis	Crab-eating macaque	NC_012670	Yi et al., unpub.
Macaca thibetana	Pere David’s macaque	NC_011519	Li et al., 2009
*Mandrillus sphinx*^a	Mandrill	KJ434963	This study
Papio hamadryas	Hamadryas baboon	NC_001992	Arnason et al., 1998
Theropithecus gelada	Gelada	FJ785426	Hodgson et al., 2009
Hominoidea
Gorilla gorilla	Western gorilla	NC_001645	Horai et al., 1995
Homo neanderthalensis	Neanderthal	AM948965	Green et al., 2008
Homo sapiens	Human	EF061150	Friedlaender et al., 2007
Homo sp. (Denisovan)	Denisova hominin	FR695060	Krause et al., 2010
Hylobates agilis	Agile gibbon	NC_014042	Matsudaira & Ishida, 2010
Hylobates lar	White-handed gibbon	NC_002082	Arnason et al., 1996
Hylobates pileatus	Pileated gibbon	NC_014045	Matsudaira & Ishida, 2010
Nomascus siki	Southern white-cheeked gibbon	NC_014051	Matsudaira & Ishida, 2010
Pan paniscus	Pygmy chimpanzee	D38116	Horai et al., 1995
Pan troglodytes	Common chimpanzee	EU095335	Flynn & Carr, 2007
Pongo abelii	Sumatran orangutan	X97707	Xu & Arnason, 1996
Pongo pygmaeus	Bornean orangutan	NC_001646	Horai et al., 1995
Symphalangus syndactylus	Siamang	NC_014047	Matsudaira & Ishida, 2010
Non-primate mammals
Euarchontoglires
Dermoptera
Galeopterus variegatus	Sunda flying lemur	NC_004031	Arnason et al., 2002
Galeopterus variegatus	Sunda flying lemur	AF460846	Schmitz et al., 2002a
Rodentia
Cavia porcellus	Guinea pig	AJ222767	D’Erchia et al., 1996
Cricetulus griseus	Chinese hamster	NC_007936	Partridge et al., 2007
Glis glis	Fat dormouse	NC_001892	Reyes et al., 1998
Mus musculus	Mouse	NC_005089	Bayona-Bafaluy et al., 2003
Rattus norvegicus	Brown rat	AJ428514	Nilsson et al., 2003
Sciurus vulgaris	Squirrel	AJ238588	Reyes et al., 2000
Lagomorpha
Lepus europaeus	European hare	AJ421471	Arnason et al., 2002
Ochotona collaris	Collared pika	NC_003033	Lin et al., 2002
Oryctolagus cuniculus	Rabbit	NC_001913	Gissi et al., 1998
Laurasiatheria
Carnivora
Canis familiaris	Dog	NC_002008	Kim et al., 1998
Felis catus	Domestic cat	U20753	Lopez et al., 1996
Perissodactyla
Equus caballus	Horse	NC_001640	Xu & Arnason, 1994
Rhinoceros unicornis	Greater Indian rhinoceros	NC_001779	Xu et al., 1996
Cetartiodactyla
Balaenoptera musculus	Blue whale	NC_001601	Arnason et al., 1993
Balaenoptera physalus	Finback whale	X61145	Arnason et al., 1991
Bos taurus	Cow	NC_006853	Chung,and Ha, unpub.
Hippopotamus amphibius	Hippopotamus	AJ010957	Ursing & Arnason, 1998b
Lama pacos	Alpaca	NC_002504	Ursing et al., 2000
Ovis aries	Sheep	AF010406	Hiendleder et al., 1998
Physeter catodon	Sperm whale	NC_002503	Arnason et al., 2000
Sus scrofa	Pig	AJ002189	Ursing & Arnason, 1998a
Afrotheria
Proboscidea
Elephas maximus	Asiatic elephant	NC_005129	Rogaev et al., 2006
Loxodonta africana	African elephant	NC_000934	Hauf et al., 2000

in bold new sequences generated for this study