Downloads for data in this track are available:

• Cactus alignments (MAF format), and phylogenetic trees, and PhyloP conservation (WIG and bigWig format)

Description

Warning: Unlike other alignment tracks on the genome browser, this one does not show insertions in the query genomes. Also, all other alignment tracks show one query genome sequence for target target genome sequence, but in this track, each target genome sequence can be aligned to multiple query genome sequences. Only the first sequence is shown on the genome browser itself, the others are shown on the details page, when one clicks on the alignment. If you are interested in this track and want these shortcomings to be fixed, please contact us.

This track shows multiple alignments of 241 vertebrate species and measurements of evolutionary conservation from the Zoonomia Project.

The multiple alignments were generated using the Cactus comparative genomics alignment system. Cactus produces reference-free, whole-genome multiple alignments.

The base-wise conservation scores are computed using phyloP from the PHAST package, for all species. This version was prepared by Michael Dong (Uppsala U) with an improved neutral model incorporating better versions of ancestral repeats.

For genome assemblies not available in the genome browser, there are alternative assembly hub genome browsers. Missing sequence in any assembly is highlighted in the track display by regions of yellow when zoomed out and by Ns when displayed at base level (see Gap Annotation, below).

count	common name	CLADE	group	scientific name	sequencing source	NCBI assembly	species status
1	Cape golden mole	AFROSORICIDA	Chrysochloridae	Chrysochloris asiatica	1. Zoonomia	GCA_004027935.1	LC
2	Small madagascar hedgehog	AFROSORICIDA	Tenrecidae	Echinops telfairi	2. Existing assembly	GCF_000313985.1	LC
3	Talazac's shrew tenrec	AFROSORICIDA	Tenrecidae	Microgale talazaci	1. Zoonomia	GCA_004026705.1	LC
4	Cheetah	CARNIVORA	Felidae	Acinonyx jubatus	2. Existing assembly	GCF_001443585.1	CR
5	Giant panda	CARNIVORA	Ursidae	Ailuropoda melanoleuca	2. Existing assembly	GCA_002007445.1	VU
6	Lesser panda	CARNIVORA	Ailuridae	Ailurus fulgens	2. Existing assembly	GCA_002007465.1	EN
7	Domestic dog	CARNIVORA	Canidae	Canis lupus familiaris	2. Existing assembly	GCF_000002285.3	LC
8	Domestic dog (village dog)	CARNIVORA	Canidae	Canis lupus familiaris	1. Zoonomia	GCA_004027395.1	LC
9	Fossa	CARNIVORA	Eupleridae	Cryptoprocta ferox	1. Zoonomia	GCA_004023885.1	VU
10	Sea otter	CARNIVORA	Mustelidae	Enhydra lutris	2. Existing assembly	GCF_002288905.1	EN
11	Domestic cat	CARNIVORA	Felidae	Felis catus	2. Existing assembly	GCF_000181335.2	LC
12	Black-footed cat	CARNIVORA	Felidae	Felis nigripes	1. Zoonomia	GCA_004023925.1	VU
13	Dwarf mongoose	CARNIVORA	Herpestidae	Helogale parvula	1. Zoonomia	GCA_004023845.1	LC
14	Striped hyena	CARNIVORA	Hyaenidae	Hyaena hyaena	1. Zoonomia	GCA_004023945.1	NT
15	Weddell seal	CARNIVORA	Phocidae	Leptonychotes weddellii	2. Existing assembly	GCF_000349705.1	LC
16	African hunting dog	CARNIVORA	Canidae	Lycaon pictus	2. Existing assembly	GCA_001887905.1	EN
17	Honey badger	CARNIVORA	Mustelidae	Mellivora capensis	1. Zoonomia	GCA_004024625.1	LC
18	Northern elephant seal	CARNIVORA	Phocidae	Mirounga angustirostris	1. Zoonomia	GCA_004023865.1	LC
19	South African banded mongoose	CARNIVORA	Herpestidae	Mungos mungo	1. Zoonomia	GCA_004023785.1	LC
20	Domestic ferret	CARNIVORA	Mustelidae	Mustela putorius	2. Existing assembly	GCF_000239315.1	LC
21	Hawaiian monk seal	CARNIVORA	Phocidae	Neomonachus schauinslandi	2. Existing assembly	GCA_002201575.1	EN
22	Pacific walrus	CARNIVORA	Odobenidae	Odobenus rosmarus	2. Existing assembly	GCF_000321225.1	DD
23	Jaguar	CARNIVORA	Felidae	Panthera onca	1. Zoonomia	GCA_004023805.1	NT
24	Leopard	CARNIVORA	Felidae	Panthera pardus	2. Existing assembly	GCA_001857705.1	VU
25	Amur tiger	CARNIVORA	Felidae	Panthera tigris	2. Existing assembly	GCF_000464555.1	EN
26	Asian palm civet	CARNIVORA	Viverridae	Paradoxurus hermaphroditus	1. Zoonomia	GCA_004024585.1	LC
27	Giant otter	CARNIVORA	Mustelidae	Pteronura brasiliensis	1. Zoonomia	GCA_004024605.1	EN
28	Puma	CARNIVORA	Felidae	Puma concolor	2. Existing assembly	GCF_003327715.1	LC
29	Western spotted skunk	CARNIVORA	Mephitidae	Spilogale gracilis	1. Zoonomia	GCA_004023965.1	LC
30	Meerkat	CARNIVORA	Herpestidae	Suricata suricatta	1. Zoonomia	GCA_004023905.1	LC
31	Polar bear	CARNIVORA	Ursidae	Ursus maritimus	2. Existing assembly	GCF_000687225.1	VU
32	Arctic fox	CARNIVORA	Canidae	Vulpes lagopus	1. Zoonomia	GCA_004023825.1	LC
33	California sea lion	CARNIVORA	Otariidae	Zalophus californianus	1. Zoonomia	GCA_004024565.1	LC
34	Aoudad	CETARTIODACTYLA	Bovidae	Ammotragus lervia	2. Existing assembly	GCA_002201775.1	VU
35	Pronghorn	CETARTIODACTYLA	Antilocapridae	Antilocapra americana	1. Zoonomia	GCA_004027515.1	LC
36	Minke whale	CETARTIODACTYLA	Balaenopteridae	Balaenoptera acutorostrata	2. Existing assembly	GCF_000493695.1	LC
37	Antarctic minke whale	CETARTIODACTYLA	Balaenopteridae	Balaenoptera bonaerensis	2. Existing assembly	GCA_000978805.1	DD
38	Hirola	CETARTIODACTYLA	Bovidae	Beatragus hunteri	1. Zoonomia	GCA_004027495.1	CR
39	American bison	CETARTIODACTYLA	Bovidae	Bison bison	2. Existing assembly	GCF_000754665.1	NT
40	Zebu cattle	CETARTIODACTYLA	Bovidae	Bos indicus	2. Existing assembly	GCA_000247795.2	LC
41	Wild yak	CETARTIODACTYLA	Bovidae	Bos mutus	2. Existing assembly	GCF_000298355.1	VU
42	Cattle	CETARTIODACTYLA	Bovidae	Bos taurus	2. Existing assembly	GCF_000003205.7	LC
43	Water buffalo	CETARTIODACTYLA	Bovidae	Bubalus bubalis	2. Existing assembly	GCF_000471725.1	LC
44	Bactrian camel	CETARTIODACTYLA	Camelidae	Camelus bactrianus	2. Existing assembly	GCF_000767855.1	LC
45	Arabian camel	CETARTIODACTYLA	Camelidae	Camelus dromedarius	2. Existing assembly	GCF_000767585.1	LC
46	Wild bactrian camel	CETARTIODACTYLA	Camelidae	Camelus ferus	2. Existing assembly	GCF_000311805.1	CR
47	Wild goat	CETARTIODACTYLA	Bovidae	Capra aegagrus	2. Existing assembly	GCA_000978405.1	VU
48	Goat	CETARTIODACTYLA	Bovidae	Capra hircus	2. Existing assembly	GCF_001704415.1	LC
49	Chacoan peccary	CETARTIODACTYLA	Tayassuidae	Catagonus wagneri	1. Zoonomia	GCA_004024745.1	EN
50	Beluga whale	CETARTIODACTYLA	Monodontidae	Delphinapterus leucas	2. Existing assembly	GCF_002288925.1	LC
51	Pere david's deer	CETARTIODACTYLA	Cervidae	Elaphurus davidianus	2. Existing assembly	GCA_002443075.1	CR
52	Grey whale	CETARTIODACTYLA	Eschrichtiidae	Eschrichtius robustus	1. Zoonomia	GCA_004363415.1	LC
53	North Pacific right whale	CETARTIODACTYLA	Balaenidae	Eubalaena japonica	1. Zoonomia	GCA_004363455.1	EN
54	Giraffe	CETARTIODACTYLA	Giraffidae	Giraffa tippelskirchi	2. Existing assembly	GCA_001651235.1	VU
55	Nilgiri tahr	CETARTIODACTYLA	Bovidae	Hemitragus hylocrius	1. Zoonomia	GCA_004026825.1	EN
56	Hippopotamus	CETARTIODACTYLA	Hippopotamidae	Hippopotamus amphibius	1. Zoonomia	GCA_004027065.1	VU
57	Amazon river dolphin	CETARTIODACTYLA	Iniidae	Inia geoffrensis	1. Zoonomia	GCA_004363515.1	DD
58	Pygmy sperm whale	CETARTIODACTYLA	Physeteridae	Kogia breviceps	1. Zoonomia	GCA_004363705.1	DD
59	Yangtze river dolphin	CETARTIODACTYLA	Iniidae	Lipotes vexillifer	2. Existing assembly	GCF_000442215.1	CR
60	Sowerby's beaked whale	CETARTIODACTYLA	Ziphiidae	Mesoplodon bidens	1. Zoonomia	GCA_004027085.1	DD
61	Narwhal	CETARTIODACTYLA	Monodontidae	Monodon monoceros	1. Zoonomia	GCA_004026685.1	LC
62	Siberian musk deer	CETARTIODACTYLA	Moschidae	Moschus moschiferus	1. Zoonomia	GCA_004024705.1	VU
63	Yangtze finless porpoise	CETARTIODACTYLA	Phocoenidae	Neophocaena asiaeorientalis	2. Existing assembly	GCA_003031525.1	EN
64	White-tailed deer	CETARTIODACTYLA	Cervidae	Odocoileus virginianus	2. Existing assembly	GCA_002102435.1	LC
65	Okapi	CETARTIODACTYLA	Giraffidae	Okapia johnstoni	2. Existing assembly	GCA_001660835.1	EN
66	Killer whale	CETARTIODACTYLA	Delphinidae	Orcinus orca	2. Existing assembly	GCF_000331955.2	DD
67	Sheep	CETARTIODACTYLA	Bovidae	Ovis aries	2. Existing assembly	GCF_000298735.2	LC
68	Peninsular bighorn sheep	CETARTIODACTYLA	Bovidae	Ovis canadensis cremnobates	1. Zoonomia	GCA_004026945.1	EN
69	Chiru	CETARTIODACTYLA	Bovidae	Pantholops hodgsonii	2. Existing assembly	GCF_000400835.1	NT
70	Harbor porpoise	CETARTIODACTYLA	Phocoenidae	Phocoena phocoena	1. Zoonomia	GCA_004363495.1	LC
71	Indus river dolphin	CETARTIODACTYLA	Platanistidae	Platanista gangetica minor	1. Zoonomia	GCA_004363435.1	EN
72	Siberian reindeer	CETARTIODACTYLA	Cervidae	Rangifer tarandus	1. Zoonomia	GCA_004026565.1	VU
73	Russian saiga	CETARTIODACTYLA	Bovidae	Saiga tatarica tatarica	1. Zoonomia	GCA_004024985.1	CR
74	Pig	CETARTIODACTYLA	Suidae	Sus scrofa	2. Existing assembly	GCF_000003025.5	LC
75	Java lesser chevrotain	CETARTIODACTYLA	Tragulidae	Tragulus javanicus	1. Zoonomia	GCA_004024965.1	DD
76	Bottlenose dolphin	CETARTIODACTYLA	Delphinidae	Tursiops truncatus	2. Existing assembly	GCA_001922835.1	LC
77	Alpaca	CETARTIODACTYLA	Camelidae	Vicugna pacos	2. Existing assembly	GCA_000767525.1	LC
78	Cuvier's beaked whale	CETARTIODACTYLA	Ziphiidae	Ziphius cavirostris	1. Zoonomia	GCA_004364475.1	LC
79	Tailed tailless bat	CHIROPTERA	Phyllostomidae	Anoura caudifer	1. Zoonomia	GCA_004027475.1	LC
80	Jamacian fruit-eating bat	CHIROPTERA	Phyllostomidae	Artibeus jamaicensis	1. Zoonomia	GCA_004027435.1	LC
81	Seba's short-tailed bat	CHIROPTERA	Phyllostomidae	Carollia perspicillata	1. Zoonomia	GCA_004027735.1	LC
82	Bumblebee bat	CHIROPTERA	Craseonycteridae	Craseonycteris thonglongyai	1. Zoonomia	GCA_004027555.1	VU
83	Common vampire bat	CHIROPTERA	Phyllostomidae	Desmodus rotundus	2. Existing assembly	GCA_002940915.2	LC
84	Straw-colored fruit bat	CHIROPTERA	Pteropodidae	Eidolon helvum	2. Existing assembly	GCA_000465285.1	NT
85	Big brown bat	CHIROPTERA	Vespertilionidae	Eptesicus fuscus	2. Existing assembly	GCF_000308155.1	LC
86	Great roundleaf bat	CHIROPTERA	Hipposideridae	Hipposideros armiger	2. Existing assembly	GCA_001890085.1	LC
87	Cantor's leaf-nosed bat	CHIROPTERA	Hipposideridae	Hipposideros galeritus	1. Zoonomia	GCA_004027415.1	LC
88	Eastern red bat	CHIROPTERA	Vespertilionidae	Lasiurus borealis	1. Zoonomia	GCA_004026805.1	LC
89	Long-tongued fruit bat	CHIROPTERA	Pteropodidae	Macroglossus sobrinus	1. Zoonomia	GCA_004027375.1	LC
90	Greater false vampire bat	CHIROPTERA	Megadermatidae	Megaderma lyra	1. Zoonomia	GCA_004026885.1	LC
91	Hairy big-eared bat	CHIROPTERA	Phyllostomidae	Micronycteris hirsuta	1. Zoonomia	GCA_004026765.1	LC
92	Natal long-fingered bat	CHIROPTERA	Vespertilionidae	Miniopterus natalensis	2. Existing assembly	GCF_001595765.1	LC
93	Common bent-wing bat	CHIROPTERA	Vespertilionidae	Miniopterus schreibersii	1. Zoonomia	GCA_004026525.1	NT
94	Ghost-faced bat	CHIROPTERA	Mormoopidae	Mormoops blainvillei	1. Zoonomia	GCA_004026545.1	LC
95	Ashy-gray tube-nosed bat	CHIROPTERA	Vespertilionidae	Murina feae	1. Zoonomia	GCA_004026665.1	LC
96	Brandt's bat	CHIROPTERA	Vespertilionidae	Myotis brandtii	2. Existing assembly	GCF_000412655.1	LC
97	David's myotis bat	CHIROPTERA	Vespertilionidae	Myotis davidii	2. Existing assembly	GCF_000327345.1	LC
98	Little brown bat	CHIROPTERA	Vespertilionidae	Myotis lucifugus	2. Existing assembly	GCF_000147115.1	LC
99	Greater mouse-eared bat	CHIROPTERA	Vespertilionidae	Myotis myotis	1. Zoonomia	GCA_004026985.1	LC
100	Greater bulldog bat	CHIROPTERA	Noctilionidae	Noctilio leporinus	1. Zoonomia	GCA_004026585.1	LC
101	Common pipistrelle	CHIROPTERA	Vespertilionidae	Pipistrellus pipistrellus	1. Zoonomia	GCA_004026625.1	LC
102	Parnell's mustached bat	CHIROPTERA	Mormoopidae	Pteronotus parnellii	2. Existing assembly	GCA_000465405.1	LC
103	Black flying fox	CHIROPTERA	Pteropodidae	Pteropus alecto	2. Existing assembly	GCF_000325575.1	LC
104	Large flying fox	CHIROPTERA	Pteropodidae	Pteropus vampyrus	2. Existing assembly	GCF_000151845.1	NT
105	Chinese rufous horseshoe bat	CHIROPTERA	Rhinolophidae	Rhinolophus sinicus	2. Existing assembly	GCA_001888835.1	LC
106	Egyptian fruit bat	CHIROPTERA	Pteropodidae	Rousettus aegyptiacus	1. Zoonomia	GCA_004024865.1	LC
107	Mexican free-tailed bat	CHIROPTERA	Molossidae	Tadarida brasiliensis	1. Zoonomia	GCA_004025005.1	LC
108	Stripe-headed round-eared bat	CHIROPTERA	Phyllostomidae	Tonatia saurophila	1. Zoonomia	GCA_004024845.1	LC
109	Screaming hairy armadillo	CINGULATA	Dasypodidae	Chaetophractus vellerosus	1. Zoonomia	GCA_004027955.1	LC
110	Nine-banded armadillo	CINGULATA	Dasypodidae	Dasypus novemcinctus	2. Existing assembly	GCF_000208655.1	LC
111	Southern three-banded armadillo	CINGULATA	Dasypodidae	Tolypeutes matacus	1. Zoonomia	GCA_004025125.1	NT
112	Sunda flying lemur	DERMOPTERA	Cynocephalidae	Galeopterus variegatus	1. Zoonomia	GCA_004027255.1	LC
113	Star-nosed mole	EULIPOTYPHLA	Talpidae	Condylura cristata	2. Existing assembly	GCF_000260355.1	LC
114	Indochinese shrew	EULIPOTYPHLA	Soricidae	Crocidura indochinensis	1. Zoonomia	GCA_004027635.1	LC
115	Western european hedgehog	EULIPOTYPHLA	Erinaceidae	Erinaceus europaeus	2. Existing assembly	GCF_000296755.1	LC
116	Eastern mole	EULIPOTYPHLA	Talpidae	Scalopus aquaticus	1. Zoonomia	GCA_004024925.1	LC
117	Hispaniolan solenodon	EULIPOTYPHLA	Solenodontidae	Solenodon paradoxus	1. Zoonomia	GCA_004363575.1	EN
118	European shrew	EULIPOTYPHLA	Soricidae	Sorex araneus	2. Existing assembly	GCF_000181275.1	LC
119	Gracile shrew-like mole	EULIPOTYPHLA	Talpidae	Uropsilus gracilis	1. Zoonomia	GCA_004024945.1	LC
120	African yellow-spotted rock hyrax	HYRACOIDEA	Procaviidae	Heterohyrax brucei	1. Zoonomia	GCA_004026845.1	LC
121	South African rock hyrax	HYRACOIDEA	Procaviidae	Procavia capensis	1. Zoonomia	GCA_004026925.1	LC
122	Snowshoe hare	LAGOMORPHA	Leporidae	Lepus americanus	1. Zoonomia	GCA_004026855.1	LC
123	American pika	LAGOMORPHA	Ochotonidae	Ochotona princeps	2. Existing assembly	GCF_000292845.1	LC
124	Rabbit	LAGOMORPHA	Leporidae	Oryctolagus cuniculus	2. Existing assembly	GCF_000003625.3	NT
125	Cape elephant shrew	MACROSCELIDEA	Macroscelididae	Elephantulus edwardii	1. Zoonomia	GCA_004027355.1	LC
126	Southern white rhinoceros	PERISSODACTYLA	Rhinocerotidae	Ceratotherium simum	2. Existing assembly	GCF_000283155.1	NT
127	Northern white rhino	PERISSODACTYLA	Rhinocerotidae	Ceratotherium simum cottoni	1. Zoonomia	GCA_004027795.1	CR
128	Sumatran rhinoceros	PERISSODACTYLA	Rhinocerotidae	Dicerorhinus sumatrensis	2. Existing assembly	GCA_002844835.1	CR
129	Black rhinocerous	PERISSODACTYLA	Rhinocerotidae	Diceros bicornis	1. Zoonomia	GCA_004027315.1	CR
130	Ass	PERISSODACTYLA	Equidae	Equus asinus	2. Existing assembly	GCF_001305755.1	LC
131	Horse	PERISSODACTYLA	Equidae	Equus caballus	2. Existing assembly	GCF_000002305.2	LC
132	Przewalski's horse	PERISSODACTYLA	Equidae	Equus przewalskii	2. Existing assembly	GCF_000696695.1	EN
133	Malayan tapir	PERISSODACTYLA	Tapiridae	Tapirus indicus	1. Zoonomia	GCA_004024905.1	EN
134	South American tapir	PERISSODACTYLA	Tapiridae	Tapirus terrestris	1. Zoonomia	GCA_004025025.1	VU
135	Malayan pangolin	PHOLIDOTA	Manidae	Manis javanica	2. Existing assembly	GCF_001685135.1	CR
136	Chinese pangolin	PHOLIDOTA	Manidae	Manis pentadactyla	2. Existing assembly	GCA_000738955.1	CR
137	Linnaeus's two toed sloth	PILOSA	Megalonychidae	Choloepus didactylus	1. Zoonomia	GCA_004027855.1	LC
138	Hoffmann's two-fingered sloth	PILOSA	Megalonychidae	Choloepus hoffmanni	2. Existing assembly	GCA_000164785.2	LC
139	Giant anteater	PILOSA	Myrmecophagidae	Myrmecophaga tridactyla	1. Zoonomia	GCA_004026745.1	VU
140	Southern tamandua	PILOSA	Myrmecophagidae	Tamandua tetradactyla	1. Zoonomia	GCA_004025105.1	LC
141	Mexican howler monkey	PRIMATES	Atelidae	Alouatta palliata mexicana	1. Zoonomia	GCA_004027835.1	CR
142	Ma's night monkey	PRIMATES	Aotidae	Aotus nancymaae	2. Existing assembly	GCA_000952055.2	VU
143	Geoffroy's spider monkey	PRIMATES	Atelidae	Ateles geoffroyi	1. Zoonomia	GCA_004024785.1	EN
144	White-eared titi	PRIMATES	Pitheciidae	Callicebus donacophilus	1. Zoonomia	GCA_004027715.1	LC
145	White-tufted-ear marmoset	PRIMATES	Cebidae	Callithrix jacchus	2. Existing assembly	GCA_002754865.1	LC
146	White-fronted capuchin	PRIMATES	Cebidae	Cebus albifrons	1. Zoonomia	GCA_004027755.1	LC
147	White-faced sapajou	PRIMATES	Cebidae	Cebus capucinus	2. Existing assembly	GCF_001604975.1	LC
148	Sooty mangabey	PRIMATES	Cercopithecidae	Cercocebus atys	2. Existing assembly	GCF_000955945.1	NT
149	De brazza's monkey	PRIMATES	Cercopithecidae	Cercopithecus neglectus	1. Zoonomia	GCA_004027615.1	LC
150	Fat-tailed dwarf lemur	PRIMATES	Cheirogaleidae	Cheirogaleus medius	1. Zoonomia	GCA_004024725.1	LC
151	Green monkey	PRIMATES	Cercopithecidae	Chlorocebus sabaeus	2. Existing assembly	GCF_000409795.2	LC
152	Angolan colobus	PRIMATES	Cercopithecidae	Colobus angolensis	2. Existing assembly	GCF_000951035.1	VU
153	Aye-aye	PRIMATES	Daubentoniidae	Daubentonia madagascariensis	1. Zoonomia	GCA_004027145.1	EN
154	Patas monkey	PRIMATES	Cercopithecidae	Erythrocebus patas	1. Zoonomia	GCA_004027335.1	LC
155	Sclater's lemur	PRIMATES	Lemuridae	Eulemur flavifrons	2. Existing assembly	GCA_001262665.1	CR
156	Common brown lemur	PRIMATES	Lemuridae	Eulemur fulvus	1. Zoonomia	GCA_004027275.1	NT
157	Western lowland gorilla	PRIMATES	Hominidae	Gorilla gorilla	2. Existing assembly	GCA_900006655.3	CR
158	Human	PRIMATES	Hominidae	Homo sapiens	2. Existing assembly	GCA_000001405.27	LC
159	Indri	PRIMATES	Indridae	Indri indri	1. Zoonomia	GCA_004363605.1	CR
160	Ring tailed lemur	PRIMATES	Lemuridae	Lemur catta	1. Zoonomia	GCA_004024665.1	EN
161	Crab-eating macaque	PRIMATES	Cercopithecidae	Macaca fascicularis	2. Existing assembly	GCF_000364345.1	DD
162	Rhesus monkey	PRIMATES	Cercopithecidae	Macaca mulatta	2. Existing assembly	GCF_000772875.2	LC
163	Pig-tailed macaque	PRIMATES	Cercopithecidae	Macaca nemestrina	2. Existing assembly	GCF_000956065.1	VU
164	Drill	PRIMATES	Cercopithecidae	Mandrillus leucophaeus	2. Existing assembly	GCF_000951045.1	EN
165	Gray mouse lemur	PRIMATES	Cheirogaleidae	Microcebus murinus	2. Existing assembly	GCA_000165445.3	LC
166	Coquerel's giant mouse lemur	PRIMATES	Cheirogaleidae	Mirza coquereli	1. Zoonomia	GCA_004024645.1	EN
167	Proboscis monkey	PRIMATES	Cercopithecidae	Nasalis larvatus	1. Zoonomia	GCA_004027105.1	EN
168	Northern white-cheeked gibbon	PRIMATES	Hylobatidae	Nomascus leucogenys	2. Existing assembly	GCF_000146795.2	CR
169	Sunda slow loris	PRIMATES	Lorisidae	Nycticebus coucang	1. Zoonomia	GCA_004027815.1	VU
170	Small-eared galago	PRIMATES	Galagidae	Otolemur garnettii	2. Existing assembly	GCF_000181295.1	LC
171	Pygmy chimpanzee	PRIMATES	Hominidae	Pan paniscus	2. Existing assembly	GCF_000258655.2	EN
172	Chimpanzee	PRIMATES	Hominidae	Pan troglodytes	2. Existing assembly	GCA_002880755.3	EN
173	Olive baboon	PRIMATES	Cercopithecidae	Papio anubis	2. Existing assembly	GCA_000264685.2	LC
174	Ugandan red colobus	PRIMATES	Cercopithecidae	Piliocolobus tephrosceles	2. Existing assembly	GCA_002776525.1	EN
175	White-faced saki	PRIMATES	Pitheciidae	Pithecia pithecia	1. Zoonomia	GCA_004026645.1	LC
176	Sumatran orangutan	PRIMATES	Hominidae	Pongo abelii	2. Existing assembly	GCA_002880775.3	CR
177	Coquerel's sifaka	PRIMATES	Indridae	Propithecus coquereli	2. Existing assembly	GCF_000956105.1	EN
178	Red-shanked douc	PRIMATES	Cercopithecidae	Pygathrix nemaeus	1. Zoonomia	GCA_004024825.1	EN
179	Black snub-nosed monkey	PRIMATES	Cercopithecidae	Rhinopithecus bieti	2. Existing assembly	GCF_001698545.1	EN
180	Golden snub-nosed monkey	PRIMATES	Cercopithecidae	Rhinopithecus roxellana	2. Existing assembly	GCF_000769185.1	EN
181	Emperor tamarin	PRIMATES	Cebidae	Saguinus imperator	1. Zoonomia	GCA_004024885.1	LC
182	Bolivian squirrel monkey	PRIMATES	Cebidae	Saimiri boliviensis	2. Existing assembly	GCF_000235385.1	LC
183	Northern Plains gray langur	PRIMATES	Cercopithecidae	Semnopithecus entellus	1. Zoonomia	GCA_004025065.1	LC
184	African savanna elephant	PROBOSCIDEA	Elephantidae	Loxodonta Africana	2. Existing assembly	GCF_000001905.1	VU
185	Cairo spiny mouse	RODENTIA	Muridae	Acomys cahirinus	1. Zoonomia	GCA_004027535.1	LC
186	Gobi jerboa	RODENTIA	Dipodidae	Allactaga bullata	1. Zoonomia	GCA_004027895.1	LC
187	Mountain beaver	RODENTIA	Aplodontiidae	Aplodontia rufa	1. Zoonomia	GCA_004027875.1	LC
188	Desmarest's hutia	RODENTIA	Capromyidae	Capromys pilorides	1. Zoonomia	GCA_004027915.1	LC
189	North American beaver	RODENTIA	Castoridae	Castor canadensis	1. Zoonomia	GCA_004027675.1	LC
190	Brazilian guinea pig	RODENTIA	Caviidae	Cavia aperea	2. Existing assembly	GCA_000688575.1	LC
191	Domestic guinea pig	RODENTIA	Caviidae	Cavia porcellus	2. Existing assembly	GCF_000151735.1	LC
192	Montane guinea pig	RODENTIA	Caviidae	Cavia tschudii	1. Zoonomia	GCA_004027695.1	LC
193	Long-tailed chinchilla	RODENTIA	Chinchillidae	Chinchilla lanigera	2. Existing assembly	GCF_000276665.1	EN
194	Gambian pouched rat	RODENTIA	Nesomyidae	Cricetomys gambianus	1. Zoonomia	GCA_004027575.1	LC
195	Chinese hamster	RODENTIA	Nesomyidae	Cricetulus griseus	2. Existing assembly	GCA_900186095.1	LC
196	Common gundi	RODENTIA	Ctenodactylidae	Ctenodactylus gundi	1. Zoonomia	GCA_004027205.1	LC
197	Social tuco-tuco	RODENTIA	Ctenomyidae	Ctenomys sociabilis	1. Zoonomia	GCA_004027165.1	CR
198	Lowland paca	RODENTIA	Cuniculidae	Cuniculus paca	1. Zoonomia	GCA_004365215.1	LC
199	Central American agouti	RODENTIA	Dasyproctidae	Dasyprocta punctata	1. Zoonomia	GCA_004363535.1	LC
200	Pacarana	RODENTIA	Dinomyidae	Dinomys branickii	1. Zoonomia	GCA_004027595.1	LC
201	Ord's kangaroo rat	RODENTIA	Heteromyidae	Dipodomys ordii	2. Existing assembly	GCF_000151885.1	LC
202	Stephen's kangaroo rat	RODENTIA	Heteromyidae	Dipodomys stephensi	1. Zoonomia	GCA_004024685.1	VU
203	Patagonian mara	RODENTIA	Caviidae	Dolichotis patagonum	1. Zoonomia	GCA_004027295.1	NT
204	Transcaucasian mole vole	RODENTIA	Cricetidae	Ellobius lutescens	2. Existing assembly	GCA_001685075.1	LC
205	Northern mole vole	RODENTIA	Cricetidae	Ellobius talpinus	2. Existing assembly	GCA_001685095.1	LC
206	Damara mole-rat	RODENTIA	Bathyergidae	Fukomys damarensis	2. Existing assembly	GCF_000743615.1	LC
207	Edible dormouse	RODENTIA	Gliridae	Glis glis	1. Zoonomia	GCA_004027185.1	LC
208	Woodland doormouse	RODENTIA	Gliridae	Graphiurus murinus	1. Zoonomia	GCA_004027655.1	LC
209	Naked mole-rat	RODENTIA	Bathyergidae	Heterocephalus glaber	2. Existing assembly	GCF_000247695.1	LC
210	Capybara	RODENTIA	Caviidae	Hydrochoerus hydrochaeris	1. Zoonomia	GCA_004027455.1	LC
211	Northern crested porcupine	RODENTIA	Hystricidae	Hystrix cristata	1. Zoonomia	GCA_004026905.1	LC
212	Thirteen-lined ground squirrel	RODENTIA	Sciuridae	Ictidomys tridecemlineatus	2. Existing assembly	GCF_000236235.1	LC
213	Lesser egyptian jerboa	RODENTIA	Dipodidae	Jaculus jaculus	2. Existing assembly	GCF_000280705.1	LC
214	Alpine marmot	RODENTIA	Sciuridae	Marmota marmota	2. Existing assembly	GCF_001458135.1	LC
215	Mongolian jird	RODENTIA	Muridae	Meriones unguiculatus	1. Zoonomia	GCA_004026785.1	LC
216	Golden hamster	RODENTIA	Cricetidae	Mesocricetus auratus	2. Existing assembly	GCF_000349665.1	VU
217	Prairie vole	RODENTIA	Cricetidae	Microtus ochrogaster	2. Existing assembly	GCF_000317375.1	LC
218	Ryukyu mouse	RODENTIA	Muridae	Mus caroli	2. Existing assembly	GCA_900094665.2	LC
219	House mouse	RODENTIA	Muridae	Mus musculus	2. Existing assembly	GCF_000001635.26	LC
220	Shrew mouse	RODENTIA	Muridae	Mus pahari	2. Existing assembly	GCA_900095145.2	LC
221	Western wild mouse	RODENTIA	Muridae	Mus spretus	2. Existing assembly	GCA_001624865.1	LC
222	Hazel dormouse	RODENTIA	Gliridae	Muscardinus avellanarius	1. Zoonomia	GCA_004027005.1	LC
223	Coypu	RODENTIA	Myocastoridae	Myocastor coypus	1. Zoonomia	GCA_004027025.1	LC
224	Upper galilee mountains blind mole rat	RODENTIA	Spalacidae	Nannospalax galili	2. Existing assembly	GCF_000622305.1	DD
225	Degu	RODENTIA	Octodontidae	Octodon degus	2. Existing assembly	GCF_000260255.1	LC
226	Muskrat	RODENTIA	Cricetidae	Ondatra zibethicus	1. Zoonomia	GCA_004026605.1	LC
227	Scorpion mouse	RODENTIA	Cricetidae	Onychomys torridus	1. Zoonomia	GCA_004026725.1	LC
228	Pacific pocket mouse	RODENTIA	Heteromyidae	Perognathus longimembris pacificus	1. Zoonomia	GCA_004363475.1	LC
229	Prairie deer mouse	RODENTIA	Cricetidae	Peromyscus maniculatus	2. Existing assembly	GCF_000500345.1	LC
230	Dassie rat	RODENTIA	Petromuridae	Petromus typicus	1. Zoonomia	GCA_004026965.1	LC
231	Fat sand rat	RODENTIA	Muridae	Psammomys obesus	2. Existing assembly	GCA_002215935.1	LC
232	Norway rat	RODENTIA	Muridae	Rattus norvegicus	2. Existing assembly	GCF_000001895.5	LC
233	Hispid cotton rat	RODENTIA	Cricetidae	Sigmodon hispidus	1. Zoonomia	GCA_004025045.1	LC
234	Daurian ground squirrel	RODENTIA	Sciuridae	Spermophilus dauricus	2. Existing assembly	GCA_002406435.1	LC
235	Greater cane rat	RODENTIA	Thryonomyidae	Thryonomys swinderianus	1. Zoonomia	GCA_004025085.1	LC
236	Cape ground squirrel	RODENTIA	Sciuridae	Xerus inauris	1. Zoonomia	GCA_004024805.1	LC
237	Meadow jumping mouse	RODENTIA	Dipodidae	Zapus hudsonius	1. Zoonomia	GCA_004024765.1	LC
238	Northern tree shrew	SCANDENTIA	Tupaiidae	Tupaia belangeri chinensis	2. Existing assembly	GCF_000334495.1	LC
239	Large treeshrew	SCANDENTIA	Tupaiidae	Tupaia tana	1. Zoonomia	GCA_004365275.1	LC
240	Florida manatee	SIRENIA	Trichechidae	Trichechus manatus	2. Existing assembly	GCF_000243295.1	EN
241	Aardvark	TUBULIDENTATA	Orycteropodidae	Orycteropus afer	1. Zoonomia	GCA_004365145.1	LC

Table 1. Genome assemblies included in the 241-way Conservation track.
Species status:LC = Least Concern; NT = Near threatened; VU = Vulnerable; EN = Endangered; CR = Critically endangered

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Pairwise alignments of each species to the human genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.

Gap Annotation

The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:

• Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the human genome or a lineage-specific deletion between the aligned blocks in the aligning species.
• Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
• Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Genomic Breaks

Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:

• Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement.
• Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the human genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence.

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the human sequence at those alignment positions relative to the longest non-human sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

• No codon translation: The gene annotation is not used; the bases are displayed without translation.
• Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment.
• Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding.
• Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation:

Gene Track	Species
UCSC Genes	Human
Ensembl Genes v104	Brazilian guinea pig, gibbon
RefSeq Genes	Angolan colobus, Balaenoptera acutorostrata, Bison bison, Black flying-fox, Brandt's myotis (bat), Bushbaby, Camelus bactrianus, Camelus ferus, Canis lupus familiaris, Cape elephant shrew, Capra hircus, Cavia porcellus, Ceratotherium simum, Cercocebus atys, Chinchilla, Chinese tree shrew, Chlorocebus sabaeus, Condylura cristata, Damara mole rat, Dasypus novemcinctus, David's myotis (bat), Delphinapterus leucas, Echinops telfairi, Enhydra lutris, Eptesicus fuscus, Equus asinus, Equus przewalskii, Erinaceus europaeus, Felis catus, Heterocephalus glaber, Jaculus jaculus, Kangaroo rat, Killer whale, Leptonychotes weddellii, Lipotes vexillifer, Little brown bat, Loxodonta africana, Macaca fascicularis, Macaca nemestrina, Mandrillus leucophaeus, Manis javanica, Marmota marmota, Mesocricetus auratus, Miniopterus natalensis, Mus musculus, Nannospalax galili, Ochotona princeps, Octodon degus, Oryctolagus cuniculus, Pacific walrus, Pan paniscus, Panthera tigris, Peromyscus maniculatus, Prairie vole, Propithecus coquereli, Pteropus vampyrus, Puma concolor, Rattus norvegicus, Rhinopithecus bieti, Shrew, Squirrel monkey, Squirrel, Sus scrofa, Trichechus manatus, Ursus maritimus, White-faced sapajou, Wild yak
no annotation	Acinonyx jubatus, Acomys cahirinus, Ailuropoda melanoleuca, Ailurus fulgens, Allactaga bullata, Alouatta palliata, Ammotragus lervia, Anoura caudifer, Antilocapra americana, Aotus nancymaae, Aplodontia rufa, Artibeus jamaicensis, Ateles geoffroyi, Balaenoptera bonaerensis, Beatragus hunteri, Bos indicus, Bos taurus, Bubalus bubalis, Callicebus donacophilus, Callithrix jacchus, Camelus dromedarius, Canis lupus, Capra aegagrus, Capromys pilorides, Carollia perspicillata, Castor canadensis, Catagonus wagneri, Cavia tschudii, Cebus albifrons, Ceratotherium simum cottoni, Cercopithecus neglectus, Chaetophractus vellerosus, Cheirogaleus medius, Choloepus didactylus, Choloepus hoffmanni, Chrysochloris asiatica, Craseonycteris thonglongyai, Cricetomys gambianus, Cricetulus griseus, Crocidura indochinensis, Cryptoprocta ferox, Ctenodactylus gundi, Ctenomys sociabilis, Cuniculus paca, Dasyprocta punctata, Daubentonia madagascariensis, Desmodus rotundus, Dicerorhinus sumatrensis, Diceros bicornis, Dinomys branickii, Dipodomys stephensi, Dolichotis patagonum, Elaphurus davidianus, Ellobius lutescens, Ellobius talpinus, Equus caballus, Erythrocebus patas, Eschrichtius robustus, Eubalaena japonica, Eulemur flavifrons, Eulemur fulvus, Felis nigripes, Galeopterus variegatus, Giraffa tippelskirchi, Glis glis, Gorilla gorilla, Graphiurus murinus, Helogale parvula, Hemitragus hylocrius, Heterohyrax brucei, Hippopotamus amphibius, Hipposideros armiger, Hipposideros galeritus, Hyaena hyaena, Hydrochoerus hydrochaeris, Hystrix cristata, Indri indri, Inia geoffrensis, Kogia breviceps, Lasiurus borealis, Lemur catta, Lepus americanus, Lycaon pictus, Macaca mulatta, Macroglossus sobrinus, Manis pentadactyla, Megaderma lyra, Mellivora capensis, Meriones unguiculatus, Mesoplodon bidens, Microcebus murinus, Microgale talazaci, Micronycteris hirsuta, Miniopterus schreibersii, Mirounga angustirostris, Mirza coquereli, Monodon monoceros, Mormoops blainvillei, Moschus moschiferus, Mungos mungo, Murina feae, Mus caroli, Mus pahari, Mus spretus, Muscardinus avellanarius, Mustela putorius, Myocastor coypus, Myotis myotis, Myrmecophaga tridactyla, Nasalis larvatus, Neomonachus schauinslandi, Neophocaena asiaeorientalis, Noctilio leporinus, Nycticebus coucang, Odocoileus virginianus, Okapia johnstoni, Ondatra zibethicus, Onychomys torridus, Orycteropus afer, Ovis aries, Ovis canadensis, Pan troglodytes, Panthera onca, Panthera pardus, Pantholops hodgsonii, Papio anubis, Paradoxurus hermaphroditus

Table 2. Gene tracks used for codon translation.

Methods

The Zoonomia alignment was composed of two sets of mammalian genomes: newly assembled DISCOVAR assemblies and GenBank assemblies. The DISCOVAR genomes were masked with RepeatMasker (commit 2d947604), using Repbase version 20170127 as the repeat library and CrossMatch as the alignment engine. The pipeline used is available at repeatMaskerPipeline (commit a6ad966). The guide-tree topology was taken from the TimeTree database (using release current in October 2018), and the branch lengths were estimated using the least-squares-fit mode of PHYLIP, version 3.695. The distance matrix used was largely based on distances from the 4d site trees from the UCSC browser. To add those species not present in the UCSC tree, approximate distances estimated by Mash (commit 541971b) to the closest UCSC species were added to the distance between the two closest UCSC species. We used the HAL package (commit 68db41d) produce the HAL file.

Phylogenetic Tree Model

The phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The all-species tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 241-way alignment (msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene set, filtered to select single-coverage long transcripts.

This same tree model was used in the phyloP calculations; however, the background frequencies were modified to maintain reversibility. The resulting tree model: all species.

PhyloP Conservation

The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements ( http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).

References

Zoonomia:

Zoonomia Consortium.. A comparative genomics multitool for scientific discovery and conservation. Nature. 2020 Nov;587(7833):240-245. PMID: 33177664; PMC: PMC7759459; DOI: 10.1038/s41586-020-2876-6

Cactus:

Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020 Nov;587(7833):246-251. PMID: 33177663; PMC: PMC7673649; DOI: 10.1038/s41586-020-2871-y

Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011 Sep;21(9):1512-28. PMID: 21665927; PMC: PMC3166836; DOI: 10.1101/gr.123356.111

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

PhyloP:

Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program., Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005 Jul;15(7):901-13. PMID: 15965027; PMC: PMC1172034; DOI: 10.1101/gr.3577405

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. DOI: 10.1007/0-387-27733-1_12

Siepel A, Pollard KS, and Haussler D. New methods for detecting lineage-specific selection. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205. DOI: 10.1007/11732990_17