Marsupial phyloSNPs

Introduction to Marsupial phyloSNPs

In this project, new genomic data from the Tasmanian devil (Sarcophilus harrisii), Tasmanian tiger (Thylacinus cynocephalus), and echidna (Tachyglossus aculeatus) are analyzed for significant changes at the protein coding level. The goal is to find single amino acid changes in one of these species at a highly invariant residue in a well-conserved exon in a gene with known or predictable tertiary structure. Such changes are thought to enrich for genetic changes with significant, adaptive biochemical or phenotypic consequences ([[Opsin_evolution:_RGR_phyloSNPs#PhyloSNPs_in_RGR|1],[[Opsin_evolution:_RGR_phyloSNPs#PhyloSNPs_in_RGR|2][[Opsin_evolution:_RGR_phyloSNPs#PhyloSNPs_in_RGR|3],[[Opsin_evolution:_LWS_PhyloSNPs#PhyloSNPs_in_LWS_opsins:_alignment_of_94_LWS_vertebrate_opsins|4]), in contrast to ordinary SNPs at positions of low conservation.

Assumed vertebrate phylogenetic tree

Marsupial relationships taken from 2009 paper establishing the mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus):

Newick tree that generates vertebrate phylogenetic tree used in the analysis here:

((((((((((((((((((homSap,panTro),gorGor),ponPyg),macMul),calJac),tarSyr),(micMur,otoGar)),tupBel),
(((((musMus,ratNor),dipOrd),cavPor),speTri),(oryCun,ochPri))),
(((((vicPac,susScr),turTru),bosTau),((equCab,(felCat,canFam)),(myoLuc,pteVam))),(eriEur,sorAra))),
(((loxAfr,proCap),echTel),(dasNov,choHof))),
(monDom,((macEug,triVul),(sarHar,thyCyn)))),
(ornAna,tacAcu)),
((galGal,taeGut),anoCar)),
xenTro),
(((tetNig,takRub),(gasAcu,oryLap)),danRer)),
calMil),
petMar);

Phylo-sorting data

46	10	52	>	10	gene	anoCar	Anolis	carolinensis	(lizard)	anoCar
29	11	30	>	11	gene	bosTau	Bos	taurus	(cow)	bosTau
15	12	15	>	12	gene	calJac	Callithrix	jacchus	(marmoset)	calJac
60	54	59	>	13	gene	calMil	Callorhinchus	milii	(elephantfish)	
32	13	33	>	14	gene	canFam	Canis	familiaris	(dog)	canFam
23	14	23	>	15	gene	cavPor	Cavia	porcellus	(guinea_pig)	cavPor
41	15	42	>	16	gene	choHof	Choloepus	hoffmanni	(sloth)	choHof
52	16	58	>	17	gene	danRer	Danio	rerio	(zebrafish)	danRer
40	17	41	>	18	gene	dasNov	Dasypus	novemcinctus	(armadillo)	dasNov
22	18	22	>	19	gene	dipOrd	Dipodomys	ordii	(kangaroo_rat)	dipOrd
39	19	40	>	20	gene	echTel	Echinops	telfairi	(tenrec)	echTel
30	20	31	>	21	gene	equCab	Equus	caballus	(horse)	equCab
35	21	36	>	22	gene	eriEur	Erinaceus	europaeus	(hedgehog)	eriEur
31	22	32	>	23	gene	felCat	Felis	catus	(cat)	felCat
44	23	50	>	24	gene	galGal	Gallus	gallus	(chicken)	galGal
50	24	56	>	25	gene	gasAcu	Gasterosteus	aculeatus	(stickleback)	gasAcu
12	25	12	>	26	gene	gorGor	Gorilla	gorilla	(gorilla)	gorGor
10	26	10	>	27	gene	homSap	Homo	sapiens	(human)	hg181
37	27	38	>	28	gene	loxAfr	Loxodonta	africana	(elephant)	loxAfr
55	55	44	>	29	gene	macEug	Macropus	eugenii	(wallaby)	
14	28	14	>	30	gene	macMul	Macaca	mulatta	(rhesus)	rheMac
17	29	17	>	31	gene	micMur	Microcebus	murinus	(mouse_lemur)	micMur
42	30	43	>	32	gene	monDom	Monodelphis	domestica	(opossum)	monDom
20	31	20	>	33	gene	musMus	Mus	musculus	(mouse)	mm91
33	32	34	>	34	gene	myoLuc	Myotis	lucifugus	(microbat)	myoLuc
26	33	26	>	35	gene	ochPri	Ochotona	princeps	(pika)	ochPri
43	34	48	>	36	gene	ornAna	Ornithorhynchus	anatinus	(platypus)	ornAna
25	35	25	>	37	gene	oryCun	Oryctolagus	cuniculus	(rabbit)	oryCun
51	36	57	>	38	gene	oryLap	Oryzias	latipes	(medaka)	oryLat
18	37	18	>	39	gene	otoGar	Otolemur	garnettii	(bushbaby)	otoGar
11	38	11	>	40	gene	panTro	Pan	troglodytes	(chimp)	panTro
53	39	60	>	41	gene	petMar	Petromyzon	marinus	(lamprey)	petMar
13	40	13	>	42	gene	ponPyg	Pongo	pygmaeus	(orang)	ponAbe
38	41	39	>	43	gene	proCap	Procavia	capensis	(hyrax)	proCap
34	42	35	>	44	gene	pteVam	Pteropus	vampyrus	(macrobat)	pteVam
21	43	21	>	45	gene	ratNor	Rattus	norvegicus	(rat)	rn41
56	56	45	>	46	gene	sarHar	Sarcophilus	harrisii	(tasmanian_devil)	
36	44	37	>	47	gene	sorAra	Sorex	araneus	(shrew)	sorAra
24	45	24	>	48	gene	speTri	Spermophilus	tridecemlineatus	(squirrel)	speTri
54	57	28	>	49	gene	susScr	Sus	scrofa	(pig)	
59	58	49	>	50	gene	tacAcu	Tachyglossus	aculeatus	(echidna)	
45	46	51	>	51	gene	taeGut	Taeniopygia	guttata	(finch)	taeGut
49	47	55	>	52	gene	takRub	Takifugu	rubripes	(fugu)	fr21
16	48	16	>	53	gene	tarSyr	Tarsius	syrichta	(tarsier)	tarSyr
48	49	54	>	54	gene	tetNig	Tetraodon	nigroviridis	(pufferfish)	tetNig
58	59	47	>	55	gene	thyCyn	Thylacinus	cynocephalus	(tasmanian_tiger)	
57	60	46	>	56	gene	triVul	Trichosurus	vulpecula	(bushytail_possum)	
19	50	19	>	57	gene	tupBel	Tupaia	belangeri	(tree_shrew)	tupBel
28	51	29	>	58	gene	turTru	Tursiops	truncatus	(dolphin)	turTru
27	52	27	>	59	gene	vicPac	Vicugna	pacos	(lama)	vicPac
47	53	53	>	60	gene	xenTro	Xenopus	tropicalis	(frog)	xenTro
										
44	44	51	f	51	gene	fasta	genus	species	common	ucsc
phy	alp	phy		alp