A database of Orthologous Mammalian Markers


SPECIES FOR WHICH ORTHOLOGOUS EXONS / CDS ARE AVAILABLE
EUARCHONTOGLIRES
Homo_sapiensHumanv01
Pan_troglodytesChimpv01
Gorilla_gorillaGorillav05
Pongo_pygmaeusOrangutanv03
Nomascus_leucogenys
 Gibbon
 v07
Macaca_mulattaMacaquev01
Papio_anubis
 Olive baboon
 v09
Chlorocebus_sabaeus
 Vervet
 v09
Callithrix_jacchusMarmosetv06
Tarsius_syrichtaTarsierv05
Otolemur_garnettii Bushbabyv02
Microcebus_murinusMouse lemurv02
Tupaia_belangeriTree shrewv02
Mus_musculusMousev01
Rattus_norvegicusRatv01
Dipodomys_ordiiKangaroo ratv05
Cavia_porcellusGuinea pigv02
Ictidomys_tridecemlineatusGround squirrelv02
Oryctolagus_cuniculusRabbitv01
Ochotona_princepsPikav02



LAURASIATHERIA
Bos_taurusCowv01
Ovis_aries
 Sheep
 v09
Tursiops_truncatusDolphinv05
Sus_scrofaPigv06
Vicugna_pacosAlpacav05
Equus_caballusHorsev03
Canis_familiarisDogv01
Ailuropoda_melanoleuca
 Panda
 v07
Mustela_putorius_furo
 Ferret
 v08
Felis_catusCatv02
Myotis_lucifugusMicrobatv02
Pteropus_vampyrusMegabatv05
Erinaceus_europaeusHedgehogv02
Sorex_araneusShrewv02



AFROTHERIA
Loxodonta_africanaElephantv01
Procavia_capensisHyraxv05
Echinops_telfairiTenrecv01



XENARTHRA
Dasypus_novemcinctusArmadillov01
Choloepus_hoffmanniSlothv05



MARSUPIALIA
Monodelphis_domesticaOpossumv01
Macropus_eugeniiWallabyv06
Sarcophilus_harrisii
 Tasmanian devil
 v07



MONOTREMATA
Ornithorhynchus_anatinusPlatypus
v02






RELATIVE EVOLUTIONARY RATE_
_
The utility of a phylogenetic marker can be described by its relative evolutionary rate (RER):
faster (respectively slower) evolving markers will be more suitable for lower (respectively deeper) taxonomic levels.

_
In a first approximation, the total branch length (TBL) of the maximum likelihood (ML) tree is a reasonable descriptor of the evolutionary rate of a given exon. 
However, the TBL will preclude fair comparisons among different exons when the taxon sampling differs: the higher the species number, the longer the TBL.

_
To circumvent this problem, we use the Super Distance Matrix (SDM) approach [Criscuolo et al. 2006], with a three-step procedure:

	(i) 	The ML tree inferred from each of the exons / CDS is converted into a matrix of additive distances by computing the path-length between each pair of species.

	(ii)	Each of the matrices is brought closer to the others by a factor (αp), according to the least-squares criterion.
		This operation is equivalent to multiplying by αp every branch length of the initial trees.

	(iii)	Optimal values of the alpha_p parameters are calculated following Criscuolo et al. (2006).
		As αp are inversely proportional to the evolutionary rates, 1/αp values provide a measure of rate heterogeneities among exons / CDS even if the number of taxa differs.
		Here, relative evolutionary rate SDM estimates range from 0.01 to 5 (OrthoMaM mean = 1.2 ; standard-error = 0.6).
		For example, if exons / CDSs X and Y are respectively characterized by relative rates rX = 0.2 and rY = 2.0, this means that Y is evolving 10 times faster than X.

_
Request guidelines: In the [0-5] range of values, type RER < 1 to query rather conserved markers, 1 < RER < 2 for more variable markers, and RER > 2 for fast-evolving ones.


 
Reference: Criscuolo A., Berry V., Douzery E. J. P. & Gascuel O., 2006.
		SDM: a fast distance-based approach for (super)tree building in phylogenomics.
		Systematic Biology 55 (5) : 740-755.



	
 

a SHAPE OF THE G DISTRIBUTION

The substitution rate heterogeneity among sites of the exon / CDS alignment is described by the Γ distribution.

Lower (respectively higher) α values correspond to strong (respectively weak) heterogeneity. If α > 1, the substitution pattern among sites is rather homogeneous.

Request guidelines: In the [0-5] range of values, type alpha < 1 to query markers with stronger among-sites variability, and alpha > 1 for alignments with more evenly distributed variability.

	
	
	
Reference:	Yang Z., 1996.
			Among-site rate variation and its impact on phylogenetic analyses.
			Trends in Ecology and Evolution 11 (9) : 367-372.
PERCENTAGE OF G+C ON THIRD CODON POSITIONS 
This parameter is a descriptor of the degree of base composition heterogeneity.
It is more contrasted on third codon positions than on the whole exon / CDS.

Request guidelines: In the [20-95] range of values, type %GC3 < 40 to query A+T rich markers, 40 < %GC3 < 60 for more equilibrated markers, and %GC3 > 60 for G+C rich markers.