Coding indels: PRNP

The prion gene PRNP exhibits a 6bp indel in its amino-terminal signal peptide that contributed historically to establishing the clade Euarchontoglires. From consideration of outgroups, the indel is a deletion rather than an insertion. It present in all sequenced species of rodents, rabbits, treeshrews, flying lemurs and primates but not in any other species of mammal.

Remarkably, this indel distribution has held up (remained homoplasy-free) even as the number of species sequenced has come to exceed 100. (A typical mammalian gene as of November 07 can only be recovered from about 40 species.)

Consequently this data set strongly conflicts with recent proposals placing mouse basal relative to dog and human, ie (mouse,(dog,human)), because it would require a global revision of the super-ordinal mammalian tree based or assume highly non-parsimonious multiple events bizarrely timed to very near these divergence stems.

However signal region indels are very rare among the 4500-odd genes with signal peptides, no doubt due to steric requirements of the binding pocket of the signal processing complex SRP, making multiple independent events within a particular gene's signal peptide highly implausible.

Below is data from 96 species:

MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Homo sapiens
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Pan troglodytes
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Gorilla gorilla
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Pongo pygmaeus
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Nomascus leucogenys
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Hylobates lar
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Macaca arctoides
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Symphalangus syndactylus
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Macaca fascicularis
MA--NAGCWLLVLFVATWSDTGLCKKRPKPG     Cavia porcellusMA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Macaca fuscata
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Macaca mulatta
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Macaca nemestrina
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Papio hamadryas
MA--NLGCWMLFLFVATWSDLGLCKKRPKPG     Callithrix jacchus
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Cebus apella
MA--NLGCWMLVVFVATWSDLGLCKKRPKPG     Cercopithecus aethiops
MA--NLGCWMLVVFVATWSDLGLCKKRPKPG     Cercopithecus dianae
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Colobus guereza
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Presbytis francoisi
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG     Saimiri sciureus
MA--KLGYWLLVLFVATWSDVGLCKKRPKPG     Tarsius syrichta
MA--NLGCWMLVVFVATWSDVGLCKKRPKPG     Microcebus murinus
MA--RLGCWMLVLFVATWSDIGLCKKRPKPG     Otolemur garnettii
ME--NLGCWMLILFVATWSDIGLCKKRPKPG     Cynocephalus variegatus
MA--QLGCWLMVLFVATWSDVGLCKKRPKPG     Tupaia belangeri
MA--NLGYWLLALFVTMWTDVGLCKKRPKPG     Mus musculus
MA--NLGYWLLALFVTTCTDVGLCKKRPKPG     Rattus norvegicus
MA--NLGYWLLALFVTTCTDVGLCKKRPKPG     Rattus rattus
MA--NLGYWLLALFVTTWTDVGLCKKRPKPG     Apodemus sylvaticus
MA--NLGCWLLVLFVATWSDLGLCKKRTKPG     Dipodomys ordii
MA--NLSYWLLAFFVTTWTDVGLCKKRPKPG     Clethrionomys glareolus
MA--NLSYWLLALFVATWTDVGLCKKRPKPG     Cricetulus griseus
MA--NLSYWLLALFVATWTDVGLCKKRPKPG     Cricetulus migratorius
MA--NLGYWLLALFVTMWTDVGLCKKRPKPG     Meriones unguiculatus
MA--NLSYWLLALFVAMWTDVGLCKKRPKPG     Mesocricetus auratus
MA--NLGYWLLALFVATWTDVGLCKKRPKPG     Sigmodon fulviventer
MA--NLGYWLLALFVATWTDVGLCKKRPKPG     Sigmodon hispiedis
MA--HLGYWMLLLFVATWSDVGLCKKRPKPG     Oryctolagus cuniculus
MA--HLSYWLLVLFVAAWSDVGLCKKRPKPG     Ochotona princeps
MV--NPGCWLLVLFVATLSDVGLCKKRPKPG     Spermophilus tridecemlineatus
MV--NPGYWLLVLFVATLSDVGLCKKRPKPG     Sciurus vulgaris
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Bos taurus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Bison bison
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Rangifer tarandus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Alces alces
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Capreolus capreolus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Kobus megaceros
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Connochaetes taurinus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Ammotragus lervia
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Hippotragus niger
MVKSHMGSWILVLFVVTWSDVGLCKKRPKPG     Camelus dromedarius
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Capris hircus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Cervus elaphus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Cervus elaphus nelsoni
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Dama dama
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Odocoileus hemionus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Odocoileus virginianus
MVKSHIGSWILVLFVAMWSDVALCKKRPKPG     Oryx leucoryx
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Ovibos moschatus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Ovis aries
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Ovis canadensis
MVKSHIGSWILVLFVAMWSDVALCKKRPKPG     Tragelaphus strepsiceros
MVKSHIGGWILVLFVAAWSDIGLCKKRPKPG     Sus scrofa
MVKSHMGSWILVLFVVTWSDMGLCKKRPKPG     Vicugna vicugna
MVKSHVGGWILVLFVATWSDVGLCKKRPKPG     Equus caballus
MVRSHVGGWILVLFVATWSDVGLCKKRPKPG     Diceros bicornis
MVKSLVGGWILLLFVATWSDVGLCKKRPKPG     Myotis lucifugus
MVKNYIGGWILVLFVATWSDVGLCKKRPKPG     Pteropus vampyrus
MVKSHIANWILVLFVATWSDMGFCKKRPKPG     Tursiops truncatus
MVKSHIGGWILLLFVATWSDVGLCKKRPKPG     Canis lupus familiaris
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Felis catus
MVKSHIGSWLLVLFVATWSDIGFCKKRPKPG     Mustela putorius
MVKSHIGSWLLVLFVATWSDIGFCKKRPKPG     Mustela vison
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG     Ailuropoda melanoleuca
MVKNHVGCWLLVLFVATWSEVGLCKKRPKPG     Erinaceus europaeus
MVTGHLGCWLLVLFMATWSDVGLCKKRPKPG     Sorex araneus
MVKSHLGCWIMVLFVATWSEVGLCKKRPKPG     Cyclopes didactylus
MVRSRVGCWLLLLFVATWSELGLCKKRPKPG     Dasypus novemcinctus
MVKGTVSCWLLVLVVAACSDMGLCKKRPKPG     Echinops telfairi
MVKSSLGCWILVLFVATWSDMGLCKKRPKPG     Elephas maximus
MVKSSLGCWILVLFVATWSDMGLCKKRPKPG     Loxodonta africana
MVKSSLGCWMLVLFVATWSDVGLCKKRPKPG     Procavia capensis
MMKSGLGCWILVLFVATWSDVGLCKKRPKPG     Orycteropus afer
MVKSGLGCWILVLFVATWSDVGVCKKRPKPG     Trichechus manatus
MAKIQLGYWILALFIVTWSELGLCKKPKTRPG    Macropus eugenii
MGKIHLGYWFLALFIMTWSDLTLCKKPKPRPG    Monodelphis domestica
MGKIQLGYWILVLFIVTWSDLGLCKKPKPRPG    Trichosurus vulpecular
MARLLTTCCLLALLLAACTDVALSKKGKGKPS    Gallus gallus
MAKLPGTSCLLLLLLLLGADLASCKKGKGKPG    Taeniopygia guttata
MGKHQMTCWLAIFLLLIQANVSLAKK-KPKPS    Anolis carolinensis
MRRFLVTCWIAVFLILLQTDVSLSKKGKNKPG    Gekko gekkko
MGRYRLTCWIVVLLVVMWSDVSFSKKGKGKGG    Trachemys scripta
MGRHLISCWIIVLFVAMWSDVSLAKKGKGKTG    Pelodiscus sinensis
MPQSLWTCLVLISLICTLTVSSKKSGGGKSKTG   Xenopus laevis
MLRSLWTSLVLISLVCALTVSSKKSGSGKSKTG   Xenopus topicalis