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 porcellus MA--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
