The experts say that in the first organisms to benefit from guts, food went through one way of the mouth, and waste the other.
However, according to them, one hole for everything became impractical when the organisms grew in size and length.
"A long gut makes sorting food and waste through a single opening inefficient. So they needed to evolve an anus," Nature magazine quoted Andreas Hejnol, a researcher at the University of Hawaii in Honolulu and one of the study's authors, as saying.
Detlev Arendt, a researcher at the European Molecular Biology Laboratory in Heidelberg, Germany, added: "The very simple question is how to get from one opening to two."
He says that punching a new hole on the opposite end from the mouth is unlikely from the evolutionary standpoint.
He believes that the mouth elongated over time, and separated into a mouth and anus.
The researcher says that once the body included a gut with two ends, the anus could migrate to the far end of animal.
Hejnol and his co-author Mark Martindale, also at the University of Hawaii, think otherwise.
They compared the patterns of gene expression during development at each end of Convolutriloba longifissura, a simple flatworm with a cul-de-sac for a gut, to those seen in more complex worms that have a mouth and an anus.
C. longifissura and the other worms expressed the same genes while building their mouths, but perhaps some genes that are expressed in the hindguts of several other species are also expressed at their posterior ends, rather than in the mouth.
The findings suggest that the anus did not develop from the mouth, but may instead have evolved in a different way.
Another way for nature to make an anus, Hejnol says, is from reproductive tissue.
The researcher says that the anuses of some of the more complex worms contain a gene that is also expressed in the reproductive tract of C. longifissura, which suggests that the reproductive tract may have evolved first and then joined with the gut.
According to Hejnol, more-complex organisms like birds, reptiles, and amphibians share a single opening for all their non-eating business, and this work may point to its origin.
Arendt, however, disagrees and points out that C. longifissura are fast-evolving creatures.
He insists that what is now a reproductive tract may have started out as an anus, rather than the other way around.
He would like to see a follow-up study of slower-evolving creatures before he will be won over.
"I'm not convinced at all. The issue remains open," he said.