Mammoth Genome Analysis Points to Pre-Extinction Genome Declines
NEW YORK (GenomeWeb) – An analysis of available ancient genome sequences suggests that the genus of the woolly mammoth, Mammuthus primigenius, began to take even more potentially harmful mutations as populations declined and species was approaching extinction – a discovery Which could have implications for the recognition of endangered species and implement appropriate conservation measures.
“There is a long history of theoretical work on how genomes of small populations could change,” said Rebekah Rogers, an integrative biology researcher at the University of California, Berkeley, in a statement. “Here we had a unique opportunity to see snapshots of ‘before’ and ‘after’ genomes of a population decline in a single species.” Rogers and co-author Montgomery Slatkin, also based at UC Berkeley, analysed the available genomic sequences of a mammalian sample from a 45,000-year-old, continental Siberian, which represents a time when the mammoth population remains robust. The researchers compared these sequences to those of a mammoth 4,300 years old from a small population on the island of Wrangel, which suffered an increase after the disappearance of the continental population. The mammoth is estimated to be missing for 3700 years.
Compared to the old genome sequences of mammoth and elephant available, the team saw a jump in deletions and retrogenes alter genes in the mammalian genome of Wrangel Island, and new point mutations predicted to pass protein function. The apparent “genomic fusion” in the island’s population declined including pseudogenes olfactory genes, and loss of gene-encoding proteins related to elephant urinary choice and mutations in genes involved in the characteristics of the mammoth layer noted researchers.
“These data carry the signature of a genomic fusion in small populations, in line with the evolution of the almost neutral genome,” wrote Rogers and Slatkin in his PLoS Genetics document. “They also suggest a number of noxious variants that elevate pre-extinction genomes, a warning to ongoing efforts to protect endangered species with small sizes of existing populations.”
For the new study, the pair proposed to characterise genetic variations, deletions, and point mutations using existing genomic sequence data for Oimyakon mammoth and mammoth Wrangel sequenced at an average depth of 11 times and 17 at both the Swedish Museum of Natural History Amor Dalen and colleagues for a 2015 study in current biology.
When we compared these sequences with sequences of an Indian elephant and an African elephant shrub reference genome, the researchers found significant differences between the two genomes of the woolly mammoth. The mammalian genome Island Wrangel contained complete deletions, deletions of genes, retrogene content and stop coding causing point mutations compared to the mammal genome Oimyakon, for example.