Thursday, March 28, 2013

[Primatology • 2012] A Genome Sequence Resource for the Aye-Aye Daubentonia madagascariensis, a Nocturnal Lemur from Madagascar


Aye-aye Daubentonia madagascariensis species distribution in Madagascar and extractive foraging behavior
photo: Francois Randrianasolo

Aye ayes have the largest brain to body ratio, making them the smartest lemurs. Humans often kill them on sight because the animals are considered a bad omen.
photo: Edward Louis 

Abstract
We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ;3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ;2.6 million scaffolds (N50 scaffold size 5 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ;10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage—a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye’s extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar’s forests.

Key words: genome assembly, molecular clock, primate evolution, lemur.

Aye-aye Daubentonia madagascariensis species distribution in Madagascar and extractive foraging behavior
photo: Francois Randrianasolo

An aye aye, a type of lemur, lives in Madagascar. A new study highlights genetic diversity among various populations, aiding conservation of the endangered species.
photo: Edward Louis




George H. Perry, Darryl Reeves, Pa´ll Melsted, Aakrosh Ratan, Webb Miller, Katelyn Michelini,
Edward E. Louis Jr, Jonathan K. Pritchard, Christopher E. Mason, and Yoav Gilad1. 2012. A Genome Sequence Resource for the Aye-Aye (Daubentonia madagascariensis), a Nocturnal Lemur from Madagascar. Genome Biology and Evolution. 4 (2): 126-135. doi: 10.1093/gbe/evr132

Aye aye! Sequence genomes to save species

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