Data from: Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant subfossil koala lemur Megaladapis edwardsi

No endemic Madagascar animal with body mass >10 kg survived a
relatively recent wave of extinction on the island. From morphological and
isotopic analyses of skeletal ‘subfossil’ remains we can reconstruct some
of the biology and behavioral ecology of giant lemurs (primates; up to
~160 kg), elephant birds (up to ~860 kg), and other extraordinary Malagasy
megafauna that survived well into the past millennium. Yet much about the
evolutionary biology of these now extinct species remains unknown, along
with persistent phylogenetic uncertainty in some cases. Thankfully,
despite the challenges of DNA preservation in tropical and sub-tropical
environments, technical advances have enabled the recovery of ancient DNA
from some Malagasy subfossil specimens. Here we present a nuclear genome
sequence (~2X coverage) for one of the largest extinct lemurs, the koala
lemur Megaladapis edwardsi (~85kg). To support the testing of key
phylogenetic and evolutionary hypotheses we also generated new
high-coverage complete nuclear genomes for two extant lemur species,
Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences
with previously published genomes for three other extant lemur species and
47 non-lemur vertebrates. Our phylogenetic results confirm that
Megaladapis is most closely related to the extant Lemuridae (typified in
our analysis by E. rufifrons) to the exclusion of L. mustelinus, which
contradicts morphology-based phylogenies. Our evolutionary analyses
identified significant convergent evolution between M. edwardsi and extant
folivorous primates (colobine monkeys) and ungulate herbivores (horses) in
genes encoding protein products that function in the biodegradation of
plant toxins and nutrient absorption. These results suggest that koala
lemurs were highly adapted to a leaf-based diet, which may also explain
their convergent craniodental morphology with the small-bodied folivore
Lepilemur.