A deer named Abraham gives up his genome to save his species

In a breeding enclosure in Dumaguete City, a captive Visayan spotted deer called Abraham yielded the DNA that became the first draft genome of his kind. What it revealed was uncomfortable: the animals bred to rescue the species have grown too closely related. Fewer than 700 mature deer remain in the wild.

For decades the answer came from paper. Studbooks, pedigrees, hand-kept records of who fathered whom — the same method zoos have used since the programme began in 1990 with twenty-one founder animals, under an agreement between the Philippine environment department and Mulhouse Zoo in France. Pedigrees work only as far back as the records go, and they say nothing about what the chromosomes actually carry.

So the CENTROP team, working with the Philippine Genome Center Visayas, sequenced Abraham. Bioinformatics director Albert Noblezada and biologists Persie Mark Sienes and Robert Guino-o assembled 2.5 billion DNA letters and annotated 24,531 genes. Then they measured heterozygosity — the simplest index of genetic variety an individual carries. Abraham scored 0.17. Below 0.3, the population is considered to be running down its reserves.

The animals saved from extinction had begun, quietly, to become copies of one another.

The same data carried better news. In one sexually active individual the team found a rare allele absent elsewhere in the captive stock — a fragment of variation that, bred deliberately rather than by chance, could widen the narrow channel the species has been swimming down.

What follows is logistics. Deer exchanges between the three Philippine facilities — CENTROP, Mari-it Wildlife and Conservation Park, Negros Forest Park — are to resume, this time matched by genome rather than by ledger. And at the 300-hectare Bayawan Nature Reserve, the team intends to test something no studbook could ever have justified: mixing captive-bred deer with wild ones, and watching what the genes do next.

The species was described in 1870 from a specimen shipped to London by Prince Alfred, Duke of Edinburgh, and for a century afterwards it was not even granted the status of a species of its own. It took until 1983 for taxonomists to concede it was distinct. On Panay, in 2009, an expedition recovered the first physical proof in more than twenty-five years that any survived in the wild at all.

Now, at last, someone knows what is inside them.