Genome map guides captive breeding for Visayan spotted deer

Scientists have created the first genetic road map for the critically endangered Visayan spotted deer. This genome could guide captive breeding efforts to save the Philippine species from extinction, reports contributor Pippo Carmona for Mongabay.

The Visayan spotted deer was once found across six islands. Deforestation and hunting have reduced its range to just Negros and Panay. A 2016 count recorded only about 700 mature individuals.

A genome from a captive deer

To assess the species' genetic health, researchers from Silliman University and the Philippine Genome Center Visayas collaborated. They sequenced the genome using a tissue sample from a captive deer named Abraham, who was raised and died at Silliman University’s Center for Tropical Conservation Studies (CENTROP). The resulting genome contains 2.5 billion DNA letters and 24,531 genes. It is the first genome sequenced for any of the Philippines’ endangered mammals.

The analysis revealed a troubling lack of genetic diversity. Abraham’s heterozygosity score, a measure of genetic differences, was just 0.17.

This low score is far below the 0.3 typical of healthy, wild populations. It indicates his parents were closely related.

“Since Abraham is from a captive population, we expected to get a low heterozygosity result,” said Albert Noblezada of the Philippine Genome Center Visayas. Noblezada explained that decades of isolation have allowed inbreeding to take hold in the captive colony.

A marker for better breeding

Despite the low overall diversity, researchers wanted to see what valuable genetic variation remained. Biologist Persie Mark Sienes at Silliman University scanned the genome and identified a rare genetic marker in one individual. “We have identified a rare allele found only in one individual here, and luckily this individual is still sexually active,” he said.

This finding provides a tangible tool for improving the captive population's genetics. Silliman University biologist Robert Guino-o called it the proof needed to revamp CENTROP’s breeding program. “We are pursuing a genome-based breeding protocol,” Guino-o said. This new method will replace the old system based solely on pedigree tracing.

Next steps for genetic rescue

The researchers agree that boosting overall diversity requires renewed cooperation between captive facilities. They recommend resuming deer exchanges between CENTROP and two other centers: Mari-it Wildlife and Conservation Park and Negros Forest Park. The last such exchange occurred in 2007.

The ultimate goal is to bridge the genetic gap between captive and wild deer. Researchers hope to test mixing individuals from both groups at the 300-hectare Bayawan Nature Reserve on Negros, which is home to 70 deer.