Scientists have sequenced the first-ever draft genome of the Philippines’ highly threatened Visayan spotted deer. The genome could guide efforts to save it from extinction, reports contributor Pippo Carmona for Mongabay.
The Visayan spotted deer (Rusa alfredi) was once found across six islands in the central Philippines. But deforestation and hunting decimated its population, prompting the IUCN, the global wildlife conservation authority, to list it as endangered in 1988. By 2019, Philippine authorities had classified the species as nationally critically endangered. The last count from 2016 recorded only about 700 mature individuals, now only found on the islands of Negros and Panay.
To understand the genetic health of the species, researchers from Silliman University and the Philippine Genome Center Visayas collaborated to map its DNA.
They used a tissue sample from Abraham, a captive Visayan spotted deer that was raised and died at Silliman University’s Center for Tropical Conservation Studies (CENTROP). The sequenced genome contains 2.5 billion DNA letters and 24,531 genes. It’s the first genome that’s been sequenced for any of the Philippines’ endangered mammals.
The researchers found Abraham’s heterozygosity score, a measure of genetic differences, was just 0.17, far below the 0.3 score typical of healthy, genetically diverse wild populations. The low score indicates his parents were genetically closely related.
“Since Abraham is from a captive population, we expected to get a low heterozygosity result,” said Albert Noblezada, who runs the bioinformatics pipeline at the Philippine Genome Center Visayas. Noblezada added that decades of isolation have allowed inbreeding to quietly take hold in the captive colony.
Despite this, biologist Persie Mark Sienes at Silliman University said he wanted to see just how much genetic diversity remained in the population and whether there are individuals that carry genetic variations that could improve breeding outcomes. So he scanned the genome and identified a genetic marker that could help restore the colony’s genetic health. “We have identified a rare allele found only in one individual here, and luckily this individual is still sexually active,” he said.
Silliman University biologist Robert Guino-o said this finding was the proof they needed to revamp CENTROP’s captive breeding. “We are pursuing a genome-based breeding protocol,” Guino-o said, adding this will replace the old method based entirely on pedigree tracing.
The researchers agree that to boost overall genetic diversity, deer exchanges between CENTROP and two other captive facilities — Mari-it Wildlife and Conservation Park and Negros Forest Park — should resume. The last exchange, between CENTROP and Negros Forest Park, was in 2007.
The researchers said they hope to test mixing of individuals from captive and wild populations to close the genetic gap between the two. They plan on testing this at the 300-hectare (741-acre) Bayawan Nature Reserve on Negros, which hosts 70 deer.
Read the full story by Pippo Carmona here.
Banner image: A Visayan spotted deer at Silliman University’s Center for Tropical Conservation Studies. Image by Pippo Carmona for Mongabay.
