This breakthrough is expected to boost local conservation efforts
There used to be a time when the primarily nocturnal Visayan spotted deer (Rusa alfredi) could be found in large numbers across inland areas of the Visayas. Considered one of the most beautiful deer in the world, it is now among the most endangered. A mix of indiscriminate hunting and habitat destruction has reduced the deer population to just a few hundred in the rainforests of Panay and Negros.
One of the important barriers for local scientists to successfully revitalize the Visayan spotted deer population is just how little we know about it in the first place. Despite its cultural prominence, most of our knowledge about R. alfredi was limited to its physical traits and its role in the local ecosystem.
Realizing this, a team led by scientists Carmel Javier, Albert Noblezada, and Dr. Victor Marco Emmanuel Ferriols from the ĚěĂŔĘÓƵ—Philippine Genome Center (UP-PGC) Visayas lent their expertise to conservation efforts on R. alfredi at Silliman University (SU). Specifically, the team mapped the first-ever draft genome of the Visayan spotted deer.
The genome of the Visayan spotted deer is the first endangered endemic species to be sequenced and assembled exclusively in the country. It marks a foundational step in Philippine conservation genetics and promises to play a pivotal role in efforts to revitalize the local deer population.
The trio was joined in the project by Silliman University’s Persie Mark Q. Sienes, Dr. Robert S. Guino-o, and Dr. Nadia Palomar; as well as Dr. Maria Celia Malay of the UP Marine Science Institute (UP-MSI) and Dr. Carmelo del Castillo of UPV’s National Institute of Molecular Biology and Biotechnology.
While the project does indeed, to quote Ferriols, highlight the capabilities of our local genomics experts, it must be asked: how exactly does one go from a reconstruction of an endangered deer’s genome to the all too real demands of breeding and conservation?
Desirable Traits
Having a large-scale reference genome of endangered species affords conservationists several advantages. An organism’s genome is the complete set of all DNA instructions found in a cell. It contains all the information necessary for that organism to function, including genes, which code for proteins and RNA, some areas that regulate these genes, as well as areas that have no apparent function.
Having this in their toolkit, scientists can identify an animal’s important genetic traits, track evolutionary changes, and guide breeding programs with data that maximize any desirable traits. For the Visayan spotted deer, which has a captive breeding program initiated in Negros by SU, such information could be a literal lifesaver. However, previously, there was no such information available for the Visayan spotted deer nor its genus, Rusa.
To address this, the team ethically collected a tissue sample from the ear of a male deer named Abraham that was part of SU’s Center for Tropical Conservation Studies (CENTROP) captive population in Negros Oriental. From that sample, the team used a technology called short-read sequencing from Illumina that generates a large amount of raw DNA sequence data in the form of short DNA fragments or reads.
The team then used bioinformatics tools to assemble these short DNA fragments into a draft genome for the species, which measured around 2.5 gigabases (similar to other cervid or deer species) with a high degree of accuracy. The team used the genome from the closely related genus Cervus, the red deer (C. elaphus) as a reference in the assembly.
The Visayan spotted deer’s genome was found to be quite similar compositionally to species like the sika deer. This was because the draft genome was around 44% composed of “repetitive sequences” or segments of DNA that repeat multiple times in the genome. The team was able to annotate a total of 24,531 genes.
The team also found a very low level of genetic diversity in the assembled genome. This “low heterozygosity” happens when an individual or group carries the same variant of particular genes. It can be common in captive populations where inbreeding or population bottlenecks can drastically reduce diversity in small, isolated groups of animals.
Finally, by reconstructing the Visayan spotted deer’s mitochondrial DNA as well, the team confirmed that it is indeed closely related to other deer in the genus Cervus and its genus Rusa, though more genetic evidence is needed from more specimens and other Rusa species to better explain its evolutionary history and distinctiveness.
To Save a Dwindling Population
In a media release, Persie Mark Sienes from SU’s Biology Department said that the release of R. alfredi’s reference genome can help in the production of species-specific genetic markers. These, in turn, can inform studies on its genetic diversity as well as help assess the level of inbreeding in captive populations.
Currently, SU CENTROP has the largest captive population of Visayan spotted deer in the world. The Center has been breeding them for three decades, intending to release these offspring back into the wild to replenish the deer’s dwindling population. According to Sienes, the genome can help improve current breeding efforts, as well as help mitigate the negative effects of breeding animals with a small population size. With the UP-PGC Visayas’ help, he says, “the first breeding intervention using the Visayan’s Spotted Deer’s genome is now possible”.
Carmel Javier who, with Albert Noblezada, led the sequencing charge from UP-PGC Visayas, echoed these sentiments and expressed her wish that their research would open doors to new, exciting scientific collaborations that help save our native wildlife.
“The value of genomic studies may not be so obvious, or not yet fully recognized in the Philippines,” she said, “however, sequencing the genome of the Visayan Spotted Deer opens more opportunities for research and collaboration to safeguard species conservation and preservation.” These intentions were reiterated by her home institution, which affirmed the UP-PGC’s Visayas’ willingness to partner with organizations nationwide for knowledge sharing, capacity building, or conservation-focused projects on the country’s rich flora and fauna.
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