George Mason scientists partner to create genetic markers for endangered species

Scientists have long recognized that both wild and captive populations of endangered species are at a high risk for loss of genetic diversity due to their rarity. With small or isolated populations, genetic diversity can be lost through stochastic or random genetic drift, or through breeding between close relatives. Therefore, proper management of captive populations is critical to ensure long-term sustainability.

The struggle, however, is how to efficiently and economically collect and analyze high-resolution genetic data that can fill the knowledge information gaps in effective breeding practices. 

Haw Chuan Lim, associate professor in George Mason University’s Department of Biology, saw an opportunity to combine the experience and knowledge of other experts in the field to develop a novel genomic tool to address this issue. 

Lim’s proposal, “Development of a novel genotyping panel for powerful and cost-effective evaluations of population structure and kinship in the critically endangered mountain bongo,” was approved for funding by the 4-VA @ Mason Advisory Board. 

Lim and his PhD student Karen Holm assembled their team — Aakrosh Ratan, assistant professor, University of Virginia; Klaus-Peter Koepfli, senior research scientist, Smithsonian-Mason School of Conservation; and Budhan Pukazhenthi, research physiologist, Smithsonian Conservation Biology Institute. 4VA funding was used to purchase the necessary supplies, reagents, and equipment, including DNA tests and probe sets. 

The team reasoned that a study conducted on one animal could provide a platform for application to other endangered species. The Eastern mountain bongo, or antelope, a critically endangered native to Kenya, was chosen as a test species. Although fewer than 140 bongos remain in the wild, there are approximately 160 bongos in U.S. zoos and several hundred more on private ranches.  As such, breeding and transfer strategies that increase genetic diversity and reduce inbreeding of captive animals are critical for the survival of the species. 

The researchers created and validated the application of a novel genetic probe-set that was used to generate data from different types of genetic markers,  such as ease of genotyping, presence throughout the genome, and high information content. 

Researchers collected four types of samples—whole blood, fecal swabs, tissues, and extracted DNA—from 39 North American conservation centers and zoos to begin the project. This resulted in a total of 207 samples from both current and historical ex situ populations (populations outside of the native ranges).  

Lim and his team evaluated the effectiveness of the probe-set in generating high-quality genetic data from different sample types and for different genetic marker types. The data obtained are now being accessed for their ability to produce accurate information on animal kinship, genetic diversity, and population structure, which will ultimately be used to guide precise captive breeding programs. 

Some preliminary data, as well as a chromosome-level genome assembly, have already been published by the National Center for Biotechnology Information and online at DNA Zoo, a conservation consortium website.  

A high-quality genome serves as an invaluable resource for species conservation because it can be used for many types of research such as those focused on detecting deleterious mutations. The results from this study will contribute to the Association of Zoos and Aquariums Species Survival Plan for the species. 

“The 4-VA@Mason funding got us started, and now we have obtained external funding to move the research even further,” said Lim.