Partnerships and Genomic Management

The long-term sustainability of ungulate populations was one of the primary concerns driving the creation of the Conservation Centers for Species Survival (C2S2) in 2005. All five of the founding members of C2S2 had long histories of successfully managing ungulate breeding programs, and they believed that their large, naturalistic enclosures and social groupings gave them an advantage in promoting population growth and sustainability.

Some of the first collaborative efforts by the consortium were focused on developing and testing alternative management strategies for ungulates. C2S2 ungulate programs have evolved as we delved deeper into the science behind these management strategies. This article draws from an article authored by C2S2 personnel published in the journal Bioscience last year. Please refer to that article (Wildt, et al., 2019) for a more in-depth review of C2S2’s efforts to save ungulates.

We are all aware of the threats facing animals in their native habitats. Ungulate species are particularly vulnerable because most require large areas of land to roam, feed, and defend mating territories. The zoo community has played an increasingly important role in managing ex situ insurance populations for these threatened and endangered species. Zoo breeding programs have traditionally used pedigree data to make breeding decisions (Ballou and Lacy 1995), with a goal of maintaining 90 percent of the existing genetic diversity of the population for over 100 years (Soule et al. 1986).

This target was predicted to preserve species integrity and evolutionary potential (Lacy 2013). Frankham et al (2017) proposed that the effective size of a population of wildlife should be at least 500 animals to minimize loss of genetic variation and retain the long-term ability to adapt to environmental change. Because the effective population is usually only a small proportion of the total population, a genetically viable ex situ population might require thousands of individuals (Ballou and Traylor-Holzer 2011). Although there is some disagreement with these projections (Jamieson and Allendorf 2012), it is important to recognize that large ex situ populations of endangered species are necessary to ensure species sustainability. 

We now recognize that many of our managed programs fail to meet population sustainability goals. Of 622 Association of Zoos and Aquariums animal programs, only 44 are considered to be self-sustaining. Only 31.5 percent of AZA ungulate populations have more than 100 animals. It is difficult for these zoo-based programs to increase animal numbers due to lack of interest, limited resources, and space (Monfort and Christen 2018, Powell 2018). Changes in exhibit design to meet visitor expectations and improve animal welfare require keeping fewer animals in larger spaces. In a recent analysis of 472 AZA Species Survival Plan® programs, Powell found that we would need an additional 12,997 spaces just to bring these populations up to a minimum of 100 individuals in each program (Powell 2018).

As C2S2 developed population models for various ungulates, it became clear that even large consortia like C2S2 could not provide enough space to meet the needs of all of the priority species currently managed within C2S2 and AZA facilities. We did, however, recognize that there were facilities that could help manage large populations of ungulates in the private sector. 

There are over 5,000 private ranches in Texas alone, many with animals living in spaces far larger than C2S2 facilities and most AZA facilities. These ranches are operated for a variety of reasons and managed in different ways. Many ranch operators are interested in helping wildlife and eager to become more involved with global conservation programs including reintroductions.      

C2S2 created the Source Population Alliance (SPA) to build partnerships between traditional zoo-based conservation programs and ranchers with large ungulate herds on private land. The goal of SPA is to produce sustainable populations of rare species that are available for a variety of conservation and research programs.

Members include C2S2 breeding centers or ranches, but a small number of zoos also have joined this alliance. Herds maintained within SPA make up larger metapopulations. Initially, SPA focused on four target species, scimitar-horned oryx, addax, dama gazelle, and sable antelope.  Currently, the alliance has 35 participants managing over 1,500 animals of these target species on over 32,000 hectares. SPA is also actively evaluating potential demographic, genetic, and welfare benefits of managing ungulates in large herds.  

Population modeling exercises compared animals managed in a typical zoo setting to those managed on a ranch, with differences in carrying capacity, breeding strategies, and calf survival. In this model, zoo populations saw initial growth, but this slowed as the population reached carrying capacity. Eventually, the population began to decline due to random variation and gradual increases in the levels of inbreeding.

By comparison, results revealed that the larger SPA population would be able to maintain ~94 percent of its original genetic diversity after 100 years compared to about 88 percent in the traditional zoo population. Predictions suggested that the zoo population would maintain greater genetic diversity early in the models due to the more intensive genetic management, but after about 35 years, the larger SPA population lost genetic diversity at a slower rate (Wildt et al. 2019).

One of the concerns for working with animals managed on ranches is the lack of pedigree information. If individual animals are not permanently identified and tracked, it is virtually impossible to integrate these animals into traditional population management programs. SPA believes advances in empirical genomics can provide new tools for managing these populations. 

Specifically, we can now estimate genetic diversity, inbreeding status, lineage integrity, ancestry, and kinship of unknown populations (Gooley et al. in press).  This type of information can provide valuable input for management decisions, especially when little else is known about an individual animal’s pedigree or breeding history. To facilitate these efforts, SPA and C2S2 partners have generated genome assemblies for the sable antelope (Koepfli, et al. 2019), dama gazelle (Dobrynin et al., in preparation), and scimitar-horned oryx (Humble, et al. in press). These genomes provide a reference for mapping whole or reduced representation genome data from multiple intraspecific individuals, from which variants in the form of single-nucleotide polymorphisms (SNPs) can be identified and used to characterize genomic diversity and relatedness with great precision.

The lack of pedigree information is not limited to animals on ranches. Sable antelope are currently managed as a Yellow SSP. Only 10.3 percent of the pedigree for this species is known. Even with significant assumptions, that number only rises to 30.4 percent. As a result, we don’t know enough information to be able to calculate the gene diversity for this population (Piltz and Ferrie 2020).

A recent study of sable antelope used empirical genomic data to evaluate genetic diversity and structure of a sample from traditional zoo populations, a conservation center, and private ranches (Gooley et al. 2020). Due to more intensive genetic management, the zoo and conservation center had higher genetic diversity and lower inbreeding levels than the ranch populations. Each population showed a distinct genetic cluster, which may reflect genetic drift as a result of these populations being independently managed. However, this may also be due in part to founder effects dating back to when the populations were established.  Selection pressure caused by management in human care may have amplified genetic drift due to small effective population sizes, especially in zoos (Gooley et al. 2020).

This work also demonstrated that exchange of animals between these distinct populations can counteract the effects of genetic drift and produce offspring with more genetic diversity. This is the essence of the SPA concept. There are 116 animals in the AZA-managed population of sable antelope (Piltz and Ferrie 2020). Best estimates tell us that there are over 3,000 sable on privately owned ranches (Mungall 2018). We have found like-minded partners in the private sector with immense interest in species conservation. Through these novel partnerships, we can build a larger metapopulation from these independent herds and potentially eliminate intensive management for genetic diversity.

We can apply new genomic tools to determine the relatedness of the individual populations and guide the exchange of animals between these herds, thereby mitigating inbreeding within any one group and enhancing the genetic diversity of the ex situ population as a whole (Gooley et al. 2020). To facilitate future genetic/genomic analyses of animals in AZA facilities or private lands, all facilities should be encouraged to opportunistically collect and bank biomaterials from all animals. Samples may be stored in their respective facilities.

Where storage resources are limited or unavailable, facilities may contact SSP coordinators for further guidance. Genome resource banking has been invaluable for the conservation of a number of endangered species (Wildt, 2000) and will become more important as genomic data are further integrated into species management programs in the future.

We are facing a critical juncture for many of our programs. Without the space to support large enough populations within AZA, we will not achieve species sustainability. There are immense animal and land resources available in the private sector for ungulate programs, and perhaps for other species groups as well. C2S2 and SPA are dedicated to building these connections between traditional zoos and ranches, and providing the expertise, resources, and tools needed to manage these self-sustaining populations of ungulates. 

Citations

Ballou JD, Traylor-Holzer K. 2011. Captive populations and genetic stability.  World Association of Zoos and Aquariums Magazine 12: 19–22.

Ballou JD, Lacy RC. 1995. Identifying genetically important individuals for management of genetic diversity in pedigreed populations. Pages 76–111 in Ballou JD, Gilpin M, Foose TJ, eds. Population Management for Species Survival and Recovery. Columbia Press.

Frankham R, Ballou JD, Ralls K, Eldridge MDB, Dudash MR, Fenster CB, Lacy RC, Sunnucks. 2017. Genetic Management of Fragmented Animal and Plant Populations. Pages 41–86. Cambridge University Press.

Gooley RM, Tamazian G, Castañeda-Rico S, Murphy KR, Dobrynin P, Ferrie GM, Maldonado JE, Wildt DE, Pukazhenthi BS, Edwards CW, Koepfli KP.  2020. Comparison of genomic diversity and structure of sable antelope (Hippotragus niger) in zoos, breeding centers and private ranches in North America. Evolutionary Applications 10 April 2020. https://doi.org/10.1111/eva.12976.

Humble E, Dobrynin P, Senn H, Chuven J, Scott AF, Mohr DW, Dudchenko O, Lieberman-Aiden E, Wildt D, Pukazhenthi B, Ogden R, Koepfli KP. Chromosomal-level genome assembly of the extinct in the wild scimitar-horned oryx: insights into diversity and demography. Molecular Ecology Resources (in press).

Jamieson IG, Allendorf FW. 2012. How does the 50/500 rule apply to MVPs? Trends in Ecology and Evolution 27: 578–584.

Koepfli KP, et al. 2019.  Whole genome sequencing and re-sequencing of the sable antelope (Hippotragus niger): A resource for monitoring diversity in ex situ and in situ populations. G3: Genes, Genomes, Genetics 9:1785–1793.

Lacy RC. 2013. Achieving true sustainability of zoo populations. Zoo Biology 32: 19–26.

Long S, Dorsey C, Boyle P. 2011. Status of Association of Zoos and Aquariums cooperatively managed populations. World Association of Zoos and Aquariums Magazine 12: 15–18.

Monfort SLM, Christen CA. 2018. Sustaining wildlife populations in human care: An existential value proposition for zoos. Pages 313–319 in Minter BA, Maienschein J, Collins JP, eds. The Ark and Beyond: The Evolution of Zoo and Aquarium Conservation. The University of Chicago Press.

Mungall EC. 2018. Species numbers throughout the years. Exotic Wildlife 6: 61–62.

Piltz J, Ferrie GM. 2020. Population Analysis and Breeding and Transfer Plan: Sable Antelope (Hippotragus niger) AZA Species Survival Plan Yellow Program. AZA Population Management Center.

Powell DM. 2018. Collection planning for the next 100 years: What will we commit to save in zoos and aquariums? Zoo Biology 38: 139–148.

Soulé M, Gilpin M, Conway W, Foose T. 1986. The millennium ark: How long a voyage, how many staterooms, how many passengers? Zoo Biology 5: 101–113.

Wildt, DE. 2000. Genome Resource Banking for Wildlife Research, Management, and Conservation. ILAR Journal 41: 228–234.

Wildt, D, Miller P, Koepfli K, Pukazhenthi B, Palfrey K, Livingston G, Beetem D, Shurter S, Gregory J, Takacs M, and Snodgrass K.  2019.  Breeding Centers, Private Ranches, and Genomics for Creating Sustainable Wildlife Populations.  BioScience. 69: 928-943  https://doi.org/10.1093/biosci/biz091

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