Investigating the Role of Conservation Genetics in the Field of Conservation using Two Case Studies: The Florida Panther, Puma concolour coryi, and The Kihansi Spray Toad, Nectophrynoides asperginis

PLEASE NOTE: The Kihansi Spray Toad section is in the process of being rewritten due to contact by individuals involved in the project. Currently, the original will stay put until I gather all the interviews and literature previously overlooked. This will take time as I apply to graduate schools, work multiple jobs, and go abroad for a while. Be patient and, for now, take that section with a grain – nay a shaker – of salt.


Conservation, until recently, has been about conserving morphological traits at the species level, and, now, is incorporating the conservation of genes. Conservation genetics is a relatively new field that studies gene dynamics at a population level with the intent to avoid species extinction. This paper investigates how conservation genetics is implemented in the field of conservation. Two case studies, the Florida panther and the Kihansi spray toad, are used to illustrate the role and importance of conservation genetics and its implications on wildlife management and species viability. Conservation genetics proved extremely useful in increasing genetic fitness and population numbers in the Florida panther, and its oversight in the captive breeding of the Kihansi spray toad may prove to be the reason for the species’ extinction. This paper concludes the role of conservation genetics in the field of conservation is vital to the proper management of endangered species, but the importance of habitat preservation should not be diminished in comparison.


Conservation genetics arose in the 1950s from the field of applied population genetics. Genetic data became increasingly important to conservation management in the mid-1900s in response to the spread of invasive carps and a desperate need for a way to analyze environmental DNA (eDNA). However, it was not until the 1970s when technological advances in molecular genetics made made species-level analysis of genetic diversity possible that conservation genetics became a field of its own. The goal of conservation genetics is to conserve genetic diversity within small populations. Species management plans now include conservation genetics to determine population viability. Assessing population viability is done using demographic and stochastic genetic models to assess whether a population can maintain itself over an agreed period of time without significant management involvement. Another modeling method is viability modeling which examines small populations and predicts their future viability based on dispersal barriers, population size, and potential gene flow. Viability modeling helps managers determine which individuals to relocate and what the male to female ratio should be in a new breeding population over a certain time period (Haig et al. 2015). Using these methods, wildlife managers are achieving more than simple numerical population goals and are instead focusing on the genetic viability of a population.

Legal protection of a species is difficult to obtain especially when taxonomic disputes are ever changing the concept of a species. The monetary cost of conservation can greatly influence whether a species is listed or not, and uncertainty of a species’ genetic status can delay a listing due to uncertainty of investment payoff. Further complications can arise when a protected species interbreeds with a non-protected species. Molecular genetic data have greatly helped in defining a species and identifying unique gene loci, settling debates about species with high mobility.

Mitochondrial DNA (mtDNA) is used to distinguish between populations. For example, testing mtDNA in preserved specimens of California condors has disproved the existence of multiple species of condors, ultimately providing wildlife managers with the option of reintroducing condors in a wider geographic range (D’Elia and Haig 2013). Combining mtDNA and nuclear DNA (nDNA) data gives a more comprehensive picture of population genetics and is used to determine breeding populations. Using both mtDNA and nDNA, researchers can screen for population-specific markers, going beyond traditional descriptions of diversity among populations and identifying specific genes potentially worthy of conservation. With time and money, migratory birds from a specific breeding population can be identified in their wintering populations. Wildlife managers can then determine if breeding populations mix with other breeding groups in their wintering habitat, helping to make better management decisions.

Florida Panther (Puma concolor coryi)

Florida panthers previously occupied a wide range in the southeastern United States, but are now restricted to the area around Big Cypress National Preserve. Fergus 1991 suggested Florida panthers are adapted to humid, wet swamps in the south, but Radetsky 1992 observed, when given the opportunity, panthers prefer higher, drier ground. Florida panther habitat has been degraded and fragmented and the species hunted so vigorously in the past that they are now found only in swamps where humans were unlikely to hunt or develop. Human activities lead to massive panther population declines and a loss of genetic variation, isolating the subspecies from outside gene flow for twenty-five generations (O’Connor 2015). In the absence of gene flow in small populations, some alleles can be eliminated and others fixated depending on the natural and sexual selections within a population. Detrimental alleles that lead to lower fitness were fixated upon in the Florida panther genome (Roelke et al. 1993). Fixation of detrimental alleles and inbreeding depression resulted in low sperm counts, malformed spermatozoa, an increase in infectious diseases, and a rise in cardiac defects (O’Brien et al. 1990, Roelke et al. 1993). Cryptorchidism, when one or both testicles does not descend, became more prevalent as population size decreased and, by the early 1990s, 80% of male Florida panthers had cryptorchidism and 94% had malformed spermatozoa (Roelke et al. 1993, Cox et al. 1978, O’Connor 2015). In order to increase the total population, genetic recovery had to become a priority.

The usual strategy in response to very low genetic variation is to establish a captive population in order to manage the genetics more intensely. However, geneticists did not believe any individuals existed in the Florida population that had enough genetic diversity to be able to begin a genetically viable captive population. There was only one haplotype of mtDNA in Florida panthers and a higher amount of band sharing in DNA fingerprints between individuals compared to other cougar populations (Hedrick 1995). The mtDNA revealed two distinct genetic stocks in the Florida population, one from the historic southeastern cougar population and the other from South American cougars. It was discovered that seven cougars of mixed inheritance from a South American population and the Florida population were released into the Everglades in 1957 and 1967. This threatened the endangered status of Florida panthers under the Hybrid Policy, which is part of the Endangered Species Act and states the protection of hybrids does not conserve a listed species and runs the risk of that species’ extinction. Indeed, hybridization has caused the extinction of many species (Allendorf et al. 2001, Levin et al. 1996). However, O’Brien and Mayr 1991 argued subspecies and populations naturally interbreed with other subspecies and populations, which is why they are not considered separate species, and the Hybrid Policy should, therefore, not apply to them. USFWS revoked the Hybrid Policy in anticipation of O’Brien and Mayr’s publication, enabling the continued protection of the Florida panther (O’Connor 2015).

The main concern for introducing new genes in a population is that even though increased gene flow would eliminate detrimental alleles from the population it would also make it harder to retain adaptive alleles. If there is too much gene flow, the subpopulation begins to resemble the source population and the subspecies is driven to genetic extinction. It was determined that Texas panthers would be introduced to the Florida populations in Big Cypress, and, using an algorithm explained in Hedrick 1995, the maximum percentage Texas genetics should influence the Florida genome to eliminate detrimental alleles while preserving adaptive alleles was 20% for the first generation and an increase of 2-4% in the following generation (Seal 1994).

Following these decisions, eight female Texas panthers were released into the Florida population and successfully bred. Cryptorchidism was absent from every male descendant of these pairings, increasing population viability and fitness (O’Connor 2015). Currently, no updated genetic report has been issued, but some geneticists expect the Florida genome to be greater than 20% Texas panther. It is unknown how this would impact future conservation of the species, but Roelke 1999 argued that all cougars in North America are members of one of six total genetic subdivisions, implying the gene flow between cougar populations should be much higher than the 20% maximum and going above this percentage would not mean genetic extinction of the subspecies.

As of 2016, in order for the Florida panthers to be delisted there must be two viable populations of at least 240 individuals where there is a 95% probability of survival for 100 years. However, there may not be enough habitat for this goal to be reached. Each male has a range of 250 square miles and each female 150 square miles. USFWS have repeatedly ignored their own panels of experts and approved development of panther habitat and ignored the highly recommended creation of a 43-square mile corridor that would allow Florida panthers to expand their range into northern Florida (O’Connor 2015). Public opinion is predicted to block any further Texas panther introduction. Only if the genetic problem regresses and populations decline to their previous numbers will the government likely take action to reintroduce more Texas panthers (O’Connor 2015). The genetic situation of the Florida panther is unknown as of 2016, but inbreeding depression appears to have been ameliorated. However, wildlife managers now struggle with policies to overcome habitat fragmentation and degradation to reach delisting goals.

Kihansi Spray Toad (Nectophrynoides asperginis)

Underestimating the necessity of genetic conservation can easily cause conservation efforts to fail. The Kihansi spray toad was discovered during an environmental assessment of the site for the Kihansi hydropower dam in Tanzania. The species had a total range of five square acres at the base of the waterfall where there existed a microhabitat created by the millions of liters of very cold spray generated every day (O’Connor 2015). These cold temperatures and enormous amounts of water were present even during the dry season which allowed the frog to evolve but is also what made the site an ideal place for a hydropower dam. The only morphologically unique aspect of the species was the absence of a tympanum and ability to detect ultrasonic noise (Arch et al. 2011). Conservation organizations mobilized to protect the species and stop construction, pointing out that going ahead with the dam would violate the environmental policies of the World Bank, which funded the project to improve the health and economic stability of Tanzania.

Conservation plans were set in place to create a captive breeding program and artificial spray system, diverting water from the dam to provide minimal habitat for the toads. The captive breeding plan allowed the World Bank to continue with the project. When the three turbines of the dam were activated, the spray volume diminished by 98% (O’Connor 2015). In a matter of weeks the toad population dropped from 20,000 to 12,000. To rescue the toads, construction of the sprinkler system and the initiation of the captive breeding program began immediately. Five hundred randomly collected individuals were used as founders to establish the captive population. Other species have avoided extinction through captive breeding programs, but breeding in captivity can rapidly lower genetic fitness and select for traits beneficial to captive rather than wild survival through unintended natural selection also known as artificial selection,  and the practice of captive breeding remains controversial in conservation management (Frankham 2008, Fischer and Lindenmayer 2000). Few cases of successful releases of captive populations without assistance exist. Figure 1 depicts the results of a study that found only 18 out of 58 released species bred successfully in the wild and only 13 became self-sustaining. Out of 110 breeding programs, 52 had no intention to reintroduce populations into the wild. Captive breeding took the focus away from the importance of maintaining the habitat and wild population.

Figure 1 (Griffiths and Pavajeau 2008). Early stage is reintroduction too recent to determine success. Future reintroduction is programs that intend to release. R = reintroduction, CB&R = captive breeding and reintroduction

In captivity, the toads initially did not reproduce and an illness wiped out most of the population so that only 70 individuals remained. Today the captive population is 6,000, but despite this large number, the genetic bottleneck caused by the reduction in population significantly reduced genetic diversity and increased the risk of low fitness and inbreeding depression in future generations (Frankham 2008). Despite the artificial spray system, the wild population continued to decrease until it went extinct. Most recorded successful reintroductions are from species with genetics from relocated wild individuals, foreshadowing failure for the Kihansi spray toad reintroduction (Griffiths and Kuzmin 2008). Other concerns existed about the program’s outcome regarding changes to the microhabitat. The microhabitat had become warmer due to reduced spray volume which had created a change in the vegetation composition, and there was doubt the frogs would be able to thrive there (O’Connor 2015). In July 2012, 2,000 Kihansi toads were released at the base of the waterfall. These toads were the 50th generation to be bred in a captive environment. The reintroduced numbers quickly diminished, and wildlife managers decided to supplement the reintroduced population with captive frogs every couple of years until the population stabilized or funding ran out. The failings of the Kihansi spray toad reintroduction and others depicted in figure 1 demonstrate captive breeding is not an effective conservation tool. In fact, there is little published literature from captive breeding and reintroduction programs that contribute to conservation (Pavajeau 2005, Griffiths and Kuzmin 2008). If captive breeding is to succeed as a conservation method, genetic monitoring of adaptive loci in captive breeding populations should become standard practice to preserve the species’ genetic viability once reintroduced to the wild (Frankham 2008).  


The future of conservation genetics will focus on metagenomics, the study of genetic material found in the environment, and has already been used to identify humans with inflammatory bowel disease using microbial genomes found in stool (Qin et al. 2010). Metagenomics will be able to determine if inbreeding depression in Florida cougars is a result of a few loci with major effects or many loci with small effects, allowing for screening of potential founders of breeding populations for both detrimental and adaptive alleles. Recent research indicates the genetic load is unevenly distributed across population founders and inbreeding depression results from a few loci with major effects, which has implications for pairing choices among captive breeding populations (Casellas et al. 2009). Metagenomics also has the potential to distinguish between natural and anthropogenic hybridization and to predict the effects of hybridization on fitness (Allendorf et al. 2001). Anthropogenic hybridization is an extreme conservation method and aims to conserve the genes of a species by interbreeding it with a close relative. This was attempted in the last Abingdon Island giant tortoise, Lonesome George. Metagenomics will further the understanding of conservation genetics and help create more efficient management plans for endangered species.

There are two conflicting schools of thought in the field of conservation. The first is that conservation should aim to protect habitats and ecosystems because they are essential to the health and continued survival of both endangered and common species. The second argues for the priority to be to conserve genetic diversity which allows species to adapt to new conditions and can lead to increased biodiversity (Frankel 1974, Erwin 1991). The two case studies discussed in this paper show a need to prioritize both. Conservation is about conserving biodiversity in the wild, and conservation genetics strives to protect biodiversity through preserving genetic diversity and the unique adaptive alleles found in species, subspecies, and populations. Conservation genetics is based on the idea that by conserving the diversity of genes, you conserve the viability of a species (Haig et al. 2015). This point is certainly clear from the Florida Panther case. Without introduction of Texas panther genes, the Florida population might have gone extinct due to inbreeding depression and low fitness. These two schools of thought should not be separated as they are both equally important to the conservation of a species. In conclusion, conservation genetics is essential to the viability of a species and is most helpful to conservation when creating management plans for isolated or endangered species, but it should not be seen as more important than habitat preservation or vice versa.

Works Cited

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Arch, Victoria S., Corinne L. Richards-Zawaki, and Albert S. Feng. (2011). “Acoustic Communication in the Kihansi Spray Toad (Nectophrynoides Asperginis): Insights from a Captive Population.” Journal of Herpetology 45.1: 45-49.

Casellas, J., Piedrafita, J., Caja, G. & Varona, L. (2009). Analysis of founder-specific inbreeding depression on birth weight in Ripollesa lambs. J. Anim. Sci. 87, 72–79.

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D’Elia, J., and S. M. Haig (2013). California Condors in the Pacific Northwest. Oregon State University Press, Corvallis, OR.

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O’Connor, M. R. (2015). Resurrection science: Conservation, de-extinction and the precarious future of wild things. New York: St. Martin’s Press.

Pavajeau, L. (2005). Captive breeding and release of amphibians. MSc dissertation. DICE, University of Kent, Canterbury.

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Roelke, M. E., J. S. Martenson, and S. J. O’Brien. (1993). The consequences of demographic reduction and genetic depletion in the endangered Florida panther. Current Biology 3:344-350

Seal, U. S. (1994). A plan for genetic restoration and management of the Florida panther (Felis concolor coryi). Report to the U.S. Fish and Wildlife Service. Conservation Breeding Specialist Group, SSC/IUCN, Apple Valley, Minnesota.

Smith, C. T., Adams, B., Bartron, M., Burnham-Curtis, M. K., Monroe, E., Olsen, J. B., . . . Wenburg, J. K. (2016). Comment on Haig et al. (): The conservation genetics juggling act: Integrating genetics and ecology, science and policy. Evolutionary Applications, 9(5), 635-637.

Thank you for reading. This was my final paper for my Genethics class. Follow my twitter to learn more about conservation biology.


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