Carbonera Pupfish

Creating a Natural Refuge Habitat for the Carbonera Pupfish Cyprinodon fontinalis

Below is a summary of our project to create a natural refuge habitat for the Carbonera pupfish, Cyprinodon fontinalis, a species endemic to a desert spring complex in Chihuahua, México. Only one native spring remains (Ojo Solo), and it is failing. This project also involved refuge population establishment of the endemic largemouth shiner Cyprinella bocagrande and the endemic Chihuahua dwarf crayfish Cambarellus chihuahuae (Hobbs 1980); the crayfish was presumed extinct until we rediscovered it. This project was funded by the Desert Fishes Council (DFC) and Pronatura Noreste, A.C. (PNE). The following text is an excerpt from our Final Report to DFC (Carson and De la Maza-Benignos 2014). Stay tuned for a more in depth treatment (manuscript to be submitted shortly for peer review).

Contributors: Evan W. Carson (UNM), Mauricio De la Maza-Benignos (PNE), Lourdes Lozano-Vilano (UANL), Lilia Vela-Valladares (PNE), and Iris Banda-Villanueva (PNE)

Drying of desert springs in Chihuahua, Mexico, is directly related to the general trend of aquifer depletion in this state, and reflective of broader declines throughout the desert southwest region of North America. The major contributors to these losses are uncontrolled groundwater exploitation and the prolonged drought; effects of these stressors are exemplified by conditions in northern Chihuahua, where resulting lowering of water tables has led directly to the extinction or extirpation of numerous endemic aquatic species (Contreras-Balderas and Lozano-Vilano, 1996).

Currently the National Water Commission (CONAGUA) recognizes 61 aquifers in the State of Chihuahua, of which around 30% exhibit signs of over-exploitation (CNA, 2010) and around 90% of ground water use in this arid to semi-arid landscape is dedicated to agricultural purposes. With increased demand for water resources and projected climate changes in the region, additional losses are expected for desert wetland habitats and the biodiversity they contain. The severity of recent effects and risk of additional loss in the region is exemplified by the plight of the Carbonera pupfish Cyprinodon fontinalis, which was known historically from 9 springs in the municipality of Villa Ahumada, Chihuahua, but now is confined to its type locality at Ojo Solo, a failing and highly modified spring in Ejido Rancho Nuevo.

The Carbonera pupfish, Cyprinodon fontinalis
Cyprinodon fontinalis (Smith and Miller 1980) was described from Ojo de Carbonera and four surrounding springs in the area of Ejido Rancho Nuevo in the Desierto de Samalayuca basin, Chihuahua, México (Figure 1). These populations represented relicts from Pluvial times when Lake Palomas inundated the basin (Smith 1981). Across these five (known) populations, a cline in morphological variation was observed (Figure 1). Populations at Ojo Solo (north) and Ojo del Apache (southwest) were represented the extremes of this morphological continuum, as well as the geographical extremes of the distribution of C. fontinalis. The intervening populations at Ojo de Carbonera (type locality), Ojo de las Varas, and Ojo el Medio formed a cluster of morphological intermediates. Smith and Miller first visited these sites in 1978, and by then all habitats except Ojo de Carbonera were highly modified and impounded. Smith and Miller (1980) suggested that the species had declined prior to their study because habitats were already altered substantially and the species was most abundant in Ojo Carbonera, the least modified spring in the system. In 1996, C. fontinalis was listed as endangered (IUCN Red List).

Figure 1


Figure 2

Ojo Solo- failing spring, last remaining population of C. fontinalis
During surveys to determine the status of the pupfishes of Chihuahua, México, we visited Ejido Rancho Nuevo in September 2012. Of the eight or nine springs that once contained C. fontinalis, all were dry except Ojo Solo, and this spring was failing (Figures 2 and 3). The pupfish, however, remained relatively abundant in this declining spring, as did the co-endemic cyprinid Cyprinella (Notropis) bocagrande (Figures 2 and 3), known only from Ojo Solo (Chernoff and Miller 1982), and the crayfish Cambarellus chihuahuae (Hobbs 1980; Figures 2 and 3), which was presumed extinct prior to our survey.

Figure 3


Phase I- Feasibility study
To prevent extinction of this C. fontinalis and associated species, some of which are also locally endemic, this project sought to establish a permanent refuge habitat within the basin in which this pupfish is endemic. Results from the first phase of this project were based on hydrological and geomorphological surveys of the native site at Ojo Solo and and Ojos Calientes.  Ojos Calientes lies within the same basin as Ojo Solo and was deemed most likely to be suitable for refuge creation and long-term management.

The study required two field excursions. First, a general prospection of the area was conducted, with emphasis on the main geological-geomorphological structures that control surface runoff, influences on topographic relief and determine the gravitational movement of groundwater were identified. Water from Ojos Calientes was also sampled for physicochemical analysis. The second visit focused on collection of soil and rock samples from the relevant topographic reliefs and determination of local hydrological elements. Water from Ojo Solo was also sampled for physicochemical analysis. Comparison of water physicochemistry at Ojos Calientes and Ojo Solo was conducted to determine environmental similarity of water conditions of these systems.

Laboratory analyses of water from both springs indicated local meteoric water origin. The surface water of Ojos Calientes was determined to emerge as a result of heating underground, whereas surface emergence of water at Ojo Solo results from infiltration at the cutting of the surface below the water table. Spring-flow at Ojo Solo was originally high due to the presence of shallow clay packets in the subsurface but has declined due to depletion of the water table and direct alteration of the system for agricultural purposes. Although these systems have different origins within the basin, water chemistry and habitat characteristics are highly similar. Both springs are located over relatively young trace faults that affect the alluvium, define the landforms of the area of study, control surface-water flows, and define the endorheic basin. The proposed refuge site is downstream of the headspring and has a temperature profile comparable to that of Ojo Solo; the headspring at Ojos Calientes emerges at approximately 50 °C.

Conclusions, Phase I
The study concluded that the marsh area adjacent to and downstream of Ojos Calientes is geohydrologically suitable for construction of a permanent refuge for C. fontinalis. This system is also ideal as it is located within the same basin as Ojo Solo. Therefore, placement of a refuge habitat in the Ojos Calientes system will maintain C. fontinalis in a system that is within the general native-range of the species.

The critical finding of the feasibility study is that Ojos Calientes, the preferred site of a refuge habitat, is a system that is resilient to prolonged drought, such that a permanent refuge can be established with high probability of long-term persistence. Specifically, the geohydrologic conceptual model for Ojos Calientes (regardless of the source of heat which gives rise to the spring-flow), indicated that the system has been functioning as a convection cell for a long time, such that the site is sufficient to develop permanent conduits to connect water flows from the depths of the system to the surface, as is necessary for refuge habitat creation and sustainability.

The aquifer beneath Ojos Calientes surrounds the spring system and is partially contained by predominantly clay material that lies over sandy lenses; this allows the convection cell of the Ojos Calientes to function with stability and will facilitate creation of a resilient and self sustaining refuge habitat for C. fontinalis. Importantly, the topographic (altitudinal) difference between Ojos Calientes and the proposed refuge site (a marsh located to the east with respect to the surrounding Ojo del Diablo Lake) is more than 10 m, which is higher than the level subject to 1000-year floods. This increases confidence that a refuge habitat placed in the Ojos Calientes system will be largely protected against high-intensity precipitation events that could otherwise damage or destroy the site and associated marsh and stream systems that would contain the refuge population of C. fontinalis. This combined evidence therefore indicates that the Ojos Calientes system would provide i) a stable site for a refuge habitat; ii) a habitat with an aquatic physicochemical profile that is sufficiently similar to that of the type locality at Ojo Solo; and iii) a protected site within the historical range of C. fontinalis.

Phase II- Refuge establishment
Following our visit to Ojo Solo in September 2012, we returned in October 2012 and identified tentatively Ojos Calientes (Figures 1 and 4) as a possible site for the refuge habitat;), Ojos Calientes is located on land owned by Ejido Villa Ahumada y Anexos and lies in the native basin of this critically endangered pupfish. Subsequent results from the feasibility study (Phase I) indicated that this site was suitable for a permanent refuge habitat for Cyprinodon fontinalis (Figures 2 and 3). This site was also deemed suitable for the co-endemic largemouth shiner Cyprinella bocagrande (Figures 2 and 3) and co-endemic Chihuahua dwarf crayfish Cambarellus chihuahua (Figures 2 and 3); the crayfish was considered extinct prior to our rediscovery of the species during our September 2012 visit to Ojo Solo (species ID confirmed from morphological assessment by Dr. Carlos Pedraza, a crayfish specialist at UNAM). In May 2013 we began the legal process for development of an MOU and also obtained permits for habitat construction and collection of species. The results indicated that this site would be suitable because it was i) stable; ii) already modified; iii) similar to Ojo Solo in its physiochemical conditions; and iv) devoid of endemic and native fishes. During this period, we also conducted education outreach workshops with landowners and municipal leaders, including representatives from Rancho Nuevo (owners of Ojo Solo) Ejido Villa Ahumada y Anexos (owners of Ojos Calientes), and the municipality of Villa Ahumada. Through this engagement, our negotiations with the supportive landowner community of Ejido Villa Ahumada y Anexos and local government, we signed an MOU in September 2013 to establish a refuge at Ojos Calientes (Figures 5), under the support of Ejido Rancho Nuevo for agreement to fish transfer. Site surveys (Figure 6) and refuge construction (Figure 7) were completed between early and middle October 2013, and a cattle-exclusion fence was added in early November (Figure 7). The refuge habitat encompasses ~300 m2, and it includes the variety of habitats documented for C. fontinalis (Smith and Miller 1980), as well as ones reported for Cyprinella bocagrande (Chernoff and Miller 1982) and for Cambarellus chihuahuae (Hobbs 1980). Following construction, the refuge system gradually re-filled to form a variety of habitats, including i) sparsely vegetated, shallow shelves and pools (<10 cm); ii) open waters of greater depth (0.5-1.0 m); and iii) inflow channels and undercut banks.

Figure 4

Figure 5Figure 6


Figure 7


Transfer of pupfish and associated endemic species
The system was allowed to recover and stabilize from October 2013 until 6-8 February 2014, when we revisited the failing Ojo Solo (Figure 8) and the refuge habitat Ojos Calientes (Figure 9) for the transfer of and collection of genetic material from endemic species. On 6 February we  assessed conditions at Ojo Solo and at Ojos Calientes, and we returned 7-8 February to collect target species at Ojo Solo and transfer them to Ojos Calientes for establishment of refuge populations. Over these two days, we collected 955 Cyprinodon fontinalis, 224 Cambarellus chihuahua, and 15 Cyprinella bocagrande for transfer to the refuge site at Ojos Calientes. Fish and crayfish were captured at Ojo Solo (Figure 8), transferred to tanks that contained spring water of appropriate temperature; water was aerated constantly and also treated with standard solutions for reduction of stress in aquarium species. We then transferred a total of 835 C. fontinalis to the refuge site (Figure 9). During this transfer, we collected genetic samples (50 mortalities, preserved whole in 95% EtOH) to establish a baseline of genetic variation and effective population size for long-term genetic monitoring of the refuge and Ojo Solo populations. Genetic analysis of these specimens are underway and include surveys of mitochondrial (mt)DNA and microsatellite DNA variation.

During this trip, we also collected and transferred 214 endemic dwarf crayfish Cambarellus chihuahuae and 13 endemic Cyprinella bocagrande (Figure 9). Future activities also will include long-term genetic, habitat, and population monitoring of each species at each site, and we will continue development of our education outreach program to teach the local community members and students about importance of biodiversity, conservation, and sustainable development. In collaboration with Pronatura Noreste A. C., a Vital Signs Monitoring Program is in development for the native site (Ojo Solo) and the refuge site (Ojos Calientes); for a comparable example, see De la Maza-Benignos et al. (2012).

Figure 8Figure 9

We thank the landowners of Ejido Villa Ahumada y Anexos for their invaluable partnership, the municipality of Villa Ahumada for machinery and equipment, and Ejido Rancho Nuevo for access to and assistance at Ojo Solo. For the feasibility study, site survey, and construction advisement, we also thank Dr. Ignacio Reyes and Ing. René Carrasco (professor of topography) and their team of students in the Facultad de Ingeniería de la Universidad Autonóma de Chihuahua. The award of a Desert Fishes Council Conservation Grant and matching funding from Pronatura Noreste, A.C., made this project possible.

Carson, E. W., R. R. Beasley, K. L. Jones, S. L. Lance, M. de L. Lozano-Vilano, L. Vela-Valladares, I. Banda-Villanueva, T. F. Turner, and M. De la Maza-Benignos. 2013. Development of polymorphic microsatellite markers for the microendemic pupfishes Cyprinodon julimes and C. pachycephalus. Conservation Genetics Resources 5:853-856.

Carson, E. W., M. De la Maza-Benignos, Ma. de L. Lozano-Vilano, L. Vela-Valladares, I. Banda-Villanueva, and T. F. Turner. 2014. Conservation genetic assessment of the critically endangered Julimes pupfish, Cyprinodon julimes. Conservation Genetics 15:483-488. DOI:10.1007/s10592-013-0548-x.

Chernoff, B., and R. R. Miller. 1982. Notropis bocagrande, a new cyprinid fish from Chihuahua, Mexico, with comments on Notropis formosus. Copeia 1982:514-522.

De la Maza-Benignos M., J. A. Rodriguez-Pineda, A. De la Mora-Covarrubias, E. W. Carson, M. Quiñones-Martínez, P. Lavín-Murcio, L. Vela-Valladares, Ma de L. Lozano-Vilano, H. Parra-Gallo, A. Macías-Duarte, T. Lebgue-Keleng, E. Pando-Pando, M. Pando-Pando, M. Andazola-González, A. Anchondo-Najera, G. Quintana-Martínez, J. Zapata-López, I. A. Banda-Villanueva, H. J. Ibarrola-Reyes. 2012. “Planes de Manejo y Programa de Monitoreo de Signos Vitales para las Áreas de Manantiales de la UMA El Pandeño; y San Diego de Alcalá en el Desierto Chihuahuense” (Management plans and monitoring program of “vital signs” of the spring areas of UMA-El Padeño and San Diego de Alcalá in the Chihuahuan Desert). Vol 1. Pronatura Noreste, A. C. (Editor). Amigos del Pandeño, A. C. 162 pp.

Hobbs Jr, H. H. 1980. New dwarf crayfishes (Decapoda: Cambaridae) from Mexico and Florida. Proc. Biol. Soc. Wash 93:194-207.

Smith G. R. 1981. Effects of habitat size on species richness and adult body sizes of desert fishes. In: Naiman RJ , and D. L. Soltz (eds) Fishes in North American deserts. Wiley, New York, pp125-172.

Smith, M. L., and R. R. Miller. 1980. Systematics and variation of a new cyprinodontid fish, Cyprinodon fontinalis, from Chihuahua, Mexico. Proc. Biol. Soc. Wash, 93:405-416. 

website security

4 Responses to Carbonera Pupfish

  1. Michael says:

    Hello Evan,

    is there an update on the project? I keep, since 2011, the population Ojo del Apache.


    • evanwcarson says:

      Hi, Michael. I would like to hear more about the fish you have from Ojo del Apache. I have heard that some fish from that spring might still survive in captivity in Europe.

      I will have an update to to the Carbonera pupfish page soon- probably in a few weeks. Thanks for your interest.


      • Chris says:

        Greetings, Evan! Great website and keep up the great conservation work!

        I wanted to chime in that our Cyprinodon Species Maintenance Group in the US also has captive colonies of both the Carbonera and Ojo del Apache populations. They are inbred, but still hanging on. It would be great to re-introduce these to the wild and we would happily support your efforts. Please let me know if you would like tissue samples/live animals.

        Chris Martin

        • evanwcarson says:

          Thanks, Chris! Much appreciated. We’re very excited- and hopeful- about the work we are doing to conserve these spectacular fish.

          Unfortunately, reintroduction of the captive C. fontinalis to the wild is a tall order at this point. Of the native springs, only Ojo Solo remains, and it is failing. The site where we created the refuge for the Ojo Solo population also is problematic for other introductions because the area is small and connectivity among springs is high, among other reasons. Its a real shame. As I’m sure you are aware, the Carbonera and Apache populations more or less fill out the range of morphological diversity of the species, at least as has thus far been described.

          I definitely would like to chat with you more about Carbonera pupfish and the Cyprinodon Species Maintenance Group in the US. Let me know if you’re interested. Please feel free to email me at


Leave a Reply