A simulation model of the Devils Hole pupfish population using monthly length-frequency distributions

The Devils Hole pupfish, Cyprinodon diabolis, is a federally-endangered fish that is endemic to Devils Hole, a discontiguous part of Death Valley National Park in Nye County, Nevada. Due to its status, Devils Hole pupfish monitoring must be non-obtrusive and thereby exclude techniques that require handling fish. Due to a recent decline in pupfish abundance, Devils Hole pupfish managers have expressed a need for a model that describes population dynamics. This population model would be used to identify vulnerable life history stage(s) and inform management actions. We constructed a set of individual-based simulation models designed to explore effects of population processes and evaluate assumptions. We developed a baseline model, whose output best resembled both observed length-frequency data and predicted intra-annual abundance patterns. We then ran simulations with 5 % increases in egg-larval, juvenile, and adult survival rates to better understand Devils Hole pupfish life history, thereby helping identify vulnerable life history stages that should become the target of management actions. Simulation models with temporally constant adult, juvenile, and egg-larval survival rates were able to reproduce observed length-frequency distributions and predicted intra-annual population patterns. In particular, models with monthly adult and juvenile survival rates of 80 % and an egg-larval survival rate of 4.7 % replicated patterns in observed data. Population growth was most affected by 5 % increases in egg-larval survival, whereas adult and juvenile survival rates had similar but lesser effects on population growth. Outputs from the model were used to assess factors suspected of influencing Devils Hole pupfish population decline.     

Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish

The Devils Hole pupfish (Cyprinodon diabolis; DHP) is an icon of conservation biology. Isolated in a 50 m² pool (Devils Hole), DHP is one of the rarest vertebrate species known and an evolutionary anomaly, having survived in complete isolation for thousands of years. However, recent findings suggest DHP might be younger than commonly thought, potentially introduced to Devils Hole by humans in the past thousand years. As a result, the significance of DHP from an evolutionary and conservation perspective has been questioned. Here we present a high‐resolution genomic analysis of DHP and two closely related species, with the goal of thoroughly examining the temporal divergence of DHP. To this end, we inferred the evolutionary history of DHP from multiple random genomic subsets and evaluated four historical scenarios using the multispecies coalescent. Our results provide substantial information regarding the evolutionary history of DHP. Genomic patterns of secondary contact present strong evidence that DHP were isolated in Devils Hole prior to 20–10 ka and the model best supported by geological history and known mutation rates predicts DHP diverged around 60 ka, approximately the same time Devils Hole opened to the surface. We make the novel prediction that DHP colonized and have survived in Devils Hole since the cavern opened, and the two events (colonization and collapse of the cavern's roof) were caused by a common geologic event. Our results emphasize the power of evolutionary theory as a predictive framework and reaffirm DHP as an important evolutionary novelty, worthy of continued conservation and exploration.     

Dramatic shifts in the gene pool of a managed population of an endangered species may be exacerbated by high genetic load

The Devils Hole pupfish, Cyprinodon diabolis, is restricted to a small habitat in southwestern Nevada. In 1972 the species was federally listed as an endangered species. Management efforts to mitigate extinction risks have been plagued by the inability to propagate the species in aquaria—anomalous for the genus—and repeated failure of propagation attempts in large, outdoor, artificial pools designed to mimic natural conditions in Devils Hole. These difficulties indicate that the species either has niche requirements that are not adequately recreated under artificial conditions or that it harbors a relatively large genetic load of deleterious mutations that compromises propagation. We used variation at 12 microsatellite loci to evaluate the results of natural, uncontrolled hybridization involving a population of C. diabolis inhabiting an artificial pool and invaders from a nearby population of the closely related C. nevadensis. The results suggest that following invasion of the pool by three C. nevadensis individuals, the gene pool underwent a rapid shift from pure C. diabolis to one comprised mostly of C. nevadensis alleles. Alleles diagnostic for C. nevadensis increased from about 0.03 to an average of 0.76 across four diagnostic loci over the course of 8 years or less. Although we cannot exclude explanations based on adaptation to Devils Hole, genetic drift, or demographic variability, these results and various other aspects of the biology of C. diabolis are best explained by the genetic load hypothesis. The work suggest avenues for future experimental work to evaluate these possibilities directly and provide an explanation for why some previous propagation efforts designed to mitigate extinction risk have failed.     

Population dynamics of the Devils Hole pupfish

Synopsis A model is constructed to simulate fluctuations in monthly population sizes of the Devils Hole pupfish between January 1973 and August 1976. A variety of biological parameters is estimated, and adult mortality is partitioned into natural and environmentally-dependent components. The simulations capture the seasonal fluctuations in population size, and only seven predicted population sizes differ from those observed by 20% or more. The model is used to make testable predictions about the life history of this species and interactions of the parameters are discussed.     

The devil's in the details: genetic and phenotypic divergence between artificial and native populations of the endangered pupfish (Cyprinodon diabolis)

Propagation of threatened or endangered species in artificial habitats is a common strategy for reducing the probability of extinction by demographic or stochastic forces. Differential selection, founder effects and genetic drift can conspire to cause artificial populations to differ irreversibly from native populations for characters important for fitness, thereby compromising conservation efforts. Here we show that artificial propagation of the endangered Devil's Hole pupfish Cyprinodon diabolis resulted in rapid divergence for phenotypic and genetic characteristics despite attempts to replicate key characteristics of the species' native habitat when designing the artificial environments. Although differences in behavior and morphology between the native pool population and the two artificial pools may reflect phenotypic plasticity, the results underscore the need to monitor and control (to the extent possible) closely the evolutionary process when propagating native species in artificial pools for multiple generations.     

Historical and contemporary forces shape genetic variation in the Olympic mudminnow (Novumbra hubbsi), an endemic fish from Washington State,USA

Genetic data have become increasingly useful for conservation planning when data regarding population status and long-term viability is limited. The Olympic mudminnow is the only fish species endemic to Washington State, USA. The species is an increasing priority for conservation given its limited distribution and increasing habitat loss. Presently, information important for developing conservation plans including population abundance data, knowledge of population boundaries, and estimates of gene flow among populations are limited. We used microsatellite markers to assess the level of genetic variation within and among Olympic mudminnow collections from 23 sites across the species range. Genetic variation within collections ranged widely and was greatest within the Chehalis River Basin, a former glacial refugium. Analysis of population boundaries showed that each collection site represented a unique population with the exception of collections made within two large wetland and stream complexes. Genetic variation among populations appears to be strongly influenced by glacial history and the species’ life history. Populations originating from the Chehalis River glacial refugium clustered together in multiple analyses and populations from the Olympic Coast, which persisted in separate refugia and have limited capacity for dispersal, showed a high level of differentiation. Competing theories existed regarding the origins of disjunct populations in east Puget Sound and genetic data showed that these populations represent undocumented introductions rather than a glacial remnant or historic colonization from the Chehalis refugium. Data presented in this study will help fill important information gaps and advance conservation planning for this species.     

Evaluating an icon of population persistence: the Devil's Hole pupfish

The Devil''s Hole pupfish Cyprinodon diabolis has iconic status among conservation biologists because it is one of the World''s most vulnerable species. Furthermore, C. diabolis is the most widely cited example of a persistent, small, isolated vertebrate population; a chronic exception to the rule that small populations do not persist long in isolation. It is widely asserted that this species has persisted in small numbers (less than 400 adults) for 10 000–20 000 years, but this assertion has never been evaluated. Here, we analyse the time series of count data for this species, and we estimate time to coalescence from microsatellite data to evaluate this hypothesis. We conclude that mean time to extinction is approximately 360–2900 years (median 410–1800), with less than a 2.1% probability of persisting 10 000 years. Median times to coalescence varied from 217 to 2530 years, but all five approximations had wide credible intervals. Our analyses suggest that Devil''s Hole pupfish colonized this pool well after the Pleistocene Lakes receded, probably within the last few hundred to few thousand years; this could have occurred through human intervention.     

Preservation of behavior after fifteen years of isolation: comparisons of wild and captive endangered pupfish in their natural habitat

Endangered species are often maintained in captivity to serve as a safeguard in the event of an extirpation of natural populations. However, wild and captive populations can rapidly diverge in genetic and phenotypic characteristics, including behavior, when maintained in isolation and under different environmental conditions. Here, we compare two populations of the endangered Leon Springs pupfish (Cyprinodon bovinus): a captive population maintained at the Southwestern Native Aquatic Resources and Recovery Center (SNARRC) and the only remaining wild population. Wild fish in the natural Texan Diamond Y desert spring are remnants of a past reintroduction of captive SNARRC fish, which occurred in 1998. The fifteen years of isolation have led to genetic and morphologic differences between the two populations. To assess the behavioral implications of such divergence, we released previously captive C. bovinus into natural habitat and quantified behaviors under natural conditions and in semi-controlled mesocosms and then replicated these conditions with the established natural population. Both populations exhibited similar levels of reproduction, foraging, and agonistic behavior. Despite divergence in genetic and morphometric characteristics, overall behavioral patterns of C. bovinus remained consistent in similar environments. This stability suggests that captive C. bovinus could again be successful establishing in their natural habitat. It is our hope that this investigation will help focus future conservation efforts towards monitoring the persistence of reintroduced C. bovinus in addition to providing a framework for other recovery plans reintroducing captive stock into ancestral habitats.     

Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish,Cyprinodon bovinus

The Leon Springs pupfish (Cyprinodon bovinus) is an endangered species currently restricted to a single desert spring and a separate captive habitat in southwestern North America. Following establishment of the captive population from wild stock in 1976, the wild population has undergone natural population size fluctuations, intentional culling to purge genetic contamination from an invasive congener (Cyprinodon variegatus) and augmentation/replacement of wild fish from the captive stock. A severe population decline following the most recent introduction of captive fish prompted us to examine whether the captive and wild populations have differentiated during the short time they have been isolated from one another. If so, the development of divergent genetic and/or morphologic traits between populations could contribute to a diminished ability of fish from one location to thrive in the other. Examination of genomewide single nucleotide polymorphisms and morphologic variation revealed no evidence of residual C. variegatus characteristics in contemporary C. bovinus samples. However, significant genetic and morphologic differentiation was detected between the wild and captive populations, some of which might reflect local adaptation. Our results indicate that genetic and physical characteristics can diverge rapidly between isolated subdivisions of managed populations, potentially compromising the value of captive stock for future supplementation efforts. In the case of C. bovinus, our findings underscore the need to periodically inoculate the captive population with wild genetic material to help mitigate genetic, and potentially morphologic, divergence between them and also highlight the utility of parallel morphologic and genomic evaluation to inform conservation management planning.     

Evolution of population genetic structure of the British roe deer by natural and anthropogenic processes (Capreolus capreolus)

Human influence typically impacts on natural populations of conservation interest. These interactions are varied and sometimes complex, and may be negative and unintended or associated with conservation and management strategy. Understanding the details of how these interactions influence and are influenced by natural evolutionary processes is essential to the development of effective conservation strategies. In this study, we investigate a species in Britain that has experienced both negative impact through overhunting in historical times and management efforts through culls and translocations. At the same time, there are regional populations that have been less affected by human influence. We use mtDNA and nuclear microsatellite DNA markers to investigate patterns of connectivity and diversity and find multiple insular populations in Britain that probably evolved within the Holocene (when the habitat was free of ice). We identify three concurrent processes. First, surviving indigenous populations show highly provincial patterns of philopatry, maintaining and generating population structure on a small geographic scale. Second, founder populations into habitat extirpated of native populations have expanded, but remained largely insular. Third, introductions into established populations generate some admixture. We discuss the implications for the evolution of diversity of the integration of natural processes with anthropogenic influences on population size and distribution.     

Distribution,habitat and conservation status of desert pupfish (Cyprinodon macularius) in the Lower Colorado River Basin,Mexico

In order to better determine the currentstatus of desert pupfish populations (Cyprinodon macularius macularius) in the LowerColorado River Basin of Mexico, bimonthly fishsampling and habitat evaluations were carriedout from September 1996 to August 1997 in sixlocalities of Baja California and Sonora.Desert pupfish were collected using minnowseines and traps. Four sampling sites are inSonora, in shallow marginal habitats of theCiénega Santa Clara (Hunters' Camp, Outletof the Welton-Mohawk channel, El Doctor andFlor del Desierto) and two are in BajaCalifornia (Cerro Prieto and streams south ofCerro Prieto). The most abundant fish speciessampled was native desert pupfish (C.macularius, 59%) followed by sailfin molly(Poecilia latipinna, 19%), redbellytilapia (Tilapia cf. zilli, 10%) and western mosquito fish (Gambusiaaffinis, 7%). Significant temporalfluctuations in distribution and abundance ofdesert pupfish populations, as previouslyreported for these populations, was againdocumented. The main anthropogenic factorsaffecting distribution and abundance of desertpupfish populations in the Mexican portion ofthe Lower Colorado River Basin are progressivealteration of aquatic and riparian habitats, aswell as presence of exotic fishes that havecaused the displacement or elimination ofnative fish populations. Both habitat andpresence of the desert pupfish populations inthe study area are controlled by theperiodicity, quality and volume of dischargesinto the Mexican portion of the basin from theUnited States.     

Moths in fragments: insights into the biology and ecology of the Australian endangered golden sun moth Synemon plana (Lepidoptera: Castniidae) in natural temperate and exotic grassland remnants

The conservation and management of endangered species requires an adequate understanding of their biology and ecology. Although there has been an increasing appreciation in Australia of the need for greater efforts to conserve insects, there is only limited information available that can be used to underpin conservation efforts. The endangered golden sun moth, Synemon plana (Lepidoptera: Castniidae) is a flagship species endemic to natural temperate grassland in south-eastern Australia. Most populations of this species are at considerable risk from habitat loss, weed invasion and inadequate management. Despite the considerable knowledge that exists about the species biology and ecology, efforts to improve the species conservation status are hampered because there are still critical gaps in our understanding of the species’ natural history. In particular, the ecology of the larvae is not known. Our study examined the abundance, population structure and reproductive biology of the moths in a broad sample of both natural temperate and exotic grassland remnants in and near Canberra in the Australian Capital Territory (ACT) in south-eastern Australia. The results fill critical gaps in the knowledge needed to achieve effective conservation management. From our findings, it is clear that the species inhabits grasslands dominated by a mixture of native wallaby grasses (Rytidosperma spp. (formerly Austrodanthonia)) and spear grasses (Austrostipa spp.). In contrast to earlier suggestions that S. plana is entirely confined to natural temperate grassland, mature and immature life stages of the species were also present in grasslands comprised entirely of the exotic Chilean needlegrass (Nassella neesiana). Most of the S. plana populations surveyed in the ACT were characterised by low relative abundance with only very few large populations being recorded. The conservation of exotic grasslands as substitute habitat for S. plana is discussed and suggestions regarding future monitoring and research of the species are provided.     

Conservation implications of a long-term decline in body condition of the Brothers Island tuatara (Sphenodon guntheri)

Understanding the factors that drive the dynamics of remnant populations of long-lived species presents a unique challenge for conservation management. The long-lived Brothers Island tuatara Sphenodon guntheri is represented by one natural, self-sustaining population on 4-ha North Brother Island, New Zealand, and two small, translocated populations. The North Brother Island population was almost driven to extinction by extreme habitat modification and collecting in the late 19th century. Analysis of a long-term (1957–2001) dataset, following the population's recovery, reveals a significant decline in tuatara body condition over time, which is more pronounced in females. Declining body condition, coupled with very low reproductive output, may be symptomatic of a density-dependent response to elevated population size exacerbated by resource limitation. Sex-specific effects that disadvantage females could compromise this small population, particularly as it exhibits a male-biased sex ratio. We recommend removal of infrequently used structures and habitat restoration to alleviate intense resource competition. Population-level manipulation should be considered if future monitoring indicates an increasingly male-biased sex ratio and continued decline of female body condition.     

Population Dynamics of the Andean Lizard Anolis heterodermus: Fast‐slow Demographic Strategies in Fragmented Scrubland Landscapes

Habitat fragmentation and loss affect population stability and demographic processes, increasing the extinction risk of species. We studied Anolis heterodermus populations inhabiting large and small Andean scrubland patches in three fragmented landscapes in the Sabana de Bogotá (Colombia) to determine the effect of habitat fragmentation and loss on population dynamics. We used the capture‐mark‐recapture method and multistate models to estimate vital rates for each population. We estimated growth population rate and the most important processes that affect λ by elasticity analysis of vital rates. We tested the effects of habitat fragmentation and loss on vital rates of lizard populations. All six isolated populations showed a positive or an equilibrium growth rate (λ = 1), and the most important demographic process affecting λ was the growth to first reproduction. Populations from landscapes with less scrubland natural cover showed higher stasis of young adults. Populations in highly fragmented landscapes showed highest juvenile survival and growth population rates. Independent of the landscape's habitat configuration and connectivity, populations from larger scrubland patches showed low adult survivorship, but high transition rates. Populations varied from a slow strategy with low growth and delayed maturation in smaller patches to a fast strategy with high growth and early maturation in large patches. This variation was congruent with the fast‐slow continuum hypothesis and has serious implications for Andean lizard conservation and management strategies. We suggest that more stable lizard populations will be maintained if different management strategies are adopted according to patch area and habitat structure.     

Condition status of the endangered desert pupfish,Cyprinodon macularius Baird and Girard, 1853, in the Lower Colorado River Basin (Mexico)

The length‐weight relationship (LWR) was used to test differences in the fish somatic condition factor among four populations of the endangered desert pupfish, Cyprinodon macularius, from the Lower Colorado River Basin, Mexico. Bimonthly fish sampling and habitat assessments were carried out from September 1996 to August 1997 for four sites in Baja California and Sonora. Slope b of the WLR varied from 3.238 (Cerro Prieto population) to 3.613 (Welton‐Mohawk population), showing in all populations a positive allometric growth. Male b values were higher than those of females for Cerro Prieto (3.303 vs 3.071), Welton‐Mohawk (3.866 vs 3.579), and Flor del Desierto (3.357 vs 3.169) populations. The Cerro Prieto population showed the highest somatic condition (y‐intercept, a = ?11.759). Water depth and salinity were the ecological variables that better accounted for most of the variation in the somatic condition of this pupfish, with a negative and a positive effect, respectively.     

Assessment of Potential Impacts of Exotic Species on Populations of a Threatened Species, White Sands Pupfish, Cyprinodon tularosa

The potential impact of introduced species on rare taxa is of particular concern to conservation biologists. We evaluate the impacts of western mosquitofish (Gambusia affinis) and virile crayfish (Orconectes virilis) on experimental populations of a threatened species, the White Sands pupfish (Cyprinodon tularosa). Forty experimental pupfish populations were exposed to one of four treatments; (a) 1 crayfish, (b) 4 crayfish, (c) 5 adult mosquitofish and (d) control. Pupfish population size and biomass was monitored over the duration of one breeding season. A repeated measure multiple analysis of covariance revealed a significant effect of treatments on response variables (population size and biomass) (P<0.0001). Mosquitofish had a significant effect on population size and biomass (P=0.0330). The effect of one crayfish was not significant (P=0. 0683). However, 4 crayfish had a significant effect (P<0.0001) on population size. We use these data, along with information on environmental tolerances of crayfish and mosquitofish, to evaluate risks for specific pupfish populations. An erratum to this article is available at .     

Estimating the genetic diversity and spatial structure of Bulgarian Castanea sativa populations by SSRs: implications for conservation

Sweet chestnut (Castanea sativa Mill.) is a multipurpose species of great ecological and economic importance in southwest Bulgaria. Bulgarian chestnut forests are severely degraded, however, due to the intensive exploitation and bad management that have occurred over the last 2000 years. Given the urgent need to define conservation strategies to preserve the biodiversity of Bulgarian chestnut, we estimated its genetic variability. A set of eight microsatellite primers were used to analyze the genetic diversity and structure of six C. sativa populations distributed throughout the range of species in Bulgaria. Results showed a generally high level of genetic diversity but little divergence among populations. A significant, positive, within-population inbreeding coefficient (Fis) was observed in four populations. A STRUCTURE analysis revealed three genetic clusters. Using a landscape approach, significant genetic barriers among populations were found by integrating genetics with geographical distance. We hypothesize that one population is a relict from a glacial refugium; the structure of the remaining populations is probably the result of a combination of natural events and human impacts. For the purposes of conservation planning, we have identified populations that are particularly rich in diversity and private alleles that are good candidates for preservation.     

New evidence for the recent divergence of Devil's Hole pupfish and the plausibility of elevated mutation rates in endangered taxa

Sa?lam et al. recently argued that the Devil's Hole pupfish (Cyprinodon diabolis), a conservation icon with the smallest known species range, was isolated 60 kya based on a new genomic data set. If true, this would be a radically long timescale for any species to persist at population sizes <500 individuals, in contrast to conservation genetics theory. However, here we argue that their analyses and interpretation are inappropriate. They placed highly restrictive prior distributions on divergence times, which do not appropriately model the large uncertainty and result in removing nearly all uncertainty from their analyses, and chose among models by assuming that pupfishes exhibit human mutation rates. We reanalysed their data with their same methods, only using an informative prior for the plausible range of mutation rates observed across vertebrates, including an estimate of the genomewide mutation rate from a pedigree analysis of cichlid fishes. In fact, Saglam et al.'s phylogenetic data support much younger median divergence times for C. diabolis, ranging from 6.2 to 19.9 kya, overlapping with our previous phylogenetic divergence time estimates of 2.5–6.5 kya. There are many reasons to suspect an even younger age and higher mutation rate in C. diabolis, as we previously estimated, due to their high metabolism, small adult size, small population size and severe environmental stressors. In conclusion, our results highlight the need for measuring mutation rate in this fascinating species and suggest that the ages of endangered taxa present in small, isolated populations may frequently be overestimated.     

The conservation-refugium value of small and disturbed Brazilian Atlantic forest fragments for the endemic ovoviviparous cockroach Monastria biguttata (Insecta: Dictyoptera, Blaberidae, Blaberinae)

The Brazilian Atlantic forest is a biodiversity hotspot and harbors many endemic species showing peculiar and unique traits. However, it has been reduced to less than 8% of its original surface and is distributed in scattered fragments, the great majority of which are smaller than 20 hectares and very disturbed, making it worth asking about their value for conservation. In this paper we assess the refugium value of small fragments to the conservation of one of the endemics of the Atlantic forest, the ovoviviparous cockroach Monastria biguttata. Our results showed that this species was ubiquitous in large and small forest fragments, but never present in plantations or pastures. The population age structure and sex ratio were balanced in every fragment, and total population size in the smallest fragments was at least several hundreds of individuals. Colony size, sex ratio, age structure, and density per piece of dead tree trunk indicated that populations from small fragments were not unbalanced or at risk of extinction. According to the analysis of resource availability, small fragments can provide suitable habitat for this species. In this situation, even very small forest fragments have a high refugium value for some endemic insect species. Considering their number in the landscape, these fragments should be considered with more attention in strategies of biodiversity conservation.     

Characterization of microsatellite markers in a threatened species,the White Sands pupfish (Cyprinodon tularosa)

We report the characterization of nine new microsatellite markers for a threatened species, the White Sands pupfish (Cyprinodon tularosa), using an enriched library method. These markers show moderate levels of variation (two to five alleles per locus) in the two native populations of this species and reveal substantial divergence between these two populations as indicated by a high percentage of private alleles. These markers will prove very useful in the conservation management of this rare species.