Care and propagation of captive pupfish from the genus Cyprinodon: insight into conservation

Burg, George C.; Johnson, Jaimie; Spataro, Savannah; O’Keefe, Amelia; Urbina, Natasha; Puentedura, Georgina; Heuton, Matt; Harris, Sean; Hillyard, Stanley D.; Breukelen, Frank van

doi:10.1007/s10641-019-00887-2

Cited by 7 publications

(4 citation statements)

References 14 publications

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“…Of these, five were associated with hypoxia, a known environmental stressor in the system, suggesting that C. diabolis could be poorly equipped to physiologically deal with the stressful hypoxic environment in Devils Hole. Indeed, previous studies have noted that C. diabolis has low fecundity [24,69], low egg viability and juvenile survivorship [29] and lays more eggs at lower temperatures (28°C) compared to the higher constant temperature of 33°C in Devils Hole [70]. At present, we cannot rule out the possibility that some of these fixed variants are potentially the result of local adaptation; distinguishing between selection and genetic drift in small populations is extremely difficult because both processes leave similar signatures in allele frequencies [71].…”

Section: Discussionmentioning

confidence: 99%

Severe inbreeding, increased mutation load and gene loss-of-function in the critically endangered Devils Hole pupfish

et al. 2022

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Small populations with limited range are often threatened by inbreeding and reduced genetic diversity, which can reduce fitness and exacerbate population decline. One of the most extreme natural examples is the Devils Hole pupfish ( Cyprinodon diabolis ), an iconic and critically endangered species with the smallest known range of any vertebrate. This species has experienced severe declines in population size over the last 30 years and suffered major bottlenecks in 2007 and 2013, when the population shrunk to 38 and 35 individuals, respectively. Here, we analysed 30 resequenced genomes of desert pupfishes from Death Valley, Ash Meadows and surrounding areas to examine the genomic consequences of small population size. We found extremely high levels of inbreeding ( F ROH = 0.34–0.81) and an increased amount of potentially deleterious genetic variation in the Devils Hole pupfish as compared to other species, including unique, fixed loss-of-function alleles and deletions in genes associated with sperm motility and hypoxia. Additionally, we successfully resequenced a formalin-fixed museum specimen from 1980 and found that the population was already highly inbred prior to recent known bottlenecks. We thus document severe inbreeding and increased mutation load in the Devils Hole pupfish and identify candidate deleterious variants to inform management of this conservation icon.

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Section: Discussionmentioning

confidence: 99%

Severe inbreeding, increased mutation load and gene loss-of-function in the critically endangered Devils Hole pupfish

et al. 2022

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“…Refuge pupfish that have been described as Cyprinado diabolis and Cyprinadon nevadensis mionectes hybrids [ 26 ] were maintained at 28 °C as described previously [ 27 ]. Pupfish were either left untreated ( n = 12) or exposed ( n = 12) to a cocktail of kanamycin (400 μg • ml − 1 ), gentamicin (35 μg • ml − 1 ), colistin (850 IU • ml − 1 ), metronidazole (215 μg • ml − 1 ), and vancomycin (45 μg • ml − 1 ) for 48 h prior to oxygen consumption measurement.…”

Section: Methodsmentioning

confidence: 99%

The gut microbiome and its potential role in paradoxical anaerobism in pupfishes of the Mojave Desert

et al. 2020

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Background: Pupfishes frequently enter paradoxical anaerobism in response to endogenously produced or exogenously supplied ethanol in a dose-dependent manner. To decipher the role of the gut microbiota in ethanolassociated paradoxical anaerobism, gut microbial communities were depleted using a cocktail of antibiotics and profiled using 16S rRNA gene sequencing. Results: Compared to the control group (n = 12), microbiota-depleted fish (n = 12) spent more time in paradoxical anaerobism. Our analysis indicated that the bacterial phyla Proteobacteria, Fusobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Patescibacteria, and Dependentiae dominated the pupfish gut, which is consistent with other fish gut microbiota. Although the gut microbial communities with and without antibiotic treatment were similarly diverse, they were distinct and the greatest contribution to the dissimilarity (27.38%) was the common fish commensal Cetobacterium. Conclusions: This study reports the first characterization of gut microbial communities of pupfish and suggests the microbiome may play a critical role in regulating metabolic strategies that are critical for survival in extremes of temperature and oxygen concentration. We speculate that Cetobacterium, a primary fermenter, also consumes ethanol through secondary fermentation via an alcohol dehydrogenase and therefore regulates the transition from paradoxical anaerobism to aerobic respiration in fish. Given the wide distribution and abundance of Cetobacterium in warm-water fishes, this process may be of broad importance, and suggests that the microbiome be carefully considered for both conservation and aquaculture.

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“…The copyright holder for this preprint this version posted August 14, 2021. ; https://doi.org/10.1101/2021.08.13.456274 doi: bioRxiv preprint Devils Hole and that putatively deleterious mutations in key genes likely hamper reproduction and population growth. Inbreeding depression often influences phenotypes such as survival, reproduction, and resistance to disease and environmental stress (Keller and Waller 2002); previous studies noted that C. diabolis has low fecundity (James 1969;Liu, R.K. 1969), low egg viability and juvenile survivorship (Deacon et al 1995), and lays more eggs at lower temperatures (28 °C) compared to the higher constant temperature of 33 °C in Devils Hole (Burg et al 2019). These results highlight the importance of investigating deletions and structural variants to more comprehensively understand deleterious variation in endangered populations.…”

Section: Degradation Of Hypoxia and Reproductive Pathways In C Diabolismentioning

confidence: 99%

Severe inbreeding and gene loss in the historical and extant population of the critically endangered Devils Hole pupfish

Tian

Turner

Martin

2021

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Small populations with limited geographic distributions are predicted to be threatened by inbreeding and lack of genetic diversity, both of which may negatively impact fitness and exacerbate population decline. One of the most extreme natural examples is the Devils Hole pupfish (Cyprinodon diabolis), an iconic and critically endangered species with the smallest known habitat range of any vertebrate. This imperiled species has experienced severe declines in population size over the last thirty years and suffered major, repeated bottlenecks in 2007 and 2013, when the population sunk to 38 and 35 individuals, respectively. Here we sequenced contemporary and historical genomes of Devils Hole and neighboring Death Valley and Ash Meadows desert pupfishes to examine the genomic consequences of small population size. We found extreme inbreeding (FROH = 0.71 - 0.82) and increased genetic load in the Devils Hole pupfish. We also document unique fixed loss-of-function (LOF) alleles and deletions in genes associated with sperm motility, stress, and hypoxia within the extant Devils Hole pupfish population that likely reduce fitness. Comparisons between contemporary samples (2008 - 2012) and a genome sequenced from a 1980 formalin-fixed museum specimen suggest that inbreeding has increased 6% as the population has declined, but that many putatively deleterious variants have been segregating in the population since at least 1980. This includes a fixed early stop codon in cfap43 (n = 8/8 samples), which is associated with sperm flagellum defects and causes infertility in humans and mice. Out of ninety-four unique deletions, fifteen were detected within 2 kb of annotated genes. Five have roles in physiological responses to hypoxia and mitochondrial activity, such as redd1 (n = 7/7 samples), suggesting impaired hypoxia tolerance in this species despite the low oxygen concentrations of Devils Hole. We thus document one of the most extreme inbreeding events in a natural population and a set of candidate deleterious variants to inform management and potential genetic rescue in this conservation icon.

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Care and propagation of captive pupfish from the genus Cyprinodon: insight into conservation

Cited by 7 publications

References 14 publications

Severe inbreeding, increased mutation load and gene loss-of-function in the critically endangered Devils Hole pupfish

Severe inbreeding, increased mutation load and gene loss-of-function in the critically endangered Devils Hole pupfish

The gut microbiome and its potential role in paradoxical anaerobism in pupfishes of the Mojave Desert

Severe inbreeding and gene loss in the historical and extant population of the critically endangered Devils Hole pupfish

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