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

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.

Most natural-forming calcites precipitate at isotopic equilibrium

Based on thermodynamic equilibrium isotope fractionation theory, this letter reasonably understands the clumping 13C-18O (Δ47 ), as well as carbon and oxygen isotope fractionation in calcites with extremely slow-growing rates from Devils Hole and Laghetto Basso (Corchia Cave) at atomic level with solid physical precipitation models and quantum-mechanical backgrounds. It is found that most calcites in nature precipitate in at equilibrium.

‘An exceedingly simple, little ecosystem’: Devils Hole, endangered species conservation, and scientific environments

This article explores the history of the Devils Hole pupfish ( Cyprinodon diabolis ), regarded by scientists as having the smallest range of any vertebrate species in the world, a single 10 × 60 ft pool in the Amargosa Valley of southern Nye County, Nevada, USA. It considers the impact of ‘scientific environments’ on the possibilities for pupfish survival as well as potential human uses of the desert. Scientific environment is defined as the knowledge and conceptualization of the environment produced from particular questions and methods and that influence how a species, habitat or region is managed. Three successive scientific environments have shaped the conservation of the pupfish since the 1890s: the first led by taxonomic analyses of the pupfish, the second by ecological and hydrological investigations of Devils Hole, as well as its surrounding desert, and the third by genetic analysis of pupfish DNA. The science in each era has shaped (and responded to) the way in which federal and state agencies have worked to conserve this critically endangered species. The article contributes to an understanding of how concepts and practices at the heart of ecological sciences develop from, and impact, particular spaces and species.

Novel method for determining 234U-238U ages of Devils Hole 2 cave calcite (Nevada)

<p>Uranium-uranium (<sup>234</sup>U-<sup>238</sup>U) disequilibrium dating can determine the age of secondary carbonates over greater time intervals than the well-established <sup>230</sup>Th-<sup>234</sup>U dating method. Yet it is rarely applied due to unknowns in the initial d<sup>234</sup>U (d<sup>234</sup>U<sub>i</sub>) value, which result in significant age uncertainties. In order to understand the d<sup>234</sup>U<sub>i</sub> in Devils Hole 2 cave, Nevada, we have determined 110 d<sup>234</sup>U<sub>i</sub> values from phreatic calcite using <sup>230</sup>Th-<sup>234</sup>U disequilibrium dating. The sampled calcite was deposited in Devils Hole 2 between 4 and 590 ka, providing a long-term look at d<sup>234</sup>U<sub>i</sub> variability over time. We then performed multi-linear regression among the d<sup>234</sup>U<sub>i</sub> values and correlative d<sup>18</sup>O and d<sup>13</sup>C values. The regression can be used to estimate the d<sup>234</sup>U<sub>i</sub> value of Devils Hole calcite based upon its measured d<sup>18</sup>O and d<sup>13</sup>C values. Using this approach and the measured present-day d<sup>234</sup>U values of Devils Hole 2 calcite, we calculated 110 independent <sup>234</sup>U-<sup>238</sup>U ages. In addition, we used newly measured d<sup>18</sup>O, d<sup>13</sup>C, and present-day d<sup>234</sup>U values to calculate 10 <sup>234</sup>U-<sup>238</sup>U ages that range between 676 and 731 ka, thus allowing us to extend the Devils Hole chronology beyond the <sup>230</sup>Th-<sup>234</sup>U-dated chronology while maintaining an age precision of ~2 %. Our results indicate that calcite deposition at Devils Hole 2 cave began no later than 736 ± 11 kyr ago. The novel method presented here may be applied to future speleothem studies in similar hydrogeological settings, given appropriate calibration studies.</p>

Novel method for determining ²³⁴U–²³⁸U ages of Devils Hole 2 cave calcite (Nevada)

Uranium–uranium (234U–238U) disequilibrium dating can determine the age of secondary carbonates over greater time intervals than the well-established 230Th–234U dating method. Yet it is rarely applied due to unknowns in the initial δ234U (δ234Ui) value, which result in significant age uncertainties. In order to understand the δ234Ui in Devils Hole 2 cave, Nevada, we have determined 110 δ234Ui values from phreatic calcite using 230Th–234U disequilibrium dating. The sampled calcite was deposited in Devils Hole 2 between 4 and 590 ka, providing a long-term look at δ234Ui variability over time. We then performed multi-linear regression among the δ234Ui values and correlative δ18O and δ13C values. The regression can be used to estimate the δ234Ui value of Devils Hole calcite based upon its measured δ18O and δ13C values. Using this approach and the measured present-day δ234U values of Devils Hole 2 calcite, we calculated 110 independent 234U–238U ages. In addition, we used newly measured δ18O, δ13C, and present-day δ234U values to calculate 10 234U–238U ages that range between 676 and 731 ka, thus allowing us to extend the Devils Hole chronology beyond the 230Th–234U-dated chronology while maintaining an age precision of ∼ 2 %. Our results indicate that calcite deposition at Devils Hole 2 cave began no later than 736 ± 11 kyr ago. The novel method presented here may be applied to future speleothem studies in similar hydrogeological settings, given appropriate calibration studies.

Novel method for determining ²³⁴U-²³⁸U ages of Devils Hole 2 cave calcite

Uranium-uranium (234U-238U) dating can determine the age of secondary carbonates over greater time intervals than the well-established 230Th-234U dating method. Yet it is rarely applied due to unknowns surrounding the initial δ234U (δ234Ui) value, which result in significant age uncertainties. In order to understand the δ234Ui in Devils Hole 2 cave, we have precisely determined 110 δ234Ui values from phreatic calcite crusts using a 230Th-234U chronology. The sampled calcite crusts were deposited in Devils Hole 2 between 4 and 590 thousand years, providing a long-term look at δ234Ui variability over time. We then performed multi-linear regressions among the δ234Ui values and correlative δ18O and δ13C values. These regressions allow us to predict the δ234Ui value of Devils Hole calcite based upon its δ18O and δ13C. Using this approach and measured present-day &felta;234U values, we calculate 110 independent 234U-238U ages of Devils Hole 2 cave deposits. In addition, we used newly measured δ18O, δ13C, and present-day δ234U values to calculate 10 234U-238U ages that range between 676 and 731 thousand years, thus allowing us to extend the Devils Hole chronology beyond the 230Th-234U-dated chronology while maintaining an age precision of ~2 %. Our results indicate that calcite deposition at Devils Hole 2 cave began no later than 736 ± 11 thousand years ago. The novel method presented here may be used in future speleothem studies in similar hydrogeological settings, given appropriate calibration studies.

Combined clumped isotope measurements resolve kinetic biases in carbonate formation temperatures

<p>Reaction kinetics involved in the precipitation of carbonates can introduce large scatter and inaccuracies in the temperatures derived from their <em>δ</em><sup>18</sup>O and ∆<sub>47</sub> values. Advances in mass spectrometry instrumentation recently enabled high-precision analysis of the <sup>18</sup>O–<sup>18</sup>O clumping in carbonate minerals (<em>∆</em><sub>48</sub>), despite the relatively low natural abundance of <sup>12</sup>C<sup>18</sup>O<sup>18</sup>O, the main isotopologue contributing to the <em>∆</em><sub>48</sub> signal (1). Measurements of <em>∆</em><sub>48</sub>, when combined with <em>∆</em><sub>47,</sub> can yield additional insights into kinetic effects and the carbonate formation environment (2).</p><p>Here we report high-precision <em>∆</em><sub>47</sub> and <em>∆</em><sub>48</sub> values of speleothem carbonates, modern coral skeletons, a brachiopod, and a belemnite. We constrained equilibrium in <em>∆</em><sub>47</sub> vs <em>∆</em><sub>48</sub> space by anchoring empirically derived <em>∆</em><sub>47</sub> vs temperature and <em>∆</em><sub>48</sub> vs temperature relationships to a Devils Hole mammillary calcite, known to be precipitated at extremely slow rates at a constant 33.7(±0.8) °C and water oxygen isotope composition. Our results, compared to theoretical predictions, provide the most substantial evidence to date that the isotopic disequilibrium commonly observed in speleothems and scleractinian coral skeletons is inherited from the dissolved inorganic carbon pool of their parent solutions. Data from an ancient belemnite imply it precipitated near isotopic equilibrium and confirm the warmer-than-present temperatures at Early Cretaceous southern high latitudes. The presence of similar kinetic departure in a brachiopod but not in a belemnite suggests that the current discrepancy between belemnite and brachiopod-based temperature estimates in the geologic record is most likely related to a greater kinetic bias in the isotopic composition of brachiopod shells.</p><p>We demonstrate that the combined clumped isotope method makes it possible to identify carbonates that did not precipitate in thermodynamic equilibrium from their parent water. Our results highlight the potential that the combined clumped isotope analyses hold for accurate paleoclimate reconstructions and the identification of the kinetic fractionation processes dominant in carbonate (bio)mineralisation.</p><p>(1) Fiebig et al. (2019), https://doi.org/10.1016/j.chemgeo.2019.05.019</p><p>(2) Guo, W. (2020), https://doi.org/10.1016/j.gca.2019.07.055</p>