Rio Grande Silvery Minnow Research Articles

Small Fish, Big Problems: Life History, Conservation, and the Future of the Rio Grande Silvery Minnow

The Rio Grande Silvery Minnow Hybognathus amarus is a small‐bodied minnow emblematic of a reproductive guild endemic to rivers of the North American Great Plains. This species has been lost from over 90% of its historical range. The species was federally listed as endangered in 1994 and intensive conservation efforts over the past three decades have averted its extinction in the wild. This article synthesizes the life history of the species, causes of decline and existing threats, and prospects for recovery considering ongoing conservation efforts. Restoring multiple self‐sustaining populations remains questionable given large‐scale, irreversible changes to the Rio Grande basin, though the resiliency of the species and established conservation programs hold at least some potential for advancing recovery beyond simply preventing extinction.

Mitogenomics of a declining species, the Rio Grande silvery minnow (Hybognathus amarus), with boom–bust population dynamics

Abstract Large mitochondrial DNA fragments and nearly complete mitogenomes were obtained from nextera-tagmented reductively amplified DNA (nextRAD) data from the Rio Grande silvery minnow (Hybognathus amarus). We used these data to characterize variation across the mitogenome and to evaluate changes in mitochondrial diversity across a 20 year time series punctuated by marked species decline. We observed different evolutionary rates among protein-coding genes and inflated values of the ratio of non-synonymous change to non-synonymous sites to synonymous changes per synonymous site for several protein-coding genes, violating assumptions of selective neutrality. Analyses suggested that non-synonymous substitutions are effectively neutral, and our results were not consistent with genetic draft. Mitogenomes revealed large long-term effective population size for Rio Grande silvery minnow, and time-series data indicated recent reductions in mitochondrial diversity via genetic drift associated with population bottlenecks. The results presented in this study show that in some cases, nextRAD sequences contain informative mitochondrial DNA data.

Movement patterns of a small-bodied minnow suggest nomadism in a fragmented, desert river

BackgroundUnfettered movement among habitats is crucial for fish to access patchily distributed resources and complete their life cycle, but many riverscapes in the American Southwest are fragmented by dams and dewatering. The endangered Rio Grande silvery minnow (Hybognathus amarus, RGSM) persists in a fragmented remnant of its former range (ca. 5%), and its movement ecology is understudied.MethodsWe tracked movements of hatchery-reared RGSM, tagged with passive integrated transponder tags, using stationary and mobile antennas from 2019 to 2022. We quantified probability of movement and total distance moved by RGSM released above and below a dam. We then assessed how well two prevailing riverine movement theories (i.e., restricted movement paradigm [RMP] and colonization cycle hypothesis [CCH]) explained RGSM movement patterns.ResultsWe detected 36.8% of released RGSM (n = 37,215) making at least one movement. Movements were leptokurtic and substantially greater than expected based on the RMP for both stationary (1.7–5.9 m) and mobile (30.3–77.8 m) individuals. On average, RGSM were detected at large for 75 days and moved a total of 12.2 rkm within a year. The maximum total distance moved by RGSM was 103 rkm. Similarly, we observed a multimodal distribution of detected range sizes with a mean detected range of 2.4 rkm and a maximum detected range of 78.2 rkm. We found little support for an upstream movement bias, as expected under the CCH, and most movements (74%) were directed downstream.ConclusionsOur data suggest RGSM are highly mobile, with the ability to make long-distance movements. Neither movement theory adequately described movement patterns of RGSM; instead, our findings support a nomadic movement pattern and an apparent drift paradox matching recent studies of other pelagic-broadcast spawning minnows where populations persist upstream despite experiencing downstream drift as larvae. Resolution of the drift paradox may be achieved through further, targeted studies into different aspects of the species’ life history. Quantification of RGSM movement provides crucial insights into the species’ movement ecology and may help define the appropriate scale of recovery efforts.

Developing a habitat suitability index with field data and hydraulic models

AbstractLinking habitat availability with hydraulic models integrates river engineering in the ecological field. Field observation for species presence and physical habitat availability mapping is inherently limited due to time and access constraints for field data collection. This study leverages hydraulic modeling to supplement larval fish population monitoring data, effectively expanding mapped physical habitat and allowing for monitoring bias analysis. The inundation extents and character of streamflow from hydraulic modeling were used to refine habitat suitability indices relative to total habitat availability from discrete fish monitoring events. Given the flexibility in hydraulic modeling to simulate a range of flows, the habitat suitability index is then translated to an effective habitat curve according to areal inundation and hydrologic frequency. With this framework, forecasting the impacts of long‐term trends, such as geomorphic or hydrologic change, can be reasonably and quantitatively assessed. This manuscript uses a case study of Rio Grande silvery minnow monitoring at restoration sites where the floodplain has been lowered via earthwork. Comparisons are made for habitat suitability indices developed from field observation data alone and field observation supplemented by hydraulic modeling. Known biases of field sampling data (targeting slow, shallow areas where fish are most often found) were confirmed based on simulated hydraulic conditions across entire restoration sites. In the case of Rio Grande silvery minnow, a heavily studied species, such field monitoring biases are an effective use of resources. However, this framework may be helpful for assessing alternative management approaches and monitoring strategies of species that are less studied.

Habitat associations of the Rio Grande Silvery Minnow, an endangered desert river fish, from a retrospective analysis based on a period of high abundance

AbstractObjectiveCharacterizing habitat associations is useful to aid in understanding the habitat requirements of native fishes, particularly those of conservation concern. Our study objective was to characterize mesoscale habitat associations of the only remaining wild population of the Rio Grande Silvery Minnow Hybognathus amarus (a federally endangered desert river fish), and provide comparisons with mesohabitat availability in the middle Rio Grande, New Mexico, from 1994 to 1996.MethodsWe collected fish monthly at two sites (separated by 160 km) near the northern and southern limits of the species' current range, and we recorded depth, velocity, substrate, and mesohabitat type for each habitat surveyed. Mesohabitat availability was recorded across 10 equally spaced and fixed transect lines at both study sites.ResultRio Grande Silvery Minnow most frequently occupied mesohabitats characterized by relatively shallow depths (≤25 cm) and low to near‐zero water velocities (≤15 cm/s). Statistical analyses indicated that mesohabitats occupied by the species were not the most frequently available at the study sites, suggesting a preference for shallow, low‐velocity habitats. Relatively high abundance of Rio Grande Silvery Minnow (n = 10,971), especially compared with post‐2009 abundance, facilitated robust characterization of species‐specific habitat associations.ConclusionComparison of our results with other studies of pelagic broadcast‐spawning leuciscids (pelagophils) endemic to the Great Plains and desert rivers of North America suggested broad overlap in mesohabitat associations among members of this reproductive guild. Our work contributes to a growing body of research aimed at conserving this declining reproductive ecotype of freshwater fishes and suggests that increasing hydraulic diversity through innovative management approaches (e.g., habitat creation, restoration of fluvial processes, and preservation of natural streamflow characteristics) will be crucial for their long‐term recovery and conservation.

Genetic erosion in an endangered desert fish during a megadrought despite long-term supportive breeding.

Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We used demographic and genetic data from wild and hatchery individuals to examine the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d = 1.34) and remained low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size based on linkage disequilibrium (LD Ne ) were positively associated (r = 0.53) with wild abundance and total abundance, but as the proportion of hatchery-origin spawners increased, LD Ne declined (r = -0.55). Megadrought limited wild spawner abundance and precluded refreshment of hatchery brood stocks with wild fish; hence, we predict a riverine population increasingly dominated by hatchery-origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.

Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes: Leuciscidae).

Sex determination systems and genetic sex differentiation across fishes are highly diverse but are unknown for most Cypriniformes, including Rio Grande silvery minnow (Hybognathus amarus). In this study, we aimed to detect and validate sex-linked markers to infer sex determination system and to demonstrate the utility of combining several methods for sex-linked marker detection in nonmodel organisms. To identify potential sex-linked markers, Nextera-tagmented reductively amplified DNA (nextRAD) libraries were generated from 66 females, 64 males, and 60 larvae of unknown sex. These data were combined with female and male de novo genomes from Nanopore long-read sequences. We identified five potential unique male nextRAD-tags and one potential unique male contig, suggesting an XY sex determination system. We also identified two single-nucleotide polymorphisms (SNPs) in the same contig with values of FST, allele frequencies, and heterozygosity conforming with expectations of an XY system. Through PCR we validated the marker containing the sex-linked SNPs and a single nextRAD-tag sex-associated marker but it was not male specific. Instead, more copies of this locus in the male genome were suggested by enhanced amplification in males. Results are consistent with an XY system with low differentiation between sex-determining regions. Further research is needed to confirm the level of differentiation between the sex chromosomes. Nonetheless, this study highlighted the power of combining reduced representation and whole-genome sequencing for identifying sex-linked markers, especially when reduced representation sequencing does not include extensive variation between sexes, either because such variation is not present or not captured.

Hatchery supplementation increases potential spawning stock of Rio Grande Silvery Minnow after population bottlenecks

AbstractObjectiveSupplementation of imperiled wild fish stocks with captively raised fish is a commonly used conservation tool. Programs designed to maintain or improve fish populations through supplementation should be evaluated to determine whether they are meeting conservation objectives. The Rio Grande Silvery Minnow Hybognathus amarus is a small‐bodied, endangered minnow endemic to the Rio Grande basin of the southwestern United States. The wild population of Rio Grande Silvery Minnow has been supplemented with captive‐reared fish since 2002. Our objective was to determine whether supplementation measurably increases the number of spawning fish after years of population bottlenecks; this objective was simplified because nearly all hatchery‐released fish have been given identifying markings.MethodsWe leveraged a long‐term fish sampling data set (18 years) covering the species' contemporary range and a single‐season, high spatial coverage fish sampling data set to determine whether the number of potential spawners was increased by the addition of hatchery fish.ResultHatchery‐reared fish increased the catch rates of spawners by up to an order of magnitude in some years. We also observed that most hatchery‐reared fish were recaptured near the point of release. We were able to determine that supplementation with hatchery fish increased the abundance and distribution of Rio Grande Silvery Minnow and provided the desired demographic boost after severe population bottlenecks.ConclusionReleasing hatchery‐reared fish may be a useful tool for conservation of imperiled freshwater fishes. However, there is a need for spawning and rearing infrastructure that matches the life‐history of the species and sufficient postrelease monitoring to evaluate the effectiveness of hatchery supplementation. Use of hatchery‐reared fish has been beneficial for improving population resiliency of Rio Grande Silvery Minnow following recruitment bottlenecks; however, natural recruitment can greatly exceed hatchery supplementation and conditions promoting natural recruitment should be restored.

Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years.

Many long-term genetic monitoring programmes began before next-generation sequencing became widely available. Older programmes can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programmes should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.

Quantifying flow and nonflow management impacts on an endangered fish by integrating data, research, and expert opinion

AbstractManagers charged with recovering endangered species in regulated river segments often have limited flexibility to alter flow regimes and want estimates of the expected population benefits associated with both flow and nonflow management actions. Disentangling impacts on different life stages from concurrently applied actions is essential for determining the effectiveness of each action, but difficult without models that integrate multiple information sources. Here, we develop and fit an integrated population model for endangered Rio Grande Silvery Minnow (Hybognathus amarus) in the Middle Rio Grande, New Mexico. We integrate catch per unit effort monitoring data collected during 2002–2018 with population estimates, data collected during rescue of minnow from drying pools, habitat availability estimates, laboratory results, releases of hatchery reared minnow, and expert opinion. We use expert elicitation to develop a larval carrying capacity index as an informed proxy for the complex interactions among flow, habitat, and life history in this species. We evaluate the model using out‐of‐sample forecasts of 2019 and 2020, develop an algorithm to identify supplemental water releases that maximize benefits to the minnow, and quantify the effectiveness of various actions. Experts generally agreed on the duration and timing of flow requirements and disagreed regarding the importance of different magnitudes. The integrated model with the larval carrying capacity index outperformed two alternative models in forecasting catch in 2019 and 2020. The model estimates that minnow abundance varied by more than three orders of magnitude between 2002 and 2018 and that in a few years recruitment was limited by spawner abundance. Evaluation of the expected benefits of flow and nonflow management actions to fall population abundance across different years suggests that efficient addition of water to the base hydrograph is the most effective action in most, but not all years. Many actions are effective only under certain hydrologic and population conditions and the effectiveness of different actions varies in different sections of the study area. Widespread water extraction and river regulation combined with periodic drought and ongoing climate change may necessitate creative management of federally listed fish species in arid systems informed by thorough analyses of management effectiveness.

Effects of flow recession regime on stranding of Rio Grande silvery minnow suggests that conservation actions must overcome evolutionary traps

Abstract Flow intermittence is a major disturbance for riverine fishes. Many species of fishes that evolved in naturally intermittent streams have specialized adaptations to survive drought such as movement to refuge habitats. Conservation of fishes in river systems with highly altered flow regimes requires understanding of how individuals and populations respond to flow intermittence. Here, flow was manipulated in two 16‐km segments of the Rio Grande, New Mexico, to determine whether managed flow recession could reduce stranding imperilled Rio Grande silvery minnow in isolated pools. Slower flow recessions did not decrease stranding in isolated pools over the range tested. Flow recession rate appeared to have an adverse impact on stranding; fewer fish were stranded under faster recession rates, but complex interactions were evident. Fish were stranded throughout both segments regardless of flow recession rate. No evidence of a synchronized movement response was observed. Instead, many Rio Grande silvery minnows were probably trapped within proximal habitats, which dry completely and function as evolutionary traps, rather than moving to areas of perennial flow. Use of proximal habitats during streamflow intermittence has implications for management of the species and mitigation of mortality, including managed flow recession rates, and position and function of refuge habitats. Effective mitigation for flow intermittence and stranding in streams with highly modified flow regimes will depend on the life history and behavioural response of the species. For Rio Grande silvery minnow, facilitating adaptive behaviour would require creating refuge areas that increase fish survival for weeks to months, as reducing the attractiveness of the traps is likely to be impossible given lack of a synchronized movement response to declining flows. Mismatching life‐history strategies, behaviour, and scale of conservation actions may result in ineffective management and continued dependence on intensive management actions such as augmentation with hatchery fish.

Water quality in three potential drought refuges in an arid-land river: assessing habitat suitability for at-risk fish species

Drought is a common disturbance in arid-land streams and rivers. The survival of aquatic species depends on access to refuge habitats where water quality remains high. Over the past century, modified flow regimes and altered watershed and instream characteristics have led to the extinction and endangerment of numerous fish species endemic to the southwestern United States. We assessed the water quality of potential drought refuges in the Middle Rio Grande (MRG), with an emphasis on suitability for the endangered Rio Grande Silvery Minnow (RGSM). We examined three types of potential drought refuges: three agricultural return drain outfalls; three isolated pools that remained during streamflow intermittency; and a reach with perennial flow below an agricultural diversion dam. All potential refuges are known to contain RGSM and other fishes. Two out of three drain outfalls, one out of three isolated pools, and three out of ten kilometers of perennially wetted stream below a dam met basic water quality criteria necessary to support RGSM populations. These findings suggest that refuge habitability is context dependent, that generalizations regarding the suitability of a specific refuge type should be avoided, and that careful assessment is required to determine if a specific location will support fish assemblages. Although some areas may contain water, they may represent ecological traps if fish are exposed to poor water quality conditions compared to other potential refuge habitats.

Shrinkage of Rio Grande Silvery Minnow after Preservation in Formalin and Storage in Ethanol

Understanding how the preservation process affects fish morphology is important for studies that use museum collections as voucher specimens. Sixty-nine Rio Grande silvery minnows (standard length [SL] 32.14–81.65 mm) were observed over 545 days during a formalin-to-water-to-ethanol preservation procedure. Median standard length decreased by the end of each preservation step; specimens shrank 1.06 mm in formalin solution, 1.97 mm in 35% ethanol, 2.17 mm in 50% ethanol, and 2.48 mm in 70% ethanol. Peak shrinkage occurred at 365 d, with a median decrease of 3.86 mm (SL 29.57–75.98 mm). After 545 days, Rio Grande silvery minnows began to increase in length, exhibiting a median shrinkage of 2.04 mm from live length. Research on museum specimens that includes morphological measurements should consider that changes in length or body shape may influence or hinder the ability to detect changes in morphology over time.

An empirically based simulation model to inform flow management for endangered species conservation

Increasing water demand, water development, and ongoing climate change have driven extensive changes to the hydrology, geomorphology and biology of arid-land rivers globally, driving an increasing need to understand how annual hydrologic conditions affect the distribution and abundance of imperiled desert fish populations. We analyzed the relationship between annual hydrologic conditions and the endangered Rio Grande silvery minnow (Hybognathus amarus) in the Middle Rio Grande, New Mexico, USA, using hurdle models to predict both presence and density as a function of integrated annual hydrologic metrics. Both presence and density were positively related to spring high flow magnitude and duration and negatively related to summer drying, as indicated by an integrated flow metric. Simulations suggest hydrologic conditions near the wettest observed in the data set would be required to meet recovery goals in a single year in all reaches. We demonstrate how the models developed herein can be used to examine alternative water management strategies, including strategies that may currently be socially and logistically infeasible to implement, to identify strategies minimizing trade-offs between conservation and other management goals.

Linking Reclaimed Water Consumption with Quantitative Downstream Flow Impacts

Although reclaimed water—municipal wastewater treatment plant effluent—can serve as a locally sustainable alternative water resource, this additional consumptive use of reclaimed water may cause impacts downstream. This paper seeks to quantitatively assess these impacts by employing scenario analysis coupled with a two-sample t-test to evaluate the statistical significance of streamflow alteration. Further, the potential for lower volumes of streamflow is linked to impacts on downstream stakeholders through the use of stakeholder performance metrics. To demonstrate the applicability of this approach, two diverse regions are evaluated: (1) the Illinois River downstream from the greater Chicago, Illinois, area, and (2) the Middle Rio Grande River downstream from Albuquerque, New Mexico. In Illinois, impacts to barge transportation are marginal and decrease with distance downstream of effluent consumption. In the Rio Grande, impacts to the Rio Grande silvery minnow worsen downstream such that a proposed consumption would be unlikely to be established under federal regulations. The extent of downstream impacts is important in legal and policy contexts regarding the sustainability of reclaimed water projects.

Use of restored floodplains by fishes of the Middle Rio Grande, New Mexico, USA

AbstractNearly 1600 ha of habitat have been restored at 300 floodplain sites of the Middle Rio Grande (MRG), New Mexico, USA, as part of a cooperative effort of the Middle Rio Grande Endangered Species Collaborative Program to conserve the endangered Rio Grande silvery minnow (RGSM). These riverside sites are designed to inundate during spring run‐off and create ephemeral habitats for other aquatic and riparian species. This study of four restored floodplain sites in May–June 2017 found that of 14 fish species captured with fyke nets, common carp (41%), red shiner (32%), RGSM (16%) and white sucker (9%) dominated total numbers. Adult RGSM included 42% gravid females, 36% ripe males and 22% spent females, suggesting that this endangered species was spawning in and near these floodplains. Larval sampling also showed that restored sites and adjacent mainstem banklines were being used as nursery habitats, where RGSM larvae dominated six and nine species with 80% and 74% of total numbers, respectively. System‐wide proportions of RGSM larvae by phase suggest that larvae leave the floodplains and move to mainstem banklines beginning as late mesolarvae and metalarvae (14–22 days post‐hatch), and most depart by the juvenile stage. Altogether, 15 fish species were encountered in restored floodplain sites in 2017, compared to 16 species reported in concurrent annual mainstem monitoring. This study and others show that most fish species of the MRG move onto restored and natural floodplains equally in spring, and many use these habitats for spawning and as larval nurseries.

Fish Rescue during Streamflow Intermittency May Not Be Effective for Conservation of Rio Grande Silvery Minnow

Streamflow intermittency can reshape fish assemblages and present challenges to recovery of imperiled species. During streamflow intermittency, fish can be subjected to a variety of stressors, including exposure to crowding, high water temperatures, and low dissolved oxygen, resulting in sublethal effects or mortality. Rescue of fishes is often used as a conservation tool to mitigate the negative impacts of streamflow intermittency. The effectiveness of such actions is rarely evaluated. Here, we use multi-year water quality data collected from isolated pools during rescue of Rio Grande silvery minnow Hybognathus amarus, an endangered minnow. We examined seasonal and diel water quality patterns to determine if fishes are exposed to sublethal and critical water temperatures or dissolved oxygen concentrations during streamflow intermittency. Further, we determined survival of rescued Rio Grande silvery minnow for 3–5 weeks post-rescue. We found that isolated pool temperatures were much warmer (>40 °C in some pools) compared to upstream perennial flows, and had larger diel fluctuations, >10 °C compared to ~5 °C, and many pools had critically low dissolved oxygen concentrations. Survival of fish rescued from isolated pools during warmer months was <10%. Reactive conservation actions such as fish rescue are often costly, and in the case of Rio Grande silvery minnow, likely ineffective. Effective conservation of fishes threatened by streamflow intermittency should focus on restoring natural flow regimes that restore the natural processes under which fishes evolved.

Wild at heart: Programs to diminish negative ecological and evolutionary effects of conservation hatcheries

Hatchery programs are critical for conservation and management of many imperiled fishes. Most traditional aquaculture programs negatively affect ecological performance, genetic, and phenotypic diversity of hatchery-origin fish compared with wild counterparts. Here, we synthesize outcomes of three conservation programs aimed at enhancing ‘wildness’. Each program focuses on a different species: lake sturgeon, razorback sucker, and Rio Grande silvery minnow. These species differ in key life history traits including size and age at sexual maturity, reproductive and migratory behavior, and habitat requirements. Threats to persistence of the focal taxa, however, exemplify common pressures experienced by freshwater fishes worldwide. Conservation hatchery programs for lake sturgeon, razorback sucker, and Rio Grande silvery minnow capitalize on natural spawning in the wild followed by collections of wild-fertilized eggs/larvae for hatchery rearing. Individuals are repatriated to the wild after rearing to body sizes less susceptible to mortality. Protocols include collections of eggs or larvae across the entire spawning period and at appropriate geographic scales to maximize retention of genetic diversity and, to increase the likelihood of preserving variation for heritable life history traits. Using direct and indirect evidence we show that hatchery programs that allow individuals to fulfill parts of the life-cycle in their native habitats can be conducted without compromising genetic diversity. Adoption of similar strategies in other imperiled fishes would improve understanding of species life history, and provide an incentive to protect native habitats so they may eventually support self-sustaining populations.

No quarter: Lack of refuge during flow intermittency results in catastrophic mortality of an imperiled minnow

Abstract Many once‐perennial rivers have become intermittent. Channel drying can result in fish mortality if refuges are not available. Understanding where refuges occur and if fishes use these refuges can provide insight for species persistence and help stakeholders manage limited resources. Streamflow diversions in the Rio Grande of New Mexico can result in >60 km losses of aquatic habitat, affecting up to 30% of the range of imperiled Rio Grande silvery minnow (Hybognathus amarus). Potential refuges include areas with perennial flow below diversion dams, isolated pools, and irrigation return flows. We examined spatial and temporal patterns of both adult and young‐of‐year Rio Grande silvery minnow collected in isolated pools that formed during streamflow intermittency from 2009 to 2019. We hypothesised that: (1) Rio Grande silvery minnow would be more numerous in pools that persisted longer; (2) they would be more numerous in isolated pools located closer to upstream areas of perennial flow, due to upstream movement to escape drying; and (3) increased rate of aquatic habitat loss each day would result in more Rio Grande silvery minnow in isolated pools. During the 12 years of the study, we counted Rio Grande silvery minnow in 3,985 isolated pools that formed during streamflow intermittency. We related counts of Rio Grande silvery minnow in each pool to the maximum pool depth, rate of loss of aquatic habitat that occurred that day, and distance each pool was to an upstream barrier. In 2016, we examined persistence of 290 isolated pools until complete desiccation or reconnection with continuous flows occurred, and the factors that influenced pool persistence. Deeper pools persisted for longer, but depth had a small positive effect on counts of adult Rio Grande silvery minnow and no effect on counts of young‐of‐year in isolated pools. Adults were more numerous in upstream isolated pools, whereas young‐of‐year were more numerous in downstream isolated pools. Rate of channel drying had little effect on the numbers of adult Rio Grande silvery minnow in isolated pools, but more young‐of‐year were stranded when the rate of drying was faster. On average, pools persisted <4 days and 263 of 290 dried completely before continuous flows returned. Only 66 of 4,749 Rio Grande silvery minnow occurred in pools that did not dry completely. Rio Grande silvery minnow did not appear to escape channel intermittency; instead, they became stranded in shrinking isolated pools that did not persist long enough to act as refuges for fishes. Lack of refuge during channel intermittency would result in catastrophic mortality of fishes through complete desiccation of pools if there were no management actions, such as translocating fish. To increase persistence through streamflow intermittency, conservation actions should match the species response to intermittency by ensuring the availability of perennial‐water refuges at the appropriate spatial and temporal scale.

Relationship of Effective Size to Hatchery Supplementation and Habitat Connectivity in a Simulated Population of Rio Grande Silvery Minnow

Simultaneous management actions often are used to improve the status of imperiled species, yet the effects of these actions can be difficult to determine. The endangered Rio Grande Silvery Minnow Hybognathus amarus is a short‐lived fish with a dispersive life history and thus requires—but does not occupy—unfragmented habitat for recruitment and survival. We used Rio Grande Silvery Minnow as a model system for an individual‐based simulation study to evaluate responses of genetic effective size to hatchery supplementation and fish passage in a managed population. Simulations were designed to test effects of fish passage on the relationship between estimates of inbreeding (NeI) and variance (NeV) effective sizes, which differ consistently (NeI >> NeV) in long‐term genetic‐monitoring data from hatchery‐supplemented Rio Grande Silvery Minnow populations. Values of different effective population size measures should be identical in a demographically stable and connected (admixed) population but can differ substantially under nonequilibrium conditions. When a barrier prevented upstream dispersal, NeI was associated negatively with rate of downstream dispersal and positively with supplementation rate, whereas NeV was associated negatively with both. This mirrored observations from Rio Grande Silvery Minnow. Individual effects of dispersal and supplementation, however, were difficult to discern due to significant interaction between these factors. When connectivity was restored, NeI and NeV depended on supplementation rate, with positive association between NeI and supplementation rate versus a negative association for NeV and interaction terms, and effects of dispersal were nonsignificant. Although fish passage did not alter the difference between NeI and NeV, our study suggests that for Rio Grande Silvery Minnow, and potentially other intensively managed species in regulated rivers, fish passage may help to distinguish effects of management actions, such as supplementation, from effects of other demographic influences. More generally, explicit analytical consideration of differences in effective population size estimates can provide important details of genetic responses to management.