Using genetic data to advance stream fish reintroduction science: a case study in brook trout

Widespread extirpation of native fish populations has led to a rise in species reintroduction efforts worldwide. Most efforts have relied on demographic data alone to guide project design and evaluate success. However, the genetic characteristics of many imperiled fish populations including low diversity, local adaptation, and hatchery introgression emphasize the importance of genetic data in the design and monitoring of reintroduction efforts. Focusing on a case study of brook trout (Salvelinus fontinalis) in North Carolina, we show how the combined use of genetic and demographic data can support reintroduction efforts by improving source population selection and providing opportunities to evaluate genetic viability and adaptive potential in restored populations. Using this combined approach, we reintroduced brook trout into a restored stream from two source populations and monitored changes in genetic diversity and population size in source and recipient populations. Three years after the initial translocation, the reintroduced population had comparable density, but higher genetic diversity, than either source population. This study demonstrates the utility of genetic and demographic data for reintroduction efforts, particularly when extant populations are genetically depauperate and maintaining adaptive potential is a primary restoration goal. However, we emphasize the value of continued monitoring at longer temporal and spatial scales to determine the effects of stochastic process on the long-term adaptive capacity and persistence of reintroduced populations. Overall, inclusion of genetic data in reintroduction efforts offers increased ability to meet project goals while simultaneously conserving critical sources of adaptive variation that exist across the landscape.     

Plant reintroduction: an overview

The reintroduction of plants will become an increasingly utilized strategy in plant conservation and protected area management. Reintroduction is the deliberate establishment of individuals of a species into an area and/or habitat where it has become extirpated with the specific aim of establishing a viable self-sustaining population for conservation purposes. Plant reintroduction can involve the establishment of an extirpated species into a relatively intact habitat or it can be part of the restoration of a degraded habitat. This will be performed as species become extinct for a number of reasons, such as collecting, introduced herbivores or pathogens and potentially climate change. Although plant reintroductions have the potential to play an important role in species' conservation the long term viability of many reintroductions has yet to be assessed. For the technique to reach it's full potential it requires greater integration with habitat management, restoration and increased international coordination between both theex situ andin situ agencies. In addition the value of introducing stocks of endangered species lacking viable sites for reintroduction to non native sites is discussed.     

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

Salmonid fishes exhibit extensive local adaptations owing to abundant environmental variation and precise natal homing. This extensive local adaptation makes conservation and restoration of salmonids a challenge. For example, defining unambiguous units of conservation is difficult, and restoration attempts often fail owing to inadequate adaptive matching of translocated populations. A better understanding of the genetic architecture of local adaptation in salmonids could provide valuable information to assist in conserving and restoring natural populations of these important species. Here, we use a combination of laboratory crosses and next-generation sequencing to investigate the genetic architecture of the parallel adaptation of rapid development rate in two geographically and genetically distant populations of rainbow trout (Oncorhynchus mykiss). Strikingly, we find that not only is a parallel genetic mechanism used but that a conserved haplotype is responsible for this intriguing adaptation. The repeated use of adaptive genetic variation across distant geographical areas could be a general theme in salmonids and have important implications for conservation and restoration.     

Genetic consequences of trumpeter swan (Cygnus buccinator) reintroductions

Relocation programs are often initiated to restore threatened species to previously occupied portions of their range. A primary challenge of restoration efforts is to translocate individuals in a way that prevents loss of genetic diversity and decreases differentiation relative to source populations—a challenge that becomes increasingly difficult when remnant populations of the species are already genetically depauperate. Trumpeter swans were previously extirpated in the entire eastern half of their range. Physical translocations of birds over the last 70 years have restored the species to portions of its historical range. Despite the long history of management, there has been little monitoring of the genetic outcomes of these restoration attempts. We assessed the consequences of this reintroduction program by comparing patterns of genetic variation at 17 microsatellite loci across four restoration flocks (three wild-released, one captive) and their source populations. We found that a wild-released population established from a single source displayed a trend toward reduced genetic diversity relative to and significant genetic differentiation from its source population, though small founder population effects may also explain this pattern. Wild-released flocks restored from multiple populations maintained source levels of genetic variation and lacked significant differentiation from at least one of their sources. Further, the flock originating from a single source revealed significantly lower levels of genetic variation than those established from multiple sources. The distribution of genetic variation in the captive flock was similar to its source. While the case of trumpeter swans provides evidence that restorations from multiple versus single source populations may better preserve natural levels of genetic diversity, more studies are needed to understand the general applicability of this management strategy.     

Mixing source populations increases genetic diversity of restored rare plant populations

The genetic diversity of germplasm used in reintroduction and restoration efforts can influence how resulting populations establish, reproduce, and evolve over time, particularly in disturbed and changing conditions. Regional admixture provenancing, mixing seeds derived from multiple populations within the same region as the target site, has been suggested to produce genetically diverse germplasm. Yet little empirical evidence shows how genetic diversity in germplasm resulting from this approach compares to source populations, or how it varies in restored populations. Here, we use neutral molecular markers to follow genetic diversity through production and use of germplasm when mixing multiple source populations in nursery production beds. Castilleja levisecta is a rare species experiencing inbreeding depression in remaining populations, with a federal recovery plan requiring the re‐establishment of populations in areas where it has been extirpated. Specifically, we track diversity from wild‐collected source populations through different production approaches and reintroductions using two propagule types. We show that measures of genetic diversity, inbreeding, and relatedness change during the production and use of material produced with a regional admixture provenancing approach, with the step at which source populations are mixed and germplasm type used influencing whether all source populations are equally represented. While genetic diversity increased throughout the process, inbreeding and relatedness increased in nursery production beds but decreased in reintroductions, with the lowest inbreeding and relatedness in populations restored using seeds rather than plugs. The results highlight the importance of taking an integrated approach informed by research when planning and implementing reintroductions with mixed‐source germplasm.     

Restoration of a bighorn sheep population impeded by Mycoplasma ovipneumoniae exposure

Bighorn sheep (Ovis canadensis) were once extirpated from the Black Hills region of South Dakota, U.S.A., mirroring declining populations throughout North America. Since the 1960s, several reintroductions have occurred in the Black Hills to reestablish populations, with varying success. We translocated 26 bighorn sheep from Alberta, Canada, to the Black Hills (February 2015) to restore bighorn sheep to their historic range. Due to prior examinations of cause‐specific survival, subsequent genetic diversity and disease prevalence analyses were required to evaluate success of the restoration effort. We measured a mean allelic diversity of 5.23 (SE = 0.44 [mean number of alleles]) and an observed heterozygosity of 0.71 (SE = 0.06; expected = 0.64 ± 0.05) in the translocated individuals. Translocated bighorn sheep tested negative for Mycoplasma ovipneumoniae at capture. An autogenous vaccine was administered prior to release in an attempt to safeguard the translocated bighorn sheep from infection with a strain known to be resident in adjacent bighorn sheep populations. However, the year following the translocation, a different strain of M. ovipneumoniae was associated with a pneumonia outbreak that resulted in 57.9% mortality. Our results suggest that allelic diversity and heterozygosity were sufficient for long‐term herd establishment, reducing the potential for founder effects. However, the overwhelming mortality associated with pneumonia, via the transfer of M. ovipneumoniae from an unknown source, limited the success or our reintroduction efforts. Successful attempts to restore bighorn sheep to their historic ranges must consider and mitigate potential routes for M. ovipneumoniae transmission pre‐ and post‐reintroduction.     

Genetic Diversity and the Reintroduction of Meadow Species

Abstract: Restoration of formerly nutrient‐poor and species‐rich grasslands generally leads to an increase in species diversity. However, species without a persistent seed bank and with poor dispersal ability often do not re‐establish spontaneously. Here, reintroduction is an option. If existing populations are comparable in their genetic composition, any population will do. This is not the case if populations have local adaptations. Unfortunately, whether populations are adapted locally is not easily determined, in contrast to assessing differentiation using neutral genetic markers. We used AFLP to study genetic diversity of Cirsium dissectum and Succisa pratensis within and among several Junco‐Molinion plant communities in the Netherlands (up to 200 km apart) that were potential source populations, and followed the reintroduction using seeds from these populations. Also, vegetative growth phase characteristics of three populations of C. dissectum were analyzed under controlled conditions. Most of the genetic variation in these cross‐fertilizing species was found within populations. Small but significant genetic differences in band frequencies were found among populations (F_st 0.100 ‐ 0.135). The first generation of reintroduced plants contained less polymorphic bands than the source populations. The genetic differences caused by reintroduction using a limited number of seeds (founder effects) were significant in all except one case (F_st 0.012 ‐ 0.101 between source and corresponding reintroduced population), but the magnitude was smaller than the source population differentiation. In assignment tests, reintroduced populations resembled their source population more than any other population, but all populations contained sizeable proportions of plants that were assigned to most similar plants from other populations, indicating that the populations are only marginally distinct. Calculations show that reintroduction from more than one source population introduces significantly more polymorphic bands into the new population, capitalizing on the existence of band frequency differences among populations.     

A Century of Elk Restoration in Eastern North America

Over a century has passed since elk were extirpated in eastern North America. During that time, numerous attempts to reintroduce elk into eastern North America have resulted in varying degrees of success and failure. An overview of restoration efforts during the last 100 years is presented here with emphasis on the differences in rates of population change among regions and differences in major causes of elk mortality during both the pre‐ and post‐acclimation periods. Approximately 40% of recorded elk reintroduction attempts in eastern North America resulted in failure, with the majority of these having occurred in the first half of the 20th century. Although rates of population change in elk were highly variable, they were not related to founding population size. Major causes of mortality varied among regions and should be considered in future reintroduction attempts.     

Evaluating where and how habitat restoration is undertaken for animals

Habitat restoration is vital to ameliorate the effects of anthropogenic disturbances on animal habitats. We reviewed the peer‐reviewed literature to examine where and how habitat restoration is undertaken. Our aim was to identify key knowledge gaps as well as research and monitoring needs that can inform future restoration actions. We found: (1) marine and terrestrial actions focus most commonly on restoring vegetation, and freshwater actions focus on restoring the in‐channel habitat; (2) arthropods are the most common focal group; (3) there is often no collection of pre‐restoration data, so certainty in attributing environmental changes to restoration actions is limited; and (4) population and community measures are most commonly used in monitoring programs, which only show if animals are present at restored sites and not whether they are able to grow, survive, and reproduce. We highlight three important considerations for future restoration actions. First, more integration of knowledge among freshwater, marine, and terrestrial systems will help us to understand how, and why, restoration outcomes might vary in different contexts. Second, where possible, restoration projects should be assessed using before‐after‐control‐impact designs, which will provide the strongest evidence if desired restoration responses occur. Third, if the goal of restoration is to develop self‐sustaining breeding populations of target animals, then measures of fitness (i.e. breeding, survival) should be collected. These recommendations will hopefully help guide more effective restoration practices and monitoring in the future.     

Evaluating the genome-wide impacts of species translocations: the greater prairie-chicken as a case study

A variety of conservation management strategies have been developed to address rapid, anthropogenically-driven biodiversity loss. The translocation of individuals from viable populations to those experiencing significant decline is one such strategy to increase genetic diversity and avoid extirpation, yet efficacy of this strategy has rarely been examined in detail utilizing genomic data. Here, we employ a conservation icon, the greater prairie-chicken (Tympanuchus cupido pinnatus), as a case study to demonstrate how genome-wide SNPs derived from RADseq offer the ability to assess translocation success with respect to the genomic aspects of genetic restoration, encompassing (1) the alleviation of inbreeding (2) the restoration of evolutionary potential, and (3) the maintenance of local variation. Genome-wide diversity estimates calculated from 356,778 SNPs demonstrate that translocations rescued the Illinois population from severe inbreeding and lack of genetic diversity, restoring variation to levels comparable to the three non-bottlenecked source populations. Delineation of genetic structure using non-linked and ubiquitously genotyped SNPs reveal distinct genetic variation among the source and recipient populations as well as high levels of admixture in the post-translocation population resulting from translocations. Estimated ancestry derived from private alleles uncover introgression of unique variation from each source population as well as the maintenance of substantial levels of variation unique to Illinois. Our findings demonstrate that genome-wide analysis of variation is a valuable management tool for measuring the genomic effects of translocations and, subsequently, gauging genetic restoration success.

     

Resolving the value of the dingo in ecological restoration

There is global interest in restoring populations of apex predators, both to conserve them and to harness their ecological services. In Australia, reintroduction of dingoes (Canis dingo) has been proposed to help restore degraded rangelands. This proposal is based on theories and the results of studies suggesting that dingoes can suppress populations of prey (especially medium‐ and large‐sized herbivores) and invasive predators such as red foxes (Vulpes vulpes) and feral cats (Felis catus) that prey on threatened native species. However, the idea of dingo reintroduction has met opposition, especially from scientists who query the dingo's positive effects for some species or in some environments. Here, we ask ‘what is a feasible experimental design for assessing the role of dingoes in ecological restoration?’ We outline and propose a dingo reintroduction experiment—one that draws upon the existing dingo‐proof fence—and identify an area suitable for this (Sturt National Park, western New South Wales). Although challenging, this initiative would test whether dingoes can help restore Australia's rangeland biodiversity, and potentially provide proof‐of‐concept for apex predator reintroductions globally.     

Causes of reintroduction failure of the brown treecreeper: Implications for ecosystem restoration

Reintroductions are conducted to re‐establish a self‐sustaining population of a species and contribute to ecosystem restoration. The brown treecreeper (Climacteris picumnus) reintroduction into two nature reserves in the Australian Capital Territory in south‐eastern Australia failed to meet its predetermined criteria for success. This occurred despite prior habitat restoration within the reserves where reintroduction occurred. Low survival of reintroduced brown treecreepers, particularly due to predation by native predators, has previously been highlighted as a key factor in the failure of the programme. We compared bird behaviour and habitat characteristics between the reintroduction reserves and the sites where brown treecreepers were sourced (which support stable brown treecreeper populations). We did not identify an indication of significantly higher predation pressure in the reintroduction reserves in comparison with the source sites. However, our results revealed that reintroduced individuals may be more vulnerable to predation because of an increased flight time to reach a refuge area. This was a result of a significantly lower number of refuge areas in logs and trees and a higher number of shrubs (which may obstruct escape paths and hinder detection of predators) in the reintroduction reserves compared with the source sites. We identified a lower ground foraging habitat quality in the reintroduction reserves because of lower numbers of ant mounds and lower areas of forageable ground. However, brown treecreepers were able to disperse extensively throughout the reserves and settle in areas with generally higher‐quality foraging habitat. Therefore, the negative effect of low ground foraging habitat quality would have been most pronounced immediately after release. This study emphasizes the inherent complexities of species reintroductions and ecosystem restoration. Despite experimental restoration activities within the reintroduction reserves, there were still deficiencies in habitat quality. We emphasize that further habitat restoration is required within these reserves to achieve more complete restoration.     

Genetic assessment of population restorations of the critically endangered Silene hifacensis in the Iberian Peninsula

In order to preserve endangered plant populations and recover their evolutionary potential and ecological behavior, some restoration measures generally involve the reinforcement of the population size in existing natural populations or the reintroduction of new populations. Genetic monitoring of both natural and restored populations can provide an assessment of restoration protocol success in establishing populations that maintain levels of genetic diversity similar to those in natural populations. The highly threatened Spanish species Silene hifacensis (Caryophyllaceae) has only three natural reduced mainland populations in the Iberian Peninsula, following decline and extinction that occurred during the late 20th century. Preterit restoration strategies were essentially based on the implantation of new populations and reinforcement of certain existing populations using transplants mostly cultivated in greenhouses. In the present contribution, levels and patterns of genetic variability within natural and restored populations of Silene hifacensis were assessed using the molecular technique AFLP. Our results pointed out significant genetic diversity differences across the three existing natural populations though their population fragmentation and progressive loss of individuals have not had an impact on the global genetic diversity of this species. For restored populations, their levels of genetic diversity were similar and even higher than in natural populations. As a result, the past restoration protocols were successful in capturing similar and even higher levels of genetic diversity than those observed within natural pools. However, inbreeding processes have been detected for two restored populations. Finally, the main source of plant material for the long-time restored transplants appears to be the natural population of Cova de les Cendres. This study demonstrates, once again, how genetic markers are useful tools to be taken in consideration for endangered plant species conservation plans.     

Tidal marsh restoration stimulates the growth of winter shorebird populations in a temperate estuary

The regional responses of winter shorebird populations in the nearly 3,000 ha estuary of Tomales Bay, California, to the restoration of 223 ha of historic tidal wetlands were evaluated for 27 years: 19 years prior to tidal reintroduction and 8 years after tidal reintroduction. We used interrupted time series analyses to measure the spatial extent of the restoration effect and to model the magnitude and length of time associated with the gradual, restoration‐induced growth of winter shorebird populations in the bay. Expanded, regional benefits of the restoration were revealed by consistent patterns of winter shorebird population growth. Eight years after tidal reintroduction, overall shorebird abundances in southern Tomales Bay nearly tripled in response to the restoration. Substantial winter population growth by most species in southern Tomales Bay was evident within 3 years after tidal reintroduction, and maximum responses to the restoration were estimated to be predominantly achieved within 8 years. In contrast to strong effects of tidal marsh restoration on winter shorebird populations in southern Tomales Bay, no significant overall responses were exhibited by shorebirds in the northern portion of the bay, although marginal evidence of expanded effects on a few species in northern Tomales Bay were suggested. The results illustrate the importance of accounting for restoration effects beyond the spatial and temporal boundaries of the restored habitat, to consider both the potentially expanded benefits and the spatial limits of those benefits to regional wildlife populations.     

Which species,how many,and from where: Integrating habitat suitability,population genomics,and abundance estimates into species reintroduction planning

Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multispecies approaches. We used an interdisciplinary, multispecies, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple‐criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species‐habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information‐based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances in the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.     

Stress and adaptation in conservation genetics

Stress, adaptation and evolution are major concerns in conservation biology. Stresses from pollution, climatic changes, disease etc. may affect population persistence. Further, stress typically occurs when species are placed in captivity. Threatened species are usually managed to conserve their ability to adapt to environmental changes, whilst species in captivity undergo adaptations that are deleterious upon reintroduction into the wild. In model studies using Drosophila melanogaster, we have found that; (a) inbreeding and loss of genetic variation reduced resistance to the stress of disease, (b) extinction rates under inbreeding are elevated by stress, (c) adaptive evolutionary potential in an increasingly stressful environment is reduced in small population, (d) rates of inbreeding are elevated under stressful conditions, (e) genetic adaptation to captivity reduces fitness when populations are reintroduced into the 'wild', and (f) the deleterious effects of adaptation on reintroduction success can be reduced by population fragmentation.     

Genotypic and phenotypic consequences of reintroduction history in the black-footed ferret (<Emphasis Type="Italic">Mustela nigripes</Emphasis>)

Population augmentation with translocated individuals has been shown to alleviate the effects of bottlenecks and drift. The first step to determine whether restoration for genetic considerations is warranted is to genetically monitor reintroduced populations and compare results to those from the source. To assess the need for genetic restoration, we evaluated genetic diversity and structure of reintroduced (n = 3) and captive populations of the endangered black-footed ferret (Mustela nigripes). We measured genotypic changes among populations using seven microsatellite markers and compared phenotypic changes with eight morphometric characters. Results indicated that for the population which rapidly grew post-reintroduction, genetic diversity was equivalent to the captive, source population. When growth languished, only the population that was augmented yearly maintained diversity. Without augmentation, allelic diversity declined precipitously and phenotypic changes were apparent. Ferrets from the genetically depaupertate population had smaller limbs and smaller overall body size than ferrets from the two populations with greater diversity. Population divergence (F _ST = 0.10 ± 0.01) was surprisingly high given the common source of populations. Thus, it appears that 5–10 years of isolation resulted in both genotypic divergence and phenotypic changes to populations. We recommend translocation of 30–40 captive individuals per annum to reintroduction sites which have not become established quickly. This approach will maximize the retention of genetic diversity, yet maintain the beneficial effects of local adaptation without being swamped by immigration.     

American Chestnut Past and Future: Implications of Restoration for Resource Pulses and Consumer Populations of Eastern U.S. Forests

Forests dominated by oak, beech, hornbeam, and boreal conifers are characterized by resource pulses. Contemporary eastern U.S. oak forests may exhibit dramatic resource pulses in part because of the loss of American chestnut, which comprised 25–50% of the canopy throughout its range. Chestnut loss may have reduced mast resources for wildlife. A newly developed, blight‐resistant hybrid makes reintroduction feasible within several years. We use historical data to model the effects of American chestnut mast on consumer populations, illuminating the potential ecological effects of a successful restoration. We parameterized a stochastic population growth model with mast production data to compare consumer population dynamics both pre‐ and post‐blight. We explored the effect of maximum intrinsic population growth rate, degree of density dependence, and reliance upon mast on consumer response to chestnut loss. We parameterized the models for white‐footed mouse, eastern chipmunk, gray squirrel, and white‐tailed deer. At a northern site 14 years post‐blight, simulated annual mast production decreased 80% and the coefficient of variation (CV) increased 60%. At a southern site 35 years post‐blight, annual mast production decreased by 35% and the CV increased by 76%. Smaller, more variable mast crops translated to reduced abundance and increased variability in simulated consumer populations. White‐footed mice were the most responsive, exhibiting a 48% decrease in population size and 57% increase in interannual variation post‐blight. The reintroduction of blight‐resistant chestnut may fundamentally alter predator–prey interactions, gypsy moth outbreaks, and Lyme disease hot spots through its effect on the character of resource pulses that drive consumer dynamics.     

Large‐scale movement behavior in a reintroduced predator population

Understanding movement behavior and identifying areas of landscape connectivity is critical for the conservation of many species. However, collecting fine‐scale movement data can be prohibitively time consuming and costly, especially for rare or endangered species, whereas existing data sets may provide the best available information on animal movement. Contemporary movement models may not be an option for modeling existing data due to low temporal resolution and large or unusual error structures, but inference can still be obtained using a functional movement modeling approach. We use a functional movement model to perform a population‐level analysis of telemetry data collected during the reintroduction of Canada lynx to Colorado. Little is known about southern lynx populations compared to those in Canada and Alaska, and inference is often limited to a few individuals due to their low densities. Our analysis of a population of Canada lynx fills significant gaps in the knowledge of Canada lynx behavior at the southern edge of its historical range. We analyzed functions of individual‐level movement paths, such as speed, residence time, and tortuosity, and identified a region of connectivity that extended north from the San Juan Mountains, along the continental divide, and terminated in Wyoming at the northern edge of the Southern Rocky Mountains. Individuals were able to traverse large distances across non‐boreal habitat, including exploratory movements to the Greater Yellowstone area and beyond. We found evidence for an effect of seasonality and breeding status on many of the movement quantities and documented a potential reintroduction effect. Our findings provide the first analysis of Canada lynx movement in Colorado and substantially augment the information available for conservation and management decisions. The functional movement framework can be extended to other species and demonstrates that information on movement behavior can be obtained using existing data sets.