Conspecifics can be aliens too: A review of effects of restocking practices in vertebrates

The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards

The translocation of individuals around the world is leading to rising incidences of anthropogenic hybridization, particularly between domestic and wild congeners. We apply a landscape genomics approach for thousands of mallard (Anas platyrhynchos) samples across continental and island populations to determine the result of over a century of supplementation practices. We establish that a single domestic game-farm mallard breed is the source for contemporary release programs in Eurasia and North America, as well as for established feral populations in New Zealand and Hawaii. In particular, we identify central Europe and eastern North America as epicenters of ongoing anthropogenic hybridization, and conclude that the release of game-farm mallards continues to affect the genetic integrity of wild mallards. Conversely, self-sustaining feral populations in New Zealand and Hawaii not only show strong differentiation from their original stock, but also signatures of local adaptation occurring in less than a half-century since game-farm mallard releases have ceased. We conclude that 'wild' is not singular, and that even feral populations are capable of responding to natural processes. Although considered paradoxical to biological conservation, understanding the capacity for wildness among feral and feral admixed populations in human landscapes is critical as such interactions increase in the Anthropocene.

Population genetics and geographic origins of mallards harvested in northwestern Ohio

The genetic composition of mallards in eastern North America has been changed by release of domestically-raised, game-farm mallards to supplement wild populations for hunting. We sampled 296 hatch-year mallards harvested in northwestern Ohio, October-December 2019. The aim was to determine their genetic ancestry and geographic origin to understand the geographic extent of game-farm mallard introgression into wild populations in more westward regions of North America. We used molecular analysis to detect that 35% of samples were pure wild mallard, 12% were early generation hybrids between wild and game-farm mallards (i.e., F1-F3), and the remaining 53% of samples were assigned as part of a hybrid swarm. Percentage of individuals in our study with some form of hybridization with game-farm mallard (65%) was greater than previously detected farther south in the mid-continent (~4%), but less than the Atlantic coast of North America (~ 92%). Stable isotope analysis using δ2Hf suggested that pure wild mallards originated from areas farther north and west than hybrid mallards. More specifically, 17% of all Ohio samples had δ2Hf consistent with more western origins in the prairies, parkland, or boreal regions of the mid-continent of North America, with 55%, 35%, and 10% of these being genetically wild, hybrid swarm, and F3, respectively. We conclude that continued game-farm introgression into wild mallards is not isolated to the eastern population of mallards in North America, and may be increasing and more widespread than previously detected. Mallards in our study had greater incidence of game-farm hybridization than other locales in the mid-continent but less than eastern North American regions suggesting further need to understand game-farm mallard genetic variation and movement across the continent.

Unexpected genetic integrity boosts hope for the conservation of the red-legged partridge (Alectoris rufa, Galliformes) in Italy

The red-legged partridge (Alectoris rufa) is a medium-sized galliform endemic to southwestern Europe. In the easternmost part of the species' range, the population inhabiting Elba Island (Tuscan Archipelago National Park, Italy) is of undisputed conservation value. While we found nuclear and maternal DNA introgression with the exotic chukar partridge (A. chukar) in previous studies based on microsatellite DNA (n = 25) and two mitochondrial markers (n = 103), respectively, we disclosed a limited or null admixture in a few Elban partridges (n = 4) in a recent genomic investigation relying on 168,675 Single Nucleotide Polymorphisms (SNPs). We herein carried out an extended microsatellite DNA survey including additional 65 samples (total, 90) and six loci (total, 11) to determine both spatial structure and genetic integrity of local A. rufa. A sharp divergence between the subpopulations inhabiting the two sides of the island was disclosed, and the microsatellites indicated that all Elban partridges were not admixed with the chukar, thus fully reflecting the picture inferred using SNPs. We hypothesized that the spreading of chukar genes was constrained by negative selection, with the persistence of only the maternal lineage being indicative of thermal adaptation. The two subpopulations should be treated as distinct Management Units, and an envisaged plan to secure a stock onto nearby Pianosa Island could not only warrant endurance of the Elban population but also establish a source of valuable founders for the ex-situ management of the species in Italy. Our study exemplifies how a suitable samples/loci combination is the key to solve wildlife issues dealing with introgression.

Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming

Simple Summary

The pikeperch Sander lucioperca (Linnaeus, 1758) is an important fish species in the development of European aquaculture. The aquaculture of a fish species can be facilitated by knowing the genetic variability within and among populations. Here, we assessed the genetic background of 8 wild populations along with 13 broodstocks (i.e., from fish farms) of pikeperch through a combination of genetic markers. We underlined that current broodstocks have a genetic diversity similar to wild populations. When focusing on genetic differentiation, we highlight that European pikeperch populations are divided into two groups: one predominantly present in Northern Europe and around the Baltic Sea and another mainly in Central Europe. Broodstocks appear to contain fish of a single origin with only a few exceptions. Ultimately, we have proposed baseline information about genetic diversity of pikeperch along with a genetic tool that can help pikeperch producers manage and improve their fish stock.

Abstract

The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions.

Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S

As anthropogenic disturbances continue to drive habitat loss and range contractions, the maintenance of evolutionary processes will increasingly require targeting measures to the population level, even for common and widespread species. Doing so requires detailed knowledge of population genetic structure, both to identify populations of conservation need and value, as well as to evaluate suitability of potential donor populations. We conducted a range-wide analysis of the genetic structure of red foxes in the contiguous western U.S., including a federally endangered distinct population segment of the Sierra Nevada subspecies, with the objectives of contextualizing field observations of relative scarcity in the Pacific mountains and increasing abundance in the cold desert basins of the Intermountain West. Using 31 autosomal microsatellites, along with mitochondrial and Y-chromosome markers, we found that populations of the Pacific mountains were isolated from one another and genetically depauperate (e.g., estimated Ne range = 3–9). In contrast, red foxes in the Intermountain regions showed relatively high connectivity and genetic diversity. Although most Intermountain red foxes carried indigenous western matrilines (78%) and patrilines (85%), the presence of nonindigenous haplotypes at lower elevations indicated admixture with fur-farm foxes and possibly expanding midcontinent populations as well. Our findings suggest that some Pacific mountain populations could likely benefit from increased connectivity (i.e., genetic rescue) but that nonnative admixture makes expanding populations in the Intermountain basins a non-ideal source. However, our results also suggest contact between Pacific mountain and Intermountain basin populations is likely to increase regardless, warranting consideration of risks and benefits of proactive measures to mitigate against unwanted effects of Intermountain gene flow.

When Ecological Analysis Reveals Hidden Human Dimensions: Building on Long-Term Community Participation to Enable a Conservation Translocation of Mountain Bongo in Kenya

Conservation translocations have traditionally focused on ecological aspects while overlooking or underestimating the importance of human dimensions. Here, we present a feasibility analysis for a conservation translocation that up front took a holistic approach by investigating both ecological and socio-economic suitability of reinforcing mountain bongo in Eburu National Forest, Kenya. From 2018 to 2019, we set up 50 cameras to detect mountain bongo and searched for secondary signs in a grid overlaying Eburu. We also conducted surveys with 200 households surrounding the forest and interviewed 300 students to understand local perceptions of and interactions with Eburu Forest and their desire for a mountain bongo translocation. We used data from camera trapping and secondary signs in a MaxEnt model to determine the amount and location of available habitat for a bongo conservation translocation. Camera traps recorded only five bongo events in the 2-year study, and MaxEnt models revealed that these antelopes were relegated to less than 2.5 km of available habitat. Socio-economic surveys indicated local support for the conservation of bongo and their habitat, and yet our camera traps uncovered threatening illicit activities that could jeopardize both bongo survival and any attempt at boosting the remnant population with captive-bred individuals. We report how we built on long-term community and stakeholder engagement to mitigate these threats and provide concrete recommendations for how to proceed with a conservation translocation in terms of both the biological aspects and continued efforts to integrate socio-economic needs and community engagement.

Genomic Hatchery Introgression in Brown Trout (Salmo trutta L.): Development of a Diagnostic SNP Panel for Monitoring the Impacted Mediterranean Rivers

Brown trout (Salmo trutta L.) populations have been restocked during recent decades to satisfy angling demand and counterbalance the decline of wild populations. Millions of fertile brown trout individuals were released into Mediterranean and Atlantic rivers from hatcheries with homogeneous central European stocks. Consequently, many native gene pools have become endangered by introgressive hybridization with those hatchery stocks. Different genetic tools have been used to identify and evaluate the degree of introgression starting from pure native and restocking reference populations (e.g., LDH-C* locus, microsatellites). However, due to the high genetic structuring of brown trout, the definition of the "native pool" is hard to achieve. Additionally, although the LDH-C* locus is useful for determining the introgression degree at the population level, its consistency at individual level is far from being accurate, especially after several generations were since releases. Accordingly, the development of a more powerful and cost-effective tool is essential for an appropriate monitoring to recover brown-trout-native gene pools. Here, we used the 2b restriction site-associated DNA sequencing (2b-RADseq) and Stacks 2 with a reference genome to identify single-nucleotide polymorphisms (SNPs) diagnostic for hatchery-native fish discrimination in the Atlantic and Mediterranean drainages of the Iberian Peninsula. A final set of 20 SNPs was validated in a MassARRAY® System genotyping by contrasting data with the whole SNP dataset using samples with different degree of introgression from those previously recorded. Heterogeneous introgression impact was confirmed among and within river basins, and was the highest in the Mediterranean Slope. The SNP tool reported here should be assessed in a broader sample scenario in Southern Europe considering its potential for monitoring recovery plans.

Captive breeding and the conservation of the threatened houbara bustards

Translocation of captive-bred individuals to reinforce wild populations may be an important conservation approach for some species, but can be detrimental when employed to boost exploited wild populations, particularly where repeated long-term reinforcement aims to compensate for repeated unregulated offtake. We review evidence that captive breeding alters multiple physiological, life-history and temperamental traits through founder effects, genetic drift and unintended adaption to captivity; degrades learnt behaviours; and compromises biogeography, population structure and viability through introgression. We highlight these risks for the globally threatened African houbara Chlamydotis undulata and Asian houbara C. macqueenii, 2 bustard species hunted throughout much of their ranges and now subject to multiple large-scale captive-breeding programmes and translocations. In eastern Morocco, annual releases of captive-bred African houbara are 2‒3 times higher than original wild numbers, but no investigation of their potentially deleterious effects has, to our knowledge, been published, although most wild populations may now have been replaced by captive-bred domestic stock, which are reportedly not self-sustaining. Despite multiple decades of reinforcement, we are not aware of any analysis of the contribution of captive breeding to African houbara population dynamics, or of the genomic consequences. Asian houbara release programmes may also be promoting rather than preventing declines, and need to contextualise themselves through rigorous analyses of wild population numbers, demographic rates and threats, maintenance of phylogeographic concordance of released with supplemented populations, profiling of traits crucial to survival and the measurement and modelling of the impacts of reinforcement on physiological and behavioural fitness of wild populations.

Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose

Interspecific introgression is considered a potential threat to endangered taxa. One example where this has had a major impact on conservation policy is the lesser white-fronted goose (LWfG). After a dramatic decline in Sweden, captive breeding birds were released between 1981-1999 with the aim to reinforce the population. However, the detection of greater white-fronted goose (GWfG) mitochondrial DNA in the LWfG breeding stock led to the release program being dismantled, even though the presence of GWfG introgression in the actual wild Swedish LWfG population was never documented. To examine this, we sequenced the complete genomes of 21 LWfG birds from the Swedish, Russian and Norwegian populations, and compared these with genomes from other goose species, including the GWfG. We found no evidence of interspecific introgression into the wild Swedish LWfG population in either nuclear genomic or mitochondrial data. Moreover, Swedish LWfG birds are genetically distinct from the Russian and Norwegian populations and display comparatively low genomic diversity and high levels of inbreeding. Our findings highlight the utility of genomic approaches in providing scientific evidence that can help improve conservation management as well as policies for breeding and reinforcement programmes.

Differences in the growth rate and immune strategies of farmed and wild mallard populations

Individuals reared in captivity are exposed to distinct selection pressures and evolutionary processes causing genetic and phenotypic divergence from wild populations. Consequently, restocking with farmed individuals may represent a considerable risk for the fitness of free-living populations. Supportive breeding on a massive scale has been established in many European countries to increase hunting opportunities for the most common duck species, the mallard (Anas platyrhynchos). It has previously been shown that mallards from breeding facilities differ genetically from wild populations and there is some indication of morphological differences. Using a common-garden experiment, we tested for differences in growth parameters between free-living populations and individuals from breeding facilities during the first 20 days of post-hatching development, a critical phase for survival in free-living populations. In addition, we compared their immune function by assessing two haematological parameters, H/L ratio and immature erythrocyte frequency, and plasma complement activity. Our data show that farmed ducklings exhibit larger morphological parameters, a higher growth rates, and higher complement activity. In haematological parameters, we observed high dynamic changes in duckling ontogeny in relation to their morphological parameters. In conclusion, our data demonstrate pronounced phenotype divergence between farmed and wild mallard populations that can be genetically determined. We argue that this divergence can directly or indirectly affect fitness of farmed individuals introduced to the breeding population as well as fitness of farmed x wild hybrids.

Surveillance and habitat diversity affect European brown hare (Lepus europaeus) density in protected breeding areas

The European brown hare (Lepus europaeus) is an important game species throughout Europe. In Italy, for preventing the introduction of allochthonous strains, the management of brown hare populations has focused on the establishment of small protected areas (ZRCs), appositely managed for disposing of wild-born hares for restocking hunting territories. We investigated the effects of both land cover and surveillance on hare density and habitat preferences in 20 ZRCs, monitored twice per year (pre- and post-breeding periods) between 1997 and 2017. Density, as assessed by spotlight counts, ranged between 2.8 and 47.0 ind/km2 in spring and 5.0 and 68.4 ind/km2 in autumn. Surveillance, percent length of protected boundaries, year of institution and habitat diversity, as assessed by Shannon’s Index, were the main factors affecting hare density. During their foraging activity, hares selected ryegrass, hayfields and lucerne, while avoided maize stubble and ploughed fields and were never recorded in poplar plantations or next to human settlements. While the effects of habitat heterogeneity on hare density have been widely studied, we suggest that the involvement of local stakeholders may be of paramount importance for ensuring effective conservation measures.

Multi-generational genetic consequences of reinforcement in a bird metapopulation

Translocation of conspecific individuals to reduce extinction risk of small, isolated populations and prevent genetic depletion is a powerful tool in conservation biology. An important question is how the translocated individuals influence the long-term genetic composition of the recipient population. Here, we experimentally reinforced a house sparrow (Passer domesticus) population, and examined the impact of this translocation on allele frequencies, levels of heterozygosity and genetic differentiation over six cohorts. We found no permanent increase in the mean number of alleles across loci or levels of observed heterozygosity, but a few alleles private to the translocated individuals remained in the population and we found a short-term increase in heterozygosity. Consequently, genetic differentiation of the recipient population compared to the genetic composition prior to reinforcement was small. The limited genetic impact was due to combined effects of a small probability of establishment and low mating success for the translocated individuals, together with increased genetic drift in the recipient population. Our findings emphasize the importance of selection and genetic drift as forces that may decrease the genetic contribution of reinforcement, especially in small populations. Conservation managers should aim to improve habitat quality in the recipient population to reduce genetic drift following translocation and thereby avoid the need for continued reinforcement. Furthermore, by facilitating establishment success and selecting individuals expected to have high mating success, possibly indicated by sexually selected traits, genetic contribution of released individuals is increased which in turn will decrease reproductive skew and genetic drift.

Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks

Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.

Non-native and hybrid in a changing environment: conservation perspectives for the last Italian red-legged partridge (Alectoris rufa) population with long natural history

The ever-increasing biotic homogenization - especially when associated with introgressive hybridization - raises concern for the reduction of the spatial component of diversity in wildlife worldwide. Nonetheless, there is a growing attention to the potential conservation value of hybridization in fastening the adaptive evolutionary responses to rapidly changing selective pressures. Under these premises, we investigated the genetic affinity of the red-legged partridge (Alectoris rufa) population inhabiting Elba Island (Italy) in the context of the overall species phylogeography and particularly of the nominate subspecies it is traditionally ascribed to. Although notoriously hybrid with the congeneric A. chukar, this island population is of undisputedly value because of its long natural history and self-sustainability. As such, its adaptive conservation management calls for a comprehensive knowledge including the assessment of its geographic origin. For this purpose, 110 fecal samples were collected across Elba, genotyped at their joint Cytochrome-b and Control Region genes (2,249 characters), and compared with 149 conspecifics from all over the species distribution range. We confirmed a widespread A. chukar mitochondrial DNA introgression in Elba partridges, whereas their expected formal assignment to the nominate subspecies from Italy and France was rejected, since these turned out to be closely related to conspecifics from the Iberian Peninsula. This counterintuitive result found support in a large variety of literary sources and compelling evidences from personal testimonies revealing recent intense management with farm-reared birds of Spanish origin. Although the nativeness of Elba partridges was disproved, we advise local authorities to keep warranting the ongoing conservation efforts - and especially restore the connectivity between the western and eastern island sub-populations - as this resource may still be conceived as the ultimate repository for part of the otherwise extinct Italian A. r. rufa genome. Indeed, the admixture with conspecifics from the Iberian Peninsula does not necessarily mean that the entirety of the native nuclear genome of Elba partridges has been wiped out. Furthermore, these latter represent an interesting case study in conservation biology to investigate the possible role played by introgressive hybridization in the adaptation to recent land use and vegetation cover changes associated with rural abandonment in an insular yet heavily anthropized context.

Subpopulation augmentation among habitat patches as a tool to manage an endangered Mojave Desert wetlands-dependent rodent during anthropogenic restricted water climate regimes

Intensive management may be necessary to protect some highly vulnerable endangered species, particularly those dependent on water availability regimes that might be disrupted by ongoing climate change. The Amargosa vole (Microtus californicus scirpensis) is an increasingly imperiled rodent constrained to rare wetland habitat in the Mojave Desert. In 2014 and 2016, we trapped and radio-collared 30 voles, 24 were translocated and six remained at donor and recipient marshes as resident control voles. Soft-release was performed followed by remote camera and radio-telemetry monitoring. Although comparative metrics were not statistically significant, the mean maximum known distance moved (MDM) was longer for translocated (82.3 ± 14.6 m) vs. resident-control voles (74.9 ± 17.5 m) and for female (98.4 ± 19.9 m) vs. male (57.8 ± 9.1 m) voles. The mean area occupied (AO) tended to be greater in female (0.15 ± 0.04 ha) vs. male (0.12 ± 0.03 ha) voles, and control voles (0.15 ± 0.05 ha) compared with translocated voles (0.13 ± 0.03 ha). The mean minimum known time alive (MTA) was 38.2 ± 19.4 days for resident-control voles and 47.0 ± 10.6 days for translocated voles. Female survival (55.7 ± 14.3 days) exceeded that of males (31.5 ± 9.4 days) regardless of study group. Activity in bulrush/rushes mix and bulrush vegetation types was strongly and significantly overrepresented compared with salt grass and rushes alone, and habitat selection did not differ between resident and translocated voles. Our results provide ecological and methodological insights for future translocations as part of a strategy of promoting long-term survival of an extremely endangered small mammal in a wild desert environment.

Enhancing population stability with combined adaptive limiter control and finding the optimal harvesting-restocking balance

Fluctuations in population size may have negative consequences (e.g., an increased risk of extinction or the occurrence of repeated outbreaks), and many management strategies are aimed at avoiding them by either only restocking or only harvesting the population. Two of these strategies are adaptive limiter control (ALC) and adaptive threshold harvesting (ATH). With ALC the population is controlled by only restocking and with ATH by only harvesting. We propose the strategy of combined adaptive limiter control (CALC) as the combination of ALC and ATH and study the potential advantages of CALC over ALC and ATH. We consider two different population models, namely a stochastic overcompensatory model and a host-pathogen-predator model. For the first model, our results show that the combination of restocking and harvesting under CALC improves the constancy stability of the managed populations when the harvesting and restocking intensities are high enough. Otherwise the effect is marginal or in rare cases negative. For the second model, we show that combining harvesting with restocking reduces the outbreak risk only if the harvesting intensity is low. For medium harvesting intensities the effect is marginal and for high harvesting intensities the risk of outbreaks is increased. In addition, we study the optimal harvesting-restocking balance by considering a proxy of the benefit obtained in terms of the reduction in the outbreak risk and the harvesting and restocking costs.

Back home? Uncertainties for returning seized animals to the source-areas under climate change

Regardless of the economic, social and environmental impacts caused by wild animal trafficking worldwide, the suitable destination of seized specimens is one of the main challenges faced by environmental managers and authorities. In Brazil, returning seized animals to the wild has been the most frequent path in population restoration programs, and has been carried out, as a priority, in areas where the animals were captured. However, in addition to the difficulty in identifying the locations of illegal captures, little scientific knowledge is available on the future viability of the source-areas to global climate change. Thus, the current work aims to evaluate the impacts of climate change on the main source-municipalities for animal trafficking in Brazil, referred to herein as source-areas. For this, using ecological niche modeling, the environmental suitability of the source-areas for illegal animal captures was evaluated in two scenarios at two different time horizons: optimistic (RCP 26) and pessimistic (RCP 85) emission scenarios in both 2050 and 2070 projections. Moreover, the source-areas were compared with the Brazilian Federal protected areas, used here as the control group. According to the results, Brazilian source-municipalities are not always the best option for maintaining the most seized species in the future simulations, and, therefore, seem not be the best option for projects that aim for the return of these animals to the wild. In this sense, despite the genetic and ecological issues inherent in translocation projects, our results suggest that population restoration programs for seized species need to be rethought, and furthermore other suitable areas could be considered for truly ensuring the survival and maintenance of overexploited populations in the long term.

A framework to measure the wildness of managed large vertebrate populations

As landscapes continue to fall under human influence through habitat loss and fragmentation, fencing is increasingly being used to mitigate anthropogenic threats and enhance the commercial value of wildlife. Subsequent intensification of management potentially erodes wildness by disembodying populations from landscape-level processes, thereby disconnecting species from natural selection. Tools are needed to measure the degree to which populations of large vertebrate species in formally protected and privately owned wildlife areas are self-sustaining and free to adapt. We devised a framework to measure such wildness based on 6 attributes relating to the evolutionary and ecological dynamics of vertebrates (space, disease and parasite resistance, exposure to predation, exposure to limitations and fluctuations of food and water supply, and reproduction). For each attribute, we set empirical, species-specific thresholds between 5 wildness states based on quantifiable management interventions. We analysed data from 205 private wildlife properties with management objectives spanning ecotourism to consumptive utilization to test the framework on 6 herbivore species representing a range of conservation statuses and commercial values. Wildness scores among species differed significantly, and the proportion of populations identified as wild ranged from 12% to 84%, which indicates the tool detected site-scale differences both among populations of different species and populations of the same species under different management regimes. By quantifying wildness, this framework provides practitioners with standardized measurement units that link biodiversity with the sustainable use of wildlife. Applications include informing species management plans at local scales; standardizing the inclusion of managed populations in red-list assessments; and providing a platform for certification and regulation of wildlife-based economies. Applying this framework may help embed wildness as a normative value in policy and mitigate the shifting baseline of what it means to truly conserve a species.

Tracking genetic diversity in a large-scale oyster restoration program: effects of hatchery propagation and initial characterization of diversity on restored vs. wild reefs

The release of hatchery-propagated fish and shellfish is occurring on a global scale, but the genetic impacts of these practices are often not fully understood and rarely monitored. Slow recovery of depleted eastern oyster populations in the Chesapeake Bay, USA has prompted a hatchery-based restoration program focused in the Choptank River, Maryland consisting of the mass release of hatchery-produced juveniles from local, wild broodstock. To evaluate potential genetic effects of this program, we (1) examined changes in genetic diversity (allelic richness, heterozygosity) and the effective number of breeders (Nb) over the hatchery production cycle with microsatellite-based parentage of natural, mass- and controlled-spawned cohorts, and (2) compared genetic diversity and effective population size (Ne) of a restored reef to wild source populations. Mass-spawned cohorts showed high variance in reproductive contribution, particularly among males, leading to a 45% average reduction in Nb from spawning adult numbers and higher relatedness-lower magnitude reductions in heterozygosity and significant reductions in allelic richness were also observed. While controlled-spawns (single-male fertilizations of pooled eggs) reduced male variance, overall reproductive variance (Vk) remained high. Finally, oysters sampled from a restored reef displayed comparable Ne, genetic diversity, and relatedness to samples from wild populations, with no significant genetic differentiation among them. Overall, the hatchery-based results and initial field-based population genetic analyses suggest that despite reductions in diversity from parents to offspring owing to high Vk, enhancement with rotated, wild broodstock appears to have maintained genetic diversity in a restored reef population compared to proximal wild populations.

Human-modified biogeographic patterns and conservation in game birds: The dilemma of the black francolin (Francolinus francolinus, Phasianidae) in Pakistan

The ever-increasing human-mediated wildlife reshuffling is raising concern for the conservation of biodiversity. The loss of biological distinctiveness among regions lessens the genetic diversity and consequently the evolutionary potential of local biotas to tackle present-day global change and human disturbance. This process may be sometimes cryptic unless investigated by means of a molecular approach. In this respect, game birds are a paradigmatic case. The black francolin (Francolinus francolinus, Phasianidae) is a medium-sized galliform whose distribution range stretches from Cyprus to the Gulf of Bengal. Six morphologic subspecies are known, with three of which occurring in Pakistan, where the species is heavily hunted and used as pet for chirping competitions. We genotyped 98 samples (feathers) at both the entire mitochondrial DNA Control Region gene and nine microsatellite loci to get a deeper insight into the genetic diversity of the black francolin in Pakistan in order to offer cogent recommendations for its conservation management. We identified several mtDNA lineages that were consistent with the currently described subspecies/taxonomy whose pattern of co-occurrence is compatible with the geological history and the faunal movement routes of the region under study. However, the biparentally inherited microsatellites returned a quite discordant picture of an extensive, sex-biased genetic mixing due to the intensive relocations of already overharvested male individuals for chirping competitions. Our results indicated that the genetic integrity of the black francolin in Pakistan could be seriously at risk and call for monitoring and limiting its trade other than enhancing the public awareness of the importance of local biodiversity resources.

Red Fox Ancestry and Connectivity Assessments Reveal Minimal Fur Farm Introgression in Greater Yellowstone Ecosystem

Rocky Mountain red foxes Vulpes vulpes macroura potentially encounter other red fox Vulpes vulpes lineages at lower elevations, which may include nonindigenous red foxes derived from fur farms. Introgression from nonindigenous red foxes could have negative evolutionary consequences for the rare Rocky Mountain red fox subspecies. Red foxes at high elevations in the Greater Yellowstone Ecosystem exhibit lighter coat colors than those at lower elevations, potentially indicating that they represent the indigenous subspecies and that gene flow across the elevational gradient is restricted. We collected tissue samples across a 1,750-m elevation range and examined mitochondrial DNA sequences and nuclear DNA microsatellite genotypes to assess the ancestry and genetic population structure of red foxes in the northern Greater Yellowstone Ecosystem. We also used reference samples from fur farm red foxes and indigenous red foxes of the western United States to assess the extent of nonindigenous introgression across the ecosystem. We found little overlap in the elevational distribution of maternally inherited mitochondrial DNA haplotypes: above 1,600 m, we only found indigenous Rocky Mountain haplotypes (n = 4), whereas below 1,600 m, we found haplotypes not indigenous to the Rocky Mountains (n = 5) that were associated with fur farms or indigenous to the Great Plains. In contrast, biparentally inherited microsatellite variation showed little population structure across the elevational gradient. Despite this evidence of nuclear gene flow across the elevational gradient, we found little fur farm introgression in the microsatellite genotypes. It is possible that long-standing nuclear (but apparently not mitochondrial) gene flow between Rocky Mountain red foxes and indigenous red foxes on the Great Plains explained the low nuclear differentiation of these populations. Importantly, our results suggested that high elevations of the northern Greater Yellowstone Ecosystem remained free of significant fur farm introgression. Mitonuclear discordance could reflect sex-biased dispersal, which we hypothesize could be the effect of elevational differences in reproductive phenology.

Swift action increases the success of population reinforcement for a declining prairie grouse

Translocations have become an increasingly valuable tool for conservation in recent years, but assessing the successfulness of translocations and identifying factors that contribute to their success continue to challenge biologists. As a unique class of translocation, population reinforcements have received relatively little attention despite representing a substantial portion of translocation programs. Here, we conducted population viability analyses to quantify the effects of 216 reinforcement scenarios on the long-term viability of four populations of Greater Prairie-Chickens (Tympanuchus cupido pinnatus) in Wisconsin, USA, and used multiple linear regression to identify factors that had the greatest relative influence on population viability. We considered reinforcements from outside of the study area in addition to translocations among Wisconsin populations. We observed the largest decreases in site-specific extinction probability and the largest increases in the number of sites persisting for 50 years when more vulnerable populations were targeted for reinforcement. Conversely, reinforcing the most stable sites caused the greatest reduction in regional extinction probability. We found that the number of translocated hens was a comparatively poor predictor of changes in long-term population viability, whereas the earlier onset of reinforcement was consistently associated with the greatest increases in viability. Our results highlight the value of evaluating alternative reinforcement strategies a priori and considering the effects of reinforcement on metrics of long-term population persistence.

Impacts of taxonomic inertia for the conservation of African ungulate diversity: an overview

We review the state of African ungulate taxonomy over the last 120 years, with an emphasis on the introduction of the polytypic species concept and the discipline's general neglect since the middle of the 20th century. We single out negative consequences of 'orthodox' taxonomy, highlighting numerous cases of neglect of threatened lineages, unsound translocations that led to lineage introgression, and cases of maladaptation to local conditions including parasitic infections. Additionally, several captive breeding programmes have been hampered by chromosome rearrangements caused by involuntary lineage mixing. We advocate that specimen-based taxonomy should regain its keystone role in mammal research and conservation biology, with its scientific values augmented with genomic evidence. While integration with molecular biology, ecology and behaviour is needed for a full understanding of ungulate alpha diversity, we stress that morphological diversity has been neglected despite its tremendous practical importance for some groups of 'utilizers' such as trophy hunters, wildlife tourists and conservationists. We conclude that there is no evidence that purported 'taxonomic inflation' has adverse effects on ungulate conservation: rather, it is taxonomic inertia that has such adverse effects. We stress that sound science, founded on robust taxonomy, should underpin effective sustainable management (hunting, ranching, captive breeding and reintroduction programmes) of this unique African natural resource.

Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape

The streams draining of into San Francisco Bay, California, have been impacted by habitat alteration for over 150 years, and roads, dams, water diversions, and other impediments now block the paths of many aquatic migratory species. These changes can affect the genetic structure of fish populations, as well as driving adaptive evolution to novel environmental conditions. Here, we determine the evolutionary relationships of San Francisco Bay Area steelhead/rainbow trout (Oncorhynchus mykiss) populations and show that (i) they are more closely related to native coastal steelhead than to the California Central Valley lineage, with no evidence of introgression by domesticated hatchery rainbow trout, (ii) populations above and below barriers within watersheds are each other's closest relatives, and (iii) adaptive genomic variation associated with migratory life-history traits in O. mykiss shows substantial evolutionary differences between fish above and below dams. These findings support continued habitat restoration and protection of San Francisco Bay Area O. mykiss populations and demonstrate that ecological conditions in novel habitats above barriers to anadromy influence life-history evolution. We highlight the importance of considering the adaptive landscape in conservation and restoration programs for species living in highly modified habitats, particularly with respect to key life-history traits.

Genetic guidelines for captive breeding and reintroductions of the endangered Black-fronted Piping Guan, Aburria jacutinga (galliformes, cracidae), an Atlantic Forest endemic

The survival of a number of birds rely on captive breeding and reintroduction into the wild, but captive populations are often small and can be exposed to the negative effects of inbreeding and genetic drift. Then, managers are concerned not only with producing as much offspring as possible, but also with the retention of the maximum genetic variability within and between populations. The Black-fronted Piping Guan, Aburria jacutinga, is an endangered cracid endemic to the Atlantic Forest of southeastern South America. Because of its conservation status and functional importance, a captive breeding program started independently, mainly in three aviaries, in the decade of 1980. Although they have supplied animals for reintroductions, genetic variability aspects have never been considered. Here we addressed levels of genetic variability within and between these aviaries. Bayesian clustering analyses revealed two lineages. Inbreeding was not detected, although we found evidences for a recent bottleneck in one of the aviaries. Then, our main management recommendations are: i) reintroducing the species in areas where it has been extinct is more prudent than supplementing natural populations, as it could involve risks of disrupting local adaptive complexes; ii) as far as inbreeding can be avoided, the captive groups should be managed separately to minimize adaptation to captivity; iii) crossbreedings in pre-release generations could improve reintroduction success; and iv) a studbook should be implemented. As populations of Black-fronted Piping Guan from conservation units are progressively declining, these captive genetic repositories may gain importance in a near future. Zoo Biol. 35:313-318, 2016. © 2016 Wiley Periodicals, Inc.

Potential contribution of fish restocking to the recovery of deteriorated coral reefs: an alternative restoration method?

Counteracting the worldwide trend of coral reef degeneration is a major challenge for the scientific community. A crucial management approach to minimizing stress effects on healthy reefs and helping the recovery of disturbed reefs is reef protection. However, the current rapid decline of the world’s reefs suggests that protection might be insufficient as a viable stand-alone management approach for some reefs. We thus suggest that the ecological restoration of coral reefs (CRR) should be considered as a valid component of coral reef management, in addition to protection, if the applied method is economically applicable and scalable. This theoretical study examines the potential applicability and outcomes of restocking grazers as a restoration tool for coral reef recovery—a tool that has not been applied so far in reef restoration projects. We studied the effect of restocking grazing fish as a restoration method using a mathematical model of degrading reefs, and analyzed the financial outcomes of the restocking intervention. The results suggest that applying this restoration method, in addition to protection, can facilitate reef recovery. Moreover, our analysis suggests that the restocking approach almost always becomes profitable within several years. Considering the relatively low cost of this restoration approach and the feasibility of mass production of herbivorous fish, we suggest that this approach should be considered and examined as an additional viable restoration tool for coral reefs.

Do hatchery-reared sea urchins pose a threat to genetic diversity in wild populations?

In salmonids, the release of hatchery-reared fish has been shown to cause irreversible genetic impacts on wild populations. However, although responsible practices for producing and releasing genetically diverse, hatchery-reared juveniles have been published widely, they are rarely implemented. Here, we investigated genetic differences between wild and early-generation hatchery-reared populations of the purple sea urchin Paracentrotus lividus (a commercially important species in Europe) to assess whether hatcheries were able to maintain natural levels of genetic diversity. To test the hypothesis that hatchery rearing would cause bottleneck effects (that is, a substantial reduction in genetic diversity and differentiation from wild populations), we compared the levels and patterns of genetic variation between two hatcheries and four nearby wild populations, using samples from both Spain and Ireland. We found that hatchery-reared populations were less diverse and had diverged significantly from the wild populations, with a very small effective population size and a high degree of relatedness between individuals. These results raise a number of concerns about the genetic impacts of their release into wild populations, particularly when such a degree of differentiation can occur in a single generation of hatchery rearing. Consequently, we suggest that caution should be taken when using hatchery-reared individuals to augment fisheries, even for marine species with high dispersal capacity, and we provide some recommendations to improve hatchery rearing and release practices. Our results further highlight the need to consider the genetic risks of releasing hatchery-reared juveniles into the wild during the establishment of restocking, stock enhancement and sea ranching programs.

Marshes as "Mountain Tops": Genetic Analyses of the Critically Endangered São Paulo Marsh Antwren (Aves: Thamnophilidae)

Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The São Paulo Marsh Antwren (Formicivora paludicola) is a recently-described and critically endangered bird from São Paulo State (Brazil) whose total estimated population is around 250-300 individuals, distributed in only 15 isolated marshes around São Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall FST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8-99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants.