Building evolutionary resilience for conserving biodiversity under climate change

Accounting for adaptive capacity and uncertainty in assessments of species' climate-change vulnerability

Climate-change vulnerability assessments (CCVAs) are valuable tools for assessing species' vulnerability to climatic changes, yet failure to include measures of adaptive capacity and to account for sources of uncertainty may limit their effectiveness. We took a more comprehensive approach that incorporates exposure, sensitivity, and capacity to adapt to climate change. We applied our approach to anadromous steelhead trout (Oncorhynchus mykiss) and nonanadromous bull trout (Salvelinus confluentus), threatened salmonids within the Columbia River Basin (U.S.A.). We quantified exposure on the basis of scenarios of future stream temperature and flow, and we represented sensitivity and capacity to adapt to climate change with metrics of habitat quality, demographic condition, and genetic diversity. Both species were found to be highly vulnerable to climate change at low elevations and in their southernmost habitats. However, vulnerability rankings varied widely depending on the factors (climate, habitat, demographic, and genetic) included in the CCVA and often differed for the 2 species at locations where they were sympatric. Our findings illustrate that CCVA results are highly sensitive to data inputs and that spatial differences can complicate multispecies conservation. Based on our results, we suggest that CCVAs be considered within a broader conceptual and computational framework and be used to refine hypotheses, guide research, and compare plausible scenarios of species' vulnerability to climate change.

Ecosystem restoration: recent advances in theory and practice

Restoration of damaged ecosystems is receiving increasing attention worldwide as awareness increases that humanity must sustain ecosystem structure, functioning, and diversity for its own wellbeing. Restoration will become increasingly important because our planet will sustain an increasingly heavy human footprint as human populations continue to increase. Restoration efforts can improve desirable ecological functioning, even when restoration to a historic standard is not feasible with current practice. Debate as to whether restoration is feasible is coupled to long-standing disputes regarding the definition of restoration, whether more-damaged lands are worthy of restoration efforts given limited financial resources, and ongoing conflicts as to whether the novel ecosystem concept is a help or a hindrance to restoration efforts. A willingness to consider restoration options that have promise, yet would have previously been regarded as ‘taboo’ based on the precautionary principle, is increasing. Functional restoration is becoming more prominent in the scientific literature, as evidenced by an increased emphasis on functional traits, as opposed to a simple inventory of vascular plant species. Biodiversity continues to be important, but an increasingly expansive array of provenance options that are less stringent than the traditional ‘local is best’ is now being considered. Increased appreciation for soil health, plant–soil feedbacks, biological crusts, and water quality is evident. In the United States, restoration projects are becoming increasingly motivated by or tied to remediation of major environmental problems or recovery of fauna that are either charismatic, for example, the monarch butterfly, or deliver key ecosystem services, for example, hymenopteran pollinators.

Native seed for restoration: a discussion of key issues using examples from the flora of southern Australia

Land clearing across southern Australia since European settlement has fundamentally changed the amount and distribution of native vegetation; it has also substantially reduced genetic diversity in plant species throughout Australia, especially in agricultural regions. The most recent State of the Environment report indicates that Australian biodiversity continues to decline. Many approaches to restoration are used in Australia including re-establishing plant populations using tube stock or by direct seeding. Native seed for these projects is often assumed to be plentiful and available for the majority of species we wish to restore but these assumptions are rarely true. We also rely on a small number of species for the majority of restoration projects despite the vast number of species required to fully restore complex plant communities. The majority of seed for restoration is still primarily collected from native vegetation despite longstanding concerns regarding the sustainability of this practice and the globally recognised impacts of vegetation fragmentation on seed production and genetic diversity. Climate change is also expected to challenge seed production as temperatures rise and water availability becomes more limited; changes to current planting practices may also be required. Until now native seed collection has relied on market forces to build a strong and efficient industry sector, but in reality the Australian native seed market is primarily driven by Federal, State and Territory funding. In addition, unlike other seed-based agri-businesses native seed collection lacks national industry standards. A new approach is required to support development of the native seed collection and use sector into an innovative industry.

Nature conservation and ecological restoration in a changing climate: what are we aiming for?

Principles underpinning the goals of nature conservation and ecological restoration have traditionally involved preventing ecological change or restoring ecosystems or populations towards preferred historical states. Under global climate change, it is increasingly recognised that this may no longer be achievable, but there has been limited debate regarding new principles that can help guide goal-setting for nature conservation and ecological restoration in dynamic environments. To stimulate such debate, we established a framework of human motivations implicit in historically focussed nature conservation approaches. We drew on this and a literature survey to propose a palette of five principles to guide goal-setting for nature conservation and ecological restoration in a changing climate. Our framework proposes three broad sets of human motivations relevant to nature conservation: (1) basic survival and material needs (akin to provisioning and regulating ecosystem services), (2) psychological and cultural needs such as a sense of place (reflecting cultural ecosystem services), and (3) the need to fulfil moral or ethical obligations (e.g. intergenerational and interspecies equity). Meeting basic needs for current and future generations is supported by a commonly proposed principle to optimise ecological processes and functions (Principle 1); which in turn is dependent on maintaining the ongoing evolutionary potential in the world’s biota (Principle 2). Beyond this, motivations relating to psychological, cultural and moral needs demand not only an emphasis on healthy ecosystem functioning, but on the character and diversity of the ecosystems and species that contribute to these functions. Our subsequent three principles, minimise native species losses (Principle 3), maintain the evolutionary character and biogeographic structuring of the biota (Principle 4), and maintain wild natural ecosystems (Principle 5) contribute to these further goals. Although these principles can sometimes be conflicting, we argue that by connecting directly with underlying motivations, this broader palette will help take us forward towards more effective nature conservation in a rapidly changing world.

Supplying trees in an era of environmental uncertainty: Identifying challenges faced by the forest nursery sector in Great Britain

In recent years, numerous articles have addressed management strategies aimed at assisting forests to adapt to climate change. However, these seldom take into account the practical and economic implications of implementing these strategies, notably, supply of forest plants and seed. Using semi-structured interviews with practitioners involved in the plant and seed supply chain in Great Britain, we highlight a series of practical and economic bottlenecks commonly encountered in the supply of locally sourced seed and domestically produced planting stock for native woodland and hedging markets. We find that adoption of alternative seed sourcing strategies, designed specifically to account for directional climate warming, is likely to exacerbate existing problems by adding further complexity to decisions nurseries make about tree species and seed origins to produce. The lack of long-term market predictability brought about by the current configuration of forestry grants and regulations and, in particular, the administrative systems for processing grant applications is identified as a major impediment to having a sustainable and competitive supply of home-grown and currently adapted planting stock. Finally, the time and effort it takes to supply healthy plants for native woodland creation projects deserves much wider recognition throughout the industry and will be crucial if planting objectives are to be met sustainably.

Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box)

In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape-wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated remnants and revegetation sites were assessed across the now highly fragmented distribution of this species using the DArTseq genomic approach. Genomic diversity was similar within all three types of remnant patches analysed, although often significantly but only slightly lower in revegetation sites compared with natural remnants. Differences in diversity between stand types varied across chromosomes. Genomic differentiation was higher between small, isolated remnants, and among revegetated sites compared with natural stands. We conclude that small remnants and revegetated sites of our E. microcarpa samples largely but not completely capture patterns in genomic diversity across the landscape. Genomic approaches provide a powerful tool for assessing restoration efforts across the landscape.

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

Highly fecund marine species with dispersive life-history stages often display large population sizes and wide geographic distribution ranges. Consequently, they are expected to experience reduced genetic drift, efficient selection fueled by frequent adaptive mutations, and high migration loads. This has important consequences for understanding how local adaptation proceeds in the sea. A key issue in this regard, relates to the genetic architecture underlying fitness traits. Theory predicts that adaptation may involve many genes but with a high variance in effect size. Therefore, the effect of selection on allele frequencies may be substantial for the largest effect size loci, but insignificant for small effect genes. In such a context, the performance of population genomic methods to unravel the genetic basis of adaptation depends on the fraction of adaptive genetic variance explained by the cumulative effect of outlier loci. Here, we address some methodological challenges associated with the detection of local adaptation using molecular approaches. We provide an overview of genome scan methods to detect selection, including those assuming complex demographic models that better describe spatial population structure. We then focus on quantitative genetics approaches that search for genotype-phenotype associations at different genomic scales, including genome-wide methods evaluating the cumulative effect of variants. We argue that the limited power of single locus tests can be alleviated by the use of polygenic scores to estimate the joint contribution of candidate variants to phenotypic variation.

Cunningham's skinks show low genetic connectivity and signatures of divergent selection across its distribution

Establishing corridors of connecting habitat has become a mainstay conservation strategy to maintain gene flow and facilitate climate‐driven range shifts. Yet, little attention has been given to ascertaining the extent to which corridors will benefit philopatric species, which might exhibit localized adaptation. Measures of genetic connectivity and adaptive genetic variation across species’ ranges can help fill this knowledge gap. Here, we characterized the spatial genetic structure of Cunningham's skink (Egernia cunninghami), a philopatric species distributed along Australia's Great Dividing Range, and assessed evidence of localized adaptation. Analysis of 4,274 SNPs from 94 individuals sampled at four localities spanning 500 km and 4° of latitude revealed strong genetic structuring at neutral loci (mean F_ST ± SD = 0.603 ± 0.237) among the localities. Putatively neutral SNPs and those under divergent selection yielded contrasting spatial patterns, with the latter identifying two genetically distinct clusters. Given low genetic connectivity of the four localities, we suggest that the natural movement rate of this species is insufficient to keep pace with spatial shifts to its climate envelope, irrespective of habitat availability. In addition, our finding of localized adaptation highlights the risk of outbreeding depression should the translocation of individuals be adopted as a conservation management strategy.

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations

BACKGROUND

Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population's ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population's adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).

METHODS

The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers.

RESULTS

SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and Φ PT for SSR (20%) and Φ PT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers.

CONCLUSIONS

The results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species

Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available.

A call to insect scientists: challenges and opportunities of managing insect communities under climate change

As climate change moves insect systems into uncharted territory, more knowledge about insect dynamics and the factors that drive them could enable us to better manage and conserve insect communities. Climate change may also require us to revisit insect management goals and strategies and lead to a new kind of scientific engagement in management decision-making. Here we make five key points about the role of insect science in aiding and crafting management decisions, and we illustrate those points with the monarch butterfly and the Karner blue butterfly, two species undergoing considerable change and facing new management dilemmas. Insect biology has a strong history of engagement in applied problems, and as the impacts of climate change increase, a reimagined ethic of entomology in service of broader society may emerge. We hope to motivate insect biologists to contribute time and effort toward solving the challenges of climate change.

Identifying environmental correlates of intraspecific genetic variation

Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

Phylogeography of the genus Podococcus (Palmae/Arecaceae) in Central African rain forests: Climate stability predicts unique genetic diversity

The tropical rain forests of Central Africa contain high levels of species diversity. Paleovegetation or biodiversity patterns suggested successive contraction/expansion phases on this rain forest cover during the last glacial maximum (LGM). Consequently, the hypothesis of the existence of refugia e.g. habitat stability that harbored populations during adverse climatic periods has been proposed. Understory species are tightly associated to forest cover and consequently are ideal markers of forest dynamics. Here, we used two central African rain forest understory species of the palm genus, Podococcus, to assess the role of past climate variation on their distribution and genetic diversity. Species distribution modeling in the present and at the LGM was used to estimate areas of climatic stability. Genetic diversity and phylogeography were estimated by sequencing near complete plastomes for over 120 individuals. Areas of climatic stability were mainly located in mountainous areas like the Monts de Cristal and Monts Doudou in Gabon, but also lowland coastal forests in southeast Cameroon and northeast Gabon. Genetic diversity analyses shows a clear North-South structure of genetic diversity within one species. This divide was estimated to have originated some 500,000years ago. We show that, in Central Africa, high and unique genetic diversity is strongly correlated with inferred areas of climatic stability since the LGM. Our results further highlight the importance of coastal lowland rain forests in Central Africa as harboring not only high species diversity but also important high levels of unique genetic diversity. In the context of strong human pressure on coastal land use and destruction, such unique diversity hotspots need to be considered in future conservation planning.

Applying gene flow science to environmental policy needs: a boundary work perspective

One application of gene flow science is the policy arena. In this article, we describe two examples in which the topic of gene flow has entered into the U.S. national environmental policymaking process: regulation of genetically engineered crops and clarification of the jurisdictional scope of the Clean Water Act. We summarize both current scientific understanding and the legal context within which gene flow science has relevance. We also discuss the process by which scientific knowledge has been synthesized and communicated to decision-makers in these two contexts utilizing the concept of 'boundary work'. Boundary organizations, the work they engage in to bridge the worlds of science, policy, and practice, and the boundary objects they produce to translate scientific knowledge existed in both examples. However, the specific activities and attributes of the objects produced varied based on the needs of the decision-makers. We close with suggestions for how scientists can contribute to or engage in boundary work with policymakers.

Global change, life-history complexity and the potential for evolutionary rescue

Most organisms have complex life cycles, and in marine taxa, larval life‐history stages tend to be more sensitive to environmental stress than adult (reproductive) life‐history stages. While there are several models of stage‐specific adaptation across the life history, the extent to which differential sensitivity to environmental stress (defined here as reductions in absolute fitness across the life history) affects the tempo of adaptive evolution to change remains unclear. We used a heuristic model to explore how commonly observed features associated with marine complex life histories alter a population's capacity to cope with environmental change. We found that increasing the complexity of the life history generally reduces the evolutionary potential of taxa to cope with environmental change. Our model also predicted that genetic correlations in stress tolerance between stages, levels of genetic variance in each stage, and the relative plasticity of different stages, all interact to affect the maximum rate of environmental change that will permit species persistence. Our results suggest that marine organisms with complex life cycles are particularly vulnerable to anthropogenic global change, but we lack empirical estimates of key parameters for most species.

A Socio-Ecological Approach for Identifying and Contextualising Spatial Ecosystem-Based Adaptation Priorities at the Sub-National Level

Climate change adds an additional layer of complexity to existing sustainable development and biodiversity conservation challenges. The impacts of global climate change are felt locally, and thus local governance structures will increasingly be responsible for preparedness and local responses. Ecosystem-based adaptation (EbA) options are gaining prominence as relevant climate change solutions. Local government officials seldom have an appropriate understanding of the role of ecosystem functioning in sustainable development goals, or access to relevant climate information. Thus the use of ecosystems in helping people adapt to climate change is limited partially by the lack of information on where ecosystems have the highest potential to do so. To begin overcoming this barrier, Conservation South Africa in partnership with local government developed a socio-ecological approach for identifying spatial EbA priorities at the sub-national level. Using GIS-based multi-criteria analysis and vegetation distribution models, the authors have spatially integrated relevant ecological and social information at a scale appropriate to inform local level political, administrative, and operational decision makers. This is the first systematic approach of which we are aware that highlights spatial priority areas for EbA implementation. Nodes of socio-ecological vulnerability are identified, and the inclusion of areas that provide ecosystem services and ecological resilience to future climate change is innovative. The purpose of this paper is to present and demonstrate a methodology for combining complex information into user-friendly spatial products for local level decision making on EbA. The authors focus on illustrating the kinds of products that can be generated from combining information in the suggested ways, and do not discuss the nuance of climate models nor present specific technical details of the model outputs here. Two representative case studies from rural South Africa demonstrate the replicability of this approach in rural and peri-urban areas of other developing and least developed countries around the world.

Plants adapted to warmer climate do not outperform regional plants during a natural heat wave

With ongoing climate change, many plant species may not be able to adapt rapidly enough, and some conservation experts are therefore considering to translocate warm‐adapted ecotypes to mitigate effects of climate warming. Although this strategy, called assisted migration, is intuitively plausible, most of the support comes from models, whereas experimental evidence is so far scarce. Here we present data on multiple ecotypes of six grassland species, which we grew in four common gardens in Germany during a natural heat wave, with temperatures 1.4–2.0°C higher than the long‐term means. In each garden we compared the performance of regional ecotypes with plants from a locality with long‐term summer temperatures similar to what the plants experienced during the summer heat wave. We found no difference in performance between regional and warm‐adapted plants in four of the six species. In two species, regional ecotypes even outperformed warm‐adapted plants, despite elevated temperatures, which suggests that translocating warm‐adapted ecotypes may not only lack the desired effect of increased performance but may even have negative consequences. Even if adaptation to climate plays a role, other factors involved in local adaptation, such as biotic interactions, may override it. Based on our results, we cannot advocate assisted migration as a universal tool to enhance the performance of local plant populations and communities during climate change.

Life-history and phenotypic traits of insectivorous songbirds breeding on reclaimed mine land reveal ecological constraints

Studies assessing impacts of industrial activities on wildlife typically examine population- or community-level responses. However, changes in measures such as species abundance or diversity are driven by cumulative responses of individuals to disturbance, and may take time to detect. Quantifying individual responses could allow us to foresee and mitigate future population declines resulting from industrial activities, while providing ecologically informative indices to assess quality of reclaimed land. We examined life-history and phenotypic traits of mountain bluebirds (Sialia currucoides) and tree swallows (Tachycineta bicolor) breeding on reclaimed copper mine lands in Canada over two years in comparison to a nearby undisturbed reference area. Bluebirds feed on terrestrial invertebrates, whereas swallows feed on adult forms of insects with aquatic larvae, allowing us to assess quality of both reclaimed terrestrial and aquatic systems as habitat for insectivorous birds. Supplemental feeding of bluebirds also was used to experimentally assess nutritional limitation of birds feeding on terrestrial invertebrates. Bluebirds on reclaimed land initiated clutches later, and in one year had lower fledging success compared to birds on the reference area. Tree swallows also bred later in the season on reclaimed land, but were otherwise comparable to or exceeded performance of birds on the reference area. Annual differences in responses of nestling bluebirds on the mine to supplemental feeding revealed an apparent switch in life-history strategy of parents between years, from brood reduction to brood survival, suggesting greater annual fluctuations in ecological conditions within terrestrial systems on reclaimed land. Sex differences in response of nestling bluebirds to food supplementation additionally suggested high within-brood competition for food on reclaimed land. We suggest that measures of avian life-history and phenotypic traits, particularly when assessed over multiple years using experimental approaches such as food supplementation, are informative and sensitive indices of the health of reclaimed terrestrial and aquatic systems.

Regional Genetic Structure and Environmental Variables Influence our Conservation Approach for Feather Heads (Ptilotus macrocephalus)

Continued alterations to the Australian environment compromise the long-term viability of many plant species. We investigate the population genetics of Ptilotus macrocephalus, a perennial herb that occurs in 2 nationally endangered communities on the Victorian Volcanic Plain Bioregion (VVP), Australia, to answer key questions regarding regional differentiation and to guide conservation strategies. We evaluate genetic structure and diversity within and among 17 P. macrocephalus populations from 3 regions of southeastern Australia using 17 microsatellite markers developed de novo. Genetic structure was present in P. macrocephalus between the 3 regions but not at the population level. Environmental factors, namely temperature and precipitation, significantly explained differentiation between the North region and the other 2 regions indicating isolation by environment. Within regions, genetic structure currently shows a high level of gene flow and genetic variation. Our results suggest that within-region gene flow does not reflect current habitat fragmentation in southeastern Australia whereas temperature and precipitation are likely to be responsible for the differentiation detected among regions. Climate change may severely impact P. macrocephalus on the VVP and test its evolutionary resilience. We suggest taking a proactive conservation approach to improve long-term viability by sourcing material for restoration to assist gene flow to the VVP region to promote an increased adaptive capacity.

Does origin always matter? Evaluating the influence of nonlocal seed provenances for ecological restoration purposes in a widespread and outcrossing plant species

For restoration purposes, nature conservation generally enforces the use of local seed material based on the "local-is-best" (LIB) approach. However, in some cases recommendations to refrain from this approach have been made. Here we test if a common widespread species with no obvious signs of local adaptation may be a candidate species for abandoning LIB during restoration. Using 10 microsatellite markers we compared population genetic patterns of the generalist species Daucus carota in indigenous and formerly restored sites (nonlocal seed provenances). Gene diversity overall ranged between H e = 0.67 and 0.86 and showed no significant differences between the two groups. Hierarchical AMOVA and principal component analysis revealed very high genetic population admixture and negligible differentiation between indigenous and restored sites (F CT = 0.002). Moreover, differentiation between groups was caused by only one outlier population, where inbreeding effects are presumed. We therefore conclude that the introduction of nonlocal seed provenances in the course of landscape restoration did not jeopardize regional species persistence by contributing to inbreeding or outbreeding depressions, or any measurable adverse population genetic effect. On the basis of these results, we see no obvious objections to the current practice to use the 10-fold cheaper, nonlocal seed material of D. carota for restoration projects.

Targeted gene flow for conservation

Anthropogenic threats often impose strong selection on affected populations, causing rapid evolutionary responses. Unfortunately, these adaptive responses are rarely harnessed for conservation. We suggest that conservation managers pay close attention to adaptive processes and geographic variation, with an eye to using them for conservation goals. Translocating pre-adapted individuals into recipient populations is currently considered a potentially important management tool in the face of climate change. Targeted gene flow, which involves moving individuals with favorable traits to areas where these traits would have a conservation benefit, could have a much broader application in conservation. Across a species' range there may be long-standing geographic variation in traits or variation may have rapidly developed in response to a threatening process. Targeted gene flow could be used to promote natural resistance to threats to increase species resilience. We suggest that targeted gene flow is a currently underappreciated strategy in conservation that has applications ranging from the management of invasive species and their impacts to controlling the impact and virulence of pathogens.

The eastern migratory caribou: the role of genetic introgression in ecotype evolution

Understanding the evolutionary history of contemporary animal groups is essential for conservation and management of endangered species like caribou (Rangifer tarandus). In central Canada, the ranges of two caribou subspecies (barren-ground/woodland caribou) and two woodland caribou ecotypes (boreal/eastern migratory) overlap. Our objectives were to reconstruct the evolutionary history of the eastern migratory ecotype and to assess the potential role of introgression in ecotype evolution. STRUCTURE analyses identified five higher order groups (i.e. three boreal caribou populations, eastern migratory ecotype and barren-ground). The evolutionary history of the eastern migratory ecotype was best explained by an early genetic introgression from barren-ground into a woodland caribou lineage during the Late Pleistocene and subsequent divergence of the eastern migratory ecotype during the Holocene. These results are consistent with the retreat of the Laurentide ice sheet and the colonization of the Hudson Bay coastal areas subsequent to the establishment of forest tundra vegetation approximately 7000 years ago. This historical reconstruction of the eastern migratory ecotype further supports its current classification as a conservation unit, specifically a Designatable Unit, under Canada's Species at Risk Act. These findings have implications for other sub-specific contact zones for caribou and other North American species in conservation unit delineation.

Adaptive introgression as a resource for management and genetic conservation in a changing climate

Current rates of climate change require organisms to respond through migration, phenotypic plasticity, or genetic changes via adaptation. We focused on questions regarding species' and populations' ability to respond to climate change through adaptation. Specifically, the role adaptive introgression, movement of genetic material from the genome of 1 species into the genome of another through repeated interbreeding, may play in increasing species' ability to respond to a changing climate. Such interspecific gene flow may mediate extinction risk or consequences of limited adaptive potential that result from standing genetic variation and mutation alone, enabling a quicker demographic recovery in response to changing environments. Despite the near dismissal of the potential benefits of hybridization by conservation practitioners, we examined a number of case studies across different taxa that suggest gene flow between sympatric or parapatric sister species or within species that exhibit strong ecotypic differentiation may represent an underutilized management option to conserve evolutionary potential in a changing environment. This will be particularly true where advanced-generation hybrids exhibit adaptive traits outside the parental phenotypic range, a phenomenon known as transgressive segregation. The ideas presented in this essay are meant to provoke discussion regarding how we maintain evolutionary potential, the conservation value of natural hybrid zones, and consideration of their important role in adaptation to climate.

Loss of genetic integrity and biological invasions result from stocking and introductions of Barbus barbus: insights from rivers in England

Anthropogenic activities, including the intentional releases of fish for enhancing populations (stocking), are recognized as adversely impacting the adaptive potential of wild populations. Here, the genetic characteristics of European barbel Barbus barbus were investigated using 18 populations in England, where it is indigenous to eastern‐flowing rivers and where stocking has been used to enhance these populations. Invasive populations are also present in western‐flowing rivers following introductions of translocated fish. Two genetic clusters were evident in the indigenous range, centered on catchments in northeast and southeast England. However, stocking activities, including the release of hatchery‐reared fish, have significantly reduced the genetic differentiation across the majority of this range. In addition, in smaller indigenous rivers, populations appeared to mainly comprise fish of hatchery origin. In the nonindigenous range, genetic data largely aligned to historical stocking records, corroborating information that one particular river (Kennet) in southeast England was the original source of most invasive B. barbus in England. It is recommended that these genetic outputs inform management measures to either restore or maintain the original genetic diversity of the indigenous rivers, as this should help ensure populations can maintain their ability to adapt to changing environmental conditions. Where stocking is considered necessary, it is recommended that only broodstock from within the catchment is used.

Genetic delineation of local provenance defines seed collection zones along a climate gradient

Efforts to re-establish native plant species should consider intraspecific variation if we are to restore genetic diversity and evolutionary potential. Data describing spatial genetic structure and the scale of adaptive differentiation are needed for restoration seed sourcing. Genetically defined provenance zones provide species-specific guidelines for the distance within which seed transfer likely maintains levels of genetic diversity and conserves locally adapted traits. While a growing number of studies incorporate genetic marker data in delineation of local provenance, they often fail to distinguish the impacts of neutral and non-neutral variation. We analysed population genetic structure for 134 amplified fragment length polymorphism (AFLP) markers in Stylidium hispidum (Stylidiaceae) along a north-south transect of the species' range with the goal to estimate the distance at which significant genetic differences occur among source and recipient populations in restoration. In addition, we tested AFLP markers for signatures of selection, and examined the relationship of neutral and putatively selected markers with climate variables. Estimates of population genetic structure revealed significant levels of differentiation (ΦPT = 0.23) and suggested a global provenance distance of 45 km for pairwise comparisons of 16 populations. Of the 134 markers, 13 exhibited evidence of diversifying selection (ΦPT = 0.52). Using data for precipitation and thermal gradients, we compared genetic, geographic and environmental distance for subsets of neutral and selected markers. Strong isolation by distance was detected in all cases, but positive correlations with climate variables were present only for markers with signatures of selection. We address findings in light of defining local provenance in ecological restoration.

Low genetic diversity, restricted dispersal, and elevation-specific patterns of population decline in American pikas in an atypical environment

In the face of climate change, there is a growing need for research into the ability of organisms to persist at the limits of their bioclimatic envelope. American pikas ( Ochotona princeps ) have emerged as a focal mammalian species for investigating extinction risk related to climate change; however, most studies have occurred in characteristic alpine talus habitat within the range core. In the Columbia River Gorge (CRG), Oregon, American pikas inhabit low-elevation talus slopes previously considered outside the species’ bioclimatic range. We used microsatellite genotypic data to reconstruct levels of genetic variation, population connectivity, and demographic history at 11 CRG sites spanning an elevational gradient (104–1,292 m). Sampled sites separated into 2 genetic clusters largely explained by elevation, topography, and geographic proximity, with pairwise estimates of differentiation and migration rates suggesting little gene flow may be occurring. Sites were characterized by levels of allelic richness and heterozygosity substantially lower than values reported at characteristic alpine sites from the range core. Evidence of recent demographic contraction was found almost exclusively at high-elevation sites despite these areas being considered refuges from climate warming in more typical habitat. Given their unique genetic characteristics and persistence in an atypical environment, the CRG pika populations likely constitute a significant component of intraspecific biodiversity with high conservation value.

The conservation genetics juggling act: integrating genetics and ecology, science and policy

The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980s following the development of polymerase chain reaction and now into the genomics era. Our laboratory has ‘grown up’ with the field, having worked on these issues for over three decades. Our multidisciplinary approach entails understanding the behavior and ecology of species as well as the underlying processes that contribute to genetic viability. Taking this holistic approach provides a comprehensive understanding of factors that influence species persistence and evolutionary potential while considering annual challenges that occur throughout their life cycle. As a federal laboratory, we are often addressing the needs of the U.S. Fish and Wildlife Service in their efforts to list, de‐list, or recover species. Nevertheless, there remains an overall communication gap between research geneticists and biologists who are charged with implementing their results. Therefore, we outline the need for a National Center for Small Population Biology to ameliorate this problem and provide organizations charged with making status decisions firmer ground from which to make their critical decisions.

Facilitating climate-change-induced range shifts across continental land-use barriers

Climate changes impose requirements for many species to shift their ranges to remain within environmentally tolerable areas, but near-continuous regions of intense human land use stretching across continental extents diminish dispersal prospects for many species. We reviewed the impact of habitat loss and fragmentation on species' abilities to track changing climates and existing plans to facilitate species dispersal in response to climate change through regions of intensive land uses, drawing on examples from North America and elsewhere. We identified an emerging analytical framework that accounts for variation in species' dispersal capacities relative to both the pace of climate change and habitat availability. Habitat loss and fragmentation hinder climate change tracking, particularly for specialists, by impeding both propagule dispersal and population growth. This framework can be used to identify prospective modern-era climatic refugia, where the pace of climate change has been slower than surrounding areas, that are defined relative to individual species' needs. The framework also underscores the importance of identifying and managing dispersal pathways or corridors through semi-continental land use barriers that can benefit many species simultaneously. These emerging strategies to facilitate range shifts must account for uncertainties around population adaptation to local environmental conditions. Accounting for uncertainties in climate change and dispersal capabilities among species and expanding biological monitoring programs within an adaptive management paradigm are vital strategies that will improve species' capacities to track rapidly shifting climatic conditions across landscapes dominated by intensive human land use.

Implications of genetics and current protected areas for conservation of 5 endangered primates in China

Most of China's 24-28 primate species are threatened with extinction. Habitat reduction and fragmentation are perhaps the greatest threats. We used published data from a conservation genetics study of 5 endangered primates in China (Rhinopithecus roxellana, R. bieti, R. brelichi, Trachypithecus francoisi, and T. leucocephalus); distribution data on these species; and the distribution, area, and location of protected areas to inform conservation strategies for these primates. All 5 species were separated into subpopulations with unique genetic components. Gene flow appeared to be strongly impeded by agricultural land, meadows used for grazing, highways, and humans dwellings. Most species declined severely or diverged concurrently as human population and crop land cover increased. Nature reserves were not evenly distributed across subpopulations with unique genetic backgrounds. Certain small subpopulations were severely fragmented and had higher extinction risk than others. Primate mobility is limited and their genetic structure is strong and susceptible to substantial loss of diversity due to local extinction. Thus, to maximize preservation of genetic diversity in all these primate species, our results suggest protection is required for all sub-populations. Key priorities for their conservation include maintaining R. roxellana in Shennongjia national reserve, subpopulations S4 and S5 of R. bieti and of R. brelichi in Fanjingshan national reserve, subpopulation CGX of T. francoisi in central Guangxi Province, and all 3 T. leucocephalus sub-populations in central Guangxi Province.

Community rescue in experimental metacommunities

The conditions that allow biodiversity to recover following severe environmental degradation are poorly understood. We studied community rescue, the recovery of a viable community through the evolutionary rescue of many populations within an evolving community, in metacommunities of soil microbes adapting to a herbicide. The metacommunities occupied a landscape of crossed spatial gradients of the herbicide (Dalapon) and a resource (glucose), whereas their constituent communities were either isolated or connected by dispersal. The spread of adapted communities across the landscape and the persistence of communities when that landscape was degraded were strongly promoted by dispersal, and the capacity to adapt to lethal stress was also related to community size and initial diversity. After abrupt and lethal stress, community rescue was most frequent in communities that had previously experienced sublethal levels of stress and had been connected by dispersal. Community rescue occurred through the evolutionary rescue of both initially common taxa, which remained common, and of initially rare taxa, which grew to dominate the evolved community. Community rescue may allow productivity and biodiversity to recover from severe environmental degradation.

Plants and climate change: complexities and surprises

BACKGROUND

Anthropogenic climate change (ACC) will influence all aspects of plant biology over coming decades. Many changes in wild species have already been well-documented as a result of increased atmospheric CO2 concentrations, warming climate and changing precipitation regimes. A wealth of available data has allowed the use of meta-analyses to examine plant-climate interactions on more sophisticated levels than before. These analyses have revealed major differences in plant response among groups, e.g. with respect to functional traits, taxonomy, life-history and provenance. Interestingly, these meta-analyses have also exposed unexpected mismatches between theory, experimental, and observational studies.

SCOPE

We reviewed the literature on species' responses to ACC, finding ∼42 % of 4000 species studied globally are plants (primarily terrestrial). We review impacts on phenology, distributions, ecophysiology, regeneration biology, plant-plant and plant-herbivore interactions, and the roles of plasticity and evolution. We focused on apparent deviations from expectation, and highlighted cases where more sophisticated analyses revealed that unexpected changes were, in fact, responses to ACC.

CONCLUSIONS

We found that conventionally expected responses are generally well-understood, and that it is the aberrant responses that are now yielding greater insight into current and possible future impacts of ACC. We argue that inconclusive, unexpected, or counter-intuitive results should be embraced in order to understand apparent disconnects between theory, prediction, and observation. We highlight prime examples from the collection of papers in this Special Issue, as well as general literature. We found use of plant functional groupings/traits had mixed success, but that some underutilized approaches, such as Grime's C/S/R strategies, when incorporated, have improved understanding of observed responses. Despite inherent difficulties, we highlight the need for ecologists to conduct community-level experiments in systems that replicate multiple aspects of ACC. Specifically, we call for development of coordinating experiments across networks of field sites, both natural and man-made.