Building evolutionary resilience for conserving biodiversity under climate change

Genetic diversity and population structure of an important wild berry crop

The success of plant breeding in the coming years will be associated with access to new sources of variation, which will include landraces and wild relatives of crop species. In order to access the reservoir of favourable alleles within wild germplasm, knowledge about the genetic diversity and the population structure of wild species is needed. Bilberry (Vaccinium myrtillus) is one of the most important wild crops growing in the forests of Northern European countries, noted for its nutritional properties and its beneficial effects on human health. Assessment of the genetic diversity of wild bilberry germplasm is needed for efforts such as in situ conservation, on-farm management and development of plant breeding programmes. However, to date, only a few local (small-scale) genetic studies of this species have been performed. We therefore conducted a study of genetic variability within 32 individual samples collected from different locations in Iceland, Norway, Sweden, Finland and Germany, and analysed genetic diversity among geographic groups. Four selected inter-simple sequence repeat primers allowed the amplification of 127 polymorphic loci which, based on analysis of variance, made it possible to identify 85 % of the genetic diversity within studied bilberry populations, being in agreement with the mixed-mating system of bilberry. Significant correlations were obtained between geographic and genetic distances for the entire set of samples. The analyses also highlighted the presence of a north-south genetic gradient, which is in accordance with recent findings on phenotypic traits of bilberry.

Assessing the components of adaptive capacity to improve conservation and management efforts under global change

Natural-resource managers and other conservation practitioners are under unprecedented pressure to categorize and quantify the vulnerability of natural systems based on assessment of the exposure, sensitivity, and adaptive capacity of species to climate change. Despite the urgent need for these assessments, neither the theoretical basis of adaptive capacity nor the practical issues underlying its quantification has been articulated in a manner that is directly applicable to natural-resource management. Both are critical for researchers, managers, and other conservation practitioners to develop reliable strategies for assessing adaptive capacity. Drawing from principles of classical and contemporary research and examples from terrestrial, marine, plant, and animal systems, we examined broadly the theory behind the concept of adaptive capacity. We then considered how interdisciplinary, trait- and triage-based approaches encompassing the oft-overlooked interactions among components of adaptive capacity can be used to identify species and populations likely to have higher (or lower) adaptive capacity. We identified the challenges and value of such endeavors and argue for a concerted interdisciplinary research approach that combines ecology, ecological genetics, and eco-physiology to reflect the interacting components of adaptive capacity. We aimed to provide a basis for constructive discussion between natural-resource managers and researchers, discussions urgently needed to identify research directions that will deliver answers to real-world questions facing resource managers, other conservation practitioners, and policy makers. Directing research to both seek general patterns and identify ways to facilitate adaptive capacity of key species and populations within species, will enable conservation ecologists and resource managers to maximize returns on research and management investment and arrive at novel and dynamic management and policy decisions.

Biodiversity and Resilience of Ecosystem Functions

Accelerating rates of environmental change and the continued loss of global biodiversity threaten functions and services delivered by ecosystems. Much ecosystem monitoring and management is focused on the provision of ecosystem functions and services under current environmental conditions, yet this could lead to inappropriate management guidance and undervaluation of the importance of biodiversity. The maintenance of ecosystem functions and services under substantial predicted future environmental change (i.e., their 'resilience') is crucial. Here we identify a range of mechanisms underpinning the resilience of ecosystem functions across three ecological scales. Although potentially less important in the short term, biodiversity, encompassing variation from within species to across landscapes, may be crucial for the longer-term resilience of ecosystem functions and the services that they underpin.

Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

‘Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl.4, 326–337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.

Population Genetic Diversity in the Australian 'Seascape': A Bioregion Approach

Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitude squared. Removing region as an explanatory variable greatly reduced model performance (delta DIC 23.4). Several bioregions were identified as possessing notably high genetic diversity. Genetic diversity increased towards the equator with a 'hump' in diversity across the range studied (-9.4 to -43.7°S). Our results suggest that factors correlated with both region and latitude play a role in shaping intra-specific genetic diversity, and that bioregion can be a useful management unit for intra-specific as well as species biodiversity. Our novel statistical model should prove useful for future analyses of within species genetic diversity at broad taxonomic and geographic scales.

Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4-7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = -0.77; P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.

The theory behind, and the challenges of, conserving nature's stage in a time of rapid change

Most conservation planning to date has focused on protecting today's biodiversity with the assumption that it will be tomorrow's biodiversity. However, modern climate change has already resulted in distributional shifts of some species and is projected to result in many more shifts in the coming decades. As species redistribute and biotic communities reorganize, conservation plans based on current patterns of biodiversity may fail to adequately protect species in the future. One approach for addressing this issue is to focus on conserving a range of abiotic conditions in the conservation-planning process. By doing so, it may be possible to conserve an abiotically diverse "stage" upon which evolution will play out and support many actors (biodiversity). We reviewed the fundamental underpinnings of the concept of conserving the abiotic stage, starting with the early observations of von Humboldt, who mapped the concordance of abiotic conditions and vegetation, and progressing to the concept of the ecological niche. We discuss challenges posed by issues of spatial and temporal scale, the role of biotic drivers of species distributions, and latitudinal and topographic variation in relationships between climate and landform. For example, abiotic conditions are not static, but change through time-albeit at different and often relatively slow rates. In some places, biotic interactions play a substantial role in structuring patterns of biodiversity, meaning that patterns of biodiversity may be less tightly linked to the abiotic stage. Furthermore, abiotic drivers of biodiversity can change with latitude and topographic position, meaning that the abiotic stage may need to be defined differently in different places. We conclude that protecting a diversity of abiotic conditions will likely best conserve biodiversity into the future in places where abiotic drivers of species distributions are strong relative to biotic drivers, where the diversity of abiotic settings will be conserved through time, and where connectivity allows for movement among areas providing different abiotic conditions.

Incorporating evolutionary processes into population viability models

We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence.

Temporal patterns in adult salmon migration timing across southeast Alaska

Pacific salmon migration timing can drive population productivity, ecosystem dynamics, and human harvest. Nevertheless, little is known about long-term variation in salmon migration timing for multiple species across broad regions. We used long-term data for five Pacific salmon species throughout rapidly warming southeast Alaska to describe long-term changes in salmon migration timing, interannual phenological synchrony, relationships between climatic variation and migratory timing, and to test whether long-term changes in migration timing are related to glaciation in headwater streams. Temporal changes in the median date of salmon migration timing varied widely across species. Most sockeye populations are migrating later over time (11 of 14), but pink, chum, and especially coho populations are migrating earlier than they did historically (16 of 19 combined). Temporal trends in duration and interannual variation in migration timing were highly variable across species and populations. The greatest temporal shifts in the median date of migration timing were correlated with decreases in the duration of migration timing, suggestive of a loss of phenotypic variation due to natural selection. Pairwise interannual correlations in migration timing varied widely but were generally positive, providing evidence for weak region-wide phenological synchrony. This synchrony is likely a function of climatic variation, as interannual variation in migration timing was related to climatic phenomenon operating at large- (Pacific decadal oscillation), moderate- (sea surface temperature), and local-scales (precipitation). Surprisingly, the presence or the absence of glaciers within a watershed was unrelated to long-term shifts in phenology. Overall, there was extensive heterogeneity in long-term patterns of migration timing throughout this climatically and geographically complex region, highlighting that future climatic change will likely have widely divergent impacts on salmon migration timing. Although salmon phenological diversity will complicate future predictions of migration timing, this variation likely acts as a major contributor to population and ecosystem resiliency in southeast Alaska.

Resilience as a universal criterion of health

To promote and maintain health in agricultural and food systems, appropriate criteria are needed for the description and assessment of the health of soils, plants, animals, humans and ecosystems. Here we identify the concept of resilience as a universally applicable and fundamentally important criterion of health in all relevant areas of agriculture. We discuss definitions of resilience for soils, plants, animals, humans and ecosystems, and explore ways in which resilience can be applied as a criterion of health in different agricultural contexts. We show how and why resilience can be seen as a key criterion of health. Based on this, we discuss how resilience can be used as a link between soil, plant, animal, human and ecosystem health. Finally, we highlight four key areas for future research on resilience in agriculture, namely spatial and temporal scaling of resilience; effects of diversity; the role of networks for resilience; and stakeholder involvement.

Relating adaptive genetic traits to climate for Sandberg bluegrass from the intermountain western United States

Genetic variation for potentially adaptive traits of the key restoration species Sandberg bluegrass (Poa secunda J. Presl) was assessed over the intermountain western United States in relation to source population climate. Common gardens were established at two intermountain west sites with progeny from two maternal parents from each of 130 wild populations. Data were collected over 2 years at each site on fifteen plant traits associated with production, phenology, and morphology. Analyses of variance revealed strong population differences for all plant traits (P < 0.0001), indicating genetic variation. Both the canonical correlation and linear correlation established associations between source populations and climate variability. Populations from warmer, more arid climates had generally lower dry weight, earlier phenology, and smaller, narrower leaves than those from cooler, moister climates. The first three canonical variates were regressed with climate variables resulting in significant models (P < 0.0001) used to map 12 seed zones. Of the 700 981 km² mapped, four seed zones represented 92% of the area in typically semi-arid and arid regions. The association of genetic variation with source climates in the intermountain west suggested climate driven natural selection and evolution. We recommend seed transfer zones and population movement guidelines to enhance adaptation and diversity for large-scale restoration projects.

Mapping evolutionary process: a multi-taxa approach to conservation prioritization

Human-induced land use changes are causing extensive habitat fragmentation. As a result, many species are not able to shift their ranges in response to climate change and will likely need to adapt in situ to changing climate conditions. Consequently, a prudent strategy to maintain the ability of populations to adapt is to focus conservation efforts on areas where levels of intraspecific variation are high. By doing so, the potential for an evolutionary response to environmental change is maximized. Here, we use modeling approaches in conjunction with environmental variables to model species distributions and patterns of genetic and morphological variation in seven Ecuadorian amphibian, bird, and mammal species. We then used reserve selection software to prioritize areas for conservation based on intraspecific variation or species-level diversity. Reserves selected using species richness and complementarity showed little overlap with those based on genetic and morphological variation. Priority areas for intraspecific variation were mainly located along the slopes of the Andes and were largely concordant among species, but were not well represented in existing reserves. Our results imply that in order to maximize representation of intraspecific variation in reserves, genetic and morphological variation should be included in conservation prioritization.

Prescriptive Evolution to Conserve and Manage Biodiversity

We are witnessing a global, but unplanned, evolutionary experiment with the biodiversity of the planet. Anthropogenic disturbances such as habitat degradation and climate change result in evolutionary mismatch between the environments to which species are adapted and those in which they now exist. The impacts of unmanaged evolution are pervasive, but approaches to address them have received little attention. We review the evolutionary challenges of managing populations in the Anthropocene and introduce the concept of prescriptive evolution, which considers how evolutionary processes may be leveraged to proactively promote wise management. We advocate the planned management of evolutionary processes and explore the advantages of evolutionary interventions to preserve and sustain biodiversity. We show how an evolutionary perspective to conserving biodiversity is fundamental to effective management. Finally, we advocate building frameworks for decision-making, monitoring, and implementation at the boundary between management and evolutionary science to enhance conservation outcomes.

Using genomics to characterize evolutionary potential for conservation of wild populations

Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.

Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion

Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80-90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

Applying evolutionary biology to address global challenges

Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens, and pests that evolve too quickly and the second, from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This Review highlights both progress and gaps in genetic, developmental, and environmental manipulations across the life sciences that either target the rate and direction of evolution or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development.

Characterisation of adaptive genetic diversity in environmentally contrasted populations of Eucalyptus camaldulensis Dehnh. (river red gum)

As an increasing number of ecosystems face departures from long standing environmental conditions under climate change, our understanding of the capacity of species to adapt will become important for directing conservation and management of biodiversity. Insights into the potential for genetic adaptation might be gained by assessing genomic signatures of adaptation to historic or prevailing environmental conditions. The river red gum (Eucalyptus camaldulensis Dehnh.) is a widespread Australian eucalypt inhabiting riverine and floodplain habitats which spans strong environmental gradients. We investigated the effects of adaptation to environment on population level genetic diversity of E. camaldulensis, examining SNP variation in candidate gene loci sampled across 20 climatically diverse populations approximating the species natural distribution. Genetic differentiation among populations was high (F(ST) = 17%), exceeding previous estimates based on neutral markers. Complementary statistical approaches identified 6 SNP loci in four genes (COMT, Dehydrin, ERECTA and PIP2) which, after accounting for demographic effects, exhibited higher than expected levels of genetic differentiation among populations and whose allelic variation was associated with local environment. While this study employs but a small proportion of available diversity in the eucalyptus genome, it draws our attention to the potential for application of wide spread eucalypt species to test adaptive hypotheses.

Next generation restoration genetics: applications and opportunities

Restoration ecology is a young scientific discipline underpinning improvements in the rapid global expansion of ecological restoration. The application of molecular tools over the past 20 years has made an important contribution to understanding genetic factors influencing ecological restoration success. Here we illustrate how recent advances in next generation sequencing (NGS) methods are revolutionising the practical contribution of genetics to restoration. Novel applications include a dramatically enhanced capacity to measure adaptive variation for optimal seed sourcing, high-throughput assessment and monitoring of natural and restored biological communities aboveground and belowground, and gene expression analysis as a measure of genetic resilience of restored populations. Challenges remain in data generation, handling and analysis, and how best to apply NGS for practical outcomes in restoration.

Coming to terms with the concept of moving species threatened by climate change - a systematic review of the terminology and definitions

Intentional moving of species threatened by climate change is actively being discussed as a conservation approach. The debate, empirical studies, and policy development, however, are impeded by an inconsistent articulation of the idea. The discrepancy is demonstrated by the varying use of terms, such as assisted migration, assisted colonisation, or managed relocation, and their multiple definitions. Since this conservation approach is novel, and may for instance lead to legislative changes, it is important to aim for terminological consistency. The objective of this study is to analyse the suitability of terms and definitions used when discussing the moving of organisms as a response to climate change. An extensive literature search and review of the material (868 scientific publications) was conducted for finding hitherto used terms (N = 40) and definitions (N = 75), and these were analysed for their suitability. Based on the findings, it is argued that an appropriate term for a conservation approach relating to aiding the movement of organisms harmed by climate change is assisted migration defined as follows: Assisted migration means safeguarding biological diversity through the translocation of representatives of a species or population harmed by climate change to an area outside the indigenous range of that unit where it would be predicted to move as climate changes, were it not for anthropogenic dispersal barriers or lack of time. The differences between assisted migration and other conservation translocations are also discussed. A wide adoption of the clear and distinctive term and definition provided would allow more focused research on the topic and enable consistent implementation as practitioners could have the same understanding of the concept.

Model-based conservation planning of the genetic diversity of Phellodendron amurense Rupr due to climate change

Climate change affects both habitat suitability and the genetic diversity of wild plants. Therefore, predicting and establishing the most effective and coherent conservation areas is essential for the conservation of genetic diversity in response to climate change. This is because genetic variance is a product not only of habitat suitability in conservation areas but also of efficient protection and management. Phellodendron amurense Rupr. is a tree species (family Rutaceae) that is endangered due to excessive and illegal harvesting for use in Chinese medicine. Here, we test a general computational method for the prediction of priority conservation areas (PCAs) by measuring the genetic diversity of P. amurense across the entirety of northeast China using a single strand repeat analysis of twenty microsatellite markers. Using computational modeling, we evaluated the geographical distribution of the species, both now and in different future climate change scenarios. Different populations were analyzed according to genetic diversity, and PCAs were identified using a spatial conservation prioritization framework. These conservation areas were optimized to account for the geographical distribution of P. amurense both now and in the future, to effectively promote gene flow, and to have a long period of validity. In situ and ex situ conservation, strategies for vulnerable populations were proposed. Three populations with low genetic diversity are predicted to be negatively affected by climate change, making conservation of genetic diversity challenging due to decreasing habitat suitability. Habitat suitability was important for the assessment of genetic variability in existing nature reserves, which were found to be much smaller than the proposed PCAs. Finally, a simple set of conservation measures was established through modeling. This combined molecular and computational ecology approach provides a framework for planning the protection of species endangered by climate change.

Splitting or lumping? A conservation dilemma exemplified by the critically endangered dama gazelle (Nanger dama)

Managers of threatened species often face the dilemma of whether to keep populations separate to conserve local adaptations and minimize the risk of outbreeding, or whether to manage populations jointly to reduce loss of genetic diversity and minimise inbreeding. In this study we examine genetic relatedness and diversity in three of the five last remaining wild populations of dama gazelle and a number of captive populations, using mtDNA control region and cytochrome b data. Despite the sampled populations belonging to the three putative subspecies, which are delineated according to phenotypes and geographical location, we find limited evidence for phylogeographical structure within the data and no genetic support for the putative subspecies. In the light of these data we discuss the relevance of inbreeding depression, outbreeding depression, adaptive variation, genetic drift, and phenotypic variation to the conservation of the dama gazelle and make some recommendations for its future conservation management. The genetic data suggest that the best conservation approach is to view the dama gazelle as a single species without subspecific divisions.

Nuclear and mitochondrial genetic structure in the Eurasian beaver (Castor fiber) - implications for future reintroductions

Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conducting postrelease monitoring. In this study, we use a panel of 306 SNP (single nucleotide polymorphism) markers and 487-489 base pairs of mitochondrial DNA control region sequence data to examine 321 individuals from possible source populations of the Eurasian beaver for a reintroduction to Scotland. We use this information to reassess the phylogenetic history of the Eurasian beavers, to examine the genetic legacy of past reintroductions on the Eurasian landmass and to assess the future power of the genetic markers to conduct ongoing monitoring via parentage analysis and individual identification. We demonstrate the capacity of medium density genetic data (hundreds of SNPs) to provide information suitable for applied conservation and discuss the difficulty of balancing the need for high genetic diversity against phylogenetic best fit when choosing source population(s) for reintroduction.

From myopia to clarity: sharpening the focus of ecosystem management through the lens of palaeoecology

Maintaining biodiversity and ecosystem services in a changing environment requires a temporal perspective that informs realistic restoration and management targets. Such targets need to be dynamic, adaptive, and responsive to changing boundary conditions. However, the application of long-term data from palaeoecology is often hindered as the management and policy implications are not made explicit, and because data sets are often not accessible or amenable to stakeholders. Focussing on this translation gap, we explore how a palaeoecological perspective can change the focus of biodiversity management and conservation policy. We embed a long-term perspective (decades to millennia) into current adaptive management and policy frameworks, with the aim of encouraging better integration between palaeoecology, conservation management, and mainstreaming viable provision of ecosystem services.

Imaging spectroscopy links aspen genotype with below-ground processes at landscape scales

Fine-scale biodiversity is increasingly recognized as important to ecosystem-level processes. Remote sensing technologies have great potential to estimate both biodiversity and ecosystem function over large spatial scales. Here, we demonstrate the capacity of imaging spectroscopy to discriminate among genotypes of Populus tremuloides (trembling aspen), one of the most genetically diverse and widespread forest species in North America. We combine imaging spectroscopy (AVIRIS) data with genetic, phytochemical, microbial and biogeochemical data to determine how intraspecific plant genetic variation influences below-ground processes at landscape scales. We demonstrate that both canopy chemistry and below-ground processes vary over large spatial scales (continental) according to aspen genotype. Imaging spectrometer data distinguish aspen genotypes through variation in canopy spectral signature. In addition, foliar spectral variation correlates well with variation in canopy chemistry, especially condensed tannins. Variation in aspen canopy chemistry, in turn, is correlated with variation in below-ground processes. Variation in spectra also correlates well with variation in soil traits. These findings indicate that forest tree species can create spatial mosaics of ecosystem functioning across large spatial scales and that these patterns can be quantified via remote sensing techniques. Moreover, they demonstrate the utility of using optical properties as proxies for fine-scale measurements of biodiversity over large spatial scales.

Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes

Comprising 50%-75% of the world's fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including "invasive species" in various ecosystems as they may become disrupted in different ways by rapid climate change. "Invasive genes" (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. "Genetic rescue" via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced "reshuffling" (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge.

Deep genetic divergence between disjunct Refugia in the Arctic-Alpine King's Crown, Rhodiola integrifolia (Crassulaceae)

Despite the strength of climatic variability at high latitudes and upper elevations, we still do not fully understand how plants in North America that are distributed between Arctic and alpine areas responded to the environmental changes of the Quaternary. To address this question, we set out to resolve the evolutionary history of the King's Crown, Rhodiola integrifolia using multi-locus population genetic and phylogenetic analyses in combination with ecological niche modeling. Our population genetic analyses of multiple anonymous nuclear loci revealed two major clades within R. integrifolia that diverged from each other ~ 700 kya: one occurring in Beringia to the north (including members of subspecies leedyi and part of subspecies integrifolia), and the other restricted to the Southern Rocky Mountain refugium in the south (including individuals of subspecies neomexicana and part of subspecies integrifolia). Ecological niche models corroborate our hypothesized locations of refugial areas inferred from our phylogeographic analyses and revealed some environmental differences between the regions inhabited by its two subclades. Our study underscores the role of geographic isolation in promoting genetic divergence and the evolution of endemic subspecies in R. integrifolia. Furthermore, our phylogenetic analyses of the plastid spacer region trnL-F demonstrate that among the native North American species, R. integrifolia and R. rhodantha are more closely related to one another than either is to R. rosea. An understanding of these historic processes lies at the heart of making informed management decisions regarding this and other Arctic-alpine species of concern in this increasingly threatened biome.

Adaptive divergence along environmental gradients in a climate-change-sensitive mammal

In the face of predicted climate change, a broader understanding of biotic responses to varying environments has become increasingly important within the context of biodiversity conservation. Local adaptation is one potential option, yet remarkably few studies have harnessed genomic tools to evaluate the efficacy of this response within natural populations. Here, we show evidence of selection driving divergence of a climate-change-sensitive mammal, the American pika (Ochotona princeps), distributed along elevation gradients at its northern range margin in the Coast Mountains of British Columbia (BC), Canada. We employed amplified-fragment-length-polymorphism-based genomic scans to conduct genomewide searches for candidate loci among populations inhabiting varying environments from sea level to 1500 m. Using several independent approaches to outlier locus detection, we identified 68 candidate loci putatively under selection (out of a total 1509 screened), 15 of which displayed significant associations with environmental variables including annual precipitation and maximum summer temperature. These candidate loci may represent important targets for predicting pika responses to climate change and informing novel approaches to wildlife conservation in a changing world.

When local isn't best

This paper attempts to explain circumstances under which local may be or may not be best. Natural selection may lead to local adaptation (LA), or it may be constrained by gene flow, founder effects, small population size, genetic drift, and archetype. ‘Specialist’ species display greater LA than ‘generalist’ species. Local genotypes are to a certain extent transient, being a consequence of past historical genetic patterns. Two recent meta-analyses found that while local performance exceeded the performance of a randomly chosen nonlocal population in 71% of comparisons, general adaptation across environments was as frequent as LA. Genotypes for restoration are most likely to be effective if they are adapted to current site conditions. As environmental change accelerates, both globally and locally, exceptions to ‘local is best’ may increase. For these reasons, ‘local is best’ may be better thought of as a testable hypothesis rather than as a general assumption. While either local or nonlocal plant material may be most effective for restoration practice depending on individual circumstances, local material will continue to be the first choice for restoration practitioners whenever this option is feasible and effective.