Building evolutionary resilience for conserving biodiversity under climate change

Worlds that collide: conservation applications of behaviour and culture in human-wildlife interactions

The behaviour of both humans and wildlife is central to the conservation of biodiversity because conservation requires human actions at multiple scales. In species with evidence of socially learned behaviour and culture, the juxtaposition of human and animal culture increases the complexity of human-wildlife interactions and their investigation but also offers opportunities to mitigate negative interactions. In this paper, we consider the language used to analyse human-animal interactions and we review the effect of culture and socially learned behaviours on those interactions. We investigate how knowledge of culture and theory from behavioural studies can be used to negotiate the complex interactions between humans and wildlife, providing specific examples of how culture can be mined for developing policies regarding negative interactions. We highlight that interactions between animal and human culture are central to the conservation of wildlife, and that such human-wildlife interactions are a key target for studies of biodiversity conservation. Integrating culture and social learning into conservation research offers scope to leverage knowledge gaps, misconceptions and concerns into conservation actions that are targeted, relevant and meaningful.This article is part of the theme issue 'Animal culture: conservation in a changing world'.

Assessment of Stress and Immune Gene Expression in Australasian Snapper (Chrysophrys auratus) Exposed to Chronic Temperature Change

Background: Snapper is a significant commercial, recreational, and cultural teleost species in New Zealand, with aquaculture potential. The impact of long-term (chronic) temperature changes on immune and stress responses have not been studied in snapper, yet they have a critical importance to the health status of the fish. Methods: We investigated a set of genes in 30 individual snapper including fin, head kidney, and liver tissue, fish (10 per group) were exposed to either warm (22 °C), cold (14 °C), or ambient temperatures (10.5-18.6 °C) for 3 months. Results: Analyses of experimental fish using NanoString technologies to assess stress- and immune-related genes in the three tissue types showed that 22 out of 25 genes changed significantly in the experiment, indicating the significant impacts of chronic temperature changes on stress and immune responses. Furthermore, using a combined dataset based on this study and a previous one testing the impact of acute temperature changes in snapper, we identified five genes in the non-lethal fin-clip samples that can predict internal organ health status. Conclusions: Taken together, our experiments demonstrate the potential of the NanoString gene expression assessment tool for the rapid monitoring of stress responses in snapper, which can aid in the selection of stress-resilient wild stocks, monitor species in aquaculture environments, and inform the selection of locations for aquaculture.

Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustris L.)

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic, annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of North America. In this study, we assembled and genotyped a diverse collection of 839 NWR individuals using genotyping-by-sequencing (GBS) and obtained 5955 single-nucleotide polymorphisms (SNPs). This collection consisted of samples from 12 wild NWR populations collected across Minnesota and Western Wisconsin, some of which were collected over two time points; a representative collection of cultivated NWR varieties and breeding populations; and a Zizania aquatica outgroup. Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their geographical location, with some clustering patterns likely influenced by historical ecosystem management. Cultivated populations were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. The first genome-wide scans of putative selection events in cultivated NWR suggest that the crop is undergoing heavy selection pressure for traits conducive to irrigated paddy conditions. Overall, this study presents a large set of SNP markers for use in NWR genetic studies and provides new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.

Genetic Diversity and Environmental Adaptation Signatures of the Great Seahorse (Hippocampus kelloggi) in the Coastal Regions of the Indo-Pacific as Revealed by Whole-Genome Re-Sequencing

The great seahorse (Hippocampus kelloggi) is one of the larger species within the seahorse group and is widely distributed in coastal areas of the Indo-Pacific. However, the natural resources of this species continue to decrease, rendering it a vulnerable species that faces a high risk of extinction. Therefore, there is an urgent need to conduct research on the genetic diversity of this species to protect its genetic resources. In this study, we conducted whole-genome re-sequencing (WGRS) on three H. kelloggi populations from the Red Sea (RS, n = 30), the Andaman Sea (AS, n = 13), and the South China Sea (SCS, n = 13), and a total of 1,398,936 high-quality single-nucleotide polymorphisms (SNPs) were identified. The results indicate that the average observed heterozygosity (Ho) and the average expected heterozygosity (He) for the RS, AS, and SCS populations are 0.2031 and 0.1987, 0.1914 and 0.1822, and 0.2083 and 0.2001, respectively. The three geographic populations exhibit a high degree of genetic differentiation with only a minimal gene flow between them. Consistently, in a population structure analysis, the three groups are also clearly distinguished, which is consistent with the results of the population differentiation coefficient. Demographic analyses revealed that the effective population size (Ne) of the SCS population underwent a dramatic bottleneck during the Last Glacial Maximum (LGM), followed by a substantial recovery, whereas the RS and AS populations maintained stable Ne values throughout this period. To investigate adaptive responses to climate change in the SCS population, we employed selective elimination analysis, which identified 21 candidate genes potentially involved in environmental adaptation. Of particular significance were myo5a, hps4, znf385a, msh3, and pfkfb4, which likely play crucial roles in the adaptive mechanisms of H. kelloggi. This comprehensive study not only illuminates the genetic diversity patterns of H. kelloggi but also provides a valuable foundation for future investigations into the species' evolutionary adaptations.

Identifying key monitoring areas for tree insect pest risks in China under climate change

Climate change can exacerbate pest population growth, posing significant threats to ecosystem functions and services, social development, and food security. Risk assessment is a valuable tool for effective pest management that identifies potential pest expansion and ecosystem dispersal patterns. We applied a habitat suitability model coupled with priority protection planning software to determine key monitoring areas (KMA) for tree insect pest risks under climate change and used forest ecoregions and nature reserves to assess the ecological risk of insect pest invasion. Finally, we collated the prevention and control measures for reducing future pest invasions. The KMA for tree insect pests in our current and future climate is mainly concentrated in eastern and southern China. However, with climate change, the KMA gradually expands from southeastern to northeastern China. In the current and future climate scenarios, ecoregions requiring high monitoring levels were restricted to the eastern and southern coastal areas of China, and nature reserves requiring the highest monitoring levels were mainly distributed in southeastern China. Tree insect pest invasion assessment using ecoregions and nature reserves identified that future climates increase the risk of pest invasions in forest ecoregions and nature reserves, especially in northeastern China. The increased risk and severity of tree insect pest invasions require implementing monitoring and preventative measures in these areas. We effectively assessed the pest invasion risks using forest ecoregions and nature reserves under climate change. Our assessments suggest that monitoring and early prevention should focus on southeastern and northeastern China.

Intra-specific diversity and adaptation modify regime shifts dynamics under environmental change

Environmental changes are a growing concern, as they exert pressures on ecosystems. In some cases, such changes lead to shifts in ecosystem structure. However, species can adapt to changes through evolution, and it is unclear how evolution interacts with regime shifts, which restricts ecosystem management strategies. Here, we used a model of prey population with evolution and intra-specific trait diversity, and simulated regime shifts through changes in predation pressure. We then explored interactions between evolution, diversity, and shifts in population density. Evolution induced delayed or early regime shifts, and altered the recovery of populations. Such changes depended on the relative speed of evolution and change of predation pressure, as well as on the initial state of the population. Evolution also influenced population resilience, which was important when considering strong environmental variability. For instance, storms can spontaneously increase mortality and induce shifts. Furthermore, environmental variability induced even higher mortality if the phenotypic diversity of populations is large. Some phenotypes were more vulnerable to environmental changes, and such increases in mortality favor shifts to decreases in density. Thus, population management needs to consider diversity, evolution, and environmental change altogether to better anticipate regime shifts on eco-evolutionary time scales. Here, evolution and diversity showed complex interactions with population shift dynamics. Investigating the influence of higher diversity levels, such as diversity at a community level, should be another step towards anticipating changes in ecosystems and communities.

Linking extinction risk to the economic and nutritional value of sharks in small-scale fisheries

To achieve sustainable shark fisheries, it is key to understand not only the biological drivers and environmental consequences of overfishing, but also the social and economic drivers of fisher behavior. The extinction risk of sharks is highest in coastal tropical waters, where small-scale fisheries are most prevalent. Small-scale fisheries provide a critical source of economic and nutritional security to coastal communities, and these fishers are among the most vulnerable social and economic groups. We used Kenya's and Zanzibar's small-scale shark fisheries, which are illustrative of the many data-poor, small-scale shark fisheries worldwide, as case studies to explore the relationship between extinction risk and the economic and nutritional value of sharks. To achieve this, we combined existing data on shark landings, extinction risk, and nutritional value with sales data at 16 key landing sites and information from interviews with 476 fishers. Shark fisheries were an important source of economic and nutritional security, valued at >US$4 million annually and providing enough nutrition for tens of thousands of people. Economically and nutritionally, catches were dominated by threatened species (72.7% and 64.6-89.7%, respectively). The most economically valuable species were large and slow to reproduce (e.g. mobulid rays, wedgefish, and bull, silky, and mako sharks) and therefore more likely to be threatened with extinction. Given the financial incentive and intensive fishing pressure, small-scale fisheries are undoubtedly major contributors to the decline of threatened coastal shark species. In the absence of effective fisheries management and enforcement, we argue that within small-scale fisheries the conditions exist for an economically incentivized feedback loop in which vulnerable fishers are driven to persistently overfish vulnerable and declining shark species. To protect these species from extinction, this feedback loop must be broken.

The Sixth Mass Extinction and Amphibian Species Sustainability Through Reproduction and Advanced Biotechnologies, Biobanking of Germplasm and Somatic Cells, and Conservation Breeding Programs (RBCs)

Primary themes in intergenerational justice are a healthy environment, the perpetuation of Earth's biodiversity, and the sustainable management of the biosphere. However, the current rate of species declines globally, ecosystem collapses driven by accelerating and catastrophic global heating, and a plethora of other threats preclude the ability of habitat protection alone to prevent a cascade of amphibian and other species mass extinctions. Reproduction and advanced biotechnologies, biobanking of germplasm and somatic cells, and conservation breeding programs (RBCs) offer a transformative change in biodiversity management. This change can economically and reliably perpetuate species irrespective of environmental targets and extend to satisfy humanity's future needs as the biosphere expands into space. Currently applied RBCs include the hormonal stimulation of reproduction, the collection and refrigerated storage of sperm and oocytes, sperm cryopreservation, in vitro fertilization, and biobanking of germplasm and somatic cells. The benefits of advanced biotechnologies in development, such as assisted evolution and cloning for species adaptation or restoration, have yet to be fully realized. We broaden our discussion to include genetic management, political and cultural engagement, and future applications, including the extension of the biosphere through humanity's interplanetary and interstellar colonization. The development and application of RBCs raise intriguing ethical, theological, and philosophical issues. We address these themes with amphibian models to introduce the Multidisciplinary Digital Publishing Institute Special Issue, The Sixth Mass Extinction and Species Sustainability through Reproduction Biotechnologies, Biobanking, and Conservation Breeding Programs.

Coral recruits demonstrate thermal resilience

Marine heatwaves are becoming more frequent during summer and pose a significant threat to coral reef ecosystems. Restoration efforts have the potential to support native coral populations and guard them against some degree of environmental change, while global action against climate change takes place. Interspecific hybridization is one approach through which resilient coral stock could be generated for restoration. Here we compared the performance of Acropora kenti and A. loripes hybrid and purebred coral recruits under a simulated thermal stress event. A. kenti eggs were successfully fertilized by A. loripes sperm to produce 'KL' hybrids, but no 'LK' hybrids could be produced from A. loripes eggs and A. kenti sperm. Despite corals in the elevated treatment accruing thermal stress (>12 degree heating weeks over 2 months) known to result in mass bleaching, both purebred and hybrid recruits showed no signs of stress under the simulated temperature regime, based on the performance indicators survivorship, size, color (a proxy of bleaching), and photochemical efficiency of photosystem II. Comparisons between the hybrids and purebreds studied here must be interpreted with caution because hybrid sample sizes were small. The hybrids did not outperform both of their purebred counterparts for any metrics studied here, demonstrating that there are limitations to the extent to which interspecific hybridization may boost the performance of coral stock. In general, the purebred A. loripes recruits performed best under both ambient and elevated conditions. The performance of the KL hybrid corals was similar to the maternal parental species, A. kenti, or not significantly different to either parental purebred species. The Symbiodiniaceae communities of the KL hybrids were characteristic of their maternal counterparts and may have underpinned the performance differences between the A. kenti/KL hybrid and A. loripes recruits.

Reef Adapt: A tool to inform climate-smart marine restoration and management decisions

A critical component of ecosystem restoration projects involves using genetic data to select source material that will enhance success under current and future climates. However, the complexity and expense of applying genetic data is a barrier to its use outside of specialised scientific contexts. To help overcome this barrier, we developed Reef Adapt ( www.reefadapt.org ), an innovative, globally applicable and expandable web platform that incorporates genetic, biophysical and environmental prediction data into marine restoration and assisted gene flow planning. The Reef Adapt tool provides maps that identify areas with populations suited to user-specified restoration/recipient sites under current and future climate scenarios. We demonstrate its versatility and practicality with four case studies of ecologically and evolutionarily diverse taxa: the habitat-forming corals Pocillopora damicornis and Acropora kenti, and macroalgae Phyllospora comosa and Ecklonia radiata. Reef Adapt is a management-ready tool to aid restoration and conservation efforts amidst ongoing habitat degradation and climate change.

Plant conservation in the age of genome editing: opportunities and challenges

Numerous plant taxa are threatened by habitat destruction or overexploitation. To overcome these threats, new methods are urgently needed for rescuing threatened and endangered plant species. Here, we review the genetic consequences of threats to species populations. We highlight potential advantages of genome editing for mitigating negative effects caused by new pathogens and pests or climate change where other approaches have failed. We propose solutions to protect threatened plants using genome editing technology unless absolutely necessary. We further discuss the challenges associated with genome editing in plant conservation to mitigate the decline of plant diversity.

Using the Constrained Disorder Principle to Navigate Uncertainties in Biology and Medicine: Refining Fuzzy Algorithms

Uncertainty in biology refers to situations in which information is imperfect or unknown. Variability, on the other hand, is measured by the frequency distribution of observed data. Biological variability adds to the uncertainty. The Constrained Disorder Principle (CDP) defines all systems in the universe by their inherent variability. According to the CDP, systems exhibit a degree of variability necessary for their proper function, allowing them to adapt to changes in their environments. Per the CDP, while variability differs from uncertainty, it can be viewed as a regulated mechanism for efficient functionality rather than uncertainty. This paper explores the various aspects of un-certainties in biology. It focuses on using CDP-based platforms for refining fuzzy algorithms to address some of the challenges associated with biological and medical uncertainties. Developing a fuzzy decision tree that considers the natural variability of systems can help minimize uncertainty. This method can reveal previously unidentified classes, reduce the number of unknowns, improve the accuracy of modeling results, and generate algorithm outputs that are more biologically and clinically relevant.

Patterns and effects of gene flow on adaptation across spatial scales: implications for management

Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.

Lessons from Ethiopian coffee landscapes for global conservation in a post-wild world

The reality for conservation of biodiversity across our planet is that all ecosystems are modified by humans in some way or another. Thus, biodiversity conservation needs to be implemented in multifunctional landscapes. In this paper we use a fascinating coffee-dominated landscape in southwest Ethiopia as our lens to derive general lessons for biodiversity conservation in a post-wild world. Considering a hierarchy of scales from genes to multi-species interactions and social-ecological system contexts, we focus on (i) threats to the genetic diversity of crop wild relatives, (ii) the mechanisms behind trade-offs between biodiversity and agricultural yields, (iii) underexplored species interactions suppressing pest and disease levels, (iv) how the interactions of climate change and land-use change sometimes provide opportunities for restoration, and finally, (v) how to work closely with stakeholders to identify scenarios for sustainable development. The story on how the ecology and evolution of coffee within its indigenous distribution shape biodiversity conservation from genes to social-ecological systems can inspire us to view other landscapes with fresh eyes. The ubiquitous presence of human-nature interactions demands proactive, creative solutions to foster biodiversity conservation not only in remote protected areas but across entire landscapes inhabited by people.

Complex parental effects impact variation in larval thermal tolerance in a vertically transmitting coral

Coral populations must be able to adapt to changing environmental conditions for coral reefs to persist under climate change. The adaptive potential of these organisms is difficult to forecast due to complex interactions between the host animal, dinoflagellate symbionts and the environment. Here we created 26 larval families from six Montipora capitata colonies from a single reef, showing significant, heritable variation in thermal tolerance. Our results indicate that 9.1% of larvae are expected to exhibit four times the thermal tolerance of the general population. Differences in larval thermotolerance were driven mainly by maternal contributions, but we found no evidence that these effects were driven by symbiont identity despite vertical transmission from the dam. We also document no evidence of reproductive incompatibility attributable to symbiont identity. These data demonstrate significant genetic variation within this population which provides the raw material upon which natural selection can act.

Capturing and managing genetic diversity in ex situ collections of threatened tropical trees: A case study in Karomia gigas

Premise

Although ex situ collections of threatened plants are most useful when they contain maximal genetic variation, the conservation and maintenance of genetic diversity in collections are often poorly known. We present a case study using population genomic analyses of an ex situ collection of Karomia gigas, a critically endangered tropical tree from Tanzania. Only ~43 individuals are known in two wild populations, and ex situ collections containing 34 individuals were established in two sites from wild-collected seed. The study aimed to understand how much diversity is represented in the collection, analyze the parentage of ex situ individuals, and identify efficient strategies to capture and maintain genetic diversity.

Methods

We genotyped all known individuals using a 2b-RADseq approach, compared genetic diversity in wild populations and ex situ collections, and conducted parentage analysis of the collections.

Results

Wild populations were found to have greater levels of genetic diversity than ex situ populations as measured by number of private alleles, number of polymorphic sites, observed and expected heterozygosity, nucleotide diversity, and allelic richness. In addition, only 32.6% of wild individuals are represented ex situ and many individuals were found to be the product of selfing by a single wild individual.

Discussion

Population genomic analyses provided important insights into the conservation of genetic diversity in K. gigas, identifying gaps and inefficiencies, but also highlighting strategies to conserve genetic diversity ex situ. Genomic analyses provide essential information to ensure that collections effectively conserve genetic diversity in threatened tropical trees.

Incorporating plant phenological responses into species distribution models reduces estimates of future species loss and turnover

Anthropogenetic climate change has caused range shifts among many species. Species distribution models (SDMs) are used to predict how species ranges may change in the future. However, most SDMs rarely consider how climate-sensitive traits, such as phenology, which affect individuals' demography and fitness, may influence species' ranges. Using > 120 000 herbarium specimens representing 360 plant species distributed across the eastern United States, we developed a novel 'phenology-informed' SDM that integrates phenological responses to changing climates. We compared the ranges of each species forecast by the phenology-informed SDM with those from conventional SDMs. We further validated the modeling approach using hindcasting. When examining the range changes of all species, our phenology-informed SDMs forecast less species loss and turnover under climate change than conventional SDMs. These results suggest that dynamic phenological responses of species may help them adjust their ecological niches and persist in their habitats as the climate changes. Plant phenology can modulate species' responses to climate change, mitigating its negative effects on species persistence. Further application of our framework will contribute to a generalized understanding of how traits affect species distributions along environmental gradients and facilitate the use of trait-based SDMs across spatial and taxonomic scales.

Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming

The information on how plant populations respond genetically to climate warming is scarce. Here, landscape genomic and machine learning approaches were integrated to assess genetic response of 10 wild barley (Hordeum vulgare ssp. spontaneum; WB) populations in the past and future, using whole genomic sequencing (WGS) data. The WB populations were sampled in 1980 and again in 2008. Phylogeny of accessions was roughly in conformity with sampling sites, which accompanied by admixture/introgressions. The 28-y climate warming resulted in decreased genetic diversity, increased selection pressure, and an increase in deleterious single nucleotide polymorphism (dSNP) numbers, heterozygous deleterious and total deleterious burdens for WB. Genome-environment associations identified some candidate genes belonging to peroxidase family (HORVU2Hr1G057450, HORVU4Hr1G052060 and HORVU4Hr1G057210) and heat shock protein 70 family (HORVU2Hr1G112630). The gene HORVU2Hr1G120170 identified by selective sweep analysis was under strong selection during the climate warming of the 28-y, and its derived haplotypes were fixed by WB when faced with the 28-y increasingly severe environment. Temperature variables were found to be more important than precipitation variables in influencing genomic variation, with an eco-physiological index gdd5 (growing degree-days at the baseline threshold temperature of 5 °C) being the most important determinant. Gradient forest modelling revealed higher predicted genomic vulnerability in Sede Boqer under future climate scenarios at 2041-2070 and 2071-2100. Additionally, estimates of effective population size (Ne) tracing back to 250 years indicated a forward decline in all populations over time. Our assessment about past genetic response and future vulnerability of WB under climate warming is crucial for informing conservation efforts for wild cereals and rational use strategies.

Breeding and Selecting Corals Resilient to Global Warming

Selective breeding of resilient organisms is an emerging topic in marine conservation. It can help us predict how species will adapt in the future and how we can help restore struggling populations effectively in the present. Scleractinian corals represent a potential tractable model system given their widescale phenotypic plasticity across fitness-related traits and a reproductive life history based on mass synchronized spawning. Here, I explore the justification for breeding in corals, identify underutilized pathways of acclimation, and highlight avenues for quantitative targeted breeding from the coral host and symbiont perspective. Specifically, the facilitation of enhanced heat tolerance by targeted breeding of plasticity mechanisms is underutilized. Evidence from theoretical genetics identifies potential pitfalls, including inattention to physical and genetic characteristics of the receiving environment. Three criteria for breeding emerge from this synthesis: selection from warm, variable reefs that have survived disturbance. This information will be essential to protect what we have and restore what we can.

Estimating blue mussel (Mytilus edulis) connectivity and settlement capacity in mid-latitude fjord regions

The mussel industry faces challenges such as low and inconsistent levels of larvae settlement and poor-quality spat, leading to variable production. However, mussel farming remains a vital sustainable and environmentally responsible method for producing protein, fostering ecological responsibility in the aquaculture sector. We investigate the population connectivity and larval dispersion of blue mussels (Mytilus edulis) in Scottish waters, as a case study, using a multidisciplinary approach that combined genetic data and particle modelling. This research allows us to develop a thorough understanding of blue mussel population dynamics in mid-latitude fjord regions, to infer gene-flow patterns, and to estimate population divergence. Our findings reveal a primary south-to-north particle transport direction and the presence of five genetic clusters. We discover a significant and continuous genetic material exchange among populations within the study area, with our biophysical model's outcomes aligning with our genetic observations. Additionally, our model reveals a robust connection between the southwest coast and the rest of the west coast. This study will guide the preservation of mussel farming regions, ensuring sustainable populations that contribute to marine ecosystem health and resilience.

Multidisciplinary estimates of connectivity and population structure suggest the use of multiple units for the conservation and management of meagre, Argyrosomus regius

Information on population structure and connectivity of targeted species is key for proper implementation of spatial conservation measures. We used a combination of genomics, biophysical modelling, and biotelemetry to infer the population structure and connectivity of Atlantic meagre, an important fisheries resource throughout its distribution. Genetic samples from previously identified Atlantic spawning locations (Gironde, Tejo, Guadalquivir, Banc d'Arguin) and two additional regions (Algarve and Senegal) were analysed using genome-wide SNP-genotyping and mitochondrial DNA analyses. Biophysical models were conducted to investigate larval dispersal and connectivity from the known Atlantic spawning locations. Additionally, thirteen fish were double-tagged with biotelemetry transmitters off the Algarve (Portugal) to assess movement patterns and connectivity of adult individuals. This multidisciplinary approach provided a robust overview of meagre population structure and connectivity in the Atlantic. Nuclear SNP-genotyping showed a clear differentiation between the European and African populations, with significant isolation of the few known Atlantic spawning sites. The limited level of connectivity between these subpopulations is potentially driven by adults, capable of wide-ranging movements and connecting sites 500 km apart, as evidenced by tagging studies, whilst larval dispersal inferred by modelling is much more limited (average of 52 km; 95% of connectivity events up to 174 km). Our results show sufficient evidence of population structure, particularly between Africa and Europe but also within Europe, for the meagre to be managed as separate stocks. Additionally, considering the low degree of larvae connectivity, the implementation of marine protected areas in key spawning sites could be crucial towards species sustainability.

Cities of the Anthropocene: urban sustainability in an eco-evolutionary perspective

Cities across the globe are driving systemic change in social and ecological systems by accelerating the rates of interactions and intensifying the links between human activities and Earth's ecosystems, thereby expanding the scale and influence of human activities on fundamental processes that sustain life. Increasing evidence shows that cities not only alter biodiversity, they change the genetic makeup of many populations, including animals, plants, fungi and microorganisms. Urban-driven rapid evolution in species traits might have significant effects on socially relevant ecosystem functions such as nutrient cycling, pollination, water and air purification and food production. Despite increasing evidence that cities are causing rapid evolutionary change, current urban sustainability strategies often overlook these dynamics. The dominant perspectives that guide these strategies are essentially static, focusing on preserving biodiversity in its present state or restoring it to pre-urban conditions. This paper provides a systemic overview of the socio-eco-evolutionary transition associated with global urbanization. Using examples of observed changes in species traits that play a significant role in maintaining ecosystem function and resilience, I propose that these evolutionary changes significantly impact urban sustainability. Incorporating an eco-evolutionary perspective into urban sustainability science and planning is crucial for effectively reimagining the cities of the Anthropocene. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'.

Differential patterns of within- and between-population genetically based trait variation in Lupinus angustifolius

BACKGROUND AND AIMS

Within-population genetic and phenotypic variation play a key role in the development of adaptive responses to environmental change. Between-population variation is also an essential element in assessing the evolutionary potential of species in response to changes in environmental conditions. In this context, common garden experiments are a useful tool to separate the genetic and environmental components of phenotypic variation. We aimed to assess within- and between-population phenotypic variation of Lupinus angustifolius L. in terms of its evolutionary potential to adapt to ongoing climate change.

METHODS

We evaluated populations' phenotypic variation of foliar, phenological and reproductive traits with a common garden experiment. Patterns of functional trait variation were assessed with (1) mixed model analyses and coefficients of variation (CVs) with confidence intervals, (2) principal component analyses (PCAs) and (3) correlations between pairs of traits. Analyses were performed at the population level (four populations) and at the latitude level (grouping pairs of populations located in two latitudinal ranges).

KEY RESULTS

Phenotypic variation had a significant genetic component associated with a latitudinal pattern. (1) Mixed models found lower specific leaf area, advanced flowering phenology and lower seed production of heavier seeds in southern populations, whereas CV analyses showed lower within-latitude variation especially in phenological and reproductive traits in southern populations. (2) PCAs showed a clearer differentiation of phenotypic variation between latitudes than between populations. (3) Correlation analyses showed a greater number of significant correlations between traits in southern populations (25 vs. 13).

CONCLUSIONS

Between-population phenotypic variation was determined by contrasting temperature and drought at different latitude and elevation. Southern populations had differential trait values compatible with adaptations to high temperatures and drought. Moreover, they had lower within-population variation and a greater number of trait correlations probably as a result of these limiting conditions, making them more vulnerable to climate change.

Conservation macrogenetics: harnessing genetic data to meet conservation commitments

Genetic biodiversity is rapidly gaining attention in global conservation policy. However, for almost all species, conservation relevant, population-level genetic data are lacking, limiting the extent to which genetic diversity can be used for conservation policy and decision-making. Macrogenetics is an emerging discipline that explores the patterns and processes underlying population genetic composition at broad taxonomic and spatial scales by aggregating and reanalyzing thousands of published genetic datasets. Here we argue that focusing macrogenetic tools on conservation needs, or conservation macrogenetics, will enhance decision-making for conservation practice and fill key data gaps for global policy. Conservation macrogenetics provides an empirical basis for better understanding the complexity and resilience of biological systems and, thus, how anthropogenic drivers and policy decisions affect biodiversity.

Fire-driven animal evolution in the Pyrocene

Fire regimes are a major agent of evolution in terrestrial animals. Changing fire regimes and the capacity for rapid evolution in wild animal populations suggests the potential for rapid, fire-driven adaptive animal evolution in the Pyrocene. Fire drives multiple modes of evolutionary change, including stabilizing, directional, disruptive, and fluctuating selection, and can strongly influence gene flow and genetic drift. Ongoing and future research in fire-driven animal evolution will benefit from further development of generalizable hypotheses, studies conducted in highly responsive taxa, and linking fire-adapted phenotypes to their underlying genetic basis. A better understanding of evolutionary responses to fire has the potential to positively influence conservation strategies that embrace evolutionary resilience to fire in the Pyrocene.

A conservation planning strategy applied to the evolutionary history of the mantellid frogs of Madagascar

Phylogenetic diversity is an increasingly applied metric used to maximize the representation of evolutionary history in spatial conservation planning. When following this approach, researchers commonly overlook sites with a relatively higher proportion of recently diverged endemic species, also known as centers of neo-endemism. Here we aim to demonstrate how targeting the conservation of different facets of diversity (taxonomic diversity, phylogenetic diversity and centers of endemism) can provide more cost-effective solutions to the conservation of the all evolutionary spectrum of biodiversity. We do so by using the mantellid frogs of Madagascar as a case study. Our results confirm that areas with high concentrations of neo-endemism can be effectively identified as conservation planning priorities only if we specifically target them. Neglecting areas that are poor in phylogenetic diversity may therefore compromise the maintenance of diversification processes, particularly when lesser proportions of the landscape are protected. This approach can be of particular interest to island ecosystems, since they often harbor unique and restricted evolutionary radiations.

Losing the forest for the tree? On the wisdom of subpopulation management

Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.

Understanding and applying biological resilience, from genes to ecosystems

The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system's behaviour requires knowledge of its component parts and their interactions. Here we call for increased efforts to understand 'biological resilience', or the processes that enable components across biological levels, from genes to communities, to resist or recover from perturbations. Although ecologists and evolutionary biologists have the tool-boxes to examine form and function, efforts to integrate this knowledge across biological levels and take advantage of big data (e.g. ecological and genomic) are only just beginning. We argue that combining eco-evolutionary knowledge with ecosystem-level concepts of resilience will provide the mechanistic basis necessary to improve management of human, natural and agricultural ecosystems, and outline some of the challenges in achieving an understanding of biological resilience.

Hidden genetic variation in plasticity provides the potential for rapid adaptation to novel environments

Rapid environmental change is forcing populations into environments where plasticity will no longer maintain fitness. When populations are exposed to novel environments, evolutionary theory predicts that genetic variation in fitness will increase and should be associated with genetic differences in plasticity. If true, then genetic variation in plasticity can increase adaptive potential in novel environments, and population persistence via evolutionary rescue is more likely. To test whether genetic variation in fitness increases in novel environments and is associated with plasticity, we transplanted 8149 clones of 314 genotypes of a Sicilian daisy (Senecio chrysanthemifolius) within and outside its native range, and quantified genetic variation in fitness, and plasticity in leaf traits and gene expression. Although mean fitness declined by 87% in the novel environment, genetic variance in fitness increased threefold and was correlated with plasticity in leaf traits. High fitness genotypes showed greater plasticity in gene expression, but lower plasticity in most leaf traits. Interestingly, genotypes with the highest fitness in the novel environment had the lowest fitness at the native site. These results suggest that standing genetic variation in plasticity could help populations to persist and adapt to novel environments, despite remaining hidden in native environments.

Genetic assessment of the value of restoration planting within an endangered eucalypt woodland

Assessment of woodland restoration often focusses on stand demographics, but genetic factors likely influence long-term stand viability. We examined the genetic composition of Yellow Box (Eucalyptus melliodora) trees in endangered Box-Gum Grassy Woodland in SE Australia, some 30 years after planting with seeds of reportedly local provenance. Using DArT sequencing for 1406 SNPs, we compared genetic diversity and population structure of planted E. melliodora trees with remnant bushland trees, paddock trees and natural recruits. Genetic patterns imply that natural stands and paddock trees had historically high gene flow (among group pairwise FST = 0.04-0.10). Genetic diversity was highest among relictual paddock trees (He = 0.17), while diversity of revegetated trees was identical to natural bushland trees (He = 0.14). Bayesian clustering placed the revegetated trees into six genetic groups with four corresponding to genotypes from paddock trees, indicating that revegetated stands are mainly of genetically diverse, local provenance. Natural recruits were largely derived from paddock trees with some contribution from planted trees. A few trees have likely hybridised with other local eucalypt species which are unlikely to compromise stand integrity. We show that paddock trees have high genetic diversity and capture historic genetic variety and provide important foci for natural recruitment of genetically diverse and outcrossed seedlings.

Phylogenetic diversity in conservation: A brief history, critical overview, and challenges to progress

Species that are evolutionarily distinct have long been valued for their unique and irreplaceable contribution to biodiversity. About 30 years ago, this idea was extended to the concept of phylogenetic diversity (PD): a quantitative, continuous-scale index of conservation value for a set of species, calculated by summing the phylogenetic branch lengths that connect them. This way of capturing evolutionary history has opened new opportunities for analysis, and has therefore generated a huge academic literature, but to date has had only limited impact on conservation practice or policy. In this review, I present a brief historical overview of PD research. I then examine the empirical evidence for the primary rationale of PD that it is the best proxy for "feature diversity," which includes both known and unknown phenotypic characters, contributing to utilitarian value, ecosystem function, future resilience, and evolutionary potential. Surprisingly, it is only relatively recently that this rationale has been subject to systematic empirical scrutiny, and to date, there are mixed results on the connection between PD and phenotypic diversity. Finally, I examine the least well-studied, but potentially greatest challenge for PD: its dependence on the reliability of phylogenetic inference itself. The very few studies that have investigated this so far show that the ranking of species assemblages by their PD values can vary substantially under alternative, routine, phylogenetic methods and assumptions. If PD is to become more widely adopted into conservation decision-making, it will be important to better understand the conditions under which it performs well, and those under which it performs poorly.

Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide

Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.

A resilient and connected network of sites to sustain biodiversity under a changing climate

Motivated by declines in biodiversity exacerbated by climate change, we identified a network of conservation sites designed to provide resilient habitat for species, while supporting dynamic shifts in ranges and changes in ecosystem composition. Our 12-y study involved 289 scientists in 14 study regions across the conterminous United States (CONUS), and our intent was to support local-, regional-, and national-scale conservation decisions. To ensure that the network represented all species and ecosystems, we stratified CONUS into 68 ecoregions, and, within each, we comprehensively mapped the geophysical settings associated with current ecosystem and species distributions. To identify sites most resilient to climate change, we identified the portion of each geophysical setting with the most topoclimate variability (high landscape diversity) likely to be accessible to dispersers (high local connectedness). These "resilient sites" were overlaid with conservation priority maps from 104 independent assessments to indicate current value in supporting recognized biodiversity. To identify key connectivity areas for sustaining species movement in response to climate change, we codeveloped a fine-scale representation of human modification and ran a circuit-theory-based analysis that emphasized movement potential along geographic climate gradients. Integrating areas with high values for two or more factors, we identified a representative, resilient, and connected network of biodiverse lands covering 35% of CONUS. Because the network connects climatic gradients across 250,000 biodiversity elements and multiple resilient examples of all geophysical settings in every ecoregion, it could form the spatial foundation for targeted land protection and other conservation strategies to sustain a diverse, dynamic, and adaptive world.

Conservation genomics of an endangered arboreal mammal following the 2019-2020 Australian megafire

The impacts of a changing climate threaten species, populations and ecosystems. Despite these significant and large-scale impacts on threatened species, many remain understudied and have little to no genetic information available. The greater glider, Petauroides volans, is an endangered species highly sensitive to the predicted changes in temperature under a changing climate and was recently severely impacted by a megafire natural disaster (85% estimated population loss). Baseline genetic data is essential for conservation management and for detecting detrimental changes in fire-effected populations. We collected genetic samples within 2 years post the 2019-2020 catastrophic Australian bushfires to examine adaptive potential, baseline genetic diversity and population structure, across their southern range in the state of New South Wales. Population genomic analyses were conducted using 8493 genome-wide SNPs for 86 greater glider individuals across 14 geographic locations. Substantial genetic structure was detected across locations, with low genetic diversity and effective population sizes observed in isolated areas. Additionally, we found signals of putative adaptation in response to temperature in greater gliders using a genotype-environment association analysis. These findings have important implications for the management of greater glider populations by identifying at-risk populations and identifying adaptive potential. We demonstrate the importance of baseline genetic information for endangered species as a practical approach to conservation. This is particularly important given the threat that changes in temperatures and megafire events, as predicted under a changing climate, poses for this species.

Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola

Understanding the role of genetic and nongenetic variants in modulating phenotypes is central to our knowledge of adaptive responses to local conditions and environmental change, particularly in species with such low population genetic diversity that it is likely to limit their evolutionary potential. A first step towards uncovering the molecular mechanisms underlying population-specific responses to the environment is to carry out environmental association studies. We associated climatic variation with genetic, epigenetic and microbiome variation in populations of a social spider with extremely low standing genetic diversity. We identified genetic variants that are associated strongly with environmental variation, particularly with average temperature, a pattern consistent with local adaptation. Variation in DNA methylation in many genes was strongly correlated with a wide set of climate parameters, thereby revealing a different pattern of associations than that of genetic variants, which show strong correlations to a more restricted range of climate parameters. DNA methylation levels were largely independent of cis-genetic variation and of overall genetic population structure, suggesting that DNA methylation can work as an independent mechanism. Microbiome composition also correlated with environmental variation, but most strong associations were with precipitation-related climatic factors. Our results suggest a role for both genetic and nongenetic mechanisms in shaping phenotypic responses to local environments.

Incorporating evolutionary and threat processes into crop wild relatives conservation

Crop wild relatives (CWR) intra- and interspecific diversity is essential for crop breeding and food security. However, intraspecific genetic diversity, which is central given the idiosyncratic threats to species in landscapes, is usually not considered in planning frameworks. Here, we introduce an approach to develop proxies of genetic differentiation to identify conservation areas, applying systematic conservation planning tools that produce hierarchical prioritizations of the landscape. It accounts for: (i) evolutionary processes, including historical and environmental drivers of genetic diversity, and (ii) threat processes, considering taxa-specific tolerance to human-modified habitats, and their extinction risk status. Our analyses can be used as inputs for developing national action plans for the conservation and use of CWR. Our results also inform public policy to mitigate threat processes to CWR (like crops living modified organisms or agriculture subsidies), and could advise future research (e.g. for potential germplasm collecting). Although we focus on Mesoamerican CWR within Mexico, our methodology offers opportunities to effectively guide conservation and monitoring strategies to safeguard the evolutionary resilience of any taxa, including in regions of complex evolutionary histories and mosaic landscapes.

Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster

The emergence of high resolution population genetic techniques, such as genotyping-by-sequencing (GBS), in combination with recent advances in particle modelling of larval dispersal in marine organisms, can deliver powerful new insights to support fisheries conservation and management. In this study, we used this combination to investigate the population connectivity of a commercial deep sea lobster species, the New Zealand scampi, Metanephrops challengeri, which ranges across a vast area of seafloor around New Zealand. This species has limited dispersal capabilities, including larvae with weak swimming abilities and short pelagic duration, while the reptant juvenile/adult stages of the lifecycle are obligate burrow dwellers with limited home ranges. Ninety-one individuals, collected from five scampi fishery management areas around New Zealand, were genotyped using GBS. Using 983 haplotypic genomic loci, three genetically distinct groups were identified: eastern, southern and western. These groups showed significant genetic differentiation with clear source-sink dynamics. The direction of gene flow inferred from the genomic data largely reflected the hydrodynamic particle modelling of ocean current flow around New Zealand. The modelled dispersal during pelagic larval phase highlights the strong connectivity among eastern sampling locations and explains the low genetic differentiation detected among these sampled areas. Our results highlight the value of using a transdisciplinary approach in the inference of connectivity among populations for informing conservation and fishery management.

Assessing the potential for demographic restoration and assisted evolution to build climate resilience in coral reefs

Interest is growing in developing conservation strategies to restore and maintain coral reef ecosystems in the face of mounting anthropogenic stressors, particularly climate warming and associated mass bleaching events. One such approach is to propagate coral colonies ex situ and transplant them to degraded reef areas to augment habitat for reef-dependent fauna, prevent colonization from spatial competitors, and enhance coral reproductive output. In addition to such "demographic restoration" efforts, manipulating the thermal tolerance of outplanted colonies through assisted relocation, selective breeding, or genetic engineering is being considered for enhancing rates of evolutionary adaptation to warming. Although research into such "assisted evolution" strategies has been growing, their expected performance remains unclear. We evaluated the potential outcomes of demographic restoration and assisted evolution in climate change scenarios using an eco-evolutionary simulation model. We found that supplementing reefs with pre-existing genotypes (demographic restoration) offers little climate resilience benefits unless input levels are large and maintained for centuries. Supplementation with thermally resistant colonies was successful at improving coral cover at lower input levels, but only if maintained for at least a century. Overall, we found that, although demographic restoration and assisted evolution have the potential to improve long-term coral cover, both approaches had a limited impact in preventing severe declines under climate change scenarios. Conversely, with sufficient natural genetic variance and time, corals could readily adapt to warming temperatures, suggesting that restoration approaches focused on building genetic variance may outperform those based solely on introducing heat-tolerant genotypes.

Comparing management strategies for conserving communities of climate-threatened species with a stochastic metacommunity model

Many species are shifting their ranges to keep pace with climate change, but habitat fragmentation and limited dispersal could impede these range shifts. In the case of climate-vulnerable foundation species such as tropical reef corals and temperate forest trees, such limitations might put entire communities at risk of extinction. Restoring connectivity through corridors, stepping-stones or enhanced quality of existing patches could prevent the extinction of several species, but dispersal-limited species might not benefit if other species block their dispersal. Alternatively, managers might relocate vulnerable species between habitats through assisted migration, but this is generally a species-by-species approach. To evaluate the relative efficacy of these strategies, we simulated the climate-tracking of species in randomized competitive metacommunities with alternative management interventions. We found that corridors and assisted migration were the most effective strategies at reducing extinction. Assisted migration was especially effective at reducing the extinction likelihood for short-dispersing species, but it often required moving several species repeatedly. Assisted migration was more effective at reducing extinction in environments with higher stochasticity, and corridors were more effective at reducing extinction in environments with lower stochasticity. We discuss the application of these approaches to an array of systems ranging from tropical corals to temperate forests.

This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.

Residency, movement patterns, behavior and demographics of reef manta rays in Komodo National Park

Background

The reef manta ray (Mobula alfredi) is a globally threatened species and an iconic tourist attraction for visitors to Indonesia's Komodo National Park (NP). In 2013, manta ray fishing was banned in Komodo NP and its surroundings, preceding the nationwide manta ray protection in 2014. Over a decade ago, a previous acoustic telemetry study demonstrated that reef manta rays had high fidelity to sites within the park, while more recent photo-identification data indicated that some individuals move up to 450 km elsewhere. Characterization of manta ray demographics, behavior, and a focused assessment on site use of popular tourism locations within the park is vital to assist the Komodo NP Management Authority formulate appropriate manta ray conservation and management policies.

Methods

This study uses a long-term library (MantaMatcher.org) of photo-identification data collected by researchers and citizen scientists to investigate manta ray demographics and habitat use within the park at four sites frequented by tour operators: Cauldron, Karang Makassar, Mawan, and Manta Alley. Residency and movements of manta rays were investigated with maximum likelihood analyses and Markov movement models.

Results

A total of 1,085 individual manta rays were identified from photographs dating from 2013 to 2018. In general, individual manta rays displayed a higher affinity to specific sites than others. The highest re-sighting probabilities came from the remote southern site, Manta Alley. Karang Makassar and Mawan are only ~5 km apart; however, manta rays displayed distinct site affinities. Exchange of individuals between Manta Alley and the two central sites (~35.5 km apart) occurred, particularly seasonally. More manta rays were recorded traveling from the south to the central area than vice versa. Female manta rays were more mobile than males. Similar demographic groups used Karang Makassar, Mawan, and Manta Alley for foraging, cleaning, cruising, or courtship activities. Conversely, a higher proportion of immature manta rays used the northern site, Cauldron, where foraging was commonly observed. Fishing gear-related injuries were noted on 56 individuals (~5%), and predatory injuries were present on 32 individuals (~3%). Tourism within the park increased from 2014 to 2017, with 34% more dive boats per survey at Karang Makassar and Mawan.

Discussion

The Komodo NP contains several distinct critical habitats for manta rays that encompass all demographics and accommodate seasonal manta ray movements. While the present study has not examined population trends, it does provide foundational data for such work. Continued research into manta ray abundance, long-range movements, and identifying and protecting other critical aggregation areas within the region is integral to securing the species' recovery. We provide management recommendations to limit undue pressure on manta rays and their critical habitats from tourism.

Evidence for a robust photosystem II in the photosynthetic amoeba Paulinella

Paulinella represents the only known case of an independent primary plastid endosymbiosis, outside Archaeplastida, that occurred c. 120 (million years ago) Ma. These photoautotrophs grow very slowly in replete culture medium with a doubling time of 6-7 d at optimal low light, and are highly sensitive to photodamage under moderate light levels. We used genomic and biophysical methods to investigate the extreme slow growth rate and light sensitivity of Paulinella, which are key to photosymbiont integration. All photosystem II (PSII) genes except psb28-2 and all cytochrome b₆ f complex genes except petM and petL are present in Paulinella micropora KR01 (hereafter, KR01). Biophysical measurements of the water oxidation complex, variable chlorophyll fluorescence, and photosynthesis-irradiance curves show no obvious evidence of PSII impairment. Analysis of photoacclimation under high-light suggests that although KR01 can perform charge separation, it lacks photoprotection mechanisms present in cyanobacteria. We hypothesize that Paulinella species are restricted to low light environments because they are deficient in mitigating the formation of reactive oxygen species formed within the photosystems under peak solar intensities. The finding that many photoprotection genes have been lost or transferred to the host-genome during endosymbiont genome reduction, and may lack light-regulation, is consistent with this hypothesis.

The Diversity in the Genus Canis Challenges Conservation Biology: A Review of Available Data on Asian Wolves

Taxa belonging to the Genus Canis can challenge taxonomists because species boundaries and distribution ranges are often gradual. Species delineation within Canis is currently not based on consistent criteria, and is hampered by geographical bias and lack of taxonomic research. But a consistent taxonomy is critical, given its importance for assigning legal protection, conservation priorities, and financial resources. We carried out a qualitative review of the major wolf lineages so far identified from Asia from historical to contemporary time and considered relevant morphological, ecological, and genetic evidence. We present full mitochondrial phylogenies and genetic distances between these lineages. This review aims to summarize the available data on contemporary Asian wolf lineages within the context of the larger phylogenetic Canis group and to work toward a taxonomy that is consistent within the Canidae. We found support for the presence and taxon eligibility of Holarctic gray, Himalayan/Tibetan, Indian, and Arabian wolves in Asia and recommend their recognition at the taxonomic levels consistent within the group.

Phenotypic differentiation and diversifying selection in populations of Eruca sativa along an aridity gradient

BACKGROUND

The aridity gradient in the eastern Mediterranean offers an opportunity to investigate intra-specific genetic differentiation and local adaptation in plant populations. Here we used genetic (FST) and quantitative trait (PST) differentiation to assess local adaptation among three natural populations of Eruca sativa (Brassicaceae) distributed along a climatic range representing desert, semi-arid and Mediterranean habitats.

RESULTS

Amplified fragment length polymorphism (AFLP) analysis revealed high genetic diversity in each population, but low genetic differentiation between populations and relatively high gene flow. Further phenotypic evaluation in a common garden experiment (conduced in a Mediterranean habitat) showed clear differences in phenological traits among populations (day of flowering and duration of the reproductive stage), shoot and root biomass, as well as fitness-related traits (total number of fruits and total seed weight). FST-PST comparison showed that PST values of the phenological traits, as well as below- and above-ground biomass and fitness-related traits, were higher than the FST values.

CONCLUSIONS

Overall, our results support the identification of genotypic and phenotypic differentiation among populations of E. sativa. Furthermore, the FST-PST comparison supports the hypothesis that these were subjected to past diversifying selection. Thus, the results clearly demonstrate adaptive divergence among populations along an aridity gradient, emphasize the ecological value of early flowering time in arid habitats, and contribute to our understanding of the possible impact of climate change on evolutionary processes in plant populations.