Evolution in biodiversity policy - current gaps and future needs

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.

Evolution Under Competition Increases Population Production by Reducing the Density-Dependence of Net Energy Fluxes and Growth

Competition can drive rapid evolution, but forecasting how species evolve in communities remains difficult. Life history theory predicts that evolution in crowded environments should maximize population production, with intra- and inter-specific competition producing similar outcomes if species compete for similar resources. Despite its appeal, this prediction has rarely been tested in communities. To test its generality and identify its physiological basis, we used experimental evolution to maintain four species of marine phytoplankton alone or together in a community for 4.5 months. We then quantified changes in their metabolism, demography, and competitive ability at two timepoints (~60 and 120 generations) in common garden experiments. One species was outcompeted during the evolution experiment. For the other three, we found the same evolutionary outcome: species evolved greater biovolume production regardless of competition treatment but did so either by increasing max. population size or individual cell size. Biovolume production increased because of the differential evolution of photosynthesis and respiration under intense competition. These metabolic changes meant that intraspecific competition decreased, and cells maintained higher rates of net energy production and growth as populations neared the stationary phase. Overall, these results show that intra- and inter-specific competition influence physiological and population parameters similarly in species that compete for essential resources. Life history theory thus provides a valuable base for predicting how species evolve in communities, and our results show how these predictions relate to the evolution of metabolism and competitive ability.

Socioeconomic prerequisites determine national long-term biomonitoring efforts

In the current anthropogenic era characterised by human-induced environmental changes, long-term biomonitoring has become a crucial component for understanding ecological patterns and detecting shifts in biodiversity. However, spatiotemporal inconsistencies in biomonitoring efforts hinder transboundary progress in understanding and mitigating global environmental change effectively. The International Long-Term Ecosystem Research (ILTER) network is one of the largest standardised biomonitoring initiatives worldwide, encompassing 44 countries globally, including 26 European countries that are part of the European Long-Term Ecosystem Research network (eLTER). To better understand the establishment and development of such long-term biomonitoring efforts, we analysed spatial and temporal trends within the eLTER network. Additionally, we evaluated the environmental, social, and economic factors influencing engagement in biomonitoring activities within this European network. Our findings reveal a spatial imbalance, with biomonitoring efforts concentrated in Central and Western European countries, where monitoring initiatives have typically been established for a longer duration. Furthermore, our analyses underscore the complex interplay of economic, geographic, and cultural factors in the development of long-term ecological research infrastructures. Countries with greater geographic connectivity, slower economic growth, and higher research activity are more likely to be involved in the eLTER network. The intensity of biomonitoring significantly increased with greater research investments, economic growth, and elevated levels of tourism. In contrast, it decreased in countries that are more inward-facing and exhibit a belief in their ability to control environmental outcomes independently. Addressing spatial gaps in monitoring necessitates enhanced support and funding to ensure comprehensive ecological monitoring over extended time periods. This is essential for achieving transboundary sustainability and effective biodiversity conservation in the face of global change drivers.

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'.

Genetic analyses reveal panmixia in Indian waters and population subdivision across Indian Ocean and Indo-Malay Archipelago for Decapterus russelli

The Indian Scad, Decapterus russelli is an important pelagic carangid widely distributed throughout the Indian Ocean and the Indo-West Pacific. Despite being widely distributed in the Indian Ocean, the information regarding genetic structuring and diversity has been lacking compared to its Indo Malay Archipelago counterparts. The present study was conducted to investigate the genetic stock structure of D. russelli based on mitochondrial (Cyt b) and nuclear (DrAldoB1) markers along Indian waters. The results indicated the presence of a single panmictic stock across the Indian Ocean region. High haplotype diversity associated with low nucleotide diversity suggested a population bottleneck followed by rapid population growth. Phylogenetic analysis revealed the absence of geographical clustering of lineages with the most common haplotype distributed globally. The pelagic life style, migratory capabilities, and larval dispersal may be the contributing factors to the observed spatial homogeneity of D. russelli. However, significant genetic differentiation was observed between the populations from Indian Ocean and Indo-Malay Archipelago. Hierarchical molecular variance analysis (AMOVA), pairwise FST comparisons and SAMOVA showed existence of two distinct genetic stocks of D. russelli in the Indian Ocean and IMA. The observed interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the Indo-Malay Archipelago and the Indian Ocean regions suggest the influence of historic isolation, ocean surface currents and biotic and abiotic features of the ocean. Also, there was a significant relationship between genetic distance and geographical distance between population pairs in a manner consistent with isolation-by-distance. These resulted in the evolution of a phylogeographic break for this species between these regions. The findings of these results suggest that D. russelli from the Indian Ocean shall be managed in its entire area of distribution as a single stock. Further, the Indian Ocean and Indo-Malayan stocks can be managed separately.

Detecting Darwinian Shortfalls in the Amazonian Odonata

Among the oldest winged insects, odonates are a monophyletic order that have become important models for ecological studies because of their highly diverse reproductive behaviors and their role as top predators and bioindicators. However, knowledge on evolutionary relationships within the order is still scarce compared to other taxa, and this situation is even more complicated in areas with high biodiversity, such as in the Amazon. Here, we sought to identify knowledge gaps on Amazonian Odonata regarding three main aspects: (i) how the inclusion of Amazonian taxa affects our interpretation of the evolutionary relationships of Zygoptera and Anisoptera; (ii) the position of Amazonian taxa in the existing supertree of the Odonata; (iii) dating evolutionary divergence between nodes using fossil records; (iv) assessing whether more species-rich basins (e.g., Amazon basin) have a larger phylogenetic gap when compared to basins with lower richness in South and Central America; and (v) in the light of our knowledge, we discuss diversification patterns found in the most predominant clades of Amazonian taxa. We built a supertree from currently available phylogenetic information of Odonata. The results show that there is no genetic information for 85% (n: 503) of the Amazonian species and that family level relationships are unknown for 17 genera. After compiling the data, we observed that clades belonging to Neotropical lineages are the most poorly resolved, with large polytomies. This problem was identified in many Anisoptera genera, such as Macrothemis, Dasythemis, Elasmothemis, and Erythrodiplax. Our results also suggest that not always the richest basins have the greatest phylogenetic gaps. As expected, we found important gaps in the existing Odonata phylogenies, especially in clades that include Amazonian representatives, that are also those less known from ecological and conservation perspectives.

Genetic effects of long-term captive breeding on the endangered pygmy hog

Long-term captive populations often accumulate genetic changes that are detrimental to their survival in the wild. Periodic genetic evaluation of captive populations is thus necessary to identify deleterious changes and minimize their impact through planned breeding. Pygmy hog (Porcula salvania) is an endangered species with a small population inhabiting the tall sub-Himalayan grasslands of Assam, India. A conservation breeding program of pygmy hog from six founders has produced a multi-generational captive population destined for reintroduction into the wild. However, the impact of conservation breeding on its genetic diversity remained undocumented. Here, we evaluate temporal genetic changes in 39 pygmy hogs from eight consecutive generations of a captive population using genome-wide SNPs, mitochondrial genomes, and MHC sequences, and explore the relationship between genetic diversity and reproductive success. We find that pygmy hog harbors a very low genome-wide heterozygosity (H) compared to other members of the Suidae family. However, within the captive population we find excess heterozygosity and a significant increase in H from the wild-caught founders to the individuals in subsequent generations due to the selective pairing strategy. The MHC and mitochondrial nucleotide diversities were lower in captive generations compared to the founders with a high prevalence of low-frequency MHC haplotypes and more unique mitochondrial genomes. Further, even though no signs of genetic inbreeding were observed from the estimates of individual inbreeding coefficient F and between individuals (F_IS) in each generation, the kinship coefficient showed a slightly increasing trend in the recent generations, due to a relatively smaller non-random sample size compared to the entire captive population. Surprisingly, male pygmy hogs that had higher heterozygosity also showed lower breeding success. We briefly discuss the implications of our findings in the context of breeding management and recommend steps to minimize the genetic effects of long-term captive breeding.

Genetic diversity and structure of one of the most endangered freshwater fish species in Mexico: Tlaloc hildebrandi (Miller, 1950) and recognition of its evolutionarily significant units

The endangered Chiapas killifish Tlaloc hildebrandi is an endemic freshwater species that lives in four subbasins of the Grijalva and Usumacinta basins, and one of the most geographically restricted species of the Produndulidae family. The species was originally described as endemic to springs in the high limestone plateau in San Cristóbal de Las Casas in the Río Amarillo subbasin (upper Grijalva basin). However, it was recently recorded in the Jataté and Tzaconejá subbasins in the upper Usumacinta basin, thereby expanding its known distribution range. The discovery of these populations is relevant not only for the conservation of the species but also for a better understanding of its evolutionary history. Currently, the scarce populations of T. hildebrandi, found in only a few localities in the Grijalva and Usumacinta basins, are fragmented and living under unfavorable conditions. Here, we analyzed three mitochondrial (mt-atp8&6 and mt-nd2) and one nuclear (nuc-s7) marker in order to assess the genetic diversity and population structure of T. hildebrandi. We found that, in comparison with other endangered freshwater fish species from Mexico, T. hildebrandi showed a lower level of genetic diversity (mt-nd2: h = 0.469, π = 0.0009; mt-atp8&6: h = 0.398, π = 0.001; and nuc-S7: h = 0.433, π = 0.001). Moreover, the analyzed populations exhibited a strong genetic structure in accordance with their geographic distribution, and can be placed into three genetic clusters: (1) Amarillo plus Chenhaló in the upper Grijalva basin, (2) Jataté, and (3) Tzaconejá, both in the upper Usumacinta basin. On the basis of our results, we propose the recognition of at least three evolutionarily significant units (ESUs) for the species and the urgent implementation of ex situ and in situ conservation and management efforts that consider the genetic background of the species.

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

Intraspecific diversity in an ecological engineer functionally trumps interspecific diversity in shaping community structure

Can intraspecific diversity functionally supersede interspecific diversity? Recent studies have established the ecological effects of intraspecific variation on a number of ecosystem dynamics including resilience and productivity and we hypothesised that they may functionally exceed those of species diversity. We focused on a coastal ecosystem dominated by two coexisting bioengineering mussel species, one of which, Perna perna, displays two distinct phylogeographic lineages. A manipulative field experiment revealed greater habitat structural complexity and a more benign microscale environment within beds of the eastern lineage than those of the western lineage or the second species (Mytilus galloprovincialis); the latter two did not differ. Similarly, while infaunal species abundance and biomass differed significantly between the two lineages of Perna, there was no such difference between Mytilus and the western Perna lineage. The evenness and diversity of associated infaunal assemblages responded differently. Diversity differed relatively weakly between species, while evenness showed a very strong difference between conspecific lineages. Our results show that variation within a species can functionally supersede diversity between species. As the two P. perna lineages have different physiological tolerances, we expect them to react differently to environmental change. Our findings indicate that predicting the ecosystem-level consequences of climate change requires an understanding of the relative strengths of within- and between-species differences in functionality.

IUCN Red List and the value of integrating genetics

Many species on endangered species lists such as the IUCN Red List (RL) are categorized using demographic factors such as numbers of mature individuals. Genetic factors are not currently used in the RL even though their explicit consideration, including effective population size (Ne) and expected heterozygosity-loss (H-loss), could improve the assessment of extinction risk. Here, we consider the estimation of Ne and H-loss in the context of RL species. First, we investigate the reporting of number of mature individuals for RL Endangered species, which is needed to estimate Ne and H-loss. We found 77% of species assessments studied here did not report methods used to estimate the number of mature adults, and that these assessments rarely report other important determinants of Ne (e.g., sex ratio, variance in family size). We therefore applied common rules of thumb to estimate Ne, and found that Ne was likely < 50 for at least 25% of the 170 RL Endangered species studied here. We also estimated mean expected H-loss for these species over the next 100 years, and found it to be 9–29%. These estimates of high H-loss and low Ne suggest that some species listed as Endangered likely warrant listing as Critically Endangered if genetic considerations were included. We recommend that RL and other assessment frameworks (i) report methods used for estimating the number of mature adults, (ii) include standardized information on species traits that influence Ne to facilitate Ne estimation, and (iii) consider using concepts like Ne and heterozygosity-loss in risk assessments.

On biological evolution and environmental solutions

Drawing insights from multiple disciplines is essential for finding integrative solutions that are required to tackle complex environmental problems. Human activities are causing unprecedented influence on global ecosystems, culminating in the loss of species and fundamental changes in the selective environments of organisms across the tree of life. Our collective understanding about biological evolution can help identify and mitigate many of the environmental problems in the Anthropocene. To this end, we propose a stronger integration of environmental sciences with evolutionary biology.

Substrate rugosity and temperature matters: patterns of benthic diversity at tropical intertidal reefs in the SW Atlantic

Modeling and forecasting ocean ecosystems in a changing world will require advances in observational efforts to monitor marine biodiversity. One of the observational challenges in coastal reef ecosystems is to quantify benthic and climate interactions which are key to community dynamics across habitats. Habitat complexity (i.e., substrate rugosity) on intertidal reefs can be an important variable explaining benthic diversity and taxa composition, but the association between substrate and seasonal variability is poorly understood on lateritic reefs in the South Atlantic. We asked if benthic assemblages on intertidal reefs with distinct substrate rugosity would follow similar seasonal patterns of succession following meteo-oceanographic variability in a tropical coastal area of Brazil. We combined an innovative 3D imaging for measuring substrate rugosity with satellite monitoring to monitor spatio-temporal patterns of benthic assemblages. The dataset included monthly in situ surveys of substrate cover and taxon diversity and richness, temporal variability in meteo-oceanographic conditions, and reef structural complexity from four sites on the Eastern Marine Ecoregion of Brazil. Additionally, correlation coefficients between temperature and both benthic diversity and community composition from one year of monitoring were used to project biodiversity trends under future warming scenarios. Our results revealed that benthic diversity and composition on intertidal reefs are strongly regulated by surface rugosity and sea surface temperatures, which control the dominance of macroalgae or corals. Intertidal reef biodiversity was positively correlated with reef rugosity which supports previous assertions of higher regional intertidal diversity on lateritic reefs that offer increased substrate complexity. Predicted warming temperatures in the Eastern Marine Ecoregion of Brazil will likely lead to a dominance of macroalgae taxa over the lateritic reefs and lower overall benthic diversity. Our findings indicate that rugosity is not only a useful tool for biodiversity mapping in reef intertidal ecosystems but also that spatial differences in rugosity would lead to very distinct biogeographic and temporal patterns. This study offers a unique baseline of benthic biodiversity on coastal marine habitats that is complementary to worldwide efforts to improve monitoring and management of coastal reefs.

Evolution in the Anthropocene: Informing Governance and Policy

The Anthropocene biosphere constitutes an unprecedented phase in the evolution of life on Earth with one species, humans, exerting extensive control. The increasing intensity of anthropogenic forces in the twenty-first century has widespread implications for attempts to govern both human-dominated ecosystems and the last remaining wild ecosystems. Here, we review how evolutionary biology can inform governance and policies in the Anthropocene, focusing on five governance challenges that span biodiversity, environmental management, food and other biomass production, and human health. The five challenges are: ( a) evolutionary feedbacks, ( b) maintaining resilience, ( c) alleviating constraints, ( d) coevolutionary disruption, and ( e) biotechnology. Strategies for governing these dynamics will themselves have to be coevolutionary, as eco-evolutionary and social dynamics change in response to each other.

Conservation practitioners' understanding of how to manage evolutionary processes

Both academics and practitioners consider a lack of knowledge about evolutionary theory to be a general barrier to effectively managing genetic diversity. However, it is challenging to judge practitioners' level of understanding and how this influences their management decisions. Knowledge built through experience may be difficult for practitioners to articulate, but could nonetheless result in appropriate management strategies. To date, researchers have assessed only the explicit (formal) knowledge practitioners have of evolutionary concepts. To explore practitioners' understanding of evolutionary concepts, it is necessary to consider how they might apply explicit and implicit knowledge to their management decisions. Using an online survey, we asked Australian practitioners to respond to 2 common management scenarios in which there is strong evidence that managing genetic diversity can improve outcomes: managing small, isolated populations and sourcing seeds for restoration projects. In describing their approach to these scenarios, practitioners demonstrated a stronger understanding of the effective management of genetic diversity than the definitions of the relevant concepts. However, their management of genetic diversity within small populations was closer to best practice than for restoration projects. Moreover, the risks practitioners described in implementing best practice management were more likely to affect their approach to restoration than translocation projects. These findings provide evidence that strategies to build the capacity of practitioners to manage genetic diversity should focus on realistic management scenarios. Given that practitioners recognize the importance of adapting their practices and the strong evidence for the benefits of actively managing genetic diversity, there is hope that better engagement by evolutionary biologists with practitioners could facilitate significant shifts toward evolutionarily enlightened management.

Identification of Female Sex Pheromone for Monitoring the Barred Tooth Striped Moth, Trichopteryx polycommata, a Priority Conservation Species

Pheromone-baited traps can be excellent tools for sensitive detection of insects of conservation concern. Here, identification of the sex pheromone of Trichopteryx polycommata (Denis & Schiffermüller, 1775), an under-recorded UK priority species, is reported. In analyses of extracts of the pheromone glands of female T. polycommata by gas chromatography coupled to electroantennographic recording from the antenna of a male moth, a single active component was detected. This was identified as (Z,Z)-6,9-nonadecadiene (Z,Z6,9-19:H) by comparison of its mass spectrum and retention times with those of the synthetic standard. In a pilot field trial in Kent, UK, T. polycommata males were caught in pheromone traps baited with lures loaded with 1 mg and 2 mg (Z,Z)-6,9-19:H. Optimum lure loading was identified in a further five trials in Kent, Sussex and Lancashire where lures of 0, 0.001, 0.01, 0.1, 1, 2, 5 and 10 mg loadings were tested. Traps baited with 1 to 10 mg of ZZ6,9-19:H caught significantly more T. polycommata than traps baited with 0 mg and 0.001 mg. In a pilot survey of T. polycommata using pheromone lures around Morecambe Bay, UK, T. polycommata males were captured at 122 new sites within the three counties where trials took place, demonstrating the potential of pheromone monitoring to increase knowledge of abundance, distribution and ecology of this elusive species.

A roadmap for urban evolutionary ecology

Urban ecosystems are rapidly expanding throughout the world, but how urban growth affects the evolutionary ecology of species living in urban areas remains largely unknown. Urban ecology has advanced our understanding of how the development of cities and towns change environmental conditions and alter ecological processes and patterns. However, despite decades of research in urban ecology, the extent to which urbanization influences evolutionary and eco-evolutionary change has received little attention. The nascent field of urban evolutionary ecology seeks to understand how urbanization affects the evolution of populations, and how those evolutionary changes in turn influence the ecological dynamics of populations, communities, and ecosystems. Following a brief history of this emerging field, this Perspective article provides a research agenda and roadmap for future research aimed at advancing our understanding of the interplay between ecology and evolution of urban-dwelling organisms. We identify six key questions that, if addressed, would significantly increase our understanding of how urbanization influences evolutionary processes. These questions consider how urbanization affects nonadaptive evolution, natural selection, and convergent evolution, in addition to the role of urban environmental heterogeneity on species evolution, and the roles of phenotypic plasticity versus adaptation on species' abundance in cities. Our final question examines the impact of urbanization on evolutionary diversification. For each of these six questions, we suggest avenues for future research that will help advance the field of urban evolutionary ecology. Lastly, we highlight the importance of integrating urban evolutionary ecology into urban planning, conservation practice, pest management, and public engagement.

Understanding managers' and scientists' perspectives on opportunities to achieve more evolutionarily enlightened management in conservation

Despite wide acceptance that conservation could benefit from greater attention to principles and processes from evolutionary biology, little attention has been given to quantifying the degree to which relevant evolutionary concepts are being integrated into management practices. There has also been increasing discussion of the potential reasons for a lack of evolutionarily enlightened management, but no attempts to understand the challenges from the perspective of those making management decisions. In this study, we asked conservation managers and scientists for their views on the importance of a range of key evolutionary concepts, the degree to which these concepts are being integrated into management, and what would need to change to support better integration into management practices. We found that while managers recognize the importance of a wide range of evolutionary concepts for conservation outcomes, they acknowledge these concepts are rarely incorporated into management. Managers and scientists were in strong agreement about the range of barriers that need to be overcome, with a lack of knowledge reported as the most important barrier to better integration of evolutionary biology into conservation decision-making. Although managers tended to be more focused on the need for more training in evolutionary biology, scientists reported greater engagement between managers and evolutionary biologists as most important to achieve the necessary change. Nevertheless, the challenges appear to be multifaceted, and several are outside the control of managers, suggesting solutions will need to be multidimensional.

Aligning science and policy to achieve evolutionarily enlightened conservation

There is increasing recognition among conservation scientists that long-term conservation outcomes could be improved through better integration of evolutionary theory into management practices. Despite concerns that the importance of key concepts emerging from evolutionary theory (i.e., evolutionary principles and processes) are not being recognized by managers, there has been little effort to determine the level of integration of evolutionary theory into conservation policy and practice. We assessed conservation policy at 3 scales (international, national, and provincial) on 3 continents to quantify the degree to which key evolutionary concepts, such as genetic diversity and gene flow, are being incorporated into conservation practice. We also evaluated the availability of clear guidance within the applied evolutionary biology literature as to how managers can change their management practices to achieve better conservation outcomes. Despite widespread recognition of the importance of maintaining genetic diversity, conservation policies provide little guidance about how this can be achieved in practice and other relevant evolutionary concepts, such as inbreeding depression, are mentioned rarely. In some cases the poor integration of evolutionary concepts into management reflects a lack of decision-support tools in the literature. Where these tools are available, such as risk-assessment frameworks, they are not being adopted by conservation policy makers, suggesting that the availability of a strong evidence base is not the only barrier to evolutionarily enlightened management. We believe there is a clear need for more engagement by evolutionary biologists with policy makers to develop practical guidelines that will help managers make changes to conservation practice. There is also an urgent need for more research to better understand the barriers to and opportunities for incorporating evolutionary theory into conservation practice.

Understanding and monitoring the consequences of human impacts on intraspecific variation

Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and nongovernmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variations within and among populations can have dramatic effects on ecological and evolutionary processes, including responses to environmental change, the maintenance of species diversity, and ecological stability and resilience. At the same time, environmental changes associated with many human activities, such as land use and climate change, have dramatic and often negative impacts on intraspecific variation. We argue for the need for local, regional, and global programs to monitor intraspecific genetic variation. We suggest that such monitoring should include two main strategies: (i) intensive monitoring of multiple types of genetic variation in selected species and (ii) broad-brush modeling for representative species for predicting changes in variation as a function of changes in population size and range extent. Overall, we call for collaborative efforts to initiate the urgently needed monitoring of intraspecific variation.

Comparison of conservation metrics in a case study of lemurs

Conservation planning is important to protect species from going extinct now that natural habitats are decreasing owing to human activity and climate change. However, there is considerable controversy in choosing appropriate metrics to weigh the value of species and geographic regions. For example, the added value of phylogenetic conservation-selection criteria remains disputed because high correlations between them and the nonphylogenetic criteria of species richness have been reported. We evaluated the commonly used conservation metrics species richness, endemism, phylogenetic diversity (PD), and phylogenetic endemism (PE) in a case study on lemurs of Madagascar. This enabled us to identify the conservation target of each metric and consider how they may be used in future conservation planning. We also devised a novel metric that uses a phylogeny scaled according to the rate of phenotypic evolution as a proxy for a species' ability to adapt to change. High rates of evolution may indicate generalization or specialization. Both specialization and low rates of evolution may result in an inability to adapt to changing environments. We examined conservation priorities by using the inverse of the rate of body mass evolution to account for species with low rates of evolution. In line with previous work, we found high correlations among species richness and PD (r = 0.96), and endemism and PE (r = 0.82) in Malagasy lemurs. Phylogenetic endemism in combination with rates of evolution and their inverse prioritized grid cells containing highly endemic and specialized lemurs at risk of extinction, such as Avahi occidentalis and Lepilemur edwardsi, 2 endangered lemurs with high rates of phenotypic evolution and low-quality diets, and Hapalemur aureus, a critically endangered species with a low rate of body mass evolution and a diet consisting of very high doses of cyanide.

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

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

Why evolution matters for species conservation: perspectives from three case studies of plant metapopulations

We advocate the advantage of an evolutionary approach to conservation biology that considers evolutionary history at various levels of biological organization. We review work on three separate plant taxa, spanning from one to multiple decades, illustrating extremes in metapopulation functioning. We show how the rare endemics Centaurea corymbosa (Clape Massif, France) and Brassica insularis in Corsica (France) may be caught in an evolutionary trap: disruption of metapopulation functioning due to lack of colonization of new sites may have counterselected traits such as dispersal ability or self‐compatibility, making these species particularly vulnerable to any disturbance. The third case study concerns the evolution of life history strategies in the highly diverse genus Leucadendron of the South African fynbos. There, fire disturbance and the recolonization phase after fires are so integral to the functioning of populations that recruitment of new individuals is conditioned by fire. We show how past adaptation to different fire regimes and climatic constraints make species with different life history syndromes more or less vulnerable to global changes. These different case studies suggest that management strategies should promote evolutionary potential and evolutionary processes to better protect extant biodiversity and biodiversification.

Predicting loss of evolutionary history: Where are we?

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.

Biodiversity assessment among two Nebraska prairies: a comparison between traditional and phylogenetic diversity indices

Background

Conservation of the evolutionary diversity among organisms should be included in the selection of priority regions for preservation of Earth’s biodiversity. Traditionally, biodiversity has been determined from an assessment of species richness (S), abundance, evenness, rarity, etc. of organisms but not from variation in species’ evolutionary histories. Phylogenetic diversity (PD) measures evolutionary differences between taxa in a community and is gaining acceptance as a biodiversity assessment tool. However, with the increase in the number of ways to calculate PD, end-users and decision-makers are left wondering how metrics compare and what data are needed to calculate various metrics.

New information

In this study, we used massively parallel sequencing to generate over 65,000 DNA characters from three cellular compartments for over 60 species in the asterid clade of flowering plants. We estimated asterid phylogenies from character datasets of varying nucleotide quantities, and then assessed the effect of varying character datasets on resulting PD metric values. We also compared multiple PD metrics with traditional diversity indices (including S) among two endangered grassland prairies in Nebraska (U.S.A.). Our results revealed that PD metrics varied based on the quantity of genes used to infer the phylogenies; therefore, when comparing PD metrics between sites, it is vital to use comparable datasets. Additionally, various PD metrics and traditional diversity indices characterize biodiversity differently and should be chosen depending on the research question. Our study provides empirical results that reveal the value of measuring PD when considering sites for conservation, and it highlights the usefulness of using PD metrics in combination with other diversity indices when studying community assembly and ecosystem functioning. Ours is just one example of the types of investigations that need to be conducted across the tree of life and across varying ecosystems in order to build a database of phylogenetic diversity assessments that lead to a pool of results upon which a guide through the plethora of PD metrics may be prepared for use by ecologists and conservation planners.

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.

Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication

Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.

Space, time and complexity in plant dispersal ecology

Dispersal of pollen and seeds are essential functions of plant species, with far-reaching demographic, ecological and evolutionary consequences. Interest in plant dispersal has increased with concerns about the persistence of populations and species under global change. We argue here that advances in plant dispersal ecology research will be determined by our ability to surmount challenges of spatiotemporal scales and heterogeneities and ecosystem complexity. Based on this framework, we propose a selected set of research questions, for which we suggest some specific objectives and methodological approaches. Reviewed topics include multiple vector contributions to plant dispersal, landscape-dependent dispersal patterns, long-distance dispersal events, spatiotemporal variation in dispersal, and the consequences of dispersal for plant communities, populations under climate change, and anthropogenic landscapes.

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.

Biodiversity and evolutionary history: useful extensions of the PD phylogenetic diversity assessment framework

Evolutionary biology is a core discipline in biodiversity science. Evolutionary history or phylogeny provides one natural measure of biodiversity through the popular phylogenetic diversity (PD) measure. The evolutionary model underlying PD means that it can be interpreted as quantifying the relative feature diversity of sets of species. Quantifying feature diversity measures possible future uses and benefits or option values. Interpretation of PD as counting-up features is the basis for an emerging broad family of PD calculations, of use to both biodiversity researchers and decision makers. Many of these calculations extend conventional species-level indices to the features level. Useful PD calculations include PD complementarity and endemism, Hill and Valley numbers incorporating abundance, and PD dissimilarities. A flexible analysis framework is provided by expected PD calculations, applied to either probabilities of extinction or presence-absence. Practical extensions include phylogenetic risk analysis and measures of distinctiveness and endemism. These support the integration of phylogenetic diversity into biodiversity conservation and monitoring programs.

Phylogenetic diversity and nature conservation: where are we?

To date, there is little evidence that phylogenetic diversity has contributed to nature conservation. Here, we discuss the scientific justification of using phylogenetic diversity in conservation and the reasons for its neglect. We show that, apart from valuing the rarity and richness aspect, commonly quoted justifications based on the usage of phylogenetic diversity as a proxy for functional diversity or evolutionary potential are still based on uncertainties. We discuss how a missing guideline through the variety of phylogenetic diversity metrics and their relevance for conservation might be responsible for the hesitation to include phylogenetic diversity in conservation practice. We outline research routes that can help to ease uncertainties and bridge gaps between research and conservation with respect to phylogenetic diversity.