Phylogeny, ecology, and the coupling of comparative and experimental approaches

New horizons for comparative studies and meta-analyses

Comparative analyses and meta-analyses are key tools to elucidate broad biological principles, yet the two approaches often appear different in purpose. We propose an integrated approach that can generate deeper insights into ecoevolutionary processes. Marrying comparative and meta-analytic approaches will allow for (i) a more accurate investigation of drivers of biological variation, (ii) a greater ability to account for sources of non-independence in experimental data, (iii) more effective control of publication bias, and (iv) improved transparency and reproducibility. Stronger integration of meta-analytic and comparative studies can also broaden the scope from species-centric investigations to community-level responses and function-valued traits (e.g., reaction norms). We illuminate commonalities, differences, and the transformative potential of combining these methodologies for advancing ecology and evolutionary biology.

The evolution of glandularity as a defense against herbivores in the tarweed clade

PREMISE

Glandular trichomes are implicated in direct and indirect defense of plants. However, the degree to which glandular and non-glandular trichomes have evolved as a consequence of herbivory remains unclear, because their heritability, their association with herbivore resistance, their trade-offs with one another, and their association with other functions are rarely quantified.

METHODS

We conducted a phylogenetic comparison of trichomes and herbivore resistance against the generalist caterpillar, Heliothis virescens, among tarweed species (Asteraceae: Madiinae) and a genetic correlation study comparing those same traits among maternal half-sibs of three tarweed species.

RESULTS

Within a tarweed species, we found no evidence that herbivore growth rate decreased on tarweed individuals or maternal sib groups with more glandularity or denser trichomes. However, tarweed species with more glandularity and fewer non-glandular trichomes resulted in slower-growing herbivores. Likewise, a trade-off between glandular and non-glandular trichomes was apparent among tarweed species, but not among individuals or sib groups within a species.

CONCLUSIONS

Our results suggest that this key herbivore does not select for trichomes as a direct defense in tarweed species. However, trichomes differed substantially among species and likely affect herbivore pressure on those species. Our results demonstrate that trade-offs among plant traits, as well as inference on the function of those traits, can depend on scale.

Hummingbird community structure and nectar resources modulate the response of interspecific competition to forest conversion

On-going land-use change has profound impacts on biodiversity by filtering species that cannot survive in disturbed landscapes and potentially altering biotic interactions. In particular, how land-use change reshapes biotic interactions remains an open question. Here, we used selectivity experiments with nectar feeders in natural and converted forests to test the direct and indirect effects of land-use change on resource competition in Andean hummingbirds along an elevational gradient. Selectivity was defined as the time hummingbirds spent at high resource feeders when feeders with both low and high resource values were offered in the presence of other hummingbird species. Selectivity approximates the outcome of interspecific competition (i.e., the resource intake across competing species); in the absence of competition, birds should exhibit higher selectivity. We evaluated the indirect effect of forest conversion on selectivity, as mediated by morphological dissimilarity and flower resource abundance, using structural equation models. We found that forest conversion influenced selectivity at low and mid-elevations, but the influence of morphological dissimilarity and resource availability on selectivity varied between these elevations. At mid-elevation, selectivity was more influenced by the presence of morphologically similar competitors than by resource abundance while at low-elevation resource abundance was a more important predictor of selectivity. Our results suggest that selectivity is influenced by forest conversion, but that the drivers of these changes vary across elevation, highlighting the importance of considering context-dependent variation in the composition of resources and competitors when studying competition.

Cross-disciplinary information for understanding macroevolution

Many different macroevolutionary models can produce the same observations. Despite efforts in building more complex and realistic models, it may still be difficult to distinguish the processes that have generated the biodiversity we observe. In this opinion we argue that we can make new progress by reaching out across disciplines, relying on independent data and theory to constrain macroevolutionary inference. Using mainly paleontological insights and data, we illustrate how we can eliminate less plausible or implausible models, and/or parts of parameter space, while applying comparative phylogenetic approaches. We emphasize that such cross-disciplinary insights and data can be drawn between many other disciplines relevant to macroevolution. We urge cross-disciplinary training, and collaboration using common-use databases as a platform for increasing our understanding.

A trait-based approach to determining principles of plant biogeography

Lineage-specific traits determine how plants interact with their surrounding environment. Unrelated species may evolve similar phenotypic characteristics to tolerate, persist in, and invade environments with certain characteristics, resulting in some traits becoming relatively more common in certain types of habitats. Analyses of these general patterns of geographical trait distribution have led to the proposal of general principles to explain how plants diversify in space over time. Trait-environment correlation analyses quantify to what extent unrelated lineages have similar evolutionary responses to a given type of habitat. In this synthesis, I give a short historical overview on trait-environment correlation analyses, from some key observations from classic naturalists to modern approaches using trait evolution models, large phylogenies, and massive data sets of traits and distributions. I discuss some limitations of modern approaches, including the need for more realistic models, the lack of data from tropical areas, and the necessary focus on trait scoring that goes beyond macromorphology. Overcoming these limitations will allow the field to explore new questions related to trait lability and niche evolution and to better identify generalities and exceptions in how plants diversify in space over time.

The herbarium of the future

The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.

Evolutionary interactions between thermal ecology and sexual selection

Thermal ecology and mate competition are both pervasive features of ecological adaptation. A surge of recent work has uncovered the diversity of ways in which temperature affects mating interactions and sexual selection. However, the potential for thermal biology and reproductive ecology to evolve together as organisms adapt to their thermal environment has been underappreciated. Here, we develop a series of hypotheses regarding (1) not only how thermal ecology affects mating system dynamics, but also how mating dynamics can generate selection on thermal traits; and (2) how the thermal consequences of mate competition favour the reciprocal co-adaptation of thermal biology and sexual traits. We discuss our hypotheses in the context of both pre-copulatory and post-copulatory processes. We also call for future work integrating experimental and phylogenetic comparative approaches to understand evolutionary feedbacks between thermal ecology and sexual selection. Overall, studying reciprocal feedbacks between thermal ecology and sexual selection may be necessary to understand how organisms have adapted to the environments of the past and could persist in the environments of the future.

A comparative study of plant volatiles induced by insect and gastropod herbivory

Insect and gastropod herbivores are major plant consumers and their importance in the evolution of plant defensive traits is broadly recognized. However, their respective effects on plant responses have rarely been compared. Here we focused on plant volatile emissions (VOCs) following herbivory and compared the effects of herbivory by caterpillars of the generalist insect Spodoptera littoralis and by generalist slugs of the genus Arion on the VOCs emissions of 14 cultivated plant species. Results revealed that plants consistently produced higher amounts of volatiles and responded more specifically to caterpillar than to slug herbivory. Specifically, plants released on average 6.0 times more VOCs (total), 8.9 times more green leaf volatiles, 4.2 times more terpenoids, 6.0 times more aromatic hydrocarbons, and 5.7 times more other VOCs in response to 1 cm² of insect damage than to 1 cm² of slug damage. Interestingly, four of the plant species tested produced a distinct blend of volatiles following insect damage but not slug damage. These findings may result from different chemical elicitors or from physical differences in herbivory by the two herbivores. This study is an important step toward a more inclusive view of plant responses to different types of herbivores.

Male-like ornamentation in female hummingbirds results from social harassment rather than sexual selection

Ornamentation is typically observed in sexually mature adults, is often dimorphic in expression, and is most apparent during breeding, supporting a role for sexual selection in its evolution.^1-4 Yet, increasing evidence suggests that nonsexual social selection may also have a role in the evolution of ornamentation, especially in females.^5-9 Distinguishing between these alternatives remains challenging because sexual and nonsexual factors may both play important and overlapping roles in trait evolution.^7,10 Here, we show that female ornamentation in a dichromatic hummingbird, the white-necked jacobin (Florisuga mellivora), cannot be explained by sexual selection. Although all males are ornamented, nearly 30% of females have male-like plumage. Remarkably, all juveniles of both sexes express ornamented plumage similar to adult males (androchromatism), but 80% of females acquire non-ornamented plumage (heterochromatism) as they age. This unique ontogeny excludes competition for mates as an explanation for female ornamentation because non-reproductive juveniles are more likely to be ornamented than adults. Instead, avoidance of social harassment appears to underlie this female-limited polymorphism, as heterochrome taxidermy mounts received more aggressive and sexual attention than androchrome mounts from this and other hummingbird species. Monitoring electronically tagged birds at data-logging feeders showed that androchrome females accessed feeders more than heterochrome females, presumably because of reduced harassment. Our findings demonstrate that ornamentation can arise purely through nonsexual social selection, and this hypothesis must be considered in the evolution of not only female-limited polymorphism but also the spectacular ornamentation often assumed to result from sexual selection.

Lack of Phylogenetic Differences in Ectomycorrhizal Fungi among Distinct Mediterranean Pine Forest Habitats

Understanding whether the occurrences of ectomycorrhizal species in a given tree host are phylogenetically determined can help in assessing different conservational needs for each fungal species. In this study, we characterized ectomycorrhizal phylogenetic composition and phylogenetic structure in 42 plots with five different Mediterranean pine forests: i.e., pure forests dominated by P. nigra, P. halepensis, and P. sylvestris, and mixed forests of P. nigra-P. halepensis and P. nigra-P. sylvestris, and tested whether the phylogenetic structure of ectomycorrhizal communities differs among these. We found that ectomycorrhizal communities were not different among pine tree hosts neither in phylogenetic composition nor in structure and phylogenetic diversity. Moreover, we detected a weak abiotic filtering effect (4%), with pH being the only significant variable influencing the phylogenetic ectomycorrhizal community, while the phylogenetic structure was slightly influenced by the shared effect of stand structure, soil, and geographic distance. However, the phylogenetic community similarity increased at lower pH values, supporting that fewer, closely related species were found at lower pH values. Also, no phylogenetic signal was detected among exploration types, although short and contact were the most abundant types in these forest ecosystems. Our results demonstrate that pH but not tree host, acts as a strong abiotic filter on ectomycorrhizal phylogenetic communities in Mediterranean pine forests at a local scale. Finally, our study shed light on dominant ectomycorrhizal foraging strategies in drought-prone ecosystems such as Mediterranean forests.

Evolution of shade tolerance is associated with attenuation of shade avoidance and reduced phenotypic plasticity in North American milkweeds

PREMISE

Mismatches between light conditions and light-capture strategy can reduce plant performance and prevent colonization of novel habitats. Although light-capture strategies tend to be highly conserved among closely related species, evolutionary transitions from shaded to unshaded habitats (and vice versa) occur in numerous plant lineages.

METHODS

We combined phylogenetic approaches with field and greenhouse experiments to investigate evolutionary constraints on light-capture strategy in North American milkweeds (genus Asclepias) and to determine whether colonization of shaded habitats in this heliophilic clade is associated with reduced plasticity and attenuation of the shade avoidance response.

RESULTS

Colonization of shaded habitats has occurred at least 10 times in this genus, including at least once in each major North American clade. Evolutionary transitions between habitats exhibit strong directional bias, with shifts from full-sun to shaded habitats occurring at least three times as often as the opposite transition. In field and greenhouse experiments, sun species responded to shade by increasing internode length, height, and specific leaf area, consistent with the shade avoidance response; paired shade species exhibited reduced plasticity overall, and only one trait (specific leaf area) responded to experimental shade.

CONCLUSIONS

Our results suggest that milkweeds colonized shaded environments multiple times using a light-capture strategy distinct from the ancestral (putatively shade avoidant) strategy, including a general attenuation of plasticity in response to variable light conditions. This pattern bolsters the notion that shade avoidance and tolerance represent divergent evolutionary strategies for maximizing performance under qualitatively different types of shade.

Macroevolutionary foundations of a recently evolved innate immune defense

Antagonistic interactions between hosts and parasites may drive the evolution of novel host defenses, or new parasite strategies. Host immunity is therefore one of the fastest evolving traits. But where do the novel immune traits come from? Here, we test for phylogenetic conservation in a rapidly evolving immune trait—peritoneal fibrosis. Peritoneal fibrosis is a costly defense against a specialist tapeworm, Schistocephalus solidus (Cestoda), expressed in some freshwater populations of threespine stickleback fish (Gasterosteus aculeatus, Perciformes). We asked whether stickleback fibrosis is a derived species‐specific trait or an ancestral immune response that was widely distributed across ray‐finned fish (Actinopterygii) only to be employed by threespine stickleback against the specialist parasite. We combined literature review on peritoneal fibrosis with a comparative experiment using either parasite‐specific, or nonspecific, immune challenge in deliberately selected species across fish tree of life. We show that ray‐finned fish are broadly, but not universally, able to induce peritoneal fibrosis when challenged with a generic stimulus (Alum adjuvant). The experimental species were, however, largely indifferent to the tapeworm antigen homogenate. Peritoneal fibrosis, thus, appears to be a common and deeply conserved fish immune response that was co‐opted by stickleback to adapt to a new selective challenge.

Phylogenetic history of vascular plant metabolism revealed using a macroevolutionary common garden

While the fundamental biophysics of C3 photosynthesis is highly conserved across plants, substantial leaf structural and enzymatic variation translates into variability in rates of carbon assimilation. Although this variation is well documented, it remains poorly understood how photosynthetic rates evolve, and whether macroevolutionary changes are related to the evolution of leaf morphology and biochemistry. A substantial challenge in large-scale comparative studies is disentangling evolutionary adaptation from environmental acclimation. We overcome this by using a 'macroevolutionary common garden' approach in which we measured metabolic traits (Jmax and Vcmax) from 111 phylogenetically diverse species in a shared environment. We find substantial phylogenetic signal in these traits at moderate phylogenetic timescales, but this signal dissipates quickly at deeper scales. Morphological traits exhibit phylogenetic signal over much deeper timescales, suggesting that these are less evolutionarily constrained than metabolic traits. Furthermore, while morphological and biochemical traits (LMA, Narea and Carea) are weakly predictive of Jmax and Vcmax, evolutionary changes in these traits are mostly decoupled from changes in metabolic traits. This lack of tight evolutionary coupling implies that it may be incorrect to use changes in these functional traits in response to global change to infer that photosynthetic strategy is also evolving.

Evolutionary history and ecology shape the diversity and abundance of phytochemical arsenals across monkeyflowers

We examine the extent to which phylogenetic effects and ecology are associated with macroevolutionary patterns of phytochemical defence production across the Mimulus phylogeny. We grew plants from 21 species representing the five major sections of the Mimulus phylogeny in a common garden to assess how the arsenals (NMDS groupings) and abundances (concentrations) of a phytochemical defence, phenylpropanoid glycosides (PPGs), vary across the phylogeny. Very few PPGs are widespread across the genus, but many are common to multiple sections of the genus. Phytochemical arsenals cluster among sections in an NMDS and are not associated with total concentration of PPGs. There is a strong phylogenetic signal for phytochemical arsenal composition across the Mimulus genus, whereas ecological variables such as growing season length, latitude, and elevation do not significantly influence arsenal. In contrast, there is little phylogenetic signal for total PPG concentration, and this trait is significantly influenced by several ecological factors. Phytochemical arsenals and abundances are influenced by plant life history form. Both phylogenetic effects and ecology are related to phytochemical patterns across species, albeit in different ways. The independence of phytochemical defence concentrations from arsenal compositions indicates that these aspects of defence may continue to evolve independently of one another.

Data on Herbivore Performance and Plant Herbivore Damage Identify the Same Plant Traits as the Key Drivers of Plant-Herbivore Interaction

Data on plant herbivore damage as well as on herbivore performance have been previously used to identify key plant traits driving plant-herbivore interactions. The extent to which the two approaches lead to similar conclusions remains to be explored. We determined the effect of a free-living leaf-chewing generalist caterpillar, Spodoptera littoralis (Lepidoptera: Noctuidae), on leaf damage of 24 closely related plant species from the Carduoideae subfamily and the effect of these plant species on caterpillar growth. We used a wide range of physical defense leaf traits and leaf nutrient contents as the plant traits. Herbivore performance and leaf damage were affected by similar plant traits. Traits related to higher caterpillar mortality (higher leaf dissection, number, length and toughness of spines and lower trichome density) also led to higher leaf damage. This fits with the fact that each caterpillar was feeding on a single plant and, thus, had to consume more biomass of the less suitable plants to obtain the same amount of nutrients. The key plant traits driving plant-herbivore interactions identified based on data on herbivore performance largely corresponded to the traits identified as important based on data on leaf damage. This suggests that both types of data may be used to identify the key plant traits determining plant-herbivore interactions. It is, however, important to carefully distinguish whether the data on leaf damage were obtained in the field or in a controlled feeding experiment, as the patterns expected in the two environments may go in opposite directions.

Ecological Interactions and Macroevolution: A New Field with Old Roots

Linking interspecific interactions (e.g., mutualism, competition, predation, parasitism) to macroevolution (evolutionary change on deep timescales) is a key goal in biology. The role of species interactions in shaping macroevolutionary trajectories has been studied for centuries and remains a cutting-edge topic of current research. However, despite its deep historical roots, classic and current approaches to this topic are highly diverse. Here, we combine historical and contemporary perspectives on the study of ecological interactions in macroevolution, synthesizing ideas across eras to build a zoomed-out picture of the big questions at the nexus of ecology and macroevolution. We discuss the trajectory of this important and challenging field, dividing research into work done before the 1970s, research between 1970 and 2005, and work done since 2005. We argue that in response to long-standing questions in paleobiology, evidence accumulated to date has demonstrated that biotic interactions (including mutualism) can influence lineage diversification and trait evolution over macroevolutionary timescales, and we outline major open questions for future research in the field.

Evolutionary trade-offs in the chemical defense of floral and fruit tissues across genus Cornus

PREMISE

Defense investment in plant reproductive structures is relatively understudied compared to the defense of vegetative organs. Here the evolution of chemical defenses in reproductive structures is examined in light of the optimal defense, apparency, and resource availability hypotheses within the genus Cornus using a phylogenetic comparative approach in relation to phenology and native habitat environmental data.

METHODS

Individuals representing 25 Cornus species were tracked for reproductive phenology over a full growing season at the Arnold Arboretum of Harvard University. Floral, fruit, and leaf tissue was sampled to quantify defensive chemistry as well as fruit nutritional traits relevant to bird dispersal. Native habitat environmental characteristics were estimated using locality data from digitized herbarium records coupled with global soil and climate data sets.

RESULTS

The evolution of later flowering was correlated with increased floral tannins, and the evolution of later fruiting was correlated with increased total phenolics. Leaves were found to contain the highest tannin activity, while inflorescences contained the highest total flavonoids. Multiple aspects of fruit defensive chemistry were correlated with fruit nutritional traits. Floral and fruit defensive chemistry were evolutionarily correlated with aspects of native habitat temperature, precipitation, and soil characteristics.

CONCLUSIONS

Results provide tentative support for the apparency hypothesis with respect to both flower and fruit phenology, while relative concentrations of secondary metabolites across organs provide mixed support for the optimal defense hypothesis. The evolution of reproductive defense with native habitat provides, at best, mixed support for the resource availability hypothesis.

The Role of Evolution in Shaping Ecological Networks

The structure of ecological networks reflects the evolutionary history of their biotic components, and their dynamics are strongly driven by ecoevolutionary processes. Here, we present an appraisal of recent relevant research, in which the pervasive role of evolution within ecological networks is manifest. Although evolutionary processes are most evident at macroevolutionary scales, they are also important drivers of local network structure and dynamics. We propose components of a blueprint for further research, emphasising process-based models, experimental evolution, and phenotypic variation, across a range of distinct spatial and temporal scales. Evolutionary dimensions are required to advance our understanding of foundational properties of community assembly and to enhance our capability of predicting how networks will respond to impending changes.

Effects of host phylogeny, habitat and spatial proximity on host specificity and diversity of pathogenic and mycorrhizal fungi in a subtropical forest

Soil plant-pathogenic (PF) and mycorrhizal fungi (MF) are both important in maintaining plant diversity, for example via host-specialized effects. However, empirical knowledge on the degree of host specificity and possible factors affecting the fungal assemblages is lacking. We identified PF and MF in fine roots of 519 individuals across 45 subtropical tree species in southern China in order to quantify the importance of host phylogeny (including via its effects on functional traits), habitat and space in determining fungal communities. We also compared host specificity in PF and MF at different host-phylogenetic scales. In both PF and MF, host phylogeny independently accounted for > 19% of the variation in fungal richness and composition, whereas environmental and spatial factors each explained no more than 4% of the variation. Over 77% of the variation explained by phylogeny was attributable to covariation in plant functional traits. Host specificity was phylogenetically scale-dependent, being stronger in PF than in MF at low host-phylogenetic scales (e.g. within genus) but similar at larger scales. Our study suggests that host-phylogenetic effects dominate the assembly of both PF and MF communities, resulting from phylogenetically clustered plant traits. The scale-dependent host specificity implies that PF were specialized at lower-level and MF at higher-level host taxa.

Sterile marginal flowers increase visitation and fruit set in the hobblebush (Viburnum lantanoides, Adoxaceae) at multiple spatial scales

BACKGROUND AND AIMS

Enlarged sterile flowers on the periphery of inflorescences increase the attractiveness of floral displays, and previous studies have generally demonstrated that these have positive effects on insect visitation and/or reproductive success. However, experiments have not specifically been designed to examine the benefits of sterile flowers under conditions that reflect the early stages in their evolution, i.e. when plants that produce sterile flowers are at low frequency.

METHODS

Over three years, three experiments were performed in natural populations of Viburnum lantanoides, which produces sterile marginal flowers (SMFs). The first experiment established that fruit production in V. lantanoides increases with the receipt of outcross pollen. The second tested the role of SMFs under extant conditions, comparing fruit production in two populations composed entirely of intact plants or entirely of plants with the SMFs removed. The third was designed to mimic the presumed context in which SMFs first evolved; here, SMFs were removed from all but a few plants in a population, and rates of insect visitation and fruit set were compared between plants with intact and denuded SMFs.

KEY RESULTS

In comparing whole populations, the presence of SMFs nearly doubled fruit set. Under simulated 'ancestral' conditions within a population, plants with intact SMFs received double the insect visits and produced significantly more fruits than denuded plants. There was no significant effect of the number of inflorescences or fertile flowers on insect visitation or fruit set, indicating that the presence of SMFs accounted for these differences.

CONCLUSIONS

The presence of SMFs significantly increased pollinator attraction and female reproductive success both in contemporary and simulated ancestral contexts, indicating that stabilizing selection is responsible for their maintenance, and directional selection likely drove their evolution when they first appeared. This study demonstrates a novel approach to incorporating historically relevant scenarios into experimental studies of floral evolution.

Towards a predictive model of species interaction beta diversity

Species interactions are fundamental to community dynamics and ecosystem processes. Despite significant progress in describing species interactions, we lack the ability to predict changes in interactions across space and time. We outline a Bayesian approach to separate the probability of species co-occurrence, interaction and detectability in influencing interaction betadiversity. We use a multi-year hummingbird-plant time series, divided into training and testing data, to show that including models of detectability and occurrence improves forecasts of mutualistic interactions. We then extend our model to explore interaction betadiversity across two distinct seasons. Despite differences in the observed interactions among seasons, there was no significant change in hummingbird occurrence or interaction frequency between hummingbirds and plants. These results highlight the challenge of inferring the causes of interaction betadiversity when interaction detectability is low. Finally, we highlight potential applications of our model for integrating observations of local interactions with biogeographic and evolutionary histories of co-occurring species. These advances will provide new insight into the mechanisms that drive variation in patterns of biodiversity.

Host and parasite morphology influence congruence between host and parasite phylogenies

Comparisons of host and parasite phylogenies often show varying degrees of phylogenetic congruence. However, few studies have rigorously explored the factors driving this variation. Multiple factors such as host or parasite morphology may govern the degree of phylogenetic congruence. An ideal analysis for understanding the factors correlated with congruence would focus on a diverse host-parasite system for increased variation and statistical power. In this study, we focused on the Brueelia-complex, a diverse and widespread group of feather lice that primarily parasitise songbirds. We generated a molecular phylogeny of the lice and compared this tree with a phylogeny of their avian hosts. We also tested for the contribution of each host-parasite association to the overall congruence. The two trees overall were significantly congruent, but the contribution of individual associations to this congruence varied. To understand this variation, we developed a novel approach to test whether host, parasite or biogeographic factors were statistically associated with patterns of congruence. Both host plumage dimorphism and parasite ecomorphology were associated with patterns of congruence, whereas host body size, other plumage traits and biogeography were not. Our results lay the framework for future studies to further elucidate how these factors influence the process of host-parasite coevolution.

Convergence, Consilience, and the Evolution of Temperate Deciduous Forests

The deciduous habit of northern temperate trees and shrubs provides one of the most obvious examples of convergent evolution, but how did it evolve? Hypotheses based on the fossil record posit that deciduousness evolved first in response to drought or darkness and preadapted certain lineages as cold climates spread. An alternative is that evergreens first established in freezing environments and later evolved the deciduous habit. We monitored phenological patterns of 20 species of Viburnum spanning tropical, lucidophyllous (subtropical montane and warm temperate), and cool temperate Asian forests. In lucidophyllous forests, all viburnums were evergreen plants that exhibited coordinated leaf flushes with the onset of the rainy season but varied greatly in the timing of leaf senescence. In contrast, deciduous species exhibited tight coordination of both flushing and senescence, and we found a perfect correlation between the deciduous habit and prolonged annual freezing. In contrast to previous stepwise hypotheses, a consilience of independent lines of evidence supports a lockstep model in which deciduousness evolved in situ, in parallel, and concurrent with a gradual cooling climate. A pervasive selective force combined with the elevated evolutionary accessibility of a particular response may explain the massive convergence of adaptive strategies that characterizes the world's biomes.

Toward a Predictive Framework for Convergent Evolution: Integrating Natural History, Genetic Mechanisms, and Consequences for the Diversity of Life

A charm of biology as a scientific discipline is the diversity of life. Although this diversity can make laws of biology challenging to discover, several repeated patterns and general principles govern evolutionary diversification. Convergent evolution, the independent evolution of similar phenotypes, has been at the heart of one approach to understand generality in the evolutionary process. Yet understanding when and why organismal traits and strategies repeatedly evolve has been a central challenge. These issues were the focus of the American Society of Naturalists Vice Presidential Symposium in 2016 and are the subject of this collection of articles. Although naturalists have long made inferences about convergent evolution and its importance, there has been confusion in the interpretation of the pattern of convergence. Does convergence primarily indicate adaptation or constraint? How often should convergence be expected? Are there general principles that would allow us to predict where and when and by what mechanisms convergent evolution should occur? What role does natural history play in advancing our understanding of general evolutionary principles? In this introductory article, I address these questions, review several generalizations about convergent evolution that have emerged over the past 15 years, and present a framework for advancing the study and interpretation of convergence. Perhaps the most important emerging conclusion is that the genetic mechanisms of convergent evolution are phylogenetically conserved; that is, more closely related species tend to share the same genetic basis of traits, even when independently evolved. Finally, I highlight how the articles in this special issue further develop concepts, methodologies, and case studies at the frontier of our understanding of the causes and consequences of convergent evolution.

Evolution in a Community Context: On Integrating Ecological Interactions and Macroevolution

Despite a conceptual understanding that evolution and species interactions are inextricably linked, it remains challenging to study ecological and evolutionary dynamics together over long temporal scales. In this review, we argue that, despite inherent challenges associated with reconstructing historical processes, the interplay of ecology and evolution is central to our understanding of macroevolution and community coexistence, and cannot be safely ignored in community and comparative phylogenetic studies. We highlight new research avenues that foster greater consideration of both ecological and evolutionary dynamics as processes that occur along branches of phylogenetic trees. By promoting new ways forward using this perspective, we hope to inspire further integration that creatively co-utilizes phylogenies and ecological data to study eco-evolutionary dynamics over time and space.

Phylogenetic congruence between subtropical trees and their associated fungi

Recent studies have detected phylogenetic signals in pathogen–host networks for both soil‐borne and leaf‐infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next‐generation high‐throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK, rbcL, atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host–fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant–fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant–fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.

From the Lab to the Farm: An Industrial Perspective of Plant Beneficial Microorganisms

Any successful strategy aimed at enhancing crop productivity with microbial products ultimately relies on the ability to scale at regional to global levels. Microorganisms that show promise in the lab may lack key characteristics for widespread adoption in sustainable and productive agricultural systems. This paper provides an overview of critical considerations involved with taking a strain from discovery to the farmer's field. In addition, we review some of the most effective microbial products on the market today, explore the reasons for their success and outline some of the major challenges involved in industrial production and commercialization of beneficial strains for widespread agricultural application. General processes associated with commercializing viable microbial products are discussed in two broad categories, biofertility inoculants and biocontrol products. Specifically, we address what farmers desire in potential microbial products, how mode of action informs decisions on product applications, the influence of variation in laboratory and field study data, challenges with scaling for mass production, and the importance of consistent efficacy, product stability and quality. In order to make a significant impact on global sustainable agriculture, the implementation of plant beneficial microorganisms will require a more seamless transition between laboratory and farm application. Early attention to the challenges presented here will improve the likelihood of developing effective microbial products to improve crop yields, decrease disease severity, and help to feed an increasingly hungry planet.

Nematode endoparasites do not codiversify with their stick insect hosts

Host-parasite coevolution stems from reciprocal selection on host resistance and parasite infectivity, and can generate some of the strongest selective pressures known in nature. It is widely seen as a major driver of diversification, the most extreme case being parallel speciation in hosts and their associated parasites. Here, we report on endoparasitic nematodes, most likely members of the mermithid family, infecting different Timema stick insect species throughout California. The nematodes develop in the hemolymph of their insect host and kill it upon emergence, completely impeding host reproduction. Given the direct exposure of the endoparasites to the host's immune system in the hemolymph, and the consequences of infection on host fitness, we predicted that divergence among hosts may drive parallel divergence in the endoparasites. Our phylogenetic analyses suggested the presence of two differentiated endoparasite lineages. However, independently of whether the two lineages were considered separately or jointly, we found a complete lack of codivergence between the endoparasitic nematodes and their hosts in spite of extensive genetic variation among hosts and among parasites. Instead, there was strong isolation by distance among the endoparasitic nematodes, indicating that geography plays a more important role than host-related adaptations in driving parasite diversification in this system. The accumulating evidence for lack of codiversification between parasites and their hosts at macroevolutionary scales contrasts with the overwhelming evidence for coevolution within populations, and calls for studies linking micro- versus macroevolutionary dynamics in host-parasite interactions.

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees

Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host-parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a "compass" when "walking" through jungles of tangled phylogenetic trees.

Patterns of Specificity of the Pathogen Escovopsis across the Fungus-Growing Ant Symbiosis

Parasites evolve within complex abiotic and biotic environments. Because of this, it is often challenging to ascertain how evolutionary and ecological processes together affect parasite specialization. Here, we use the fungus-growing ant system, which consists of ancient, likely coevolved, complex communities, to explore the ecological and evolutionary forces shaping host-parasite specificity. We use a comparative phylogenetic framework to determine whether patterns of specificity between the fungal parasite Escovopsis and its host fungi at fine phylogenetic scales reflect patterns of specificity at broader phylogenetic levels. In other words, we ask whether parasite specificity across broad host phylogenetic relationships is maintained by specificity toward more closely related hosts. We couple this exploration with manipulations of the community context within which host-parasite interactions are taking place to evaluate how community complexity alters parasite specificity. Regardless of host community complexity, parasites displayed a consistent pattern of specialization on native hosts, that is, those that they are found attacking in nature, with the potential for occasional switching to hosts distantly related to their native hosts. These results suggest that, even within a complex community context, pairwise host and parasite adaptation and coadaptation can be the primary drivers of the evolution and maintenance of parasite specificity.

Integrating Studies on Plant-Pollinator and Plant-Herbivore Interactions

Research on herbivore-induced plant defence and research on pollination ecology have had a long history of separation. Plant reproduction of most angiosperm species is mediated by pollinators, and the effects of herbivore-induced plant defences on pollinator behaviour have been largely neglected. Moreover, there is expected to be a trade-off between plant reproductive strategies and defence mechanisms. To investigate this trade-off, it is essential to study herbivore-induced plant resistance and allocation of resources by plants, within the same system, and to test if indirect plant resistance can conflict with pollinator attraction. Here, I review the key literature highlighting connection between plant defence and reproduction, and propose to exploit natural variation among plant species to assess the ecological costs of plant responses to herbivores and pollinators.

Strong phylogenetic signals and phylogenetic niche conservatism in ecophysiological traits across divergent lineages of Magnoliaceae

The early diverged Magnoliaceae shows a historical temperate-tropical distribution among lineages indicating divergent evolution, yet which ecophysiological traits are phylogenetically conserved, and whether these traits are involved in correlated evolution remain unclear. Integrating phylogeny and 20 ecophysiological traits of 27 species, from the four largest sections of Magnoliaceae, we tested the phylogenetic signals of these traits and the correlated evolution between trait pairs. Phylogenetic niche conservatism (PNC) in water-conducting and nutrient-use related traits was identified, and correlated evolution of several key functional traits was demonstrated. Among the three evergreen sections of tropical origin, Gwillimia had the lowest hydraulic-photosynthetic capacity and the highest drought tolerance compared with Manglietia and Michelia. Contrastingly, the temperate centred deciduous section, Yulania, showed high rates of hydraulic conductivity and photosynthesis at the cost of drought tolerance. This study elucidated the regulation of hydraulic and photosynthetic processes in the temperate-tropical adaptations for Magnoliaceae species, which led to strong phylogenetic signals and PNC in ecophysiological traits across divergent lineages of Magnoliaceae.

Confluence, synnovation, and depauperons in plant diversification

We review the empirical phylogenetic literature on plant diversification, highlighting challenges in separating the effects of speciation and extinction, in specifying diversification mechanisms, and in making convincing arguments. In recent discussions of context dependence, key opportunities and landscapes, and indirect effects and lag times, we see a distinct shift away from single-point/single-cause 'key innovation' hypotheses toward more nuanced explanations involving multiple interacting causal agents assembled step-wise through a tree. To help crystalize this emerging perspective we introduce the term 'synnovation' (a hybrid of 'synergy' and 'innovation') for an interacting combination of traits with a particular consequence ('key synnovation' in the case of increased diversification rate), and the term 'confluence' for the sequential coming together of a set of traits (innovations and synnovations), environmental changes, and geographic movements along the branches of a phylogenetic tree. We illustrate these concepts using the radiation of Bromeliaceae. We also highlight the generality of these ideas by considering how rate heterogeneity associated with a confluence relates to the existence of particularly species-poor lineages, or 'depauperons.' Many challenges are posed by this re-purposed research framework, including difficulties associated with partial taxon sampling, uncertainty in divergence time estimation, and extinction.

Estimating and mapping ecological processes influencing microbial community assembly

Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.