Eco‐evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations

Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here, we investigate whether coevolution and eco‐evolutionary feedback dynamics in a predator‐prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer‐algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco‐evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco‐evolutionary feedback dynamics on the overall evolutionary change has been underestimated.     

Trait adaptation promotes species coexistence in diverse predator and prey communities

Species can adjust their traits in response to selection which may strongly influence species coexistence. Nevertheless, current theory mainly assumes distinct and time‐invariant trait values. We examined the combined effects of the range and the speed of trait adaptation on species coexistence using an innovative multispecies predator–prey model. It allows for temporal trait changes of all predator and prey species and thus simultaneous coadaptation within and among trophic levels. We show that very small or slow trait adaptation did not facilitate coexistence because the stabilizing niche differences were not sufficient to offset the fitness differences. In contrast, sufficiently large and fast trait adaptation jointly promoted stable or neutrally stable species coexistence. Continuous trait adjustments in response to selection enabled a temporally variable convergence and divergence of species traits; that is, species became temporally more similar (neutral theory) or dissimilar (niche theory) depending on the selection pressure, resulting over time in a balance between niche differences stabilizing coexistence and fitness differences promoting competitive exclusion. Furthermore, coadaptation allowed prey and predator species to cluster into different functional groups. This equalized the fitness of similar species while maintaining sufficient niche differences among functionally different species delaying or preventing competitive exclusion. In contrast to previous studies, the emergent feedback between biomass and trait dynamics enabled supersaturated coexistence for a broad range of potential trait adaptation and parameters. We conclude that accounting for trait adaptation may explain stable and supersaturated species coexistence for a broad range of environmental conditions in natural systems when the absence of such adaptive changes would preclude it. Small trait changes, coincident with those that may occur within many natural populations, greatly enlarged the number of coexisting species.     

Eco‐evolutionary feedbacks between private and public goods: evidence from toxic algal blooms

The importance of ‘eco‐evolutionary feedbacks’ in natural systems is currently unclear. Here, we advance a general hypothesis for a particular class of eco‐evolutionary feedbacks with potentially large, long‐lasting impacts in complex ecosystems. These eco‐evolutionary feedbacks involve traits that mediate important interactions with abiotic and biotic features of the environment and a self‐driven reversal of selection as the ecological impact of the trait varies between private (small scale) and public (large scale). Toxic algal blooms may involve such eco‐evolutionary feedbacks due to the emergence of public goods. We review evidence that toxin production by microalgae may yield ‘privatised’ benefits for individual cells or colonies under pre‐ and early‐bloom conditions; however, the large‐scale, ecosystem‐level effects of toxicity associated with bloom states yield benefits that are necessarily ‘public’. Theory predicts that the replacement of private with public goods may reverse selection for toxicity in the absence of higher level selection. Indeed, blooms often harbor significant genetic and functional diversity: bloom populations may undergo genetic differentiation over a scale of days, and even genetically similar lineages may vary widely in toxic potential. Intriguingly, these observations find parallels in terrestrial communities, suggesting that toxic blooms may serve as useful models for eco‐evolutionary dynamics in nature. Eco‐evolutionary feedbacks involving the emergence of a public good may shed new light on the potential for interactions between ecology and evolution to influence the structure and function of entire ecosystems.     

Large‐scale molecular barcoding of prey DNA reveals predictors of intrapopulation feeding diversity in a marine predator

Predator–prey interactions are critical in understanding how communities function. However, we need to describe intraspecific variation in diet to accurately depict those interactions. Harbor seals (Phoca vitulina) are an abundant marine predator that prey on species of conservation concern. We estimated intrapopulation feeding diversity (variation in feeding habits between individuals of the same species) of harbor seals in the Salish Sea. Estimates of feeding diversity were examined relative to sex, month, and location using a novel approach that combined molecular techniques, repeated cross‐sectional sampling of scat, and a specialization metric (within‐individual consistency in diet measured by the Proportional Similarity Index ()). Based on 1,083 scat samples collected from five haul‐out sites during four nonsequential years, we quantified diet using metabarcoding techniques and determined the sex of the scat depositor using a molecular assay. Results suggest that intrapopulation feeding diversity was present. Specialization was high over short periods (24–48 hr,  = 0.392, 95% CI = 0.013, R = 100,000) and variable in time and space. Females showed more specialization than males, particularly during summer and fall. Additionally, demersal and benthic prey species were correlated with more specialized diets. The latter finding suggests that this type of prey likely requires specific foraging strategies and that there are trade‐offs between pelagic and benthic foraging styles for harbor seals. This differential feeding on prey species, as well as between sexes of harbor seals, indicates that predator–prey interactions in harbor seals are complex and that each sex may have a different impact on species of conservation concern. As such, describing intrapopulation feeding diversity may unravel hitherto unknown complex predator–prey interactions in the community.     

Genome‐wide linkage disequilibrium and past effective population size in three Korean cattle breeds

The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high‐density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (N_e), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and N_e in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15–0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small N_e values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and N_e for each breed reflect the breeding strategy applied. The N_e for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract.     

A process‐based metacommunity framework linking local and regional scale community ecology

The metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: (1) density‐independent responses to abiotic conditions, (2) density‐dependent biotic interactions and (3) dispersal. Stochasticity is incorporated in the demographic realisation of each of these processes. We formalise this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning and stability within metacommunities.     

Nucleotide diversity patterns of three divergent soybean populations: evidences for population‐dependent linkage disequilibrium and taxonomic status of Glycine gracilis

The level of linkage disequilibrium (LD) is a major factor to determine DNA polymorphism pattern of a population and to construct high‐resolution maps useful in localizing and gene cloning of complicated traits. Here, we investigated LD level of three soybean populations with different genetic backgrounds and taxonomic status of G. gracilis by comparing the DNA polymorphism patterns of four high‐diversity single‐copy nuclear genes. A total of 152, 22, and 77 accessions of G. soja, G. gracilis, and G. max were observed. The results indicated that G. max retained only 75.3 (π) and 39% (θ) of the nucleotide polymorphism found in G. soja. Four gene loci evolved according to neutrality in both G. max and G. gracilis populations, and three gene loci evolved according to neutrality in G. soja population by Tajima's and Fu and Li's test. However, one gene locus deviated from neutrality by Fu and Li's test in the G. soja population. Further, medial level of LD (average r² = 0.2426) was found in intragene in G. max and G. gracilis populations, but unexpected low level of LD (r² ≤ 0.0539) was found in G. soja population. Significant genetic differentiation was detected between G. max and G. soja populations and also between G. max and G. gracilis populations; however, nonsignificant genetic differentiation was found between G. gracilis and G. soja populations. The results suggest that LD level depends on genetic background of soybean population, and implicit that G. gracilis should be regarded as the variant of G. soja, not as an independent species.     

Multicoloured greenbeards,bacteriocin diversity and the rock‐paper‐scissors game

Greenbeard genes identify copies of themselves in other individuals and cause their bearer to behave nepotistically towards those individuals. Bacterial toxins (bacteriocins) exemplify the greenbeard effect because producer strains carry closely linked genes for immunity, such that toxicity is limited to nonproducer strains. Bacteriocin producers can be maintained in a dynamic polymorphism, known as rock‐paper‐scissors (RPS) dynamics, with immune and susceptible strains. However, it is unclear whether and how such dynamics will be maintained in the presence of multiple toxin types (multiple beard ‘colours’). Here, we analyse strain dynamics using models of recurrent patch colonization and population growth. We find that (i) polymorphism is promoted by a small number of founding lineages per patch, strong local resource competition and the occurrence of mutations; (ii) polymorphism can be static or dynamic, depending on the intensity of local interactions and the costs of toxins and immunity; (iii) the occurrence of multiple toxins can promote RPS dynamics; and (iv) strain diversity can be maintained even when toxins differ in toxicity or lineages can exhibit multitoxicity/multi‐immunity. Overall, the factors that maintain simple RPS dynamics can also promote the coexistence of multiple toxin types (multiple beard colours), thus helping to explain the remarkable levels of bacteriocin diversity in nature. More generally, we contrast these results with the maintenance of marker diversity in genetic kin recognition.     

Intra‐ and interspecific interactions between aphidophagous ladybirds: the role of prey in predator coexistence

Cannibalism (CANN) and intraguild predation (IGP) may provide energy and nutrients to individuals and eliminate potential competitors. These negative competitive interactions could also affect the coexistence of predatory species. The co‐occurrence of aphidophagous ladybird species in crops creates opportunities for CANN and IGP, especially when aphids become scarce. The Lotka–Volterra model predicts the coexistence of two species if intraspecific competition is stronger than interspecific interference interactions. Cycloneda sanguinea L. and Eriopis connexa (Germar) (both Coleoptera: Coccinellidae) coexist in sweet pepper crops in La Plata (Argentina) consuming mainly Myzus persicae (Sulzer) (Hemiptera: Aphididae). The present study used laboratory experiments to estimate levels of CANN and IGP by adults and larvae on eggs, and by adults on larvae, in both the presence and absence of prey (i.e., M. persicae), to explain the effect of prey on coexistence of these two predators. Levels of CANN by C. sanguinea and E. connexa were high in the absence of aphids, and decreased when prey was present. Intraguild predation was bidirectional and asymmetric. Adults and larvae of E. connexa were more voracious IG predators of C. sanguinea than vice versa, the former being the stronger IG predator and interference competitor. Eriopis connexa always won when larvae of the same instar were compared, whereas the larger larva always won when larvae were of different instars, regardless of species. In the presence of prey, CANN by both species decreased, but IGP by E. connexa on C. sanguinea remained high, suggesting that E. connexa could displace C. sanguinea via interspecific interference competition. Other factors potentially affecting the coexistence of C. sanguinea and E. connexa in sweet pepper crops are discussed.     

Eco‐evolutionary partitioning metrics: assessing the importance of ecological and evolutionary contributions to population and community change

Interest in eco‐evolutionary dynamics is rapidly increasing thanks to ground‐breaking research indicating that evolution can occur rapidly and can alter the outcome of ecological processes. A key challenge in this sub‐discipline is establishing how important the contribution of evolutionary and ecological processes and their interactions are to observed shifts in population and community characteristics. Although a variety of metrics to separate and quantify the effects of evolutionary and ecological contributions to observed trait changes have been used, they often allocate fractions of observed changes to ecology and evolution in different ways. We used a mathematical and numerical comparison of two commonly used frameworks – the Price equation and reaction norms – to reveal that the Price equation cannot partition genetic from non‐genetic trait change within lineages, whereas the reaction norm approach cannot partition among‐ from within‐lineage trait change. We developed a new metric that combines the strengths of both Price‐based and reaction norm metrics, extended all metrics to analyse community change and also incorporated extinction and colonisation of species in these metrics. Depending on whether our new metric is applied to populations or communities, it can correctly separate intraspecific, interspecific, evolutionary, non‐evolutionary and interacting eco‐evolutionary contributions to trait change.     

Ecology shapes the evolutionary trade‐off between predator avoidance and defence in coral reef butterflyfishes

Antipredator defensive traits are thought to trade‐off evolutionarily with traits that facilitate predator avoidance. However, complexity and scale have precluded tests of this prediction in many groups, including fishes. Using a macroevolutionary approach, we test this prediction in butterflyfishes, an iconic group of coral reef inhabitants with diverse social behaviours, foraging strategies and antipredator adaptations. We find that several antipredator traits have evolved adaptively, dependent primarily on foraging strategy. We identify a previously unrecognised axis of diversity in butterflyfishes where species with robust morphological defences have riskier foraging strategies and lack sociality, while species with reduced morphological defences feed in familiar territories, have adaptations for quick escapes and benefit from the vigilance provided by sociality. Furthermore, we find evidence for the constrained evolution of fin spines among species that graze solely on corals, highlighting the importance of corals, as both prey and structural refuge, in shaping fish morphology.     

天童森林植被的群落稳定性与物种多样性关系的研究

本文依据天童森林群落样地的数据,分析了群落稳定性与物种多样性的关系。结果表明不能单纯以物种多样性的高低来判断某具体群落的稳定性,使用群落各层次的物种多样性指数和群落优势种群的年龄结构来衡量群落的稳定性较为合适     

Distance‐dependent seedling mortality and long‐term spacing dynamics in a neotropical forest community

Negative distance dependence (NDisD), or reduced recruitment near adult conspecifics, is thought to explain the astounding diversity of tropical forests. While many studies show greater mortality at near vs. far distances from adults, these studies do not seek to track changes in the peak seedling curve over time, thus limiting our ability to link NDisD to coexistence. Using census data collected over 12 years from central Panama in conjunction with spatial mark‐connection functions, we show evidence for NDisD for many species, and find that the peak seedling curve shifts away from conspecific adults over time. We find wide variation in the strength of NDisD, which was correlated with seed size and canopy position, but other life‐history traits showed no relationship with variation in NDisD mortality. Our results document shifts in peak seedling densities over time, thus providing evidence for the hypothesized spacing mechanism necessary for diversity maintenance in tropical forests.     

Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neighboring joining tree distinguished the modern from the original populations. The F_ST‐outlier identified several genes putatively involved in the genetic differentiation between the two groups, such as stature and growth, behavior, and adaptability to local environments. The ROH islands within both the original and the modern populations overlapped with QTL associated with relevant traits. In modern Brown (Brown Swiss and Italian Brown), ROH islands harbored candidate genes associated with milk production traits, in evident agreement with the artificial selection conducted to improve this trait in these populations. In original Brown (Original Braunvieh and Braunvieh), we identified candidate genes related with fat deposition, confirming that breeding strategies for the original Brown populations aimed to produce dual‐purpose animals. Our study highlighted the presence of several genomic regions that vary between Brown populations, in line with their different breeding histories.     

Single‐nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula

Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single‐nucleotide polymorphism (SNP) markers in M. truncatula through large‐scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency <0.01). The substantial polymorphism detected at the species and population levels, the high marker quality and the potential to survey large samples of individuals make this set of SNP markers a valuable tool to improve our understanding of the effect of demographic and selective factors that shape the natural genetic diversity within the selfing species Medicago truncatula.     

Effects of evolutionary changes in prey use on the relationship between food web complexity and stability

The relationship between food web complexity and stability has been the subject of a long-standing debate in ecology. Although rapid changes in the food web structure through adaptive foraging behavior can confer stability to complex food webs, as reported by Kondoh (Science 299:1388–1391, 2003), the exact mechanisms behind this adaptation have not been specified in previous studies; thus, the applicability of such predictions to real ecosystems remains unclear. One mechanism of adaptive foraging is evolutionary change in genetically determined prey use. We constructed individual-based models of evolution of prey use by predators assuming explicit population genetics processes, and examined how this evolution affects the stability (i.e., the proportion of species that persist) of the food web and whether the complexity of the food web increased the stability of the prey–predator system. The analysis showed that the stability of food webs decreased with increasing complexity regardless of evolution of prey use by predators. The effects of evolution on stability differed depending on the assumptions made regarding genetic control of prey use. The probabilities of species extinctions were associated with the establishment or loss of trophic interactions via evolution of the predator, indicating a clear link between structural changes in the food web and community stability.     

Diversity and coexistence are influenced by time‐dependent species interactions in a predator–prey system

Although numerous studies show that communities are jointly influenced by predation and competitive interactions, few have resolved how temporal variability in these interactions influences community assembly and stability. Here, we addressed this challenge in experimental microbial microcosms by employing empirical dynamic modelling tools to: (1) detect causal interactions between prey species in the absence and presence of a predator; (2) quantify the time‐varying strength of these interactions and (3) explore stability in the resulting communities. Our findings show that predators boost the number of causal interactions among community members, and lead to reduced dynamic stability, but higher coexistence among prey species. These results correspond to time‐varying changes in species interactions, including emergence of morphological characteristics that appeared to reduce predation, and indirectly facilitate growth of predator‐susceptible species. Jointly, our findings suggest that careful consideration of both context and time may be necessary to predict and explain outcomes in multi‐trophic systems.     

No correlation between the diversity and productivity of assemblages: evidence from the phytophage and predator assemblages in various cotton agroecosystems

Biodiversity research has shown that primary productivity increases with plant species number, especially in many experimental grassland systems. Here, we assessed the correlation between productivity and diversity of phytophages and natural enemy assemblages associated with planting date and intercropping in four cotton agroecosystems. Twenty-one pairs of data were used to determine Pearson correlations between species richness, total number of individuals, diversity indices and productivity for each assemblage every five days from 5 June to 15 September 2012. At the same trophic level, the productivity exhibited a significant positive correlation with species richness of the phytophage or predator assemblage. A significant correlation was found between productivity and total number of individuals in most cotton fields. However, no significant correlations were observed between productivity and diversity indices (including indices of energy flow diversity and numerical diversity) in most cotton fields for either the phytophage or the predator assemblages. Species richness of phytophage assemblage and total individual numbers were significantly correlated with primary productivity. Also, species richness of natural enemy assemblage and total number of individuals correlated with phytophage assemblage productivity. A negative but not significant correlation occurred between the indices of numerical diversity and energy flow diversity and lower trophic-level productivity in the cotton-phytophage and phytophage-predator assemblages for most intercropped cotton agroecosystems. Our results clearly showed that there were no correlations between diversity indices and productivity within the same or lower trophic levels within the phytophage and predator assemblages in cotton agroecosystems, and inter-cropped cotton fields had a stronger ability to support the natural enemy assemblage and potentially to reduce phytophages.