Seasonal niche differentiation among closely related marine bacteria

Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.Subject terms: Microbial ecology, Microbial ecology     

Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model

There is growing interest in the integration of macroecology and palaeoecology towards a better understanding of past, present, and anticipated future biodiversity dynamics. However, the empirical basis for this integration has thus far been limited. Here we review prospects for a macroecology–palaeoecology integration in biodiversity analyses with a focus on marine microfossils [i.e. small (or small parts of) organisms with high fossilization potential, such as foraminifera, ostracodes, diatoms, radiolaria, coccolithophores, dinoflagellates, and ichthyoliths]. Marine microfossils represent a useful model system for such integrative research because of their high abundance, large spatiotemporal coverage, and good taxonomic and temporal resolution. The microfossil record allows for quantitative cross‐scale research designs, which help in answering fundamental questions about marine biodiversity, including the causes behind similarities in patterns of latitudinal and longitudinal variation across taxa, the degree of constancy of observed gradients over time, and the relative importance of hypothesized drivers that may explain past or present biodiversity patterns. The inclusion of a deep‐time perspective based on high‐resolution microfossil records may be an important step for the further maturation of macroecology. An improved integration of macroecology and palaeoecology would aid in our understanding of the balance of ecological and evolutionary mechanisms that have shaped the biosphere we inhabit today and affect how it may change in the future.     

Ecological traits influence the phylogenetic structure of bird species co‐occurrences worldwide

The extent to which species’ ecological and phylogenetic relatedness shape their co‐occurrence patterns at large spatial scales remains poorly understood. By quantifying phylogenetic assemblage structure within geographic ranges of >8000 bird species, we show that global co‐occurrence patterns are linked – after accounting for regional effects – to key ecological traits reflecting diet, mobility, body size and climatic preference. We found that co‐occurrences of carnivorous, migratory and cold‐climate species are phylogenetically clustered, whereas nectarivores, herbivores, frugivores and invertebrate eaters tend to be more phylogenetically overdispersed. Preference for open or forested habitats appeared to be independent from the level of phylogenetic clustering. Our results advocate for an extension of the tropical niche conservatism hypothesis to incorporate ecological and life‐history traits beyond the climatic niche. They further offer a novel species‐oriented perspective on how biogeographic and evolutionary legacies interact with ecological traits to shape global patterns of species coexistence in birds.     

Palaeoniches get stitches: analyses of niches informing macroevolutionary theory

The concept of the niche is fundamental to ecology and palaeoecology, and an extensive body of scientific literature exists on the subject Here we discuss how recent palaeontological studies, particularly those focusing on species’ niche dynamics through time, continue to integrate palaeoecology with macroevolutionary theory.     

Niche versus neutrality in structuring the beta diversity of damselfly assemblages

1. Differences among communities in taxonomic composition – beta diversity – are frequently expected to result from taxon‐specific responses to spatial variation in ecological conditions, through niche partitioning. Such process‐derived patterns are in sharp contrast to arguments from neutral theory, where taxa are ecologically equivalent and beta diversity results primarily from dispersal limitation. 2. Here, we compared beta diversity among assemblages of damselflies (Odonata: Zygoptera), for which previous experiments have shown that niche differences maintain genera within a community, but patterns of relative abundance for species within each genus are shaped primarily by neutral dynamics. 3. Using null‐model and ordination‐based methods, we find that both genera and (in contrast to neutral theory) species assemblage composition vary across the landscape in a deterministic fashion, shaped by environmental and spatial factors. 4. While the observed patterns in species composition conflict with theory, we suggest that this a result of weak ecological filters acting to produce spatial variation in assemblages of ecologically similar species undergoing ecological drift within communities. Such patterns are especially likely in systems of relatively weak dispersers like damselflies.     

Matching consumer feeding behaviours and resource traits: a fourth‐corner problem in food‐web theory

For decades, food web theory has proposed phenomenological models for the underlying structure of ecological networks. Generally, these models rely on latent niche variables that match the feeding behaviour of consumers with their resource traits. In this paper, we used a comprehensive database to evaluate different hypotheses on the best dependency structure of trait‐matching patterns between consumers and resource traits. We found that consumer feeding behaviours had complex interactions with resource traits; however, few dimensions (i.e. latent variables) could reproduce the trait‐matching patterns. We discuss our findings in the light of three food web models designed to reproduce the multidimensionality of food web data; additionally, we discuss how using species traits clarify food webs beyond species pairwise interactions and enable studies to infer ecological generality at larger scales, despite potential taxonomic differences, variations in ecological conditions and differences in species abundance between communities.     

Trait-dependent declines of species following conversion of rain forest to oil palm plantations

Conversion of natural habitats to agriculture reduces species richness, particularly in highly diverse tropical regions, but its effects on species composition are less well-studied. The conversion of rain forest to oil palm is of particular conservation concern globally, and we examined how it affects the abundance of birds, beetles, and ants according to their local population size, body size, geographical range size, and feeding guild or trophic position. We re-analysed data from six published studies representing 487 species/genera to assess the relative importance of these traits in explaining changes in abundance following forest conversion. We found consistent patterns across all three taxa, with large-bodied, abundant forest species from higher trophic levels, declining most in abundance following conversion of forest to oil palm. Best-fitting models explained 39–66 % of the variation in abundance changes for the three taxa, and included all ecological traits that we considered. Across the three taxa, those few species found in oil palm tended to be small-bodied species, from lower trophic levels, that had low local abundances in forest. These species were often hyper-abundant in oil palm plantations. These results provide empirical evidence of consistent responses to land-use change among taxonomic groups in relation to ecological traits.     

Case studies and mathematical models of ecological speciation. 2. Palms on an oceanic island

A recent study of a pair of sympatric species of palms on the Lord Howe Island is viewed as providing probably one of the most convincing examples of sympatric speciation to date. Here we describe and study a stochastic, individual-based, explicit genetic model tailored for this palms system. Overall, our results show that relatively rapid (<50,000 generations) colonization of a new ecological niche, and sympatric or parapatric speciation via local adaptation and divergence in flowering periods are theoretically plausible if (i) the number of loci controlling the ecological and flowering period traits is small; (ii) the strength of selection for local adaptation is intermediate; and (iii) an acceleration of flowering by a direct environmental effect associated with the new ecological niche is present. We discuss patterns and time-scales of ecological speciation identified by our model, and we highlight important parameters and features that need to be studied empirically in order to provide information that can be used to improve the biological realism and power of mathematical models of ecological speciation.     

A multivariate approach reveals diversity of ontogenetic niche shifts across taxonomic and functional groups

1. Shifts in the fundamental and realised niche of individuals during their ontogeny are ubiquitous in nature, but we know little about what aspects of the niche change and how these changes vary across species within communities. However, this knowledge is essential to predict the dynamics of populations and communities and how they respond to environmental change.
2. Here I introduce a range of metrics to describe different aspects of shifts in the realised trophic niche of individuals based on stable isotopes. Applying this multi-variate approach to 2,272 individuals from 13 taxonomic and functional distinct species (Amphibia, Hemiptera, Coleoptera, Odonata) sampled in natural pond communities allowed me to: (1) describe and quantify the diversity of trophic niche shift patterns over ontogeny in multi-dimensional space, and (2) identify what aspects of ontogenetic shifts vary across taxa, and functional groups.
3. Results revealed that species can differ substantially in which aspects of the trophic niche change and how they change over ontogeny. Interestingly, patterns of ontogenetic niche shifts grouped in distinct taxonomic clusters in multi-variate space, including two distinct groups of predators (Hemiptera versus Odonata). Given the differences in traits (especially feeding mode) across groups, this suggests that differences in ontogenetic niche shifts across species could at least partially be explained by variation in traits and functional roles of species.
4. These results emphasise the importance of a multivariate approach to capture the large diversity of trophic niche shifts patterns possible in natural communities and suggest that differences in ontogenetic niche shifts follow general patterns.

     

Individual Cell Based Traits Obtained by Scanning Flow-Cytometry Show Selection by Biotic and Abiotic Environmental Factors during a Phytoplankton Spring Bloom

In ecology and evolution, the primary challenge in understanding the processes that shape biodiversity is to assess the relationship between the phenotypic traits of organisms and the environment. Here we tested for selection on physio-morphological traits measured by scanning flow-cytometry at the individual level in phytoplankton communities under a temporally changing biotic and abiotic environment. Our aim was to study how high-frequency temporal changes in the environment influence biodiversity dynamics in a natural community. We focused on a spring bloom in Lake Zurich (Switzerland), characterized by rapid changes in phytoplankton, water conditions, nutrients and grazing (mainly mediated by herbivore ciliates). We described bloom dynamics in terms of taxonomic and trait-based diversity and found that diversity dynamics of trait-based groups were more pronounced than those of identified phytoplankton taxa. We characterized the linkage between measured phytoplankton traits, abiotic environmental factors and abundance of the main grazers and observed weak but significant correlations between changing abiotic and biotic conditions and measured size-related and fluorescence-related traits. We tested for deviations in observed community-wide distributions of focal traits from random patterns and found evidence for both clustering and even spacing of traits, occurring sporadically over the time series. Patterns were consistent with environmental filtering and phenotypic divergence under herbivore pressure, respectively. Size-related traits showed significant even spacing during the peak of herbivore abundance, suggesting that morphology-related traits were under selection from grazing. Pigment distribution within cells and colonies appeared instead to be associated with acclimation to temperature and water chemistry. We found support for trade-offs among grazing resistance and environmental tolerance traits, as well as for substantial periods of dynamics in which our measured traits were not under selection.     

宏生态学(Macroecology)及其研究

宏生态学是生态学与其他宏观学科不断交叉和融合后的产物。它以个体、种群和物种的生态特征在大时空尺度上的格局和变化规律为主要研究内容,它比其他生态学更强调归纳和推论,也更依赖数据的积累。近年来,宏生态学在对物种一面积关系进行探讨的基础上,对生物类群间的物种数量的协同变化以及物种和高级分类单元间的关系等进行了新的研究;宏生态学试图将有机论和个体论结合来探讨和总结群落结构中的物种组成规律;并对物种多度和分布格局间的关系从生态位和异质种群角度进行新的解释;个体大小频次分布规律是宏生态学一重要内容,对其深入研究和探讨已与物种多度、能量、分布面积、历史起源等多方面特征相结合,并得到一些普遍性规律;最后,宏生态学还探讨物种在地理区域上的普遍性的分布模式,并对其假说进行检验和探讨。宏生态学在中国还处于刚起步阶段,但中国具有资源的优势,并具有一定的数据积累,将在宏生态学研究中发挥越来越重要的作用。     

Dispersal evolution in temporally variable environments: implications for plant range dynamics

Dispersal—the movement of an individual from the site of birth to a different site for reproduction—is an ecological and evolutionary driver of species ranges that shapes patterns of colonization, connectivity, gene flow, and adaptation. In plants, the traits that influence dispersal often vary within and among species, are heritable, and evolve in response to the fitness consequences of moving through heterogeneous landscapes. Spatial and temporal variation in the quality and quantity of habitat are important sources of selection on dispersal strategies across species ranges. While recent reviews have evaluated the interactions between spatial variation in habitat and dispersal dynamics, the extent to which geographic variation in temporal variability can also shape range-wide patterns in dispersal traits has not been synthesized. In this paper, we summarize key predictions from metapopulation models that evaluate how dispersal evolves in response to spatial and temporal habitat variability. Next, we compile empirical data that quantify temporal variability in plant demography and patterns of dispersal trait variation across species ranges to evaluate the hypothesis that higher temporal variability favors increased dispersal at plant range limits. We found some suggestive evidence supporting this hypothesis while more generally identifying a major gap in empirical work evaluating plant metapopulation dynamics across species ranges and geographic variation in dispersal traits. To address this gap, we propose several future research directions that would advance our understanding of the interplay between spatiotemporal variability and dispersal trait variation in shaping the dynamics of current and future species ranges.     

Divergent parasite infections in sympatric cichlid species in Lake Victoria

Parasitism has been proposed as a factor in host speciation, as an agent affecting coexistence of host species in species‐rich communities and as a driver of post‐speciation diversification. Young adaptive radiations of closely related host species of varying ecological and genomic differentiation provide interesting opportunities to explore interactions between patterns of parasitism, divergence and coexistence of sympatric host species. Here, we explored patterns in ectoparasitism in a community of 16 fully sympatric cichlid species at Makobe Island in Lake Victoria, a model system of vertebrate adaptive radiation. We asked whether host niche, host abundance or host genetic differentiation explains variation in infection patterns. We found significant differences in infections, the magnitude of which was weakly correlated with the extent of genomic divergence between the host species, but more strongly with the main ecological gradient, water depth. These effects were most evident with infections of Cichlidogyrus monogeneans, whereas the only host species with a strictly crevice‐dwelling niche, Pundamilia pundamilia, deviated from the general negative relationship between depth and parasitism. In accordance with the Janzen–Connell hypothesis, we also found that host abundance tended to be positively associated with infections in some parasite taxa. Data on the Pundamilia sister species pairs from three other islands with variable degrees of habitat (crevice) specialization suggested that the lower parasite abundance of P. pundamilia at Makobe could result from both habitat specialization and the evolution of specific resistance. Our results support influences of host genetic differentiation and host ecology in determining infections in this diverse community of sympatric cichlid species.     

Conservatism of ecological niche characteristics in North American plant species over the Pleistocene-to-Recent transition

Aim  To provide a test of the conservatism of a species' niche over the last 20,000 years by tracking the distribution of eight pollen taxa relative to climate type as they migrated across eastern North America following the Last Glacial Maximum (LGM).
Location  North America.
Methods  We drew taxon occurrence data from the North American pollen records in the Global Pollen Database, representing eight pollen types – all taxa for which ≥5 distinct geographic occurrences were available in both the present day and at the LGM (21,000 years ago ± 3000 years). These data were incorporated into ecological niche models based on present-day and LGM climatological summaries available from the Palaeoclimate Modelling Intercomparison Project to produce predicted potential geographic distributions for each species at present and at the LGM. The output for each time period was projected onto the 'other' time period, and tested using independent known occurrence information from that period.
Results  The result of our analyses was that all species tested showed general conservatism in ecological characteristics over the climate changes associated with the Pleistocene-to-Recent transition.
Main conclusions  This analysis constitutes a further demonstration of general and pervasive conservatism in ecological niche characteristics over moderate periods of time despite profound changes in climate and environmental conditions. As such, our results reinforce the application of ecological niche modelling techniques to the reconstruction of Pleistocene biodiversity distribution patterns, and to project the future potential distribution range of species in the face of global-scale climatic changes.     

Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree

Whether bacteria display spatial patterns of distribution and at which level of taxonomic organization such patterns can be observed are central questions in microbial ecology. Here we investigated how the total and relative abundances of eight bacterial taxa at the phylum or class level were spatially distributed in a pasture by using quantitative PCR and geostatistical modelling. The distributions of the relative abundance of most taxa varied by a factor of 2.5–6.5 and displayed strong spatial patterns at the field scale. These spatial patterns were taxon‐specific and correlated to soil properties, which indicates that members of a bacterial clade defined at high taxonomical levels shared specific ecological traits in the pasture. Ecologically meaningful assemblages of bacteria at the phylum or class level in the environment provides evidence that deep branching patterns of the 16S rRNA bacterial tree are actually mirrored in nature.     

ASYNCHRONOUS EVOLUTION OF PHYSIOLOGY AND MORPHOLOGY IN ANOLIS LIZARDS

Species‐rich adaptive radiations typically diversify along several distinct ecological axes, each characterized by morphological, physiological, and behavioral adaptations. We test here whether different types of adaptive traits share similar patterns of evolution within a radiation by investigating patterns of evolution of morphological traits associated with microhabitat specialization and of physiological traits associated with thermal biology in Anolis lizards. Previous studies of anoles suggest that close relatives share the same “structural niche” (i.e., use the same types of perches) and are similar in body size and shape, but live in different “climatic niches” (i.e., use habitats with different insolation and temperature profiles). Because morphology is closely tied to structural niche and field active body temperatures are tied to climatic niches in Anolis, we expected phylogenetic analyses to show that morphology is more evolutionarily conservative than thermal physiology. In support of this hypothesis, we find (1) that thermal biology exhibits more divergence among recently diverged Anolis taxa than does morphology; and (2) diversification of thermal biology among all species often follows diversification in morphology. These conclusions are remarkably consistent with predictions made by anole biologists in the 1960s and 1970s.     

Models for assessing local‐scale co‐abundance of animal species while accounting for differential detectability and varied responses to the environment

We developed a new modeling framework to assess how the local abundance of one species influences the local abundance of a potential competitor while explicitly accounting for differential responses to environmental conditions. Our models also incorporate imperfect detection as well as abundance estimation error for both species. As a case study, we applied the model to four pairs of mammal species in Borneo, surveyed by extensive and spatially widespread camera trapping. We detected different responses to elevation gradients within civet, macaque, and muntjac deer species pairs. Muntjac and porcupine species varied in their response to terrain ruggedness, and the two muntjac responded different to river proximity. Bornean endemic species of civet and muntjac were more sensitive than their widespread counterparts to habitat disturbance (selective logging). Local abundance within several species pairs was positively correlated, but this is likely due to the species having similar responses to (unmodeled) environmental conditions or resources rather than representing facilitation. After accounting for environment and correcting for false absences in detection, negative correlations in local abundance appear rare in tropical mammals. Direct competition may be weak in these species, possibly because the ‘ghost of competition past’ or habitat filtering have already driven separation of the species in niche space. The analytical framework presented here could increase basic understanding of how ecological interactions shape patterns of abundance across the landscape for a range of taxa, and also provide a powerful tool for forecasting the impacts of global change.     

Trait-based community assembly of understory palms along a soil nutrient gradient in a lower montane tropical forest

Two opposing niche processes have been shown to shape the relationship between ecological traits and species distribution patterns: habitat filtering and competitive exclusion. Habitat filtering is expected to select for similar traits among coexisting species that share similar habitat conditions, whereas competitive exclusion is expected to limit the ecological similarity of coexisting species leading to trait differentiation. Here, we explore how functional traits vary among 19 understory palm species that differ in their distribution across a gradient of soil resource availability in lower montane forest in western Panama. We found evidence that habitat filtering influences species distribution patterns and shifts community-wide and intraspecific trait values. Differences in trait values among sites were more strongly related to soil nutrient availability than to variation in light or rainfall. Soil nutrient availability explained a significant amount of variation in site mean trait values for 4 of 15 functional traits. Site mean values of leaf nitrogen and phosphorus increased 37 and 64%, respectively, leaf carbon:nitrogen decreased 38%, and specific leaf area increased 29% with increasing soil nutrient availability. For Geonoma cuneata, the only species occurring at all sites, leaf phosphorus increased 34% and nitrogen:phosphorus decreased 42% with increasing soil nutrients. In addition to among-site variation, most morphological and leaf nutrient traits differed among coexisting species within sites, suggesting these traits may be important for niche differentiation. Hence, a combination of habitat filtering due to turnover in species composition and intraspecific variation along a soil nutrient gradient and site-specific niche differentiation among co-occurring species influences understory palm community structure in this lower montane forest.     

Rates of phenotypic evolution of ecological characters and sexual traits during the Tanganyikan cichlid adaptive radiation

Theory suggests that sexual traits evolve faster than ecological characters. However, characteristics of a species niche may also influence evolution of sexual traits. Hence, a pending question is whether ecological characters and sexual traits present similar tempo and mode of evolution during periods of rapid ecological divergence, such as adaptive radiation. Here, we use recently developed phylogenetic comparative methods to analyse the temporal dynamics of evolution for ecological and sexual traits in Tanganyikan cichlids. Our results indicate that whereas disparity in ecological characters was concentrated early in the radiation, disparity in sexual traits remained high throughout the radiation. Thus, closely related Tanganyikan cichlids presented higher disparity in sexual traits than ecological characters. Sexual traits were also under stronger selection than ecological characters. In sum, our results suggest that ecological characters and sexual traits present distinct evolutionary patterns, and that sexual traits can evolve faster than ecological characters, even during adaptive radiation.     

Niche evolution in Australian terrestrial mammals? Clarifying scale-dependencies in phylogenetic and functional drivers of co-occurrence

Interactive forces between competition and habitat filtering drive many biogeographic patterns over evolutionary time scales. However, the responsiveness of assemblages to these two forces is highly influenced by spatial scale, forming complex patterns of niche separation. We explored these spatial dependencies by quantifying the influence of phylogeny and functional traits in shaping present day native terrestrial mammal assemblages at multiple scales, principally by identifying the spatial scales at which niche evolution operates. We modelled the distribution of 53 native terrestrial mammal species across New South Wales, Australia. Using predicted distributions, we estimated the range overlap between each pair of species at increasing grain sizes (~0.8, 5.1, 20, 81, 506, 2,025, 8,100 km²). We employed a decision tree to identify how interactions among functional traits and phylogenetic relatedness translated to levels of sympatry at increasing spatial scales. We found that Australian terrestrial mammals displayed phylogenetic over-dispersion that was inversely related to spatial scale, suggesting that ecological processes were more influential than biogeographic sympatry patterns in defining assemblages of species. While the contribution of phylogenetic relatedness to patterns of co-occurrence decreased as spatial scale increased, the reverse was true for habitat preferences. At the same time, functional traits also operated at different scales, as dietary preferences dominated at local spatial scales (<10 km²) while body mass has a stronger effect at larger spatial scales. Our findings show that ecological and evolutionary processes operate at different scales and that Australian terrestrial mammals diverged slower along their micro-scale niche compared to their macro-scale niche. By combining phylogenetic and niche methods through the modelling of species distributions, we assessed whether specific traits were related to a particular niche. More importantly, conducting multi-scale spatial analysis avoids categorical assignment of traits-to-niches, providing a clearer relationship between traits and a species ecological niche and a more precise scaling for the axes of niche evolution.