Predicting insect phenology across space and time

Many species appear to be undergoing shifts in phenology, arising from climate change. To predict the direction and magnitude of future changes requires an understanding of how phenology depends on climatic variation. Species show large‐scale spatial variation in phenology (affected by differentiation among populations) as well as variation in phenology from year‐to‐year at the same site (affected predominantly by local plasticity). Teasing apart spatial and temporal variation in phenology should allow improved predictions of phenology under climate change. This study is the first to quantify large‐scale spatial and temporal variation in the entire emergence pattern of species, and to test the relationships found by predicting future data. We use data from up to 33 years of permanent transect records of butterflies in the United Kingdom to fit and test models for 15 butterfly species. We use generalized additive models to model spatial and temporal variation in the distribution of adult butterflies over the season, allowing us to capture changes in the timing of emergence peaks, relative sizes of peaks and/or number of peaks in a single analysis. We develop these models using data for 1973–2000, and then use them to predict phenologies from 2001 to 2006. For six of our study species, a model with only spatial variation in phenology is the best predictor of the future, implying that these species have limited plasticity. For the remaining nine species, the best predictions come from a model with both spatial and temporal variation in phenology; for four of these, growing degree‐days have similar effects over space and time, implying high levels of plasticity. The results show that statistical phenology models can be used to predict phenology shifts in a second time period, suggesting that it should be feasible to project phenologies under climate change scenarios, at least over modest time scales.     

Plastid division: across time and space

Plastid division is executed by the coordinated action of at least two molecular machineries--an internal machinery situated on the stromal side of the inner envelope membrane that was contributed by the cyanobacterial endosymbiont from which plastids evolved, and an external machinery situated on the cytosolic side of the outer envelope membrane that was contributed by the host. Here we review progress in defining the components of the plastid division complex and understanding the mechanisms of envelope constriction and division-site placement in plants. We also highlight recent work identifying the first molecular linkage between the internal and external division machineries, shedding light on how their mid-plastid positioning is coordinated across the envelope membranes. Little is known about the mechanisms that regulate plastid division in plant cells, but recent studies have begun to hint at potential mechanisms.     

Similarity of mammalian body size across the taxonomic hierarchy and across space and time

Although it is commonly assumed that closely related animals are similar in body size, the degree of similarity has not been examined across the taxonomic hierarchy. Moreover, little is known about the variation or consistency of body size patterns across geographic space or evolutionary time. Here, we draw from a data set of terrestrial, nonvolant mammals to quantify and compare patterns across the body size spectrum, the taxonomic hierarchy, continental space, and evolutionary time. We employ a variety of statistical techniques including "sib-sib" regression, phylogenetic autocorrelation, and nested ANOVA. We find an extremely high resemblance (heritability) of size among congeneric species for mammals over approximately 18 g; the result is consistent across the size spectrum. However, there is no significant relationship among the body sizes of congeneric species for mammals under approximately 18 g. We suspect that life-history and ecological parameters are so tightly constrained by allometry at diminutive size that animals can only adapt to novel ecological conditions by modifying body size. The overall distributions of size for each continental fauna and for the most diverse orders are quantitatively similar for North America, South America, and Africa, despite virtually no overlap in species composition. Differences in ordinal composition appear to account for quantitative differences between continents. For most mammalian orders, body size is highly conserved, although there is extensive overlap at all levels of the taxonomic hierarchy. The body size distribution for terrestrial mammals apparently was established early in the Tertiary, and it has remained remarkably constant over the past 50 Ma and across the major continents. Lineages have diversified in size to exploit environmental opportunities but only within limits set by allometric, ecological, and evolutionary constraints.     

Modeling microbial community structure and functional diversity across time and space

Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways.     

Effects of drought on fish across axes of space, time and ecological complexity

• 1 We evaluate the position of 50 previously published studies of fish and drought with respect to spatial scale of study (individual stream pools to subcontinents), length of the dry period (weeks to centuries), and level of system complexity (individual fish to ecosystems). Most papers address short (months to a year) droughts or dry periods, in local reaches of streams, and impacts on populations or local assemblages. In these 50 papers, the most frequently demonstrated effects of drought were population declines, loss of habitat, changes in the community, negative effects from changes in water quality, movement within catchments, and crowding of fish in reduced microhabitats. Thirteen other less frequent effects also were identified.
• 2 Gaps in knowledge exist on effects of long‐term droughts (decades to centuries), influence of drought on fish effects in ecosystems, and at the spatial scale of river basins to subcontinents. However, some of these gaps have recently been addressed, particularly additive effects of repeated drying episodes and whole‐lake or basin‐wide effects of drought, and in using molecular techniques to seek signals of drought at wide geographic scales because of events in the deep past. Gaps in knowledge remain for effects of very short dry periods, on drought effects on higher levels of complexity, and on the manner in which droughts at the scale of decades affect fish.
• 3 Data from streams in Oklahoma and elsewhere in the south‐western U.S.A. suggest that most droughts may leave little persistent signal in the existing fish fauna, i.e. that recovery from drought by fish populations or assemblages in the region can be rapid. However, species that are vulnerable to drought or water loss in streams may have disappeared from some basins in the region before the mid‐1900s, and recent evidence also suggests that extreme droughts do sometimes alter fish assemblages.
• 4 Little is known about mechanisms by which droughts have direct or indirect effects on fish, the roles of droughts in the evolution of fish species, and the ways droughts alter effects of fish in ecosystems. Global climate changes may have serious consequences for future local or regional fish faunas, but ongoing studies of fish experiencing drought may aid in future conservation of what will become species at risk under climate‐change scenarios.

     

The future of plant-pollinator diversity: understanding interaction networks across time, space, and global change

Structural analysis of plant-pollinator networks has revealed remarkably high species and interaction diversity and highlighted the species important for pollination services. Although techniques to analyze plant-pollinator networks began to emerge a decade ago, the characterization of spatiotemporal variation of interactions is still in its infancy. Understanding the ecological and evolutionary causes and consequences of spatial and temporal variation in plant-pollinator interactions is important for both basic and applied questions in community structure and function, the evolution of floral traits, and the development of optimal conservation strategies. Here we review observational, theoretical, and experimental studies of temporal and spatial variation in plant-pollinator interaction networks to establish a foundation for future studies to incorporate perspectives in spatiotemporal variation. Such perspectives are crucial given the rapid environmental changes associated with habitat loss, climate change, and biological invasions, which we discuss in this context. The inherent plasticity of plant-pollinator interactions and network structure suggests that many species should be able to persist by responding to environmental changes quickly, even though the identity of their mutualistic partners may change.     

An ecological framework linking scales across space and time based on self-thinning

Scaling up from measurements made at small spatial and short temporal scales is a central challenge in the ecological and related sciences, where predictions at larger scales and over long time periods are required. It involves two quite distinct aspects: a formulation of a theoretical framework for calculating space-time averages, and an acquisition of data to support that framework. In this paper, we address the theoretical part of the question, and although our primary motivation was an understanding of carbon accounting our formulation is more general. To that end, we adopt a dynamical systems approach, and incorporate a new dynamical formulation of self-thinning. We show how to calculate rates of change for total (and average) plant dry mass, volume, and carbon, in terms of the properties of the individual plants. The results emphasize how local scale statistics (such as, variation in the size of individuals) lead to nonlinear variation at larger scales. Further, we describe how regular and stochastic disturbance can be readily incorporated into this framework. It is shown that stochastic disturbance at patch-scales, results in (to first approximation) regular disturbance at ecosystem scales, and hence can be formulated as such. We conclude that a dynamical formulation of self-thinning can be used as a generic framework for scaling ecological processes in space and time.     

Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time

In this study, we collected water from different locations in 32 drinking water distribution networks in the Netherlands and analysed the spatial and temporal variation in microbial community composition by high‐throughput sequencing of 16S rRNA gene amplicons. We observed that microbial community compositions of raw source and processed water were very different for each distribution network sampled. In each network, major differences in community compositions were observed between raw and processed water, although community structures of processed water did not differ substantially from end‐point tap water. End‐point water samples within the same distribution network revealed very similar community structures. Network‐specific communities were shown to be surprisingly stable in time. Biofilm communities sampled from domestic water metres varied distinctly between households and showed no resemblance to planktonic communities within the same distribution networks. Our findings demonstrate that high‐throughput sequencing provides a powerful and sensitive tool to probe microbial community composition in drinking water distribution systems. Furthermore, this approach can be used to quantitatively compare the microbial communities to match end‐point water samples to specific distribution networks. Insight in the ecology of drinking water distribution systems will facilitate the development of effective control strategies that will ensure safe and high‐quality drinking water.     

Fatty acid composition of consumers in boreal lakes – variation across species,space and time

1. Fatty acids (FAs) have been widely applied as trophic biomarkers in aquatic food web studies. However, current knowledge of inter‐ and intraspecific variation in consumer FA compositions across spatial and temporal scales is constrained to a few pelagic taxa. 2. We analysed the FAs of 22 taxa of benthic macroinvertebrates, zooplankton and fish collected from the littoral, pelagic and profundal habitats of nine boreal oligotrophic lakes over spring, summer and autumn. We quantified and compared the FA variance partitions contributed by species identity (i.e. an integrative effect of phylogenetic origin, life history and functional feeding guild of individual taxa), site and season using partial redundancy analysis both on all consumers and on benthic arthropods alone. 3. Species identity alone contributed 84.4 and 72.8% of explained FA variation of all consumers and benthic arthropods, respectively. Influences of site, season and all joint effects accounted for 0–11.3% only. Fatty acid profiles of primary consumers differentiated below class level, but those of predators were distinguishable only when they became more taxonomically distinct (i.e. among classes or higher). 4. Pelagic and profundal consumers showed stronger reliance on autochthonous resources than did their littoral counterparts as reflected by their higher ω3 to ω6 FA ratios. Polyunsaturated FAs (PUFAs) were increasingly retained with trophic levels, and saturated FAs (e.g. FA 16 : 0) gradually reduced. Ecologically, this trade‐off enhances the trophic transfer efficiency and confirms the importance of PUFA‐rich autotrophs in aquatic food webs. 5. Our findings indicate strong interspecific differences in FA requirements and assimilation among aquatic consumers from a wide range of taxonomic levels, habitats and lakes. Consumers were able to maintain homoeostasis in FA compositions across spatial and temporal changes in resource FAs, but consumer homoeostasis did not limit the effectiveness of FAs as trophic biomarkers.     

Modelling,inference and big data in biophysics

In recognition of the increasing importance of big data in biophysics, a new session called ‘Modelling, inference, big data’ is incorporated into the IUPAB/EBSA Congress on 18 July 2017 at Edinburgh, UK.     

The causes of species richness patterns across space, time, and clades and the role of "ecological limits"

A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by "ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new "alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.     

Gene family evolution across 12 Drosophila genomes

Comparison of whole genomes has revealed large and frequent changes in the size of gene families. These changes occur because of high rates of both gene gain (via duplication) and loss (via deletion or pseudogenization), as well as the evolution of entirely new genes. Here we use the genomes of 12 fully sequenced Drosophila species to study the gain and loss of genes at unprecedented resolution. We find large numbers of both gains and losses, with over 40% of all gene families differing in size among the Drosophila. Approximately 17 genes are estimated to be duplicated and fixed in a genome every million years, a rate on par with that previously found in both yeast and mammals. We find many instances of extreme expansions or contractions in the size of gene families, including the expansion of several sex- and spermatogenesis-related families in D. melanogaster that also evolve under positive selection at the nucleotide level. Newly evolved gene families in our dataset are associated with a class of testes-expressed genes known to have evolved de novo in a number of cases. Gene family comparisons also allow us to identify a number of annotated D. melanogaster genes that are unlikely to encode functional proteins, as well as to identify dozens of previously unannotated D. melanogaster genes with conserved homologs in the other Drosophila. Taken together, our results demonstrate that the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss. It is likely that this genomic revolving door has played a large role in shaping the morphological, physiological, and metabolic differences among species.     

Algorithm for large-scale clustering across multiple genomes

Identifying genomic regions that descended from a common ancestor helps us study the gene function and genome evolution. In distantly related genomes, clusters of homologous gene pairs are evidently used in function prediction, operon detection, etc. Currently, there are many kinds of computational methods that have been proposed defining gene clusters to identify gene families and operons. However, most of those algorithms are only available on a data set of small size. We developed an efficient gene clustering algorithm that can be applied on hundreds of genomes at the same time. This approach allows for large-scale study of evolutionary relationships of gene clusters and study of operon formation and destruction. An analysis of proposed algorithms shows that more biological insight can be obtained by analyzing gene clusters across hundreds of genomes, which can help us understand operon occurrences, gene orientations and gene rearrangements.     

Survival of the currently fittest: genetics of rainbow trout survival across time and space

As a fitness trait, survival is assumed to exhibit low heritability due to strong selection eroding genetic variation and/or spatio-temporal variation in mortality agents reducing genetic and increasing residual variation. The latter phenomenon in particular may contribute to low heritability in multigeneration data, even if certain cohorts exhibit significant genetic variation. Analysis of survival data from 10 year classes of rainbow trout reared at three test stations showed that treating survival as a single trait across all generations resulted in low heritability (h(2) = 0.08-0.17). However, when heritabilities were estimated from homogeneous generation and test station-specific cohorts, a wide range of heritability values was revealed (h(2) = 0.04-0.71). Of 64 genetic correlations between different cohorts, 20 were positive, but 16 were significantly negative, confirming that genetic architecture of survival is not stable across generations and environments. These results reveal the existence of hidden genetic variation for survival and demonstrate that treating survival as one trait over several generations may not reveal its true genetic architecture. Negative genetic correlations between cohorts indicate that overall survival has limited potential to predict general resistance, and care should be taken when using it as selection criterion.