Cue identification in phenology: A case study of the predictive performance of current statistical tools

Modelling asynchrony in phenology considering a dynamic representation of meteorological variables

Shifts in the timing of phenological events across many taxa and ecosystems are a result of climate change. Within a trophic network, phenological mismatches between interlinked species can have negative impacts for biodiversity, ecosystems, and the trophic network. Here we developed interaction indices that quantify the level of synchrony and asynchrony among groups of species in three interlinked trophic levels, as well as accounting for a dynamic representation of meteorology. Insect first flight, vegetation green-up and arrival of migrant birds were the phenological indicators, obtained from a combination of spatially and temporally explicit species observations from citizen science programmes and remote sensing platforms (i.e., Landsat). To determine phenological shifts in interlinked taxa we created and applied several phenological indices of synchrony-asynchrony, combining information from the phenological events and critical time windows of meteorological variables. To demonstrate our method of incorporating a meteorological component in our new interaction index, we implemented the relative sliding time window analysis, a stepwise regression model, to identify critical time windows preceding the phenological events on a yearly basis. The new indices of phenological change identified several asynchronies within trophic levels, allowing exploration of potential interactions based on synchrony among interlinked species. Our novel index of synchrony-asynchrony including a meteorological dimension could be highly informative and should open new pathways for studying synchrony among species and interaction networks.

Space-for-time substitutions in climate change ecology and evolution

In an epoch of rapid environmental change, understanding and predicting how biodiversity will respond to a changing climate is an urgent challenge. Since we seldom have sufficient long-term biological data to use the past to anticipate the future, spatial climate-biotic relationships are often used as a proxy for predicting biotic responses to climate change over time. These 'space-for-time substitutions' (SFTS) have become near ubiquitous in global change biology, but with different subfields largely developing methods in isolation. We review how climate-focussed SFTS are used in four subfields of ecology and evolution, each focussed on a different type of biotic variable - population phenotypes, population genotypes, species' distributions, and ecological communities. We then examine the similarities and differences between subfields in terms of methods, limitations and opportunities. While SFTS are used for a wide range of applications, two main approaches are applied across the four subfields: spatial in situ gradient methods and transplant experiments. We find that SFTS methods share common limitations relating to (i) the causality of identified spatial climate-biotic relationships and (ii) the transferability of these relationships, i.e. whether climate-biotic relationships observed over space are equivalent to those occurring over time. Moreover, despite widespread application of SFTS in climate change research, key assumptions remain largely untested. We highlight opportunities to enhance the robustness of SFTS by addressing key assumptions and limitations, with a particular emphasis on where approaches could be shared between the four subfields.

Environmental Drivers of Amphibian Breeding Phenology across Multiple Sites

A mechanistic understanding of phenology, the seasonal timing of life history events, is important for understanding species’ interactions and the potential responses of ecological communities to a rapidly changing climate. We present analysis of a seven-year dataset on the breeding phenology of wood frogs (Rana sylvatica), tiger salamanders (Ambystoma tigrinum), blue-spotted salamanders (Ambystoma laterale), and associated unisexual Ambystoma salamanders from six wetlands in Southeast Michigan, USA. We assess whether the ordinal date of breeding migrations varies among species, sexes, and individual wetlands, and we describe the specific environmental conditions associated with breeding migrations for each species/sex. Breeding date was significantly affected by species/sex identity, year, wetland, and the interactions between species/sex and year as well as wetland and year. There was a great deal of variation among years, with breeding occurring nearly synchronously among groups in some years but widely spaced between groups in other years. Specific environmental triggers for movement varied for each species and sex and changed as the breeding season progressed. In general, salamanders responded to longer temperature lags (more warmer days in a row) than wood frogs, whereas wood frogs required longer precipitation lags (more rainy days in a row) than salamanders. Wood frogs were more likely to migrate around the time of a new moon, whereas in contrast, Ambystoma salamander migration was not associated with a moon phase. Ordinal day was an important factor in all models, suggesting that these amphibians require a latency period or similar mechanism to avoid breeding too early in the year, even when weather conditions appear favorable. Male wood frogs migrated earlier than female wood frogs, and male blue-spotted salamanders migrated earlier than female A. laterale and associated unisexual females. Larger unisexual salamanders migrated earlier than smaller individuals. Differences in species’ responses to environmental cues led to wood frogs and A. laterale breeding later than tiger salamanders in colder years but not in warmer years. This suggests that, as the climate warms, wood frog and A. laterale larvae may experience less predation from tiger salamander larvae due to reduced size differences when they breed simultaneously. Our study is one of few to describe the proximate drivers of amphibian breeding migrations across multiple species, wetlands, and years, and it can inform models predicting how climate change may shift ecological interactions among pond-breeding amphibian species.

A reaction norm framework for the evolution of learning: how cumulative experience shapes phenotypic plasticity

Learning is a familiar process to most people, but it currently lacks a fully developed theoretical position within evolutionary biology. Learning (memory and forgetting) involves adjustments in behaviour in response to cumulative sequences of prior experiences or exposures to environmental cues. We therefore suggest that all forms of learning (and some similar biological phenomena in development, aging, acquired immunity and acclimation) can usefully be viewed as special cases of phenotypic plasticity, and formally modelled by expanding the concept of reaction norms to include additional environmental dimensions quantifying sequences of cumulative experience (learning) and the time delays between events (forgetting). Memory therefore represents just one of a number of different internal neurological, physiological, hormonal and anatomical ‘states’ that mediate the carry‐over effects of cumulative environmental experiences on phenotypes across different time periods. The mathematical and graphical conceptualisation of learning as plasticity within a reaction norm framework can easily accommodate a range of different ecological scenarios, closely linking statistical estimates with biological processes. Learning and non‐learning plasticity interact whenever cumulative prior experience causes a modification in the reaction norm (a) elevation [mean phenotype], (b) slope [responsiveness], (c) environmental estimate error [informational memory] and/or (d) phenotypic precision [skill acquisition]. Innovation and learning new contingencies in novel (laboratory) environments can also be accommodated within this approach. A common reaction norm approach should thus encourage productive cross‐fertilisation of ideas between traditional studies of learning and phenotypic plasticity. As an example, we model the evolution of plasticity with and without learning under different levels of environmental estimation error to show how learning works as a specific adaptation promoting phenotypic plasticity in temporally autocorrelated environments. Our reaction norm framework for learning and analogous biological processes provides a conceptual and mathematical structure aimed at usefully stimulating future theoretical and empirical investigations into the evolution of plasticity across a wider range of ecological contexts, while providing new interdisciplinary connections regarding learning mechanisms.

Sex-differences in Phenology: A Tinbergian Perspective

Shifts in the timing of cyclic seasonal life-history events are among the most commonly reported responses to climate change, with differences in response rates among interacting species leading to phenological mismatches. Within a species, however, males and females can also exhibit differential sensitivity to environmental cues and may therefore differ in their responsiveness to climate change, potentially leading to phenological mismatches between the sexes. This occurs because males differ from females in when and how energy is allocated to reproduction, resulting in marked sex-differences in life-history timing across the annual cycle. In this review, we take a Tinbergian perspective and examine sex differences in timing of vertebrates from adaptive, ontogenetic, mechanistic, and phylogenetic viewpoints with the goal of informing and motivating more integrative research on sexually dimorphic phenologies. We argue that sexual and natural selection lead to sex-differences in life-history-timing and that understanding the ecological and evolutionary drivers of these differences is critical for connecting climate-driven phenological shifts to population resilience. Ontogeny may influence how and when sex differences in life-history timing arise because the early-life environment can profoundly affect developmental trajectory, rates of reproductive maturation, and seasonal timing. The molecular mechanisms underlying these organismal traits are relevant to identifying the diversity and genetic basis of population- and species-level responses to climate change, and promisingly, the molecular basis of phenology is becoming increasingly well-understood. However, because most studies focus on a single sex, the causes of sex-differences in phenology critical to population resilience often remain unclear. New sequencing tools and analyses informed by phylogeny may help generate hypotheses about mechanism as well as insight into the general "evolvability" of sex differences across phylogenetic scales, especially as trait and genome resources grow. We recommend that greater attention be placed on determining sex-differences in timing mechanisms and monitoring climate change responses in both sexes, and we discuss how new tools may provide key insights into sex-differences in phenology from all four Tinbergian domains.

Bird populations most exposed to climate change are less sensitive to climatic variation

The phenology of many species shows strong sensitivity to climate change; however, with few large scale intra-specific studies it is unclear how such sensitivity varies over a species' range. We document large intra-specific variation in phenological sensitivity to temperature using laying date information from 67 populations of two co-familial European songbirds, the great tit (Parus major) and blue tit (Cyanistes caeruleus), covering a large part of their breeding range. Populations inhabiting deciduous habitats showed stronger phenological sensitivity than those in evergreen and mixed habitats. However, populations with higher sensitivity tended to have experienced less rapid change in climate over the past decades, such that populations with high phenological sensitivity will not necessarily exhibit the strongest phenological advancement. Our results show that to effectively assess the impact of climate change on phenology across a species' range it will be necessary to account for intra-specific variation in phenological sensitivity, climate change exposure, and the ecological characteristics of a population.

Fluctuating selection driven by global and local climatic conditions leads to stasis in breeding time in a migratory bird

The origin of natural selection is linked to environmental heterogeneity, which influences variation in relative fitness among phenotypes. However, individuals in wild populations are exposed to a plethora of biotic and abiotic environmental factors. Surprisingly, the relative influence of multiple environmental conditions on the relative fitness of phenotypes has rarely been tested in wild populations. Identifying the main selection agent(s) is crucial when the target phenotype is tightly linked to reproduction and when temporal variation in selection is expected to affect evolutionary responses. By using individual-based data from a 29-year study of a short-lived migratory songbird, the pied flycatcher (Ficedula hypoleuca), we studied the relative influence of 28 temperature- and precipitation-based factors at local and global scales on selection on breeding time (egg laying) at the phenotypic level. Selection, estimated using the number of recruits as a proxy for fitness, penalized late breeders. Minimum temperatures in April and May were the environmental drivers that best explained selection on laying date. In particular, there was negative directional selection on laying date mediated by minimum temperature in April, being strongest in cold years. In addition, nonlinear selection on laying date was influenced by minimum temperatures in May, with selection on laying date changing from null to negative as the breeding season progressed. The intensity of selection on late breeders increased when minimum temperatures in May were highest. Our results illustrate the complex influence of environmental factors on selection on laying date in wild bird populations. Despite minimum temperature in April being the only variable that changed over time, its increase did not induce a shift in laying date in the population. In this songbird population, stabilizing selection has led to a three-decade stasis in breeding time. We suggest that variation in the effects of multiple climatic variables on selection may constrain phenotypic change.

Strengthening the evidence base for temperature-mediated phenological asynchrony and its impacts

Climate warming has caused the seasonal timing of many components of ecological food chains to advance. In the context of trophic interactions, the match-mismatch hypothesis postulates that differential shifts can lead to phenological asynchrony with negative impacts for consumers. However, at present there has been no consistent analysis of the links between temperature change, phenological asynchrony and individual-to-population-level impacts across taxa, trophic levels and biomes at a global scale. Here, we propose five criteria that all need to be met to demonstrate that temperature-mediated trophic asynchrony poses a growing risk to consumers. We conduct a literature review of 109 papers studying 129 taxa, and find that all five criteria are assessed for only two taxa, with the majority of taxa only having one or two criteria assessed. Crucially, nearly every study was conducted in Europe or North America, and most studies were on terrestrial secondary consumers. We thus lack a robust evidence base from which to draw general conclusions about the risk that climate-mediated trophic asynchrony may pose to populations worldwide.

Best environmental predictors of breeding phenology differ with elevation in a common woodland bird species

Temperatures in mountain areas are increasing at a higher rate than the Northern Hemisphere land average, but how fauna may respond, in particular in terms of phenology, remains poorly understood. The aim of this study was to assess how elevation could modify the relationships between climate variability (air temperature and snow melt-out date), the timing of plant phenology and egg-laying date of the coal tit (Periparus ater). We collected 9 years (2011-2019) of data on egg-laying date, spring air temperature, snow melt-out date, and larch budburst date at two elevations (~1,300 m and ~1,900 m asl) on a slope located in the Mont-Blanc Massif in the French Alps. We found that at low elevation, larch budburst date had a direct influence on egg-laying date, while at high-altitude snow melt-out date was the limiting factor. At both elevations, air temperature had a similar effect on egg-laying date, but was a poorer predictor than larch budburst or snowmelt date. Our results shed light on proximate drivers of breeding phenology responses to interannual climate variability in mountain areas and suggest that factors directly influencing species phenology vary at different elevations. Predicting the future responses of species in a climate change context will require testing the transferability of models and accounting for nonstationary relationships between environmental predictors and the timing of phenological events.

Cascading effects of temperature alterations on trophic ecology of European grayling (Thymallus thymallus)

The aims of this project were to study: diet composition, food selectivity and the phenology of different prey items in grayling’s (Thymallus thymallus) diet. It was hypothesized, that alterations in mayfly emergence, caused by reservoir-induced thermal changes, have consequences for trophic ecology of drift-feeding fish. Sampling of fish and macroinvertebrates were conducted in two closely located rivers, one human-modified and the other an undisturbed river. Grayling preyed mainly on aquatic insects, but only mayflies were preferred. Seasonal changes of the fish diet were observed, and air temperature is considered a predictor of prey occurrence with different time lags, depending on the biology of the organisms. Significant differences in the abundances and probability of mayfly occurrence between two studied rivers were shown. The observed phenological shift suggests that distorted environmental cues were experienced by the Ephemeroptera in the modified river. The “lost generation” of insects which failed to complete development became a new food for fish. The results presented indicate that reservoir-induced thermal alterations in the rivers, similarly to climate change, can lead to a chain of consequences in the ecosystems. Taking into consideration the projected climate scenarios, further monitoring and forecasting of these effects are considered an important step for future mitigating actions and adaptive management of water resources.

The environmental predictors of spatio-temporal variation in the breeding phenology of a passerine bird

Establishing the cues or constraints that influence avian timing of breeding is the key to accurate prediction of future phenology. This study aims to identify the aspects of the environment that predict the timing of two measures of breeding phenology (nest initiation and egg laying date) in an insectivorous woodland passerine, the blue tit (Cyanistes caeruleus). We analyse data collected from a 220 km, 40-site transect over 3 years and consider spring temperatures, tree leafing phenology, invertebrate availability and photoperiod as predictors of breeding phenology. We find that mean night-time temperature in early spring is the strongest predictor of both nest initiation and lay date and suggest this finding is most consistent with temperature acting as a constraint on breeding activity. Birch budburst phenology significantly predicts lay date additionally to temperature, either as a direct cue or indirectly via a correlated variable. We use cross-validation to show that our model accurately predicts lay date in two further years and find that similar variables predict lay date well across the UK national nest record scheme. This work refines our understanding of the principal factors influencing the timing of tit reproductive phenology and suggests that temperature may have both a direct and indirect effect.