Aim Spatial analysis of the distribution and density of species is of continuing interest within theoretical and applied ecology. Species distribution models (SDMs) are being increasingly used to analyse count, presence–absence and presence‐only data sets. There is a growing literature on dynamic SDMs (which incorporate temporal variation in species distribution), joint SDMs (which simultaneously analyse the correlated distribution of multiple species) and geostatistical models (which account for similarity between nearby sites caused by unobserved covariates). However, no previous study has combined all three attributes within a single framework. Innovation We develop spatial dynamic factor analysis for use as a ‘joint, dynamic SDM’ (JDSDM), which uses geostatistical methods to account for spatial similarity when estimating one or more ‘factors’. Each factor evolves over time following a density‐dependent (Gompertz) process, and the log‐density of each species is approximated as a linear combination of different factors. We demonstrate a JDSDM using two multispecies case studies (an annual survey of bottom‐associated species in the Bering Sea and a seasonal survey of butterfly density in the continental USA), and also provide our code publicly as an R package. Main conclusions Case study applications show that that JDSDMs can be used for species ordination, i.e. showing that dynamics for butterfly species within the same genus are significantly more correlated than for species from different genera. We also demonstrate how JDSDMs can rapidly identify dominant patterns in community dynamics, including the decline and recovery of several Bering Sea fishes since 2008, and the ‘flight curves’ typical of early or late‐emerging butterflies. We conclude by suggesting future research that could incorporate phylogenetic relatedness or functional similarity, and propose that our approach could be used to monitor community dynamics at large spatial and temporal scales.

1. Phenology is one of the most immediate responses to global climate change, but data limitations have made examining phenology patterns across greater taxonomic, spatial and temporal scales challenging. One significant opportunity is leveraging rapidly increasing data resources from digitized museum specimens and community science platforms, but this assumes reliable statistical methods are available to estimate phenology using presence-only data. Estimating the onset or offset of key events is especially difficult with incidental data, as lower data densities occur towards the tails of an abundance distribution. 2. The Weibull distribution has been recognized as an appropriate distribution to estimate phenology based on presence-only data, but Weibull-informed estimators are only available for onset and offset. We describe the mathematical framework for a new Weibull-parameterized estimator of phenology appropriate for any percentile of a distribution and make it available in an r package, phenesse. We use simulations and empirical data on open flower timing and first arrival of monarch butterflies to quantify the accuracy of our estimator and other commonly used phenological estimators for 10 phenological metrics: onset, mean and offset dates, as well as the 1st, 5th, 10th, 50th, 90th, 95th and 99th percentile dates. Root mean squared errors and mean bias of the phenological estimators were calculated for different patterns of abundance and observation processes. 3. Results show a general pattern of decay in performance of estimates when moving from mean estimates towards the tails of the seasonal abundance curve, suggesting that onset and offset continue to be the most difficult phenometrics to estimate. However, with simple phenologies and enough observations, our newly developed estimator can provide useful onset and offset estimates. This is especially true for the start of the season, when incidental observations may be more common. 4. Our simulation demonstrates the potential of generating accurate phenological estimates from presence-only data and guides the best use of estimators. The estimator that we developed, phenesse, is the least biased and has the lowest estimation error for onset estimates under most simulated and empirical conditions examined, improving the robustness of these estimates for phenological research.

Butterflies are a diverse and charismatic insect group that are thought to have evolved with plants and dispersed throughout the world in response to key geological events. However, these hypotheses have not been extensively tested because a comprehensive phylogenetic framework and datasets for butterfly larval hosts and global distributions are lacking. We sequenced 391 genes from nearly 2,300 butterfly species, sampled from 90 countries and 28 specimen collections, to reconstruct a new phylogenomic tree of butterflies representing 92% of all genera. Our phylogeny has strong support for nearly all nodes and demonstrates that at least 36 butterfly tribes require reclassification. Divergence time analyses imply an origin ~100 million years ago for butterflies and indicate that all but one family were present before the K/Pg extinction event. We aggregated larval host datasets and global distribution records and found that butterflies are likely to have first fed on Fabaceae and originated in what is now the Americas. Soon after the Cretaceous Thermal Maximum, butterflies crossed Beringia and diversified in the Palaeotropics. Our results also reveal that most butterfly species are specialists that feed on only one larval host plant family. However, generalist butterflies that consume two or more plant families usually feed on closely related plants.

The maximum per capita rate of population growth, r, is a central measure of population biology. However, researchers can only directly calculate r when adequate time series, life tables and similar datasets are available. We instead view r as an evolvable, synthetic life-history trait and use comparative phylogenetic approaches to predict r for poorly known species. Combining molecular phylogenies, life-history trait data and stochastic macroevolutionary models, we predicted r for mammals of the Caniformia and Cervidae. Cross-validation analyses demonstrated that, even with sparse life-history data, comparative methods estimated r well and outperformed models based on body mass. Values of r predicted via comparative methods were in strong rank agreement with observed values and reduced mean prediction errors by approximately 68 per cent compared with two null models. We demonstrate the utility of our method by estimating r for 102 extant species in these mammal groups with unknown life-history traits.

Mate finding, which is essential to both population growth and gene exchange, involves both spatial and temporal components. From a population dynamics perspective, spatial mate-finding problems are well studied, and decreased mate-finding efficiency at low population densities is a well-recognized mechanism for the Allee effect. Temporal aspects of mate finding have been rarely considered, but reproductive asynchrony may engender an Allee effect in which some females go mateless by virtue of temporal isolation. Here we develop and explore a model that unifies previously disparate theoretical considerations of spatial and temporal aspects of mate finding. Specifically, we develop a two-sex reaction-diffusion system to examine the interplay between reproductive asynchrony and the dispersal of individuals out of a patch. We also consider additional behavioral complications, including several alternative functional forms for mating efficiency and advective movements in which males actively seek out females. By calculating the fraction of females expected to go mateless as a joint function of reproductive asynchrony and patch size, we find that the population-level reproductive rates necessary to offset female matelessness may be quite high. These results suggest that Allee effects engendered by reproductive asynchrony will be greatly exacerbated in spatially isolated populations.

Population growth and persistence depend on the collective ability of individuals to find mates in both space and time. When individuals are reproductively mature for only a portion of a population's breeding season, reproductive asynchrony can cause mating failure and a temporal Allee effect, which is exacerbated by spatial constraints in isolated populations. However, the effect of phenological variation by sex (protandry, protogyny) in spatiotemporal mate finding is not well understood. Here, we examine the interacting roles of sex-specific and population-wide individual asynchrony on female matelessness in spatially isolated populations. By incorporating sex-specific phenology into a two-sex reaction-diffusion system, we explore female matelessness as a function of phenology, movement behavior, and patch size. Although individual asynchrony may lead to female mating failure in small and isolated populations, we find that moderate protandry reduces female mating failure across a variety of scenarios. We go on to examine model behavior for a case study based on the bagworm, Thyridopteryx ephemeraeformis Haworth (Lepidoptera: Psychidae), where many populations exhibit pronounced protogyny. Overall, we find a consistent benefit of moderate protandry, which may mitigate female matelessness for many populations.

Natural history collections (NHCs) have been indispensable to understanding longer‐term trends of the timing of seasonal events. Massive‐scale digitization of specimens promises to further enable phenological research, especially the ability to move towards a deeper understanding of drivers of change and how trait–environment interactions shape phenological sensitivity. Despite the promise of NHCs to answer fundamental phenology questions, the use of these data resources presents unique and often overlooked challenges requiring specialized workflow steps, such as assembling multisource data, accounting for date imprecision and making decisions about trade‐offs between data density and spatial resolution. We provide a set of key best practice recommendations and showcase these via a case study that utilizes NHC data to test hypotheses about spatiotemporal trends in adult Lepidoptera (i.e. butterflies and moths) flight timing across North America. Our case study is a worked example of these best practices, helping practitioners recognize and overcome potential pitfalls at each step, from data acquisition and cleaning, to delineating spatial units and proper estimation of phenological metrics and associated uncertainty, to building appropriate models. We confirm and extend the critical importance of voltinism and diapause strategy, but less‐so daily activity patterns, for predicting Lepidoptera phenology spatiotemporal trends. Our case study also showcases the unique power of NHC data to test existing hypotheses and generate new insights about temporal phenological trends. Specifically, migratory species and species that enter diapause as adults are advancing the start of flight periods in more recent years, even after accounting for climate context. These results highlight the physiological and adaptive differences between species with different overwintering strategies. We close by noting the value of partnerships between data scientists, museum experts and ecological modellers to fully harness the power of digital data resources to address pressing global change challenges. These partnerships can extend approaches for integrating multiple data types to fully unlock our understanding of the tempo, mode, drivers and outcomes of phenological changes at greater spatial, temporal and taxonomic scales. Read the free Plain Language Summary for this article on the Journal blog.

Disruptive effects of climate change include range shifts, phenological mismatches among consumers and producers, and population declines. While these biological alterations have been widely documented, studies identifying specific mechanisms linking climate change to population declines are scarce. Extreme events, such as heatwaves can have devastating effects on living organisms and are increasing in frequency as Earth warms. Hence, understanding the effects of heatwaves on insects is necessary to inform conservation efforts and to develop predictions of population dynamics under future climate scenarios. Here, we experimentally evaluated the effects of heatwaves on the survival and phenology of the Baltimore Checkerspot (Euphydryas phaeton phaeton), a wetland butterfly with imperiled populations that has incorporated a novel host. We performed laboratory manipulations (implementing realistic temperature regimes) to assess the effect of heatwaves during summer and winter on the survival and phenology of E. p. phaeton. In addition, we analyzed historical temperature records to quantify the incidence of heatwaves within E. p. phaeton's range to assess their potential role in the decline of southeastern populations. We found that winter heatwaves with maximum temperatures of 20 • C can have more devastating effects on survival than summer heatwaves (up to 41 • C). Eggs endured acute heat stress during summer with no significant effects on phenology and survival; similarly, pre-overwintering larvae were robust to heatwave exposure, as only the most intense heatwave treatment reduced their survival (37% reduction compared to control conditions). By contrast, dormant larvae were the most vulnerable stage, as they lost from 2 to 6% of their body mass after a three-day summer heatwave. Furthermore, their exposure to winter heatwaves resulted in 75 to 100% mortality. Feeding on the native host provided higher resilience under thermal stress than feeding on the invasive, recently acquired host. Finally, both heatwave incidence and severity have increased in the southern range of E. p. phaeton in the period from 1894 to 2011. We show that warm winter days induced severe mortality, providing a mechanistic explanation of how climate change can trigger population declines in E. p. phaeton and other insects.