The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence ( Dendroica , Plethodon and Heliconius ). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.
Abstract Advances in spring phenology are among the clearest biological responses to climate warming. There has been much interest in how climate impacts on phenology because the timings of key events have implications for species interactions, nutrient cycling and ecosystem services. To date most work has focused on only one aspect of population phenology, the effects of temperature on the average timing. In comparison, effects of temperature on the abundance of individuals and their seasonal spread are understudied, despite their potential to have profound impacts on species interactions. Here we develop a new method that directly estimates the effect of spring temperatures on the timing, height and width of the phenological distribution and apply it to temperate forest caterpillars, a guild that has been the focus of much research on phenology and trophic mismatch. We find that warmer spring conditions advance the timing of the phenological distribution of abundance by −4.96 days °C −1 and increase its height by 34% °C −1 but have no significant effect on the duration of the distribution. An increase in the maximum density of arboreal caterpillars with rising temperatures has implications for understanding climate impacts on forest food chains, both in terms of herbivory pressure and the resources available to secondary consumers. The new method we have developed allows the thermal sensitivity in the full phenological distribution to be modelled directly from raw data, providing a flexible approach that has broad applicability within global change research. Read the free Plain Language Summary for this article on the Journal blog.
Revealing processes that structure species interactions is central to understanding community assembly and dynamics. Species interact via their phenotypes, but identifying and quantifying the traits that structure species-specific interactions (links) can be challenging. Where these traits show phylogenetic signal, however, link properties may be predictable using models that incorporate phylogenies in place of trait data. We analysed variation in link richness, frequency, and species identity in a multi-site dataset of interactions between oak cynipid galls and parasitoid natural enemies, using a Bayesian mixed modelling framework allowing concurrent fitting of phylogenetic effects of both trophic levels. In both link incidence (presence/absence) and link frequency datasets, we identified strong signatures of cophylogeny (related parasitoids attack related host galls) alongside patterns independent of either phylogeny. Our results are robust to simulations of substantially reduced sample completeness, and are consistent with the structuring of trophic interactions by a combination of phylogenetically conserved and convergently evolving traits in both trophic levels. We discuss our results in light of phenotypic traits thought to structure gall-parasitoid interactions and consider wider applications of this approach, including inference of underlying community assembly processes and prediction of economically important trophic interactions.
Habitat data collected for the manuscript entitled 'The phenology and clutch size of UK Blue Tits does not differ with woodland composition'. All other data associated with the manuscript is available on request. Bird breeding data are housed with the British Trust for Ornithology as part of the maintained National Database on Bird Ringing and Nest Recording. Data can be requested via https://www.bto.org/our-science/data/data-request-system. All temperature data are available on request from the MET Office.
Over the past four decades, rising temperatures have impacted the breeding phenology of many bird species, in some cases with consequences for their reproductive success. Migratory birds face particular challenges in shifting breeding phenology to track warmer springs, and understanding the impacts of rising spring temperatures on migratory birds' breeding is urgent. Here, we use over 4000 UK observations of Common Redstart nests, and spring temperature data from 1974 to 2020, to examine the effect of spring temperatures on laying date, clutch size and brood size. We use a sliding window approach to detect periods over which traits are most sensitive to temperature, and compare phenotypic responses to temperature over space and time with the aim of identifying causal effects of temperature and inferring the contributions of plasticity and local adaptation. We found that redstart laying date was sensitive to spring temperature from mid‐April to late May, with a relatively shallow response of 1–2 days/°C that was similar across space and time, but shallower than the phenological response of many of the resource species. Over the study period, laying date has advanced by more than 11 days, which is substantially more than can be explained based on the temperature plasticity estimates we obtained. Spring temperature had a weak, but positive, impact on clutch size, but with no evidence of an effect of spatial variation in temperature. The rate of brood size reduction from hatching to fledging became more negative at higher temperatures, but after taking into account a non‐significant but positive effect of temperature on brood size at hatching, there was no net effect of temperature on fledging success. Taken together, we found little evidence that higher temperatures in the UK lead to lower reproductive output.
Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry. Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32 %–95 % of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved. Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on "strict and " "relaxed" biological species concepts (BSC), as well as on a surrogate for the widely-used "diagnostic" version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two groups. To establish whether heliconiines are exceptional will require biogeographic comparative studies for a wider range of animal taxa including many more invertebrates.
'%3e%3cpath fill='%23012169' d='M0 0v30h60V0z'/%3e%3cpath stroke='%23fff' stroke-width='6' d='m0 0 60 30m0-30L0 30'/%3e%3cpath stroke='%23C8102E' stroke-width='4' d='m0 0 60 30m0-30L0 30' clip-path='url(%23b)'/%3e%3cpath stroke='%23fff' stroke-width='10' d='M30 0v30M0 15h60'/%3e%3cpath stroke='%23C8102E' stroke-width='6' d='M30 0v30M0 15h60'/%3e%3c/g%3e%3c/svg%3e)
