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How sensitive are elasticities of long-run stochastic growth to how environmental variability is modelled?

A variable environment leaves a signature in a population's dynamics. Deriving statistical and mathematical models of how environmental variability affects population projections has – in the wake of reports of substantial climatic fluctuations – received much recent attention. If the model changes, then so too does the population projection. This is because a different model of environmental variability changes estimates of long-run stochastic growth, which is a function of demographic rates and their temporal sequence. Decomposing elasticities of long-run stochastic growth into constituent parts can assess the relative influence of different components. Here, we investigate the consequences of changing the environmental state definition, and therefore altering the shape of demographic rate distributions and their temporal sequence, by using age-structured matrix models to project vertebrate populations into the future under a range of environmental scenarios. The identity of the most influential demographic rate was consistent among all approaches that perturbed only the mean, but was not when only the variance was perturbed. Furthermore, the influence of each demographic rate fluctuated among projections by up to factors of six and two for changes to the variance and mean, respectively. These changes in influence depend in part upon how environmental variability – in particular, the color of environmental noise – is incorporated. In the light of predictions of increasing climatic variability in the future, these results suggest caution when drawing quantitative conclusions from stochastic population projections

Inclusion of a near-complete fossil record reveals speciation-related molecular evolution

The rate of genetic evolution is often too variable among lineages to be explained by a strict molecular clock, prompting alternative ecological and evolutionary hypotheses to explain this rate heterogeneity. One controversial hypothesis is that speciation provokes a burst of rapid genetic change, giving molecular evolution a punctuational component. The amount of root-to-tip genetic change therefore tends to increase with the number of identified speciation events (nodes) along the root-to-tip path in molecular phylogenies. The controversy arises because nodes on molecular phylogenies can typically only be counted if both descendants are extant. Here, using stratigraphic, phylogenetic and ecological data from the exceptional fossil record of Cenozoic macroperforate planktonic foraminifera, we test whether among-lineage rate heterogeneity is explained by ecological factors (abundance, life history and environment) and by the numbers of speciation events according to fossil lineage, fossil morphospecies and molecular species concepts. The number of nodes between root and tips on the fossil lineage phylogeny was a statistically significant correlate of the rate of molecular evolution over the same root-to-tip path. The speciation counts from other species concepts and hypothesized ecological drivers had considerably less support. Our results showcase how the fossil record contains signals of biological processes that drive genetic evolution, justifying calls to further marry fossil and molecular data when studying macroevolution over geological time-scales

Correlations between age, phenotype, and individual contribution to population growth in common terns

There have been numerous reports of changes in phenology, which are frequently attributed to environmental change. Age-dependent change in phenotypic traits, fledgling production, and the timing of events in the life cycle is also widespread. This means that changes in the age structure of a population could generate changes in phenology, which may be incorrectly attributed to environmental change or microevolution. Here, estimates of selection for arrival date, arrival mass, and laying date are compared when age is and is not corrected for. This is achieved using long-term individual-based data collected from a breeding colony of Common Terns (Sterna hirundo) and a novel fitness measure: individual contributions to population growth. The failure to correct for age generated deceptive estimates of selection in eight out of nine comparisons. In six out of nine comparisons, the direction of selection differed between age-corrected and uncorrected estimates. Persistent individual differences were detected: individuals remained within the same part of the phenotype distribution throughout life. The age-corrected estimates of selection were weak and explained little variation in fitness, suggesting that arrival date, arrival mass, and laying date are not under intense selection in this population. These results also demonstrate the importance of correcting for age when identifying factors associated with changes in seabird phenology

Algorithmic approaches to aid species' delimitation in multidimensional morphospace

BackgroundThe species is a fundamental unit of biological pattern and process, but its delimitation has proven a ready source of argument and disagreement. Here, we discuss four key steps that utilize statistical thresholds to describe the morphological variability within a sample and hence assess whether there is evidence for one or multiple species. Once the initial set of biologically relevant traits on comparable individuals has been identified, there is no need for the investigator to hypothesise how specimens might be divided among groups, nor the traits on which groups might be separated. ResultsPrincipal components are obtained using robust covariance estimates and retained only if they exceed threshold amounts of explanatory power, before model-based clustering is performed on the dimension-reduced space. We apply these steps in an attempt to resolve ongoing debates among taxonomists working on the extinct Eocene planktonic foraminifera Turborotalia, providing statistical evidence for two species shortly before the lineage's extinction near the Eocene/Oligocene boundary. ConclusionBy estimating variance robustly (samples containing incipient species are unlikely to be scaled optimally by means and standard deviations) and identifying thresholds relevant to a particular system rather than universal standards, the steps of the framework aim to optimize the chances of delineation without imposing pre-conceived patterns onto estimates of species limits. <br/

Calibration of the repeatability of foraminiferal test size and shape measures with recommendations for future use

The fossil record of planktonic foraminifera is ideally suited to defining stratigraphic age controls and exploring fundamental questions in evolutionary biology due to its excellent preservation potential that yields continuous, high-resolution fossil archives of large numbers of individuals. For full morphometric analyses foraminifera tests are generally mounted, oriented and imaged manually, while data are processed using standard software such as ImageJ or Image Pro. However, manually induced orientation errors are a source of potential bias in trait measurements even when quantified using the same computational subroutine. Here we test the repeatability of four measures of foraminiferal test shape on six morphologically distinct species and present a calibration (power analysis) of the number of individuals needed to determine a given percentage change in these traits. We mounted and measured every individual twice and analysed the difference between the two measurements to determine the effects of small orientation changes on the studied traits. We show that measurements of test area and aspect ratio are statistically indistinguishable between runs for all species studied, and a power law calibration suggests that between 25 and 50 individuals are needed to detect at least a 10% in- or decrease in either trait. However, despite mounting tests on glass slides to clarify perimeter outlines, test perimeter was only repeatable in the spherical species Orbulina universa, and test roundness was not repeatable for three out of six studied species. We recommend the use of lengths and avoidance of perimeters and their dependent metrics to reduce orientation induced bias

Prospectors’ colony attendance is sex-specific and increases future recruitment chances in a seabird

In most long-lived vertebrates, including seabirds, young non-breeders often attend potential breeding sites. In seabird colonies, this prospecting behaviour has nearly never been studied with respect to potential sex-specific benefits, and its fitness consequences are largely unknown. We compared attendance patterns of sexed common tern prospectors at six subcolonies with future breeding status and nesting site choice. We also tested for potential effects of population density. Birds that arrived earlier at the colony were recorded more often along the season. This arrival effect was stronger in males, which generally spent more time at the colony. Birds prospecting for two consecutive years attended the colony more intensively in the second year. A high colony attendance enhanced recruitment probability in both sexes, but only in females, it was linked with a higher probability to return. Attendance at a preferred subcolony increased during the season. For first breeding, individuals favoured the subcolony where they had prospected most intensively in the previous season. In males, this subcolony fidelity was stronger and increased simultaneously to breeding pair density. We conclude that prospecting is a process of integration into the community of breeders, and that benefits are higher for males, the more territorial sex in this species

The challenges to inferring the regulators of biodiversity in deep time

Attempts to infer the ecological drivers of macroevolution in deep time have long drawn inspiration from work on extant systems, but long-term evolutionary and geological changes complicate the simple extrapolation of such theory. Recent efforts to incorporate a more informed ecology into macroevolution have moved beyond the descriptive, seeking to isolate generating mechanisms and produce testable hypotheses of how groups of organisms usurp each other or coexist over vast timespans. This theme issue aims to exemplify this progress, providing a series of case studies of how novel modelling approaches are helping infer the regulators of biodiversity in deep time. In this Introduction, we explore the challenges of these new approaches. First, we discuss how our choices of taxonomic units have implications for the conclusions drawn. Second, we emphasize the need to embrace the interdependence of biotic and abiotic changes, because no living organism ignores its environment. Third, in the light of parts 1 and 2, we discuss the set of dynamic signatures that we might expect to observe in the fossil record. Finally, we ask whether these dynamics represent the most ecologically informative foci for research efforts aimed at inferring the regulators of biodiversity in deep time. The papers in this theme issue contribute in each of these areas

Evolutionary history biases inferences of ecology and environment from δ13C but not δ18O values

Closely related taxa are, on average, more similar in terms of their physiology, morphology and ecology than distantly related ones. How this biological similarity affects geochemical signals, and their interpretations, has yet to be tested in an explicitly evolutionary framework. Here, we compile and analyze planktonic foraminiferal size-specific stable carbon and oxygen isotope values (δ13C and δ18O) spanning the last 107 million years. After controlling for dominant drivers of size-δ13C and δ18O trends, such as geological preservation, presence of algal photosymbionts and global environmental trends, we identify that shared evolutionary history has shaped the evolution of species-specific “vital effects” in δ13C, but not in δ18O. Our results lay the groundwork for using a phylogenetic approach to ‘correct’ species δ13C vital effects through time, thereby reducing systematic biases in interpretations of long-term δ13C records – a key measure of holistic organismal biology and of the global carbon cycle