Environmentally driven extinction and opportunistic origination explain fern diversification patterns

Combining palaeontological and neontological data offers a unique opportunity to investigate the relative roles of biotic and abiotic controls of species diversification, and the importance of origination versus extinction in driving evolutionary dynamics. Ferns comprise a major terrestrial plant radiation with an extensive evolutionary history providing a wealth of modern and fossil data for modelling environmental drivers of diversification. Here we develop a novel Bayesian model to simultaneously estimate correlations between diversification dynamics and multiple environmental trajectories. We estimate the impact of different factors on fern diversification over the past 400 million years by analysing a comprehensive dataset of fossil occurrences and complement these findings by analysing a large molecular phylogeny. We show that origination and extinction rates are governed by fundamentally different processes: originations depend on within-group diversity but are largely unaffected by environmental changes, whereas extinctions are strongly affected by external factors such as climate and geology. Our results indicate that the prime driver of fern diversity dynamics is environmentally driven extinction, with origination being an opportunistic response to diminishing ecospace occupancy

Elevation gradients of lemur abundance emphasise the importance of Madagascar’s lowland rainforest for the conservation of endemic taxa

1. Elevation gradients correlate with changes in several environmental conditions and are known to be related to animal abundance. Animals in regions with a naturally limited extent of lowland rainforest are expected to have evolved adaptations to intermediate elevations that provided a stable environment during their evolution. 2. Since the lowland rainforest of Madagascar has a limited extent and suffers from increasing anthropogenic pressure, it is essential to understand how well species tolerate intermediate and high elevations. In this study, we aim to quantify the relationship between lemur abundance and elevation in the eastern rainforest of Madagascar. 3. We correlated abundance data on 26 lemur species (10 genera), including 492 records from 26 studies, with elevation. We analysed the consistency of correlations across species with a meta‐analytical approach. We controlled for species’ body mass, elevational range and median elevation. We then ran generalised linear mixed models to determine whether lemur abundance was related to elevation, body mass, plant productivity and anthropogenic disturbance. 4. Overall, the abundance of lemur species in Malagasy rainforests was negatively correlated with elevation, and species occupying broader elevational ranges showed stronger correlations. Body mass was not related to species’ tolerance of high elevations. Even though several lemur species are able to occupy the entire elevation gradient, the few remaining patches of lowland rainforests host lemur species at greater abundances than other sites. Abundance across species was negatively related to body mass, elevation and seasonality in plant productivity and positively related to plant productivity. 5. Despite the ecological flexibility of many lemur species, the remnant patches of lowland rainforests host the highest levels of lemur abundance and are key to lemur conservation. It is crucial to preserve this priority habitat both for biodiversity conservation and for our understanding of lemur adaptations

Climate drives community-wide divergence within species over a limited spatial scale: evidence from an oceanic island

Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the spatial scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance are restricted, microclimatic variation over distances of only a few kilometres can maintain strong geographic isolation extending back several millions of years. Further to this, we demonstrate congruent diversification with gene flow across species, mediated by Quaternary climate oscillations that have facilitated a dynamic of isolation and secondary contact. The unprecedented scale of parallel species responses to a common environmental driver for evolutionary change has profound consequences for understanding past and future species responses to climate variation

Disturbance indicator values for European plants

Motivation Indicator values are numerical values used to characterize the ecological niches of species and to estimate their occurrence along gradients. Indicator values on climatic and edaphic niches of plant species have received considerable attention in ecological research, whereas data on the optimal positioning of species along disturbance gradients are less developed. Here, we present a new data set of disturbance indicator values identifying optima along gradients of natural and anthropogenic disturbance for 6382 vascular plant species based on the analysis of 736,366 European vegetation plots and using expert-based characterization of disturbance regimes in 236 habitat types. The indicator values presented here are crucial for integrating disturbance niche optima into large-scale vegetation analyses and macroecological studies. Main types of variables contained We set up five main continuous indicator values for European vascular plants: disturbance severity, disturbance frequency, mowing frequency, grazing pressure and soil disturbance. The first two indicators are provided separately for the whole community and for the herb layer. We calculated the values as the average of expert-based estimates of disturbance values in all habitat types where a species occurs, weighted by the number of plots in which the species occurs within a given habitat type. Spatial location and grain Europe. Vegetation plots ranging in size from 1 to 1000 m(2). Time period and grain Vegetation plots mostly sampled between 1956 and 2013 (= 5th and 95th quantiles of the sampling year, respectively). Major taxa and level of measurement Species-level indicator values for vascular plants. Software format csv file

Root traits explain plant species distributions along climatic gradients yet challenge the nature of ecological trade-offs

Ecological theory is built on trade-offs, where trait differences among species evolved as adaptations to different environments. Trade-offs are often assumed to be bidirectional, where opposite ends of a gradient in trait values confer advantages in different environments. However, unidirectional benefits could be widespread if extreme trait values confer advantages at one end of an environmental gradient, whereas a wide range of trait values are equally beneficial at the other end. Here, we show that root traits explain species occurrences along broad gradients of temperature and water availability, but model predictions only resembled trade-offs in two out of 24 models. Forest species with low specific root length and high root tissue density (RTD) were more likely to occur in warm climates but species with high specific root length and low RTD were more likely to occur in cold climates. Unidirectional benefits were more prevalent than trade-offs: for example, species with large-diameter roots and high RTD were more commonly associated with dry climates, but species with the opposite trait values were not associated with wet climates. Directional selection for traits consistently occurred in cold or dry climates, whereas a diversity of root trait values were equally viable in warm or wet climates. Explicit integration of unidirectional benefits into ecological theory is needed to advance our understanding of the consequences of trait variation on species responses to environmental change.</p

PaleoClim, high spatial resolution paleoclimate surfaces for global land areas

High-resolution, easily accessible paleoclimate data are essential for environmental, evolutionary, and ecological studies. The availability of bioclimatic layers derived from climatic simulations representing conditions of the Late Pleistocene and Holocene has revolutionized the study of species responses to Late Quaternary climate change. Yet, integrative studies of the impacts of climate change in the Early Pleistocene and Pliocene – periods in which recent speciation events are known to concentrate – have been hindered by the limited availability of downloadable, user-friendly climatic descriptors. Here we present PaleoClim, a free database of downscaled paleoclimate outputs at 2.5-minute resolution (~5 km at equator) that includes surface temperature and precipitation estimates from snapshot-style climate model simulations using HadCM3, a version of the UK Met Office Hadley Centre General Circulation Model. As of now, the database contains climatic data for three key time periods spanning from 3.3 to 0.787 million years ago: the Marine Isotope Stage 19 (MIS19) in the Pleistocene (~787 ka), the mid-Pliocene Warm Period (~3.264–3.025 Ma), and MIS M2 in the Late Pliocene (~3.3 Ma)

ENM2020: A Free Online Course and Set of Resources on Modeling Species' Niches and Distributions

The field of distributional ecology has seen considerable recent attention, particularly surrounding the theory, protocols, and tools for Ecological Niche Modeling (ENM) or Species Distribution Modeling (SDM). Such analyses have grown steadily over the past two decades-including a maturation of relevant theory and key concepts-but methodological consensus has yet to be reached. In response, and following an online course taught in Spanish in 2018, we designed a comprehensive English-language course covering much of the underlying theory and methods currently applied in this broad field. Here, we summarize that course, ENM2020, and provide links by which resources produced for it can be accessed into the future. ENM2020 lasted 43 weeks, with presentations from 52 instructors, who engaged with >2500 participants globally through >14,000 hours of viewing and >90,000 views of instructional video and question-and-answer sessions. Each major topic was introduced by an "Overview" talk, followed by more detailed lectures on subtopics. The hierarchical and modular format of the course permits updates, corrections, or alternative viewpoints, and generally facilitates revision and reuse, including the use of only the Overview lectures for introductory courses. All course materials are free and openly accessible (CC-BY license) to ensure these resources remain available to all interested in distributional ecology

Marine Biodiversity in the Caribbean: Regional Estimates and Distribution Patterns

This paper provides an analysis of the distribution patterns of marine biodiversity and summarizes the major activities of the Census of Marine Life program in the Caribbean region. The coastal Caribbean region is a large marine ecosystem (LME) characterized by coral reefs, mangroves, and seagrasses, but including other environments, such as sandy beaches and rocky shores. These tropical ecosystems incorporate a high diversity of associated flora and fauna, and the nations that border the Caribbean collectively encompass a major global marine biodiversity hot spot. We analyze the state of knowledge of marine biodiversity based on the geographic distribution of georeferenced species records and regional taxonomic lists. A total of 12,046 marine species are reported in this paper for the Caribbean region. These include representatives from 31 animal phyla, two plant phyla, one group of Chromista, and three groups of Protoctista. Sampling effort has been greatest in shallow, nearshore waters, where there is relatively good coverage of species records; offshore and deep environments have been less studied. Additionally, we found that the currently accepted classification of marine ecoregions of the Caribbean did not apply for the benthic distributions of five relatively well known taxonomic groups. Coastal species richness tends to concentrate along the Antillean arc (Cuba to the southernmost Antilles) and the northern coast of South America (Venezuela – Colombia), while no pattern can be observed in the deep sea with the available data. Several factors make it impossible to determine the extent to which these distribution patterns accurately reflect the true situation for marine biodiversity in general: (1) highly localized concentrations of collecting effort and a lack of collecting in many areas and ecosystems, (2) high variability among collecting methods, (3) limited taxonomic expertise for many groups, and (4) differing levels of activity in the study of different taxa

The importance of understanding annual and shorter-term temperature patterns and variation in the surface levels of polar soils for terrestrial biota

Ground temperatures in the top few centimetres of the soil profile are key in many biological processes yet remain very poorly documented, especially in the polar regions or over longer timescales. They can vary greatly seasonally and at various spatial scales across the often highly complex and heterogeneous polar landscapes. It is challenging and often impossible to extrapolate soil profile temperatures from meteorological air temperature records. Furthermore, despite the justifiably considerable profile given to contemporary large-scale climate change trends, with the exception of some sites on Greenland, few biological microclimate datasets exist that are of sufficient duration to allow robust linkage and comparison with these large-scale trends. However, it is also clear that the responses of the soil-associated biota of the polar regions to projected climate change cannot be adequately understood without improved knowledge of how landscape heterogeneity affects ground and sub-surface biological microclimates, and of descriptions of these microclimates and their patterns and trends at biologically relevant physical and temporal scales. To stimulate research and discussion in this field, we provide an overview of multi-annual temperature records from 20 High Arctic (Svalbard) and maritime Antarctic (Antarctic Peninsula and Scotia Arc) sites. We highlight important features in the datasets that are likely to have influence on biology in polar terrestrial ecosystems, including (a) summer ground and sub-surface temperatures vary much more than air temperatures; (b) winter ground temperatures are generally uncoupled from air temperatures; (c) the ground thawing period may be considerably shorter than that of positive air temperatures; (d) ground and air freeze–thaw patterns differ seasonally between Arctic and Antarctic; (e) rates of ground temperature change are generally low; (f) accumulated thermal sum in the ground usually greatly exceeds air cumulative degree days. The primary purpose of this article is to highlight the utility and biological relevance of such data, and to this end the full datasets are provided here to enable further analyses by the research community, and incorporation in future wider comparative studies