Frédérik Saltré

Climate refugia: joint inference from fossil records, species distribution models and phylogeography

Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining biodiversity through the glacial-interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia - fossil records, species distribution models and phylogeographic surveys - in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths, limitations and new advances for these three approaches. We provide case studies to illustrate their combined application, and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with European beech, Qinghai spruce and Douglas-fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance, in particular by elucidating the fine-scale processes and the particular geographic locations that buffer species against rapidly changing climate.

Climate change not to blame for late Quaternary megafauna extinctions in Australia

Late Quaternary megafauna extinctions impoverished mammalian diversity worldwide. The causes of these extinctions in Australia are most controversial but essential to resolve, because this continent-wide event presaged similar losses that occurred thousands of years later on other continents. Here we apply a rigorous metadata analysis and new ensemble-hindcasting approach to 659 Australian megafauna fossil ages. When coupled with analysis of several high-resolution climate records, we show that megafaunal extinctions were broadly synchronous among genera and independent of climate aridity and variability in Australia over the last 120,000 years. Our results reject climate change as the primary driver of megafauna extinctions in the worlds most controversial context, and instead estimate that the megafauna disappeared Australia-wide ∼13,500 years after human arrival, with shorter periods of coexistence in some regions. This is the first comprehensive approach to incorporate uncertainty in fossil ages, extinction timing and climatology, to quantify mechanisms of prehistorical extinctions.

Modelling range dynamics under global change: which framework and why?

Summary To conserve future biodiversity, a better understanding of the likely effects of climate and land-use change on the geographical distributions of species and the persistence of ecological communities is needed. Recent advances have integrated population dynamic processes into species distribution models (SDMs), to reduce potential biases in predictions and to better reflect the demographic nuances of incremental range shifts. However, there is no clear framework for selecting the most appropriate demographic-based model for a given data set or scientific question. We review the computer-based modelling platforms currently used for the development of either population- or individual-based species range dynamics models. We describe the features and requirements of 20 software platforms commonly used to generate simulations of species ranges and abundances. We classify the platforms according to particular capabilities or features that account for user requirements and constraints, such as (i) ability to simulate simple to complex population dynamics, (ii) organism specificity or (iii) their computational capacities. Using this classification, we develop a protocol for choosing the most appropriate framework for modelling species range dynamics based in data availability and research requirements. We find that the main differences between modelling platforms are related to the way in which they simulate population dynamics, the type of organisms they are able to model and the ecological processes they incorporate. We show that some platforms can be used as generic modelling software to investigate a broad range of ecological questions related to the range dynamics of most species, and how these are likely to change in the future in response to forecast climate and land-use change. We argue that model predictions will be improved by reducing usage to a smaller number of highly flexible freeware platforms. Our approach provides ecologists and conservation biologists with a clear method for selecting the most appropriate software platform that meets their needs when developing SDMs coupled with population-dynamic processes. We argue that informed tool choice will translate to better predictions of species responses to climate and land-use change and improved conservation management.

How climate, migration ability and habitat fragmentation affect the projected future distribution of European beech

Recent efforts to incorporate migration processes into species distribution models (SDMs) are allowing assessments of whether species are likely to be able to track their future climate optimum and the possible causes of failing to do so. Here, we projected the range shift of European beech over the 21st century using a process-based SDM coupled to a phenomenological migration model accounting for population dynamics, according to two climate change scenarios and one land use change scenario. Our model predicts that the climatically suitable habitat for European beech will shift north-eastward and upward mainly because (i) higher temperature and precipitation, at the northern range margins, will increase survival and fruit maturation success, while (ii) lower precipitations and higher winter temperature, at the southern range margins, will increase drought mortality and prevent bud dormancy breaking. Beech colonization rate of newly climatically suitable habitats in 2100 is projected to be very low (1-2% of the newly suitable habitats colonised). Unexpectedly, the projected realized contraction rate was higher than the projected potential contraction rate. As a result, the realized distribution of beech is projected to strongly contract by 2100 (by 36-61%) mainly due to a substantial increase in climate variability after 2050, which generates local extinctions, even at the core of the distribution, the frequency of which prevents beech recolonization during more favourable years. Although European beech will be able to persist in some parts of the trailing edge of its distribution, the combined effects of climate and land use changes, limited migration ability, and a slow life-history are likely to increase its threat status in the near future.

What caused extinction of the pleistocene megafauna of sahul

During the Pleistocene, Australia and New Guinea supported a rich assemblage of large vertebrates. Why these animals disappeared has been debated for more than a century and remains controversial. Previous synthetic reviews of this problem have typically focused heavily on particular types of evidence, such as the dating of extinction and human arrival, and have frequently ignored uncertainties and biases that can lead to misinterpretation of this evidence. Here, we review diverse evidence bearing on this issue and conclude that, although many knowledge gaps remain, multiple independent lines of evidence point to direct human impact as the most likely cause of extinction.

High-quality fossil dates support a synchronous, Late Holocene extinction of devils and thylacines in mainland Australia

The last large marsupial carnivores—the Tasmanian devil (Sarcophilis harrisii) and thylacine (Thylacinus cynocephalus)—went extinct on mainland Australia during the mid-Holocene. Based on the youngest fossil dates (approx. 3500 years before present, BP), these extinctions are often considered synchronous and driven by a common cause. However, many published devil dates have recently been rejected as unreliable, shifting the youngest mainland fossil age to 25 500 years BP and challenging the synchronous-extinction hypothesis. Here we provide 24 and 20 new ages for devils and thylacines, respectively, and collate existing, reliable radiocarbon dates by quality-filtering available records. We use this new dataset to estimate an extinction time for both species by applying the Gaussian-resampled, inverse-weighted McInerney (GRIWM) method. Our new data and analysis definitively support the synchronous-extinction hypothesis, estimating that the mainland devil and thylacine extinctions occurred between 3179 and 3227 years BP.

A comprehensive database of quality-rated fossil ages for Sahul's Quaternary vertebrates.

The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.

Where to Dig for Fossils: Combining Climate-Envelope, Taphonomy and Discovery Models

Fossils represent invaluable data to reconstruct the past history of life, yet fossil-rich sites are often rare and difficult to find. The traditional fossil-hunting approach focuses on small areas and has not yet taken advantage of modelling techniques commonly used in ecology to account for an organism’s past distributions. We propose a new method to assist finding fossils at continental scales based on modelling the past distribution of species, the geological suitability of fossil preservation and the likelihood of fossil discovery in the field, and apply it to several genera of Australian megafauna that went extinct in the Late Quaternary. Our models predicted higher fossil potentials for independent sites than for randomly selected locations (mean Kolmogorov-Smirnov statistic = 0.66). We demonstrate the utility of accounting for the distribution history of fossil taxa when trying to find the most suitable areas to look for fossils. For some genera, the probability of finding fossils based on simple climate-envelope models was higher than the probability based on models incorporating current conditions associated with fossil preservation and discovery as predictors. However, combining the outputs from climate-envelope, preservation, and discovery models resulted in the most accurate predictions of potential fossil sites at a continental scale. We proposed potential areas to discover new fossils of Diprotodon, Zygomaturus, Protemnodon, Thylacoleo, and Genyornis, and provide guidelines on how to apply our approach to assist fossil hunting in other continents and geological settings.

Supplementary Table 1 from High-quality fossil dates support a synchronous, Late Holocene extinction of devils and thylacines in mainland Australia

Details of new and previously published ages of mainland thylacines and devils analysed in this study