bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complementarity, completeness and quality of long-term faunal archives in an Asian biodiversity hotspot
Authors: Turvey Samuel T. , Walsh Connor , Hansford James P. , Crees Jennifer J. , Bielby Jon , Duncan Clare , Hu Kaijin , Hudson Michael A. 
Published: November 2019

Long-term baselines on biodiversity change through time are crucial to inform conservation decision-making in biodiversity hotspots, but environmental archives remain unavailable for many regions. Extensive palaeontological, zooarchaeological and historical records and indigenous knowledge about past environmental conditions exist for China, a megadiverse country experiencing large-scale biodiversity loss, but their potential to understand past human-caused faunal turnover is not fully assessed. We investigate a series of complementary environmental archives to evaluate the quality of the Holocene–historical faunal record of Hainan Island, China's southernmost province, for establishing new baselines on postglacial mammalian diversity and extinction dynamics. Synthesis of multiple archives provides an integrated model of long-term biodiversity change, revealing that Hainan has experienced protracted and ongoing human-caused depletion of its mammal fauna from prehistory to the present, and that past baselines can inform practical conservation management. However, China's Holocene–historical archives exhibit substantial incompleteness and bias at regional and country-wide scales, with limited taxonomic representation especially for small-bodied species, and poor sampling of high-elevation landscapes facing current-day climate change risks. Establishing a clearer understanding of the quality of environmental archives in threatened ecoregions, and their ability to provide a meaningful understanding of the past, is needed to identify future conservation-relevant historical research priorities.
This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Differing climatic mechanisms control transient and accumulated vegetation novelty in Europe and eastern North America
Authors: Burke Kevin D. , Williams John W. , Brewer Simon , Finsinger Walter , Giesecke Thomas , Lorenz David J. , Ordonez Alejandro 
Published: November 2019

Understanding the mechanisms of climate that produce novel ecosystems is of joint interest to conservation biologists and palaeoecologists. Here, we define and differentiate transient from accumulated novelty and evaluate four climatic mechanisms proposed to cause species to reshuffle into novel assemblages: high climatic novelty, high spatial rates of change (displacement), high variance among displacement rates for individual climate variables, and divergence among displacement vector bearings. We use climate simulations to quantify climate novelty, displacement and divergence across Europe and eastern North America from the last glacial maximum to the present, and fossil pollen records to quantify vegetation novelty. Transient climate novelty is consistently the strongest predictor of transient vegetation novelty, while displacement rates (mean and variance) are equally important in Europe. However, transient vegetation novelty is lower in Europe and its relationship to climatic predictors is the opposite of expectation. For both continents, accumulated novelty is greater than transient novelty, and climate novelty is the strongest predictor of accumulated ecological novelty. These results suggest that controls on novel ecosystems vary with timescale and among continents, and that the twenty-first century emergence of novelty will be driven by both rapid rates of climate change and the emergence of novel climate states.
This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Anthropocene refugia: integrating history and predictive modelling to assess the space available for biodiversity in a human-dominated world
Authors: Monsarrat Sophie , Jarvie Scott , Svenning Jens-Christian 
Published: November 2019

During periods of strong environmental change, some areas may serve as refugia, where components of biodiversity can find protection, persist and potentially expand from should conditions again become favourable. The refugia concept has previously been used in the context of climatic change, to describe climatically stable areas in which taxa survived past Quaternary glacial–interglacial oscillations, or where they might persist in the future under anthropogenic climate change. However, with the recognition that Earth has entered the Anthropocene, an era in which human activities are the dominant driving force on ecosystems, it is critical to also consider human pressures on the environment as factors limiting species distributions. Here, we present a novel concept, Anthropocene refugia, to refer to areas that provide spatial and temporal protection from human activities and that will remain suitable for a given taxonomic unit in the long-term. It integrates a deep-time perspective on species biogeography that provides information on the natural rather than current-day relictual distribution of species, with spatial information on modern and future anthropogenic threats. We define the concept and propose a methodology to effectively identify and map realized and potential current and future refugia, using examples for two megafaunal species as a proof of concept. We argue that identifying Anthropocene refugia will improve biodiversity conservation and restoration by allowing better prediction of key areas for conservation and potential for re-expansions today and in the future. More generally, it forms a new conceptual framework to assess and manage the impact of anthropogenic activities on past, current and future patterns of species distributions.
This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
The Burramys Project: a conservationist's reach should exceed history's grasp, or what is the fossil record for?
Authors: Archer Michael , Bates Hayley , Hand Suzanne J. , Evans Trevor , Broome Linda , McAllan Bronwyn , Geiser Fritz , Jackson Stephen , Myers Troy , Gillespie Anna , Palmer Chris , Hawke Tahneal , Horn Alexis M. 
Published: November 2019

The fossil record provides important information about changes in species diversity, distribution, habitat and abundance through time. As we understand more about these changes, it becomes possible to envisage a wider range of options for translocations in a world where sustainability of habitats is under increasing threat. The Critically Endangered alpine/subalpine mountain pygmy-possum,Burramys parvus(Marsupialia, Burramyidae), is threatened by global heating. Using conventional strategies, there would be no viable pathway for stopping this iconic marsupial from becoming extinct. The fossil record, however, has inspired an innovative strategy for saving this species. This lineage has been represented over 25 Myr by a series of species always inhabiting lowland, wet forest palaeocommunities. These fossil deposits have been found in what is now the Tirari Desert, South Australia (24 Ma), savannah woodlands of the Riversleigh World Heritage Area, Queensland (approx. 24–15 Ma) and savannah grasslands of Hamilton, Victoria (approx. 4 Ma). This palaeoecological record has led to the proposal overviewed here to construct a lowland breeding facility with the goal of monitoring the outcome of introducing this possum back into the pre-Quaternary core habitat for the lineage. If this project succeeds, similar approaches could be considered for other climate-change-threatened Australian species such as the southern corroboree frog (Pseudophryne corroboree) and the western swamp tortoise (Pseudemydura umbrina).This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Addressing priority questions of conservation science with palaeontological data
Authors: Kiessling Wolfgang , Raja Nussaïbah B. , Roden Vanessa Julie , Turvey Samuel T. , Saupe Erin E. 
Published: November 2019

Palaeontologists often ask identical questions to those asked by ecologists. Despite this, ecology is considered a core discipline of conservation biology, while palaeontologists are rarely consulted in the protection of species, habitats and ecosystems. The recent emergence of conservation palaeobiology presents a big step towards better integration of palaeontology in conservation science, although its focus on historical baselines may not fully capture the potential contributions of geohistorical data to conservation science. In this essay we address previously defined priority questions in conservation and consider which of these questions may be answerable using palaeontological data. Using a statistical assessment of surveys, we find that conservation biologists and younger scientists have a more optimistic view of potential palaeontological contributions to the field compared to experienced palaeontologists. Participants considered questions related to climate change and marine ecosystems to be the best addressable with palaeontological data. As these categories are also deemed most relevant by ecologists and receive the greatest research effort in conservation, they are the natural choice for future academic collaboration.This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Using historical and palaeoecological data to inform ambitious species recovery targets
Authors: Grace Molly , Akçakaya H. Resit , Bennett Elizabeth , Hilton-Taylor Craig , Long Barney , Milner-Gulland E. J. , Young Richard , Hoffmann Michael 
Published: November 2019

Historical data are a valuable resource for addressing present-day conservation issues, for example by informing the establishment of appropriate recovery targets. However, while the recovery of threatened species is the end goal of many conservation programmes, data made available through the efforts of palaeoecologists and historical ecologists are rarely consulted. The proposal of a ‘Green List of Species’ by the International Union for Conservation of Nature (IUCN) will soon change this. The Green List of Species measures recovery against historical baselines; in particular, the method requires estimates of species range and abundance in previous centuries. In this paper, we present the case for why setting species recovery against a historical baseline is necessary to produce ambitious conservation targets, and we highlight examples from palaeoecology and historical ecology where fossil and archival data have been used to establish historical species baselines. Finally, we introduce Conservation Archive (https://conservationarchive.shinyapps.io/ConservationArchive/), a database of resources that can be used to infer baseline species conditions, and invite contributions to this database.This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Opening the Black Box of Artificial Intelligence for Clinical Decision Support: A Study Predicting Stroke Outcome
Authors: Zihni Esra , Madai Vince Istvan , Livne Michelle , Galinovic Ivana , Khalil Ahmed A. , Fiebach Jochen B. , Frey Dietmar 
Published: November 2019

AbstractBackgroundState-of-the-art machine learning (ML) artificial intelligence methods are increasingly leveraged in clinical predictive modeling to provide clinical decision support systems to physicians. Modern ML approaches such as artificial neural networks (ANNs) and tree boosting often perform better than more traditional methods like logistic regression. On the other hand, these modern methods yield a limited understanding of the resulting predictions. However, in the medical domain, understanding of applied models is essential, in particular, when informing clinical decision support. Thus, in recent years, interpretability methods for modern ML methods have emerged to potentially allow explainable predictions paired with high performance.MethodsTo our knowledge, we present in this work the first explainability comparison of two modern ML methods, tree boosting and multilayer perceptrons (MLPs), to traditional logistic regression methods using a stroke outcome prediction paradigm. Here, we used clinical features to predict a dichotomized 90 days post-stroke modified Rankin Scale (mRS) score. For interpretability, we evaluated clinical features’ importance with regard to predictions using deep Taylor decomposition for MLP, Shapley values for tree boosting and model coefficients for logistic regression.ResultsWith regard to performance as measured by AUC values on the test dataset, all models performed comparably: Logistic regression AUCs were 0.82, 0.82, 0.79 for three different regularization schemes; tree boosting AUC was 0.81; MLP AUC was 0.81. Importantly, the interpretability analysis demonstrated consistent results across models by rating age and stroke severity consecutively amongst the most important predictive features. For less important features, some differences were observed between the methods.ConclusionsOur analysis suggests that modern machine learning methods can provide explainability which is compatible with domain knowledge interpretation and traditional method rankings. Future work should focus on replication of these findings in other datasets and further testing of different explainability methods.
Mating enhances immune function of Drosophila melanogaster populations against bacterial pathogens
Authors: Bansal Nitin , Shit Biswajit , Aparajita  , Hegde Tejashwini , Dutta Rochishnu , Prasad Nagaraj Guru 
Published: November 2019

AbstractImmunity and reproduction are two important processes that affect fitness of an organisms. Sexual activity has been previously shown to determine the degree to which a population is able to survive various infections. While many studies have demonstrated a trade-off between immune function and reproduction, many studies have found synergistic relation between the two fitness determinants. Besides it is generally hypothesised that sexes may differ in immunity due to relative cost they incur during reproduction with males losing in immunity to rather increase their reproductive success. In this study, we test the effect of immune function on the survival of mated and virgin replicates of a large outbred baseline D. melanogaster population that was infected with four different bacterial infections. We find enhanced survival in mated flies than virgin flies in response to all four bacterial infections across all replicates. While investigating sexual dimorphism in immune function, we find no difference in sexes in their ability to survive the imposed bacterial infections. Synergistic interaction between reproduction and immunity may exist if it improves Darwinian fitness of either sexes of a population under selection, and are not necessarily limited by each other due to trade-off over finite resources.
Afrotropical Tree Communities May Have Distinct Responses to Forecasted Climate Change
Authors: Nuñez Chase L. , Clark James S. , Poulsen John R. 
Published: November 2019

AbstractMore refined knowledge of how tropical forests respond to changes in the abiotic environment and human disturbance is necessary to mitigating climate change, maintain biodiversity, and preserve ecosystem services. To evaluate the unique response of Afrotropical forests to changes in the abiotic environment and disturbance, we employ species inventories, remotely sensed historic climatic data, and future climate predictions collected from 104 1-ha plots in the central African country of Gabon. We forecast a 3 - 8% decrease in Afrotropical forest species richness by the end of the century, in contrast to the 30-50% loss of plant diversity predicted to occur with equivalent warming in the Neotropics. This work reveals that community forecasts are not generalizable across regions, and more representative studies are needed in understudied biomes like the Afrotropics. This study serves as an important counterpoint to work done in the Neotropics by providing contrasting predictions for Afrotropical forests with substantially different ecological, evolutionary, and anthropogenic histories.
Close relationship between coral-associated Chromera strains despite major differences within the Symbiodiniaceae
Authors: Mohamed Amin R. , Chan Cheong Xin , Ragan Mark A. , Zhang Jia , Cooke Ira , Ball Eldon E. , Miller David J. 
Published: November 2019

SummaryReef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress; as little as a 1°C increase often leading to collapse of the association. This sensitivity has led to interest in the potential of more stress tolerant algae to supplement or substitute for the normal Symbiodiniaceae mutualists. In this respect, the apicomplexan-like microalga Chromera is of particular interest due to its greater temperature tolerance. We generated a de novo transcriptome for a Chromera strain isolated from a GBR coral (“GBR Chromera”) and compared to those of the reference strain of Chromera (“Sydney Chromera”), and to those of Symbiodiniaceae (Fugacium, Cladocopium and Breviolum), as well as the apicomplexan parasite, Plasmodium falciparum. By contrast with the Symbiodiniaceae, the two Chromera strains had a high level of sequence similarity evident by very low levels of divergence in orthologous genes. Although KEGG categories provide few criteria by which true coral mutualists might be identified, they do supply a molecular rationalization for the ubiquitous association of Cladocopium strains with Indo-Pacific reef corals. The presence of HSP20 genes may underlie the higher thermal tolerance of Chromera.
High complexity and degree of genetic variation inBrettanomyces bruxellensispopulation
Authors: Gounot Jean-Sébastien , Neuvéglise Cécile , Freel Kelle C. , Devillers Hugo , Piškur Jure , Friedrich Anne , Schacherer Joseph 
Published: November 2019

AbstractGenome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype-phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms,Saccharomyces cerevisiaeandSchizosaccharomyces pombe. In this context, we sought to explore an uncharacterized yeast species,Brettanomyces bruxellensis, which is a major cause of wine spoilage but also can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53B. bruxellensisstrains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in theB. bruxellensisspecies. Genomes are punctuated by multiple loss-of-heterozygosity regions while aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared toS. cerevisiae. The pangenome is composed of 4,923 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.
Neuro-computational account of arbitration between imitation and emulation during human observational learning
Authors: Charpentier Caroline C. , Iigaya Kiyohito , O’Doherty John P. 
Published: November 2019

AbstractIn observational learning (OL), organisms learn from observing the behavior of others. There are at least two distinct strategies for OL. Imitation involves learning to repeat the previous actions of other agents, while in emulation, learning proceeds from inferring the goals and intentions of others. While putative neural correlates for these forms of learning have been identified, a fundamental question remains unaddressed: how does the brain decides which strategy to use in a given situation? Here we developed a novel computational model in which arbitration between the strategies is determined by the predictive reliability, such that control over behavior is adaptively weighted toward the strategy with the most reliable prediction. To test the theory, we designed a novel behavioral task in which our experimental manipulations produced dissociable effects on the reliability of the two strategies. Participants performed this task while undergoing fMRI in two independent studies (the second a pre-registered replication of the first). Behavior manifested patterns consistent with both emulation and imitation and flexibly changed between the two strategies as expected from the theory. Computational modelling revealed that behavior was best described by an arbitration model, in which the reliability of the emulation strategy determined the relative weights allocated to behavior for each strategy. Emulation reliability - the model’s arbitration signal - was encoded in the ventrolateral prefrontal cortex, temporoparietal junction and rostral cingulate cortex. Being replicated across two fMRI studies, these findings suggest a neuro-computational mechanism for allocating control between emulation and imitation during observational learning.
Variation in the life history strategy of cells underlies tumor’s functional diversity
Authors: Li Tao , Liu Jialin , Feng Jing , Liu Zhenzhen , Liu Sixue , Zhang Minjie , Zhang Yuezheng , Hou Yali , Wu Dafei , Li Chunyan , Chen Young-Bin , Wu Chung-I , Chen Hua , Lu Xuemei 
Published: November 2019

AbstractClassicalr- vs.K-selection theory describes the trade-offs between high reproductive output and competitiveness and guides research in evolutionary ecology1–5. While its impact has waned in the recent past, cancer evolution may rekindle it6–10. Indeed, solid tumors are an ideal theater forr- andK-selection and, hence, a good testing ground for ideas on life-history strategy evolution11,12. In this study, we imposer- orK-selection on HeLa cells to obtain strongly proliferative r cells and highly competitive K cells. RNA-seq analysis indicates that phenotypic trade-offs in r and K cells are associated with distinct patterns of expression of genes involved in the cell cycle, adhesion, apoptosis, and contact inhibition. Both empirical observations and simulations based on an ecological competition model show that the trade-off between cell proliferation and competitiveness can evolve adaptively and rapidly in naïve cell lines. It is conceivable that the contrasting selective pressure may operate in a realistic ecological setting of actual tumors. When the r and K cells are mixedin vitro, they exhibit strikingly different spatial and temporal distributions in the resultant cultures. Thanks to this niche separation, the fitness of the entire tumor increases. Our analyses of life-history trade-offs are pertinent to evolutionary ecology as well as cancer biology.