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27 results for “extinction prediction”
Data and Scripts from: Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa
<p>Morphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Futhermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals, and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa, but yields new insights about the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet, but serves as a general framework for predicting multivariate ecology from phenotypic traits.</p>
Data and code of "Post-trauma behavioral phenotype predicts the degree of vulnerability to fear relapse after extinction in male rats"
<p>This dataset contains behavioral and transcriptomic data, and the original code related to the following article:</p> <p>Post-trauma behavioral phenotype predicts the degree of vulnerability to fear relapse after extinction in male rats. Fanny Demars, Ralitsa Todorova, Gabriel Makdah, Antonin Forestier, Marie-Odile Krebs, Bill P Godsil, Thérèse M Jay, Sidney I Wiener, & Marco N Pompili (2022) Current Biology <em>32. https://doi.org/10.1016/j.cub.2022.05.050</em></p>
Code and data for "Global warming generates predictable extinctions of warm- and cold-water marine benthic invertebrates via thermal habitat loss"
<pre>This repository contains the following information: Datasets S1 to S4 can all be loaded, manipulated, and analysed in R using script provided in Data S5 to obtain the results of the paper, Reddin et al. 2022, "Global warming generates predictable extinctions of warm and cold-water marine benthic invertebrates via thermal habitat loss". Data S1. (separate file) The original downloaded PaleoDB dataset. Data S2. (separate file) The pre-prepared dataset of occurrences. Data S3. (separate file) The finished environmental dataset. Data S4. (separate file) Additional environmental dataset. Data S5. (separate file) The R-code for the main analysis. Data S6. (compressed directory) Output data and code from the simulations. Table S7 (separate file). List of data source publications for PaleoDB data used in our study. Listed are the data source author list (ref_author), year (ref_pubyr), and reference number as appears in the PaleoDB (reference_no). </pre>
Data from: Evolvability predicts evolutionary divergence in extant and extinct species
Heritable variation is a prerequisite for evolutionary change. Yet, whether genetic potential for microevolution is relevant on macroevolutionary timescales is debated. Here we show that evolutionary divergence among populations, and to a lesser extent among species, increases with microevolutionary evolvability in both extant and extinct taxa. We evaluate and reject a number of hypotheses put forward to explain this relationship and propose that an effect of evolvability on population and species divergence can be explained by the influence of genetic constraints on population's ability to track rapid stationary environmental fluctuations.
Data and Scripts from: Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa
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Bushmeat yields, species extinction rates and ecosystem-level impacts of bushmeat harvesting as predicted by the Madingley General Ecosystem Model
<p>The datasets contain data generated using the Madingley General Ecosystem Model for experiments decribed in the paper: "T. Barychka, G.M.Mace and D.W.Purves (2021) The Madingley General Ecosystem Model predicts bushmeat yields, species extinction rates and ecosystem-level impacts of bushmeat harvesting. Oikos."</p> <p>The Madingley General Ecosystem Model was used to generate predictions of bushmeat yields, extinction rates and broader ecosystem impacts for a range of harvesting intensities of duiker-sized endothermic herbivores. Duiker antelope (such as <i>Cephalophus callipygus</i> and <i>Cephalophus dorsalis</i>) are the most heavily hunted species in sub-Saharan Africa, contributing 34%-95% of all bushmeat in the Congo Basin. In the Madingley, the harvested group was described as "Heterotroph – Herbivore – Terrestrial – Mobile – Iteroparous– Endotherm", with adult bodymasses of 13-21 kg and juvenile bodymasses of >100 g. Harvesting period was set at 30 years (<em>n </em>=30).</p> <p>In the first experiment, we used the Madingley model to predict bushmeat yields ("Harvested Biomasses") and extinction rates ("Density") from harvesting duiker-sized herbivores using proportional harvesting strategy, with harvest rates ranging from 0 to 0.90. These were compared to the estimates of bushmeat yields and survival probabilities for two duiker antelope species (<i>Cephalophus callipygus</i> and <i>Cephalophus dorsalis) </i>from conventional single-species Beverton-Holt model. </p> <p>In the second experiment, we used the Madingley model to generate data on the state ("State") of the harvested ecosystem. The datasets contain estimates of biomasses, abundances, adult and juvenile bodymasses, etc. of the harvested duiker-sized herbivores as well as unharvested herbivores, omnivores and carnivores present in the simulated ecosystem. In the paper we focused on abundances; however, other estimates e.g., adult bodymasses can be used to conduct further studies on the effects of harvesting in tropical ecosystems.</p> <p>Main results of the experiments are that: 1) the Madingley model gave estimates for optimal harvesting rate, and extinction rate, that were qualitatively and quantitatively similar to the estimates from conventional single-species Beverton-Holt model; 2) the Madingley model predicted a background local extinction probability for the target species of at least 10%; 3) at medium and high levels of harvesting of duiker-sized herbivores, the Madingley model predicted statistically significant, but moderate, reductions in the densities of the targeted functional group; increases in small-bodied herbivores; decreases in large-bodied carnivores; and minimal ecosystem-level impacts overall.</p>
Bushmeat yields, species extinction rates and ecosystem-level impacts of bushmeat harvesting as predicted by the Madingley General Ecosystem Model
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Data supporting the article "Replication of extinction retrieval prediction by prefrontal reactivations and non-replication of L-DOPA effects on retrieval and reactivations in males"
<p>These datasets contain sAA, sCORT, US expectancy, questionnaire and rating raw data generated in this replication study. Furthermore, the processed MRI data (vmPFC reactivations) and derived SCR data are available. The custom-made analysis script for scoring SCR can be run on Matlab 2015b.</p>
Geographic range size, water temperature and extrinsic threats predict the extinction risk in global cetaceans
<p><span>Despite that cetaceans provide significant ecological contributions to the health and stability of aquatic ecosystems, they are highly endangered with nearly one-third of species assessed as threatened with extinction. Nevertheless, to date, few studies have explicitly examined the patterns and processes of extinction risk and threats for this taxon, and even less between the two subclades (Mysticeti and Odontoceti). To fill this gap, we compiled a dataset of six intrinsic traits (active region, geographic range size, body weight, diving depth, school size and reproductive cycle), six environmental factors relating to sea surface temperature and chlorophyll concentration, and two human-related threat indices that are commonly recognized for cetaceans. We then employed phylogenetic generalized least square (PGLS) models and model selection to identify the key predictors of extinction risk in all cetaceans, as well as in the two subclades. We found that geographic range size, sea surface temperature and human threat index were the most important predictors of extinction risk in all cetaceans and in odontocetes. Interestingly, maximum body weight was positively associated with the extinction risk in mysticetes, but negatively related to that for odontocetes. By linking seven major threat types to extinction risk, we further revealed that fisheries bycatch was the most common threat, yet the impacts of certain threats could be overestimated when considering all species rather than just threatened ones. Overall, we suggest that conservation efforts should focus on small-ranged cetaceans and species living in warmer waters or under strong anthropogenic pressures. Moreover, further studies should consider the extinction risk of species when superimposing risk maps and quantifying risk severity. Finally, we emphasize that mysticetes and odontocetes should be conserved with different strategies, because their extinction risk patterns and major threat types are </span><span>considerably</span><span> different. For instance, large-bodied mysticetes and small-ranged odontocetes require special conservation priority.</span></p>
Data from: Assessing bite force estimates in extinct mammals and archosaurs using phylogenetic predictions
Bite force is an ecologically important biomechanical performance measure is informative in inferring the ecology of extinct taxa. However, biomechanical modelling to estimate bite force is associated with some level of uncertainty. Here, I assess the accuracy of bite force estimates in extinct taxa using a Bayesian phylogenetic prediction model. I first fitted a phylogenetic regression model on a training set comprising extant data. The model predicts bite force from body mass and skull width while accounting for differences owning to biting position. The posterior predictive model has a 93% prediction accuracy as evaluated through leave-one-out cross-validation. I then predicted bite force in 37 species of extinct mammals and archosaurs from the posterior distribution of predictive models. Biomechanically estimated bite forces fall within the posterior predictive distributions for all except four species of extinct taxa and are thus as accurate as that predicted from body size and skull width, given the variation inherent in extant taxa and the amount of time available for variance to accrue. Biomechanical modelling remains a valuable means to estimate bite force in extinct taxa and should be reliably informative of functional performances and serve to provide insights into past ecologies.
Data from: Niche width predicts extinction from climate change and vulnerability of tropical species
<p>Climate change may be a major threat to global biodiversity, especially to tropical species. Yet, why tropical species are more vulnerable to climate change remains unclear. Tropical species are thought to have narrower physiological tolerances to temperature, and they have already experienced a higher estimated frequency of climate-related local extinctions. These two patterns suggest that tropical species are more vulnerable to climate change because they have narrower thermal niche widths. However, no studies have tested whether species with narrower climatic niche widths for temperature have experienced more local extinctions, and if these narrower niche widths can explain the higher frequency of tropical local extinctions. Here, we test these ideas using resurvey data from 538 plant and animal species from 10 studies. We found that mean niche widths among species and the extent of climate change (increase in maximum annual temperatures) together explained most variation (>75%) in the frequency of local extinction among studies. Surprisingly, neither latitude nor occurrence in the tropics alone significantly predicted local extinction among studies, but latitude and niche widths were strongly inversely related. Niche width also significantly predicted local extinction among species, as well as among and (sometimes) within studies. Overall, niche width may offer a relatively simple and accessible predictor of the vulnerability of populations to climate change. Intriguingly, niche width has the best predictive power to explain extinction from global warming when it incorporates coldest yearly temperatures.</p>
Data from: Can body mass and skull morphology predict seed and fruit ingestion potential for mammal species? A test using extant species and its application to extinct species
<p>Larger animals are assumed to ingest larger seeds and consume larger fruits, but empirical studies reveal inconsistent trends between body mass and the average size of fruits and seeds ingested. Further, no studies have explored seed size relationships with morphological traits, such as skull dimensions. Such characteristics might provide more reliable estimates of ingestion ability and allow for accurate predictions of seed dispersal capacity in species for which we lack empirical data, especially extinct species. To determine whether (i) mammalian skull dimensions are better predictors of the maximum size of ingested seeds and fruits, compared to body mass and (ii) body mass are the better predictors of mean fruit and seed sizes, we studied these relationships across three mammalian orders: Chiroptera, Primates, and Carnivora.</p> <p>We collected novel data on skull dimensions and collated available data on body mass and maximum and mean sizes of ingested fruits and seeds for mammals (N=100) across the Neotropics, Asia, Africa, and Madagascar. We explored the relationships between anatomical traits and fruit and seed sizes of extant species and made predictions for five extinct species.</p> <p>Our results revealed that body mass and skull dimensions are essential determinants of ingested fruit and seed size in mammals. The latter traits can generate predictions for extinct species, especially coronoid height and maximum jaw gape. Nevertheless, body mass predicted larger ingested fruits and seeds than skull dimensions and explained a greater part of the variance for both maximum and mean sizes in our dataset.</p> <p>Our results show how body mass and cranial anatomy constrain seed size and reinforce the importance of maintaining functional diversity in seed dispersers to maintain tropical forest structure. We also show that scientists can use morphological characteristics to predict the seed dispersal potential of extinct mammals allowing better inferences on past and future consequences of frugivore extinctions within tropical forests.</p>
Data from: Biting mechanics determines craniofacial morphology among extant diprotodont herbivores: dietary predictions for the giant extinct short-faced kangaroo, Simosthenurus occidentalis.
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Data from: Climate change predicts Quaternary extinctions and extant genetic diversity in a threatened Australian lizard
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Data from: Can body mass and skull morphology predict seed and fruit ingestion potential for mammal species? A test using extant species and its application to extinct species
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Geographic range size, water temperature and extrinsic threats predict the extinction risk in global cetaceans
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Data from: Niche width predicts extinction from climate change and vulnerability of tropical species
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Data from: Assessing bite force estimates in extinct mammals and archosaurs using phylogenetic predictions
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Biological traits of seabirds predict extinction risk and vulnerability to anthropogenic threats
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Data from: Sexual traits are sensitive to genetic stress and predict extinction risk in the stalk-eyed fly, Diasemopsis meigenii
The handicap principle predicts that sexual traits are more susceptible to inbreeding depression than nonsexual traits. However, this hypothesis has received little testing and results are inconsistent. We used 11 generations of full-sibling mating to test the effect of inbreeding on sexual and nonsexual traits in the stalk-eyed fly Diasemopsis meigenii. Consistent with the theoretical predictions, the male sexual trait (eyespan) decreased more than nonsexual traits (female eyespan and male wing length), even after controlling for body size variation. In addition, male eyespan was a reliable predictor of line extinction, unlike other nonsexual traits. After 11 generations, inbred lines were crossed to generate inbred and outbred families. All morphological traits were larger in outbred individuals than inbred individuals. This heterosis was greater in male eyespan than in male wing length, but not female eyespan. The elevated response in male eyespan to genetic stress mirrored the result found using environmental stress during larval development and suggests that common mechanisms underlie the patterns observed. Overall, these results support the hypothesis that male sexual traits suffer more from inbreeding depression than nonsexual traits and are in line with predictions based on the handicap principle.
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