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53 results for “extinction selectivity”
Data from: An extinction event in planktonic Foraminifera preceded by stabilizing selection
Unless they adapt, populations facing persistent stress are threatened by extinction. Theoretically, populations facing stress can react by either disruption (increasing trait variation and potentially generating new traits) or stabilization (decreasing trait variation). In the short term, stabilization is more economical, because it quickly transfers a large part of the population closer to a new ecological optimum. However, canalization is deleterious in the face of persistently increasing stress, because it reduces variability and thus decreases the ability to react to further changes. Understanding how natural populations react to intensifying stress reaching terminal levels is key to assessing their resilience to environmental change such as that caused by global warming. Because extinctions are hard to predict, observational data on the adaptation of populations facing extinction are rare. Here, we make use of the glacial salinity rise in the Red Sea as a natural experiment allowing us to analyse the reaction of planktonic Foraminifera to stress escalation in the geological past. We analyse morphological trait state and variation in two species across a salinity rise leading to their local extinction. One species reacted by stabilization in shape and size, detectable several thousand years prior to extinction. The second species reacted by trait divergence, but each of the two divergent populations remained stable or reacted by further stabilization. These observations indicate that the default reaction of the studied Foraminifera is canalization, and that stress escalation did not lead to the emergence of adapted forms. An inherent inability to breach the global adaptive threshold would explain why communities of Foraminifera and other marine protists reacted to Quaternary climate change by tracking their zonally shifting environments. It also means that populations of marine plankton species adapted to response by migration will be at risk of extinction when exposed to stress outside of the adaptive range.
Heterogeneous selectivity and morphological evolution of marine clades during the Permian-Triassic mass extinction
<p>This is a supplementary repository, including the dataset and codes we used in this manuscript. we developed a new method, called DeepMorph to analyze the morphological evolution of six marine clades (i.e., ammonoids, bivalves, brachiopods, gastropods, ostracods, and conodonts ) during the Permian-Triassic mass extinction events. The taxonomy dataset was uploaded and contains 599 genera and 656 images, spanning from the latest Permian (Changhsingian) to the earliest Triassic (Induan). </p>
Text-fig. 3. Phylogenetic relationship of Peignecyon felinoides n. gen. et n. sp., within some selected Amphicyonidae, and some extinct caniform carnivorans. Paramiacis exilis is the outgroup. Searches were performed by means of the Branch and Bound and a Bootstrap analysis through 1,000 replicates. One tree is obtained (length 73 steps, consistency index (CI) = 0.6301, retention index (RI) = 0.7000). The numbers below nodes are Bremer indices, and the numbers above nodes are Bootstrap support percentages (only shown ≥ 50). in A New Thaumastocyoninae (Amphicyonidae, Carnivora) From The Early Miocene Of Tuchořice, The Czech Republic
Text-fig. 3. Phylogenetic relationship of Peignecyon felinoides n. gen. et n. sp., within some selected Amphicyonidae, and some extinct caniform carnivorans. Paramiacis exilis is the outgroup. Searches were performed by means of the Branch and Bound and a Bootstrap analysis through 1,000 replicates. One tree is obtained (length 73 steps, consistency index (CI) = 0.6301, retention index (RI) = 0.7000). The numbers below nodes are Bremer indices, and the numbers above nodes are Bootstrap support percentages (only shown ≥ 50).
Reduced strength and increased variability of extinction selectivity during mass extinctions
<p>Two of the traits most often observed to correlate with extinction risk in marine animals are geographic range and body size. However, the relative effects of these two traits on extinction risk has not been investigated systematically for either background times or during mass extinctions. To close this knowledge gap, we measure and compare extinction selectivity of geographic range and body size of genera within five classes of benthic marine animals across the Phanerozoic using capture-mark-recapture models. During background intervals, narrow geographic range is strongly associated with greater extinction probability, whereas smaller body size is more weakly associated with greater extinction probability. During mass extinctions, the association between geographic range and extinction probability is reduced in every class and fully eliminated in some, whereas the association between body size and extinction probability varies in strength and direction across classes. While geographic range is universally the stronger predictor of survival during background intervals, variation among classes during mass extinction suggests a fundamental shift in extinction processes during these global catastrophes.</p>
Reduced strength and increased variability of extinction selectivity during mass extinctions
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Data from: An extinction event in planktonic Foraminifera preceded by stabilizing selection
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Selective extinctions resulting from random habitat destruction lead to under‐estimates of local and regional biodiversity loss in a manipulative field experiment
<p>Land-use change is a significant cause of anthropogenic extinctions, which are likely to continue and accelerate as habitat conversion proceeds in most biomes. One way to understand the effects of habitat loss on biodiversity is through improved tools for predicting the number and identity of species losses in response to habitat loss. There are relatively few methods for predicting extinctions and even fewer opportunities for rigorously assessing the quality of these predictions. In this paper we address these issues by applying a new method based on rarefaction to predict species losses after random, but aggregated, habitat loss. We compare predictions from three rarefaction models, individual-based, sample-based, and spatially-clustered, to those derived from a commonly-used extinction estimation method, the Species-Area Relationship (SAR). We apply each method to a mesocosm experiment, in which we aim to predict species richness and extinctions of arthropods immediately following 50% habitat loss. While each model produced strikingly accurate predictions of species richness immediately after the habitat loss disturbance, each model significantly underestimated the number of extinctions occurring at both the local (within-mesocosm) and regional (treatment-wide) scales. Despite the stochastic nature of our small-scale, short-term, and randomly applied habitat loss experiment, we found surprisingly clear evidence for extinction selectivity, for example when abundant species with low extinction probabilities were extirpated following habitat loss. The important role played by selective extinction even in this contrived experimental system suggests that ecologically driven, trait-based extinctions play an equally important role to stochastic extinction, even when the disturbance itself has no clear selectivity. As a result, neutrally stochastic null models such as the SAR and rarefaction are likely to underestimate extinctions caused by habitat loss. Nevertheless, given the difficulty of predicting extinctions, null models provide useful benchmarks for conservation planning by providing minimum estimates and probabilities of species extinctions.</p>
Data from: When are extinctions simply bad luck? rarefaction as a framework for disentangling selective and stochastic extinctions
1. A key challenge in conservation biology is that not all species are equally likely to go extinct when faced with a disturbance. Traditionally, differences in species extinction risk are considered a form of extinction selectivity, a nanrondom process by which species' extinction risks are associated with their traits. While selectivity clearly contributes to varation in extinction among taxa, it is also clear that rare species are more likely to go extinct than are common species. While obvious, this law of extinction suggests that random chance, operating on species abundance, plays an important role in the extinction process. Unless ecologists and conservation biologists can disentangle random and nonrandom extinction processes, then the prediction and prevention of future extinctions will continue to be an elusive challenge. 2. We suggest that a modified version of a common null model procedure, rarefaction, can be used to disentangle the influence of stochastic species loss from selective nonrandom processes. To this end we applied a rarefaction based null model to three published data sets to characterize the influence of species rarity in driving biodiversity loss following three disturbance events: i) disease-associated bat declines; ii) disease-associated amphibian declines; and iii) habitat loss and invasive species-associated gastropod declines. For each case study, we used rarefaction to generate null expectations of stochastic biodiversity loss and species-specific extinction probabilities. 3. In each of our case studies we find evidence for random and nonrandom (selective) extinctions. Our findings highlight the importance of explicitly considering that some species extinctions are the result of stochastic processes, i.e., bad luck. 4. Policy Implications If there is a first law of extinction, it is that rare species are most likely than common species to go extinct. We suggest that taking this law into account in analyses of extinction risk is critical to the identification of selective extinctions. Our results suggest that rarefaction can be used to identify nonrandom decline, extirpation, and extinction events and provide an important baseline comparison point for future extinction analyses.12-Jul-2019
Data from: Machine learning identifies ecological selectivity patterns across the end-Permian mass extinction
<p>The end-Permian mass extinction occurred alongside a large swathe of environmental changes that are often invoked as extinction mechanisms, even when a direct link is lacking. One way to elucidate the cause(s) of a mass extinction is to investigate extinction selectivity as it can reveal critical information on organismic traits as key determinants of extinction and survival. Here we show that machine learning algorithms, specifically gradient boosted decision trees, can be used to identify determinants of extinction as well as predict extinction risk. To understand which factors led to the end-Permian mass extinction during an extreme global warming event, we quantified the ecological selectivity of marine extinctions in the well-studied South China region. We find that extinction selectivity varies between different groups of organisms and that a synergy of multiple environmental stressors best explains the overall end-Permian extinction selectivity pattern. Extinction risk was greater for genera that had a low species richness, had narrow bathymetric ranges limited to deep-water habitats, had a stationary mode of life, possessed a siliceous skeleton or, less critically, had calcitic skeletons. These selective losses directly link the extinction to the environmental effects of rapid injections of carbon dioxide into the ocean-atmosphere system, specifically the combined effects of expanded oxygen minimum zones, rapid warming, and potentially ocean acidification.</p>
Data from: Extinction selectivity obscures patterns of trait-dependent endangerment in Columbiformes
<p>Understanding how extinction has occurred in the recent past is crucial to unravel its main drivers as well as to implement effective conservation practices to minimize global biodiversity loss. It has long been hypothesized that extinction risk is not randomly distributed among traits of species. However, the actual traits making species more prone to extinction may have been overlooked because already extinct species are often not considered in comparative analyses of extinction risk. We characterized the drivers of extinction in a cosmopolitan bird clade, including Holocene and contemporary extinctions potentially related to human impacts, and provided evidence of an 'extinction selectivity' in species traits. We constructed a new phylogenetic hypothesis of the Columbiformes, a cosmopolitan bird clade consisting of 33 recently extinct and 351 extant species. Then, we integrated data on geography, behaviour, and morphology to reveal the drivers of extinction risk. We used phylogenetic generalized least square models to test the effect of geography, behaviour, and morphology on the risk of extinction and identified differences in the drivers of extinction when including vs. excluding recently extinct species. Our analysis revealed that Columbiformes endemic from islands with ground-foraging habits, weak flying abilities, migratory behaviour, and larger body sizes are more vulnerable to extinction. Our results also show that excluding recently extinct species identifies extinction drivers differently from those when including recently extinct species. Only by accurately identifying the traits that increase extinction risk can we develop targeted conservation measures that promote the long-term persistence of threatened species. Extinction selectivity has important implications for the conservation of biological communities and ultimately ecosystem functioning, considering the critical role Columbiformes often play as seed dispersers.</p>
Respiratory protein-driven selectivity during the Permian–Triassic mass extinction
<p><strong>Fossil occurrence data</strong></p> <p>Fossil data used to calculate diversity variation were obtained from a previously published database of Permian‒Triassic marine fossils (Song et al., 2018; Song et al., 2020). The database contains 52,322 occurrences at the generic level from 1,768 published papers and the Paleobiology Database, spanning the Late Permian Changhsingian to the Late Triassic Rhaetian (Data 1). Our analysis is based on the occurrences of genera, as taphonomy prevents species-level identifications. Within the considered interval, a total of 1,097 genera belong to 13 major clades, including two clades of protozoa (foraminifera and radiolarians), nine clades of invertebrates (corals, sponges, brachiopods, bryozoans, ostracods, cephalopods, gastropods, bivalves, and echinoderms), and two clades of vertebrates (conodonts and fishes). For marine arthropods, we used only ostracod data because ostracods are abundant in the fossil record during the late Permian. Other marine arthropods are very rare in this time interval. For example, only two genera of trilobite, one genus of chelicera, and one genus of decapod are recorded in the Changhsingian bin compared to > 100 genera of ostracods in the Paleobiology Database. We did not consider background extinction in the Late Permian because many studies have shown that the background extinction rate of marine taxa in the Changhsingian is negligible compared to the mass extinction interval around the Permian‒Triassic boundary (Yin et al., 2007; Shen et al., 2011; Song et al., 2013; Fan et al., 2020). Therefore, the results using the Changhsingian and Induan fossil data reflect a selectivity pattern of the Permian‒Triassic mass extinction rather than background extinction.</p> <p> </p> <p><strong>Body size data</strong></p> <p>We used the comprehensive database of Schaal et al. (2016) to assign body size expressed as the maximum length for each species. Using the maximum size for each taxon is a common approach for body size studies, as the effects of juvenile specimens in the database can be avoided (Stanley, 1973; Jablonski, 1997; Lockwood, 2005; Heim et al., 2015; Payne et al., 2016; Schaal et al., 2016). We followed the same methods to compile additional data for taxa not included in this database. A number of recently published databases were used to compile the size data, including references (Romano et al., 2016; Shi et al., 2016; Foster et al., 2018; Chen et al., 2019; Feng et al., 2020; Foster et al., 2020). Other size data were mainly obtained from the published taxonomic literature (see Data 2). Only common taxa from both Changhsingian and Induan are included because these taxa have abundant fossil data to study their size change during the Permian-Triassic interval, i.e., foraminifera, brachiopods, ostracods, gastropods, cephalopods, bivalves, conodonts, and fishes. Other taxa including corals, sponges, radiolarians, bryozoans, and echinoderms are absent/very rare in the Induan bin (see Data 1), and accordingly are not included in this study. The Changhsingian and Induan body size dataset is composed of 1495 species in 635 genera belonging to eight common clades.</p> <p> </p> <p>Other data were obtained from the above fossil occurrence and body size datasets.</p> <p> </p> <p><strong>References</strong></p> <p>Chen, J., Song, H., He, W., Tong, J., Wang, F., Wu, S., 2019. Size variation of brachiopods from the Late Permian through the Middle Triassic in South China: Evidence for the Lilliput Effect following the Permian-Triassic extinction. Palaeogeography, Palaeoclimatology, Palaeoecology, 519: 248–257.</p> <p>Fan, J.-x., Shen, S.-z., Erwin, D.H., Sadler, P.M., MacLeod, N., Cheng, Q.-m., Hou, X.-d., Yang, J., Wang, X.-d., Wang, Y., 2020. A high-resolution summary of Cambrian to Early Triassic marine invertebrate biodiversity. Science, 367(6475): 272–277.</p> <p>Feng, Y., Song, H., Bond, D.P.G., 2020. Size variations in foraminifers from the early Permian to the Late Triassic: implications for the Guadalupian–Lopingian and the Permian–Triassic mass extinctions. Paleobiology, 46(4): 511–532.</p> <p>Foster, W., Gliwa, J., Lembke, C., Pugh, A., Hofmann, R., Tietje, M., Varela, S., Foster, L., Korn, D., Aberhan, M., 2020. Evolutionary and ecophenotypic controls on bivalve body size distributions following the end-Permian mass extinction. Global and Planetary Change, 185: 103088.</p> <p>Foster, W., Lehrmann, D., Yu, M., Ji, L., Martindale, R., 2018. Persistent environmental stress delayed the recovery of marine communities in the aftermath of the latest Permian mass extinction. Paleoceanography and Paleoclimatology, 33(4): 338–353.</p> <p>Heim, N.A., Knope, M.L., Schaal, E.K., Wang, S.C., Payne, J.L., 2015. Cope's rule in the evolution of marine animals. Science, 347(6224): 867–870.</p> <p>Jablonski, D., 1997. Body-size evolution in Cretaceous molluscs and the status of Cope's rule. Nature, 385(6613): 250–252.</p> <p>Lockwood, R., 2005. Body size, extinction events, and the early Cenozoic record of veneroid bivalves: a new role for recoveries? Paleobiology, 31(4): 578–590.</p> <p>Payne, J.L., Bush, A.M., Heim, N.A., Knope, M.L., McCauley, D.J., 2016. Ecological selectivity of the emerging mass extinction in the oceans. Science, 353(6305): 1284–1286.</p> <p>Romano, C., Koot, M.B., Kogan, I., Brayard, A., Minikh, A.V., Brinkmann, W., Bucher, H., Kriwet, J., 2016. Permian–Triassic Osteichthyes (bony fishes): diversity dynamics and body size evolution. Biological Reviews, 91(1): 106–147.</p> <p>Schaal, E.K., Clapham, M.E., Rego, B.L., Wang, S.C., Payne, J.L., 2016. Comparative size evolution of marine clades from the Late Permian through Middle Triassic. Paleobiology, 42(1): 127–142.</p> <p>Shen, S., Crowley, J.L., Wang, Y., Bowring, S.A., Erwin, D.H., Sadler, P.M., Cao, C., Rothman, D.H., Henderson, C.M., Ramezani, J., Zhang, H., Shen, Y., Wang, X., Wang, W., Mu, L., Li, W., Tang, Y., Liu, X., Liu, L., Zeng, Y., Jiang, Y., Jin, Y., 2011. Calibrating the end-Permian mass extinction. Science, 334(6061): 1367–1372.</p> <p>Shi, G.R., Zhang, Y.-c., Shen, S.-z., He, W.-h., 2016. Nearshore–offshore–basin species diversity and body size variation patterns in Late Permian (Changhsingian) brachiopods. Palaeogeography, Palaeoclimatology, Palaeoecology, 448: 96–107.</p> <p>Song, H., Huang, S., Jia, E., Dai, X., Wignall, P.B., Dunhill, A.M., 2020. Flat latitudinal diversity gradient caused by the Permian–Triassic mass extinction. Proceedings of the National Academy of Sciences, 117(30): 17578–17583.</p> <p>Song, H., Wignall, P.B., Dunhill, A.M., 2018. Decoupled taxonomic and ecological recoveries from the Permo-Triassic extinction. Science Advances, 4(10): eaat5091.</p> <p>Song, H., Wignall, P.B., Tong, J., Yin, H., 2013. Two pulses of extinction during the Permian-Triassic crisis. Nature Geoscience, 6(1): 52–56.</p> <p>Stanley, S.M., 1973. An explanation for Cope's rule. Evolution, 27(1): 1–26.</p> <p>Yin, H., Feng, Q., Lai, X., Baud, A., Tong, J., 2007. The protracted Permo-Triassic crisis and multi-episode extinction around the Permian-Triassic boundary. Global and Planetary Change, 55(1–3): 1–20.</p> <p> </p> <p> </p>
Sexually-selected male weapon increases the risk of population extinction under environmental change: An experimental evidence
<p><span>Exaggerated sexually-selected traits, occurring more commonly in males, help individuals to increase reproductive success, but are costly to produce and maintain. These costs on the one hand may improve population fitness by intensifying selection against maladapted males, but on the other hand may increase the risk of extinction under environmental challenge. However, the impact of sexually selected traits on extinction risk have not been investigated experimentally. We used replicate populations of a male-dimorphic mite, <em>Rhizoglyphus robini</em>, to test if prevalence of a sexually-selected weapon affected the risk of extinction under gradual temperature increase (20C per generation). In two independent experiments that utilized either inbred lines or lines mass selected for or against the weapon to establish experimental replicate populations differing in the prevalence of the weapon, we found that populations with high weapon prevalence were more likely to go extinct. Extinctions occurred despite partial suppression of the weapon expression at increased temperature and were not explained by increased male mortality. Our results provide the first, to our knowledge, experimental evidence demonstrating dramatic effect of elaborated sexual traits on the risk of extinction under environmental challenge.</span></p>
Illuminating the mystery of thylacine extinction: A role for relaxed selection and gene loss
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Data from: When are extinctions simply bad luck? rarefaction as a framework for disentangling selective and stochastic extinctions
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Data from: Machine learning identifies ecological selectivity patterns across the end-Permian mass extinction
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Sexually-selected male weapon increases the risk of population extinction under environmental change: An experimental evidence
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Data from: Extinction selectivity obscures patterns of trait-dependent endangerment in Columbiformes
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Selective extinctions resulting from random habitat destruction lead to under‐estimates of local and regional biodiversity loss in a manipulative field experiment
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Data from: A framework for the integrated analysis of the magnitude, selectivity, and biotic effects of extinction and origination
The taxonomic and ecologic composition of Earth's biota has shifted dramatically through geologic time, with some clades going extinct while others diversified. Here, we derive a metric that quantifies the change in biotic composition due to extinction or origination and show that it equals the product of extinction/origination magnitude and selectivity (variation in magnitude among groups). We also define metrics that describe the extent to which a recovery (1) reinforced or reversed the effects of extinction on biotic composition and (2) changed composition in ways uncorrelated with the extinction. To demonstrate the approach, we analyzed an updated compilation of stratigraphic ranges of marine animal genera. We show that mass extinctions were not more selective than background intervals at the phylum level; rather, they tended to drive greater taxonomic change due to their higher magnitudes. Mass extinctions did not represent a separate class of events with respect to either strength of selectivity or effect. Similar observations apply to origination during recoveries from mass extinctions, and on average, extinction and origination were similarly selective and drove similar amounts of biotic change. Elevated origination during recoveries drove bursts of compositional change that varied considerably in effect. In some cases, origination partially reversed the effects of extinction, returning the biota towards the pre-extinction composition; in others, it reinforced the effects of the extinction, magnifying biotic change. Recoveries were as important as extinction events in shaping the marine biota, and their selectivity deserves systematic study alongside that of extinction.
Shifts in sexual dimorphism across a mass extinction in ostracods: implications for sexual selection as a factor in extinction risk
<p>Sexual selection often favors investment in expensive sexual traits that help individuals compete for mates. In a rapidly changing environment, however, allocation of resources to traits related to reproduction at the expense of those related to survival may elevate extinction risk. Empirical testing of this hypothesis in the fossil record, where extinction can be directly documented, is largely lacking. The rich fossil record of cytheroid ostracods offers a unique study system in this context: the male shell is systematically more elongate than that of females, and thus the sexes can be distinguished, even in fossils. Using mixture models to identify sex clusters from size and shape variables derived from the digitized valve outlines of adult ostracods, we estimated sexual dimorphism in ostracod species before and after the Cretaceous/Paleogene mass extinction in the United States Coastal Plain. Across this boundary, we document a substantial shift in sexual dimorphism, driven largely by a pronounced decline in the taxa with dimorphism indicating both very high and very low male investment. The shift away from high male investment, which arises largely from evolutionary changes within genera that persist through the extinction, parallels extinction selectivity previously documented during the Late Cretaceous under a background extinction regime. Our results suggest that sexual selection and the allocation of resources towards survival versus reproduction may be an important factor for species extinction during both background and mass extinctions. </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.