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opencc-zeroFeb 2023View details →

The end of the line: Competitive exclusion and the extinction of historical entities

Identifying competitive exclusion at the macroevolutionary scale has typically relied on demonstrating a reciprocal, contradictory response by two co-occurring, functionally similar clades. Finding definitive examples of such a response in fossil time-series has proven challenging however, as has controlling for the effects of a changing physical environment. We take a novel approach to this issue by quantifying variation in trait values that capture almost the entirety of function for steam locomotives (SL), a known example of competitive exclusion from material culture, with the goal of identifying patterns suitable for assessing clade replacement in the fossil record. Our analyses find evidence of an immediate, directional response to the first appearance of a direct competitor, with subsequent competitors further reducing the realized niche of SLs, until extinction was the inevitable outcome. These results demonstrate when interspecific competition should lead to extinction and suggest that clade replacement may only occur when niche overlap between an incumbent and its competitors is near absolute and where the incumbent is incapable of transitioning to a new adaptive zone. Our findings provide the basis for a new approach to analyze putative examples of competitive exclusion that is largely free of a priori assumptions.

opencc-by-4.0Feb 2023View details →

Fig. 2 in Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber

Fig. 2 Artistic reconstruction of Neoponera vejestoria sp. nov. Artist: Minsoo Dong

opencc-zeroFeb 2023View details →

Reconstructing locomotor ecology of extinct avialans: a case study of Ichthyornis comparing sternum morphology and skeletal proportions

Avian skeletal morphology is associated with locomotor function, including flight style, swimming and terrestrial locomotion, and permits informed inferences on locomotion in extinct taxa. The fossil taxon Ichthyornis (Avialae: Ornithurae) has long been regarded as highly aerial, with flight similar to terns or gulls (Laridae), and skeletal features resembling foot-propelled diving adaptations. However, rigorous testing of locomotor hypotheses has yet to be performed on Ichthyornis, despite its notable phylogenetic position as one of the most crownward stem birds. We analysed separate datasets of 3D sternal shape (geometric morphometrics) and skeletal proportions (linear measurements across the skeleton), to examine how well these data types predict locomotor traits in Neornithes. We then used this information to infer locomotor capabilities of Ichthyornis. We find strong support for both soaring and foot-propelled swimming capabilities in Ichthyornis. Further, sternal shape and skeletal proportions provide complementary information on avian locomotion: skeletal proportions allow better predictions of the capacity for flight, whereas sternal shape predicts variation in more specific locomotor abilities such as soaring, foot-propelled swimming, and escape burst flight. These results have important implications for future studies of extinct avialan ecology, and underscore the importance of closely considering sternum morphology in investigations of fossil bird locomotion.

opencc-zeroApr 2023View details →

Data from: Bivalves from the Changhsingian (Upper Permian) Bellerophon Formation of the Dolomites (Italy): ancestors of the Lower Triassic post extinction benthic communities

The diverse shallow marine fossil assemblages from the Changhsingian Bellerophon Formation of the Dolomites record the late Palaeozoic marine life immediately before the end-Permian mass extinction. Here, based on the collection of c. 6500 bivalve specimens from different localities of the western Dolomites, we have taxonomically classified 26 species, including 10 new species, 3 new genera and 1 new family: Acharax frenademezi sp. nov., Bakevellia (Bakevellia) preromangica sp. nov., Edmondia hautmanni sp. nov., Etheripecten stuflesseri sp. nov., Ladinomya fosteri gen. et sp. nov., Lovaralucina covidi gen. et sp. nov., Palaeolima badiotica sp. nov., Promytilus merlai sp. nov., Tambanella? stetteneckensis sp. nov., Volsellina carinata sp. nov., Gardenapecten gen. nov., Ladinomyidae fam. nov. The occurrence of three Eumorphotis species with a different and superimposed stratigraphic distribution led us to propose an upper Permian 'lower Eumorphotis Zone' in contrast to the already known Lower Triassic Eumorphotis Zone which is consequently renamed as 'upper Eumorphotis Zone'. The 'lower Eumorphotis Zone' is divided, in ascending stratigraphic order, into E. praecurrens, E. striatocostata and E. lorigae subzones. A palaeoecological analysis of the bivalves contained in each sampled bed has allowed us to recognize 6 biofacies and 4 ecofacies, based on richness, dominance and ecological lifestyle. The bivalves from Bellerophon Formation inhabited lagoonal to nearshore environments affected by stressed conditions, mostly represented by high temperatures, high salinity, shallow water depths, low oxygen and high terrigenous input. The upper Bellerophon Fm is characterized by increasing fully marine conditions, although the occurrence of eurytopic taxa still suggests stressed marine conditions.

opencc-zeroMay 2023View details →

Genomes of the extinct Bachman's Warbler show high divergence and no evidence of admixture with other extant Vermivora Warblers

Bachman's Warbler (Vermivora bachmanii) – last sighted in 1988 – is one of the only North American passerines to have gone extinct. Given extensive ongoing hybridization of its two extant congeners – the Blue-Winged Warbler (V. cyanoptera) and Golden-Winged Warbler (V. chrysoptera) – and shared patterns of plumage variation between Bachman's Warbler and hybrids between those extant species, it has been suggested that Bachman's Warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genomes of Bachman's Warblers collected at the turn of the 20th century to address this. We combine these data with the two extant Vermivora species to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent with V. bachmanii having been a highly divergent, reproductively isolated species, with no evidence of introgression. We show that these three species have similar levels of runs of homozygosity (ROH), consistent with effects of a small long-term effective population size or population bottlenecks, with one V. bachmanii outlier showing numerous long ROH and an FROH greater than 5%. We also found—using population branch statistic estimates—previously undocumented evidence of lineage-specific evolution in V. chrysoptera near a pigmentation gene candidate, CORIN, which is a known modifier of ASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species.

opencc-by-4.0Nov 2020View details →

Figure 2. Dental measurements taken from the left M and the right M1 in A New Species of Extinct False Vampire Bat (Megadermatidae: Macroderma) from the Kimberley Region of Western Australia

Figure 2. Dental measurements taken from the left M and the right M1, based on Hand (1985).

opencc-by-4.0Nov 2020View details →

Figure 1 in A New Species of Extinct False Vampire Bat (Megadermatidae: Macroderma) from the Kimberley Region of Western Australia

Figure 1. Location of Dingo Gap (star) in the Kimberley region of Western Australia,

opencc-zeroJun 2023View details →

Dataset: Corridor quality buffers extinction under extreme droughts in experimental metapopulations

Corridors with good-quality habitats maintain the spatial dynamics of metapopulations by promoting dispersal between habitat patches, potentially buffering populations and communities against continued global change. However, this function is threatened by habitats becoming increasingly fragmented, and habitat matrices becoming increasingly inhospitable, potentially reducing the resilience and persistence of populations. Yet, we lack a clear understanding of how reduced corridor quality interacts with rates of environmental change to destabilise populations. Using laboratory microcosms containing metapopulations of the Collembola Folsomia candida, we investigate the impact of corridor quality on metapopulation persistence under a range of simulated droughts, a key stressor for this species. We manipulated both drought severity and the number of patches affected by drought across landscapes connected by either good or poor-quality corridors. We measured the time of metapopulation extinction, the maximum rate of metapopulation decline, and the variability of abundance among patches as criteria to evaluate the persistence ability of metapopulations. We show that whilst drought severity negatively influenced the time of metapopulation extinction and the increase in drought patches caused metapopulation decline, these results were mitigated by good quality corridors, which increased metapopulation persistence time and decreased both how fast metapopulations declined and the inter-patch variability in abundances. Our results suggest that enhancing corridor quality can increase the persistence of metapopulations, increasing the time available for conservation actions to take effect, and/or for species to adapt or move in the face of continued stress. Given that fragmentation increases the isolation of habitats, improving the quality of habitat corridors may provide a useful strategy to enhance the resistance of spatially structured populations.

opencc-by-4.0Jun 2023View details →

Respiratory protein-driven selectivity during the Permian–Triassic mass extinction

Fossil occurrence data 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.   Body size data 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.   Other data were obtained from the above fossil occurrence and body size datasets.   References 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. 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. 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. 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. 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. 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. Jablonski, D., 1997. Body-size evolution in Cretaceous molluscs and the status of Cope's rule. Nature, 385(6613): 250–252. 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. 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. 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. 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. 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. 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. 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. Song, H., Wignall, P.B., Dunhill, A.M., 2018. Decoupled taxonomic and ecological recoveries from the Permo-Triassic extinction. Science Advances, 4(10): eaat5091. 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. Stanley, S.M., 1973. An explanation for Cope's rule. Evolution, 27(1): 1–26. 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.

opencc-by-4.0Feb 2023View details →

Supplement to: Early Cretaceous climate for the southern Tethyan Ocean: insights from the geochemical and paleoecological analyses of extinct cephalopods

One file (excel) containing XRPD results and Table S1-S6 with details of the clumped isotope, stable carbon isotope, and trace elements analyses that refers to the manuscript.

opencc-by-4.0Feb 2023View details →

Supplement to: Early Cretaceous climate for the southern Tethyan Ocean: insights from the geochemical and paleoecological analyses of extinct cephalopods

One file (excel) containing XRPD results and Table S1-S6 with details of the clumped isotope, stable carbon isotope, and trace elements analyses that refers to the manuscript.

opencc-zeroJul 2023View details →

Sexually-selected male weapon increases the risk of population extinction under environmental change: An experimental evidence

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, Rhizoglyphus robini, 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.

opencc-zeroAug 2023View details →

Data for: Lipid biomarkers recording marine microbial community structure changes through the Frasnian‐Famennian mass extinction event

This dataset contains data for a research article published on Geobiology. The article is entitled " Lipid biomarkers recording marine microbial community structure changes through the Frasnian‐Famennian mass extinction event". This study aims to reconstruct changes in the marine microbial community structure through the Late Devonian Frasnian‐Famennian (F‐F) transition. We performed a multiproxy investigation on a drill core of the Upper Devonian New Albany Shale from the Illinois Basin (western Kentucky, USA). Detailed information regarding the data collection, analysis, and interpretation can be found in the following paper: Chen J., Hogancamp N., Lu M., Ikejiri T., Malina N., Ojeda A., Sun Y., Lu Y. 2023. Lipid Biomarkers Recording Marine Microbial Community Structure Changes Through the Frasnian‐Famennian Mass Extinction Event. Geobiology <a href="https://doi.org/10.1111/gbi.12568">https://doi.org/10.1111/gbi.12568</a>

opencc-zeroSep 2023View details →

Spatial sorting promotes rapid (mal)adaptation in the red-shouldered soapberry bug after hurricane-driven local extinctions

Predicting future evolutionary change is a critical challenge in the Anthropocene as geographic range shifts and local extinction emerge as hallmarks of planetary change. Hence, spatial sorting – a driver of rapid evolution in which dispersal-associated traits accumulate along expanding range edges and within recolonized habitats – might be of growing importance in ecology and conservation. We report on the results of a natural experiment that monitored re-colonization of host plants by the seed-feeding, red-shouldered soapberry bug, Jadera haematoloma, after local extinctions from catastrophic flooding in an extreme hurricane. We tested the contribution of spatial sorting to generate rapid and persistent evolution in dispersal traits, as well as in feeding traits unrelated to dispersal. Long-winged dispersal forms accumulated in re-colonized habitats, and due to genetic correlation, mouthparts also became longer, and this shift persisted across generations. Those longer mouthparts were likely adaptive on one host plant species but maladaptive on two others based on matching the optimum depth of seeds within their host fruits. Moreover, spatial sorting eroded recently evolved adaptive divergence in mouthpart length among all host-associated biotypes, an outcome pointing to profound practical consequences of the extreme weather event for local adaptation, population resilience, and evolutionary futures.

opencc-zeroSep 2023View details →

The effects of sex on extinction dynamics of Chlamydomonas reinhardtii depend on the rate of environmental change

The continued existence of sex, despite many the costs it entails, still lacks an adequate explanation, as previous studies demonstrated that the effects of sex are environment-dependent: sex enhances the rate of adaptation in changing environments, but the benefits level off in benign conditions. To the best of our knowledge, the potential impact of different patterns of environmental change on the magnitude of these benefits received less attention in theoretical studies. In this paper, we begin to explore this issue by examining the effect of the rate of environmental deterioration (negatively correlated with population survival rate), on the benefits of sex. To investigate the interplay of sex and the rate of environmental deterioration, we carried out a long-term selection experiment with a unicellular alga (Chlamydomonas reinhardtii), by manipulating mode of reproduction (asexual, facultative or obligate sexual) and the rate of environmental deterioration (an increase of salt concentration). We monitored both the population size and extinction dynamics. The results revealed that the relative advantage of sex increased at the intermediate rate and plateaued at the highest rate of environmental deterioration. Obligate sexual populations had the slowest extinction rate under the intermediate rate of environmental deterioration, while facultative sexuality was favoured under the high rate-treatment. To the best of our knowledge, our study is the first to demonstrate that the interplay of sex and the rate of environmental deterioration affects the probability of survival, which indicates that mode of reproduction may be an important determinant of survival of the anthropogenic-induced environmental change.

controlledIPD-YESFeb 2026View details →

An Attempt at Translating Novelty-enhanced Extinction of Context Conditioning From Rodents to Humans

ClinicalTrials.gov study NCT05150951. IPD Sharing: YES. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Dopamine Enhancement of Fear Extinction Learning in PTSD (1R21MH108753)

ClinicalTrials.gov study NCT02560389. IPD Sharing: NO. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

Extinction of Fear Memories With Glucocorticoids in Veterans With PTSD

ClinicalTrials.gov study NCT01090180. IPD Sharing: Not stated. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

Cannabinoid Control of Fear Extinction Neural Circuits in Post-traumatic Stress Disorder

ClinicalTrials.gov study NCT02069366. IPD Sharing: Not stated. Countries: 1. Publications: 2.