palaeoverse: A community‐driven R package to support palaeobiological analysis

Methods in Ecology and Evolution, Journal Year: 2023, Volume and Issue: 14(9), P. 2205 - 2215

Published: April 13, 2023

Abstract The open‐source programming language ‘R' has become a standard tool in the palaeobiologist's toolkit. Its popularity within palaeobiological community continues to grow, with published articles increasingly citing usage of R and packages. However, there are currently lack agreed standards for data preparation available frameworks support implementation such standards. Consequently, workflows often unclear not reproducible, even when code is provided. Moreover, due accessibility documentation, palaeobiologists forced ‘reinvent wheel’ find solutions issues already solved by other members community. Here, we introduce palaeoverse , community‐driven package aid exploration quantitative research. freely three core principles: (1) streamline analyses; (2) enhance readability; (3) improve reproducibility results. To develop these aims, assessed analytical needs broader using an online survey, addition incorporating our own experiences. In this work, first report findings which shaped development package. Subsequently, describe demonstrate functionality provide examples. Finally, discuss resources have made future plans Palaeoverse project. palaeobiology, developed intention bringing together establish high‐quality provides user‐friendly platform preparing analysis well‐documented transparency. improves accessibility, beneficial both review process

Language: Английский

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Mass extinctions and their rebounds: a macroevolutionary framework

Paleobiology, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 14

Published: Jan. 21, 2025

Abstract Mass extinctions are natural experiments on the short- and long-term consequences of pushing biotas past breaking points, often with lasting effects structure function biodiversity. General properties mass extinctions—exceptionally severe, taxonomically broad, global losses taxa—are starting to come into focus through comparisons among dimensions biodiversity, including morphological, functional, phylogenetic diversity. Notably, functional diversity tends persist despite severe taxonomic diversity, whereas taxic morphological may or not be coupled. One biggest challenges in synthesizing extracting general these events has been that they driven by multiple, interacting pressures, taxa their traits vary events, making it difficult link single stressors specific traits. Ongoing improvements stratigraphic resolution for multiple clades will sharpen tests selectivity help isolate hitchhiking effects, whereby organismal carried differential survival extinction owing other higher-level attributes, such as geographic-range size. Direct comparative analyses across also clarify impacts particular drivers taxa, traits, morphologies. It is just filter deserves attention, longer-term impact derives part from ensuing rebounds. More work needed uncover biotic abiotic circumstances spur some re-diversification while relegating others marginal shares Combined insights filters rebounds bring a macroevolutionary view approaching biodiversity crisis Anthropocene, helping pinpoint clades, groups, morphologies most vulnerable failed

Language: Английский

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Challenges and directions in analytical paleobiology

Paleobiology, Journal Year: 2023, Volume and Issue: 49(3), P. 377 - 393

Published: Feb. 27, 2023

Over the last 50 years, access to new data and analytical tools has expanded study of paleobiology, contributing innovative analyses biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability resources, paleobiology faces deep-rooted obstacles that stem from need for more equitable best practices guide fossil record. Recent progress been accelerated by a collective push toward collaborative, interdisciplinary, open science, especially early-career researchers. Here, we survey four challenges facing an perspective: (1) accounting biases when interpreting record; (2) integrating modern data; (3) building science skills; (4) increasing accessibility equity. We discuss recent efforts address each challenge, highlight persisting barriers, identify have advanced work. Given inherent linkages between these challenges, encourage discourse across disciplines find common solutions. also affirm systemic changes reevaluate how conduct share paleobiological research.

Language: Английский

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Multiple drivers and lineage-specific insect extinctions during the Permo–Triassic

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Dec. 6, 2022

The Permo-Triassic interval encompasses three extinction events including the most dramatic biological crisis of Phanerozoic, latest Permian mass extinction. However, their drivers and outcomes are poorly quantified understood for terrestrial invertebrates, which we assess here insects. We find a pattern with extinctions: Roadian/Wordian (≈266.9 Ma; 64.5% insect genera), Permian/Triassic (≈252 82.6% Ladinian/Carnian boundaries (≈237 74.8% genera). also unveil heterogeneous effect these across major clades. Because have impacted ecosystems, investigate influence abiotic biotic factors on diversification dynamics that changes in floral assemblages likely strongest insects' responses throughout Permo-Triassic. diversity dependence between guilds; an ubiquitously found current ecosystems. herbivores held central position interaction network. Our study reveals high levels profoundly shaped evolutionary history diverse non-microbial lineage.

Language: Английский

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Combining palaeontological and neontological data shows a delayed diversification burst of carcharhiniform sharks likely mediated by environmental change

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Dec. 19, 2022

Abstract Estimating deep-time species-level diversification processes remains challenging. Both the fossil record and molecular phylogenies allow estimation of speciation extinction rates, but each type data may still provide an incomplete picture dynamics. Here, we combine palaeontological (fossil occurrences) neontological (molecular phylogenies) to estimate diversity dynamics through process-based birth–death models for Carcharhiniformes, most speciose shark order today. Despite their abundant dating back Middle Jurassic, only a small fraction extant carcharhiniform species is recorded as fossils, which impedes relying on study recent diversification. Combining phylogenetic data, recover complex evolutionary history carcharhiniforms, exemplified by several variations in rates with early low period followed Cenozoic radiation. We further reveal burst last 30 million years, partially only. also find that reef expansion temperature change can explain time. These results pinpoint primordial importance these environmental variables evolution marine clades. Our highlights benefit combining address macroevolutionary questions.

Language: Английский

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Estimating spatial variation in origination and extinction in deep time: a case study using the Permian–Triassic marine invertebrate fossil record

Paleobiology, Journal Year: 2023, Volume and Issue: 49(3), P. 509 - 526

Published: Feb. 10, 2023

Abstract Understanding spatial variation in origination and extinction can help to unravel the mechanisms underlying macroevolutionary patterns. Although methods have been developed for estimating global rates from fossil record, no framework exists applying these restricted regions. Here, we test efficacy of three metrics regional analysis, using simulated occurrences. These are then applied marine invertebrate record Permian Triassic examine across latitudes. Extinction were generally uniform latitudes time intervals, including during Capitanian Permian–Triassic mass extinctions. The small magnitude this variation, combined with possibility its attribution sampling bias, cautions against linking any observed differences contrasting evolutionary dynamics. Our results indicate that levels more variable clades than

Language: Английский

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Explanations for latitudinal diversity gradients must invoke rate variation

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(33)

Published: Aug. 3, 2023

The latitudinal diversity gradient (LDG) describes the pattern of increasing numbers species from poles to equator. Although recognized for over 200 years, mechanisms responsible largest-scale and longest-known in macroecology are still actively debated. I argue here that any explanation LDG must invoke differential rates speciation, extinction, extirpation, or dispersal. These processes themselves may be governed by numerous abiotic biotic factors. Hypotheses claim not rates, such as ‘age area’ ‘time diversification’, eschew focus rate variation is assumed these explanations. There significant uncertainty how dispersal have varied regionally Earth history. However, better understand development LDGs, we need constrain this variation. Only then will drivers – they nature become clearer.

Language: Английский

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Bayesian analyses indicate bivalves did not drive the downfall of brachiopods following the Permian-Triassic mass extinction

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 9, 2023

Certain times of major biotic replacement have often been interpreted as broadly competitive, mediated by innovation in the succeeding clades. A classic example was switch from brachiopods to bivalves seabed organisms following Permian-Triassic mass extinction (PTME), ~252 million years ago. This attributed competitive exclusion better adapted or simply fact that had hit especially hard PTME. The brachiopod-bivalve is emblematic global turnover marine faunas Palaeozoic-type Modern-type triggered Here, using Bayesian analyses, we find unexpectedly two clades displayed similar large-scale trends diversification before Jurassic. Insight a multivariate birth-death model shows brachiopod during PTME set stage for switch, with differential responses high ocean temperatures post-extinction further facilitating their displacement bivalves. Our study strengthens evidence and were not competitors over macroevolutionary time scales, events environmental stresses shaping divergent fates.

Language: Английский

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New insights into Silurian–Devonian palaeophytogeography

Palaeogeography Palaeoclimatology Palaeoecology, Journal Year: 2023, Volume and Issue: 613, P. 111393 - 111393

Published: Jan. 7, 2023

The Silurian–Devonian plant radiation was an event triggered by the progressive colonization of subaerial habitats. Nevertheless, it is still unclear whether this globally uniform or alternative diversification scenarios emerged depending on geographical context. Here, we report early land diversity patterns across different previously defined palaeogeographical units (i.e., Laurussia, Siberia, Kazakhstania, NE, NW and South Gondwana). Results reveal apparent diachronous events extinction partly resulting from uneven sampling effort, especially in Gondwana. Global are most similar to Laurussian curve suggesting that observed global dynamics mostly controlled historically best-sampled continents. changes floral composition through time become less prone biases, disparities indicate a non-random distribution vegetation. Consequently, further performed set multivariate analyses revisit palaeophytogeographical signal four time-intervals Silurian–Lochkovian, Pragian–Emsian, Middle Late Devonian), which revealed spatial differentiation vegetation mainly climatic conditions lesser extent barriers. Most importantly, find maximum provincialism during cooler periods such as Silurian–Lochkovian Devonian, whilst warmer (Pragian–Emsian Devonian) coincided with increased cosmopolitanism among plants.

Language: Английский

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DeepDive: estimating global biodiversity patterns through time using deep learning

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 17, 2024

Understanding how biodiversity has changed through time is a central goal of evolutionary biology. However, estimates past are challenged by the inherent incompleteness fossil record, even when state-of-the-art statistical methods applied to adjust while correcting for sampling biases. Here we develop an approach based on stochastic simulations and deep learning model infer richness at global or regional scales incorporating spatial, temporal taxonomic variation. Our method outperforms alternative approaches across simulated datasets, especially large spatial scales, providing robust palaeodiversity under wide range preservation scenarios. We apply our two empirical datasets different scope: Permian-Triassic record marine animals Cenozoic evolution proboscideans. provide revised quantitative assessment mass extinctions in reveal rapid diversification proboscideans following their expansion out Africa >70% diversity drop Pleistocene.

Language: Английский

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