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13 results for “Avian extinction”
The global loss of avian functional and phylogenetic diversity from anthropogenic extinctions
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Supplement to Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction
<p>This repository contains the supplementary files for:</p> <p>Allen BJ, Volkova Oliveria MV, Stadler T, Vaughan TG, Warnock RCM. 2024. Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction. Cambridge Prisms: Extinction.</p> <p><strong>Description of files</strong></p> <p>This repository contains the cleaned tree files, tables of age constraints, XML files for running the analyses in BEAST2, and R code to process the datasets.</p> <p>Benson1clean.tree, Benson2clean.tree, Lloyd1clean.tree, Lloyd2clean.tree - the cleaned tree files containing the phylogenies inputted into BEAST2, with tip names matched to age data from the Paleobiology Database</p> <p>Tree modifications log.xlsx - a description of the modifications made to each input phylogeny compared to their state in the data supplement of their original papers</p> <p>dinosaur_ages.csv - the raw dinosaur age data downloaded from the Paleobiology Database</p> <p>tip_constraints.csv - the dinosaur age data converted into a format to input into BEAST2, to provide age constraints for tips</p> <p>change_times.txt - a text file describing the change times for the piecewise constant trajectories in the two phylodynamic analyses</p> <p>BDSKY.xml, PiecewiseCoalescent.xml - XML files describing the BEAST2 configuration for each of the two phylodynamic models</p> <p>BDSKY_logs.zip, BDSKY_trees.zip, Coalescent_logs.zip, Coalescent_trees.zip - compressed folders containing the output log files and inferred phylogenies for each of the 16 analysed phylogenies</p> <p>Supplementary_tables.zip - Tables containing summary statistics for each of the parameters inferred in each of the models</p> <p><strong>Description of R code</strong></p> <p>The R code is subdivided into the following files:</p> <p>Wrangle_trees.R - code for checking, cleaning, and splitting the phylogenies used in the analyses</p> <p>PBDB_tip_constraints.R - code for converting the raw age data from the Paleobiology Database into a format ready for input into BEAST2 as tip constraints</p> <p>BDSKY_post_processing.R, Coalescent_post_processing.R - code for cleaning and plotting data from the BEAST2 log files, for each of the two phylodynamic models</p>
Data from: The megaherbivore gap after the non-avian dinosaur extinctions modified trait evolution and diversification of tropical palms
<p><span>The Cretaceous–Paleogene (K-Pg) extinction of the non-avian dinosaurs (66 Ma) led to a 25 million year gap of megaherbivores (>1000 kg) before the evolution of megaherbivorous mammals in the Late Eocene (40 Ma). The botanical consequences of this 'Paleocene megaherbivore gap' (PMHG) remain poorly explored. We hypothesize that the absence of megaherbivores should result in changes in the diversification and trait evolution of associated plant lineages. We used phylogenetic time- and trait-dependent diversification models with palms (Arecaceae) and show that the PMHG was characterized by speciation slowdowns, decreased evolution of armature, and increased evolution of megafaunal (</span>≥<span>4cm) fruits. This suggests that the absence of browsing by megaherbivores during the PMHG may have led to a loss of defence traits, but absence of megaherbivorous seed dispersers did not lead to a loss of megafaunal fruits. Instead, increases in PMHG fruit sizes may be explained by Late Paleocene rising temperatures, rainforest expansion, and the subsequent radiation of seed dispersing birds and mammals. We show that the profound impact of the PMHG on plant diversification can be detected even with the overwriting of adaptations by the subsequent Late Eocene opening-up of megaherbivore-associated ecological opportunities. Our study provides a quantitative, comparative framework to assess </span>diversification and adaptation during one of the most enigmatic periods in angiosperm history.</p>
Data from: Climate matching and anthropogenic factors contribute to the colonisation and extinction of local populations during avian invasions
<p>Concern about the impacts of biological invasions has generated a great deal of interest in understanding factors that determine invasion success. Most of our current knowledge comes from static approaches that use spatial patterns as a proxy of temporal processes. These approaches assume that species are present in areas where environmental conditions are the most favourable. However, this assumption is problematic when applied to dynamic processes such as species expansions when equilibrium has not been reached. In our work, we analyse the roles played by human activities, climatic matching, and spatial connectivity on the two main underlying processes shaping the spread of invasive species (i.e., colonisation and extinction) using a dynamic modelling approach. For this, we used a large dataset that has recorded the occurrence of two invasive bird species -the ring-necked and the monk parakeets- in the Iberian Peninsula from 1991 to 2016. </p>
Data from: The megaherbivore gap after the non-avian dinosaur extinctions modified trait evolution and diversification of tropical palms
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Data from: Genomic Signature of an Avian Lilliput Effect across the K-PG Extinction
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Data from: Climate matching and anthropogenic factors contribute to the colonisation and extinction of local populations during avian invasions
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An effect size statistical framework for investigating sexual dimorphism in non-avian dinosaurs and other extinct taxa
<p>Despite reports of sexual dimorphism in extinct taxa, such claims in non-avian dinosaurs have been underrepresented recently (~the last decade) and often criticized. Since dimorphism is widespread in sexually reproducing organisms today, underrepresentation might suggest either methodological shortcomings or that this diverse group exhibited highly unusual reproductive biology. Univariate significance testing, especially for bimodality, is ineffective and prone to false negatives. Species recognition and mutual sexual selection hypotheses, therefore, may not be required to explain supposed absence of sexual dimorphism across the grade, likely a type II error. Instead, multiple lines of evidence support sexual selection and variation of structures consistent with secondary sexual characteristics, strongly suggesting sexual dimorphism in non-avian dinosaurs. We propose a framework for studying sexual dimorphism in fossils, focusing on likely secondarily sexual traits and testing against all alternate hypotheses for variation in them using multiple lines of evidence. We use effect size statistics appropriate for low sample sizes, rather than significance testing, to analyze potential divergence of growth curves in traits and constrain estimates for dimorphism magnitude. In many cases, estimates of sexual variation can be reasonably accurate, and further developments in methods to improve sex assignments and account for intrasexual variation (e.g., mixture modelling) will improve accuracy. It is better to compare estimates for the magnitude of and support for dimorphism between datasets than to dichotomously reject or fail to reject monomorphism in a single species, enabling the study of sexual selection across phylogenies and time. We defend our approach with simulated and empirical data, including dinosaur data, showing that even simple approaches can yield fairly accurate estimates of sexual variation in many cases, allowing for comparison of species with high and low support for sexual variation.</p>
Functional traits of avian frugivores have shifted following species extinction and introduction in the Hawaiian Islands
<p>The extinction and introduction of species can alter ecological processes owing to the loss or gain of species roles. In vertebrate-dependent seed dispersal, mutualisms between frugivores and fruiting plants depend, in part, on matching of functional traits. High species turnover of frugivores has occurred on the Hawaiian Islands, owing to both the loss of native frugivores and the introduction of a new suite of frugivores. How this turnover has altered the functional traits of frugivores and the potential impacts on seed dispersal remain unclear.</p> <p>We investigated how avian frugivore traits differed between historic and modern assemblages of the Hawaiian Islands. We also tested how traits shifted within foraging guilds (ground versus arboreal) to distinguish potential impacts on plants within low versus high forest strata.</p> <p>Compared to historic frugivores, the modern assemblage is smaller in gape width and body mass in both ground and arboreal guilds. Wing shape did not significantly change between assemblages. From results, we postulate that changes in the frugivore community have likely altered seed dispersal processes by reducing (1) the size of seeds consumed, (2) frugivory rates per animal, and (3) seed dispersal distances.</p> <p>Owing to seed size placing strong constraints on consumption, we reviewed recent studies on frugivory by modern birds in the Hawaiian Islands and compared the size of seeds consumed versus seeds available. We found that larger-seeded plants (>8.1mm seed width) were not consumed by modern birds and were more likely to be of conservation risk compared to smaller-seeded plants. Consequently, dispersal limitation may threaten Hawaiian plant communities, with larger-seeded plants at greatest risk of extinction.</p> <p>Broadly, we show that extensive turnover within assemblages may lead to significant changes in functional traits, with potential knock-on effects for mutualistic interactions and communities.</p>
Functional traits of avian frugivores have shifted following species extinction and introduction in the Hawaiian Islands
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An effect size statistical framework for investigating sexual dimorphism in non-avian dinosaurs and other extinct taxa
Open the record for dataset details and reuse information.
Data from: Extinction as a driver of avian latitudinal diversity gradients
The role of historical factors in driving latitudinal diversity gradients is poorly understood. Here we used an updated global phylogeny of terrestrial birds to test the role of three key historical factors – speciation, extinction and dispersal rates – in generating latitudinal diversity gradients for eight major clades. We fit a model that allows speciation, extinction and dispersal rates to differ, both with latitude and between the New and Old World. Our results consistently support extinction (all clades had lowest extinction where species richness was highest) as a key driver of species richness gradients across each of eight major clades. In contrast, speciation and dispersal rates showed no consistent latitudinal patterns across replicate bird clades, and thus are unlikely to represent general underlying drivers of latitudinal diversity gradients.
Data from: Extinction as a driver of avian latitudinal diversity gradients
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