Mark N. Puttick
YOU?
Author Swipe
View article: Why should we compare morphological and molecular disparity?
Why should we compare morphological and molecular disparity? Open
Indices of morphological disparity seek to summarise the highly multivariate morphological variation across groups of species within clades, time bins or other groups. Morphological variation can be quantified using geometric morphometric,…
View article: Phylogenetic sampling affects evolutionary patterns of morphological disparity
Phylogenetic sampling affects evolutionary patterns of morphological disparity Open
Cladistic character matrices are routinely repurposed in analyses of morphological disparity. Unfortunately, the sampling of taxa and characters within such datasets reflects their intended application (to resolve phylogeny, rather than di…
View article: Empirical distributions of homoplasy in morphological data
Empirical distributions of homoplasy in morphological data Open
Cladistic datasets of morphological characters are comprised of observations that exhibit varying degrees of consistency with underlying phylogenetic hypotheses, reflecting the acquisition and retention of character states (highly consiste…
View article: Data from Murphy et al. 2021. Empirical distributions of homoplasy in morphological data. Palaeontology
Data from Murphy et al. 2021. Empirical distributions of homoplasy in morphological data. Palaeontology Open
This dataset contains analytic code, cladistic datasets and metadata derived from analysis of these datasets, as well as a description of data sources. The data accompanies the following manuscript: Jodie L. Murphy, Mark N. Puttick, Joseph…
View article: Shifting spaces: Which disparity or dissimilarity measurement best summarize occupancy in multidimensional spaces?
Shifting spaces: Which disparity or dissimilarity measurement best summarize occupancy in multidimensional spaces? Open
Multidimensional analysis of traits are now common in ecology and evolution and are based on trait spaces in which each dimension summarizes the observed trait combination (a morphospace or an ecospace). Observations of interest will typic…
View article: Disparities in the analysis of morphological disparity
Disparities in the analysis of morphological disparity Open
Analyses of morphological disparity have been used to characterize and investigate the evolution of variation in the anatomy, function and ecology of organisms since the 1980s. While a diversity of methods have been employed, it is unclear…
View article: A Cambrian–Ordovician Terrestrialization of Arachnids
A Cambrian–Ordovician Terrestrialization of Arachnids Open
Understanding the temporal context of terrestrialization in chelicerates depends on whether terrestrial groups, the traditional Arachnida, have a single origin and whether or not horseshoe crabs are primitively or secondarily marine. Molec…
View article: Arachnid monophyly: morphological, palaeontological and molecular support for a single terrestrialization within Chelicerata
Arachnid monophyly: morphological, palaeontological and molecular support for a single terrestrialization within Chelicerata Open
Data matrices, gene trees and alignments, output files, and custom scripts used on this manuscript.
View article: MOTMOT: Models of trait macroevolution on trees (an update)
MOTMOT: Models of trait macroevolution on trees (an update) Open
The disparity in species’ traits arises through variation in the tempo and mode of evolution over time and between lineages. Understanding these patterns is a core goal in evolutionary biology. Here we present the comprehensively updated r…
View article: Origin of horsetails and the role of whole-genome duplication in plant macroevolution
Origin of horsetails and the role of whole-genome duplication in plant macroevolution Open
Whole-genome duplication (WGD) has occurred commonly in land plant evolution and it is often invoked as a causal agent in diversification, phenotypic and developmental innovation, as well as conferring extinction resistance. The ancient an…
View article: Shifting spaces: which disparity or dissimilarity metrics best summarise occupancy in multidimensional spaces?
Shifting spaces: which disparity or dissimilarity metrics best summarise occupancy in multidimensional spaces? Open
Multidimensional analysis of traits are now a common toolkit in ecology and evolution and are based on trait-spaces in which each dimension summarise the observed trait combination (a morphospace or an ecospace). Observations of interest w…
View article: Characterization of melanosomes involved in the production of non-iridescent structural feather colours and their detection in the fossil record
Characterization of melanosomes involved in the production of non-iridescent structural feather colours and their detection in the fossil record Open
Non-iridescent structural colour in avian feathers is produced by coherent light scattering through quasi-ordered nanocavities in the keratin cortex of the barbs. To absorb unscattered light, melanosomes form a basal layer underneath the n…
View article: Supplementary Figures 1 - 4 and Supplementary Table 1 from Origin of horsetails and the role of whole-genome duplication in plant macroevolution
Supplementary Figures 1 - 4 and Supplementary Table 1 from Origin of horsetails and the role of whole-genome duplication in plant macroevolution Open
Figure S1: Akaike Information Criterion and Bayesian Information Criterion assessing the fitting of Gaussian mixture models to the Ks distribution of both Equisetum hyemale and Equisetum diffusum.; Figure S2: Frequency of duplications amon…
View article: List of bird species (Common and Latin name) used in sampling of NISC (description of colour and area on the body where feather was sampled); Details of melanosomes sampling from E. brachyptera fossil and results of their measurements; Trait database used for Ancestral state reconstruction and posterior probabilities of colour state for E. brachyptera; Posterior probabilities of colour state for E. brachyptera; 1000 phylogenetic trees downloaded from birdtree.org in Nexus format; Tukey's post-hoc test results (pairwise comparison); Forward stepwise regression results and plot of the first two variables; Li et al. database with measurements of melanosomes isolated from feathers expressing non-iridescent structural colour included. Added samples are indicated with blue colour in the database.; Results of simulation of correct classification of colour categories with quadratic discriminant analysis; Figure 2D, figure 2E, figure 2F, figure 2G, figure 2H - melanosome extraction details
List of bird species (Common and Latin name) used in sampling of NISC (description of colour and area on the body where feather was sampled); Details of melanosomes sampling from E. brachyptera fossil and results of their measurements; Trait database used for Ancestral state reconstruction and posterior probabilities of colour state for E. brachyptera; Posterior probabilities of colour state for E. brachyptera; 1000 phylogenetic trees downloaded from birdtree.org in Nexus format; Tukey's post-hoc test results (pairwise comparison); Forward stepwise regression results and plot of the first two variables; Li et al. database with measurements of melanosomes isolated from feathers expressing non-iridescent structural colour included. Added samples are indicated with blue colour in the database.; Results of simulation of correct classification of colour categories with quadratic discriminant analysis; Figure 2D, figure 2E, figure 2F, figure 2G, figure 2H - melanosome extraction details Open
We have uploaded separate file in the Step 3 section where we have listed entire content of our Supplementary material.
View article: Shifting spaces: which disparity or dissimilarity metrics best summarise occupancy in multidimensional spaces?
Shifting spaces: which disparity or dissimilarity metrics best summarise occupancy in multidimensional spaces? Open
Raw data set used in "Shifting spaces: which disparity or dissimilarity metrics best summarise occupancy in multidimensional spaces?".The raw data is from:Beck, R. M., & Lee, M. S. (2014). Ancient dates or accelerated rates? Morphological …
View article: Supplementary material from "Characterization of melanosomes involved in the production of non-iridescent structural feather colours and their detection in the fossil record"
Supplementary material from "Characterization of melanosomes involved in the production of non-iridescent structural feather colours and their detection in the fossil record" Open
Non-iridescent structural colour in avian feathers is produced by coherent light-scattering through quasi-ordered nanocavities in the keratin cortex of the barbs. To absorb unscattered light, melanosomes form a basal layer underneath the n…
View article: Archosauromorph extinction selectivity during the Triassic–Jurassic mass extinction
Archosauromorph extinction selectivity during the Triassic–Jurassic mass extinction Open
Many traits have been linked to extinction risk among modern vertebrates, including mode of life and body size. However, previous work has indicated there is little evidence that body size, or any other trait, was selective during past mas…
View article: Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations
Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations Open
[no abstract]
View article: Evolution of metazoan morphological disparity
Evolution of metazoan morphological disparity Open
Significance We attempt to quantify animal “bodyplans” and their variation within Metazoa. Our results challenge the view that maximum variation was achieved early in animal evolutionary history by nonuniformitarian mechanisms. Rather, the…
View article: Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model
Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model Open
To understand patterns and processes of the diversification of life, we require an accurate understanding of taxon interrelationships. Recent studies have suggested that analyses of morphological character data using the Bayesian and maxim…
View article: Evolution of jaw disparity in fishes
Evolution of jaw disparity in fishes Open
The morphology of the vertebrate lower jaw has been used to infer feeding ecology, with transformations in mandibular shape and structure likely to have facilitated the emergence of different feeding behaviours in vertebrate evolution. Her…
View article: Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss
Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss Open
microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and …
View article: The timescale of early land plant evolution
The timescale of early land plant evolution Open
Significance Establishing the timescale of early land plant evolution is essential to testing hypotheses on the coevolution of land plants and Earth’s System. Here, we establish a timescale for early land plant evolution that integrates ov…
View article: Mixed evidence for early bursts of morphological evolution in extant clades
Mixed evidence for early bursts of morphological evolution in extant clades Open
Macroevolutionary theory predicts high rates of evolution should occur early in a clade's history as species exploit ecological opportunity. Evidence from the fossil record has shown a high prevalence of early bursts in morphological evolu…