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opencc-zeroOct 2019View details →

Data from: A Bayesian approach for inferring the impact of a discrete character on rates of continuous-character evolution in the presence of background-rate variation

Understanding how and why rates of character evolution vary across the Tree of Life is central to many evolutionary questions; e.g., does the trophic apparatus (a set of continuous characters) evolve at a higher rate in fish lineages that dwell in reef versus non-reef habitats (a discrete character)? Existing approaches for inferring the relationship between a discrete character and rates of continuous-character evolution rely on comparing a null model (in which rates of continuous-character evolution are constant across lineages) to an alternative model (in which rates of continuous-character evolution depend on the state of the discrete character under consideration). However, these approaches are susceptible to a "straw-man" effect: the influence of the discrete character is inflated because the null model is extremely unrealistic. Here, we describe MuSSCRat, a Bayesian approach for inferring the impact of a discrete trait on rates of continuous-character evolution in the presence of alternative sources of rate variation ("background-rate variation"). We demonstrate by simulation that our method is able to reliably infer the degree of state-dependent rate variation, and show that ignoring background-rate variation leads to biased inferences regarding the degree of state-dependent rate variation in grunts (the fish group Haemulidae).

opencc-zeroJan 2024View details →

Fast Bayesian inference of phylogenies from multiple continuous characters

<p>Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remains challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.</p>

publicNov 2019View details →

Data from: A Bayesian approach for inferring the impact of a discrete character on rates of continuous-character evolution in the presence of background-rate variation

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Fast Bayesian inference of phylogenies from multiple continuous characters

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opennotspecifiedJan 2016View details →

FIGURE 2. Discretized continuous characters. Each point denotes a in Revision and phylogenetic analysis of the orb-weaving spider genus Glenognatha Simon, 1887 (Araneae, Tetragnathidae)

FIGURE 2. Discretized continuous characters. Each point denotes a measured individual (up to three for each species) and the horizontal lines are the limits between states (Mann-Whitney U=0.0, p<0.001). PDP: paracymbium distal portion. PBP: paracymbium basal portion. Ret: Retromarginal tooth.

opennotspecifiedMay 2003View details →

text-fig. 28. Sacra of theropod dinosaurs, illustrating different states for character 116. a, sacrum and ilium of Herrerasaurus ischigualastensis in lateral view; the shaded area indicates the attachment area of the very massive sacral ribs on the medial side of the ilium; modified from Novas (1993). B, sacrum and ilia of Syntarsus rhodesiensis in dorsal view, showing the almost continuous sheet of bone formed by the sacral ribs between the sacrum and the iliac blades; based on Raath (1990) and QG1. Abbreviations: ib, iliac blade; il, ilium; ns: neural spine; SI, S2, sacral vertebrae; sac, supraacetabular crest; sr, sacral ribs; st, spine table. Scale bars represent 50 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 28. Sacra of theropod dinosaurs, illustrating different states for character 116. a, sacrum and ilium of Herrerasaurus ischigualastensis in lateral view; the shaded area indicates the attachment area of the very massive sacral ribs on the medial side of the ilium; modified from Novas (1993). B, sacrum and ilia of Syntarsus rhodesiensis in dorsal view, showing the almost continuous sheet of bone formed by the sacral ribs between the sacrum and the iliac blades; based on Raath (1990) and QG1. Abbreviations: ib, iliac blade; il, ilium; ns: neural spine; SI, S2, sacral vertebrae; sac, supraacetabular crest; sr, sacral ribs; st, spine table. Scale bars represent 50 mm.

FIGURE 43 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 43. Cladogram of species of Pinnunavis, Pinnularia and Caloneis based on 6 morphological characters using Mayamaea atomus as an outgroup. Tree length = 41, consistency index= 0.366, retention index = 0.381, rescaled consistency index = 0.139, homoplasy index = 0.634.

FIGURE 42 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 42. Prediction belts for inter-raphe distance in Pinnunavis yarrensis in this study. The thick black line is the linear regression line (n = 41). Six pairs of symmetrically disposed upper and lower 95% prediction belts are indicated by the thinner lines for unknown samples with sizes of 1, 2, 3, 5, 10 and 25 specimens. Those for sample size 1 are furthest from the regression line, and the limits move closer to the regression line as sample size increases. The double-headed red arrow indicates the 95% prediction interval for the mean inter-raphe distance of 3 unknown specimens, each 100 µm long. If the 3 unknown specimens were P. yarrensis and 100 µm long, then 95% of the time their mean would be expected to fall within the interval of 2.7–3.5 µm.

FIGURE 40 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 40. Inter-raphe distance as a function of valve length in Pinnunavis edkuensis, P. yarrensis and the Port Elizabeth sample. Regression lines (solid) represent the entire sample; the 95% prediction belts for the mean inter-raphe distance based on new sample size of 2 (dashed lines) are shown for each taxon.

FIGURE 39 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 39. Transect location of the maximum striae slope as a function of valve length for the 3 Pinnunavis species. Dashed regressions lines are not significantly different from zero (all p> 0.05).

FIGURE 38 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 38. Maximal striae slope in degrees versus specimen size for 3 species of Pinnunavis. Dashed regression line slopes are not significantly different from zero (p> 0.05). The circled P. yarrensis specimen (at c. x = 150, y = 10) was included in the analysis; its exclusion would not have changed the conclusions.

FIGURE 41 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 41. Comparison of the gap size in the continuous character inter-raphe distance and the t-values from paired t-tests on random samples (n = 20) of inter-raphe distance from two hypothetical groups. Four sets of 1000-replicate simulations show the effects of varying the distance between the parametric means of Group A (µA = 1.5, fixed) and Group B (variable, values shown on the chart). In all simulation sA = sB = 0.29. The dashed red line indicates the critical t-value (one-tailed) for all comparisons except µB = 1.5, for which the dashed blue line indicates the two-tailed critical t-value. Positive gap distances (shaded light blue) between paired samples indicate no range overlap, i.e. a gap, while negative inter-raphe distances indicate range overlap, i.e. no gap.

FIGURE 37 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 37. Striae slope within valves (individuals) in three taxa as a function of transect location. Each regression line is a quartic polynomial describing the pattern of striae slope in a single valve. For P. yarrensis, only the curves for Yarra Yarra are plotted, but both Yarra Yarra and South Yarra samples were pooled and used in the statistical analysis. The triangles denote taxon means at three semivalve transect locations. The P. yarrensis YY23 curve is a statistical outlier which was included in the analysis; its exclusion does not affect the conclusions of the analysis. Inset charts (a–c) are striae slopes at specific semivalve transect locations versus valve length. Inset regression lines significantly (p <0.05) different from zero are solid; those not significant are dashed.

FIGURE 36 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 36. Quartic polynomial regressions of striae orientation (degrees) along a semivalve transect in 3 species. Individual points are single stria slope measurements; solid lines are polynomial regression lines for all measured orientations in a taxon.

FIGURE 35 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 35. Quadratic regressions of striae orientation (degrees) along a semivalve transect in 3 species. Individual points are single stria slope measurements; solid lines are polynomial regression lines for all measured orientations in a taxon

FIGURE 34 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 34. The distribution of proximal interstriae distances along semi-valve transects in Pinnunavis edkuensis, P. yarrensis, P. zalatii ("aegyptiaca" subset) and the Port Elizabeth sample. Each quadratic regression line represents a single valve based on c. 50–140 proximal interstriae distances. Transect distance is measured in µm from the transapical axis. Taxon means are indicated by triangles at transect locations x = 0, 10 and 20 µm. Each of the 3 graphic insets (a)–(c) shows for the 3 species the interstriae distances at transect locations x = 0, 10 and 20 µm, respectively, regressed against valve length. The axis in the inset graphs are the same as on the larger plot. The Port Elizabeth sample was not part of the anova, its means were not plotted in the larger graph, and it was not plotted in the insets. A traditional striae density scale is provided on the right side of the plot.

FIGURE 33 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 33. The distribution of proximal interstriae distances along the semivalve transect in Pinnunavis edkuensis, P. yarrensis, P. zalatii ("aegyptiaca" subset only) and the Port Elizabeth samples. Regression lines are solid; 98% confidence intervals for the regression lines are indicated by dashed lines. A traditional striae density scale is provided along the right side of the plot.

FIGURE 30 in A morphometric diagnosis using continuous characters of Pinnunavis edkuensis, sp. nov. (Bacillariophyta: Bacillariophyceae), a brackish-marine species from Egypt

FIGURE 30. The relationship of valve face surface area (solid regression lines) and axial area surface area (dashed regression lines) to valve length in 3 species of Pinnunavis and the Port Elizabeth sample.