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FIGURE 4 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 4. FMNH PR2081, Tyrannosaurus rex. Skull in ventral view (A, photograph; B, line interpretation of cranial sutures). Scale = 30 cm. See Appendix 1 for abbreviations. Photograph by J. Weinstein.

FIGURE 3 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 3. FMNH PR2081, Tyrannosaurus rex. Skull in dorsal view (A, photograph; B, line interpretation of cranial sutures). Scale = 30 cm. See Appendix 1 for abbreviations.

FIGURE 59 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 59. FMNH PR2081, Tyrannosaurus rex. Caudal vertebrae, posterior view. Scale = 15 cm. Photographs by J. Weinstein.

FIGURE 51 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 51. FMNH PR2081, Tyrannosaurus rex. Cervical vertebrae (p2 through p9), right lateral view. A is axis. Scale = 15 cm. See Appendix 1 for abbreviations. Photographs by J. Weinstein.

FIGURE 54 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 54. FMNH PR2081, Tyrannosaurus rex. Presacral vertebrae (p14 through p23), posterior view. Scale = 15 cm. See Appendix 1 for abbreviations. Photographs by J. Weinstein.

FIGURE 2 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 2. FMNH PR2081, Tyrannosaurus rex. Skull in right lateral view (A, photograph; B, line interpretation of cranial sutures). Scale = 30 cm. See Appendix 1 for abbreviations. Photograph by J. Weinstein.

FIGURE 50 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 50. FMNH PR2081, Tyrannosaurus rex. Cervical vertebrae (p2 through p9), left lateral view. A is axis. Scale = 1 5 cm. See Appendix 1 for abbreviations. Photographs by J. Weinstein.

FIGURE 69 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 69. FMNH PR2081, Tyrannosaurus rex. Haemal arches, dorsal view. Scale = 10 cm. Photographs by J. Weinstein.

FIGURE 53 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 53. FMNH PR2081, Tyrannosaurus rex. Presacral vertebrae (p14 through p23), anterior view. Scale =15 cm. See Appendix 1 for abbreviations. Photographs by J. Weinstein.

FIGURE 68 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 68. FMNH PR2081, Tyrannosaurus rex. Haemal arches, right lateral view. Scale = 10 cm. Photographs by J. Weinstein.

FIGURE 61 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 61. FMNH PR2081, Tyrannosaurus rex. Caudal vertebrae, dorsal view. Scale = 15 cm. Photographs by J. Weinstein.

FIGURE 67 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 67. FMNH PR2081, Tyrannosaurus rex. Haemal arches, posterior view. Scale = 10 cm. Photographs by J. Weinstein.

FIGURE 60 in Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull

FIGURE 60. FMNH PR2081, Tyrannosaurus rex. Caudal vertebrae, left lateral view. Scale = 1 5 cm. Photographs by J. Weinstein.

opencc-zeroDec 2016View details →

Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS: We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree–species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization. KEY RESULTS: Phylogenetic estimates from species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches. CONCLUSIONS: Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.

opencc-zeroDec 2015View details →

Data from: Root heterogeneity along an arctic elevational gradient: the importance of resolution

Spatial heterogeneity affects plant performance and is influenced by plants, but the scale at which fine roots react to or generate spatial heterogeneity has received little attention. Fine roots might be expected to respond to heterogeneity at a scale comparable to their diameter (mm), but studies to date have been conducted at much coarser resolutions (cm – m). Here we quantify root heterogeneity in contrasting habitats with special attention to the influence of resolution. We measured fine root length heterogeneity at resolutions ranging from 1 to 300 mm2, at four elevations along an arctic alpine gradient from 500 m a.s.l. (forest) to 1100 m (tundra). We calculated the magnitude of heterogeneity as the coefficient of variation of root length, and the scale of heterogeneity using semivariance analysis. The magnitude of heterogeneity was about twofold greater at fine than coarse resolution. Further, the magnitude of heterogeneity was generally greatest at the highest elevation, suggesting that soil at 1100 m was less evenly occupied by plant roots than soils at lower elevations. The exception to this was at the 1 mm2 resolution, for which the magnitude of heterogeneity did not vary with elevation, possibly because heterogeneity at this scale is related to ecophysiological processes common to all vegetation types. The scale of root length heterogeneity increased significantly with resolution coarseness, suggesting that roots respond to or generate patchiness at small scales that have not previously been examined. In contrast, the scale of heterogeneity did not vary significantly with elevation and the accompanying turnover in growth form. Our results suggest that roots in four vegetation types respond to or generate very fine scales of spatial heterogeneity, including scales much smaller than those that have previously been examined. Both the magnitude and scale of heterogeneity varied with sampling resolution, suggesting resolutions as small as a few millimetres are relevant to studies of spatial root interactions and below-ground processes.

opencc-zeroDec 2014View details →

Data from: The influence of data resolution on predicted distribution and estimates of extent of current protection of three 'listed' deep-sea habitats

Modelling approaches have the potential to significantly contribute to the spatial management of the deep-sea ecosystem in a cost effective manner. However, we currently have little understanding of the accuracy of such models, developed using limited data, of varying resolution. The aim of this study was to investigate the performance of predictive models constructed using non-simulated (real world) data of different resolution. Predicted distribution maps for three deep-sea habitats were constructed using MaxEnt modelling methods using high resolution multibeam bathymetric data and associated terrain derived variables as predictors. Model performance was evaluated using repeated 75/25 training/test data partitions using AUC and threshold-dependent assessment methods. The overall extent and distribution of each habitat, and the percentage contained within an existing MPA network were quantified and compared to results from low resolution GEBCO models. Predicted spatial extent for scleractinian coral reef and Syringammina fragilissima aggregations decreased with an increase in model resolution, whereas Pheronema carpenteri total suitable area increased. Distinct differences in predicted habitat distribution were observed for all three habitats. Estimates of habitat extent contained within the MPA network all increased when modelled at fine scale. High resolution models performed better than low resolution models according to threshold-dependent evaluation. We recommend the use of high resolution multibeam bathymetry data over low resolution bathymetry data for use in modelling approaches. We do not recommend the use of predictive models to produce absolute values of habitat extent, but likely areas of suitable habitat. Assessments of MPA network effectiveness based on calculations of percentage area protection (policy driven conservation targets) from low resolution models are likely to be fit for purpose.

opencc-zeroDec 2013View details →

Data from: Choice of resolution by functional trait or taxonomy affects allometric scaling in soil food webs

Belowground organisms often display a shift in their mass-abundance scaling relationships due to environmental factors such as soil chemistry and atmospheric deposition. Here we present new empirical data that show strong differences in allometric scaling according to whether the resolution at the local scale is based on a taxonomic or a functional classification, while only slight differences arise according to soil environmental conditions. For the first time, isometry (an inverse 1∶1 proportion) is recognized in mass-abundance relationships, providing a functional signal for constant biomass distribution in soil biota regardless of discrete trophic levels. Our findings are in contrast to those from aquatic ecosystems, in that higher trophic levels in soil biota are not a direct function of increasing body mass.

opencc-zeroDec 2014View details →

Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure

Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.

opencc-zeroDec 2014View details →

Data from: Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies

Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea.