henderson_et_al_code_README_ESM.txt from Sampling biases obscure the early diversification of the largest living vertebrate group

Extant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet spatio-temporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends, reconstruct local richness and apply richness estimation techniques to a recently assembled occurrence database for Palaeozoic ray-finned fishes. We identify substantial fossil record biases, such as geographical bias in sampling centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the occurrence distributions, reflecting historical biases in sampling and taxonomic practices, to the extent that evenness has an overriding effect on diversity estimates. Other than a genuine rise in diversity in the Tournaisian following the end-Devonian mass extinction, diversity estimates for Palaeozoic actinopterygians appear to lack biological signal, are heavily biased and are highly dependent on sampling. Increased sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the ‘global’ dataset may identify accurate local diversity trends

henderson_et_al_figures_ESM.pdf from Sampling biases obscure the early diversification of the largest living vertebrate group

Extant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet spatio-temporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends, reconstruct local richness and apply richness estimation techniques to a recently assembled occurrence database for Palaeozoic ray-finned fishes. We identify substantial fossil record biases, such as geographical bias in sampling centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the occurrence distributions, reflecting historical biases in sampling and taxonomic practices, to the extent that evenness has an overriding effect on diversity estimates. Other than a genuine rise in diversity in the Tournaisian following the end-Devonian mass extinction, diversity estimates for Palaeozoic actinopterygians appear to lack biological signal, are heavily biased and are highly dependent on sampling. Increased sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the ‘global’ dataset may identify accurate local diversity trends

henderson_et_al_data_ESM.csv from Sampling biases obscure the early diversification of the largest living vertebrate group

Extant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet spatio-temporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends, reconstruct local richness and apply richness estimation techniques to a recently assembled occurrence database for Palaeozoic ray-finned fishes. We identify substantial fossil record biases, such as geographical bias in sampling centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the occurrence distributions, reflecting historical biases in sampling and taxonomic practices, to the extent that evenness has an overriding effect on diversity estimates. Other than a genuine rise in diversity in the Tournaisian following the end-Devonian mass extinction, diversity estimates for Palaeozoic actinopterygians appear to lack biological signal, are heavily biased and are highly dependent on sampling. Increased sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the ‘global’ dataset may identify accurate local diversity trends

henderson_et_al_code_ESM.txt from Sampling biases obscure the early diversification of the largest living vertebrate group

Extant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet spatio-temporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends, reconstruct local richness and apply richness estimation techniques to a recently assembled occurrence database for Palaeozoic ray-finned fishes. We identify substantial fossil record biases, such as geographical bias in sampling centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the occurrence distributions, reflecting historical biases in sampling and taxonomic practices, to the extent that evenness has an overriding effect on diversity estimates. Other than a genuine rise in diversity in the Tournaisian following the end-Devonian mass extinction, diversity estimates for Palaeozoic actinopterygians appear to lack biological signal, are heavily biased and are highly dependent on sampling. Increased sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the ‘global’ dataset may identify accurate local diversity trends

Supplementary Information from Diversity change during the rise of tetrapods and the impact of the ‘Carboniferous rainforest collapse’

The Carboniferous and early Permian were critical intervals in the diversification of early four-limbed vertebrates (tetrapods), yet the major patterns of diversity and biogeography during this time remain unresolved. Previous estimates suggest that global tetrapod diversity rose continuously across this interval and that habitat fragmentation following the ‘Carboniferous rainforest collapse’ (CRC) drove increased endemism among communities. However, previous work failed to adequately account for spatial and temporal biases in sampling. Here, we reassess early tetrapod diversity and biogeography with a new global species-level dataset using sampling standardization and network biogeography methods. Our results support a tight relationship between observed richness and sampling, particularly during the Carboniferous. We found that subsampled species richness initially increased into the late Carboniferous, then decreased substantially across the Carboniferous/Permian boundary before slowly recovering in the early Permian. Our analysis of biogeography does not support the hypothesis that the CRC drove endemism; instead, we found evidence for increased cosmopolitanism in the early Permian. While a changing environment may have played a role in reducing diversity in the earliest Permian, our results suggest that the CRC was followed by increased global connectivity between communities, possibly reflecting both reduced barriers to dispersal and the diversification of amniotes

C Early tetrapod supertree from Diversity change during the rise of tetrapods and the impact of the ‘Carboniferous rainforest collapse’

Informal species-level supertree of early tetrapods based upon the most recent phylogenetic analyses and formal supertrees available for the major clades of Carboniferous–early Permian tetrapod

B Early tetrapod species occurrences (cleaned) from Diversity change during the rise of tetrapods and the impact of the ‘Carboniferous rainforest collapse’

Occurrence dataset which has been edited to exclude marine taxa and taxa indeterminate at species and genus leve

Supplementary Information from Diversity change during the rise of tetrapods and the impact of the ‘Carboniferous rainforest collapse’

The Carboniferous and early Permian were critical intervals in the diversification of early four-limbed vertebrates (tetrapods), yet the major patterns of diversity and biogeography during this time remain unresolved. Previous estimates suggest that global tetrapod diversity rose continuously across this interval and that habitat fragmentation following the ‘Carboniferous rainforest collapse’ (CRC) drove increased endemism among communities. However, previous work failed to adequately account for spatial and temporal biases in sampling. Here, we reassess early tetrapod diversity and biogeography with a new global species-level dataset using sampling standardization and network biogeography methods. Our results support a tight relationship between observed richness and sampling, particularly during the Carboniferous. We found that subsampled species richness initially increased into the late Carboniferous, then decreased substantially across the Carboniferous/Permian boundary before slowly recovering in the early Permian. Our analysis of biogeography does not support the hypothesis that the CRC drove endemism; instead, we found evidence for increased cosmopolitanism in the early Permian. While a changing environment may have played a role in reducing diversity in the earliest Permian, our results suggest that the CRC was followed by increased global connectivity between communities, possibly reflecting both reduced barriers to dispersal and the diversification of amniotes

Orbit size and estimated eye size in dinosaurs and other archosaurs and their implications for the evolution of visual capabilities

Vision is one of the most important senses for animals, allowing them to interact with their environment and with further implications for evolutionary histories. However, relevant soft tissues, such as the eye and associated structures, are not preserved in fossil vertebrates, limiting our knowledge of their visual capabilities. Here, we quantified absolute and relative orbit size for 400 species of dinosaurs and other extinct archosaurs using linear measurements of the preserved skeletal elements as a proxy for visual capabilities. Our results demonstrate that the orbit makes up on average 20% of skull size with a strong and consistent correlation across all sampled groups. This trend is largely independent of temporal distribution, species richness, and phylogeny. In fact, relative orbit size is narrowly constrained and did not surpass 45% of skull size, suggesting physiological and functional controls. Estimated eye size was found to be absolutely larger in herbivores, whereas carnivores tended to have smaller eyes absolutely and compared with skull size. Relatively large eyes only occurred in small-bodied species and vice versa. However, eye size alone was not sufficient to discriminate between different activity patterns or to characterize visual capabilities in detail.</p

Additional file 1 of Single vs. multiple fraction non-inferiority trial of stereotactic ablative radiotherapy for the comprehensive treatment of oligo-metastases/progression: SIMPLIFY-SABR-COMET

Additional file 1: Appendix 1. BC CANCER PROVINCIAL SABR ORGAN-AT-RISK (OAR) CONSTRAINTS. Appendix 2. Reasonable reirradiation SBRT doses to the thecal sac Pmax following common initial conventional radiotherapy regimens