Accelerated evolution and diversifying selection drove the adaptation of cetacean bone microstructure

Sun, Di; Zhou, Xuming; Yu, Zhenpeng; Xu, Shixia; Seim, Inge; Yang, Guang

doi:10.1186/s12862-019-1509-x

Cited by 7 publications

(6 citation statements)

References 70 publications

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“…find very little evidence of phylogenetic signal in their dataset, with Pagel’s λ parameter taking values 0.02≤λ≤0.07 across the various datasets and trials. This is consistent with other studies of Cg that used comparable datasets to analyze convergent features across many clades [ 45 , 46 ]. As a result, one would expect little difference between these results and those obtained with ordinary LDA.…”

Section: Methodssupporting

confidence: 91%

Diving dinosaurs? Caveats on the use of bone compactness and pFDA for inferring lifestyle

Myhrvold,

Baumgart,

Vidal

et al. 2024

PLoS ONE

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The lifestyle of spinosaurid dinosaurs has been a topic of lively debate ever since the unveiling of important new skeletal parts for Spinosaurus aegyptiacus in 2014 and 2020. Disparate lifestyles for this taxon have been proposed in the literature; some have argued that it was semiaquatic to varying degrees, hunting fish from the margins of water bodies, or perhaps while wading or swimming on the surface; others suggest that it was a fully aquatic underwater pursuit predator. The various proposals are based on equally disparate lines of evidence. A recent study by Fabbri and coworkers sought to resolve this matter by applying the statistical method of phylogenetic flexible discriminant analysis to femur and rib bone diameters and a bone microanatomy metric called global bone compactness. From their statistical analyses of datasets based on a wide range of extant and extinct taxa, they concluded that two spinosaurid dinosaurs (S. aegyptiacus, Baryonyx walkeri) were fully submerged “subaqueous foragers,” whereas a third spinosaurid (Suchomimus tenerensis) remained a terrestrial predator. We performed a thorough reexamination of the datasets, analyses, and methodological assumptions on which those conclusions were based, which reveals substantial problems in each of these areas. In the datasets of exemplar taxa, we found unsupported categorization of taxon lifestyle, inconsistent inclusion and exclusion of taxa, and inappropriate choice of taxa and independent variables. We also explored the effects of uncontrolled sources of variation in estimates of bone compactness that arise from biological factors and measurement error. We found that the ability to draw quantitative conclusions is limited when taxa are represented by single data points with potentially large intrinsic variability. The results of our analysis of the statistical method show that it has low accuracy when applied to these datasets and that the data distributions do not meet fundamental assumptions of the method. These findings not only invalidate the conclusions of the particular analysis of Fabbri et al. but also have important implications for future quantitative uses of bone compactness and discriminant analysis in paleontology.

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Section: Methodssupporting

confidence: 91%

Diving dinosaurs? Caveats on the use of bone compactness and pFDA for inferring lifestyle

Myhrvold,

Baumgart,

Vidal

et al. 2024

PLoS ONE

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show abstract

“…Although in principle the phylogenetic signal could have a strong effect, in practice, Fabbri et al find very little evidence of phylogenetic signal in their dataset, with Pagel's λ parameter taking values 0.02�λ�0.07 across the various datasets and trials. This is consistent with other studies of Cg that used comparable datasets to analyze convergent features across many clades [45,46]. As a result, one would expect little difference between these results and those obtained with ordinary LDA.…”

supporting

confidence: 91%

Diving dinosaurs? Caveats on the use of bone compactness and pFDA for inferring lifestyle

Myhrvold

Sereno

Baumgart

et al. 2023

Preprint

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Measures of bone compactness in amniote tetrapods of varying lifestyle were used to infer that two spinosaurid dinosaurs (Spinosaurus aegyptiacus, Baryonyx walkeri) were diving "subaqueous foragers," whereas a third spinosaurid (Suchomimus tenerensis) and other sampled nonavian dinosaurs were non-diving terrestrial feeders entering water only as waders. We outline shortcomings in this analysis that involve bone compactness sampling and measurement, lifestyle categorization, the inclusion and exclusion of taxa in the dataset, and flawed statistical methods and inferences. These many shortcomings undermine the evidence used to conclude that two spinosaurid taxa were avid divers. Bone compactness indices remain a valuable tool for interpretation of lifestyle in extinct species when based on sound dataset composition, robust statistical analysis, and consilience with evidence from functional, biomechanical, or paleoenvironmental considerations.

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“…The evolutionary process of genes can be well understood by selection pressure analysis. When positive selection genes were detected on the ancestral branch of cetaceans, their genes involved in osteoclast function underwent accelerated evolution, thus demonstrating that bone remodeling played an important role in their adaptation to the water environment [ 32 ]. Zhang et al have analyzed the TLR genes of 102 amphibian species and found that purification selection played a major role in amphibian TLR evolution [ 33 ].…”

Section: Discussionmentioning

confidence: 99%

Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs

Zhang

et al. 2023

IJMS

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Body size is an important biological phenotypic trait that has attracted substantial attention. Small domestic pigs can serve as excellent animal models for biomedicine and also help meet sacrificial culture needs in human societies. Although the mechanisms underlying vertebral development regulating body size variation in domestic pigs during the embryonic period have been well described, few studies have examined the genetic basis of body size variation in post embryonic developmental stages. In this study, seven candidate genes—PLIN1, LIPE, PNPLA1, SCD, FABP5, KRT10 and IVL—significantly associated with body size were identified in Min pigs, on the basis of weighted gene co-expression network analysis (WGCNA), and most of their functions were found to be associated with lipid deposition. Six candidate genes except for IVL were found to have been subjected to purifying selection. PLIN1 had the lowest ω value (0.139) and showed heterogeneous selective pressure among domestic pig lineages with different body sizes (p < 0.05). These results suggested that PLIN1 is an important genetic factor regulating lipid deposition and consequently affecting body size variation in pigs. The culture of whole pig sacrifice in Manchu during the Qing Dynasty in China might have contributed to the strong artificial domestication and selection of Hebao pigs.

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Accelerated evolution and diversifying selection drove the adaptation of cetacean bone microstructure

Cited by 7 publications

References 70 publications

Diving dinosaurs? Caveats on the use of bone compactness and pFDA for inferring lifestyle

Diving dinosaurs? Caveats on the use of bone compactness and pFDA for inferring lifestyle

Diving dinosaurs? Caveats on the use of bone compactness and pFDA for inferring lifestyle

Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs

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