Rewinding the molecular clock in the genus Carabus (Coleoptera: Carabidae) in light of fossil evidence and the Gondwana split: A reanalysis

Molecular clocks have become powerful tools given increasing sequencing and fossil resources. However, calibration analyses outcomes depend on the choice of priors. Here, we revisited the seminal dating study published by Andújar and coworkers of the genus Carabus proposing that prior choices need re-evaluation. We hypothesized that reflecting fossil evidence and the Gondwanan split properly significantly rewinds the molecular clock. We re-used the dataset including five mitochondrial and four nuclear DNA fragments with a total length of 7888 nt. Fossil evidence for Oligocene occurrence of Calosoma was considered. Root age was set based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous. Paleogene divergence of the outgroup taxa Ceroglossini and Pamborini is introduced as a new prior based on current paleontological and geological literature. The ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCA Carabus of 53.92 Ma (HPD 95% 45.01–63.18 Ma), roughly 30 Ma older than in the Andújar study. The splits among C. rugosus and C. morbillosus (A), C. riffensis from the European Mesocarabus (B), and Eurycarabus and Nesaeocarabus (C) were dated to 17.58 (12.87–22.85), 24.14 (18.02–30.58), and 21.6 (16.44–27.43) Ma. They were decidedly older than those previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven almost entirely by constraining the Carabidae time-tree root with a Harpalinae amber fossil at ~99 Ma. Utilizing the nd5 dating results of three well-supported Carabus clades as secondary calibration points for the complete MIT-NUC dataset led to a TMRCA of Carabus of 44.72 (37.54–52.22) Ma, compared with 25.16 Ma (18.41–33.04 Ma) in the previous study. Considering fossil evidence for Oligocene Calosoma and Late Cretaceous Harpalini together with the Gondwanan split as a new prior, our new approach supports the origin of genus Carabus in the Eocene. Our results are preliminary because of the heavy reliance on the nd5 gene, and thus will have to be tested with a sufficient set of nuclear markers. Additionally, uncertainties due to dating root age of the tree based on a single fossil and outgroup taxon affect the results. Improvement of the fossil database, particularly in the supertribe Carabitae, is needed to reduce these uncertainties in dating Carabus phylogeny.

Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor et al . (2020)

Through phylogenetic modelling, we previously presented strong support for diversification decline in the three major subclades of dinosaurs (Sakamoto et al . 2016 Proc. Natl Acad. Sci. USA 113 , 5036–5040. ( doi:10.1073/pnas.1521478113 )). Recently, our support for this model has been criticized (Bonsor et al . 2020 R. Soc. Open Sci. 7 , 201195. ( doi:10.1098/rsos.201195 )). Here, we highlight that these criticisms seem to largely stem from a misunderstanding of our study: contrary to Bonsor et al .'s claims, our model accounts for heterogeneity in diversification dynamics, was selected based on deviance information criterion (DIC) scores (not parameter significance), and intercepts were estimated to account for uncertainties in the root age of the phylogenetic tree. We also demonstrate that their new analyses are not comparable to our models: they fit simple, Dinosauria-wide models as a direct comparison to our group-wise models, and their additional trees are subclades that are limited in taxonomic coverage and temporal span, i.e. severely affected by incomplete sampling. We further present results of new analyses on larger, better-sampled trees ( N = 961) of dinosaurs, showing support for the time-quadratic model. Disagreements in how we interpret modelled diversification dynamics are to be expected, but criticisms should be based on sound logic and understanding of the model under discussion.

Root biomass and root traits of Alnus glutinosa show size-dependent and opposite patterns in a drained and a rewetted forest peatland

Background and Aims Forest peatlands represent 25 % of global peatlands and store large amounts of carbon (C) as peat. Traditionally they have been drained in order to increase forestry yield, which may cause large losses of C from the peat. Rewetting aims to stop these losses and to restore the initial storage function of the peatlands. As roots represent major peat-forming elements in these systems, we sampled roots with diameter <5 mm in a drained and a rewetted forest peatland in north-east Germany to evaluate differences in tree biomass investments below ground, root functional characteristics and root age. Methods We cored soil next to Alnus glutinosa stems and sorted root biomass into <1, 1–2 and 2–5 mm diameter classes. We measured biomass distribution and specific root area (SRA) in 10-cm depth increments down to 50 cm, and estimated root age from annual growth rings. Key Results Root biomass in the rewetted site was more than double that in the drained site. This difference was mostly driven by very fine roots <1 mm, which accounted for 51 % of the total root biomass and were mostly (75 %) located in the upper 20 cm. For roots <1 mm, SRA did not differ between the sites. However, SRA of the 1–2 mm and 2–5 mm diameter roots was higher in the drained than in the rewetted site. Root age did not differ between sites. Conclusions The size-dependent opposite patterns between root biomass and their functional characteristics under contrasting water regimes indicate differences between fine and coarse roots in their response to environmental changes. Root age distribution points to similar root turnover rates between the sites, while higher root biomass in the rewetted site clearly indicates larger tree C stocks below ground under rewetting, supporting the C sink function of the ecosystem.

Rewinding the molecular clock in the genus Carabus (Coleoptera: Carabidae) in light of fossil evidence and the Gondwana split: a re-analyses

1AbstractBackgroundMolecular clocks have become powerful tools given increasing sequencing and fossil resources. However, outcome of calibration analyses depend on choosing priors. Here we revisit a seminal dating study of the genus Carabus by Andujar et al. proposing that their prior choices need re-evaluation with the hypothesis that reflecting fossil evidence and the Gondwanan split properly rewinds the molecular clock significantly. We used the same dataset including five mitochondrial and four nuclear DNA fragments with 7888 nt total length. We set the root age based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous and introduce the Paleogene divergence of the outgroup taxa Ceroglossus (endemic to South-America) and Pamborus + Maoripamborus (Australia, New Zealand) as a new prior based on current paleontological and geological literature.ResultsThe ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCA Carabus age of 58.48 Ma (HPD95% 46.61-72.04), roughly 35 Ma older than in the Andujar study. The splits between C. rugosus and C. morbillosus (A), between C. riffensis from the European Mesocarabus (B), and between Eurycarabus and Nesaeocarabus (C) were dated to 19.19 (13.54-25.87), 25.95 (18.8-34.62), and 23.98 (17.28-31.47) Ma and were thus decidedly older than previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven solely by constraining the Carabidae time tree root with Harpalinae amber fossils at ∼99 Ma. Utilizing the nd5 dating results of three well supported Carabus clades as secondary calibration points for the complete MIT-NUC data set lead to a TMRCA of Carabus of 53.56 (41.25-67.05) Ma compared to 25.16 (18.41-33.04) in Andujar’s study.ConclusionTaking into account the Gondwanan split as a new prior, together with the fossil evidence of the outgroup taxon Harpalini in the Late Cretaceous, our new approach supports an origin of the genus Carabus in the Paleocene-Early Eocene. Our results are preliminary due to the heavy reliance on the nd5 gene and thus will have to be tested with sufficient set of nuclear markers. In addition, uncertainties arise from dating the root age of the tree based on a single fossil and outgroup taxon which has a major effect on the results. Improvement of the fossil data base particularly in the supertribe Carabitae is thus strongly needed to reduce the currently large uncertainties in dating Carabus phylogeny.

Genotypic and Organ Variation in Ginsenoside Contents from American Ginseng Populations

Variation in ginsenoside content was investigated as a function of population/genotype, plant organ, and age using four geographically isolated wild populations and one landrace population of american ginseng (Panax quinquefolius L.). The contents of individual and total ginsenosides were affected by the main and two-way interactions between population, organ, and age. Ginsenoside Re was not detected in roots of the wild population plants but was found in leaves and in both organs of the landrace population. A positive relationship between root age and total root ginsenosides was detected in two wild populations. Individual root ginsenosides were highly correlated with certain leaf ginsenosides in wild populations rather than in landrace populations. Therefore, the results suggest that certain leaf ginsenosides would be applied for potential biomarkers to estimate individual root ginsenosides. Principal component analysis (PCA) scores plot indicates that all wild populations were segregated from the single landrace population. However, cluster analysis indicates that differences existed between organs, and between the wild and landrace populations. Overall, the result suggests that the variation of individual and total ginsenoside contents would be influenced by a combination of population, plant organ, and root age.