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Figure 3 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460

Figure 3 Undated 18S–26S nuclear DNA repeat region BEAST 2 phylogeny of Pennantia, under the Birth-Death model. The tree was rooted to make P. cunninghamii sister to the other species of Pennantia, in accordance with the chloroplast DNA tree and the ITS tree of Keeling et al. (2004). Node posterior probability is shown next to the corresponding node. The sequences downloaded from GenBank have their accession number in round brackets; the others were generated from the samples used in this study.

Supplementary material 3 from: Paszko B, Nikel A, Mueller-Bieniek A, Paul W (2020) Zapałowicz's Conspectus florae Galiciae criticus: Clarification of publication dates for nomenclatural purposes and bibliographic notes. PhytoKeys 155: 53-85. https://doi.org/10.3897/phytokeys.155.51072

Table S3

Supplementary material 1 from: Paszko B, Nikel A, Mueller-Bieniek A, Paul W (2020) Zapałowicz's Conspectus florae Galiciae criticus: Clarification of publication dates for nomenclatural purposes and bibliographic notes. PhytoKeys 155: 53-85. https://doi.org/10.3897/phytokeys.155.51072

Table S1

Supplementary material 2 from: Paszko B, Nikel A, Mueller-Bieniek A, Paul W (2020) Zapałowicz's Conspectus florae Galiciae criticus: Clarification of publication dates for nomenclatural purposes and bibliographic notes. PhytoKeys 155: 53-85. https://doi.org/10.3897/phytokeys.155.51072

Table S2

Figure 1 from: Paszko B, Nikel A, Mueller-Bieniek A, Paul W (2020) Zapałowicz's Conspectus florae Galiciae criticus: Clarification of publication dates for nomenclatural purposes and bibliographic notes. PhytoKeys 155: 53-85. https://doi.org/10.3897/phytokeys.155.51072

Figure 1 Hugo Zapałowicz (1852–1919). Image from http://www.cotg.pttk.pl/newsy/img/zapalowicz.jpg [Accessed September 2019].

Supplementary material 2 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460

BEAST2 and RAxML files

Figure 2 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460

Figure 2 Dated chloroplast DNA BEAST 2 phylogeny of Pennantia, under the Birth-Death model. Mean node age and 95% HPD (in My) is given in the table embedded in the figure under the corresponding letter code. 95% HPD is also represented by blue bars. All node posterior probabilities are equal to 1 except if indicated otherwise. The calibrated nodes (see text) are indicated by red dots.

Supplementary material 4 from: Paszko B, Nikel A, Mueller-Bieniek A, Paul W (2020) Zapałowicz's Conspectus florae Galiciae criticus: Clarification of publication dates for nomenclatural purposes and bibliographic notes. PhytoKeys 155: 53-85. https://doi.org/10.3897/phytokeys.155.51072

Table S4

Supplementary material 1 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460

Figs S1–S5; Tables S1–S3

Figure 2 from: Paszko B, Nikel A, Mueller-Bieniek A, Paul W (2020) Zapałowicz's Conspectus florae Galiciae criticus: Clarification of publication dates for nomenclatural purposes and bibliographic notes. PhytoKeys 155: 53-85. https://doi.org/10.3897/phytokeys.155.51072

Figure 2 The illustration of binding of Volume 6B of the Rozprawy Wydziału Matematyczno-Przyrodniczego Akademii Umiejętności, Dział B. Nauki Biologiczne (Seria 3) showing its book spine and the outside covers, with the 1906 date at the foot of the front cover. Copy from the library of the W. Szafer Institute of Botany, Polish Academy of Sciences (Kraków, Poland).

Figure 1 from: Maurin KJL (2020) A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences. PhytoKeys 155: 15-32. https://doi.org/10.3897/phytokeys.155.53460

Figure 1 General distribution of the four Pennantia species. TKI = Three Kings Islands. Generated in QGIS 3.0.1 from Google Satellite data obtained through the XYZ Tiles tool (https://mt1.google.com/vt/lyrs=s&x={x}&y={y}&z={z}).

opencc-zeroSep 2020View details →

Supplementary material 1 from: Klinger YP, Eckstein RL, Horlemann D, Otte A, Ludewig K (2020) Germination of the invasive legume Lupinus polyphyllus depends on cutting date and seed morphology. NeoBiota 60: 79-95. https://doi.org/10.3897/neobiota.60.56117

Model Tables

opencc-zeroOct 2020View details →

Mind the outgroup and bare branches in total-evidence dating: a case study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

<p>Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information, but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artefact that might be detrimental for total-evidence dating: "bare-branch attraction", namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.</p>

opencc-by-4.0Jan 2021View details →

400 events with dates and times of the worst-case severe environments

<p>400 events with dates and times of the worst-case severe environments</p>

opencc-zeroDec 2015View details →

Data from: The impact of the tree prior on molecular dating of data sets containing a mixture of inter- and intraspecies sampling

In Bayesian phylogenetic analyses of genetic data, prior probability distributions need to be specified for the model parameters, including the tree. When Bayesian methods are used for molecular dating, available tree priors include those designed for species-level data, such as the pure-birth and birth-death priors, and coalescent-based priors designed for population-level data. However, molecular dating methods are frequently applied to data sets that include multiple individuals across multiple species. Such data sets violate the assumptions of both the speciation and coalescent-based tree priors, making it unclear which should be chosen and whether this choice can affect the estimation of node times. To investigate this problem, we used a simulation approach to produce data sets with different proportions of within- and between-species sampling under the multispecies coalescent model. These data sets were then analysed under pure-birth, birth-death, constant-size coalescent, and skyline coalescent tree priors. We also explored the ability of Bayesian model testing to select the best-performing priors. We confirmed the applicability of our results to empirical data sets from cetaceans, phocids, and coregonid whitefish. Estimates of node times were generally robust to the choice of tree prior, but some combinations of tree priors and sampling schemes led to large differences in the age estimates. In particular, the pure-birth tree prior frequently led to inaccurate estimates for data sets containing a mixture of inter- and intraspecific sampling, whereas the birth-death and skyline coalescent priors produced stable results across all scenarios. Model testing provided an adequate means of rejecting inappropriate tree priors. Our results suggest that tree priors do not strongly affect Bayesian molecular dating results in most cases, even when severely misspecified. However, the choice of tree prior can be significant for the accuracy of dating results in the case of data sets with mixed inter- and intraspecies sampling.

opencc-zeroMay 2016View details →

Data from: Multiple morphological clocks and total-evidence tip-dating in mammals

Morphological integration predicts that correlated characters will coevolve; thus, each distinct suite of correlated characters might be expected to evolve according to a separate clock or 'pacemaker'. Characters in a large morphological dataset for mammals were found to be evolving according to seven separate clocks, each distinct from the molecular clock. Total-evidence tip-dating using these multiple clocks inflated divergence time estimates, but potentially improved topological inference. In particular, single-clock analyses placed several meridiungulates and condylarths in a heterodox position as stem placentals, but multi-clock analyses retrieved a more plausible and orthodox position within crown placentals. Several shortcomings (including uneven character sampling) currently impact upon the accuracy of total-evidence dating, but this study suggests that when sufficiently large and appropriately constructed phenotypic datasets become more commonplace, multi-clock approaches are feasible and can affect both divergence dates and phylogenetic relationships.

opencc-zeroDec 2013View details →

Data from: Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.

opencc-zeroDec 2018View details →

Data from: Cross-species hybridization and the origin of North African date palms

Date palm (Phoenix dactylifera L.) is a major fruit crop of arid regions that were domesticated 7,000 y ago in the Near or Middle East. This species is cultivated widely in the Middle East and North Africa, and previous population genetic studies have shown genetic differentiation between these regions. We investigated the evolutionary history of P. dactylifera and its wild relatives by resequencing the genomes of date palm varieties and five of its closest relatives. Our results indicate that the North African population has mixed ancestry with components from Middle Eastern P. dactylifera and Phoenix theophrasti, a wild relative endemic to the Eastern Mediterranean. Introgressive hybridization is supported by tests of admixture, reduced subdivision between North African date palm and P. theophrasti, sharing of haplotypes in introgressed regions, and a population model that incorporates gene flow between these populations. Analysis of ancestry proportions indicates that as much as 18% of the genome of North African varieties can be traced to P. theophrasti and a large percentage of loci in this population are segregating for single-nucleotide polymorphisms (SNPs) that are fixed in P. theophrasti and absent from date palm in the Middle East. We present a survey of Phoenix remains in the archaeobotanical record which supports a late arrival of date palm to North Africa. Our results suggest that hybridization with P. theophrasti was of central importance in the diversification history of the cultivated date palm.

opencc-zeroDec 2012View details →

Data from: Molecular dating, evolutionary rates, and the age of the grasses

Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a dataset of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae around 51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important groups.