Dating the Diversification of the Major Lineages of Ascomycota (Fungi)
Establishing the dates for the origin and main diversification events in the . times for major events in fungal evolution (e.g., the time for the origin of Fungi, .. Comparison of divergence ages in several Ascomycota clades. Dating the Time of Origin of Major Clades: Molecular Clocks and the Fossil Record. Annual Review of Earth and Planetary Sciences. Vol. (Volume . divergence time, molecular dating, mutation rate, phylogeny, Poaceae estimated an origin of the BEP-PACMAD clade between 52 and 86 Ma (Vicentini et al. The ages obtained for the major clades of grasses by different methods and.
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. The accumulation of genetic mutations is not linear with respect to time, and potential variation in rates of mutation accumulation must be taken into account when inferring lineage divergence dates Magallon Several sophisticated methods are now available that consider potential variation in evolutionary rates across the phylogeny by implementing so-called relaxed molecular clocks Kishino et al.
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- Dating the time of origin of major clades: molecular clocks and the fossil record
Often, however, there is a low number of fossil calibration points relative to a large number of species and thus nodes in the phylogeny. The informativeness of any fossil depends largely on the accuracy of its assignment to a taxonomic group Magallon ; Parham et al.
Dating methods can thus be strongly influenced by both the assumptions of the underlying models and the uncertainties around the incorporation of fossil evidence Ho et al. The most commonly used methods differ mainly in how rate variation is modeled and, in particular, whether or not they assume autocorrelation of rates Kishino et al. Investigation into the appropriateness of rate autocorrelation has been inconclusive, yielding contrasting results depending on the data sets and methods used Drummond et al.
In this study, we explore the effect of variation in rates of mutation, fossil placement, and model assumptions on divergence time estimation, with the goal of inferring the age of the grasses Poaceae; monocots.
This diverse and ecologically important plant lineage of more than 11, species includes the world's major crops, such as rice, wheat, and maize, and natural grasslands cover large regions of the world's terrestrial land surface e.
Gibson ; Edwards et al. Previous dating analyses of Poaceae have typically included only a limited number of taxa outside the focal group Vicentini et al. Meanwhile, molecular dating analyses of angiosperms flowering plants are abundant in recent literature and, despite differences in methodology, independent estimates converge on a date for the split between the two major groups of flowering plants eudicots and monocots between roughly and Ma Bell et al.
The incongruence between large-scale phylogenetic analyses including a few representatives of Poaceae and densely sampled analyses focused on Poaceae likely results from important variation in rates of evolution between grasses and other angiosperms Gaut et al.
New insights into this problem might be gained from analyses of markers from different genomes that consider fossil evidence within Poaceae as well as in distant lineages.
Dating the Diversification of the Major Lineages of Ascomycota (Fungi)
We performed divergence time analyses of different data sets of plastid and nuclear genetic markers, sampling broadly from across all angiosperms. The ages obtained for the major clades of grasses by different methods and genetic markers were compared with the known fossil record. The influence of a divergent calibration point, represented here by the most recently published phytolith fossils Prasad et al.
Different methods deal with uncertainty associated with the phylogenetic position of fossil calibration points  — .
The method implemented in the Bayesian phylogenetic software BEAST  allows the user to account for uncertainty in the age of a given fossil, in the form of a prior distribution. By allowing calibrating information to be represented in the form of parametric distributions, this approach offers a high degree of flexibility to incorporate a time scale into a phylogenetic analysis .
Several estimates for divergence times in Fungi have been published during the last two decades e. Many of these studies obtained radically different age estimates for the same divergence events, with analyses based on different methods e.
Dating the time of origin of major clades - thebluetones.info
The fossil record in Fungi is very limited compared with plants and animals . This is due to a combination of the often microscopic nature of fungi, the very poor preservation potential  and probably, the relative difficulty in recognizing them in the fossil record . Many, probably most, major lineages of fungi thus currently lack fossil data. As the fossil record is fragmentary, a given fossil will very rarely possess features that place it in the crown group rather than along the stem lineage leading to the crown group .
In Fungi, one of the most noteworthy examples is Paleopyrenomycites devonicus, the oldest unequivocal euascomycete fossil from the lower Devonian ca million years ago [Mya]the systematic position of which has been widely disputed  —  — .
This was done through a graphical recalibration of nodes from a number of fungal molecular clock trees, by fixing the age of the Ascomycota-Basidiomycota origin to 1 and calculating the relative ages of major nodes in the tree pp — The fossil is morphologically complex and does not fit within any extant taxonomic group.
The presence of an ascoma opening similar to an operculum has resulted in different interpretations about its affinities, although it is clear that this structure is not homologous with the operculum in modern Pezizomycotina. Other remarkable Ascomycota fossils found in amber include an Aspergillus species growing on a springtail from the Eocene a species related to the extant anamorphic ascomycete genus Curvularia from the Cretaceous  and a Xylaria species from Dominican amber .
The resinicolous mazaediate fungus Chaenothecopsis bitterfeldensis was found in Bitterfeld amber from around 22 million years ago, near the Miocene—Oligocene boundary  and recently, two Chaenothecopsis fossils were described from Eocene Baltic and Oligocene Bitterfeld amber dating back to at least 35 and 24 Ma ago, respectively .
Well—preserved lichen fossils are found in Baltic 35—55 Mya and Dominican amber with estimates ranging from 15—20 to 30—45 Mya. Among these fossils, there is an alectorioid lichen and two specimens of Anzia from Baltic amber  — two species of Parmelia s.
Crustose lichen fossils belonging to both mazaediate genera Calicium and Chaenotheca were also found in Baltic amber . Finally, an impression of a foliose macrolichen belonging to Lobariaceae  was found from Miocene deposits. Until now, very few studies have included these fossils to calibrate phylogenetic trees and even fewer have used them to estimate the timing of the main divergence events within Ascomycota. Most of the existing dating studies provide hypotheses on divergence times for major events in fungal evolution e.
Most of these studies are also not focused on Fungi, but have a wider scope, including plants and animals, and the taxon sampling may not be optimal for calculating the origin and divergence times of lineages within Ascomycota or Basidiomycota . One exception is the study of Gueidan et al. Several fossils related to extant mazaediate genera have been found in amber, but these have not been used for calibrating phylogenetic trees.
We have recently produced a phylogeny of the Ascomycota with the aim of placing mazaedia—producing groups with previously unknown relationships . This phylogeny contains representatives of several groups in which amber—preserved fossils occur, which can now be utilized for dating. Here, we want to take advantage of this recent phylogeny and use it to date the main diversification events within Ascomycota.
To achieve this, we include all the dateable mazaediate fossils known, together with other Ascomycota fossils, to investigate the origin and divergence times of a number of major groups within Ascomycota, including lichenized fungi.