Some species that grow on wood have caps that grow out directly from the wood. In some cases the cap is semi-circular and attached by the straight edge as shown in this species of Crepidotus below while in others that grow on the underside of fallen logs or trunks the cap is circular but attached by its upper side. The second picture shows a species of Resupinatus , found growing on the underside of a rotting branch that was lying on the ground.
You can see the gills on the small, circular cap up to a centimetre in diameter. Crepidotus sp. Mushrooms and toadstools have a stalk with a cap on top. Under the cap you will see either gills, pores or spikes. Sometimes the gills are crowded together, sometimes forked or of different lengths and sometimes spaced out or distant.
The pattern that you see can be helpful in identifying the fungus fruit body. Some fruit bodies lack gills, spikes and pores but have a soft spongy layer instead. Lemon Disco has a layer like this in her cup shaped fruit body.
Spores are like seeds of a flowering plant. They are made in the fungus fruit body. Spores are microscopic. You cannot see them with the naked eye. Fruiting bodies are fungal structures that contain spores. They come in many sizes, shapes, and colors, all of which aid in identification of the specific fungus. Here is some information that is helpful but not necessary to fruiting body identification.
Fungal pathogens often have an imperfect stage also called an anomorph and sometimes a perfect stage teleomorph as well. This really confuses things because a disease might be named for either stage.
For instance, oak wilt is caused by Ceratocystis perfect stage ; but we identify its imperfect stage, Chalara, in the lab. The point is not to confuse but to alert you to the fact that more than one fungal name may be associated with a single disease. For example, powdery mildew forms white, powdery spores called Oidium imperfect stage. Through these analyses, we hope to recover plausible causatives that triggered the evolution of deliquescent fruiting bodies.
More specifically, we set out to address the following questions: 1 are there morphological characters that correlate with the emergence of deliquescent fruiting bodies?
Herbarium materials and strains for DNA extraction were selected so as to ensure appropriate representation of all lineages of the family Psathyrellaceae.
Taxa were selected on the basis of trees published formerly Hopple and Vilgalys , Padamsee et al. Of the herbarium materials at our disposal, we selected those with a worldwide distribution in the temperate zone, occurring in North America and Europe as well.
The specimens used in this study, their origins, identifier persons, and accession numbers are listed in Table 1. Specimens included in this study, herbarium numbers, locality of origin, identifier person, and GenBank accession numbers. Species from the genera Bolbitius, Agrocybe, Conocybe , and Mythicomyces corneipes were used as outgroups based on former large-scale phylogenetic studies Moncalvo et al.
Cycle amplification followed standard protocols White et al. Alignments of individual genes were computed by using the ClustalW Larkin et al. The combinability of the single-gene data sets was assessed by the approximately unbiased test implemented in Consel Shimodaira and Hasewaga , Shimodaira As it has been shown that indel characters can be phylogenetically informative in Basidiomycota e.
Concatenated single-gene alignments were merged with the indel matrix obtained with FastGap. Because gamma approximation accounts for the same phenomenon as P-invar and it has been raised that using both can reduce the identifiability of parameters in the analyses Rannala ; Nylander et al.
We evaluated the fit of five different partitioned models Table 2 : 1 treating all nucleic acid characters as one partition and indel data as a second; 2 dividing the nucleic acid data in six partitions corresponding to the ITS1, 5. Bayesian sampling of phylogenies was performed in BayesPhylogenies 1. In case of BayesPhylogenies, one Markov chain was run in five replicates, whereas in MrBayes four chains were run in two replicates with Metropolis Coupling.
Topological convergence was checked by the statistics implemented in MrBayes average standard deviation of split frequencies and Potential Scale Reduction Factor as well as by Are we there yet? Wilgenbusch et al. Comparison of different partitioned models was performed on the basis of Bayes factors BFs as proposed by Suchard et al. The BF comparison was proposed as a Bayesian equivalent of the likelihood ratio test, evaluating the relative superiority of models by approximating their marginal probabilities Suchard et al.
Maximum likelihood bootstrap analysis was performed in RaxML 7. The matrix was divided into partitions as above. One thousand nonparametric bootstrap replicates were performed, employing a GTR model of sequence evolution with a gamma approximation of rate heterogeneity for calculation of tree likelihoods in the final step GTRMIX option.
A bootstrap consensus tree was computed by using Dendroscope Huson et al. Due to the constraints imposed by the comparative method, we coded fruiting body types as a binary character. Species that deliquesce or collapse only partly e. The following morphological characters were also coded into binary matrices in order to assess their correlation with fruiting body types Fig.
Pseudoparaphyses are presumed to serve as spacers that prevent developing spores of neighboring basidia from abuting and are found in all species of Parasola, Coprinellus, Coprinopsis, Coprinus patouillardi plus Bolbitius vitellinus. Species with a plicate cap surface have distinct radially arranged ridges or grooves on the cap. Mature plicate caps resemble small expanded parasols. The third trait we tested was the anatomy of the basidia.
Taxa with bimorphic basidia possess two types of basidium, one sturdy shorter form and another that has a constricted part in the middle and is therefore much longer. Bimorphic basidia form two strata of spores, which may be viewed as a two-floored hymenium spore-bearing surface.
It would not be surprising if such an anatomy could offer improved spore discharge mechanisms for the mushroom. Hymenial cystidia are spacer cells like pseudoparaphyses, but their role is to arrest the fusion of parallelly situated gills with each other and of the gill edges with the stipe in young fruiting bodies.
Morphological features examined in this study. Pictures a , b , c , and k are from Psathyrella fibrillosa ; d , e , f , g , i , l , m , and n from Coprinellus micaceus ; h and j from Ps. For comparative analyses, a subsample of 10 3 trees including branch lengths was drawn from the trees sampled during the Bayesian Markov chain Monte Carlo MCMC analyses by using Mesquite 2.
Tests of correlated evolution were performed in BayesTraits 1. We used a hyperprior approach to define a reasonably restrictive but conservative prior distribution for the MCMC analyses.
To acquire an idea about the average values of rate parameters, we ran an empirical Bayesian analysis on the tree sample maximum likelihood option in BayesTraits, with 10 optimization attempts per tree. By allowing jumps between model classes, the RJ-MCMC approach samples both dependent and independent models in proportion to their posterior probability Pagel and Meade , given the data. Models and rate parameters were sampled every th iteration.
All analyses were replicated 5 times. The Markov model of correlated evolution that we employed allows identification of the evolutionary pathway taken by the characters from the ancestral combination of states to the observed contemporary pattern Pagel and Meade For instance, given that the ancestral combination of states was 0,0 , and the extant species have the combination 1,1 , there are two possible intermediate combinations of states 1,0 and 0,1.
Values of the rate parameters, the MCMC samples, provide information about which intermediate state is more likely, given the data. We also examined the plausibility of the two pathways by means of a BF test using BayesTraits. Accordingly, the more plausible a pathway is, the greater the decrease in the likelihood when the corresponding rates are restricted to zero. To assess whether deliquescent fruiting bodies of various lineages Parasola, Coprinopsis, Coprinellus , and C.
The nucleotide substitution process was modeled by the GTR model with gamma distribution approximated with four rate categories to account for among-site rate heterogeneity. Among-lineage rate heterogeneity was modeled by using an uncorrelated lognormal relaxed molecular clock, with the tree prior set to the pure birth Yule process.
MCMC analyses were run for 1. The convergence of the runs and effective sample sizes were checked in Tracer. We defined taxon sets in Beauti 1. All taxon sets that were constrained to monophyly during the molecular clock analyses received a bounded-error probabilistic polynomial of 1. Because the fungal fossil record is incontinuous, six different calibrations have been tested, which took advantage of former estimates for the emergence of Agaricomycotina Berbee and Taylor , Heckman et al.
Because Archaemarasmius and Protomycena are the only agaricoid fossils with more or less unambiguous taxonomic positions Hibbett and Donoghue , and is at the same time the only available direct calibration point for the Agaricomycetes, we used them for calibration as the closest applicable relatives of the Psathyrellaceae. More specifically, the six calibrations were set up as follows:.
Combinations of 1 and 3 and of 2 and 3 were used as fifth 5 and sixth 6 calibration regimes, respectively. By using such combined calibrations, we hoped to include all reliable information available on node ages of Basidiomycota. We included two taxa of Inocybaceae in the data set for which the divergence times were estimated by Matheny et al. The approximately unbiased test did not recover significant conflict between individual genes.
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