Figures (2)  Tables (2)

    • Figure 1. 

      Summary of articles on ancestral state reconstruction found on the Web of Science.

    • Figure 2. 

      ASR methods commonly used for fungal groups[54,59].

    • Principle Method
      Parsimony Maximum parsimony
      Stochastic modeling of trait evolution Maximum likelihood
      Bayesian inference

      Table 1. 

      The main approaches of ASR in mycological research.

    • SoftwareAdvantagesDisadvantages
      BeastFramework for testing evolutionary hypotheses that does not require a single tree topology to be defined.It consumes computational resources. Fossil-based phylogenetic positions inferred from morphological data still need to be considered in conjunction with other evidence (e.g. palaeontological evidence).
      DiversitreeFocuses on statistical modeling of species diversity and lineage differentiation, which can be used to explore patterns of species formation and extinction.Performs better with large amounts of data.
      MesquiteThis is professional evolutionary biology software optimized for the analysis of comparative organism data, and is ideal for small datasets and educational applications.Processing large data sets is inefficient and the functionality is relatively simple, making it unsuitable for complex analysis.
      Multi-stateAllowing the system and its components to assume more than two performance levels can provide a more realistic and accurate representation.Involves the estimation of a larger number of rate parameters.
      PHYLIPOpen source and free, supports a wide range of phylogenetic analysis methods.The interface is older, less intuitive, and the functionality is relatively basic.
      RPowerful and flexible.It cannot be used to develop web-type or internet-type applications.
      RASPSupports multiple analysis methods and allows users to select models according to data characteristics, offering greater flexibility.Running Bayesian methods or complex models on large datasets or phylogenetic trees is time-consuming and requires high-spec hardware.

      Table 2. 

      Comparison of the advantages and disadvantages of the software and online websites for constructing ASR.