History of Thai Mycology and Resolution of Taxonomy for Thai Macrofungi Confused with Europe and American Names

Reappraising adaptive radiation

Morphological characteristics have historically been used to study and identify Thai macrofungi, with many species being associated with those found in Europe and America. However, the lack of comprehensive herbarium collections, accurate descriptions, and molecular data has raised doubts on some of these identifications, making them questionable. The challenge of accurate macrofungal identification underscores the need for integrating both molecular and morphological data. Therefore, this review article is a part of the research project series “Revision and Update Checklist of Thai Macrofungi”. A new, accurate checklist of thirty genera viz. Amanita, Armillaria, Auricularia, Cacaoporus, Calocybella, Collybiopsis, Coniolepiota, Crinipellis, Cyathus, Erythrophylloporus, Gloeocantharellus, Heimioporus, Hymenagaricus, Inocybe, Lentinus, Lepiota, Macrolepiota, Marasmiellus, Panus, Paramarasmius, Parasola, Pseudosperma, Pyrenopolyporus, Retiperidiolia, Rhodactina, Rostrupomyces, Rubinosporus, Sutorius, Tuber, and Tulostoma, were revised and updated based on detailed specimen collections, description, and molecular data gathered from Thai specimens. This article contributes to the understanding of macrofungal diversity in Thailand by providing updated information on various genera, incorporating both morphological and molecular data, and highlighting their ecological significance within the diverse ecosystems.

A major challenge in the post-genomics era will be to integrate molecular sequence data from extant organisms with morphological data from fossil and extant taxa into a single, coherent picture of phylogenetic relationships; only then will these phylogenetic hypotheses be effectively applied to the study of morphological character evolution. At least two analytical approaches to solving this problem have been utilized: (1) simultaneous analysis of molecular sequence and morphological data with fossil taxa included as terminals in the analysis, and (2) the molecular scaffold approach, in which morphological data are analyzed over a molecular backbone (with constraints that force extant taxa into positions suggested by sequence data). The perceived obstacles to including fossil taxa directly in simultaneous analyses of morphological and molecular sequence data with extant taxa include: (1) that fossil taxa are missing the molecular sequence portion of the character data; (2) that morphological characters might be misleading due to convergence; and (3) character weighting, specifically how and whether to weight characters in the morphological partition relative to characters in the molecular sequence data partition. The molecular scaffold has been put forward as a potential solution to at least some of these problems. Using examples of simultaneous analyses from the literature, as well as new analyses of previously published morphological and molecular sequence data matrices for extant and fossil Chiroptera (bats), we argue that the simultaneous analysis approach is superior to the molecular scaffold approach, specifically addressing the problems to which the molecular scaffold has been suggested as a solution. Finally, the application of phylogenetic hypotheses including fossil taxa (whatever their derivation) to the study of morphological character evolution is discussed, with special emphasis on scenarios in which fossil taxa are likely to be most enlightening: (1) in determining the sequence of character evolution; (2) in determining the timing of character evolution; and (3) in making inferences about the presence or absence of characteristics in fossil taxa that may not be directly observable in the fossil record.

BackgroundMatrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.ResultsWe systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as some intermediate nodes may show large time differences between these two types of data.ConclusionsOur findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.

A phylogenetic analysis for the Cimicomorpha was conducted using 92 taxa, including eight outgroups and six species of Thaumastocoridae. Density of taxon sampling allows for tests of relationships at the family level for most taxa, whereas in the Miridae denser sampling allows for doing so on the tribal level. This level of sampling also corresponds with the availability of testable published hypotheses of relationships. Morphological data for 73 characters are coded for all taxa. Approximately 3500 base pairs of DNA were sequenced for the following gene regions for 83 taxa: 16S rDNA, 18S rDNA, 28S rDNA and COI. Results are presented for analysis of morphological data, individual molecular partitions, combined molecular data, combined morphological and molecular data for 83 taxa and combined morphological and molecular data for 92 taxa. Analyses of morphological data were performed using the parsimony programs nona and piwe : molecular and combined data were analysed using direct optimization with the program poy . Major conclusions of the present study include recognition of the following monophyletic groups: The Geocorisae is a monophyletic group. The monophyly of the Cimicomorpha – including Thaumastocoridae – is not supported in most analyses. The Reduviidae is monophyletic, with the Phymatinae Complex being the sister‐group of the remaining subfamilies. The circumscription of the Cimiciformes is altered from the prior conception of Schuh and Štys to also include the Joppeicidae, Microphysidae and Velocipedidae, as well as the recently described family Curaliidae; the monophyly of the Cimiciformes is supported in most analyses; the Cimiciformes is treated as the sister‐group of the Miroidea in most analyses. The monophyly of the Cimicoidea, including Curaliidae, is supported in all analyses including molecular data, whereas Curaliidae is treated as a more basal cimiciform in all other analyses. The monophyly and placement of the Thaumastocoridae is ambiguous across the range of analyses, and the monophyly of the Miroidea sensu Schuh and Štys receives limited support in the combined analyses of morphology + molecular data. The Tingidae and Miridae are each monophyletic and together almost invariably form a monophyletic group. Within the Miridae, several inclusive monophyletic groups at the subfamily/tribal level are more or less consistently recognized when molecular data are included; however, the interrelationships of the subfamilies vary substantially across the range of analyses. Of the individual molecular partitions, only 18S rDNA shows significant congruence with combined analyses of morphological, combined molecular or combined morphological and molecular data. Scenarios are discussed for the evolution of the metathoracic scent‐efferent system and the origin of the fossula spongiosa.

Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution, these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, that is, lacking morphological and molecular data, which we call occurrences, provide invaluable information to estimate the past number of lineages. Here, we present new methodological developments around the fossilized birth–death process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death, and sampling rates; and (iii) estimate the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions. We finally illustrate our new implementation using two empirical data sets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the coronavirus disease 2019 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics. [Birth–death model; epidemiology; fossils; macroevolution; occurrences; phylogenetics; skyline.]

Dataset supporting the use of nematodes as bioindicators of polluted sediments

It took almost a century until Schwendener’s (1867) finding that lichens belong to the fungi finally led mycologists and lichenologists to include them in the fungal system (Nannfeldt 1932; Santesson 1952). Trying to elucidate the phylogenetic relationships between lichenized and un-lichenized fungi and among lichen taxa, based solely on morphological and chemical data, has proven to be a frustrating endeavour. Lichens display few taxonomically useful characters, of which many are widely variable; the homology of character states within and between groups is difficult to assess. Often, even the interpretation of morphological characters, e.g. types of ascoma development or ascus type, proved difficult (see e.g. Henssen and Jahns 1974; Lumbsch 2000; Lumbsch et al. 2001c; Ott and Lumbsch 2001; Stenroos et al. 2002b; Lumbsch and Huhndorf 2007). In the absence of well-supported and uncontroversial phylogenetic reconstructions based on morphological data, molecular data have, therefore, gained great importance in lichen systematics. The impact of molecular data on the classification and taxonomy of lichenized ascomycetes has been summarized regularly in recent years (Lumbsch 2000, 2007; Grube and Winka 2002; DePriest 2004). This review is not an attempt to update these previous comprehensive reviews. It rather tries to shed light on the relationship between results based on molecular and morphological studies of lichens. In the late 1980s and early 1990s, morphology-based taxonomy and systematics and molecular phylogenetics of lichens more or less led their own separate lives. The first studies based on molecular data often concentrated on reconstructing phylogenetic relationships and were not so much concerned with character evolution or the reinterpretation of morphological characters in light of molecular results. Likewise, a critical evaluation of the results in light of morphological data was rarely attempted. This has changed profoundly in recent years. Most phylogenetic reconstructions of lichenized ascomycetes are now designed to test morphology-based classifications. As a result, the systematic value of morphological characters in diverse groups is now much better understood than previously and reconstructions of character evolution exist for many systematic groups. On the other hand, classical taxonomists make increasing use of molecular data because classical lichen taxonomy is riddled with problems that only independent data from molecular analyses are likely to solve. One very obvious problem that is relatively easy to solve with molecular data concerns the systematic placement of obligately sterile lichens (Stenroos and DePriest 1998; Arup and Grube 1999; Platt and Spatafora 2000; Ekman and Tonsberg 2002; Crespo et al. 2004a) or other species with doubtful systematic affinities (Printzen and Kantvilas 2004; Lucking et al. 2007; Spribille et al. 2009). Other such problems arise from the multiple description of morphologically variable species, doubtful circumscriptions of taxa and erroneous assignment of species to them, or misinterpretation of the systematic value of characters due to incorrect homology hypotheses. In all these cases, molecular analyses offer promising tools to test traditional hypotheses.

Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.

Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach.

The paper provides an overview of the concordance between molecular (nuclear ribosomal DNA ITS) and morphological data in the group of geophilic Umbelliferae of Middle Asia, which includes the genera Elwendia, Elaeosticta, Hyalolaena, Galagania, Oedibasis, Mogoltavia and Gongylotaxis. In general, a good consistency of data of different types can be observed. At the same time, at some levels of the taxonomic hierarchy, the consistency between morphological and molecular data looks much higher than at others. The identification of the group of geophilic Umbelliferae agrees much better with molecular data than the boundaries between genera within it and the proposed intrageneric groupings. Some observed cases of inconsistency, such as the position of Hyalolaena melanorrhiza among the species of the genus Elaeosticta and the polyphyly of the genera Hyalolaena and Oedibasis, are rather difficult to explain from a morphological point of view, only from a biogeography.

Chapter Six - Morphological and molecular data in the study of the evolution, population genetics and taxonomy of Rhizostomeae

The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio-temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of fossil taxa and biogeographic inferences of Cissampelideae. We assembled three data types, morphological data only, morphological data with a molecular scaffold and combined morphological and molecular data. By removing high-level homoplastic morphological data or reweighting the morphological characters, we conducted 15 parsimony, 12 undated Bayesian and four dated Bayesian analyses. Our results show that the 14 selected Cissampelideae fossil taxa are placed poorly when based only on morphological data, but the addition of molecular scaffold and combination of morphological and molecular data greatly improve the resolution of fossil nodes. We raise the monotypic Stephania subg. Botryodiscia to generic status and discover that three fossils previously assigned to Stephania should be members of Diploclisia. The Bayesian tip-dated tree recovered by removing homoplastic morphological characters with a Rescaled Consistency Index <0.25 has the highest stratigraphic fit and consequently generates more reasonable biogeographic reconstruction for Cissampelideae. Cissampelideae began to diversify in Asia in the latest Cretaceous and subsequently dispersed to South America around the Cretaceous-Palaeogene boundary. Two dispersal events from Asia to Africa occurred in the Early Eocene and the Late Eocene-Late Oligocene, respectively. These findings provide guidelines and practical methods for mitigating the effects of homoplastic morphological characters on fossil placements and Bayesian tip-dating, as well as insights into the past tropical floristic exchanges among different continents.

Analyses of living and fossil taxa are crucial for understanding changes in biodiversity through time. The Total Evidence method allows living and fossil taxa to be combined in phylogenies, by using molecular data for living taxa and morphological data for both living and fossil taxa. With this method, substantial overlap of morphological data among living and fossil taxa is crucial for accurately inferring topology. However, although molecular data for living species is widely available, scientists using and generating morphological data mainly focus on fossils. Therefore, there is a gap in our knowledge of neontological morphological data even in well-studied groups such as mammals. We investigated the amount of morphological (cladistic) data available for living mammals and how this data was phylogenetically distributed across orders. 22 of 28 mammalian orders have < 25% species with available morphological data; this has implications for the accurate placement of fossil taxa, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available data are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate Total Evidence phylogenies.

Two new species of the nudibranch genus Dendronotus, Dendronotusarcticussp. n. and Dendronotusrobilliardisp. n., are described from the Arctic and North Pacific oceans respectively, based on morphological and molecular data, and the North Pacific Dendronotusalbus is revealed to be a species complex. The species Dendronotusrobilliardisp. n. is described from the northwestern Pacific (Kamchatka) differing from the northeastern Pacific Dendronotusalbus by molecular and morphological data. The synonymy of Dendronotusdiversicolor with Dendronotusalbus is confirmed by analysis of their original descriptions. An endemic Arctic species Dendronotusarcticussp. n. is also described here, differing substantially from all species of the genus Dendronotus using morphological and molecular data. An unusual record of the recently described Dendronotuskamchaticus Ekimova, Korshunova, Schepetov, Neretina, Sanamyan, Martynov, 2015 is also presented, the first from the northeastern Pacific, geographically separated from the type locality of this species in the northwestern Pacific by a distance ca. 6000 km; molecular data show them to belong to the same species.