The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earths biota in a time of rapid global change.

https://projects.au.dk/fileadmin/projects/circe/2009_Cavender_et_al_01.pdf

The merging of community ecology and phylogenetic biology

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1550-7408.2012.00644.x

The revised classification of eukaryotes

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many ...

/pdf/revisions-to-the-classification-nomenclature-and-diversity-4opk71xv7f.pdf

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

This review summarizes data on the biogeography and dispersal of bacteria, microfungi and selected protists, such as dinoflagellates, chrysophytes, testate amoebae, and ciliates. Furthermore, it introduces the restricted distribution and dispersal of mosses, ferns and macrofungi as arguments into the discussion on the postulated cosmopolitism and ubiquity of protists. Estimation of diversity and distribution of micro-organisms is greatly disturbed by undersampling, the scarcity of taxonomists, and the frequency of misidentifications. Thus, probably more than 50% of the actual diversity has not yet been described in many protist groups. Notwithstanding, it has been shown that a restricted geographic distribution of micro-organisms occurs in limnetic, marine, terrestrial, and fossil ecosystems. Similar as, in cryptogams and macrofungi about, 30% of the extant suprageneric taxa, described and undescribed, might be morphological and/or genetic and/or molecular endemics. At the present state of knowledge, micro-organism endemicity can be proved/disproved mainly by flagship species, excluding sites (e.g., university ponds) prone to be contaminated by invaders. In future, genetic and molecular data will be increasingly helpful. The wide distribution of many micro-organisms has been attributed to their small size and their astronomical numbers. However, this interpretation is flawed by data from macrofungi, mosses and ferns, many of which occupy distinct areas, in spite of their minute and abundant means of dispersal (spores). Thus, I suggest historic events (split of Pangaea etc.), limited cyst viability and, especially, time as major factors for dispersal and provinciality of micro-organisms. Furthermore, the true number of species and their distribution can hardly be estimated by theories and statistics but require reliable investigations on the number of morphospecies in representative ecosystems. Generally, the doubts on Beijerinck's famous metaphor "in micro-organisms everything is everywhere" can be focussed on a simple question: If the world is teeming with cosmopolitan unicells, where is everybody?

Biogeography and Dispersal of Micro-organisms: A Review Emphasizing Protists

This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.

https://biblio.ugent.be/publication/8660838/file/8660843.pdf

Outline of Fungi and fungus-like taxa

The social amoebas (Dictyostelia) display conditional multicellularity in a wide variety of forms. Despite widespread interest in Dictyostelium discoideum as a model system, almost no molecular data exist from the rest of the group. We constructed the first molecular phylogeny of the Dictyostelia with parallel small subunit ribosomal RNA and a-tubulin data sets, and we found that dictyostelid taxonomy requires complete revision. A mapping of characters onto the phylogeny shows that the dominant trend in dictyostelid evolution is increased size and cell type specialization of fruiting structures, with some complex morphologies evolving several times independently. Thus, the latter may be controlled by only a few genes, making their underlying mechanisms relatively easy to unravel.

/pdf/molecular-phylogeny-and-evolution-of-morphology-in-the-2519gwx2gn.pdf

Molecular Phylogeny and Evolution of Morphology in the Social Amoebas

The frequency of occurrence of Acrasieae was determined in 28 temperate and tropical countries on five continents. Twenty-nine different cellular slime molds, including five new to science, were is...

Geographical Distribution of Acrasieae

A B S T R A C T The clonal isolation of Acrasieae from suspensions of soils or organic substrates may be accomplished by employing a dilute hay-infusion agar medium to the surface of which pregrown bacteria have been added as a source of nutrient for the myxamoebae. The method described permits quantitative sampling of cellular slime mold populations, and it has been used by the authors in a study of the occurrence and distribution of these organisms in North and Central American forests. AS A PREREQUISITE for investigating the occurrence and distribution of the Acrasieae in forest soils, a method was developed which makes possible the clonal isolation of these cellular slime molds. Hence it can be used in the comparison of populations from different localities or sources. Although the method was developed and has been employed mainly for the study of populations in forest soils, it is equally applicable to other substrates such as leaf litter, decaying plants, fruits and dung, if these are macerated prior to analyses. MATERIALS AND METHODS-Collection of samXples-Samples were collected at the soil surface or from the humus layer of forests, and, in the latter case, included a portion of the fermentation layer where decomposition is most active. Variation in slime mold populations from one site to another in a forest is considerable. Consequently, an adequate number of soils must be taken to ensure representative sampling of a particular forest population. Soils may be conveniently collected in 9-dr plastic vials with wide mouths and snap-on covers. These vials are light weight, sufficiently strong, inexpensive, and suitable for shipping by mail, if necessary. Samples are taken by scraping the soil surface with the mouth of the vial. If soils cannot be plated out immediately after collection, they should be stored at a temperature slightly above freezing. Numbers of Acrasieae diminish soon after collection, there being a 15-25% decrease after 8 weeks' storage at 4 C in a moist condition. The decrease may be explained largely by death of active myxamoebae with some loss of spore and cyst viability as well. Samples may be frozen, but freezing causes a sharper initial decrease in numbers than does

The acrasieae in nature. i. isolation.

Summary

AimThe goal of this project was to compile, organize, and present the known distributional data on the dictyostelid cellular slime moulds (CSMs) found in forest soils worldwide. The question of what factors influence CSM distribution patterns was also addressed.



LocationCSMs have been recovered from soils of temperate deciduous forest, tropical deciduous and seasonal evergreen rainforest, boreal coniferous forest, and tundra by various investigators around the world.



MethodsWithin each of these four biomes, various locations around the world have been sampled by a number of investigators. The current study attempts to synthesize the known dictyostelid distributional data and present specific patterns of distribution.



ResultsWorldwide, sixty-five species of CSM were found to occupy various forest soils. These species’ distributions fell into one of four categories: cosmopolitan, disjunct, restricted, and pantropical.



Main conclusionsGlobal CSM distribution patterns are influenced by a variety of factors other than the biota (including but not restricted to climate, latitude, altitude, soil pH, and soil-forming parent materials). The current study supports the thesis that organic inputs from specific plant associations and animal vectors have an important role as well.

https://www.jstor.org/stable/info/2656043

Global distribution of forest soil dictyostelids

Social Amoebae or Dictyostelia are eukaryotic microbes with a unique life cycle consisting of both uni- and multicellular stages. They have long fascinated molecular, developmental and evolutionary biologists, and Dictyostelium discoideum is now one of the most widely studied eukaryotic microbial models. The first molecular phylogeny of Dictyostelia included most of the species known at the time and suggested an extremely deep taxon with a molecular depth roughly equivalent to Metazoa. The group was also shown to consist of four major clades, none of which correspond to traditional genera. Potential morphological justification was identified for three of the four major groups, on the basis of which tentative names were assigned. Over the past four years, the Mycetozoan Global Biodiversity Survey has identified many new isolates that appear to be new species of Dictyostelia, along with numerous isolates of previously described species. We have determined 18S ribosomal RNA gene sequences for all of these new isolates. Phylogenetic analyses of these data show at least 50 new species, and these arise from throughout the dictyostelid tree breaking up many previously isolated long branches. The resulting tree now shows eight well-supported major groups instead of the original four. The new species also expand the known morphological diversity of the previously established four major groups, violating nearly all previously suggested deep morphological patterns. A greatly expanded phylogeny of Dictyostelia now shows even greater morphological plasticity at deep taxonomic levels. In fact, there now seem to be no obvious deep evolutionary trends across the group. However at a finer level, patterns in morphological character evolution are beginning to emerge. These results also suggest that there is a far greater diversity of Dictyostelia yet to be discovered, including novel morphologies.

/pdf/an-expanded-phylogeny-of-social-amoebas-dictyostelia-shows-3tt2rae170.pdf

James C. Cavender

Papers

Molecular Phylogeny and Evolution of Morphology in the Social Amoebas

Geographical Distribution of Acrasieae

The acrasieae in nature. i. isolation.

Global distribution of forest soil dictyostelids

An expanded phylogeny of social amoebas (Dictyostelia) shows increasing diversity and new morphological patterns.