Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids

Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as “units”. Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.

Oligocene Planktic Foraminiferal Taxonomy and Evolution: An Illustrated Revision of Ocean Drilling Program Site 803

ABSTRACT The Oligocene (33.9–23.0 Ma) has historically proven to be a difficult interval to examine with respect to planktic foraminifera; the tendency for many of the taxa to be basically globigerine in shape, with 4 or 5 chambers in the final whorl means differences between species are limited. Recently, an international working group has attempted to clarify the Oligocene planktic foraminiferal taxonomy, with the goal of establishing phylogenetically-consistent generic and species concepts. A relatively expanded and continuous Oligocene section recovered at Ocean Drilling Program Site 803 in the western equatorial Pacific was previously studied by Leckie et al. (1993) using fairly conservative species concepts. Since 1993, foraminiferal biostratigraphic datum age calibrations have changed, and so revised sedimentation rates for the 220-m thick Oligocene sequence are actually more constant than previously thought. As a part of the recent taxonomic revision, this site was reevaluated and numerous additional taxa are recorded at this location. Macroevolutionary rates are calculated from the occurrences, and increased extinction is found within the late Oligocene, counter to the expectations laid out in broader-scale macroevolutionary studies. An effort is made here to describe the diagnostic features, which can be used to distinguish all taxa under a standard binocular microscope. Finally, several figures of scanning electron microscope photomicrographs (from Site 803 and tropical Atlantic Ocean ODP Site 628) depict features used to describe and differentiate important, but difficult or homeomorphic taxa, with the hope that these figures can be used by other workers at the microscope attempting to do Oligocene taxonomy-based studies.

The Univocity of Real Essence in Locke

I argue that Locke’s various descriptions of real essence pick out one and the same thing, namely a nature that can be ascribed to many things, and in terms of which we can get matters of classification right or wrong. On my reading, Locke does not attack real essences of the sort that are the essences of real species, but rather the presumption that a sorting according to our species concepts and their names is a sorting of things according to their real essences. And the lesson of Locke’s empirical argument against that presumption, I argue, is that our species concepts often function more like higher taxa, grouping together things that knowledge of their real essences would distinguish into distinct lowest species.

The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.

The genetic species concept and its versatility

A review of the species criteria of the four most popular species concepts (typological, genetic, bio-logical, and evolutionary-phylogenetic) shows that they are essentially the same. In each of them, the fact of fixing alternative alleles in diverging populations is a key circumstance in one form or another. Such groups of populations should be considered as a kind of evolutionary genetic dis-creteness supported by a protected gene pool. Therefore, a biological species should be understood as a set of populations, individuals of which have the fixation of common unique alleles for a num-ber of structural genes. Differences between the concepts are secondary and are due to the emphasis on different sides of the same phenomenon or the use of different methods for determining the ge-netic structure. It is indicated that there are subjective difficulties in the application of the genetic concept (the reluctance of traditional taxonomists to lose their monopoly) and objective problems caused by the unequal period of divergence of taxa of the species rank and different ways of form-ing genetically discrete entities.

Mycotoxin Production in Fusarium According to Contemporary Species Concepts

Fusarium is one of the most important genera of plant-pathogenic fungi in the world and arguably the world's most important mycotoxin-producing genus. Fusarium species produce a staggering array of toxic metabolites that contribute to plant disease and mycotoxicoses in humans and other animals. A thorough understanding of the mycotoxin potential of individual species is crucial for assessing the toxicological risks associated with Fusarium diseases. There are thousands of reports of mycotoxin production by various species, and there have been numerous attempts to summarize them. These efforts have been complicated by competing classification systems based on morphology, sexual compatibility, and phylogenetic relationships. The current depth of knowledge of Fusarium genomes and mycotoxin biosynthetic pathways provides insights into how mycotoxin production is distributed among species and multispecies lineages (species complexes) in the genus as well as opportunities to clarify and predict mycotoxin risks connected with known and newly described species. Here, we summarize mycotoxin production in the genus Fusarium and how mycotoxin risk aligns with current phylogenetic species concepts. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.