scholarly journals Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 204
Author(s):  
Elvira Hörandl
Keyword(s):  
Sexual Reproduction ◽  
Species Delimitation ◽  
Species Concepts ◽  
Plant Evolution ◽  
Polyploid Species ◽  
Ecological Adaptations ◽  
As Species ◽  
Novel Approaches ◽  
Conceptual Progress

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.

scholarly journals Names of phytopathogenic fungi: a practical guide

2021 ◽  
Author(s):  
Pedro W Crous ◽  
Amy Y Rossman ◽  
Catherine Aime ◽  
Cavan Allen ◽  
Treena Burgess ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Classification System ◽  
Driving Force ◽  
Pathogenic Fungi ◽  
Phytopathogenic Fungi ◽  
Plant Pathogenic Fungi ◽  
Natural Classification ◽  
Online Databases ◽  
As Species

Names of phytopathogenic fungi and oomycetes are essential to communicate knowledge about species and their biology, control, and quarantine as well as for trade and research purposes. Many plant pathogenic fungi are pleomorphic, meaning that they produce different asexual (anamorph) and sexual (teleomorph) morphs in their lifecycles. Because of this, more than one name has been applied to different morphs of the same species, which has confused users of names. The onset of DNA technologies makes it possible to connect different morphs of the same species, resulting in a move to a more natural classification system for fungi, in which a single name for a genus as well as species can now be used. The move to a single nomenclature, as well as the advent of molecular phylogeny and the introduction of polythetic taxonomic approaches has been the main driving force for the re-classification of fungi, including pathogens. Nonetheless, finding the correct name for species remains challenging, but there is a series of steps or considerations that could greatly simplify this process, as outlined here. In addition to various online databases and resources, a list of accurate names is herewith provided of the accepted names of the most common genera and species of phytopathogenic fungi.

scholarly journals Speciation towards tetraploidization after intermediate processes of non-sexual reproduction

2008 ◽  
Vol 363 (1505) ◽  
pp. 2921-2929 ◽  
Author(s):  
Carina Cunha ◽  
Ignacio Doadrio ◽  
Maria M Coelho
Keyword(s):  
Sexual Reproduction ◽  
Mating Systems ◽  
Diploid Hybrid ◽  
Polyploid Species ◽  
Animal Evolution ◽  
Sex Ratio Bias ◽  
First Time ◽  
Normal Meiosis ◽  
Experimental Crosses ◽  
Hybrid Forms

Polyploidy, hybridization and variation in mating systems are central issues for a deeper understanding of animal evolution. The Iberian species Squalius alburnoides represents an example combining all three phenomena. Previous studies showed that S. alburnoides populations are mainly composed of triploid and diploid hybrid forms (mainly females), and that the tetraploid forms are rare or absent. Both populations from the Douro drainage reveal a distinct scenario: tetraploid individuals represent 85.6–97.5% of the population, with no sex ratio bias observed. Based on the flow cytometry measurements of blood and spermatozoa cells, microsatellite loci and experimental crosses, we describe here, for the first time, two symmetric allotetraploid populations (CCAA) that resumed normal meiosis after undergoing intermediate processes of non-sexual reproduction to give rise to a new sexually reproducing polyploid species. Prezygotic (habitat selection and assortative mating) and postzygotic mechanisms (nonviable embryos) are responsible for the reproductive isolation from other forms of the S. alburnoides complex (e.g. CA, CAA). This example illustrates how hybrid polyploid complexes may lead to speciation.

scholarly journals A phylogenetic framework for reassessing generic concepts and species delimitation in the lichenized family Trypetheliaceae (Ascomycota: Dothideomycetes)

2016 ◽  
Vol 48 (6) ◽  
pp. 739-762 ◽  
Author(s):  
Robert LÜCKING ◽  
Matthew P. NELSEN ◽  
André APTROOT ◽  
Roselvira BARILLAS DE KLEE ◽  
Paulina A. BAWINGAN ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Type Species ◽  
Species Concept ◽  
Species Concepts ◽  
Additional Species ◽  
Secondary Chemistry ◽  
The Family ◽  
Phylogenetic Framework ◽  
Phenotypic Features

AbstractWe provide an expanded and updated, 2-locus phylogeny (mtSSU, nuLSU) of the lichenized fungal family Trypetheliaceae, with a total of 196 ingroup OTUs, in order to further refine generic delimitations and species concepts in this family. As a result, the following 15 clades are recognized as separate genera, including five newly established genera: Aptrootia, Architrypethelium, Astrothelium (including the bulk of corticate species with astrothelioid ascospores; synonyms: Campylothelium, Cryptothelium, Laurera), Bathelium s. str. (excluding B. degenerans and relatives which fall into Astrothelium), the reinstated Bogoriella (for tropical, lichenized species previously placed in Mycomicrothelia), Constrictolumina gen. nov. (for tropical, lichenized species of Arthopyrenia), Dictyomeridium gen. nov. (for a subgroup of species with muriform ascospores previously placed in Polymeridium), Julella (provisionally, as the type species remains unsequenced), Marcelaria (Laurera purpurina complex), Nigrovothelium gen. nov. (for the Trypethelium tropicum group), Novomicrothelia gen. nov. (for an additional species previously placed in Mycomicrothelia), Polymeridium s. str., Pseudopyrenula, Trypethelium s. str. (T. eluteriae group), and Viridothelium gen. nov. (for the Trypethelium virens group). All recognized genera are phenotypically characterized and a discussion on the evolution of phenotypic features in the family is given. Based on the obtained phylogeny, species delimitations are revised and the importance of characters such as thallus morphology, hymenial inspersion, and secondary chemistry for taxonomic purposes is discussed, resulting in a refined species concept.

scholarly journals Phylogenetic analysis of SARS-CoV-2 data is difficult

2020 ◽  
Author(s):  
Benoit Morel ◽  
Pierre Barbera ◽  
Lucas Czech ◽  
Ben Bettisworth ◽  
Lukas Hübner ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Phylogenetic Inference ◽  
Daily Basis ◽  
Extreme Caution ◽  
Data Analyses ◽  
Phylogenetic Methods ◽  
Degree Of Confidence

Abstract Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.

The Application of the European Time Scale to the Upper Tertiary of North America

1940 ◽  
Vol 77 (1) ◽  
pp. 1-27 ◽  
Author(s):  
Guy E. Pilgrim
Keyword(s):  
North America ◽  
Time Scale ◽  
Upper Miocene ◽  
As Species ◽  
Individual Opinion

Matthew's provisional classification of the freshwater Tertiary of Western America in 1899 was succeeded ten years later by a detailed correlation of the American Tertiary Mammal horizons with those of Europe, published by Osborn and himself in 1909. At that time these authors placed the Pikermi horizon of Europe (Pontian) in the Upper Miocene and the Val d'Arno horizon (Villafranchian) in the Upper Pliocene. They in common with many later writers subsequently adopted a Lower Pliocene and Pleistocene age respectively for the two horizons named. Allowing for this change of view, Osborn's and Matthew's correlation has been substantially followed, with a few modifications due to individual opinion, by all later authorities. The reasons for it were somewhat elaborated by Osborn in his Age of Mammals (1910). It is evident that the Equidae formed the basis for it. The appearance of the genera Anchitherium (as species of Kalobatippus and Hypohippus were then named), Hipparion and Equus in North America were assumed to be approximately contemporaneous with their appearance in Europe. That North America was at any rate the main, if not the exclusive radiative centre for the distribution of the Equidae has been universally acknowledged. Hence Osborn's and Matthew's choice of this group as a standard of age seemed to be fully justified. In accordance with it the first Hipparion beds of North America were regarded as Pontian.

scholarly journals Species Concepts and Species Delimitation

2007 ◽  
Vol 56 (6) ◽  
pp. 879-886 ◽  
Author(s):  
Kevin De Queiroz
Keyword(s):  
Species Delimitation ◽  
Species Concepts

scholarly journals Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7754
Author(s):  
Dora Serdari ◽  
Evangelia-Georgia Kostaki ◽  
Dimitrios Paraskevis ◽  
Alexandros Stamatakis ◽  
Paschalia Kapli
Keyword(s):  
Species Delimitation ◽  
Ad Hoc ◽  
Hepatitis Virus ◽  
Genetic Distances ◽  
Phenotypic Traits ◽  
Virus Taxonomy ◽  
Hepatitis Viruses ◽  
Virus Classification ◽  
Distance Methods

Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.

scholarly journals Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing

2019 ◽  
Author(s):  
Yinjie Qiu ◽  
Cory D. Hirsch ◽  
Ya Yang ◽  
Eric Watkins
Keyword(s):  
Chloroplast Genome ◽  
Genome Size ◽  
Nuclear Genome ◽  
Morphological Characteristics ◽  
As Species ◽  
Estimate Genome Size ◽  
Fine Fescue ◽  
Chloroplast Genome Sequencing ◽  
Taxon Identification

AbstractFine fescues (Festuca L., Poaceae) are turfgrass species that perform well in low-input environments. Based on morphological characteristics, the most commonly-utilized fine fescues are divided into five taxa: three are subspecies within F. rubra L. and the remaining two are treated as species within the F. ovina L. complex. Morphologically, these five taxa are very similar, both identification and classification of fine fescues remain challenging. In an effort to develop identification methods for fescues, we used flow cytometry to estimate genome size, ploidy level, and sequenced the chloroplast genome of all five taxa. Fine fescue chloroplast genome sizes ranged from 133,331 to 133,841 bp and contained 113 to 114 genes. Phylogenetic relationship reconstruction using whole chloroplast genome sequences agreed with previous work based on morphology. Comparative genomics suggested unique repeat signatures for each fine fescue taxon that could potentially be used for marker development for taxon identification.

scholarly journals XII.—On the Mode of Growth and Increase amongst the Corals of the Palæozoic Period

1875 ◽  
Vol 27 (3) ◽  
pp. 237-250 ◽  
Author(s):  
H. Alleyne Nicholson
Keyword(s):  
Sexual Reproduction ◽  
Present Communication ◽  
Different Parts

The mode of growth and increase amongst the Coralligenous Actinozoa in general has been more or less fully treated of by various observers, including such distinguished naturalists as Milne-Edwards, and Haime, Dana, Martin Duncan, Fromentel, Agassiz, and others. I do not, therefore, in the present communication propose to pass the whole of this subject in review, but rather to consider the general and special peculiarities of growth and non-sexual reproduction exhibited by the corals of the Palæozoic Period alone. Many of these peculiarities are of great interest, both from the stand-point of the palæontologist, and also as concerns the systematic zoologist, and they have not yet met with all the attention they deserve. To carry out this inquiry, it will be necessary first to consider the general phenomena exhibited by the Palæozoic corals, as regards their mode of growth and increase. We may then examine the bearing of these phenomena upon various points connected with the classification of these ancient corals, and more especially upon their generic and specific affinities and differences. Finally, we may briefly consider the relations which exist between different parts of a compound corallum as regards their growth, and their influence upon the ultimate form of the colony.

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