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

2021 ◽  
Author(s):  
Teun Boekhout ◽  
M. Catherine Aime ◽  
Dominik Begerow ◽  
Toni Gabaldón ◽  
Joseph Heitman ◽  
...  
Keyword(s):  
Species Concept ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Biological Species ◽  
Species Concepts ◽  
Biological Species Concept ◽  
Sequencing Technology ◽  
Morphological Aspects ◽  
Growth Profiles ◽  
Genome Information

AbstractHere 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.

Species limits in Pteruthius (Aves: Corvida) shrike-babblers: a comparison between the Biological and Phylogenetic Species Concepts

Zootaxa ◽  
2009 ◽  
Vol 2301 (1) ◽  
pp. 29-54 ◽  
Author(s):  
FRANK E. RHEINDT ◽  
JAMES A. EATON
Keyword(s):  
Species Concept ◽  
Molecular Data ◽  
Biological Species ◽  
Species Concepts ◽  
Biological Species Concept ◽  
Phylogenetic Species ◽  
Species Status ◽  
Phylogenetic Species Concept ◽  
Sampling Regime ◽  
Morphological And Molecular Data

The question of how to define a species continues to divide biologists. Meanwhile, the application of different species concepts has led to disparate taxonomic treatments that confound conservationists and other biologists. The most widely followed guidelines to species designation in avian and other vertebrate taxonomy are Ernst Mayr’s Biological Species Concept (BSC) and Joel Cracraft’s version of the Phylogenetic Species Concept (PSC). Although the BSC is considered to be more conservative in its assignment of species status, there is a lack of research demonstrating differences in taxonomic treatment between the BSC and the PSC with reference to a multi-taxon multi-trait study system. We examined the case of five traditionally recognized species of shrike-babbler (Pteruthius) that have recently been divided into 19 species under the PSC. Re-analyzing previous morphological and molecular data and adding new vocal data, we propose a BSC classification of 9 species. However, taking into consideration geographic gaps in the sampling regime, we contend that additional data will likely reduce discrepancies between the total numbers of species designated under the PSC and BSC. The current PSC species total is a likely overestimate owing to species diagnosis based on characters that erroneously appear to be unique to a taxon at low sample size. The current BSC species total as here proposed is a likely underestimate on account of the conservative designation of taxa as subspecies in equivocal cases, e.g. where BSC species status is potentially warranted but may be masked by insufficient data.

Species

2021 ◽  
pp. 219-238
Author(s):  
Andrew V. Z. Brower ◽  
Randall T. Schuh
Keyword(s):  
Species Concept ◽  
Biological Species ◽  
Species Concepts ◽  
Biological Species Concept ◽  
Character State ◽  
Phylogenetic Species Concept ◽  
Units Of Analysis ◽  
Perceived Reality

This chapter studies the systematists' perspective on species concepts and the role of species in systematics. No matter how sophisticated the tools and methods enhancing the conceptualization of reality may become in the future, systematists will still be constrained by their perceptions. In their more modest, empirical view, systematists embrace their perceived reality and prefer species concepts that incorporate tools for identifying and delimiting species as empirical hypotheses, thereby providing them with efficacious working terminal elements for phylogenetic analysis and classification of more inclusive taxa. It is fortunate that cladists employed the notion of a “phylogenetic” species concept based on diagnosability before more metaphysically inclined authors appropriated the term for concepts founded on monophyly or common ancestors. As noted, Willi Hennig's species concept was a version of the “biological” species concept, and it fell to his followers to develop a species concept that is well suited to cladistic principles. Among the earliest of the post-Hennigian empiricists was American Museum ichthyologist Donn Rosen. Rosen's concept, sometimes called the apomorphic concept because of its requirement that every recognized species must have its own derived character state, accomplished two key advances for systematics: it proposed a cladistic criterion for recognizing species, and it defined species as the minimal units of analysis, as far as taxonomy is concerned, thus setting a lower bound for systematic inquiry.

Is the taxonomy appropriate? Delineating species for conservation purposes

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Species Concept ◽  
Conservation Management ◽  
Biological Species ◽  
Species Concepts ◽  
Outbreeding Depression ◽  
Biological Species Concept ◽  
Genetic Rescue ◽  
Low Genetic Diversity ◽  
Inbred Populations ◽  
Species Definitions

The first step in conservation management is to delineate groups for separate versus combined management. However, there are many problems with species delineation, including diverse species definitions, lack of standardized protocols, and poor repeatability of delineations. Definitions that are too broad will lead to outbreeding depression if populations are crossed, while those that split excessively may preclude genetic rescue of small inbred populations with low genetic diversity. To minimize these problems, we recommend the use of species concepts based upon reproductive isolation (such as the biological species concept) and advise against the use of phylogenetic and general lineage species concepts. We provide guidelines as to when taxonomy requires revision and outline protocols for robust species delineations.

scholarly journals An alternative species taxonomy of the birds of Mexico

2004 ◽  
Vol 4 (2) ◽  
pp. 1-32 ◽  
Author(s):  
Adolfo G. Navarro-Sigüenza ◽  
A. Townsend Peterson
Keyword(s):  
Species Concept ◽  
Bird Species ◽  
Biological Species ◽  
Species Concepts ◽  
Biological Species Concept ◽  
Phylogenetic Species ◽  
Phylogenetic Species Concept ◽  
Alternative Species ◽  
Species Taxonomy

Extensive debate has surrounded the application of alternative species concepts in Ornithology. The biological species concept (BSC) and phylogenetic species concept (PSC) have typically been set in opposition, with extensive debate on the relative merits of each. An alternative is the evolutionary species concept (ESC), which offers a perspective similar to that of the PSC, yet with several significant differences. To date, no major avifauna has been examined and compared among taxonomic viewpoints. Herein, we develop an alternative phylogenetic/evolutionary species taxonomy to the current BSC treatment for the more than 1000 bird species of Mexico. A total of 135 biological species was divided to produce a total of 323 phylogenetic/evolutionary species, 122 of which represent “new” endemic forms in Mexico.

Carboniferous fireworms (Amphinomida : Annelida), with a discussion of species taxa in palaeontology

2004 ◽  
Vol 18 (6) ◽  
pp. 693 ◽  
Author(s):  
Fredrik Pleijel ◽  
Greg W. Rouse ◽  
Jean Vannier
Keyword(s):  
New Records ◽  
Species Concept ◽  
Biological Species ◽  
Species Concepts ◽  
Late Carboniferous ◽  
Biological Species Concept ◽  
Phylogenetic Species ◽  
Object Lesson

New records of Palaeocampa anthrax Meek&Worthen, 1865 with fossilized soft parts are provided from Montceau-les-Mines in France, late Carboniferous, permitting the identification of a new clade of extinct amphinomid polychaetes. The group also provides an object lesson for problems with species concepts in palaeontology. The biological species concept, the diagnosable phylogenetic species concepts, and the monophyletic phylogenetic species concepts are applied and discussed in the case of P. anthrax, as well as more generally in palaeontology. All three are rejected, but for different reasons. Instead we advocate the application of LITUs (least inclusive taxonomic unit), which refers to the smallest currently recognised taxa, but without making the unjustified rank assignments to species.

Taxonomical uses of the species concept in the human lineage

2012 ◽  
Vol 2 (1) ◽  
pp. e1
Author(s):  
Camilo J. Cela-Conde ◽  
Marcos Nadal
Keyword(s):  
Species Concept ◽  
Biological Species ◽  
Species Concepts ◽  
Middle Pleistocene ◽  
Biological Species Concept ◽  
Human Lineage

Different species concepts, which broadened the scope of Mayr’s Biological Species Concept, have been put forward aiming to produce sound taxonomies of fossil taxa. Here, we propose using a simple one, the Evolutionary Species Concept, on the grounds of considering that separation of populations – disregarding other issues – is enough to describe the evolution of the human lineage. The question of the acceptable number of Middle Pleistocene hominin species is used as an example.

Discriminating arboviral species

2021 ◽  
Vol 102 (4) ◽  
Author(s):  
Yiyuan Li ◽  
Angela C. O’Donnell ◽  
Howard Ochman
Keyword(s):  
Evolutionary History ◽  
Viral Vectors ◽  
Species Concept ◽  
International Committee ◽  
Biological Species ◽  
Biological Species Concept ◽  
Substantial Variation ◽  
Artificial Boundaries ◽  
Human Infections

Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle – that underlying the Biological Species Concept (BSC) – to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.

Steinernema khuongin. sp. (Panagrolaimomorpha, Steinernematidae), a new entomopathogenic nematode species from Florida, USA

2018 ◽  
Vol 93 (2) ◽  
pp. 226-241 ◽  
Author(s):  
S.P. Stock ◽  
R. Campos-Herrera ◽  
F.E. El-Borai ◽  
L.W. Duncan
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Novel Species ◽  
Entomopathogenic Nematode ◽  
Biological Species ◽  
Morphological Data ◽  
Biological Species Concept ◽  
The Novel ◽  
Ecological Data ◽  
Cross Hybridization

AbstractIn this study, molecular (ribosomal sequence data), morphological and cross-hybridization properties were used to identify a newSteinernemasp. from Florida, USA. Molecular and morphological data provided evidence for placing the novel species into Clade V, or the ‘glaseri-group’ ofSteinernemaspp. Within this clade, analysis of sequence data of the rDNA genes, 28S and internal transcribed spacer (ITS), depicted the novel species as a distinctive entity and closely related toS. glaseriandS. cubanum.Additionally, cross-hybridization assays showed that the new species is unable to interbreed with either of the latter two species, reinforcing its uniqueness from a biological species concept standpoint. Key morphological diagnostic characters forS. khuongin. sp. include the mean morphometric features of the third-stage infective juveniles: total body length (average: 1066 μm), tail length (average: 65 μm), location of the excretory pore (average: 80.5 μm) and the values ofc(average: 16.4),D% (average: 60.5),E% (average: 126) andH% (average: 46.6). Additionally, males can be differentiated fromS. glaseriandS. cubanumby the values of several ratios:D% (average: 68),E% (average: 323) and SW% (average: 120). The natural distribution of this species in Florida encompasses both natural areas and citrus groves, primarily in shallow groundwater ecoregions designated as ‘flatwoods’. The morphological, molecular, phylogenetic and ecological data associated with this nematode support its identity as a new species in theS. glaseri-group.

scholarly journals Putting the Biological Species Concept to the Test: Using Mating Networks to Delimit Species

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e68267 ◽  
Author(s):  
Lélia Lagache ◽  
Jean-Benoist Leger ◽  
Jean-Jacques Daudin ◽  
Rémy J. Petit ◽  
Corinne Vacher
Keyword(s):  
Species Concept ◽  
Biological Species ◽  
Biological Species Concept

Fern nothogenera and ×Lepinema, a new hybrid genus between Ellipinema and Lepisorus (Polypodiaceae)

Phytotaxa ◽  
2020 ◽  
Vol 455 (4) ◽  
pp. 262-266
Author(s):  
LIANG ZHANG ◽  
LI-BING ZHANG
Keyword(s):  
Species Concept ◽  
Intergeneric Hybrid ◽  
Molecular Data ◽  
Biological Species ◽  
Biological Species Concept

The biological species concept is not exclusively applicable in many groups of organisms including ferns. Interspecific fern hybrids are not rare: there are 16 intergeneric hybrid genera in ferns confirmed with molecular data. Here we add one more hybrid genus in the tribe Lepisoreae of Polypodiaceae, ×Lepinema, formed via hybridization between parents in two genera: Ellipinema and Lepisorus.

Sign in / Sign up

Export Citation Format

Share Document