Choke Disease Caused by Epichloë bromicola in the Grass Agropyron repens in Poland

Agropyron repens (synonym Elymus repens, couch grass) is a species native to Europe and Asia. In Poland, it is a common weed of crop fields. In May 2008, we noticed for the first time symptoms of choke disease (caused by Epichloë spp.) on A. repens at two localities in central Poland. The localities, Pakość (52°47.531′N, 18°06.118′E) and Dulsk (52°45.329′N, 18°20.518′E), are located 16 km apart from each other. The following year, we confirmed the occurrence of choke disease on couch grass at these localities. Stromata were formed on reproductive stems that did not produce inflorescences. They ranged from 16 to 31 mm long and were covered with perithecia 520 to 560 × 160 to 250 μm at a density of 35 to 45 per mm2. Asci measured 270 to 310 × 5.2 to 6.5 μm and ascospores were 225 to 275 × 1.5 to 1.7 μm (specimen deposited in ZT). Morphological characters match with the original description of Epichloë bromicola (4). One strain was isolated from stromatal tissue and the partial DNA sequence of tubB including introns 1 to 3 was obtained as previously described (2). In a phylogenetic analysis, the isolate (GenBank Accession No. GU325782) grouped with Epichloë isolates from other Agropyron spp. from Poland (A. intermedium) and Japan (A. ciliare and A. tsukushiense) and with an isolate from a Roegneria sp. (from China). Experimental mating tests involving isolates from A. intermedium and a Roegneria sp. indicated that these isolates were sexually compatible with Epichloë bromicola from Bromus erectus. Similarly, E. yangsii was compatible with E. bromicola. This suggests that Epichloë isolates from Agropyron, Roegneria, and Bromus hosts form a common mating population, and implies that under a biological species concept the phylogenetic definition of E. bromicola has to be broadened. Epichloë on A. repens has been previously found in Poland (1), Germany (3), Hungary, and Romania (specimen deposited in herbarium of ETH Zurich, ZT) based on incidental records or on herbarium specimens that have been listed under E. typhina. Our study, based on morphology, tubB sequence similarity, and mating compatibility, suggests that the fungus infecting A. repens in Poland is E. bromicola. References: (1) I. Adamska. Acta Mycol. 36:31, 2001. (2) D. Brem and A. Leuchtmann. Evolution 57:37, 2003. (3) J. Kohlmeyer and E. Kohlmeyer. Mycologia 66:77, 1974. (4) A. Leuchtmann and C. L. Schardl. Mycol. Res. 102:1169, 1998.

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The increasing multiplicity of the species concepts

BSGF - Earth Sciences Bulletin ◽

10.2113/176.2.221 ◽

2005 ◽

Vol 176 (2) ◽

pp. 221-225

Author(s):

Jean Génermont

Keyword(s):

Species Concept ◽

Cladistic Analysis ◽

Biological Species ◽

Point Of View ◽

Biological Species Concept ◽

Phylogenetic Species ◽

Phylogenetic Species Concept ◽

Ecological Criteria ◽

Stem Species ◽

Definition Of

Abstract In 1980, Henri Tintant advocated the usefulness of the biological species concept in paleontology. At this time, this concept was still accepted by many neontologists, but it was already rather severely criticized by some others. In fact, a lot of new concepts appeared in the course of the following two decades. While a few ones are mere adjustments of the biological concept, for instance taking in account ecological criteria, in such a way that it could be applied to clonal organisms, some others, which were developed in connexion with the cladistic theory of taxonomy, are truly new from a conceptual point of view. The diagnosable version of the phylogenetic species concept is somewhat reminiscent of Simpson’s evolutionary species concept, since it accepts phyletic speciation as well as survival of the stem species after a cladogenetic event. One of its more criticizable features, from a cladistic point of view, is that the species are not necessarilly monophyletic. On another hand, according to the monophyly version of the phylogenetic species concept, species are recognized rather subjectively as monophyletic taxa revealed by some previous cladistic analysis dealing with operational taxonomic units. A consensus on the definition of species cannot be expected, since all concepts related to the biological one are founded on population grouping on the basis of potentially identical evolutionary fates, while those which are related to cladistic taxonomy are exclusively concerned with historical features.

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Bursaphelenchus acaloleptae n. sp. sharing tree and beetle carrier hosts with B. luxuriosae Kanzaki & Futai, 2003 in Japan

Nematology ◽

10.1163/15685411-00003320 ◽

2020 ◽

Vol 22 (5) ◽

pp. 515-527 ◽

Cited By ~ 1

Author(s):

Natsumi Kanzaki ◽

Taisuke Ekino ◽

Noritoshi Maehara ◽

Takuya Aikawa ◽

Robin M. Giblin-Davis

Keyword(s):

New Species ◽

Morphological Characters ◽

Biological Species ◽

Biological Species Concept ◽

Separate Species ◽

Aralia Elata ◽

Host Habitat ◽

Molecular Profiles ◽

Group Species ◽

F1 Generation

Summary Bursaphelenchus acaloleptae n. sp. is described and figured based upon its morphological characters and molecular profiles. The new species belongs to the xylophilus-group of the genus and is typologically characterised by its secretory-excretory pore being located slightly posterior to the median bulb, weakly tapering, relatively broad and straight female tail with variously shaped terminus, and rounded male bursal flap with squared terminus. The new species is phylogenetically and biologically closest to B. luxuriosae. These cryptic species share the host (habitat) tree species, Aralia elata (Araliaceae), the same carrier insect species, Acalolepta luxuriosa (Cerambycidae), and a characteristic phoretic adult form. However, the new species is typologically distinguished from all other xylophilus-group species by the combination of the above-mentioned characters and molecular profiles (SSU and LSU molecular barcodes). Further, B. acaloleptae n. sp. can be distinguished from its closest relative, B. luxuriosae, by mating experiments, i.e., these two species did not produce a viable F1 generation in reciprocal crossings, thereby confirming separate species status using the biological species concept.

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A revision of the Trimeresurus puniceus-complex (Serpentes: Viperidae: Crotalinae) based on morphological and molecular data

Zootaxa ◽

10.11646/zootaxa.1293.1.1 ◽

2006 ◽

Vol 1293 (1) ◽

pp. 1 ◽

Cited By ~ 2

Author(s):

PATRICK DAVID ◽

GERNOT VOGEL ◽

S. P. VIJAYAKUMAR ◽

NICOLAS VIDAL

Keyword(s):

Species Concept ◽

Distinct Species ◽

Morphological Characters ◽

Molecular Data ◽

Biological Species ◽

Valid Species ◽

Biological Species Concept ◽

Phylogenetic Species Concept ◽

Morphological And Molecular Data ◽

A New Species

The brown Asian pitvipers of the genus Trimeresurus related to Trimeresurus puniceus (informal Trimeresurus puniceus-complex) are revised on the basis of morphological and molecular analyses. Variation in morphological characters were investigated among 119 specimens from 62 populations of the whole range of the pitvipers currently known as Trimeresurus puniceus (Boie, 1827), Trimeresurus borneensis (Peters, 1872) and Trimeresurus brongersmai Hoge, 1969. Molecular and morphological analyses clearly differentiate two groups of taxa, referrable to the informal Trimeresurus puniceus-group and Trimeresurus borneensis-group, and confirm the distinct specific status of T. puniceus and T. borneensis. Morphological univariate and multivariate analyses differentiate six clusters of populations that are morphologically diagnosable, of which five are here considered to represent independent lineages and one is placed incertae sedis pending the availability of further specimens. These clusters are considered to be distinct species following the Biological Species Concept and the Phylogenetic Species Concept. One of them is described as a new species, Trimeresurus andalasensis spec. nov. (T. borneensis-group), which includes populations from northern Sumatra. Trimeresurus wiroti Trutnau, 1981 is revalidated to accommodate populations from Thailand and West Malaysia. Trimeresurus borneensis is here considered endemic to Borneo. Trimeresurus puniceus is known from Java and from South Sumatra, but the taxonomy of this species in Sumatra is left unresolved. Also left unresolved is the taxonomic position of specimens from western Sumatra and the Mentawai Archipelago, and from the Natuna Islands and Anamba Islands. Although belonging to the T. puniceus-group, they show some differences to other specimens of the group. They are not referred to any taxon pending the collection of additional specimens. Lastly, Trimeresurus brongersmai is confirmed as a valid species from the Mentawai Archipelago. A key to these taxa is provided.

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Birds of Prey (Falconiformes, Accipitriformes) of Northern Eurasia in the Biological Tetranary Nomenclature

Raptors Conservation ◽

10.19074/1814-8654-2020-40-16-51 ◽

2020 ◽

pp. 16-51

Author(s):

Pavel V. Pfander ◽

◽

Keyword(s):

Reproductive Isolation ◽

Species Concept ◽

Physical Object ◽

Biological Species ◽

Birds Of Prey ◽

Northern Eurasia ◽

Biological Species Concept ◽

Species Problem ◽

Nomenclature System ◽

Definition Of

The main disadvantage of the generally accepted trinary system of around-species nomenclature is the lack of a species concept. This leads to the fact that any lower taxon can be declared a species or subspecies, and any combination of these taxa of arbitrary rank is correct and legitimate, by definition, and therefore cannot even be discussed. Ambiguity of the level of divergence of species creates a “species problem” and makes the question – species or subspecies – meaningless. The solution to the “species problem” can be the creation of a nomenclature system with a "own" species concept. The only concept whose criteria are objective (reproductive isolation and sympatry) and, more importantly, correspond to a certain level of divergence, and that have a biological meaning, is a biological species concept. However, the use of this concept is difficult due to the uncertainty of the degree of reproductive isolation. Therefore, a revised definition of a biological species (B-species) as a category of taxonomy is proposed – this is a level of divergence that provides reproductive isolation sufficient for sympatry (with other closely related forms). Accordingly, as a physical object, the B-species can be defined as a set of sister populations that are incapable to sympatry with each other. The level of B-species is very high, therefore, for forms intermediate between subspecies and B-species, an additional category is needed – a semi-species. Unlike subspecies, which differ only in size and color, a semi-species must have at least one of the following features: 1 – obvious differences in the preference for environmental conditions; 2 – a certain assortative mating with other semi-species; 3 – reduced fertility of hybrids; 4 – significant differences in morphology, physiology, behavior, etc.; 5 – the hybridization zone is relatively very narrow (parapatry). The taxonomy of birds of prey (Falconiformes, Accipitriformes) of Northern Eurasia is presented in a new (genus, B-species, semi-species, subspecies) system of categories and nomenclature.

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Taxonomic position and circumscription of Cardamine barbaraeoides (Brassicaceae), a systematically challenging taxon from the Balkan Peninsula

Phytotaxa ◽

10.11646/phytotaxa.502.2.1 ◽

2021 ◽

Vol 502 (2) ◽

pp. 111-132

Author(s):

MAREK ŠLENKER ◽

MARIÁN PERNÝ ◽

JUDITA ZOZOMOVÁ-LIHOVÁ ◽

KAROL MARHOLD

Keyword(s):

Original Description ◽

Balkan Peninsula ◽

Morphological Characters ◽

Biodiversity Hotspot ◽

Morphometric Study ◽

Herbarium Specimens ◽

Endemic Plants ◽

North Central ◽

Focal Species ◽

Of Greece

The Balkan Peninsula, and the territory of Greece in particular, is a significant biodiversity hotspot in the Mediterranean that is rich in endemic plants. The focal species of this study, Cardamine barbaraeoides, is a narrow Greek endemic that has been confused taxonomically since its original description. Based on a detailed multivariate morphometric study, we provide here a set of morphological characters that enables the reliable identification of this species. In addition, we present an identification key to C. barbaraeoides and related taxa. We have revised herbarium specimens and literature data on the occurrence of this species in Greece and ascertained that it occurs only in the Pindos mountains (the Southern Pindos and partly the Northern Pindos floristic regions). All reports of this species from the Greek floristic regions of North Central, Sterea Ellas and partly also Northern Pindos were based on misidentifications of specimens of C. acris.

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Variation of plumage patterns, geographic distribution and taxonomy of the Unicolored Blackbird (Aves: Icteridae)

Zootaxa ◽

10.11646/zootaxa.4221.4.2 ◽

2017 ◽

Vol 4221 (4) ◽

pp. 431

Author(s):

LEONARDO ESTEVES LOPES

Keyword(s):

Species Concept ◽

Taxonomic Revision ◽

Morphological Characters ◽

Biological Species ◽

Sao Paulo ◽

Southeastern Brazil ◽

Biological Species Concept ◽

São Paulo ◽

Phylogenetic Species Concept ◽

Marsh Bird

The Unicolored Blackbird Agelasticus cyanopus (Vieillot, 1819) is a marsh bird with four allopatric subspecies restricted to lowlands in South America east of the Andes. I conducted a taxonomic revision of the species based on analysis of external morphological characters of 288 study skins, including all types available. My revision shows that: 1) Leistes unicolor Swainson, 1838, is a senior synonym of A. c. xenicus (Parkes, 1966) and, therefore, the correct name of the taxon should be A. c. unicolor (Swainson, 1838); 2) the range of A. c. unicolor (Swainson, 1838) is much wider than previously thought, extending from the mouth of the Rio Amazonas to the state of São Paulo, in southeastern Brazil, where it intergrades with A. c. atroolivaceus (zu Wied-Neuwied, 1831); 3) A. c. atroolivaceus extends its range well beyond the coast of Rio de Janeiro, reaching the coast of São Paulo, the central part of Minas Gerais, Bahia and Espírito Santo; and 4) specimens attributed to A. c. beniensis are highly variable, so this name must be considered a subjective junior synonym of the nominotypical taxon. Under the Biological Species Concept, two broadly parapatric species should be recognized, A. cyanopus and A. atroolivaceus (including unicolor as a subspecies). Under the Phylogenetic Species Concept or the General Lineage Concept of Species, the best taxonomic treatment is to recognize three species: A. cyanopus, A. atroolivaceus, and A. unicolor.

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Review of genera within theAxionice/Pistacomplex (Polychaeta, Terebellidae), with discussion of the taxonomic definition of other Terebellidae with large lateral lobes

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315417000923 ◽

2017 ◽

Vol 97 (5) ◽

pp. 911-934 ◽

Cited By ~ 3

Author(s):

I.A. Jirkov ◽

M.K. Leontovich

Keyword(s):

Type Species ◽

New Genus ◽

Taxonomic Status ◽

Original Description ◽

Morphological Characters ◽

The Other ◽

Considerable Confusion ◽

Definition Of ◽

Almost All ◽

A New Species

The definitions of terebellid genera have caused considerable confusion. Some genera, such asPistaMalmgren, 1866, are clearly not monophyletic and the need to revise them is widely accepted. A phylogenetic analysis of genus level morphological characters within theAxionice/Pistacomplex and other Terebellidae with large lateral lobes revealed two well defined groups; these differed in the arrangement of different forms of lateral lobes on segments 1–3, the shape of the branchiae, structure of the ventral pads and, if present, the origin of the manubrium on the uncini. One of the groups includes the type species ofPista; the other includes the type species ofAxioniceand almost all the other genera whose taxonomic status is discussed in this paper (Betapista,Eupistella,Lanice,Loimia,Paraxionice) which we propose to treat as its junior synonyms. Three other genera –Lanicides,LanicolaandScionella– did not fall within these two groups; they are accepted as distinct. A complete list of species ofAxioniceandPistais provided; 39 species currently included inPistashould be moved toAxionice, thusAxioniceincludes at least 94 species. Many authors’ descriptions of the type species ofPista(Amphitrite cristataMüller, 1776) conflict with the original description.Amphitrite cristatas. str. has been described as a new species:Scionella lornensisPearson, 1969 and the type species of a new genus:PistellaHartmann-Schröder, 1996.Scionella lornensisis here considered a junior synonym ofAmphitrite cristata. Redescriptions of the type species ofAxioniceandPistaare provided.

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A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding

10.1101/717355 ◽

2019 ◽

Cited By ~ 5

Author(s):

Miriam I. Brandt ◽

Blandine Trouche ◽

Laure Quintric ◽

Patrick Wincker ◽

Julie Poulain ◽

...

Keyword(s):

Clustering Algorithm ◽

Sequence Similarity ◽

Alpha Diversity ◽

Biological Species ◽

Biological Species Concept ◽

Ribosomal Database Project ◽

Taxonomic Assignment ◽

Deep Sea Sediment ◽

Biodiversity Inventories ◽

Identity Threshold

ABSTRACTEnvironmental metabarcoding is an increasingly popular tool for studying biodiversity in marine and terrestrial biomes. With sequencing costs decreasing, multiple-marker metabarcoding, spanning several branches of the tree of life, is becoming more accessible. However, bioinformatic approaches need to adjust to the diversity of taxonomic compartments targeted as well as to each barcode gene specificities. We built and tested a pipeline based on Illumina read correction with DADA2 allowing analyzing metabarcoding data from prokaryotic (16S) and eukaryotic (18S, COI) life compartments. We implemented the option to cluster Amplicon Sequence Variants (ASVs) into Operational Taxonomic Units (OTUs) with swarm v2, a network-based clustering algorithm, and to further curate the ASVs/OTUs based on sequence similarity and co-occurrence rates using a recently developed algorithm, LULU. Finally, flexible taxonomic assignment was implemented via Ribosomal Database Project (RDP) Bayesian classifier and BLAST. We validate this pipeline with ribosomal and mitochondrial markers using eukaryotic mock communities and 42 deep-sea sediment samples. The results show that ASVs, reflecting genetic diversity, may not be appropriate for alpha diversity estimation of organisms fitting the biological species concept. The results underline the advantages of clustering and LULU-curation for producing more reliable metazoan biodiversity inventories, and show that LULU is an effective tool for filtering metazoan molecular clusters, although the minimum identity threshold applied to co-occurring OTUs has to be increased for 18S. The comparison of BLAST and the RDP Classifier underlined the potential of the latter to deliver very good assignments, but highlighted the need for a concerted effort to build comprehensive, ecosystem-specific, databases adapted to the studied communities.

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Biological species in the viral world

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1717593115 ◽

2018 ◽

Vol 115 (23) ◽

pp. 6040-6045 ◽

Cited By ~ 20

Author(s):

Louis-Marie Bobay ◽

Howard Ochman

Keyword(s):

Gene Flow ◽

Species Concept ◽

Genome Structure ◽

Biological Species ◽

Arbitrary Sequence ◽

Biological Species Concept ◽

Host Tropism ◽

Universal Definition ◽

Definition Of ◽

Shared Gene

Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.

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A review of morphological variation in Trimeresurus popeiorum (Serpentes: Viperidae: Crotalinae), with the description of two new species

Zootaxa ◽

10.11646/zootaxa.727.1.1 ◽

2004 ◽

Vol 727 (1) ◽

pp. 1 ◽

Cited By ~ 15

Author(s):

GERNOT VOGEL ◽

PATRICK DAVID ◽

OLIVIER S.G. PAUWELS

Keyword(s):

New Species ◽

Species Concept ◽

Morphological Characters ◽

Biological Species ◽

Type Locality ◽

Biological Species Concept ◽

New Taxon ◽

Widespread Species ◽

Phylogenetic Species Concept ◽

Correct Spelling

Variation in morphological characters were investigated among 136 specimens (128 specimens examined by us and eight specimens described in the literature) from 44 populations of the whole range of the pitviper currently known as Trimeresurus popeiorum Smith, 1937. Univariate and mul-tivariate analyses of these morphological characters allowed us to recognize six clusters of populations that are morphologically diagnosable, and that are here considered to represent independent lineages. Five of these clusters are considered to be distinct species following the Biological Species Concept and the Phylogenetic Species Concept. Two of them are described as new. Trimeresurus fucatus spec. nov. includes populations from southern Thailand and most of West Malaysia. Trimeresurus nebularis spec. nov. is described for populations from Cameron Highlands of West Malaysia. A population from Toba Massif, northern Sumatra, is referred to this complex, but cannot be assigned to a species at the present time. Trimeresurus popeiorum sabahi is raised to specific status, Trimeresurus sabahi new comb., to accommodate the populations from Borneo, whereas Trimeresurus barati new comb. includes the populations from western Sumatra and the Mentawai Archipelago. Separate keys to the two sexes of the recognised species of the T. popeiorum complex are provided.KEY WORDS: Thailand, West Malaysia, Sumatra, Borneo, Serpentes, Viperidae, Trimeresurus, Trimeresurus popeiorum, Trimeresurus fucatus spec. nov., Trimeresurus nebularis spec. nov., Trimeresurus sabahi, Trimeresurus baratiBefore the paper by Pope & Pope (1933), all green Trimeresurus species were gathered under the name Trimeresurus gramineus (Shaw, 1802). In a first step towards understanding the systematics of the genus, these authors split the nominal taxon gramineus into six species. The specific nomen gramineus was applied to a widespread species, ranging from northeastern India to western Indonesia. Indian populations were referred to a new species described as Trimeresurus occidentalis. Subsequently, Smith (1937) correctly showed that Pope & Pope (1933) misunderstood the type locality of gramineus, and showed that the type locality for T. gramineus was within the range of T. occidentalis. Therefore, Trimeresurus occidentalis Pope & Pope 1933 became a subjective junior synonym of T. gramineus (Shaw, 1802), leaving unnamed the distinct eastern taxon. Smith (1937) named it as Trimeresurus popeiorum. Unfortunately, he failed to designate a type specimen and a type locality for this new taxon. This interpretation was accepted by most subsequent authors except Hoge & Romano Hoge (1981) and Welch (1988). Another issue affecting the specific nomen is its spelling. Smith (1943) corrected the original spelling as popeorum on the basis that it was indeed a clerical error. This spelling was largely accepted, and was the subject of recent controversies. This problem will be addressed in another paper (David & Vogel, submitted). We consider that the correct spelling is indeed popeiorum. Eventually, Taylor & Elbel (1958), regarded as syntypes of Trimeresurus popeiorum Smith, 1937 all specimens referred by Pope & Pope (1933) to as T. gramineus, and designated the specimen BMNH 72.4.17.137 as the lectotype of the species. Consequently, the type locality was restricted to Khasi Hills, Assam , now in the State of Meghalaya, India.

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