scholarly journals Phylogeny, morphology, and ecology resurrect previously synonymized species of North American Stereum

2020 ◽  
Author(s):  
Sarah G. Delong-Duhon ◽  
Robin K. Bagley
Keyword(s):  
North American ◽  
Sequence Data ◽  
Preliminary Investigation ◽  
Morphological Variability ◽  
Sampling Strategy ◽  
Nominal Species ◽  
Field Guides ◽  
Species Complexes ◽  
Scientific Papers ◽  
Multilocus Approach

AbstractStereum is a globally widespread genus of basidiomycete fungi with conspicuous shelf-like fruiting bodies. Several species have been extensively studied due to their economic importance, but broader Stereum taxonomy has been stymied by pervasive morphological crypsis in the genus. Here, we provide a preliminary investigation into species boundaries among some North American Stereum. The nominal species Stereum ostrea has been referenced in field guides, textbooks, and scientific papers as a common fungus with a wide geographic range and even wider morphological variability. We use ITS sequence data of specimens from midwestern and eastern North America, alongside morphological and ecological characters, to show that Stereum ostrea is a complex of at least three reproductively isolated species. Preliminary morphological analyses show that these three species correspond to three historical taxa that were previously synonymized with S. ostrea: Stereum fasciatum, Stereum lobatum, and Stereum subtomentosum. Stereum hirsutum ITS sequences taken from GenBank suggest that other Stereum species may actually be species complexes. Future work should apply a multilocus approach and global sampling strategy to better resolve the taxonomy and evolutionary history of this important fungal genus.

scholarly journals Reeling them in: taxonomy of marine annelids used as bait by anglers in the Western Cape Province, South Africa

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11847
Author(s):  
Carol Simon ◽  
Jyothi Kara ◽  
Alheit du Toit ◽  
Hendré van Rensburg ◽  
Caveshlin Naidoo ◽  
...  
Keyword(s):  
South Africa ◽  
Nominal Species ◽  
Western Cape ◽  
Western Cape Province ◽  
Mitochondrial Coi ◽  
Field Guides ◽  
Species Complexes ◽  
Coi Sequences ◽  
First Time ◽  
Mitochondrial Cytochrome Oxidase

Background Common names are frequently used inconsistently for marine annelid species used as bait in the peer-reviewed literature, field guides and legislative material. The taxonomy of many such species based on morphology only also ignores cryptic divergences not yet detected. Such inconsistencies hamper effective management of marine annelids, especially as fishing for recreation and subsistence is increasing. This study investigates the scale of the problem by studying the use and names of bait marine annelids in the Western Cape Province of South Africa. Methods Fifteen recreational and six subsistence fishers at 12 popular fishing sites in the Western Cape Province donated 194 worms which they identified by common name. Worms were assigned scientific names according to a standard identification key for polychaetes from South Africa, and mitochondrial cytochrome oxidase I (COI) amplified and sequenced. Results This study identified 11 nominal species known by 10 common names, in the families Siphonosomatidae, Arenicolidae, Sabellaridae, Lumbrineridae, Eunicidae, Onuphidae and Nereididae. Cryptic diversity was investigated through employing mitochondrial COI sequences and these data will facilitate future identifications among widely distributed species. Several species (Siphonosoma dayi, Abarenicola gilchristi, Scoletoma species, Marphysa corallina, Lysidice natalensis, Heptaceras quinquedens, Perinereis latipalpa) are reported as bait for the first time, and while the names blood- and moonshineworms were consistently applied to members of Arenicolidae and Onuphidae, respectively, coralworm was applied to members of Sabellaridae and Nereididae. Analysis of COI sequences supported morphological investigations that revealed the presence of two taxonomic units each for specimens initially identified as Gunnarea gaimardi and Scoletoma tetraura according to identification keys. Similarly, sequences for Scoletoma species and Lysidice natalensis generated in this study do not match those from specimens in China and India, respectively. Further research is required to resolve the species complexes detected and also to refine the use of names by fishermen over a wider geographic range.

Hookear sculpins (genus Artediellus) of the North American Atlantic: taxonomy, morphological variability, distribution, and aspects of life history

1986 ◽  
Vol 64 (3) ◽  
pp. 677-690 ◽  
Author(s):  
Louis Van Guelpen
Keyword(s):  
North American ◽  
Morphological Variability ◽  
Morphological Characters ◽  
Cape Cod ◽  
Nominal Species ◽  
Depth Range ◽  
Baffin Island ◽  
Northern Limit ◽  
The North ◽  
Depth Relationship

Difficulty in identifying the two nominal species of hookear sculpins (genus Artediellus) from the North American Atlantic has led to confusion in their taxonomy and reported distributions. The species were found to be separable using nine meristic and six morphological characters, as well as collection locality. Sexual dimorphism and clinal geographic variation occurred in several characters of both species. The known northern limit of A. atlanticus (the Atlantic hookear) in North America was extended to southeast Baffin Island, also the northern limit for A. uncinatus (the snowflake hookear). The southern limits were off Cape Cod for A. atlanticus and northern Nova Scotia for A. uncinatus. Artediellus uncinatus inhabited a shallower depth range (13–183 m) than A. atlanticus (0–384 m), indicating at least partial ecological separation. The latter species had a positive size–depth relationship, with the largest fish inhabiting the deep northern waters. Artediellus atlanticus seemed to prefer softer bottom sediments, while A. uncinatus showed no preference. Overall, sex ratios were similar (1.29 males to females in A. atlanticus and 1.12 in A. uncinatus). In North American waters, A. atlanticus spawns from approximately May to November and A. uncinatus during summer. Both nominal species warrant full specific status; however, subspecies designations appear unfounded.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

FUSARIUM-ID v.3.0: An updated, downloadable resource for Fusarium species identification

Plant Disease ◽  
2021 ◽  
Author(s):  
Terry Torres-Cruz ◽  
Briana Whitaker ◽  
Robert Proctor ◽  
Kirk Broders ◽  
Imane Laraba ◽  
...  
Keyword(s):  
Sequence Data ◽  
Safety Concern ◽  
Fusarium Species ◽  
Elongation Factor ◽  
Sequence Database ◽  
Accurate Identification ◽  
Dna Sequence Data ◽  
Species Complexes ◽  
Marker Loci ◽  
Feed Safety

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ~680 bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely-available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.

A molecular phylogenetic and DNA barcode assessment of the tribe Pterosiphonieae (Ceramiales, Rhodophyta) emphasizing the Northeast Pacific

Botany ◽  
2016 ◽  
Vol 94 (10) ◽  
pp. 917-939 ◽  
Author(s):  
Amanda M. Savoie ◽  
Gary W. Saunders
Keyword(s):  
South African ◽  
North American ◽  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Sensu Stricto ◽  
North American Species ◽  
African Species ◽  
Molecular Phylogenetic

Sequence data (COI-5P and rbcL) for North American members of the tribe Pterosiphonieae were compared with collections from around the world. Phylogenetic analyses resolved Pterosiphonia as polyphyletic and many species required transfer to other genera. In our analyses Pterosiphonia sensu stricto included only the type species P. cloiophylla (C. Agardh) Falkenberg and P. complanata (Clemente) Falkenberg, as well as the South African species P. stegengae sp. nov. A new genus, Xiphosiphonia gen. nov., was described for X. ardreana (Maggs & Hommersand) comb. nov., X. pennata (C. Agardh) comb. nov., and X. pinnulata (Kützing) comb. nov. Some Asian, European and North American species previously attributed to Pterosiphonia were transferred to Symphyocladia including S. baileyi (Harvey) comb. nov., S. dendroidea (Montagne) comb. nov., S. plumosa nom. nov. (for P. gracilis Kylin), and S. tanakae (S. Uwai & M. Masuda) comb. nov. We also described two new North American species, Symphyocladia brevicaulis sp. nov. and S. rosea sp. nov. Other species formed a well-supported clade for which the genus name Polyostea Ruprecht was resurrected. Included in Polyostea were P. arctica (J. Agardh) comb. nov., P. bipinnata (Postels & Ruprecht) Ruprecht, P. hamata (E.S. Sinova) comb. nov., and P. robusta (N.L. Gardner) comb. nov.

scholarly journals Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1830
Author(s):  
Victor B. Pedrosa ◽  
Flavio S. Schenkel ◽  
Shi-Yi Chen ◽  
Hinayah R. Oliveira ◽  
Theresa M. Casey ◽  
...  
Keyword(s):  
Milk Production ◽  
Genome Sequence ◽  
North American ◽  
Milk Fat ◽  
Molecular Mechanisms ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Holstein Cattle ◽  
Whole Genome ◽  
Production Traits

Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.

Additional information on Meloidogyne polycephannulata and its proposal as a junior synonym of M. incognita

Nematology ◽  
2019 ◽  
Vol 21 (2) ◽  
pp. 129-146
Author(s):  
Jessica M.S. Monteiro ◽  
Vanessa S. Mattos ◽  
Marcilene F.A. Santos ◽  
Ana C.M.M. Gomes ◽  
Valdir R. Correa ◽  
...  
Keyword(s):  
Morphological Variability ◽  
Junior Synonym ◽  
Valid Species ◽  
Bootstrap Support ◽  
Nominal Species ◽  
Aflp Data ◽  
Morphometric Characters ◽  
Additional Information ◽  
Phylogenetic Studies ◽  
Type Population

Summary The type population of Meloidogyne polycephannulata is synonymised with M. incognita based on morphological and morphometric characters, as well as biochemical, molecular and phylogenetic studies. Morphological variability and a wide host range were reported for M. incognita during its first description and later re-description. Meloidogyne polycephannulata was described in Brazil from specimens collected in a carrot field (type population). The esterase phenotype (Est) characterised for this species was identical to the phenotype Est I2 of M. incognita, the most ubiquitous phenotype used for diagnostics. Morphological and morphometric characters of the descriptions of the two nominal species showed major similarities, as well as variability within the range of variation detected in M. incognita. In PCR assays, three SCAR markers species-specific for M. incognita (incK14 F/R, Mi/FR and incB06 F/R) amplified the same fragments of 399 bp, 955 bp and 1200 bp, respectively, for populations in both species. In phylogenetic studies based either on concatenated sequences of ITS1-5.8S-ITS2, D2-D3 rRNA, mitochondrial COII regions or on RAPD and AFLP data, the populations of both species grouped in the same clade with high bootstrap support. Altogether, these results provide congruent evidence that the M. polycephannulata type isolate deposited at the Embrapa Cryopreserved National Collection of Root-knot Nematodes is not a valid species but rather a junior synonym of M. incognita.

scholarly journals Molecular forms of Anopheles subpictus and Anopheles sundaicus in the Indian subcontinent

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Ankita Sindhania ◽  
Manoj K. Das ◽  
Gunjan Sharma ◽  
Sinnathamby N. Surendran ◽  
B. R. Kaushal ◽  
...  
Keyword(s):  
Sibling Species ◽  
Molecular Form ◽  
Indian Subcontinent ◽  
Phylogenetic Analyses ◽  
Coastal Areas ◽  
Molecular Forms ◽  
Nominal Species ◽  
Anopheles Subpictus ◽  
Species Complexes ◽  
Molecular Phylogenetic

Abstract Background Anopheles subpictus and Anopheles sundaicus are closely related species, each comprising several sibling species. Ambiguities exist in the classification of these two nominal species and the specific status of members of these species complexes. Identifying fixed molecular forms and mapping their spatial distribution will help in resolving the taxonomic ambiguities and understanding their relative epidemiological significance. Methods DNA sequencing of Internal Transcribed Spacer-2 (ITS2), 28S-rDNA (D1-to-D3 domains) and cytochrome oxidase-II (COII) of morphologically identified specimens of two nominal species, An. subpictus sensu lato (s.l.) and An. sundaicus s.l., collected from the Indian subcontinent, was performed and subjected to genetic distance and molecular phylogenetic analyses. Results Molecular characterization of mosquitoes for rDNA revealed the presence of two molecular forms of An. sundaicus s.l. and three molecular forms of An. subpictus s.l. (provisionally designated as Form A, B and C) in the Indian subcontinent. Phylogenetic analyses revealed two distinct clades: (i) subpictus clade, with a single molecular form of An. subpictus (Form A) prevalent in mainland India and Sri Lanka, and (ii) sundaicus clade, comprising of members of Sundaicus Complex, two molecular forms of An. subpictus s.l. (Form B and C), prevalent in coastal areas or islands in Indian subcontinent, and molecular forms of An. subpictus s.l. reported from Thailand and Indonesia. Based on the number of float-ridges on eggs, all An. subpictus molecular Form B were classified as Species B whereas majority (80%) of the molecular Form A were classified as sibling species C. Fixed intragenomic sequence variation in ITS2 with the presence of two haplotypes was found in molecular Form A throughout its distribution. Conclusion A total of three molecular forms of An. subpictus s.l. and two molecular forms of An. sundaicus s.l. were recorded in the Indian subcontinent. Phylogenetically, two forms of An. subpictus s.l. (Form B and C) prevalent in coastal areas or islands in the Indian subcontinent and molecular forms reported from Southeast Asia are members of Sundaicus Complex. Molecular Form A of An. subpictus is distantly related to all other forms and deserve a distinct specific status.

A taxonomic review of the fish parasitic isopod family Cymothoidae Leach, 1818 (Crustacea: Isopoda: Cymothooidea) of India

Zootaxa ◽  
2019 ◽  
Vol 4622 (1) ◽  
pp. 1-99 ◽  
Author(s):  
S. RAVICHANDRAN ◽  
P. VIGNESHWARAN ◽  
G. RAMESHKUMAR
Keyword(s):  
Morphological Variability ◽  
Marine Fishes ◽  
Valid Species ◽  
Indian Species ◽  
Nominal Species ◽  
Host Preferences ◽  
As Species ◽  
The Family ◽  
Species Inquirenda ◽  
Parasitic Isopod

The parasitic isopod family Cymothoidae Leach, 1818 of the India exclusive economic zone is reviewed. A total of 56 nominal species corresponding to 48 valid species belonging to sixteen genera are reviewed from 73 host species belonging to 35 families. Mothocya plagulophora (Haller, 1880), Nerocila depressa Milne Edwards, 1840, Nerocila loveni Bovallius, 1887, Nerocila trichiura (Miers, 1877), Norileca triangulata (Richardson, 1910) and Ryukyua globosa Williams & Bunkley-Williams, 1994 are redescribed. Indusa pustulosa Pillai, 1954 is synonymised with Agarna malayi Tiwari, 1952; Cymothoa krishnai Jayadev Babu & Sanjeeva Raj, 1984 is synonymised with Cymothoa eremita (Brünnich, 1783) and Nerocila priacanthusi Kumari, Rao & Shyamasundari, 1987 is synonymised with Nerocila arres Bowman & Tareen, 1983. Ourozeuktes bopyroides (Lesueur, 1814) is revised and excluded from the Indian fauna. The Indian cymothoid species Agarna bengalensis Kumari, Rao & Shaymasundari, 1990, Cymothoa asymmetrica Pillai, 1954 and Nerocila hemirhamphusi Shyamasundari, Rao & Kumari, 1990 are regarded here as species inquirenda. A key to the Indian genera of the family Cymothoidae and keys to the Indian species of the genera Cymothoa, Joryma, Mothocya, and Nerocila are presented. A checklist of the valid Cymothoidae species until now reported from Indian marine fishes are compiled. Host preferences, morphological variability and distribution are discussed. 

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