scholarly journals Nothing in (sponge) biology makes sense – except when based on holotypes

2015 ◽  
Vol 96 (2) ◽  
pp. 305-311 ◽  
Author(s):  
Dirk Erpenbeck ◽  
Merrick Ekins ◽  
Nicole Enghuber ◽  
John N.A. Hooper ◽  
Helmut Lehnert ◽  
...  
Keyword(s):  
New Species ◽  
Reference Material ◽  
Species Identification ◽  
Dna Sequences ◽  
Morphological Plasticity ◽  
Morphological Characters ◽  
Molecular Techniques ◽  
Reference Sequences ◽  
Species Descriptions ◽  
Preservation History

Sponge species are infamously difficult to identify for non-experts due to their high morphological plasticity and the paucity of informative morphological characters. The use of molecular techniques certainly helps with species identification, but unfortunately it requires prior reference sequences. Holotypes constitute the best reference material for species identification, however their usage in molecular systematics and taxonomy is scarce and frequently not even attempted, mostly due to their antiquity and preservation history. Here we provide case studies in which we demonstrate the importance of using holotype material to answer phylogenetic and taxonomic questions. We also demonstrate the possibility of sequencing DNA fragments out of century-old holotypes. Furthermore we propose the deposition of DNA sequences in conjunction with new species descriptions.

scholarly journals Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shan Shen ◽  
Shi-Liang Liu ◽  
Ji-Hang Jiang ◽  
Li-Wei Zhou
Keyword(s):  
Species Identification ◽  
Rolling Circle Amplification ◽  
Practical Method ◽  
Morphological Characters ◽  
Its Sequences ◽  
Commercial Development ◽  
Medicinal Mushrooms ◽  
Rolling Circle ◽  
Reference Sequences ◽  
Its Barcoding

Abstract“Sanghuang” refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of “Sanghuang” in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to “Sanghuang” in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Gregory AC Singer ◽  
Donal A Hickey
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Primate Species ◽  
Dna Barcodes ◽  
Global Biodiversity ◽  
Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

scholarly journals Three new species of the genus Coddingtonia from Asia (Araneae, Theridiosomatidae)

ZooKeys ◽  
2019 ◽  
Vol 886 ◽  
pp. 113-126
Author(s):  
Chengcheng Feng ◽  
Yucheng Lin
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Current Paper ◽  
Distribution Map ◽  
Three New Species

The current paper expands knowledge of the genus Coddingtonia Miller, Griswold & Yin, 2009. Based on morphological characters and molecular data, three species are documented as new to science: C. erhuan Feng & Lin, sp. nov. (♀) from China, C. lizu Feng & Lin, sp. nov. (♀) from China, and C. huifengi Feng & Lin, sp. nov. (♂♀) from Indonesia. The type of C. euryopoides Miller, Griswold & Yin, 2009 is also reexamined. DNA sequences (COI), detailed illustrations of habitus, male palp and epigyne are provided for these four species, as well as a key and a distribution map for Coddingtonia species.

Leptolejeunea nigra (Lejeuneaceae), a new species with brownish black ocelli based upon morphology and DNA sequences

Phytotaxa ◽  
2019 ◽  
Vol 427 (1) ◽  
pp. 31-42
Author(s):  
LEI SHU ◽  
RUI-LIANG ZHU
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Time Span ◽  
Molecular Dating ◽  
Molecular Phylogenetic ◽  
Brownish Black ◽  
A New Species

Based on molecular phylogenetic analyses and morphological characters, a new species from Bangladesh, northern Vietnam, and southwestern China, Leptolejeunea nigra, is described. It is mostly similar to L. balansae but remarkable for having brownish black ocelli in its leaf lobes. In the molecular phylogeny, the samples of L. nigra are not nested within any clade and form an independent lineage. In particular, the molecular dating suggested that the divergence of L. nigra happened in time span of the formation of the Himalayas.

Male identification, generic classification and sexual dimorphism of Micronychus pardus (Kazantsev, 2018) comb. nov. (Coleoptera: Lycidae: Calochrominae)

Zootaxa ◽  
2019 ◽  
Vol 4657 (1) ◽  
pp. 177-182 ◽  
Author(s):  
MICHAL MOTYKA
Keyword(s):  
Mitochondrial Dna ◽  
Sexual Dimorphism ◽  
Species Identification ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Large Specimen ◽  
Molecular Analyses ◽  
Almost All ◽  
First Time

Almost all net-winged beetles are members of Müllerian complexes and their similarity due to phenotypic coevolution sometimes complicates species identification and generic placement. Therefore, large specimen series, detailed exhaustive examination of morphological characters and molecular data are needed to clarify the taxonomic placement. Using mitochondrial DNA sequences, I investigated the sexual dimorphism and generic placement of the recently described species Calochromus pardus Kazantsev, 2018. I found that the species does not belong in Calochromus Guérin-Méneville, 1833 and all morphological characters and molecular analyses point to its placement in Micronychus Motschulsky, 1861. Therefore, Micronychus pardus (Kazantsev, 2018), comb. nov. is proposed. Additionally, the male is described here for the first time showing the sexual dimorphism in the species. Unlike the females, the males do not superficially resemble members of Xylobanus Waterhouse, 1879 with bright coloured elytral costae and black background, but mimics the sympatrically occurring yellow and black lycids in the genus Cautires Waterhouse, 1879. 

A new entomopathogenic nematode, Steinernema xinbinense n. sp. (Nematoda: Steinernematidae), from north China

Nematology ◽  
2012 ◽  
Vol 14 (6) ◽  
pp. 723-739 ◽  
Author(s):  
Juan Ma ◽  
Juan Ma ◽  
Shulong Chen ◽  
Juan Ma ◽  
Shulong Chen ◽  
...  
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
First Generation ◽  
Galleria Mellonella ◽  
Entomopathogenic Nematode ◽  
Tail Length ◽  
Northern China ◽  
Morphological Characters ◽  
Liaoning Province ◽  
Lateral Field

During a survey for entomopathogenic nematodes in northern China, a new species of Steinernema was isolated from soil samples collected from Xinbin county, Liaoning province. This nematode was obtained by the insect-baiting technique using last instar larvae of Galleria mellonella. It is described herein as S. xinbinense n. sp. The nematode can be separated from other described species of the group by morphological and morphometric characteristics of the different stages and by characterisation and phylogeny of DNA sequences of the D2D3 domain of the LSU or ITS regions of rDNA. This new species is characterised by the following morphological characters: infective third-stage juvenile with a body length of 694 (635-744) μm, distance from head to excretory pore of 51 (46-53) μm, tail length of 73 (61-81) μm, E = 71 (65-78)%, presence of eight unevenly spaced and developed ridges in middle lateral field (i.e., nine lines). First generation male with well curved, yellowish spicules 56 (49-62) μm long and gubernaculum 35 (30-41) μm long, small mucron mostly present, first generation female with protruding vulva, tail conical with one or two small mucrons and D = 45 (41-50)%. Cross hybridisation tests with S. tielingense, S. kraussei, S. feltiae and S. hebeiense showed that this species was reproductively isolated. The analyses of ITS-rDNA and D2D3 sequence confirm that the studied nematode isolate is a valid new species belonging to the ‘feltiae-kraussei-oregonense’ group.

Description of a new genus and two new species of killifish (Cyprinodontiformes: Nothobranchiidae) from West Africa, with a discussion of the taxonomic status of Aphyosemion maeseni Poll, 1941

Zootaxa ◽  
2009 ◽  
Vol 2294 (1) ◽  
pp. 1-22 ◽  
Author(s):  
RAINER SONNENBERG ◽  
ECKHARD BUSCH
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
New Genus ◽  
Nuclear Dna ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Color Pattern ◽  
Monophyletic Group ◽  
Morphological Data ◽  
Adult Males

The phylogeny of the West African genus Archiaphyosemion was studied with mitochondrial and nuclear DNA sequences. The results of the combined dataset presented here did not support a monophyletic group. After the exclusion of the type species of the genus, A. guineense, the remaining species form a well-supported monophyletic group. Based on these molecular results and supported by morphological data, we suggest a new name for this group, Nimbapanchax, new genus. Additionally, based on a recent collection in Guinea, two new Nimbapanchax species were described. The taxon Nimbapanchax leucopterygius, new species, is described for a nothobranchiid fish formerly misidentified as Archiaphyosemion maeseni (Poll, 1941). Nimbapanchax melanopterygius, new species, is described from the Mount Nimba region in southeastern Guinea. Both new Nimbapanchax species are clearly distinguished from their congeners by the coloration pattern of adult males. The results of the DNA data support the assumption based on color pattern and morphological characters that the new described species are sister taxa. The type of Aphyosemion maeseni Poll, 1941 was reexamined and transferred to the genus Epiplatys, a decision based on diagnostic morphological characters.

scholarly journals Two new species of Hygrophorus from temperate Himalayan Oak forests of Pakistan

MycoKeys ◽  
2019 ◽  
Vol 56 ◽  
pp. 33-47 ◽  
Author(s):  
Arooj Naseer ◽  
Abdul Nasir Khalid ◽  
Rosanne Healy ◽  
Matthew E. Smith
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Large Subunit ◽  
Its Region ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Oak Forests ◽  
Rdna Genes ◽  
Two New Species ◽  
Dark Green

The genus Hygrophorus is poorly studied from Asia. From Pakistan, only one species has been reported so far. Two new species in the genus have been collected from Himalayan oak forests of Pakistan. Hygrophorusalboflavescens (section Pudorini, subgenus Colorati) is characterised by its pure white, centrally depressed pileus, occurrence of white stipe with yellow patches at lower half and broader (4.98 μm) basidiospores. Hygrophorusscabrellus (section Hygrophorus, subgenus Hygrophorus) is characterised by its yellowish-green stipe with white apex that has fine scales on the entire stipe, an off-white pileus with dark green and greyish fibrils, ovoid to ellipsoid basidiospores and clavate 4-spored basidia. Macro- and micromorphological descriptions have revealed that both these taxa are not yet described. Phylogenetic estimation based on DNA sequences from the internal transcribed spacer (ITS) region and large subunit (LSU) of the nuclear ribosomal DNA (rDNA) genes, is congruent with the morphological characters that help to delimit these as new species of Hygrophorus. Allied taxa are also compared.

Two new species of Lycianthes (Capsiceae, Solanaceae) from Mexico and Guatemala

Phytotaxa ◽  
2019 ◽  
Vol 409 (5) ◽  
pp. 261-272 ◽  
Author(s):  
ELLEN DEAN ◽  
FREDY ARCHILA ◽  
JENNIFER POORE ◽  
HANNAH KANG ◽  
MARCO ANTONIO ANGUIANO-CONSTANTE ◽  
...  
Keyword(s):  
New Species ◽  
Cloud Forest ◽  
Morphological Characters ◽  
The State ◽  
Similar Species ◽  
Forest Species ◽  
Two New Species ◽  
Geographic Distributions ◽  
Species Descriptions

Two cloud forest species of Lycianthes are newly described: L. breedlovei from the state of Chiapas, Mexico and L. fredyclaudiae from the state of Baja Verapaz, Guatemala. Both species have orange-brown, multangulate-stellate trichomes in which the rays of the trichome are rebranched, white to pale lilac flowers (with darker violet-purple lobes in L. breedlovei), and unequal stamens. Morphologically, they resemble L. hortulana of Honduras, but both new species have previously been misidentified as L. cuchumatanensis. This article provides species descriptions, maps of geographic distributions, drawings of trichomes, and images of the flowers and specimens of the two new species, as well as a comparison chart of morphological characters used to separate L. breedlovei and L. fredyclaudiae from similar species.

Calcareous sponges (Porifera, Calcarea) from Florida: new species, new records and biogeographical affinities

Zootaxa ◽  
2018 ◽  
Vol 4526 (2) ◽  
pp. 127 ◽  
Author(s):  
MATHEUS V. LOPES ◽  
ANDRÉ PADUA ◽  
BÁSLAVI CÓNDOR-LUJÁN ◽  
MICHELLE KLAUTAU
Keyword(s):  
New Species ◽  
Geographical Distribution ◽  
New Records ◽  
Florida Keys ◽  
Morphological Plasticity ◽  
Morphological Characters ◽  
Marine Biodiversity ◽  
Calcareous Sponges ◽  
Distributional Patterns ◽  
New Diagnosis

Florida is among important marine biodiversity areas with high richness and endemism of marine taxa. Despite the economic and scientific importance of the region, knowledge on the diversity and distribution of some groups, such as calcareous sponges, is still reduced and scattered in old literature. In the present work, sponges collected in the Florida Keys were studied under an integrative perspective (traditional morphology and DNA: ITS). Three calcinean species were found: Clathrina smaragda sp. nov., C. lutea, and Ernstia rocasensis. Clathrina smaragda sp. nov. is the first Clathrina described with a green cormus. The occurrence of C. lutea in Florida was confirmed, and E. rocasensis had its geographical distribution widened from the Northeastern Brazilian waters to Florida, although Floridian individuals of this species have presented differences in morphological characters that resulted in the proposition of a new diagnosis and a discussion on morphological plasticity in Clathrinidae. A complete list of the calcareous sponges from Florida is presented and their distributional patterns are discussed. 

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