scholarly journals DNA-barcode and endophallus morphology delimit congruent species in a systematic revision of the oxyporine rove beetles of Russia (Coleoptera: Staphylinidae: Oxyporinae)

2021 ◽  
pp. 1-64
Author(s):  
Alexandra S. Tokareva ◽  
Fedor V. Konstantinov ◽  
Adam J. Brunke ◽  
Alexey Solodovnikov
Keyword(s):  
Species Interactions ◽  
Species Delimitation ◽  
Morphological Traits ◽  
Dna Barcode ◽  
Phylogenetic Inference ◽  
Ancestral State ◽  
Systematic Revision ◽  
Rove Beetles ◽  
New Synonyms ◽  
The Russian Federation

Abstract Rigorous species delimitation is a challenge in biology and systematics in particular. In insects, male genitalia traditionally, and the barcoding region of the CO1 gene recently, are the main markers to identify species, even though a standalone use of CO1 for that is often criticized. In our systematic revision of the mycophagous and in other ways peculiar oxyporine rove beetles of Russia, the legacy alpha-taxonomy could not be improved by traditional investigation of genitalia as they are unusually character-poor in this group. Using phylogenetic inference and ancestral state reconstruction, we demonstrate that CO1 and endophallus are useful markers for species delimitation in Oxyporus. We also show that many morphological traits previously used for species delimitation in Oxyporus are in fact highly variable and thus inconsistent. We hypothesize that in Oxyporus diversification of the endophallic structures is driven by intense intra- and inter-species interactions of multiple individuals co-occurring in narrow spaces inside fungal bodies during mating. Our results encourage broader use of both markers, especially easy-to-generate dna barcodes, for the desired alpha-taxonomical work in Oxyporinae globally. The revision revealed 10 species of Oxyporus in the fauna of the Russian Federation; eliminated erroneous species records; established two new synonyms, Oxyporus (Oxyporus) basicornis Cameron, 1930 = O. (O.) aequicollis Bernhauer, 1935, syn.nov. = O. (O.) parvus Lee et al., 2020, syn. nov.; and raised the hypothesis that O. (O.) aokii Dvořák, 1956, O. (O.) basiventris Jarrige, 1948 and O. (O.) kobayashii Hayashi, 2015 are conspecific with O. (O.) maxillosus Fabricius, 1793. Lectotypes are designated for O. (O.) basicornis Cameron, 1930, O. (O.) germanus Sharp, 1889, O. (O.) niger Sharp, 1889, and O. (O.) triangulus Sharp, 1889. Comprehensive taxonomic treatment and an identification key are provided for all species.

Guidelines for DNA barcoding of coralline algae, focusing on Lithophylloideae (Corallinales) from Brazil

2018 ◽  
Vol 61 (2) ◽  
pp. 127-140 ◽  
Author(s):  
Beatriz N. Torrano-Silva ◽  
Bruno R. Vieira ◽  
Rafael Riosmena-Rodríguez ◽  
Mariana C. Oliveira
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Morphological Traits ◽  
Dna Barcode ◽  
Molecular Data ◽  
Coralline Algae ◽  
Integrative Approach ◽  
Interspecific Divergence ◽  
Algorithmic Approaches ◽  
Barcode Gap

AbstractMultiple-marker (COI-5P, UPA,psbA andrbcL-3P) and two algorithmic approaches [automatic barcode gap discovery (ABGD) and Poisson tree process (PTP)] were used for species delimitation of Lithophylloideae in Brazil. The integrative approach was mostly congruent between markers and algorithmic methods of species delimitation, suggesting the occurrence of 24 species. Based on morphology and molecular data,Amphiroa rigida,Amphiroa vanbosseae,Lithophyllum atlanticum,Lithophyllum kaiseri,Lithophyllum margaritae,Titanoderma pustulatum,Titanoderma prototypumandPaulsilvella huveorum, which were previously reported for Brazil, are confirmed in this work. Six new species are distinguished by both molecular and morphological traits, and they are provisionally named asAmphiroasp. 1,Amphiroasp. 2,Amphiroasp. 3,Lithophyllumsp. 1,Lithophyllumsp. 2 andLithophyllumsp. 3. Another 10 species are cryptic and cannot be distinguished based on traditionally used morphological traits. These includeAmphiroasp. 4,Lithophyllumsp. 4, three species that are morphologically named underAmphiroa beauvoisii, and six that share the morphology described forAmphiroa fragilissima. All four markers used were useful for species delimitation. However, a combination of practical aspects and levels of intra- and interspecific divergence values led us to propose the use ofrbcL-3P as a standard DNA barcode marker for the Corallinales.

Revision of the subgenus Phortica (sensu stricto) (Diptera, Drosophilidae) from East Asia, with assessment of species delimitation using DNA barcodes

Zootaxa ◽  
2019 ◽  
Vol 4678 (1) ◽  
pp. 1-75
Author(s):  
JIA HUANG ◽  
LU GONG ◽  
SHUN-CHERN TSAUR ◽  
LIN ZHU ◽  
KEYING AN ◽  
...  
Keyword(s):  
New Species ◽  
Cytochrome C Oxidase ◽  
Species Delimitation ◽  
Species Complex ◽  
Dna Barcode ◽  
Sensu Stricto ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Dna Barcodes ◽  
New Synonyms

A total of 50 (43 known and seven new) species in the subgenus Phortica (sensu stricto) were surveyed and (re)described from China: P. bicornuta (Chen & Toda, 1997); P. bipartita (Toda & Peng, 1992); P. biprotrusa (Chen & Toda, 1998); P. cardua (Okada, 1977); P. chi (Toda & Sidorenko, 1996); P. conifera (Okada, 1977); P. eparmata (Okada, 1977); P. eugamma (Toda & Peng, 1990); P. excrescentiosa (Toda & Peng, 1990); P. fangae (Máca, 1993); P. flexuosa (Zhang & Gan, 1986); P. foliata (Chen & Toda, 1997); P. gamma (Toda & Peng, 1990); P. gigas (Okada, 1977); P. glabtabula Chen & Gao, 2005; P. hainanensis (Chen & Toda, 1998); P. hongae (Máca, 1993); P. huazhii Cheng & Chen, 2008; P. iota (Toda & Sidorenko, 1996); P. jadete Zhu, Cao & Chen, 2018; P. kappa (Máca, 1977); P. lambda (Toda & Peng, 1990); P. latifoliacea Chen & Watabe, 2008; P. magna (Okada, 1960); P. okadai (Máca, 1977); P. omega (Okada, 1977); P. orientalis (Hendel, 1914); P. pangi Chen & Wen, 2005; P. paramagna (Okada, 1971); P. perforcipata (Máca & Lin, 1993); P. pi (Toda & Peng, 1990); P. protrusa (Zhang & Shi, 1997); P. pseudopi (Toda & Peng, 1990); P. pseudotau (Toda & Peng, 1990); P. psi (Zhang & Gan, 1986); P. rhagolobos Chen & Gao, 2008; P. saeta (Zhang & Gan, 1986); P. setitabula Chen & Gao, 2005; P. subradiata (Okada, 1977); P. tau (Toda & Peng, 1990); P. uncinata Chen & Gao, 2005; P. unipetala Chen & Wen, 2005; P. allomega Gong & Chen, sp. nov.; P. archikappa Gong & Chen, sp. nov.; P. dianzangensis Gong & Chen, sp. nov.; P. imbacilia Gong & Chen, sp. nov.; P. liukuni Gong & Chen, sp. nov.; P. tibeta Gong & Chen, sp. nov.; and P. xianfui Gong & Chen, sp. nov. In addition, seven new synonyms were recognized: P. acongruens (Zhang & Shi, 1997), syn. nov.; P. antillaria (Chen & Toda, 1997), syn. nov.; P. kukuanensis Máca, 2003, syn. nov.; P. linae (Máca & Chen, 1993), syn. nov.; P. shillongensis (Singh & Gupta, 1979), syn. nov.; P. takadai (Okada, 1977), syn. nov.; and P. watanabei (Máca & Lin, 1993), syn. nov. A key to all Asian species (except for the eparmata species complex) of this subgenus was provided. All currently available DNA barcode (partial mitochondrial cytochrome c oxidase subunit I (COI) gene) sequences of this subgenus (217 sequences of 54 species) are employed in a molecular analysis using different species delimitation methods. The results indicate that approximately 68.5% (37 of 54 spp.) of Phortica (s. str.) species could be clearly distinguished from closely related morphospecies or cryptic species. 

scholarly journals Morphology lies: a case-in-point with a new non-biting midge species from Oriental China (Diptera, Chironomidae)

ZooKeys ◽  
2020 ◽  
Vol 909 ◽  
pp. 67-77
Author(s):  
Chao Song ◽  
Xinhua Wang ◽  
Wenjun Bu ◽  
Xin Qi
Keyword(s):  
Species Delimitation ◽  
Morphological Traits ◽  
Morphological Characteristics ◽  
Phylogenetic Inference ◽  
Ribosomal Genes ◽  
Biting Midge ◽  
Protein Encoding ◽  
Molecular Genes ◽  
Encoding Genes ◽  
A New Species

Morphological traits are generally indicative of specific taxa, and particularly function as keys in taxonomy and species delimitation. In this study, a non-biting midge species with an Einfeldia-like superior volsella makes it hard to accurately determined based on its morphological characteristics. Molecular genes of two ribosomal genes and three protein-encoding genes were compiled to construct a related genera phylogeny and to address the taxonomic issues. Phylogenetic inference clearly supports the undetermined species as belonging to Kiefferulus. Therefore, a new species classified in the genus Kiefferulus is described and figured as an adult male from Oriental China. The species could be easily distinguished from other species in having an Einfeldia-like superior volsella and a triangular tergite IX.

Corrigendum to: Cladistic analysis and revision of Piestus Gravenhorst with remarks on related genera (Coleoptera : Staphylinidae : Piestinae)

2013 ◽  
Vol 27 (1) ◽  
pp. 129
Author(s):  
Edilson Caron ◽  
Cibele S. Ribeiro-Costa ◽  
Alfred F. Newton
Keyword(s):  
Cladistic Analysis ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Morphological Characters ◽  
Valid Species ◽  
Phylogenetic Position ◽  
Neotropical Forests ◽  
Rove Beetles ◽  
New Synonyms ◽  
Branch Support

Rove beetles of the genus Piestus Gravenhorst, 1806 are commonly captured under the bark of or inside decaying logs from Neotropical forests. Piestus belongs to the subfamily Piestinae, historically an ill-defined dumping-ground for Staphylinidae defined by plesiomorphic characters, but which has gradually been restricted in concept and currently includes only six additional extant genera worldwide. Piestinae in this restricted sense has been considered a probably monophyletic subfamily, but its status and phylogenetic position, as a possible sister-group of Osoriinae within the recently proposed Oxyteline group of staphylinid subfamilies, are uncertain and need confirmation. The main aim of the present study was to provide a morphological cladistic analysis and complete taxonomic revision of Piestus, which, as the type and most speciose genus of Piestinae, is critical for future phylogenetic studies involving the subfamily. In our study, the monophyly of Piestus is established and phylogenetic relationships among its species are proposed based on 70 adult morphological characters. Piestus is supported by 11 synapomorphies and high branch support. All species of Piestus are revised and the genus is redefined. The genus contains 43 species, including 13 species described here for the first time. The previously proposed subgenera Antropiestus Bernhauer, 1917, Eccoptopiestus Scheerpeltz, 1952, Elytropiestus Scheerpeltz, 1952, Lissopiestus Scheerpeltz, 1952, Piestus s. str., Trachypiestus Scheerpeltz, 1952 and Zirophorus Dalman, 1821 have not been confirmed, as they were found to be poly- or paraphyletic, or are here removed from Piestus, and therefore subgenera are not used. The main taxonomic changes are as follows. Lissopiestus, syn. nov. is proposed as new synonym of Eleusis Laporte, 1835 and its species, E. interrupta (Erichson, 1840), comb. rest., is transferred again to that genus. Antropiestus, syn. nov. and Eccoptopiestus, syn. nov. are proposed as new synonyms of Hypotelus Erichson, 1839 and their species, H. laevis (Solsky, 1872), comb. nov. and H. andinus (Bernhauer, 1917), comb. nov., are transferred to Hypotelus. Fourteen new synonymies are proposed (valid species listed first): P. lacordairei Laporte, 1835 = Z. furcatus Sharp, 1887, syn. nov.; P. capricornis Laporte, 1835 = P. frontalis Sharp, 1876, syn. nov.; P. pennicornis Fauvel, 1864 = P. plagiatus Fauvel, 1864, syn. nov.; P. rectus Sharp, 1876, syn. nov.; P. pygialis Fauvel, 1902, syn. nov.; P. surinamensis Bernhauer, 1928, syn. nov.; P. minutus Erichson, 1840 = P. nigrator Fauvel, 1902, syn. nov.; P. sulcatus Gravenhorst, 1806 = P. sanctaecatharinae Bernhauer, 1906, syn. nov.; P. condei Wendeler, 1955, syn. nov.; P. gounellei Fauvel, 1902 = P. wasmanni Fauvel, 1902, syn. nov.; P. mexicanus Laporte, 1835 = P. alternans Sharp, 1887, syn. nov.; P. aper Sharp, 1876 = P. schadei Scheerpeltz, 1952, syn. nov.; P. angularis Fauvel, 1864 = P. crassicornis Sharp, 1887, syn. nov.; H. andinus (Bernhauer, 1917) = P. strigipennis Bernhauer, 1921, syn. nov. One species is revalidated: P. fronticornis (Dalman, 1821), stat. rev., and one synonym is restored: P. penicillatus (Dalman, 1821) = P. erythropus Erichson, 1840, syn. rest. Neotypes are designated for P. lacordairei Laporte, 1835 and Oxytelus bicornis Olivier, 1811, and lectotypes are designated for P. puncticollis Fauvel, 1902, P. capricornis variety muticus Fauvel, 1902, P. zischkai Scheerpeltz, 1951, P. pennicornis Fauvel, 1864, P. plagiatus Fauvel, 1864, P. pygmaeus Laporte, 1835, P. niger Fauvel 1864, P. minutus Erichson, 1840, P. nigratror Fauvel, 1902, P. sulcatus Gravenhorst, 1806, P. sanctaecatharinae Bernhauer, 1906, P. sulcipennis Scheerpeltz, 1952, P. aper Sharp, 1876, P. schadei Scheerpeltz, 1952 and P. andinus Bernhauer, 1917.

scholarly journals Two new species of the feather mite genus Analges Nitzsch, 1818 (Analgoidea: Analgidae) from accentors (Passeriformes: Prunellidae) — morphological descriptions with DNA barcode data

2018 ◽  
Vol 23 (12) ◽  
pp. 2288 ◽  
Author(s):  
Jacek Dabert ◽  
Serge V. Mironov ◽  
Marián Janiga
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Dna Barcode ◽  
Feather Mites ◽  
Feather Mite ◽  
Two New Species ◽  
Mite Genus

Two new species of the genus Analges (Astigmata: Analgoidea) are described from two species of accentors (Passeriformes: Prunellidae): Analges himalayanus sp. nov. from the Altai Accentor P. himalayana (Blyth), and A. slovakiensis sp. nov. from the Alpine Accentor Prunella collaris (Scopoli). Both species are closely related to A. bidentatus Giebel, 1871 described from the Dunnock Prunella modularis (Linnaeus). We extended the standard morphological descriptions of feather mites by species delimitation analyses carried out on DNA barcode sequences.

scholarly journals Integrative taxonomy of Nearctic and Palaearctic Aleocharinae: new species, synonymies, and records (Coleoptera, Staphylinidae)

ZooKeys ◽  
2021 ◽  
Vol 1041 ◽  
pp. 27-99
Author(s):  
Adam J. Brunke ◽  
Mikko Pentinsaari ◽  
Jan Klimaszewski
Keyword(s):  
New Species ◽  
North America ◽  
Dna Barcode ◽  
Integrative Taxonomy ◽  
Eastern Canada ◽  
Rove Beetles ◽  
Adventive Species ◽  
The Status ◽  
Taxonomic Studies ◽  
Holarctic Species

A long tradition of separate Nearctic and Palaearctic taxonomic studies of the diverse aleocharine rove beetles (Coleoptera: Staphylinidae) has obscured the recognition of Holarctic species and detection of adventive species in both regions. Recently, integrated study of the two regions through detailed morphological comparisons and development of an authoritatively identified DNA barcode reference library has revealed the degree to which these two aleocharine faunas are interconnected, both naturally and through human activity. Here this approach is adopted to recognize new species, reveal Holarctic species, and recognize adventive species in both North America and Europe. The following new species are described: Isoglossa triangularis Klimaszewski, Brunke & Pentinsaari, sp. nov. from British Columbia; Gnypeta impressicollis Klimaszewski, Brunke & Pentinsaari, sp. nov., from Ontario, Maryland and North Carolina; Aloconota pseudogregaria Klimaszewski, Brunke & Pentinsaari, sp. nov., from Ontario and Virginia; and Philhygra pseudolaevicollis Klimaszewski, Brunke & Pentinsaari, sp. nov. from eastern Canada. Dasygnypeta velata and Philhygra angusticauda are revealed to be Holarctic species, resulting in the following synonymies: Dasygnypeta velata (Erichson, 1839) = Gnypeta minuta Klimaszewski & Webster, 2008, syn. nov. and Philhygra angusticauda (Bernhauer, 1909) = Atheta (Philhygra) pinegensis Muona, 1983, syn. nov. The Nearctic species Hylota ochracea (and genus Hylota), Thecturota tenuissima, and Trichiusa robustula are newly reported from the Palaearctic region as adventive, resulting in the following synonymies: Hylota ochracea Casey, 1906 = Stichoglossa (Dexiogyia) forticornis Strand, 1939, syn. nov.; Thecturota tenuissima Casey, 1893 = Atheta marchii Dodero, 1922, syn. nov.; and Trichiusa robustula Casey, 1893 = T. immigrata Lohse, 1984, syn. nov. The Palaearctic species Amarochara forticornis, Anomognathus cuspidatus, Oligota pumilio, and Parocyusa rubicunda are newly confirmed from the Nearctic region as adventive, resulting in the following synonymies: Parocyusa rubicunda (Erichson, 1837) = Chilopora americana Casey, 1906, syn. nov. and Anomognathus cuspidatus (Erichson, 1839) = Thectura americana Casey, 1893, syn. nov. The genus Dasygnypeta, sensu nov. is newly reported from North America, Paradilacra is newly reported from eastern North America, and Haploglossa is newly reported from Canada, resulting in the following synonymy: Paradilacra densissima (Bernhauer, 1909) = Gnypeta saccharina Klimaszewski & Webster, 2008, syn. nov. Native Cyphea wallisi is newly reported from across Canada and C. curtula is removed from the Nearctic fauna. The status of both Gyrophaena affinis and Homalota plana is uncertain but these species are no longer considered to be adventive in North America. Three new combinations are proposed: Dasygnypeta baranowskii (Klimaszewski, 2020) and D. nigrella (LeConte, 1863) (both from Gnypeta) and Mocyta scopula (Casey, 1893) (from Acrotona). Dolosota Casey, 1910, syn. nov. (type species Eurypronota scopula Casey), currently a subgenus of Acrotona, is therefore synonymized with Mocyta Mulsant & Rey, 1874. Additionally, four new Canadian records and 18 new provincial and state records are reported.

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.

A Taxonomic Revision of Fern Genus Pseudocyclosorus (Thelypteridaceae) from China and the Pan-Himalaya Region, with Special Reference to the Identity of Pseudocyclosorus stramineus

Phytotaxa ◽  
2019 ◽  
Vol 424 (4) ◽  
pp. 197-216
Author(s):  
ZHONG-YANG LI ◽  
XIAN-CHUN ZHANG ◽  
ZHEN-LONG LIANG ◽  
JIE LI
Keyword(s):  
Special Reference ◽  
Species Delimitation ◽  
Morphological Study ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Morphological Features ◽  
Similar Species ◽  
Spore Morphology ◽  
Distribution Map ◽  
New Synonyms

The fern genus Pseudocyclosorus (Thelypteridaceae) from China and the Pan-Himalaya region is revised based on morphological study. Reduced basal pinnae, angles between costule and costae, and glands/hairs on abaxial surfaces/indusia are considered as the most diagnostic morphological characters for species delimitation. Genus Trigonospora was excluded from genus Pseudocyclosorus. This segregation is supported by multiple morphological features. Eight species were recognized here, namely Pseudocyclosorus tylodes, P. pseudofalcilobus, P. falcilobus, P. subochthodes, P. stramineus, P. ornatipes, P. esquirolii and P. canus. Twenty-one names were reduced as new synonyms. One name (P. duclouxii) was considered a dubious species. A key to these eight species, their descriptions, spore morphology and distribution map of each species are given.         Pseudocyclosorus stramineus was a long overlooked species, which has always been misidentified as other similar species, and was wrongly reduced as a synonym of P. duclouxii. Here based on morphology characters, the identity of P. stramineus as a species was reclaimed. A more detailed description with photographs and illustrations, and its whole distribution range are given here.

scholarly journals Molecular identification of species of Physalis (Solanaceae) using a candidate DNA barcode: the chloroplast psbA–trnH intergenic region

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 15-20 ◽  
Author(s):  
Shangguo Feng ◽  
Kaili Jiao ◽  
Yujia Zhu ◽  
Hongfen Wang ◽  
Mengying Jiang ◽  
...  
Keyword(s):  
Intergenic Region ◽  
Morphological Traits ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Genetic Distances ◽  
Success Rates ◽  
Medicinal Species ◽  
Distance Methods ◽  
Identification Of Species ◽  
Related Plant

Physalis L., an important genus of the family Solanaceae, includes many commercially important edible and medicinal species. Traditionally, species identification is based on morphological traits; however, the highly similar morphological traits among species of Physalis make this approach difficult. In this study, we evaluated the feasibility of using a popular DNA barcode, the chloroplast psbA–trnH intergenic region, in the identification of species of Physalis. Thirty-six psbA–trnH regions of species of Physalis and of the closely related plant Nicandra physalodes were analyzed. The success rates of PCR amplification and sequencing of the psbA–trnH region were 100%. MEGA V6.0 was utilized to align the psbA–trnH sequences and to compute genetic distances. The results show an apparent barcoding gap between intra- and interspecific variations. Results of both BLAST1 and nearest-distance methods prove that the psbA–trnH regions can be used to identify all species examined in the present study. In addition, phylogenetic analysis using psbA–trnH data revealed a distinct boundary between species. It also confirmed the relationship between species of Physalis and closely related species, as established by previous studies. In conclusion, the psbA–trnH intergenic region can be used as an efficient DNA barcode for the identification of species of Physalis.

Sign in / Sign up

Export Citation Format

Share Document