scholarly journals SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

2020 ◽  
Vol 21 (24) ◽  
pp. 9421
Author(s):  
Lidia Skuza ◽  
Ewa Filip ◽  
Izabela Szućko ◽  
Jan Bocianowski
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Markers ◽  
Related Species ◽  
Economic Importance ◽  
Closely Related Species ◽  
Coding Sequences ◽  
Coding Regions ◽  
Genomic Regions ◽  
Tribe Triticeae

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

Species delimitation of colour polymorphic Cladophorus (Coleoptera: Lycidae) from New Guinea

Zootaxa ◽  
2017 ◽  
Vol 4320 (3) ◽  
pp. 505 ◽  
Author(s):  
ROMANA KALOUSOVA ◽  
LADISLAV BOCAK
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Related Species ◽  
Species Delimitation ◽  
Morphological Differentiation ◽  
Morphological Characters ◽  
Molecular Data ◽  
Closely Related Species ◽  
Dna Fragment ◽  
Colour Patterns

Cladophorus Guérin-Méneville, 1830 are endemic Papuan net-winged beetles which take part in highly diverse Müllerian mimicry rings. Available specimens were sequenced for cox1–tRNA-Leu–cox2 mitochondrial DNA fragment and the species delimitations were based on the genetic distance, phylogenetic analysis, and morphology. Three earlier described species were identified in the recently collected material and further 10 species are described: C. pallescens sp. nov., C. bicolor sp. nov., C. craterensis sp. nov., C. motykai sp. nov., C. mindikensis sp. nov., C. kailakiensis sp. nov., C. manokwarensis sp. nov., C. haiaensis sp. nov., C. humeralis sp. nov., and C. boceki sp. nov. DNA-based identifications provided some ambiguous results and closely related species could not be robustly delimited using solely molecular data. Additionally, the species limits were based on clearly defined morphological characters and the morphological differentiation was found unlinked from the genetic divergence. Colour patterns cannot be used for identification because all species available in more specimens were polymorphic and followed various local co-mimics. The Papuan fauna of Cladophorus is very diverse and the closely related species regularly occur in limited regions. Differentiation within restricted ranges is therefore considered as the main speciation mode. 

scholarly journals Taxonomic revision of the Campoplex difformis group (Ichneumonidae, Campopleginae), with particular reference to species of economic importance

2021 ◽  
Vol 740 ◽  
Author(s):  
Filippo Di Giovanni ◽  
Pier Luigi Scaramozzino ◽  
Augusto Loni ◽  
Andrea Lucchi
Keyword(s):  
Biological Control ◽  
Related Species ◽  
Taxonomic Status ◽  
Taxonomic Revision ◽  
Host Record ◽  
Economic Importance ◽  
Biological Control Agents ◽  
Closely Related Species

Despite their importance as potential biological control agents, species of the campoplegine genus Campoplex Gravenhorst, 1829 are hard to identify. Previous works provided short descriptions or poor illustrations of crucial characters, meaning it is often impossible to distinguish closely related species. We provide illustrations to identify species of the Campoplex difformis group and redescriptions of and illustrations for C. difformis (Gmelin, 1790), C. capitator Aubert, 1960, C. dubitator Horstmann, 1985, C. formosanae Horstmann, 2012, and C. unicingulatus (Schmiedeknecht, 1909). In addition, the taxonomic status of C. difformis is clarified; a lectotype is designated for C. capitator in Aubert’s collection in Lausanne and the host record for this species on Ancylis mitterbacheriana (Denis & Schiffermüller, 1775) is queried; Campoplex corsicator Aubert, 1960 stat. nov. is removed from synonymy with Campoplex tibialis (Szépligeti, 1916) and redescribed.

Molecular markers reconstruct the invasion history of variable leaf watermilfoil (Myriophyllum heterophyllum) and distinguish it from closely related species

2011 ◽  
Vol 13 (7) ◽  
pp. 1687-1709 ◽  
Author(s):  
Ryan A. Thum ◽  
Matthew P. Zuellig ◽  
Robert L. Johnson ◽  
Michael L. Moody ◽  
Charles Vossbrinck
Keyword(s):  
Molecular Markers ◽  
Related Species ◽  
Invasion History ◽  
Closely Related Species ◽  
History Of

Designation of a neotype for the Brazilian porcupine, Coendou prehensilis (Linnaeus, 1758)

Zootaxa ◽  
2011 ◽  
Vol 2791 (1) ◽  
pp. 30 ◽  
Author(s):  
YURI L. R. LEITE ◽  
VILACIO CALDARA JÚNIOR ◽  
ANA CAROLINA LOSS ◽  
LEONORA PIRES COSTA ◽  
ÉVERTON R. A. MELO ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Geographic Distribution ◽  
Related Species ◽  
Taxonomic Revision ◽  
Type Specimen ◽  
Northeastern Brazil ◽  
Closely Related Species ◽  
Geographic Ranges ◽  
Central Brazil ◽  
Shed Light

The Brazilian porcupine was one of several species described and illustrated by the 17 th -century naturalist Georg Marcgrave, whose text was among the primary references upon which Linnaeus based his Hystrix prehensilis. As currently understood, Coendou prehensilis is a wide-ranging polytypic taxon that has never been revised and may represent a complex of closely related species. Given that no name-bearing type specimen of C. prehensilis is believed to be extant, and in order to avoid ambiguous application of this name, we designate a specimen collected at the type locality in Pernambuco, northeastern Brazil, as the neotype for Hystrix prehensilis Linnaeus. The geographic distribution of mitochondrial DNA haplotypes suggests that specimens from west-central Brazil previously identified as “Coendou prehensilis” belong to a different species, but only a comprehensive taxonomic revision of the genus will shed light on species limits and the geographic ranges of C. prehensilis and other congeneric forms.

Molecular identification of animal isolates ofEchinococcus granulosusfrom Iran using four mitochondrial genes

2011 ◽  
Vol 86 (4) ◽  
pp. 485-492 ◽  
Author(s):  
M. Rostami Nejad ◽  
N. Taghipour ◽  
Z. Nochi ◽  
E. Nazemalhosseini Mojarad ◽  
S.R. Mohebbi ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Related Species ◽  
Mitochondrial Genes ◽  
12S Rrna ◽  
Rrna Gene ◽  
Sequence Evolution ◽  
Closely Related Species ◽  
12S Rrna Gene ◽  
Complete Sequences ◽  
Animal Isolates

AbstractMitochondrial genes have more power than nuclear genes in reconstructing phylogenetic relationships among closely related species because of their faster sequence evolution. The aim of this study was to use the complete or near-complete sequences from three mitochondrial genes (cox1,nad1andatp6) and partial sequences of the 12S rRNA gene to infer relationships among isolates ofEchinococcus granulosusfrom Iran. Two hundred and twenty-nine isolates ofE. granulosuswere collected from cattle, camels, sheep, buffalo and goats from different geographical areas. Most individuals were found to possess the G1 genotype but some of the camel samples belonged to the G6 genotype. Newly designed primers forcox1,nad1andatp6genes amplified bands of 1830, 708 and 1157 bp for the G1 genotype and 1856, 705, 1054 bp for the G6 genotype, respectively. The result of this survey showed thatatp6andnad1genes are good molecular markers for identifyingE. granulosusisolates from a range of hosts in Iran.

A reassessment of the genus Haeckeria (Asteraceae: Gnaphalieae), with definition of new species in Cassinia

2004 ◽  
Vol 17 (5) ◽  
pp. 447 ◽  
Author(s):  
A. E. Orchard
Keyword(s):  
New Species ◽  
Leaf Anatomy ◽  
Related Species ◽  
Closely Related Species ◽  
Definition Of

Variation in the species hitherto known as Haeckeria ozothamnoides F.Muell. is discussed. This taxon has well-developed paleae between the florets, and many collections show development of a pappus. These characters, along with others such as leaf anatomy and morphology, strongly distinguish H. ozothamnoides s. lat. from Haeckeria s. str. and place it in Cassinia. The taxon is also shown to comprise three closely related species, which are here described as Cassinia ozothamnoides (F.Muell.) Orchard, comb. nov., C.�scabrida Orchard, sp. nov. and C.�venusta Orchard, sp. nov. The history, taxonomy, relationships and classification of Haeckeria is reviewed, and the genus and its two remaining species, H.�cassiniiformis and H.�punctulata, are described. All five species are illustrated and their distributions mapped.

Additions to Taiwan fungal flora 2: Ophiosphaerella taiwanica sp. nov.

Phytotaxa ◽  
2019 ◽  
Vol 413 (1) ◽  
pp. 39-48 ◽  
Author(s):  
HIRAN A. ARIYAWANSA ◽  
E. B. GARETH JONES
Keyword(s):  
Dna Sequences ◽  
Related Species ◽  
Phylogenetic Reconstruction ◽  
New Taxon ◽  
The Novel ◽  
Fungal Flora ◽  
Closely Related Species ◽  
Natural Classification

The genus Ophiosphaerella contains 14 formerly illustrated species and is characterized by papillated ascomata bearing fissitunicate cylindrical asci frequently narrower near the base, with a short furcate pedicel and filamentous, pale brown, multi-septate ascospores without swollen cells or separating into part spores. We describe an Ophiosphaerella taxon that is new to science isolated from Yushania niitakayamensis in Cilai Mountain, Taiwan. We conducted polyphasic methods using single and multi-locus (ITS, LSU, SSU, and tef1-α) phylogenetic reconstruction united with morphology to evaluate the natural classification of the novel taxon. The results show that our Ophiosphaerella isolates are different from closely related species O. aquaticus and O. agrostidis based on distinct size differences of the ascomata, asci, ascospores, host and DNA sequences data, thus should be recognised here as a new taxon Ophiosphaerella taiwanica sp. nov.

scholarly journals Accuracy of a neural net classification of closely-related species of microfossils from a sparse dataset of unedited images

2018 ◽  
Author(s):  
Johan Renaudie ◽  
Ryan Gray ◽  
David B Lazarus
Keyword(s):  
Related Species ◽  
Depth Of Field ◽  
Neural Net ◽  
Automated Identification ◽  
Convolutional Network ◽  
Closely Related Species ◽  
Fossil Specimen ◽  
Focus Depth ◽  
The Cost

Identification of biologic objects in images is a major source of biodiversity data. Currently this is done by scarce taxonomic experts and data is thus limited in scope and reproducibility. Automated identification in fields such as plankton research or micropaleontology, where enormous numbers of objects are available, would significantly improve data quantity and quality, particularly in applied studies of environmental and climate change. We describe a machine learning workflow based on the MobileNet convolutional network. The software can identify closely related species of radiolarians, a morphologically challenging group of microfossils, and from complete species populations (not only ideal specimens) as they are normally identified in standard transmitted light microscope preparations. Multiple, partial focus, depth of field limited images were obtained for each fossil specimen from multiple radiolarian microslides. Images were normalized and in one test also cropped to remove most systematic slide-linked image biases (e. g. type of background particles) that could be used by a classifier as non-taxonomic clues to species assignment. An average of 60 specimens per species for 16 species in two distinct clusters of closely related forms (9 species in the Antarctissa group and 7 species in the genus Cycladophora) were used to train and test the system. An overall average classification accuracy of ca 73% was achieved, and for some species >85%. Using a cutoff for specimens with classifier-calculated low certainty values boosts overall accuracy close to 90%, but at the cost of ca 1/3 reduction in identifiable specimens. This latter accuracy is close to the reproducibility of human experts, albeit with more unidentifiable specimens. The most important constraint to broader use is the time and effort needed by taxonomic experts to collect and label images to be used in training, as many species in these diverse biotas are rare, and the numbers of taxonomic experts available are very limited.

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