scholarly journals ‘Barcode fishing’ for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mark D. Scherz ◽  
Safidy M. Rasolonjatovo ◽  
Jörn Köhler ◽  
Loïs Rancilhac ◽  
Andolalao Rakotoarison ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
High Elevation ◽  
Degraded Dna ◽  
Taxonomic Resolution ◽  
Type Specimens ◽  
Extrinsic Factors ◽  
Diagnostic Characters ◽  
Genetic Lineages ◽  
Intrinsic Factors

Abstract Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne dʼAmbre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d’Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this ‘barcode fishing’ approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.

scholarly journals Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization ofEphesiella,EphesiopsisandSphaerodorum

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5783 ◽  
Author(s):  
María Capa ◽  
Torkild Bakken ◽  
Karin Meißner ◽  
Arne Nygren
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Intraspecific Variability ◽  
Morphological Data ◽  
Nominal Species ◽  
Type Specimens ◽  
Diagnostic Features ◽  
28S Rdna Sequence

BackgroundLong-bodied sphaerodorids (Annelida, Sphaerodoridae) is the common name for members of the three closely and morphologically homogenous currently accepted genera of benthic marine bristle worms:Ephesiella,EphesiopsisandSphaerodorum. Members of this group share the presence of two dorsal and longitudinal rows of macrotubercles with terminal papillae, and two longitudinal rows of microtubercles, features that are unique among sphaerodorids. Genera are distinguished by the chaetae morphology. Members ofEphesiellaare characterised by having compound chaetae (except, sometimes, simple chaetae in the first chaetigers),Sphaerodorumbear only simple chaetae, andEphesiopsishave both compound and simple chaetae in all parapodia.MethodsMitochondrial (partial COI and 16S rDNA) and nuclear (partial 18S rDNA and 28S rDNA) sequence data of long-bodied sphaerodorids with compound and simple chaetae, and an outgroup of additional seven sphaerodorid species were analysed separately and in combination using Bayesian inference (BA), and Maximum Likelihood (ML) methods. Long-bodied sphaerodorids from around the world (including type specimens) were examined under a range of optical equipment in order to evaluate putative generic and specific diagnostic features, in addition to intraspecific variability.ResultsPhylogenetic analyses of mitochondrial and nuclear DNA sequences of specimens identified asEphesiellaandSphaerodorum,based on chaeta morphology, were performed.SphaerodorumandEphesiellawere recovered as paraphyletic and nested within each other. Revision of current nominal species diagnostic features are performed and discussed.DiscussionResults contradict current generic definitions. Recovery of paraphyletic compound and simple chaetae clades urge the synonymization of these two genera of long-bodied sphaerodorids. Morphological data also suggest the synonymization ofEphesiopsis.

scholarly journals Toward a Natural Classification of Botryosphaeriaceae: A Study of the Type Specimens of Botryosphaeria sensu lato

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Zhang ◽  
Yupei Zhou ◽  
Wei Sun ◽  
Lili Zhao ◽  
D. Pavlic-Zupanc ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Type Specimens ◽  
Natural Classification ◽  
Dna Sequence Data

The genus Botryosphaeria includes more than 200 epithets, but only the type species, Botryosphaeria dothidea and a dozen or more other species have been identified based on DNA sequence data. The taxonomic status of the other species remains unconfirmed because they lack either morphological information or DNA sequence data. In this study, types or authentic specimens of 16 “Botryosphaeria” species are reassessed to clarify their identity and phylogenetic position. nuDNA sequences of four regions, ITS, LSU, tef1-α and tub2, are analyzed and considered in combination with morphological characteristics. Based on the multigene phylogeny and morphological characters, Botryosphaeria cruenta and Botryosphaeria hamamelidis are transferred to Neofusicoccum. The generic status of Botryosphaeria aterrima and Botryosphaeria mirabile is confirmed in Botryosphaeria. Botryosphaeria berengeriana var. weigeliae and B. berengeriana var. acerina are treated synonyms of B. dothidea. Botryosphaeria mucosa is transferred to Neodeightonia as Neodeightonia mucosa, and Botryosphaeria ferruginea to Nothophoma as Nothophoma ferruginea. Botryosphaeria foliicola is reduced to synonymy with Phyllachorella micheliae. Botryosphaeria abuensis, Botryosphaeria aesculi, Botryosphaeria dasylirii, and Botryosphaeria wisteriae are tentatively kept in Botryosphaeria sensu stricto until further phylogenetic analysis is carried out on verified specimens. The ordinal status of Botryosphaeria apocyni, Botryosphaeria gaubae, and Botryosphaeria smilacinina cannot be determined, and tentatively accommodate these species in Dothideomycetes incertae sedis. The study demonstrates the significance of a polyphasic approach in characterizing type specimens, including the importance of using of DNA sequence data.

scholarly journals DNA from a 100-year-old holotype confirms the validity of a potentially extinct hummingbird species

2009 ◽  
Vol 6 (1) ◽  
pp. 112-115 ◽  
Author(s):  
Jeremy J. Kirchman ◽  
Christopher C. Witt ◽  
Jimmy A. McGuire ◽  
Gary R. Graves
Keyword(s):  
Population Growth ◽  
Human Population ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
High Elevation ◽  
Valid Species ◽  
Type Specimens ◽  
Tissue Samples ◽  
Mtdna Sequence ◽  
Well Differentiated

We used mtDNA sequence data to confirm that the controversial 100-year-old holotype of the Bogotá sunangel ( Heliangelus zusii ) represents a valid species. We demonstrate that H. zusii is genetically well differentiated from taxa previously hypothesized to have given rise to the specimen via hybridization. Phylogenetic analyses place H. zusii as sister to a clade of mid- to high-elevation Andean species currently placed in the genera Taphrolesbia and Aglaiocercus. Heliangelus zusii , presumed extinct, has never been observed in nature by biologists. We infer that the species occupied a restricted distribution between the upper tropical and temperate zones of the northern Andes and that it was most probably driven to extinction by deforestation that accompanied human population growth during the nineteenth and early twentieth centuries. We demonstrate the feasibility of obtaining DNA from nearly microscopic tissue samples from old hummingbird specimens and suggest that these methods could be used to resolve the taxonomy of dozens of avian taxa known only from type specimens.

scholarly journals High genetic connectivity in a gastropod with long-lived planktonic larvae

2019 ◽  
Vol 86 (1) ◽  
pp. 42-55 ◽  
Author(s):  
Fabio Crocetta ◽  
Luigi Caputi ◽  
Sofia Paz-Sedano ◽  
Valentina Tanduo ◽  
Angelo Vazzana ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Gross Anatomy ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Extrinsic Factors ◽  
Dna Sequence Data ◽  
Pelagic Larvae

Abstract Genetic connectivity plays a crucial role in shaping the geographic structure of species. Our aim in this study was to explore the pattern of genetic connectivity in Bursa scrobilator, an iconic marine caenogastropod with long-lived pelagic larvae. Our study was based on the analysis of DNA sequence data for the 658-bp barcoding fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. This is the largest DNA sequence dataset assembled to date for B. scrobilator. These data confirm that the two recently described subspecies B. scrobilator scrobilator (Linnaeus, 1758), from the Mediterranean and Macaronesia, and B. s. coriacea (Reeve, 1844), from West Africa, constitute two evolutionarily significant units (ESUs). We found that for the nominal subspecies, the variation in morphology (shell, radula and gross anatomy) and DNA sequences was not geographically structured, and this agrees with what we would expect in a species with high connectivity at the larval stage. The divergence between the two subspecies cannot be easily explained by isolation by distance, and we would argue that one or more extrinsic factors may have played a role in isolating the two ESUs and maintaining that isolation.

scholarly journals New acoustic and molecular data shed light on the poorly known Amazonian frog Adenomera simonstuarti (Leptodactylidae): implications for distribution and conservation

2020 ◽  
Author(s):  
Thiago R. Carvalho ◽  
Leandro J.C.L. Moraes ◽  
Ariadne Angulo ◽  
Fernanda P. Werneck ◽  
Javier Icochea ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Taxonomic Resolution ◽  
Future Research ◽  
Nominal Species ◽  
Phenotypic Data ◽  
Voucher Specimen ◽  
Genetic Lineages ◽  
Conservation Concern

Adenomera simonstuarti is a poorly known species complex inhabiting western Amazonia. Here we reevaluate the species diversity within this complex based on previously documented and newly acquired molecular and phenotypic data. We also redescribe the calling pattern of the nominal species based on the original recording (Peru) and a new recording (Brazil). Our results indicate eight geographically structured genetic lineages and the nominal species with a multi-note call pattern. This is the first association of calls and DNA sequence from a voucher specimen, thereby enabling the assignment of A. simonstuarti to one specific lineage within the complex. The multi-note call was not previously reported and represents an important additional diagnostic character within Adenomera. The geographic distribution of A. simonstuarti is substantially narrowed down to the southwestern portion of the entire geographic range recognized for the complex. The lack of taxonomic resolution in the complex is a major conservation concern by preventing us from evaluating the potential threats and extinction risks of each of the lineages. Future research should follow the protocol of combining calls and DNA sequences associated with voucher specimens as a means to address the taxonomic status of genetic lineages within the A. simonstuarti complex.

Institutional Environment, Entrepreneurial Self-Efficacy and Entrepreneurial Intention of Company Employees

1970 ◽  
Vol 3 (1) ◽  
pp. 1-9
Author(s):  
Devi Angrahini Anni Lembana ◽  
Yu Yu Chang ◽  
Wen Ke Liang
Keyword(s):  
Self Efficacy ◽  
Institutional Environment ◽  
Practical Experience ◽  
Entrepreneurial Intention ◽  
Entrepreneurial Intentions ◽  
New Venture ◽  
Hierarchical Regression ◽  
Market Demand ◽  
Extrinsic Factors ◽  
Intrinsic Factors

From the intentionality-based view, individuals' actual behaviors to initiate a new venture is driven by their entrepreneurial intentions. Company employees have accumulated professionalism and practical experience, which both enable them to discover some unmet market demand and industrial gaps. However, in establishing a new business, not everyone with certain knowledge or expertise has the desire to become an entrepreneur. Prior research has shown that entrepreneurial intentions are under the profound influences of intrinsic factors and extrinsic factors. On the one hand, entrepreneurial self-efficacy is one of the key psychological states that makes someone dare to initiate entrepreneurial activities. Institutional environment, on the other hand, can either enhance and hinder an individuals' entrepreneurial motivation by offering incentives or causing barriers. Little work has been done to understand how the institutional environment and entrepreneurial self-efficacy jointly affect company employees' intention to quit their job and start an enterprising career. By using hierarchical regression on a sample of 325 Indonesian company employees, this paper shows that the entrepreneurial cognition and entrepreneurial self-efficacy are positively related to employees' entrepreneurial intentions. Also, entrepreneurial self-efficacy strengthens the effect of normative Approval on entrepreneurial intention, whereas the regulatory Support from Government is detrimental to company employees' intention to start a new venture regardless the entrepreneurial self-efficacy is high or low.

scholarly journals Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kuldeepsingh A. Kalariya ◽  
Ram Prasnna Meena ◽  
Lipi Poojara ◽  
Deepa Shahi ◽  
Sandip Patel
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Competitive Inhibition ◽  
Sequence Data ◽  
Homology Model ◽  
Squalene Synthase ◽  
Gymnema Sylvestre ◽  
Gardenia Jasminoides ◽  
Ramachandran Plots ◽  
Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

scholarly journals Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

2021 ◽  
Vol 9 (3) ◽  
pp. 666
Author(s):  
Niccolò Forin ◽  
Alfredo Vizzini ◽  
Federico Fainelli ◽  
Enrico Ercole ◽  
Barbara Baldan
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Illumina Miseq ◽  
Botanical Garden ◽  
Molecular Study ◽  
Its2 Sequence ◽  
Type Specimens ◽  
Its1 Sequence ◽  
Dna Sequence Data ◽  
Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

scholarly journals Modulation of odour-guided behaviour in mosquitoes

2021 ◽  
Vol 383 (1) ◽  
pp. 195-206
Author(s):  
Sharon R. Hill ◽  
Rickard Ignell
Keyword(s):  
Functional Genomics ◽  
Life Stage ◽  
Blood Feeding ◽  
Model Systems ◽  
Extrinsic Factors ◽  
Intrinsic Factors ◽  
Host Seeking ◽  
Enhancing Resources ◽  
Maturation Age ◽  
Behavioural Repertoire

AbstractMosquitoes are emerging as model systems with which to study innate behaviours through neuroethology and functional genomics. Decades of work on these disease vectors have provided a solid behavioural framework describing the distinct repertoire of predominantly odour-mediated behaviours of female mosquitoes, and their dependence on life stage (intrinsic factors) and environmental cues (extrinsic factors). The purpose of this review is to provide an overview of how intrinsic factors, including adult maturation, age, nutritional status, and infection, affect the attraction to plants and feeding on plant fluids, host seeking, blood feeding, supplemental feeding behaviours, pre-oviposition behaviour, and oviposition in female mosquitoes. With the technological advancements in the recent two decades, we have gained a better understanding of which volatile organic compounds are used by mosquitoes to recognise and discriminate among various fitness-enhancing resources, and characterised their neural and molecular correlates. In this review, we present the state of the art of the peripheral olfactory system as described by the neural physiology, functional genomics, and genetics underlying the demonstrated changes in the behavioural repertoire in female mosquitoes. The review is meant as a summary introduction to the current conceptual thinking in the field.

scholarly journals Landscape Characteristics Based on Effectiveness of Wildlife Crossing Structures in South Korea

2021 ◽  
Vol 13 (2) ◽  
pp. 675
Author(s):  
Hyunjin Seo ◽  
Chulhyun Choi ◽  
Kyeongjun Lee ◽  
Donggul Woo
Keyword(s):  
Landscape Management ◽  
Spatial Pattern Analysis ◽  
Extrinsic Factors ◽  
Intrinsic Factors ◽  
Landscape Characteristics ◽  
Crossing Structures ◽  
Significant Difference ◽  
Management Plans ◽  
Wildlife Crossing Structures ◽  
Surrounding Landscape

Roads are notable and responsible for the loss of biodiversity and disruption of wildlife habitats connectivity. Wildlife crossing structures (WCS) help wildlife move between habitats by connecting fragmented habitats. Their effectiveness is affected by various factors. Here, to identify methods for improving the effectiveness of wildlife crossing structures, we controlled the effect of intrinsic factors, such as size, that are difficult to improve in an already installed area, and then, evaluated the differences in extrinsic factors using 12 landscape characteristics. Our results show that 18 wildlife crossing structures were selected with propensity-score (PS) matching method. The surrounding landscape characteristics differed between high-effectiveness wildlife crossing structures and low-effectiveness wildlife crossing structures. Particularly, there was a significant difference between the ‘statutory protected area’ and the ‘edge’ index of the morphological spatial pattern analysis among the landscape characteristic variables derived within 1 km2 of wildlife crossing structures. We empirically demonstrate that characteristics around highly effective WCS, statutory protected areas are widely distributed, and the ratio of edge of MSPA is low (within 1 km2). Therefore, an important outcome of our research is the demonstration that management of WCS itself is important, but conservation of surrounding habitats and landscape management plans are also significant.

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