SPECIES DISCOVERY AND CHANGING SPECIES INCLUSIVENESS IN CENOZOIC MOLLUSCS – WHAT EMERGES FROM A POPULAR HANDBOOK AFTER MORE THAN 50 YEARS OF NEGLECT?

2017 ◽  
Author(s):  
Jonathan A. Todd ◽  
◽  
Kenneth G. Johnson
Keyword(s):  
Species Discovery

PROBABILISTIC MODELS OF SPECIES DISCOVERY AND BIODIVERSITY COMPARISONS

2016 ◽  
Author(s):  
Stewart M. Edie ◽  
◽  
Peter D. Smits ◽  
David Jablonski
Keyword(s):  
Probabilistic Models ◽  
Species Discovery

scholarly journals Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Amrita Srivathsan ◽  
Emily Hartop ◽  
Jayanthi Puniamoorthy ◽  
Wan Ting Lee ◽  
Sujatha Narayanan Kutty ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Low Cost ◽  
Small Body ◽  
Small Subset ◽  
Similar Species ◽  
Large Species ◽  
Morphological Examination ◽  
Species Discovery ◽  
Short Period

Abstract Background More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such “molecular operational taxonomic units” (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries. Results We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8 weeks. We discovered > 650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; > 99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genus Megaselia. We demonstrate for one Megaselia species how the molecular data can guide the description of a new species (Megaselia sepsioides sp. nov.). Conclusions We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.

scholarly journals Notes on the threatened lowland forests of Mt Cameroon and their endemics including Drypetes burnleyae sp. nov., with a key to species of Drypetes sect. Stipulares (Putranjivaceae)

Kew Bulletin ◽  
2021 ◽  
Author(s):  
Martin Cheek ◽  
Nouhou Ndam ◽  
Andrew Budden
Keyword(s):  
Conservation Management ◽  
Conservation Status ◽  
Central Africa ◽  
Habitat Destruction ◽  
Coastal Forests ◽  
Key To Species ◽  
International Union ◽  
Species Discovery ◽  
Mount Cameroon ◽  
Lowland Forests

SummaryThis paper reports a further discovery of a new endemic threatened species to science in the context of botanical surveys in the lowland coastal forests of Mount Cameroon in the Cross River-Sanaga interval of west-central Africa. These studies now focus on species discovery and conservation through the Tropical Important Plant Areas programme. New species to science continue to be discovered from Mt Cameroon. Most of these species are rare, highly localised, and threatened by habitat destruction, increasing the justification for improved conservation management of surviving habitat. Drypetes burnleyae is placed in and keyed out in Drypetes sect. Stipulares, a group mostly confined to Lower Guinea, here adjusted to accommodate nine species. The conservation status of Drypetes burnleyae is assessed as Endangered (EN B1+2ab(iii)) according to the 2012 criteria of the International Union for the Conservation of Nature. An updated overview of the plant endemics of Mt Cameroon is presented.

Avifaunal Diversity of Khata Corridor Forest

2009 ◽  
pp. 48-56 ◽  
Author(s):  
Umesh Kumar Chaudhari ◽  
Gandhiv Kafle ◽  
Hem Sagar Baral
Keyword(s):  
Species Diversity ◽  
Threatened Species ◽  
Mixed Forest ◽  
Habitat Type ◽  
Distribution Map ◽  
Species Discovery ◽  
Area Distribution ◽  
High Species Diversity ◽  
List Method ◽  
Index Of Diversity

The study was made to assess the species diversity of avians, habitat type, their presence/absence in the different habitats and to produce a distribution map of globally threatened species in Khata Corridor forest of Bardia district. Species discovery curve and richness curve was produced through McKinnon list method in which each list contains 15-species. Habitat type was distinguished by modified DAFOR scale. Riverine sissoo-khair forest, Moist-mixed forest, and Riverine grassland were found to be prominent habitat type in the intensive study area. Distribution map of threatened species was assembled through Arc View 3.2a. Shannon's Index of Diversity (H = 3.114) and species evenness (0.629) indicates the high species diversity of avians in Khata corridor forest. Further study is essential to incorporate remaining part of the forest and to survey winter birds. Key words: Avifauna, corridor, species diversity, habitatDOI: 10.3126/jowe.v2i1.1857 Journal of Wetlands Ecology, (2009) vol. 2, pp 48-56

scholarly journals On the synergy between Ariel and ground-based high-resolution spectroscopy

2022 ◽  
Author(s):  
Gloria Guilluy ◽  
Alessandro Sozzetti ◽  
Paolo Giacobbe ◽  
Aldo S. Bonomo ◽  
Giuseppina Micela
Keyword(s):  
High Resolution ◽  
Near Infrared ◽  
Major Axis ◽  
High Resolution Spectroscopy ◽  
Correlation Technique ◽  
Temperature Structure ◽  
Low Resolution ◽  
Semi Major Axis ◽  
Species Discovery ◽  
Orbital Parameters

AbstractSince the first discovery of an extra-solar planet around a main-sequence star, in 1995, the number of detected exoplanets has increased enormously. Over the past two decades, observational instruments (both onboard and on ground-based facilities) have revealed an astonishing diversity in planetary physical features (i. e. mass and radius), and orbital parameters (e.g. period, semi-major axis, inclination). Exoplanetary atmospheres provide direct clues to understand the origin of these differences through their observable spectral imprints. In the near future, upcoming ground and space-based telescopes will shift the focus of exoplanetary science from an era of “species discovery” to one of “atmospheric characterization”. In this context, the Atmospheric Remote-sensing Infrared Exoplanet Large (Ariel) survey, will play a key role. As it is designed to observe and characterize a large and diverse sample of exoplanets, Ariel will provide constraints on a wide gamut of atmospheric properties allowing us to extract much more information than has been possible so far (e.g. insights into the planetary formation and evolution processes). The low resolution spectra obtained with Ariel will probe layers different from those observed by ground-based high resolution spectroscopy, therefore the synergy between these two techniques offers a unique opportunity to understanding the physics of planetary atmospheres. In this paper, we set the basis for building up a framework to effectively utilise, at near-infrared wavelengths, high-resolution datasets (analyzed via the cross-correlation technique) with spectral retrieval analyses based on Ariel low-resolution spectroscopy. We show preliminary results, using a benchmark object, namely HD 209458 b, addressing the possibility of providing improved constraints on the temperature structure and molecular/atomic abundances.

scholarly journals Shortfalls and opportunities in terrestrial vertebrate species discovery

2020 ◽  
Author(s):  
Mario R. Moura ◽  
Walter Jetz
Keyword(s):  
Sustainable Management ◽  
Vertebrate Species ◽  
Species Discovery ◽  
Terrestrial Vertebrate ◽  
Policy Goals ◽  
Discovery Potential ◽  
Living Species ◽  
Automated Sensors ◽  
Species Descriptions ◽  
Terrestrial Vertebrate Species

AbstractMeter-resolution imagery of our world and myriad biodiversity records collected through citizen scientists and automated sensors belie the fact that much of the planet’s biodiversity remains undiscovered. Conservative estimates suggest only 13 to 18% of all living species may be known at this point 1–4, although this number could be as low as 1.5% 5. This biodiversity shortfall 6,7 strongly impedes the sustainable management of our planet’s resources, as the potential ecological and economic relevance of undiscovered species remains unrecognized 8. Here we use model-based predictions of terrestrial vertebrate species discovery to estimate future taxonomic and geographic discovery opportunities. Our model identifies distinct taxonomic and geographic unevenness in future discovery potential, with greatest opportunities for amphibians and reptiles and for Neotropical and IndoMalayan forests. Brazil, Indonesia, Madagascar, and Colombia emerge as holding greatest discovery opportunities, with a quarter of future species descriptions expected there. These findings highlight the significance of international support for taxonomic initiatives and the potential of quantitative models to aid the discovery of species before their functions are lost in ignorance 8. As nations draw up new policy goals under the post-2020 global biodiversity framework, a better understanding of the magnitude and geography of this known unknown is critical to inform goals and priorities 9 and to minimize future discoveries lost to extinction10.

scholarly journals debar, a sequence-by-sequence denoiser for COI-5P DNA barcode data

2021 ◽  
Author(s):  
Cameron M. Nugent ◽  
Tyler A. Elliott ◽  
Sujeevan Ratnasingham ◽  
Paul D. N. Hebert ◽  
Sarah J. Adamowicz
Keyword(s):  
High Throughput Sequencing ◽  
Dna Barcode ◽  
R Package ◽  
Error Rates ◽  
Real World Data ◽  
Species Discovery ◽  
Consensus Sequences ◽  
In Silico Studies ◽  
Coi Sequences

AbstractDNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising —the separation of biological signal from instrument (technical) noise—of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochrome c oxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.

Laboulbeniomycetes: Intimate Fungal Associates of Arthropods

2021 ◽  
Vol 66 (1) ◽  
pp. 257-276 ◽  
Author(s):  
Danny Haelewaters ◽  
Meredith Blackwell ◽  
Donald H. Pfister
Keyword(s):  
Population Biology ◽  
Life Histories ◽  
Invasion Biology ◽  
Species Discovery ◽  
Phylogenetic Studies ◽  
Intimate Association ◽  
Red Algal ◽  
Molecular Phylogenetic ◽  
Parasitic Worms ◽  
Host Parasite

Arthropod–fungus interactions involving the Laboulbeniomycetes have been pondered for several hundred years. Early studies of Laboulbeniomycetes faced several uncertainties. Were they parasitic worms, red algal relatives, or fungi? If they were fungi, to which group did they belong? What was the nature of their interactions with their arthropod hosts? The historical misperceptions resulted from the extraordinary morphological features of these oddly constructed ectoparasitic fungi. More recently, molecular phylogenetic studies, in combination with a better understanding of life histories, have clearly placed these fungi among filamentous Ascomycota (subphylum Pezizomycotina). Species discovery and research on the classification of the group continue today as arthropods, and especially insects, are routinely collected and examined for the presence of Laboulbeniomycetes. Newly armed with molecular methods, mycologists are poisedto use Laboulbeniomycetes–insect associations as models for the study of a variety of basic evolutionary and ecological questions involving host–parasite relationships, modes of nutrient intake, population biology, host specificity, biological control, and invasion biology. Collaboration between mycologists and entomologists is essential to successfully advance knowledge of Laboulbeniomycetes and their intimate association with their hosts.

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