scholarly journals Molecular and anatomical analyses reveal that Peronia verruculata (Gastropoda: Onchidiidae) is a cryptic species complex

2018 ◽  
Vol 87 (3) ◽  
pp. 149-165 ◽  
Author(s):  
Jia Jin Marc Chang ◽  
Ywee Chieh Tay ◽  
Hui Ping Ang ◽  
Karenne Phyu Phyu Tun ◽  
Loke Ming Chou ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Dna Sequence ◽  
Sequence Data ◽  
Accessory Gland ◽  
Sequence Information ◽  
Dna Sequence Data ◽  
Distinct Sequence ◽  
Cryptic Species Complex ◽  
Taxonomic Approach ◽  
Intertidal Environments

Recent years have seen an increase in the number of studies that use DNA sequence information in addition to morphological methods, as the latter alone can be inadequate for morphologically similar, cryptic species. Marine onchidiid slugs (Mollusca: Gastropoda: Onchidiidae), which commonly inhabit intertidal environments and have a near-global distribution, comprise 11 genera and 86 described species. Singapore has 19 recorded species of onchidiids with Peronia verruculata (Cuvier, 1830) being the most abundant. Here we present mitochondrial DNA sequence data from 63 P. verruculata-like specimens to show that they constitute two closely-related clades with distinct sequence signatures and a clear barcode gap. Intraclade distances are 0–1.8% while interclade distances range from 4.7 to 6.0%. Scanning electron microscopy of internal copulation organs reveals that the two clades have distinct penial and accessory gland spine structures, which also differ in size. Using an integrative taxonomic approach, we propose that what was initially thought to be P. verruculata in Singapore, actually are two different species of Peronia.

scholarly journals DNA sonification for public engagement in bioinformatics

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Heleen Plaisier ◽  
Thomas R. Meagher ◽  
Daniel Barker
Keyword(s):  
Dna Sequence ◽  
Public Engagement ◽  
Sequence Data ◽  
Sensory Perception ◽  
Data Representation ◽  
Sequence Information ◽  
Dna Sequence Data ◽  
Public Events ◽  
Dna Base ◽  
Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

Revision of Australian jumping spider genus Servaea Simon 1887 (Aranaea: Salticidae) including use of DNA sequence data and predicted distributions

Zootaxa ◽  
2012 ◽  
Vol 3350 (1) ◽  
pp. 1 ◽  
Author(s):  
BARRY J. RICHARDSON ◽  
NICOLE L. GUNTER
Keyword(s):  
Nucleotide Sequence ◽  
Dna Sequence ◽  
Type Species ◽  
Sequence Data ◽  
Sandy Soils ◽  
Soil Types ◽  
Sequence Information ◽  
Suitable Material ◽  
Dna Sequence Data ◽  
Nucleotide Sequence Information

The genus Servaea Simon 1887 is revised and redefined. Descriptions and identification keys are provided to the following sixspecies, of which three are described as new: Servaea incana (Karsch 1878), Servaea narraweena n. sp., Servaea melaina n.sp., Servaea spinibarbis Simon 1909, Servaea villosa (Keyserling 1881) and Servaea zabkai n. sp. The type species of thegenus, Servaea vestita (L. Koch 1879), is proposed here to be a junior synonym of Servaea incana. In addition to the diagnosesand descriptions, distributional and nucleotide sequence information are provided. DNA sequence data for the segment of COIused in other salticid studies was obtained for the five species for which suitable material was available. Intraspecific variationin S. villosa and S. incana were studied in more detail. Within-species divergence was S. melaina and S spinibarbis, had adjacent predicted distributions, one coastal on sandy soils and one inland on other soil types.

scholarly journals First records of the fanged frogs Limnonectes bannaensis Ye, Fei & Jiang, 2007 and L. utara Matsui, Belabut & Ahmad, 2014 (Amphibia: Anura: Dicroglossidae) in Thailand

2021 ◽  
Vol 9 ◽  
Author(s):  
Chatmongkon Suwannapoom ◽  
Ke Jiang ◽  
Yun-He Wu ◽  
Parinya Pawangkhanant ◽  
Sengvilay Lorphengsy ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Species Complex ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Morphological Data ◽  
Integrative Approach ◽  
Species Identity ◽  
Dna Sequence Data ◽  
Species Complexes ◽  
Cryptic Species Complex

The taxonomic status of the Thai populations belonging to the Limnonectes kuhlii species complex is controversial, due to phenotypic similarity in the cryptic species complex. Recently, some studies on this group in Thailand have discovered four new species: L. taylori, L. megastomias, L. jarujini and L. isanensis. Even so, the diversity of this group is still incomplete. Based on an integrative approach encompassing genetic and morphological analyses, we conclude that the Limnonectes populations from Nan Province (northern) and Yala Province (southern) of Thailand are conspecific with L. bannaensis Ye, Fei & Jiang, 2007 and L. utara Matsui, Belabut & Ahmad, 2014, respectively. These are the first records of these species in Thailand. Our study highlights the importance of using DNA sequence data in combination with morphological data to accurately document species identity and diversity. This is especially important for morphologically cryptic species complexes and sympatrically occurring congeners.

scholarly journals DNA Sonification For Public Engagement in Bioinformatics

2021 ◽  
Author(s):  
Heleen Plaisier ◽  
Thomas Robert Meagher ◽  
Daniel Barker
Keyword(s):  
Dna Sequence ◽  
Public Engagement ◽  
Sequence Data ◽  
Sensory Perception ◽  
Data Representation ◽  
Sequence Information ◽  
Dna Sequence Data ◽  
Public Events ◽  
Dna Base ◽  
Alternative Means

Abstract Objective: Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound – sonification – represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification.Results: We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

Assessment of the order Rhodymeniales (Rhodophyta) from British Columbia using an integrative taxonomic approach reveals overlooked and cryptic species diversity

Botany ◽  
2018 ◽  
Vol 96 (6) ◽  
pp. 359-383 ◽  
Author(s):  
Gina V. Filloramo ◽  
Gary W. Saunders
Keyword(s):  
British Columbia ◽  
Species Diversity ◽  
Dna Sequence ◽  
Sequence Data ◽  
The Novel ◽  
Additional Species ◽  
Dna Sequence Data ◽  
Species Groups ◽  
Taxonomic Approach ◽  
Genetic Species

Molecular-assisted alpha taxonomy using COI-5P and rbcL-3P was employed to reassess species diversity for the Rhodymeniales (Rhodophyta) in British Columbia. A total of 563 collections from British Columbia were resolved as 16 genetic species groups, whereas 13 were previously reported. Collections attributed to Botryocladia pseudodichotoma from British Columbia were resolved as distinct from collections of that species from California (type locality) and were assigned to Botryocladia hawkesii sp. nov. DNA sequence data also resolved an additional species of Fryeella. Although two species of Gloiocladia were recognized, genetic analyses resolved three: G. fryeana, G. laciniata, and Gloiocladia vigneaultii sp. nov. Data also resolved Gloiocladia media comb. nov. from California. For the genus Rhodymenia, where two species were expected, DNA sequence data resolved four. Both R. californica and R. pacifica were confirmed in British Columbia, whereas some collections field-identified as R. californica were genetically distinct and assigned to the novel species, Rhodymenia bamfieldensis sp. nov. Some collections initially identified as R. pacifica were assigned to the resurrected species R. rhizoides. Anatomical development for the monospecific genus Minium was also reassessed owing to that taxon’s assignment to the Fryeellaceae. Our investigation clarified the number of rhodymenialean species in British Columbia and resolved taxonomic and distributional uncertainties associated with some of these taxa.

A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia

Zootaxa ◽  
2020 ◽  
Vol 4766 (3) ◽  
pp. 472-484
Author(s):  
HANNAH E. SOM ◽  
L. LEE GRISMER ◽  
PERRY L. JR. WOOD ◽  
EVAN S. H. QUAH ◽  
RAFE M. BROWN ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Dna Sequence ◽  
Rare Species ◽  
Sequence Data ◽  
Peninsular Malaysia ◽  
Tropical Asia ◽  
Dna Sequence Data ◽  
A New Species ◽  
Lines Of Evidence

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12. 

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