scholarly journals DNA Barcoding of Marine Mollusks Associated with Corallina officinalis Turfs in Southern Istria (Adriatic Sea)

Diversity ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 196
Author(s):  
Moira Buršić ◽  
Ljiljana Iveša ◽  
Andrej Jaklin ◽  
Milvana Arko Pijevac ◽  
Mladen Kučinić ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Adriatic Sea ◽  
Gastropod Species ◽  
Invertebrate Species ◽  
Research Areas ◽  
New Findings ◽  
Corallina Officinalis ◽  
Coi Sequences ◽  
Mollusk Species ◽  
Mollusk Assemblages

Presence of mollusk assemblages was studied within red coralligenous algae Corallina officinalis L. along the southern Istrian coast. C. officinalis turfs can be considered a biodiversity reservoir, as they shelter numerous invertebrate species. The aim of this study was to identify mollusk species within these settlements using DNA barcoding as a method for detailed identification of mollusks. Nine locations and 18 localities with algal coverage range above 90% were chosen at four research areas. From 54 collected samples of C. officinalis turfs, a total of 46 mollusk species were identified. Molecular methods helped identify 16 gastropod, 14 bivalve and one polyplacophoran species. COI sequences for two bivalve species (Musculus cf. costulatus (Risso, 1826) and Gregariella semigranata (Reeve, 1858)) and seven gastropod species (Megastomia winfriedi Peñas & Rolán, 1999, Eatonina sp. Thiele, 1912, Eatonina cossurae (Calcara, 1841), Crisilla cf. maculata (Monterosato, 1869), Alvania cf. carinata (da Costa, 1778), Vitreolina antiflexa (Monterosato, 1884) and Odostomia plicata (Montagu, 1803)) represent new BINs in BOLD database. This study contributes to new findings related to the high biodiversity of mollusks associated with widespread C. officinalis settlements along the southern coastal area of Istria.

scholarly journals Extremal Values of the Sackin Tree Balance Index

2021 ◽  
Author(s):  
Mareike Fischer
Keyword(s):  
Phylogenetic Trees ◽  
Theoretical Computer Science ◽  
Search Trees ◽  
Formal Proofs ◽  
Birth Process ◽  
Ordered Trees ◽  
Research Areas ◽  
New Findings ◽  
Mathematical Phylogenetics ◽  
Extremal Values

AbstractTree balance plays an important role in different research areas like theoretical computer science and mathematical phylogenetics. For example, it has long been known that under the Yule model, a pure birth process, imbalanced trees are more likely than balanced ones. Also, concerning ordered search trees, more balanced ones allow for more efficient data structuring than imbalanced ones. Therefore, different methods to measure the balance of trees were introduced. The Sackin index is one of the most frequently used measures for this purpose. In many contexts, statements about the minimal and maximal values of this index have been discussed, but formal proofs have only been provided for some of them, and only in the context of ordered binary (search) trees, not for general rooted trees. Moreover, while the number of trees with maximal Sackin index as well as the number of trees with minimal Sackin index when the number of leaves is a power of 2 are relatively easy to understand, the number of trees with minimal Sackin index for all other numbers of leaves has been completely unknown. In this manuscript, we extend the findings on trees with minimal and maximal Sackin indices from the literature on ordered trees and subsequently use our results to provide formulas to explicitly calculate the numbers of such trees. We also extend previous studies by analyzing the case when the underlying trees need not be binary. Finally, we use our results to contribute both to the phylogenetic as well as the computer scientific literature using the new findings on Sackin minimal and maximal trees to derive formulas to calculate the number of both minimal and maximal phylogenetic trees as well as minimal and maximal ordered trees both in the binary and non-binary settings. All our results have been implemented in the Mathematica package SackinMinimizer, which has been made publicly available.

scholarly journals Imposex in endemic volutid from Northeast Brazil (Mollusca: Gastropoda)

2008 ◽  
Vol 51 (5) ◽  
pp. 1065-1069 ◽  
Author(s):  
Ítalo Braga de Castro ◽  
Carlos Augusto Oliveira de Meirelles ◽  
Helena Matthews-Cascon ◽  
Cristina de Almeida Rocha-Barreira ◽  
Pablo Penchaszadeh ◽  
...  
Keyword(s):  
First Record ◽  
Reproductive Organs ◽  
Organotin Compounds ◽  
Northeast Brazil ◽  
Gastropod Species ◽  
Antifouling Paints ◽  
Tin Compounds ◽  
Stramonita Haemastoma ◽  
Mollusk Species ◽  
Female Reproductive Organs

Imposex is characterized by the development of masculine sexual organs in neogastropod females. Almost 120 mollusk species are known to present imposex when exposed to organic tin compounds as tributyltin (TBT) and triphenyltin (TPT). These compounds are used as biocide agents in antifouling paints to prevent the incrustations on boats. Five gastropod species are known to present imposex in Brazil: Stramonita haemastoma, Stramonita rustica, Leucozonia nassa, Cymathium parthenopeum and Olivancillaria vesica. This paper reports the first record of imposex observed in the endemic gastropod Voluta ebraea from Pacheco Beach, Northeast Brazil. Animals presenting imposex had regular female reproductive organs (capsule gland, oviduct and sperm-ingesting gland) and an abnormal penis. As imposex occurs in mollusks exposed to organotin compounds typically found at harbors, marinas, shipyards and areas with high shipping activities, probably contamination of Pacheco Beach is a consequence of a shipyard activity located in the nearest areas.

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav K Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

Paralarval and juvenile stages as a proxy for cephalopod diversity in the Juan Fernández and Desventuradas ecoregion, southeast Paific Ocean

2020 ◽  
Vol 96 (2) ◽  
pp. 263-280
Author(s):  
Sergio A Carrasco ◽  
Andrea I Varela ◽  
Christian M Ibáñez ◽  
Javier Sellanes ◽  
Martin Thiel
Keyword(s):  
Dna Barcoding ◽  
Early Life ◽  
Current Knowledge ◽  
Morphological Characteristics ◽  
Oceanic Islands ◽  
Life Stages ◽  
Early Life Stages ◽  
Marine Park ◽  
Coi Sequences ◽  
Juan Fernández Archipelago

Southeast Pacific (SEP) oceanic islands are characterized by their extreme isolation and high degree of endemism. To date, most research has focused on species composition and distributions, with little information available on early life stages. In this study, we provide new records of early life stages of cephalopods based on planktonic collections carried out during October and November 2016 around three oceanic islands: San Félix, San Ambrosio (Desventuradas Islands; 26.3°S, 79.8°W), and Alejandro Selkirk (Juan Fernández Archipelago; 33.7°S, 80.7°W), which are part of the Nazca-Desventuradas Marine Park, the largest marine park in the Americas. Twenty-four paralarvae and juveniles were obtained and identified based on morphological characteristics [i.e., mantle length (ML), chromatophore patterns, number and shape of suckers on arms and tentacles] and DNA barcoding [i.e., mitochondrial Cytochrome c Oxidase subunit I (COI) sequences]. Six families were recorded, including Brachioteuthidae, Onychoteuthidae, Tremoctopodidae, Octopodidae, Octopoteuthidae, and Lycoteuthidae. Most individuals (92%) corresponded to larger stages of 4–12 mm ML (Brachioteuthidae, Onychoteuthidae, Tremoctopodidae, and Lycoteuthidae), and 8% were newly hatched paralarvae of around 1 mm ML (Octopodidae and Octopoteuthidae). The DNA barcoding approach validated the identity of Brachioteuthis sp., Onykia aff. robsoni , Octopus mimus, and Tremoctopus sp., with two specific identities (Octopoteuthidae and Lycoteuthis sp.) remaining to be evaluated. ese records provide new information on cephalopod diversity and distribution around SEP islands, adding to the current knowledge about zoogeographic patterns of this group and evidencing their potential relationships with continental or nearby habitats.

A test of DNA barcoding in crayfish of the upper James River basin, Virginia

2015 ◽  
Vol 21 (1) ◽  
pp. 179-183
Author(s):  
Paul R. Cabe ◽  
Bradleigh E. Navalsky ◽  
Ainsley K. Bloomer ◽  
Ryan Doherty ◽  
Jordan Edgren ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
River Basin ◽  
Native Species ◽  
Biological Diversity ◽  
Coi Gene ◽  
Test Case ◽  
Accurate Identification ◽  
James River ◽  
Coi Sequences ◽  
Current Sequence

Abstract Crayfish populations in North America face many conservation threats, including habitat loss, degradation, and the introduction of non-native species. The management of biological diversity requires accurate identification of species, and for crayfish, many species are difficult to identify using standard morphological approaches. We investigated DNA barcoding using cytochrome oxidase I (COI) gene sequences to determine if this widely used method is useful in the identification of crayfish. As a test case, we sampled crayfish from the middle and upper James River basin in Virginia. This area had been recently surveyed by experienced crayfish biologists, and hosts a moderate number of species. We collected nearly 300 COI sequences, which clustered clearly into seven groups, mirroring the seven species reported for this watershed. Despite the unambiguous clustering, the range of sequence variation within species overlapped the range of variation between species; we detected no clear "barcode gap." Although this method holds promise as an aid to crayfish identification, current sequence databases (GenBank, BOLD) do not contain enough appropriate COI sequences to allow unequivocal identification in this unique and understudies fauna.

Systematics and DNA barcoding of free-living marine nematodes with emphasis on tropical desmodorids using nuclear SSU rDNA and mitochondrial COI sequences

Nematology ◽  
2014 ◽  
Vol 16 (8) ◽  
pp. 979-989 ◽  
Author(s):  
Maickel Armenteros ◽  
Ariadna Rojas-Corzo ◽  
Alexei Ruiz-Abierno ◽  
Sofie Derycke ◽  
Thierry Backeljau ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Sister Group ◽  
Ssu Rdna ◽  
Reference Database ◽  
Cryptic Diversity ◽  
Marine Nematodes ◽  
Free Living ◽  
Mitochondrial Coi ◽  
The Family ◽  
Coi Sequences

The diversity and phylogenetic relationships of the Desmodoridae, a widespread tropical family of free-living marine nematodes, is hitherto poorly known both from molecular and taxonomic points of view. We performed a molecular phylogenetic analysis of marine nematodes to: i) disentangle relationships among tropical desmodorid species; and ii) compare the performance of the nuclear SSU rDNA and mitochondrial COI nucleotide sequences in 42 and 45 nominal species, respectively, to identify species. We generated 27 new sequences of SSU rDNA belonging to five genera not previously sequenced, and 34 new sequences of COI belonging to six genera and four families not previously sequenced. The SSU rDNA tree confirmed the Enoplida to be a monophyletic sister group to the Chromadorida. The family Comesomatidae is a sister group of the Xyalidae within the Monhysterida. Both DNA markers confirmed the congruence between the morphology- and molecular-based phylogenetic inferences for most of the families. Desmodoridae was a monophyletic group, but the relationships within the family could not be recovered; the subfamilies Desmodorinae and Spiriniinae were not monophyletic meanwhile the monophyly of Stilbonematinae was not fully supported due to a few specimens of questionable identity. COI performed better than SSU rDNA to disentangle relationships among closely related species and suggested the presence of cryptic diversity within Desmodoridae. COI is effective to explore cryptic diversity and barcode species within Nematoda, with a possible threshold of genetic distance of 5% between conspecific and interspecific sequences, but DNA barcoding is limited by the poor knowledge of the diversity and taxonomy of the group and the lack of a good reference database of vouchered COI sequences.

scholarly journals First Record of Traumatic Myiasis Obtained From Forest Musk Deer (Moschus Berezovskii) Using DNA Barcoding

2020 ◽  
Author(s):  
Yunyun Gao ◽  
Yajun Fu ◽  
Liping Yan ◽  
Defu Hu ◽  
Benmo Jiang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Animal Husbandry ◽  
First Record ◽  
Coi Gene ◽  
Common Disease ◽  
Human Society ◽  
Musk Deer ◽  
Two Samples ◽  
Nucleotide Divergence ◽  
Coi Sequences

Abstract Background: Myiasis is a common disease occurring in humans and livestock all over the world. It is closely related to human society and of great significance to animal husbandry, forensic science, and medicine. Myiasis is known to occur in wild animals, while no information is reported in forest musk deer. On July 6, 2019, we found severe traumatic myiasis of an injured forest musk deer (Moschus berezovskii) (Flerov, 1929), infected by lots of maggots and clusters of eggs. However, the precise identification of the larvae that we collected was difficult with few specific morphology characteristics.Methods: DNA barcoding is an efficient technique for species diagnosis, therefore is employed to identify the samples collected from the infected forest musk deer. Firstly, we extracted genomic DNA from one larva and one egg respectively. The cytochrome oxidase I (COI) gene barcoding region was amplified by polymerase chain reaction (PCR) and bidirectionally sequenced by Sanger sequencing. The sequences were searched for similarity using BLAST and the best hits were Lucilia. To identify these blowflies accurately, these newly generated sequences were subsequently analyzed with COI sequences of Lucilia and Calliphora downloaded from GenBank, to calculate nucleotide divergence, and to construct a neighbor-joining tree.Results: Our results suggest that nucleotide divergence between the two samples is 0.0033cM, between two samples and Lucilia caesar (Diptera: Calliphoridae) (Linnaeus, 1758) is 0.0016–0.0050cM. Furthermore, the NJ tree construction indicates that the flies collected from the musk deer are Lucilia caesar.Conclusions: Our results indicate that DNA barcoding can successfully identify pathogenic species. As far as the authors know, this is the first time that myiasis is detected in forest musk deer caused by a traumatic infection in China. The affected individual was clinically treated immediately and apparently recovered.

Projected research trends in invertebrate physiology and biochemistry

1987 ◽  
Vol 65 (4) ◽  
pp. 797-802
Author(s):  
Roger G. H. Downer
Keyword(s):  
Rational Design ◽  
Research Progress ◽  
Future Research ◽  
Invertebrate Species ◽  
Research Areas ◽  
Modern Molecular Biology ◽  
Highly Sensitive ◽  
Physiology And Biochemistry ◽  
Invertebrate Physiology ◽  
Increased Activity

The direction of future research is likely to be influenced by major conceptual advances and technological breakthroughs, neither of which can be predicted with certainty. However, it is possible to identify general areas in which conceptual advances may be anticipated as a result of studies on invertebrate physiology and biochemistry and, in this regard, neurobiology and developmental biology offer particular promise. It is reasonable to predict also that the technologies of modern molecular biology and the development of highly sensitive analytical instrumentation will greatly facilitate research progress. Increased activity may also be predicted in strategic research areas including those that will lead to the rational design of pesticides and the improvement of "farming" procedures for invertebrate species that are used as sources of food. Invertebrates are also expected to continue to be used as models for biomedical research.

Molecular Confirmation on the Presence of Anadara Kagoshimensis (Tokunaga, 1906) (Mollusca: Bivalvia: Arcidae) in the Black Sea / Confirmarea moleculară a prezenţei speciei Anadara Kagoshimensis (Tokunaga, 1906) (Mollusca: Bivalvia: Arcidae) în Marea Neagră

2015 ◽  
Vol 57 (1) ◽  
pp. 9-12 ◽  
Author(s):  
Ana Maria Krapal ◽  
Oana Paula Popa ◽  
Alexandra Levarda ◽  
Elena Iulia Iorgu ◽  
Luis Ovidiu Popa ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Genetic Markers ◽  
Black Sea ◽  
Genetic Similarity ◽  
Molecular Level ◽  
The Black Sea ◽  
Anadara Kagoshimensis ◽  
Ark Shell ◽  
Coi Sequences ◽  
High Genetic Similarity

Abstract The use of DNA barcoding in alien invasions has recently proved to be a powerful tool in delineating dispersal pathways and clarifying doubtful identifications. Morphological similarities between Anadara kagoshimensis (Tokunaga, 1906) and Anadara inaequivalvis (Bruguière, 1789) require the use of genetic markers in identifying the ark shell species that has recently invaded the Black Sea. The high genetic similarity (99.8-100%) hereby found between COI sequences obtained from the Black Sea samples and Japanese A. kagoshimensis confirms at a molecular level that the ark clam species invading the Romanian Black Sea belong to this taxon.

scholarly journals First report of lionfish prey from Western Florida waters as identified by DNA barcoding

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9922 ◽  
Author(s):  
Carlos A. Santamaria ◽  
James Locascio ◽  
Taylor M. Greenan
Keyword(s):  
Dna Barcoding ◽  
Regional Differences ◽  
Prey Species ◽  
Fish Prey ◽  
Crustacean Species ◽  
First Report ◽  
Eastern Gulf Of Mexico ◽  
Coi Barcoding ◽  
Coi Sequences ◽  
Prey Items

DNA barcoding was used to identify prey fragments recovered from the stomachs of lionfish harvested during the 2016 Sarasota Lionfish Derby. A total of 305 prey fragments were recovered from 50 stomachs (mean = 4.6 per stomach), of which 184 (60.3%) fragments could be identified to either species or genus when Cytochrome Oxidase I (COI) sequences were queried against the Barcode of Life Database. We identified 21 fish prey species which represented fourteen families and accounted for 95.7% of genetically identifiable prey items. The remaining prey items identified corresponded to six crustacean species. The four most common prey taxa in lionfish stomachs were Ptereleotris calliura (24.3%), an unidentified Microgobius species (20.4%), Diplectum formosum (14.3%), and Apogon aurolineatus (12.2%). The most frequently observed crustacean species, Metapenaeopsis goodei, was found in only three stomachs (6.1%). We also report eleven taxa as putative novel lionfish prey species, most of which are common in Florida waters. Sixteen prey items were identified as lionfish (P. volitans); however, it was not definitive whether these detections were due to cross contamination or cannibalization. This represents the first report of lionfish diets from Florida waters in the Eastern Gulf of Mexico based on barcoding efforts. Our results are largely congruent with previous COI barcoding based studies of lionfish diets, indicating these predators to be generalists exhibiting preferences for specific prey traits but with regional differences in their diets.

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