Molecular identification of <i>Auxis</i> spp. larvae (Pisces: Scombridae) from the Gulf of California: Solving morphological identification limits

The larvae of the Auxis genus are abundant in the Gulf of California during summer; however, their identification to the species level by morphological methods is a challenge. The goal of this study was to identify A. thazard and A. rochei larvae for first time, through molecular markers using COI sequences of mtDNA, and look for distinctive morphological characteristics between species, mainly in pigmentation patterns. Larvae were obtained by zooplankton tows in 3 oceanographic cruises in the southern Gulf of California and adjacent waters. The presence of A. thazard and A. rochei larvae was genetically confirmed. The sequences of 7 larvae showed genetic divergences lower than 1% when were compared to sequences of A. thazard adults, while 15 larvae showed genetic divergences lower than 2% when where compared to sequences of A. rochei adults. Genetic divergences between both Auxis species were higher than 2%. These results suggest the spawning of both species in the Gulf of California. On the other hand, pigmentation patterns and morphometric characteristics, in all larval stages, did not permit the secure differentiation between species. Thus, the use of molecular identification by COI is recommended to identify Auxis larvae to the species level, as well as in other marine fish larvae collected in other regions of the world, that have identification troubles.

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Fish larvae from the Gulf of California to Colima, Mexico: an update

Check List ◽

10.15560/10.1.106 ◽

2014 ◽

Vol 10 (1) ◽

pp. 106 ◽

Cited By ~ 3

Author(s):

Raymundo Avendaño-Ibarra ◽

Gerardo Aceves-Medina ◽

Enrique Godínez-Domínguez ◽

Roxana De Silva-Dávila ◽

S. Patricia A. Jiménez-Rosenberg ◽

...

Keyword(s):

New Taxa ◽

Marine Fish ◽

Gulf Of California ◽

Fish Larvae ◽

Abundant Species ◽

Species Level ◽

Marine Fish Larvae

An updated taxonomic list of marine fish larvae from the Gulf of California to Colima, Mexico is presented. A total of 579 taxa belonging to 119 families, 256 genera, and 423 species were recorded. The list was compiled using 14 publications on fish larvae research (1974-2012), and the fish larvae identified from 315 samples collected with Bongo nets during 10 oceanographic cruises made from the Gulf of California to Bahía de Banderas, Mexico, from 2003 to 2007 (this study). The most important families in this study were the Myctophidae (28.3%), Engraulidae (25.0%), and Clupeidae (15.4%). The most abundant species were Cetengraulis mysticetus (18.2%), Benthosema panamense (13.9%), and Opisthonema libertate (12.7%). The compiled taxonomic list shows the addition of 296 new taxa to the previous list published 10 years ago, and also the need of an increase in the effort on the taxonomy of fish larvae forms not identified to species level.

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Validation of an Effective Protocol for Culicoides Latreille (Diptera: Ceratopogonidae) Detection Using eDNA Metabarcoding

Insects ◽

10.3390/insects12050401 ◽

2021 ◽

Vol 12 (5) ◽

pp. 401

Author(s):

Yoamel Milián-García ◽

Lauren A. A. Janke ◽

Robert G. Young ◽

Aruna Ambagala ◽

Robert H. Hanner

Keyword(s):

Molecular Identification ◽

Molecular Detection ◽

Morphological Characteristics ◽

Species Level ◽

Morphological Identification ◽

Culicoides Species ◽

Nacl Solution ◽

Identification Method

eDNA metabarcoding is an effective molecular-based identification method for the biosurveillance of flighted insects. An eDNA surveillance approach maintains specimens for secondary morphological identification useful for regulatory applications. This study identified Culicoides species using eDNA metabarcoding and compared these results to morphological identifications of trapped specimens. Insects were collected using ultraviolet (UV) lighted fan traps containing a saturated salt (NaCl) solution from two locations in Guelph, Ontario, Canada. There were forty-two Culicoides specimens collected in total. Molecular identification detected four species, C. biguttatus, C. stellifer, C. obsoletus, and C. mulrennani. Using morphological identification, two out of these four taxonomic ranks were confirmed at the species level (C. biguttatus and C. stellifer) and one was confirmed at the subgenus level (Avaritia [C. obsoletus]). No molecular detection of Culicoides species occurred in traps with an abundance of less than three individuals per taxon. The inconsistency in identifying Culicoides specimens to the species level punctuates the need for curated DNA reference libraries for Culicoides. In conclusion, the saturated salt (NaCl) solution preserved the Culicoides’ morphological characteristics and the eDNA.

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An emended description of Stemphylium amaranthi with its first record for Iran mycobiota

Phytotaxa ◽

10.11646/phytotaxa.371.2.3 ◽

2018 ◽

Vol 371 (2) ◽

pp. 93

Author(s):

ALIREZA POURSAFAR ◽

YOUBERT GHOSTA ◽

MOHAMMAD JAVAN-NIKKHAH

Keyword(s):

Morphological Characteristics ◽

First Record ◽

Its Rdna ◽

Morphological Identification ◽

Sexual Morph ◽

Species Circumscription ◽

New Information ◽

Emended Description ◽

First Time

Stemphylium amaranthi was originally described from the leaves of Amaranthus retroflexous in China based only on asexual morphological characteristics. New collections of S. amaranthi from wheat and barley plants with symptoms of black (sooty) head mould in Golestan and Qazvin Provinces, Iran, revealed abundant formation of a sexual morph. The morphological identification was confirmed by sequences obtained from ITS-rDNA and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genomic loci. New information on the sexual morph of S. amaranthi is provided and the species circumscription is emended. Wheat and barley are reported as new substrates for S. amaranthi, and this species is recorded for the first time in Iran.

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Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae)

Bulletin of Entomological Research ◽

10.1017/s0007485315000486 ◽

2015 ◽

Vol 106 (1) ◽

pp. 34-46 ◽

Cited By ~ 7

Author(s):

A.J. Failla ◽

A.A. Vasquez ◽

P. Hudson ◽

M. Fujimoto ◽

J.L. Ram

Keyword(s):

Sequence Data ◽

Species Group ◽

Species Level ◽

Morphological Identification ◽

Neighbor Joining ◽

Chironomid Larvae ◽

Western Lake ◽

Individual Sequences ◽

Aquatic Food ◽

Coi Sequences

AbstractEstablishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or ‘species group’ level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor-joining analysis reported here describes the application and confirmation of a useful tool that can accelerate identification and bioassesment of chironomid communities.

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Karyotype and COI sequences of Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera,Chironomidae) from the bay of Orkhon River, Mongolia

Comparative Cytogenetics ◽

10.3897/compcytogen.v15.i2.66549 ◽

2021 ◽

Vol 15 (2) ◽

pp. 149-157

Author(s):

Viktor V. Bolshakov ◽

Alexander A. Prokin

Keyword(s):

Bayesian Inference ◽

Phylogenetic Tree ◽

Genetic Distance ◽

Dna Barcoding ◽

Molecular Genetic ◽

Species Level ◽

Coi Gene ◽

High Similarity ◽

Coi Sequences ◽

First Time

Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera, Chironomidae) is recorded from Mongolia for the first time. Eleven banding sequences determined in the Mongolian population were previously known from Altai and Yenisei populations: sokA1, sokB1, sokB2, sokC1, sokC2, sokD1, sokD2, sokE1, sokF1, sokF2 and sokG1. The additional B-chromosomes are absent. DNA-barcoding of COI gene was carried out for this species for the first time. The phylogenetic tree estimated by Bayesian inference showed a high similarity of the studied species with Ch. acutiventris Wülker, Ryser et Scholl, 1983 from the Chironomus obtusidens-group. The estimated genetic distance K2P between Ch. sokolovae and Ch. acutiventris is much lower (0.38%) than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. Our results show that the accepted cytogenetic criteria of species level in the genus Chironomus are more in accordance with morphological ones of the same level, than with molecular-genetic criteria accepted for species COI genetic distance.

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CHANGES IN SPECIES COMPOSITION AND ABUNDANCE OF FISH LARVAE FROM THE GULF OF TEHUANTEPEC, MEXICO

CICIMAR Oceánides ◽

10.37543/oceanides.v27i2.112 ◽

2012 ◽

Vol 27 (2) ◽

pp. 1

Author(s):

O. López -Chávez ◽

G. Aceves -Medina ◽

R. J. Saldierna -Martínez ◽

S. P. Jiménez -Rosenberg ◽

J. P. Murad -Serrano ◽

...

Keyword(s):

Species Composition ◽

Gulf Of California ◽

Larval Fish ◽

Fish Larvae ◽

Species Level ◽

Unusual Condition ◽

Gulf Of Tehuantepec ◽

Demersal Species ◽

High Diversity ◽

Mesopelagic Species

The larval fish abundance and species composition of the Gulf of Tehuantepec are described based on the analysis of samples obtained from oblique zooplankton tows during summer 2007 and spring 2008. Changes in species composition and abundance between both periods were also described. A total of 145 taxa were obtained from which 73 were identified to species level, 43 to genus and 29 to family. The larval fish assemblage of the Gulf of Tehuantepec showed distinctive characteristics from other regions of the American Pacific, such as: A) a dominance of coastal-pelagic species (mainly Bregmaceros bathymaster); B) high diversity and abundance of shallow demersal species even along the oceanic stations of the study area; and C) a low proportion of mesopelagic species, an unusual condition in areas with narrow continental shelf. The diversity estimations suggest that Gulf of Tehuantepec is one of the most diverse ecosystems of the American Pacific, even as compared with other regions considered of highest diversity such as the Gulf of California. The high abundance, as well as the presence of the larval, juvenile and adult stages of B. bathymaster, suggests the importance of this region as a reproductive, nursery and recruitment for this species. Cambios en la composición de especies y abundancia de larvas de peces en el Golfo de Tehuantepec, México Se describen la composición de especies y abundancia de larvas de peces del Golfo de Tehuantepec a partir del análisis de muestras obtenidas en arrastres oblicuos de zooplancton. Así mismo, se describen los cambios en composición y abundancia entre un periodo de verano y uno de primavera. Se obtuvieron 145 taxa de los que 73 se identificaron a nivel especie, 43 a género y 29 a familia. La comunidad de larvas de peces del Golfo de Tehuantepec mostró rasgos distintivos de otras regiones similares del Pacífico Americano, tales como: A) dominancia de especies pelágico-costeras (particularmente Bregmaceros bathymaster); B) alta diversidad y abundancia de especies demersales someras aún en las estaciones mas oceánicas del área de estudio; y C) una proporción menor de especies de peces mesopelágicos, condición poco común en áreas con plataforma continental estrecha. Las estimaciones de diversidad ubican al Golfo de Tehuantepec como uno de los ecosistemas más diversos del Pacífico americano, aún comparándolo con regiones consideradas de alta diversidad a nivel mundial como es el caso del Golfo de California. La abundancia y la presencia de estadios larvales, juveniles y adultos de B. bathymaster reflejan la importancia de esta zona como área de reproducción, crianza y reclutamiento de esta especie.

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Molecular and Biological Analysis on Ommastrephes caroli Findings in the Central Western Mediterranean Sea (Sardinian Waters) Including First Age Investigation Using Eye Lenses and Beaks

Frontiers in Marine Science ◽

10.3389/fmars.2021.683856 ◽

2021 ◽

Vol 8 ◽

Author(s):

Blondine Agus ◽

Laura Carugati ◽

Andrea Bellodi ◽

Rita Cannas ◽

Alessandro Cau ◽

...

Keyword(s):

Mediterranean Sea ◽

Molecular Data ◽

Western Mediterranean ◽

Morphological Identification ◽

Potential Fecundity ◽

Western Mediterranean Sea ◽

Body Sizes ◽

Coi Sequences ◽

Size And Morphology ◽

First Time

Molecular identifications based on two mitochondrial markers (cytochrome c oxidase subunit I -COI- and 16S ribosomal RNA gene -16S-) have been implemented to confirm the morphological identification of eight specimens collected in the Central western Mediterranean. Molecular data show they belonged to a recently resurrected species of the genus Ommastrephes, i.e., O. caroli, known to be distributed in the Atlantic Ocean and Mediterranean Sea. Despite this, molecular analyses of COI sequences evidenced the presence of potential genetic differentiation between Mediterranean and Atlantic samples, highlighting the need for further studies, with more individuals to investigate the connectivity between individuals living in the two areas. Furthermore, morphological, biometric and reproductive features here reported, could be useful in evaluating possible distinctive biological features between the Mediterranean and Atlantic individuals. Female mature size was larger than the male. The relationships obtained between the beak measurements and body sizes (DML; TW) were better described by a power model. Asynchronous oocytes development with relatively small oocytes (0.05–1.10 mm) and a protracted intermittent spawning with active feeding were observed. This study also reported for the specie O. caroli the first data on the potential fecundity estimated (840061 oocytes), the oviducal load (90000 ripe oocytes) as well as the number of seminal receptacles and the size and morphology of the spermatangia found in the buccal mass of all mated females. Even if on a low sample size, beaks and eye lenses were used for the first time in O. caroli for age estimation. The statistically significant relationship found between increments counted in eye lenses and beaks highlighted the reliability of the lenses to estimate age in O. caroli, even if further studies will be needed for its validation. Assuming a daily increment for both structures, a mean life span of about 12–13 months was estimated for both sexes, which is consistent with the sexual maturity condition observed in all the samples and the semelparity known for cephalopods coleoids.

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Morphological and molecular identification of Fusarium spp. isolated from maize kernels in Java and Lombok, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210650 ◽

2020 ◽

Vol 21 (6) ◽

Author(s):

Ani Widiastuti ◽

Monica Lucky Karlina ◽

Kurnia Ritma Dhanti ◽

Yufita Dwi Chinta ◽

Tri Joko ◽

...

Keyword(s):

Molecular Identification ◽

Fusarium Verticillioides ◽

Animal Health ◽

Morphological Characteristics ◽

Morphological Identification ◽

Fusarium Spp ◽

Single Spore ◽

Central Java ◽

Species Specific ◽

Maize Kernels

Abstract. Widiastuti A, Karlina ML, Dhanti KR, Chinta YD, Joko T, Suryanti, Wibowo A. 2020. Morphological and molecular identification of Fusarium spp. isolated from maize kernels in Java and Lombok, Indonesia. Biodiversitas 21: 2741-2750. Fungal contamination of maize is a serious problem in Indonesia. Fusarium spp. infect maize in the field will be continuing to contaminate in the post-harvest period even though disease symptoms are not always emerged. Some Fusarium spp. produced mycotoxins which are harmful to human and animal health. Aims of this research were to reveal the presence of Fusarium spp. from both symptomatic and unsymptomatic maize, and to identify them based on morphological characteristics and molecular analysis. Samples of maize were collected from maize cultivation areas in East Java (EJ), Central Java (CJ), West Java (WJ), Yogyakarta Special Province (DIY), and Lombok, West Nusa Tenggara. Fusarium spp. were isolated in a single spore method and cultured in potato dextrose agar (PDA) medium for morphological identification of macro-and microconidia. Molecular identification was conducted by PCR assay using species-specific primers. Furthermore, unidentified species were analyzed by DNA sequence. This research found four species of mycotoxigenic Fusarium isolated from maize-based on molecular identification, which were Fusarium verticillioides (15 isolates), F. proliferatum (6 isolates), F. graminearum (1 isolate) and F. asiaticum (1 isolate). This research showed a novel report of F. asiaticum infection on maize kernel in Indonesia.

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Observations on the morphology of adults and larval stages of Oesophagostomum sp. isolated from man in northern Togo and Ghana

Journal of Helminthology ◽

10.1017/s0022149x00012840 ◽

1993 ◽

Vol 67 (1) ◽

pp. 49-61 ◽

Cited By ~ 37

Author(s):

J. Blotkamp ◽

H. P. Krepel ◽

V. Kumar ◽

S. Baeta ◽

J. M. Van't Noordende ◽

...

Keyword(s):

Morphological Characteristics ◽

Intestinal Lumen ◽

Necator Americanus ◽

Larval Stages ◽

Pyrantel Pamoate ◽

First Time

AbstractInfection with Oesophagostomum sp. appears to be extremely common in man in northern Togo and Ghana Adult specimens were recovered from the intestinal lumen by treatment with pyrantel pamoate and the morphological characteristics of oesophagostomes of man could for the first time be compared with information available on the morphology of oesophagostomes of monkeys. The observations and measurements demonstrated that the species involved is Oesophagostomum bifurcum and that the eggs of this species cannot be differentiated from those of Necator americanus. Both infections occur simultaneously in the population involved. The L1 larvae, too, cannot be differentiated from hookworm L1 larvae. The L3 however, are characteristic. Diagnoses of human Oesophagostomum infections is based on the detection of these larvae in coprocultures. In the present paper, the eggs, the L1 and L3 larval stages and the adults, carefully described and photos are given.

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Annotated and updated checklist of marine crabs (Decapoda: Brachyura) of Mozambique supported by morphological and molecular data from shelf and slope species of the “MOZAMBIQUE” surveys

Zootaxa ◽

10.11646/zootaxa.5056.1.1 ◽

2021 ◽

Vol 5056 (1) ◽

pp. 1-67

Author(s):

ISABEL MUÑOZ ◽

EVA GARCÍA-ISARCH ◽

JOSE A. CUESTA

Keyword(s):

Dna Barcode ◽

Morphological Characteristics ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Colour Pattern ◽

General Distribution ◽

Bathymetric Range ◽

Coi Sequences ◽

First Time

An updated checklist of Mozambican marine brachyuran crabs is generated based on an exhaustive revision of the existing literature, together with the additional records provided by the specimens collected throughout the three “MOZAMBIQUE” surveys carried out in Mozambican waters during three consecutive years (2007–2009) by the Instituto Español de Oceanografía, (Spanish Institute of Oceanography, IEO). A total of 269 species, grouped in 15 superfamilies, 26 families and 172 genera are reported in the checklist, and a detailed inventory is produced with the list and remarks about the brachyuran species collected. Thirty-nine crab species belonging to 19 families were identified based on morphological characteristics and/or genetic tools. DNA barcode sequences (16S rRNA and/or COI) were obtained for 37 species, including 16S and COI sequences that are new for 26 and 14 species, respectively. Colour photographs of fresh specimens illustrate the comments about most species, being the first time that the original colour pattern is described for some of them. New records in Mozambican waters are reported for the species Paromolopsis boasi, Mursia aspera, Carcinoplax ischurodous, Tanaoa pustulosus, Euclosiana exquisita, Oxypleurodon difficilis, Naxioides robillardi, Samadinia galathea, Cyrtomaia gaillardi, Paramaja gibba, Pleistacantha ori, Parathranites granosus, Parathranites orientalis, Ovalipes iridescens and Charybdis smithii, and second records for Moloha alcocki, Samadinia pulchra and Charybdis africana. In addition, Raninoides crosnieri, S. galathea and P. ori were collected for the first time after their descriptions. The female of Samadinia galathea is described for the first time, and a potential new species of Mursia is reported. Some records expand the known bathymetric range of certain species and/or their general distribution. New molecular and morphological data suggest the necessity of the revision of P. boasi, R. crosnieri, C. africana and the genera Platymaia and Carcinoplax. The variability and taxonomic validity of some morphological characters in brachyuran systematic is discussed.

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