A Mysterious World Revealed: Larval-Adult Matching of Deep-Sea Shrimps from the Gulf of Mexico

The identification of deep-sea (>200 m) pelagic larvae is extremely challenging due to the morphological diversity across ontogeny and duration of larval phases. Within Decapoda, developmental stages often differ conspicuously from their adult form, representing a bizarre and mysterious world still left to be discovered. The difficulties with sampling and rearing deep-sea larvae, combined with the lack of taxonomic expertise, argues for the use of molecular methods to aid in identification. Here, we use DNA barcoding combined with morphological methods, to match larval stages with their adult counterpart from the northern Gulf of Mexico and adjacent waters. For DNA barcoding, we targeted the mitochondrial ribosomal large subunit 16S (16S) and the protein coding cytochrome oxidase subunit 1 (COI). These data were combined with previous sequences to generate phylogenetic trees that were used to identify 12 unknown larval and two juvenile species from the infraorder Caridea and the suborder Dendrobranchiata. Once identified, we provide taxonomic descriptions and illustrations alongside the current state of knowledge for all families. For many groups, larval descriptions are missing or non-existent, so this study represents a first step of many to advance deep-sea larval diversity.

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DNA barcoding enhances large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico and adjacent waters

Journal of Crustacean Biology ◽

10.1093/jcbiol/ruab005 ◽

2021 ◽

Vol 41 (1) ◽

Author(s):

Carlos Varela ◽

Charles Golightly ◽

Laura E Timm ◽

Blake Wilkins ◽

Tamara Frank ◽

...

Keyword(s):

Gulf Of Mexico ◽

Dna Barcoding ◽

Deep Sea ◽

Large Scale ◽

Oil Spills ◽

Large Subunit ◽

Evolutionary Relationships ◽

Protein Coding ◽

Molecular Approaches ◽

Species Complexes

Abstract The application of DNA barcoding represents a complementary and efficient approach to identifying specimens at all stages of their life cycle when used in combination with traditional morphological methods. Due to difficulties obtaining samples from the deep sea (> 200 m), these methods have been less frequently applied to deep-water taxa. We used DNA-barcoding techniques to enhance large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico, a region that has recently been identified as one of the world’s four most hyperdiverse ocean ecosystems. This study was conceptualized in direct response to the Deepwater Horizon Oil Spill in 2010, which identified major knowledge gaps in our understanding of deep-sea biodiversity. We employed traditional Sanger sequencing and a genomic skimming approach to target the mitochondrial ribosomal large subunit 16S and the protein-coding cytochrome oxidase subunit 1 (COI). Alongside these molecular approaches, traditional taxonomic investigations allowed for advancements in biodiversity, evolutionary relationships, cryptic species complexes, and distributional records across four abundant and common deep-pelagic orders (Amphipoda, Euphausiacea, Lophogastrida, and Decapoda). DNA barcodes were successfully obtained from 82 species for a total of 158 and 169 new 16S and COI sequences, respectively. Evidence of cryptic diversity has been found in the genera EucopiaDana, 1852 (Lophogastrida) and Allosergestes Judkins & Kensley, 2008 (Decapoda). New records for the Gulf of Mexico of species of LanceolaSay, 1818 (Amphipoda), Eupasiphae Wood-Mason in Wood-Mason & Alcock, 1893, PasiphaeaSavigny, 1816, and MeningodoraSmith, 1882 (Caridea) are presented. Preliminary results allow us to reconsider the current classification and evolutionary relationships of several lineages. The urgency to document biodiversity in the deep-pelagic is pressing against a backdrop of future threats including oil spills and deep-sea drilling.

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Oligochaete taxonomy – The rise of earthworm DNA barcode in India

Science Vision ◽

10.33493/scivis.18.01.01 ◽

2018 ◽

Vol 18 (1) ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

H. Lalthanzara ◽

Ruth Lalfelpuii ◽

C. Zothansanga ◽

M. Vabeiryureilai ◽

N. Senthil Kumar ◽

...

Keyword(s):

Dna Barcoding ◽

Developmental Stages ◽

Dna Barcode ◽

Soil Classification ◽

Reproductive Organs ◽

Diagnostic Features ◽

Protein Coding ◽

Anatomical Characters ◽

Ecological Importance

Oligochaeta is a class of segmented worms under the phylum Annelida that are characterised by the presence of tiny setae in each body segment. Earthworms are the main members, consisting of approximately 6200 species. Their ecological importance is well known as they are the major soil macro-fauna; Aristotle had named them as “the intestines of soil”. Classification of earthworms is a controversial issue since the introduction of modern taxonomical system on earthworm by Michaelsen in 1921. This is mainly because conventional identification using morphological and anatomical characters are complicated and confusing. The key diagnostic features such as the position and structure of the reproductive organs, clitellum and the associated tubercular pubertatis are not always reliable, particularly in different developmental stages, especially when the available specimens are the juveniles. DNA barcoding has offered a potential solution, even at the levels of identifying the juveniles or cocoons. Several genes including mitochondrial cytochrome-c oxidase I, 16S, 18S and 28S ribosomal RNAs, and protein-coding histone H3 genes have been introduced in the taxonomy and phylogeny of earthworm. It is anticipated that DNA barcoding will help conflicting taxonomy and further exploration of species diversity in India.

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LEVERAGING MACHINE LEARNING TO INFORM SPATIAL AND TEMPORAL PATTERNS IN DEEP-SEA CORAL BIODIVERSITY, GULF OF MEXICO AND US WEST ATLANTIC

10.1130/abs/2019am-336777 ◽

2019 ◽

Author(s):

Alexander N. Zimmerman ◽

◽

Claudia C. Johnson ◽

Nicholas W. Bussberg ◽

Mehmet M. Dalkilic

Keyword(s):

Machine Learning ◽

Gulf Of Mexico ◽

Deep Sea ◽

Temporal Patterns ◽

Spatial And Temporal Patterns ◽

Us West

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Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽

10.3390/insects12080668 ◽

2021 ◽

Vol 12 (8) ◽

pp. 668

Author(s):

Tinghao Yu ◽

Yalin Zhang

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Strong Support ◽

Intergenic Spacer ◽

Taxonomic Status ◽

Start Codon ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

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Active prey selection in developing larvae of Atlantic bluefin tuna (Thunnus thynnus) in spawning grounds of the Gulf of Mexico

Journal of Plankton Research ◽

10.1093/plankt/fbab020 ◽

2021 ◽

Author(s):

Akihiro Shiroza ◽

Estrella Malca ◽

John T Lamkin ◽

Trika Gerard ◽

Michael R Landry ◽

...

Keyword(s):

Gulf Of Mexico ◽

Prey Selection ◽

Bluefin Tuna ◽

Gut Contents ◽

Physical Factors ◽

Larval Rearing ◽

Thunnus Thynnus ◽

Small Copepod ◽

Atlantic Bluefin Tuna ◽

Larval Stages

Abstract Bluefin tuna spawn in restricted areas of subtropical oligotrophic seas. Here, we investigate the zooplankton prey and feeding selectivity of early larval stages of Atlantic bluefin tuna (ABT, Thunnus thynnus) in larval rearing habitat of the Gulf of Mexico. Larvae and zooplankton were collected during two multi-day Lagrangian experiments during peak spawning in May 2017 and 2018. Larvae were categorized by flexion stage and standard length. We identified, enumerated and sized zooplankton from larval gut contents and in the ambient community. Ciliates were quantitatively important (up to 9%) in carbon-based diets of early larvae. As larvae grew, diet composition and prey selection shifted from small copepod nauplii and calanoid copepodites to larger podonid cladocerans, which accounted for up to 70% of ingested carbon. Even when cladoceran abundances were <0.2 m−3, they comprised 23% of postflexion stage diet. Feeding behaviors of larvae at different development stages were more specialized, and prey selection narrowed to appendicularians and primarily cladocerans when these taxa were more abundant. Our findings suggest that ABT larvae have the capacity to switch from passive selection, regulated by physical factors, to active selection of presumably energetically optimal prey.

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Holistic description of new deep sea megafauna (Cephalopoda: Cirrata) using a minimally invasive approach

BMC Biology ◽

10.1186/s12915-021-01000-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Alexander Ziegler ◽

Christina Sagorny

Keyword(s):

Minimally Invasive ◽

Dna Barcoding ◽

Deep Sea ◽

Imaging Techniques ◽

Structural Complexity ◽

Micro Computed Tomography ◽

Invasive Approach ◽

Non Invasive ◽

Additional Support ◽

Holistic Description

Abstract Background In zoology, species descriptions conventionally rely on invasive morphological techniques, frequently leading to damage of the specimens and thus only a partial understanding of their structural complexity. More recently, non-destructive imaging techniques have successfully been used to describe smaller fauna, but this approach has so far not been applied to identify or describe larger animal species. Here, we present a combination of entirely non-invasive as well as minimally invasive methods that permit taxonomic descriptions of large zoological specimens in a more comprehensive manner. Results Using the single available representative of an allegedly novel species of deep-sea cephalopod (Mollusca: Cephalopoda), digital photography, standardized external measurements, high-field magnetic resonance imaging, micro-computed tomography, and DNA barcoding were combined to gather all morphological and molecular characters relevant for a full species description. The results show that this specimen belongs to the cirrate octopod (Octopoda: Cirrata) genus Grimpoteuthis Robson, 1932. Based on the number of suckers, position of web nodules, cirrus length, presence of a radula, and various shell characters, the specimen is designated as the holotype of a new species of dumbo octopus, G. imperator sp. nov. The digital nature of the acquired data permits a seamless online deposition of raw as well as derived morphological and molecular datasets in publicly accessible repositories. Conclusions Using high-resolution, non-invasive imaging systems intended for the analysis of larger biological objects, all external as well as internal morphological character states relevant for the identification of a new megafaunal species were obtained. Potentially harmful effects on this unique deep-sea cephalopod specimen were avoided by scanning the fixed animal without admixture of a contrast agent. Additional support for the taxonomic placement of the new dumbo octopus species was obtained through DNA barcoding, further underlining the importance of combining morphological and molecular datasets for a holistic description of zoological specimens.

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Deep-sea erosional unconformity in the southeastern Gulf of Mexico

Geology ◽

10.1130/0091-7613(1983)11<215:deuits>2.0.co;2 ◽

1983 ◽

Vol 11 (4) ◽

pp. 215 ◽

Cited By ~ 6

Author(s):

D. M. Angstadt ◽

J. A. Austin ◽

R. T. Buffler

Keyword(s):

Gulf Of Mexico ◽

Deep Sea

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Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus

Insects ◽

10.3390/insects12050453 ◽

2021 ◽

Vol 12 (5) ◽

pp. 453

Author(s):

Zi-Yi Zhang ◽

Jia-Yin Guan ◽

Yu-Rou Cao ◽

Xin-Yi Dai ◽

Kenneth B. Storey ◽

...

Keyword(s):

Gene Expression ◽

Phylogenetic Trees ◽

Mitochondrial Gene ◽

Mitochondrial Protein ◽

Pine Wilt Disease ◽

Bursaphelenchus Xylophilus ◽

Monochamus Alternatus ◽

Genome Database ◽

Protein Coding ◽

Nd5 Gene

We determined the mitochondrial gene sequence of Monochamus alternatus and three other mitogenomes of Lamiinae (Insect: Coleoptera: Cerambycidae) belonging to three genera (Aulaconotus, Apriona and Paraglenea) to enrich the mitochondrial genome database of Lamiinae and further explore the phylogenetic relationships within the subfamily. Phylogenetic trees of the Lamiinae were built using the Bayesian inference (BI) and maximum likelihood (ML) methods and the monophyly of Monochamus, Anoplophora, and Batocera genera was supported. Anoplophora chinensis, An. glabripennis and Aristobia reticulator were closely related, suggesting they may also be potential vectors for the transmission of the pine wood pathogenic nematode (Bursaphelenchus xylophilus) in addition to M. alternatus, a well-known vector of pine wilt disease. There is a special symbiotic relationship between M. alternatus and Bursaphelenchus xylophilus. As the native sympatric sibling species of B. xylophilus, B. mucronatus also has a specific relationship that is often overlooked. The analysis of mitochondrial gene expression aimed to explore the effect of B. mucronatus on the energy metabolism of the respiratory chain of M. alternatus adults. Using RT-qPCR, we determined and analyzed the expression of eight mitochondrial protein-coding genes (COI, COII, COIII, ND1, ND4, ND5, ATP6, and Cty b) between M. alternatus infected by B. mucronatus and M. alternatus without the nematode. Expression of all the eight mitochondrial genes were up-regulated, particularly the ND4 and ND5 gene, which were up-regulated by 4–5-fold (p < 0.01). Since longicorn beetles have immune responses to nematodes, we believe that their relationship should not be viewed as symbiotic, but classed as parasitic.

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Seasonal occurrence of some larval stages of endoparasites in three cyprinids from the Nwanedi-Luphephe dams, the Limpopo River System, South Africa

Helminthologia ◽

10.1515/helmin-2015-0037 ◽

2015 ◽

Vol 52 (3) ◽

pp. 229-235 ◽

Cited By ~ 2

Author(s):

E. M. Mbokane ◽

J. Theron ◽

W. J. Luus-Powell

Keyword(s):

Developmental Stages ◽

River System ◽

Intestinal Wall ◽

The Body ◽

Seasonal Occurrence ◽

Seasonal Fluctuations ◽

Metazoan Parasites ◽

Larval Stages ◽

Parasite Communities ◽

Third Stage

Abstract This study provides information on seasonal occurrence of developmental stages of endoparasites infecting three cyprinids in the Nwanedi-Luphephe dams, Limpopo River System. Labeobarbus marequensis (Smith, 1841), Barbus trimaculatus Peters, 1852 and Barbus radiatus Peters, 1853 were investigated seasonally from January 2008 to October 2008. The following larvae of metazoan parasites were collected: Diplostomum sp. from the eyes of L. marequensis and B. trimaculatus; Ornithodiplostomum sp. from the gills of B. trimaculatus; Posthodiplostomum sp. from muscle, skin and fins of B. trimaculatus and B. radiatus; third-stage Contracaecum larvae (L3) from the mesentery fats and on the liver lobes of L. marequensis and B. trimaculatus and gryporynchid cestode larvae from the outer intestinal wall of B. radiatus. All the flukes encountered were metacercariae. Diplostomum sp. and Contracaecum sp. dominated the parasite communities. Their prevalence exhibited seasonal fluctuations with maxima in summer. Factors likely to influence fish infection such as the body size of fish and their condition factors were also briefly considered in this study.

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