Cephalopod DNA/Molecular/Genetic Studies/Health

DWhatley

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This is a review of the current status of ceph molecular data collection. @gjbarord is currently doing DNA work with the nautilus and hopefully will post where the information can be accessed once it is stored.

The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review A. Louise Allcock,A. Lindgren, J. M. Strugnell 2013 (subscription)

Abstract
The first DNA sequence of a cephalopod was published in 1983 and the first molecular paper focusing on cephalopods was published in 1994. In this review we trace progress in the field. We examine the placement of Cephalopoda with respect to other molluscan classes and we examine relationships within Cephalopoda. We provide a summary tree of the relationships between cephalopod orders and we examine relationships of taxa within each of these orders. Although much knowledge has been gained over the past 20 years, deeper-level relationships are still not well understood and there is still much scope for further research in this field. Genomic studies are likely to contribute significantly to our knowledge in the future.
 

gjbarord

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Interesting paper. Not sure how I missed it so thanks D!!

From a nautilus standpoint, there should be some cool stuff coming out soon...

Greg
 

GPO87

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Cranchiids of the South Atlantic Mid-Oceanic Ridge: results from the first southern MAR-ECO expedition.
Bolstad, K. S. R., Perez, J. A. A., Strugnell, J. M., & Vidal, É. A.

Abstract
Cranchiids were the most diverse squid family collected during the first southern MAR-ECO expedition in late 2009, with nine taxa identified to species. A total of 45 young specimens were collected (mantle length 7.4–59.2 mm), allowing a survey of early ontogenetic tentacular morphology in cranchiids using scanning electron micrographs. Paralarval tentacular sucker morphology appeared similar among species within the same subfamily: in the Cranchiinae, the paralarval suckers possess relatively large, narrowly polygonal or ovoid-faced pegs in the innermost ring around the aperture, and the infundibular ring lacks the dentition observed in most taoniin genera. Hook development in Galiteuthis armata appears to vary widely among small individuals. Tissue samples were also collected from five genera (Cranchia, Galiteuthis, Helicocranchia, Leachia and Teuthowenia); phylogenetic trees (maximum-likelihood and Bayesian methods) built using these cytochrome oxidase subunit I sequences and others available from GenBank show some support for the subfamilies Cranchiinae and Taoniinae, and that within the latter, the hooked taxa group together. It is hoped that reporting this opportunistic systematic and genetic information may be of eventual assistance in helping to resolve this most problematic of squid families.
 

DWhatley

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The complete mitochondrial genome of Octopus conispadiceus (Sasaki, 1917) (Cephalopoda: Octopodidae)
Yuanyuan Ma, Xiaodong Zheng, Rubin Cheng, and Qi Li 2014

Abstract
In this paper, we determined the complete mitochondrial genome of Octopus conispadiceus (Cephalopoda: Octopodidae). The whole mitogenome of O. conispadiceus is 16,027 basepairs (bp) in length with a base composition of 41.4% A, 34.8% T, 16.1% C, 7.7% G and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a major non-coding region (MNR). The gene arrangements of O. conispadiceus showed remarkable similarity to that of O. vulgaris, Amphioctopus fangsiao, Cistopus chinensis and C. taiwanicus.
 

DWhatley

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Genetic divergence and phylogenetic analysis based on cytochrome c oxidase subunit-1 sequence of enope squid Abraliaandamanica (Goodrich 1896) inhabiting Andaman Sea
Naveen Sathyan, Chaithanya, Anil Kumar, Sruthy, Rosamma Philip 2014 (pdf)

Abstract
Cytochrome c oxidase subunit-1 (CO1) gene sequence of enope squid Abralia andamanica sampled from Andaman Sea was compared with the CO1 gene sequence of A. andamanica from China Sea. Assessment of CO1 nucleotide and protein sequence of enope squid Abralia andamanica from Andaman Sea and China Sea revealed that with respect to CO1 sequence genetic divergence exist between the two enope squids. A. andamanica inhabiting Andaman Sea exhibited more affinity towards A. veranyi than to its counterpart from China Sea. Pairwise distance calculated based on Kimura 2-parameter (K2P) model for the enope squids from Andaman Sea and China Sea was found to be almost half of the mean pairwise distance determined for order Teuthida indicating high genetic variation among the two enope squids with regard to CO1 gene. Phylogenetic analysis of the CO1 nucleotide sequence of A. andamanica was performed to determine its relationship with other squids belonging to the order Teuthida. A. andamanica aligned along with the clade formed by family Enoploteuthidae. Sixteen families of order Teuthida were considered for phylogenetic analysis, overlap was observed three families. The study endorses the proficiency of CO1 based DNA barcoding in determining the phylogeny and genetic divergence of a species.
 

Tintenfisch

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Bolstad, K. S., Braid, H. E., & McBride, P. D. Molecular phylogenetic analysis of the squid family Mastigoteuthidae (Mollusca, Cephalopoda) based on three mitochondrial genes [2014].

Abstract:

Mastigoteuthid squids are ecologically important, being prey to many apex predators, yet the diversity and systematics of the family remain poorly understood. Delicate by nature, they are often damaged during capture; there is a need to accurately identify incomplete mastigoteuthid specimens from collections and stomach contents. This study aimed to test a morphological hypothesis for the division of the genera Mastigoteuthis� (Mt.), Idioteuthis, Mastigopsis (Mp.), Echinoteuthis, and Magnoteuthis (Mg.) and to assess the utility of DNA barcodes to discriminate species. Three mitochondrial genes (16S rRNA, 12S rRNA, and cytochrome c oxidase subunit I) were analysed for eight different species, representing the largest phylogenetic assessment of the family to date. Evidence was found for a potentially new species in New Zealand that has been previously misidentified as the morphologically similar species Mg. magna. Each species analysed herein exhibited unique mitochondrial DNA haplotypes for all loci, and the morphological distinction between the five proposed genera was strongly supported using a combined Bayesian and maximum-likelihood phylogenies. Of the three loci examined, the DNA barcode region shows the greatest divergence between species and should be used in future systematic work on the Mastigoteuthidae.
 

DWhatley

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Genetic diversity and population structure of Sepia officinalis from the Tunisian cost revealed by mitochondrial COI sequences
Tir Meriam, Tombari Wafa, Telahigue Khawla, Hajji Tarek, Ghram Abdeljelil, Elcafsi Mhamed 2014 (subscription)

Abstract
Population substructure of Sepia officinalis sampled along the Tunisian coastline was studied. We have scored the genetic variation of the mitochondrial gene cytochrome oxidase 1. A total of 20 specimens from four sampling sites were analysed and revealed 12 different haplotypes. Haplotype diversity showed a decreasing north to south gradient which may be explained by the hydrogeography of the study area. The overall estimate of genetic divergence (FST) revealed significant genetic differentiation between the pair-wise population comparisons supported by the AMOVA analysis which reveals significant genetic divergence. Finally, populations showed an excess of rare haplotypes. The mismatch distribution and several population genetic statistics indicate that the excess of rare variants is due to a recent expansion for Djerba and Kelibia populations. For Rades and Bizerte populations a constant population size was detected. These findings are important for fisheries management to preserve this marine resource for long-term utilization.
 

DWhatley

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Characterization of Homeobox Genes Reveals Sophisticated Regionalization of the Central Nervous System in the European Cuttlefish Sepia officinalis
Laura Focareta, Salvatore Sesso, Alison G. Cole

Abstract
Cephalopod mollusks possess a number of anatomical traits that often parallel vertebrates in morphological complexity, including a centralized nervous system with sophisticated cognitive functionality. Very little is known about the genetic mechanisms underlying patterning of the cephalopod embryo to arrive at this anatomical structure. Homeodomain (HD) genes are transcription factors that regulate transcription of downstream genes through DNA binding, and as such are integral parts of gene regulatory networks controlling the specification and patterning of body parts across lineages. We have used a degenerate primer strategy to isolate homeobox genes active during late-organogenesis from the European cuttlefish Sepia officinalis. With this approach we have isolated fourteen HD gene fragments and examine the expression profiles of five of these genes during late stage (E24-28) embryonic development (Sof-Gbx, Sof-Hox3, Sof-Arx, Sof-Lhx3/4, Sof-Vsx). All five genes are expressed within the developing central nervous system in spatially restricted and largely non-overlapping domains. Our data provide a first glimpse into the diversity of HD genes in one of the largest, yet least studied, metazoan clades and illustrate how HD gene expression patterns reflect the functional partitioning of the cephalopod brain.
 

DWhatley

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Cephalopod development: what we can learn from differences
L Bonnaud-Ponticelli, Y Bassaglia1 2014 (PDF)


Abstract
The molluscan neuro-muscular system shows extreme diversity. Cephalopods present an original body plan, a derived neuro-muscular complex and a development with drastic changes in the antero-posterior/dorso-ventral orientation. How it took place during evolution is an unresolved question that can be approached by the study of developmental genes. Studying the expression of conserved transcription factors (Pax and NK families, otx, apt) and morphogen (hedgehog) during development is a good test of the conservation of their functions. We underline here unexpected expression patterns during cephalopod development, and we aim to suggest that these patterns may be, at least partly, in relation to morphological novelties in this clade.
 

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