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Taite M, Fernández-Álvarez FÁ, Braid HE, Bush SL, Bolstad K, Drewery J, Mills S, Strugnell JM, Vecchione M, Villanueva R, Voight JR, Allcock AL. Genome skimming elucidates the evolutionary history of Octopoda. Mol Phylogenet Evol 2023; 182:107729. [PMID: 36773750 DOI: 10.1016/j.ympev.2023.107729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/10/2022] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirroteuthidae, Grimpoteuthidae, Opisthoteuthidae and Stauroteuthidae) and six families of Incirrata (Amphitretidae, Argonautidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, and Megaleledonidae) which were assembled using genome skimming. Phylogenetic trees were built using Maximum Likelihood and Bayesian Inference with several alignment matrices. All mitochondrial genomes had the 'typical' genome composition and gene order previously reported for octopodiforms, except Bathypolypus ergasticus, which appears to lack ND5, two tRNA genes that flank ND5 and two other tRNA genes. Argonautoidea was revealed as sister to Octopodidae by the mitochondrial protein-coding gene dataset, however, it was recovered as sister to all other incirrate octopods with strong support in an analysis using nuclear rRNA genes. Within Cirrata, our study supports two existing classifications suggesting neither is likely in conflict with the true evolutionary history of the suborder. Genome skimming is useful in the analysis of phylogenetic relationships within Octopoda; inclusion of both mitochondrial and nuclear data may be key.
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Affiliation(s)
- M Taite
- School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - F Á Fernández-Álvarez
- School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland; Institut de Ciències del Mar (CSIC), Passeig Marítim 37-49, E-08003 Barcelona, Spain.
| | - H E Braid
- AUT Lab for Cephalopod Ecology & Systematics, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - S L Bush
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington DC 20560, USA.
| | - K Bolstad
- AUT Lab for Cephalopod Ecology & Systematics, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.
| | - J Drewery
- Marine Scotland, Marine Laboratory, 375 Victoria Road, Aberdeen AB11 9DB, UK.
| | - S Mills
- National Institute of Water and Atmospheric Research, 301 Evans Bay Parade, Wellington, New Zealand.
| | - J M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Qld, Australia.
| | - M Vecchione
- National Systematics Laboratory, Office of Science and Technology, NOAA Fisheries, Washington, DC, USA; Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA.
| | - R Villanueva
- Institut de Ciències del Mar (CSIC), Passeig Marítim 37-49, E-08003 Barcelona, Spain.
| | - J R Voight
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S DuSable Lake Shore Dr., Chicago, IL 60605, USA.
| | - A L Allcock
- School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland.
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Morphological Description and Phylogenetic Analyses of a New Species of Callistoctopus (Cephalopoda, Octopodidae) from China. DIVERSITY 2022. [DOI: 10.3390/d14121083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new octopus species, Callistoctopus tenuipes sp. nov., was formally described from the southeastern coastal waters of China using morphological description and molecular analysis methods. C. tenuipes sp. nov. is a small- to moderate-sized octopus, which is characterized by very narrow and long arms. Although it was previously misidentified as the juvenile of Octopus minor (Sasaki, 1920), it can be recognised by spots, gill lamellae count, funnel organ shape, enlarged suckers, and ligula shape. C. tenuipes sp. nov. differs from the small-sized octopus Callistoctopus xiaohongxu, mainly in the gill lamellae count, funnel organ shape, and arm-length index. In the molecular analysis, sequences obtained from the cytochrome c-oxidase subunit I (COI) gene of eight specimens were 590 bp in length. The pairwise Kimura 2-parameter (K2P) genetic distances between Octopodidae species ranged from 8.58 to 23.79% based on the COI gene. The phylogenetic analyses suggested that C. tenuipes sp. nov. belonged to the Callistoctopus clade and may have a close affinity with C. xiaohongxu and O. minor. Moreover, three species delimitation methods all strongly supported C. tenuipes as a separate species.
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Zheng X, Xu C, Li J. Morphological description and mitochondrial DNA-based phylogenetic placement of a new species of Callistoctopus Taki, 1964 (Cephalopoda, Octopodidae) from the southeast waters of China. Zookeys 2022; 1121:1-15. [PMID: 36760765 PMCID: PMC9848676 DOI: 10.3897/zookeys.1121.86264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/10/2022] [Indexed: 11/12/2022] Open
Abstract
In this study, we described a new species of octopus and named it Callistoctopusxiaohongxu sp. nov. based on nine specimens captured in the waters of southeast China. Callistoctopusxiaohongxu sp. nov. is a small to moderate-sized octopus. The most characteristic and defining morphological features are the reddish-orange to reddish-brown skin, gills with 8 or 9 lamellae per demibranch, \∧/-shaped funnel organ, and small suckers. Fragments obtained from the mitochondrial cytochrome c oxidase subunit I (COI) gene of nine specimens were 593 bp in length, and the genetic distance among the specimens of C.xiaohongxu sp. nov. and the other 16 octopods ranged from 11.13 to 21.09%. Topologies resulting from ML and BI analyses of the COI gene showed a highly supported monophyletic clade (bootstrap value [BS] = 94%, posterior probability [PP] = 100%) containing all the specimens identified as C.xiaohongxu sp. nov.
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Affiliation(s)
- Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, ChinaOcean University of ChinaQingdaoChina
| | - Chenxi Xu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, ChinaOcean University of ChinaQingdaoChina
| | - Jiahua Li
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, ChinaOcean University of ChinaQingdaoChina
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Tang Y, Zhang X, Ma Y, Zheng X. Descriptive study of the mitogenome of the diamondback squid (
Thysanoteuthis rhombus
Troschel, 1857) and the evolution of mitogenome arrangement in oceanic squids. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan Tang
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
| | - Xiaoying Zhang
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
| | - Yuanyuan Ma
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
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Tang Y, Zheng X, Liu H, Sunxie F. Population genetics and comparative mitogenomic analyses reveal cryptic diversity of Amphioctopus neglectus (Cephalopoda: Octopodidae). Genomics 2020; 112:3893-3902. [PMID: 32603760 DOI: 10.1016/j.ygeno.2020.06.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 12/28/2022]
Abstract
This study presented 96 cox1 and 76 cox3 genes of Amphioctopus neglectus populations. Three distinct lineages were formed from phylogenetic trees and networks constructed using haplotypes. Mitogenomes of A. neglectus-a and A. neglectus-b as the representatives of two lineages separated from population genetics were sequenced to compare with A. neglectus at the genome-level. Amphioctopus neglectus-a showed significant differences with A. neglectus, mainly reflected in gene length, intergenic regions and the secondary structure of tandem repeat motifs. Notably, two sequence deletions in mitogenomes of the two representative species were detected in different positions of major non-coding regions, which were the most distinct differences with A. neglectus. Pairwise genetic distances and the phylogenetic analysis supported the relationship of (A. neglectus-a + (A. neglectus + A. neglectus-b)). This study suggested that A. neglectus-a should be considered as a potential cryptic species of this complex, while A. neglectus-b needed further verification to be defined.
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Affiliation(s)
- Yan Tang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China.
| | - Haijuan Liu
- Guangxi Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai 536000, China
| | - Feige Sunxie
- Dongshan Boguangtianxing Foods Co., Ltd., Zhangzhou 363000, China
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Tang Y, Zheng X, Li Q. Redescription of Amphioctopus ovulum (Sasaki, 1917) (Cephalopoda : Octopodidae) and comparative morphological analyses among three species of violet-ringed octopods. INVERTEBR SYST 2020. [DOI: 10.1071/is20002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Amphioctopus ovulum (Sasaki, 1917) is a small to moderate-sized octopus, which can be identified by the iridescent violet ring present in the dark ocellus on the web between the bases of arms II and III. Comprehensive taxonomic review is required to fully characterise this species because the syntypes are missing and the description is insufficiently complete for modern octopod taxonomy. In this study, the species A. ovulum is redescribed with morphological and morphometric characters of 18 specimens collected from the coastal waters of China. The distribution of A. ovulum extends from the Gulf of Thailand, through Cambodia, Vietnam, Philippines, through the South China Sea and the East China Sea to Japan. The swollen terminal organ diverticulum and long spermatophores make it possible to distinguish A. ovulum clearly from A. rex and A. neglectus, species with similar morphological characters of violet rings. Moreover, three species of violet-ringed octopods were clearly differentiated by sequences of the partial mitochondrial genes COI and COIII. Three monophyletic clades resolved in phylogenetic trees. Amphioctopus rex and A. neglectus clustered into a sister taxon, and clustered with the remaining Amphioctopus species.
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