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Kobayashi G, Abe H. Cost-efficient PCR based DNA barcoding of marine invertebrate specimens with NovaSeq amplicon sequencing. Mol Biol Rep 2024; 51:887. [PMID: 39105821 DOI: 10.1007/s11033-024-09811-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/19/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND The marine environment harbors high biodiversity; however, it is poorly understood. Nucleotide sequence data of all marine organisms should be accumulated before natural and/or anthropogenic environmental changes jeopardize the marine environment. In this study, we report a cost-effective and easy DNA barcoding method. This method can be readily adopted without using library preparation kits. It includes multiplex PCR of short targets, indexing PCR, and outsourcing to a sequencing service using the NovaSeq system. METHODS AND RESULTS We targeted four mitochondrial genes [cytochrome c oxidase subunit I (COI), COIII, 16S rRNA (16S), and 12S rRNA (12S)] and three nuclear genes [18S rRNA (18S), 28S rRNA (28S), internal transcribed spacer 2 (ITS2)] in 95 marine invertebrate specimens, which were primarily annelids. The primers, including adapters and indices for NovaSeq sequencing, were newly designed. Two PCR runs were conducted. The 1st PCR amplified specific loci with universal primers and the 2nd added sequencing adapters and indices to the 1st PCR products. The gene sequences obtained from the FASTQ files were subjected to BLAST search and phylogenetic analyses. One run using 95 specimens yielded sequences averaging 2816 bp per specimen for a total length of six loci. Nuclear genes were more successfully assembled compared with mitochondrial genes. A weak but significantly negative correlation was observed between the average length of each locus and success rate of the assembly. Some of the sequences were almost identical to the sequences obtained from specimens collected far from Japan, indicating the presence of potentially invasive species identified for the first time. CONCLUSIONS We obtained gene sequences efficiently using next-generation sequencing rather than Sanger sequencing. Although this method requires further optimization to increase the success rate for some loci, it is used as a first step to select specimens for further analyses by determining the specific loci of the targets.
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Affiliation(s)
- Genki Kobayashi
- Research Center for Creative Partnerships, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan.
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan.
| | - Hirokazu Abe
- Faculty of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
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2
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Song H, Wang Y, Shao H, Li Z, Hu P, Yap-Chiongco MK, Shi P, Zhang T, Li C, Wang Y, Ma P, Vinther J, Wang H, Kocot KM. Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting. Proc Natl Acad Sci U S A 2023; 120:e2302361120. [PMID: 37738291 PMCID: PMC10556646 DOI: 10.1073/pnas.2302361120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/18/2023] [Indexed: 09/24/2023] Open
Abstract
The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern animal biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in the animal tree of life has proven to be a major challenge, hindering understanding of early animal evolution and the fossil record. This is particularly true in the species-rich and highly varied Mollusca where dramatic inconsistency among paleontological, morphological, and molecular evidence has led to a long-standing debate about the group's phylogeny and the nature of dozens of enigmatic fossil taxa. A critical step needed to overcome this issue is to supplement available genomic data, which is plentiful for well-studied lineages, with genomes from rare but key lineages, such as Scaphopoda. Here, by presenting chromosome-level genomes from both extant scaphopod orders and leveraging complete genomes spanning Mollusca, we provide strong support for Scaphopoda as the sister taxon of Bivalvia, revitalizing the morphology-based Diasoma hypothesis originally proposed 50 years ago. Our molecular clock analysis confidently dates the split between Bivalvia and Scaphopoda at ~520 Ma, prompting a reinterpretation of controversial laterally compressed Early Cambrian fossils, including Anabarella, Watsonella, and Mellopegma, as stem diasomes. Moreover, we show that incongruence in the phylogenetic placement of Scaphopoda in previous phylogenomic studies was due to ancient incomplete lineage sorting (ILS) that occurred during the rapid radiation of Conchifera. Our findings highlight the need to consider ILS as a potential source of error in deep phylogeny reconstruction, especially in the context of the unique nature of the Cambrian Explosion.
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Affiliation(s)
- Hao Song
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yunan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Haojing Shao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Zhuoqing Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Pinli Hu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | | | - Pu Shi
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Tao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Cui Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yiguan Wang
- Institute of Ecology and Evolution, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Peizhen Ma
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jakob Vinther
- School of Biological Sciences, University of Bristol, BristolBS8 1TQ, United Kingdom
- School of Earth Sciences, University of Bristol, BristolBS8 1TQ, United Kingdom
| | - Haiyan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Kevin M. Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL35487
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL35487
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3
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Takano T, Kano Y, Mogi T, Okanishi M. Fusceulimoides kohtsukai gen. et sp. nov., a Minute Eulimid Gastropod Parasitic on the Little Brittle Star Ophiactis savignyi in Central Japan. Zoolog Sci 2023; 40:64-69. [PMID: 36744711 DOI: 10.2108/zs220050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/19/2022] [Indexed: 01/18/2023]
Abstract
Gastropods of over a dozen genera in the family Eulimidae have been identified as parasites of brittle stars, and many more remain to be discovered and described for a comprehensive understanding of the evolutionary history of their host-parasite relationships. In this study, we describe Fusceulimoides kohtsukai gen. et sp. nov., parasitic on the little brittle star, Ophiactis savignyi (Ophiactidae), in Kanagawa, central Japan. The new genus is distinguished from other eulimid genera by the combination of following seven conchological characters: (1) a very small size of up to 1.7 mm high, (2) a colorless translucent appearance, (3) a conical pupiform shape with a paucispiral protoconch, (4) slightly convex teleoconch whorls, (5) a remarkably large body whorl occupying 65-70% of the total shell height, (6) a broad, somewhat squarish and laterally expanded aperture with a strongly curved outer lip, and (7) a developed parietal callus without an indentation or depression in the umbilical area. A multi-locus molecular phylogeny revealed its distant relationship to Hemiliostraca + Pyramidelloides, a previously known clade of ophiuroid parasites, thereby suggesting multiple origins of this host-parasite association in Eulimidae.
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Affiliation(s)
- Tsuyoshi Takano
- Meguro Parasitological Museum, Meguro, Tokyo 153-0064, Japan,
| | - Yasunori Kano
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Takanobu Mogi
- Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, Miura, Kanagawa 238-0225, Japan
| | - Masanori Okanishi
- Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, Miura, Kanagawa 238-0225, Japan
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4
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Zhang T, Wang Y, Song H. The Complete Mitochondrial Genome and Gene Arrangement of the Enigmatic Scaphopod Pictodentalium vernedei. Genes (Basel) 2023; 14:210. [PMID: 36672951 PMCID: PMC9859601 DOI: 10.3390/genes14010210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial genomes in this group that are currently available. Here, we present the assembly and annotation of the complete mitochondrial genome from Dentaliida Pictodentalium vernedei, whose mitochondrial genome is 14,519 bp in size, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The nucleotide composition was skewed toward A-T, with a 71.91% proportion of AT content. Due to the mitogenome-based phylogenetic analysis, we defined P. vernedei as a sister to Graptacme eborea in Dentaliida. Although a few re-arrangements occurred, the mitochondrial gene order showed deep conservation within Dentaliida. Yet, such a gene order in Dentaliida largely diverges from Gadilida and other molluscan classes, suggesting that scaphopods have the highest degree of mitogenome arrangement compared to other molluscs.
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Affiliation(s)
- Tianzhe Zhang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yunan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 101400, China
| | - Hao Song
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 101400, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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5
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Kobayashi G, Goto R. Molecular phylogenetic assessment of Spirobranchus kraussii-complex (Annelida: Serpulidae) from the Japanese Archipelago. PeerJ 2021; 9:e11746. [PMID: 34316401 PMCID: PMC8286061 DOI: 10.7717/peerj.11746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/19/2021] [Indexed: 11/20/2022] Open
Abstract
Spirobranchus kraussii (Annelida: Serpulidae) was recognized as being widely distributed both in the Pacific and Atlantic Oceans. However, the sampling records far from its type locality (South Africa) have been questioned. Actually, recent molecular phylogenetic studies showed that S. kraussii contains genetically distinct species. In this study, we performed molecular phylogenetic analyses of S. cf. kraussii collected from Japan using the nucleotide sequences of a mitochondrial gene and two nuclear genes. Three lineages were recovered within Spirobranchus kraussii-complex in Japan, and one (Spirobranchus sp. 6) showed moderate genetic difference (approximately 4%) in the mitochondrial cytb gene sequence from Spirobranchus sp. 1, an undescribed sequenced species from Honshu Island, Japan. However, the nucleotide sequences of the 18S rRNA gene and ITS2 region were nearly indistinguishable. The other lineage was clearly distinct from the other previously sequenced species and is thus considered to be another distinct species of this species complex (Spirobranchus sp. 5). Although detailed morphological assessment of these lineages is necessary to define their taxonomic status, the present study provided further implications for the species diversity within the S. kraussii-complex.
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Affiliation(s)
- Genki Kobayashi
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Shirahama, Nishimuro, Wakayama, Japan
| | - Ryutaro Goto
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Shirahama, Nishimuro, Wakayama, Japan
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6
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Souza LS, Caetano CHS, Scarabino F, Costa PMS. New records and a new species of Scaphopoda (Mollusca) from the southwestern Atlantic Ocean. IHERINGIA. SERIE ZOOLOGIA 2020. [DOI: 10.1590/1678-4766e2020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
| | | | - Fabrizio Scarabino
- Universidad de la República, Uruguay; Museo Nacional de Historia Natural, Uruguay
| | - Paulo Márcio S. Costa
- Universidade Federal do Rio de Janeiro, Brazil; Fundação Instituto de Pesca do Estado do Rio de Janeiro, Brazil
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7
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Layton KKS, Middelfart PU, Tatarnic NJ, Wilson NG. Erecting a new family for
Spirostyliferina
, a truncatelloidean microgastropod, and further insights into truncatelloidean phylogeny. ZOOL SCR 2019. [DOI: 10.1111/zsc.12374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kara K. S. Layton
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
- Aquatic and Terrestrial Zoology & Molecular Systematics Unit Western Australian Museum Welshpool Western Australia Australia
| | - Peter U. Middelfart
- Aquatic and Terrestrial Zoology & Molecular Systematics Unit Western Australian Museum Welshpool Western Australia Australia
| | - Nikolai J. Tatarnic
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
- Aquatic and Terrestrial Zoology & Molecular Systematics Unit Western Australian Museum Welshpool Western Australia Australia
| | - Nerida G. Wilson
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
- Aquatic and Terrestrial Zoology & Molecular Systematics Unit Western Australian Museum Welshpool Western Australia Australia
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8
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Kocot KM, Wollesen T, Varney RM, Schwartz ML, Steiner G, Wanninger A. Complete mitochondrial genomes of two scaphopod molluscs. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3161-3162. [PMID: 33365899 PMCID: PMC7707011 DOI: 10.1080/23802359.2019.1666689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Complete mitochondrial genomes were determined for two scaphopod molluscs: the dentaliid Antalis entalis and an unidentified Antarctic gadilid. Both genomes are complete except, in Gadilida sp. indet., a short stretch of nad5 was undetermined and trnR could not be annotated. Organization of the Gadilida sp. genome is nearly identical to that previously reported for the gadilid Siphonodentalium whereas trnK, nad5, trnD, nad4, and nad4l are transposed to the opposite strand in the previously published Graptacme genome relative to that of Antalis. Phylogenetic analysis of the 13 protein-coding and 2 rRNA genes recovered Scaphopoda, Gadilida, and Dentaliida monophyletic with maximal support.
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Affiliation(s)
- Kevin M Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Tim Wollesen
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rebecca M Varney
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Megan L Schwartz
- School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA, USA
| | - Gerhard Steiner
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Andreas Wanninger
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
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9
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Wollesen T, Rodríguez Monje SV, Luiz de Oliveira A, Wanninger A. Staggered Hox expression is more widespread among molluscs than previously appreciated. Proc Biol Sci 2018; 285:20181513. [PMID: 30305436 PMCID: PMC6191704 DOI: 10.1098/rspb.2018.1513] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/14/2018] [Indexed: 01/07/2023] Open
Abstract
Hox genes are expressed along the anterior-posterior body axis in a colinear fashion in the majority of bilaterians. Contrary to polyplacophorans, a group of aculiferan molluscs with conserved ancestral molluscan features, gastropods and cephalopods deviate from this pattern by expressing Hox genes in distinct morphological structures and not in a staggered fashion. Among conchiferans, scaphopods exhibit many similarities with gastropods, cephalopods and bivalves, however, the molecular developmental underpinnings of these similar traits remain unknown. We investigated Hox gene expression in developmental stages of the scaphopod Antalis entalis to elucidate whether these genes are involved in patterning morphological traits shared by their kin conchiferans. Scaphopod Hox genes are predominantly expressed in the foot and mantle but also in the central nervous system. Surprisingly, the scaphopod mid-stage trochophore exhibits a near-to staggered expression of all nine Hox genes identified. Temporal colinearity was not found and early-stage and late-stage trochophores, as well as postmetamorphic individuals, do not show any apparent traces of staggered expression. In these stages, Hox genes are expressed in distinct morphological structures such as the cerebral and pedal ganglia and in the shell field of early-stage trochophores. Interestingly, a re-evaluation of previously published data on early-stage cephalopod embryos and of the gastropod pre-torsional veliger shows that these developmental stages exhibit traces of staggered Hox expression. Considering our results and all gene expression and genomic data available for molluscs as well as other bilaterians, we suggest a last common molluscan ancestor with colinear Hox expression in predominantly ectodermal tissues along the anterior-posterior axis. Subsequently, certain Hox genes have been co-opted into the patterning process of distinct structures (apical organ or prototroch) in conchiferans.
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Affiliation(s)
- Tim Wollesen
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Sonia Victoria Rodríguez Monje
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - André Luiz de Oliveira
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Andreas Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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10
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Kobayashi G, Goto R, Takano T, Kojima S. Molecular phylogeny of Maldanidae (Annelida): Multiple losses of tube-capping plates and evolutionary shifts in habitat depth. Mol Phylogenet Evol 2018; 127:332-344. [DOI: 10.1016/j.ympev.2018.04.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 04/16/2018] [Accepted: 04/23/2018] [Indexed: 11/27/2022]
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11
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Budd GE, Jackson ISC. Ecological innovations in the Cambrian and the origins of the crown group phyla. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150287. [PMID: 26598735 PMCID: PMC4685591 DOI: 10.1098/rstb.2015.0287] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Simulation studies of the early origins of the modern phyla in the fossil record, and the rapid diversification that led to them, show that these are inevitable outcomes of rapid and long-lasting radiations. Recent advances in Cambrian stratigraphy have revealed a more precise picture of the early bilaterian radiation taking place during the earliest Terreneuvian Series, although several ambiguities remain. The early period is dominated by various tubes and a moderately diverse trace fossil record, with the classical ‘Tommotian’ small shelly biota beginning to appear some millions of years after the base of the Cambrian at ca 541 Ma. The body fossil record of the earliest period contains a few representatives of known groups, but most of the record is of uncertain affinity. Early trace fossils can be assigned to ecdysozoans, but deuterostome and even spiralian trace and body fossils are less clearly represented. One way of explaining the relative lack of clear spiralian fossils until about 536 Ma is to assign the various lowest Cambrian tubes to various stem-group lophotrochozoans, with the implication that the groundplan of the lophotrochozoans included a U-shaped gut and a sessile habit. The implication of this view would be that the vagrant lifestyle of annelids, nemerteans and molluscs would be independently derived from such a sessile ancestor, with potentially important implications for the homology of their sensory and nervous systems.
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Affiliation(s)
- Graham E Budd
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
| | - Illiam S C Jackson
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
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12
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Wollesen T, Rodríguez Monje SV, McDougall C, Degnan BM, Wanninger A. The ParaHox gene Gsx patterns the apical organ and central nervous system but not the foregut in scaphopod and cephalopod mollusks. EvoDevo 2015; 6:41. [PMID: 26715985 PMCID: PMC4693441 DOI: 10.1186/s13227-015-0037-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/17/2015] [Indexed: 11/21/2022] Open
Abstract
Background It has been hypothesized that the ParaHox gene Gsx patterned the foregut of the last common bilaterian ancestor. This notion was corroborated by Gsx expression in three out of four lophotrochozoan species, several ecdysozoans, and some deuterostomes. Remarkably, Gsx is also expressed in the bilaterian anterior-most central nervous system (CNS) and the gastropod and annelid apical organ. To infer whether these findings are consistent with other mollusks or even lophotrochozoans, we investigated Gsx expression in developmental stages of representatives of two other molluscan classes, the scaphopod Antalis entalis and the cephalopod Idiosepius notoides. Results Gsx is not expressed in the developing digestive tract of Antalis entalis and Idiosepius notoides. Instead, it is expressed in cells of the apical organ in the scaphopod trochophore and in two cells adjacent to this organ. Late-stage trochophores express Aen-Gsx in cells of the developing cerebral and pedal ganglia and in cells close to the pavilion, mantle, and foot. In postmetamorphic specimens, Aen-Gsx is expressed in the cerebral and pedal ganglia, the foot, and the nascent captacula. In early squid embryos, Ino-Gsx is expressed in the cerebral, palliovisceral, and optic ganglia. In late-stage embryos, Ino-Gsx is additionally expressed close to the eyes and in the supraesophageal and posterior subesophageal masses and optic lobes. Developmental stages close to hatching express Ino-Gsx only close to the eyes. Conclusions Our results suggest that Gsx expression in the foregut might not be a plesiomorphic trait of the Lophotrochozoa as insinuated previously. Since neither ecdysozoans nor deuterostomes express Gsx in their gut, a role in gut formation in the last common bilaterian ancestor appears unlikely. Gsx is consistently expressed in the bilaterian anterior-most CNS and the apical organ of lophotrochozoan larvae, suggesting a recruitment of Gsx into the formation of this organ in the Lophotrochozoa. The cephalopod posterior subesophageal mass and optic ganglia and the scaphopod pedal ganglia also express Gsx. In summary, Gsx expression only appears to be conserved in the anterior-most brain region during evolution. Accordingly, Gsx appears to have been recruited into the formation of other expression domains, e.g., the apical organ or the foregut, in some lophotrochozoans.
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Affiliation(s)
- Tim Wollesen
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | | | - Carmel McDougall
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Andreas Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
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13
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Sumner-Rooney LH, Schrödl M, Lodde-Bensch E, Lindberg DR, Heß M, Brennan GP, Sigwart JD. A neurophylogenetic approach provides new insight to the evolution of Scaphopoda. Evol Dev 2015; 17:337-46. [DOI: 10.1111/ede.12164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lauren H. Sumner-Rooney
- School of Biological Sciences; Queen's University Belfast; Northern Ireland
- Queen's University Marine Laboratory; Queen's University Belfast; Northern Ireland
| | - Michael Schrödl
- SNSB-Zoologische Staatssammlung M; ü; nchen; Germany
- Biozentrum; Ludwig-Maximilians-Universität München; Germany
| | | | - David R. Lindberg
- Department of Integrative Biology and Museum of Palaeontology; University of California; Berkeley CA USA
| | - Martin Heß
- Biozentrum; Ludwig-Maximilians-Universität München; Germany
| | - Gerard P. Brennan
- School of Biological Sciences; Queen's University Belfast; Northern Ireland
| | - Julia D. Sigwart
- School of Biological Sciences; Queen's University Belfast; Northern Ireland
- Queen's University Marine Laboratory; Queen's University Belfast; Northern Ireland
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14
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15
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Schrödl M, Stöger I. A review on deep molluscan phylogeny: old markers, integrative approaches, persistent problems. J NAT HIST 2014. [DOI: 10.1080/00222933.2014.963184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Takano T, Kano Y. Molecular phylogenetic investigations of the relationships of the echinoderm-parasite family Eulimidae within Hypsogastropoda (Mollusca). Mol Phylogenet Evol 2014; 79:258-69. [DOI: 10.1016/j.ympev.2014.06.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/16/2014] [Accepted: 06/21/2014] [Indexed: 10/25/2022]
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Allcock AL, Lindgren A, Strugnell J. The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review. J NAT HIST 2014. [DOI: 10.1080/00222933.2013.825342] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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The continuing debate on deep molluscan phylogeny: evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora). BIOMED RESEARCH INTERNATIONAL 2013; 2013:407072. [PMID: 24350268 PMCID: PMC3856133 DOI: 10.1155/2013/407072] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 08/08/2013] [Accepted: 08/23/2013] [Indexed: 11/17/2022]
Abstract
Molluscs are a diverse animal phylum with a formidable fossil record. Although there is little doubt about the monophyly of the eight extant classes, relationships between these groups are controversial. We analysed a comprehensive multilocus molecular data set for molluscs, the first to include multiple species from all classes, including five monoplacophorans in both extant families. Our analyses of five markers resolve two major clades: the first includes gastropods and bivalves sister to Serialia (monoplacophorans and chitons), and the second comprises scaphopods sister to aplacophorans and cephalopods. Traditional groupings such as Testaria, Aculifera, and Conchifera are rejected by our data with significant Approximately Unbiased (AU) test values. A new molecular clock indicates that molluscs had a terminal Precambrian origin with rapid divergence of all eight extant classes in the Cambrian. The recovery of Serialia as a derived, Late Cambrian clade is potentially in line with the stratigraphic chronology of morphologically heterogeneous early mollusc fossils. Serialia is in conflict with traditional molluscan classifications and recent phylogenomic data. Yet our hypothesis, as others from molecular data, implies frequent molluscan shell and body transformations by heterochronic shifts in development and multiple convergent adaptations, leading to the variable shells and body plans in extant lineages.
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Comparative neuroanatomy of Caudofoveata, Solenogastres, Polyplacophora, and Scaphopoda (Mollusca) and its phylogenetic implications. ZOOMORPHOLOGY 2012. [DOI: 10.1007/s00435-012-0150-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Dzik J. Brachiopod Identity of the Alleged Monoplacophoran Ancestors of Cephalopods. MALACOLOGIA 2010. [DOI: 10.4002/040.052.0107] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Simone LRL. Comparative morphology among representatives of main taxa of Scaphopoda and basal protobranch Bivalvia (Mollusca). PAPÉIS AVULSOS DE ZOOLOGIA 2009. [DOI: 10.1590/s0031-10492009003200001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This study deals with detailed morphology and anatomy of 4 species of Scaphopoda and 5 species of protobranch Bivalvia. Both classes are traditionally grouped in the taxon Diasoma, which has been questioned by different methodologies, such as molecular and developmental. This study is developed under a phylogenetic methodology with the main concern in performing it in an intelligible and testable methodology. The analyzed Scaphopoda species came from the Brazilian coast and belong to the family Dentaliidae [(1) Coccodentalium carduus; (2) Paradentalium disparile] and Gadiliidae; [(3) Polyschides noronhensis, n. sp. from Fernando de Noronha Archipelago; (4) Gadila braziliensis]. These species represent the main branches of the class Scaphopoda. From protobranch bivalves, representatives of the families Solemyidae [(5) Solemya occidentalis, from Florida; S. notialis, n. sp. from S.E. Brazil], Nuculanidae [(6) Propeleda carpentieri from Florida], and Nuculidae [(7) Ennucula puelcha, from south Brazil] are included. These species represent the main branches of the basal Bivalvia. The descriptions on the anatomy of S. occidentalis and of P. carpentieri are published elsewhere. The remaining are included here, for which a complete taxonomical treatment is performed. Beyond these species, representatives of other taxa are operationally included as part of the ingroup (indices are then shared with them), as a procedure to test the morphological monophyly of Diasoma. These taxa are: two lamellibranch bivalves [(8) Barbatia - Arcidae; (9) Serratina - Tellinidae; both published elsewhere;, and Propilidium (10) Patellogastropoda, and (11) Nautilus, basal Cephalopoda, based on basal taxa. The effective outgroups are (12) Neopilina (Monoplacophora) and (13) Hanleya (Polyplacophora). The phylogenetic analysis based on morphology revealed that the taxon Diasoma is supported by 14 synapomorphies, and is separated from Cyrtosoma (Gastropoda + Cephalopoda). Although they are not the main goal of this paper, the taxa Scaphopoda and Bivalvia are supported by 8 and by 7 synapomorphies respectively. The taxon Protobranchia resulted paraphyletic. Both scaphopod orders resulted monophyletic. The obtained cladogram is: ((((Coccodentalium carduus - Paradentalium disparile) (Polyschides noronhensis - Gadila brasiliensis)) ((Solemya occidentalis - S. notialis) (Propeleda carpenteri (Ennucula puelcha (Barbatia cancellaria - Serratina capsoides))))) (Propilidium curumim - Nautilus pompilius - Lolliguncula brevis)).
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Simone LRL. Comparative morphology among representatives of main taxa of Scaphopoda and basal protobranch Bivalvia (Mollusca). PAPÉIS AVULSOS DE ZOOLOGIA 2009. [DOI: 10.4103/2277-8632.185432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
This study deals with detailed morphology and anatomy of 4 species of Scaphopoda and 5 species of protobranch Bivalvia. Both classes are traditionally grouped in the taxon Diasoma, which has been questioned by different methodologies, such as molecular and developmental. This study is developed under a phylogenetic methodology with the main concern in performing it in an intelligible and testable methodology. The analyzed Scaphopoda species came from the Brazilian coast and belong to the family Dentaliidae [(1) Coccodentalium carduus; (2) Paradentalium disparile] and Gadiliidae; [(3) Polyschides noronhensis, n. sp. from Fernando de Noronha Archipelago; (4) Gadila braziliensis]. These species represent the main branches of the class Scaphopoda. From protobranch bivalves, representatives of the families Solemyidae [(5) Solemya occidentalis, from Florida; S. notialis, n. sp. from S.E. Brazil], Nuculanidae [(6) Propeleda carpentieri from Florida], and Nuculidae [(7) Ennucula puelcha, from south Brazil] are included. These species represent the main branches of the basal Bivalvia. The descriptions on the anatomy of S. occidentalis and of P. carpentieri are published elsewhere. The remaining are included here, for which a complete taxonomical treatment is performed. Beyond these species, representatives of other taxa are operationally included as part of the ingroup (indices are then shared with them), as a procedure to test the morphological monophyly of Diasoma. These taxa are: two lamellibranch bivalves [(8) Barbatia - Arcidae; (9) Serratina - Tellinidae; both published elsewhere;, and Propilidium (10) Patellogastropoda, and (11) Nautilus, basal Cephalopoda, based on basal taxa. The effective outgroups are (12) Neopilina (Monoplacophora) and (13) Hanleya (Polyplacophora). The phylogenetic analysis based on morphology revealed that the taxon Diasoma is supported by 14 synapomorphies, and is separated from Cyrtosoma (Gastropoda + Cephalopoda). Although they are not the main goal of this paper, the taxa Scaphopoda and Bivalvia are supported by 8 and by 7 synapomorphies respectively. The taxon Protobranchia resulted paraphyletic. Both scaphopod orders resulted monophyletic. The obtained cladogram is: ((((Coccodentalium carduus - Paradentalium disparile) (Polyschides noronhensis - Gadila brasiliensis)) ((Solemya occidentalis - S. notialis) (Propeleda carpenteri (Ennucula puelcha (Barbatia cancellaria - Serratina capsoides))))) (Propilidium curumim - Nautilus pompilius - Lolliguncula brevis)).
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Kano Y. Vetigastropod phylogeny and a new concept of Seguenzioidea: independent evolution of copulatory organs in the deep-sea habitats. ZOOL SCR 2007. [DOI: 10.1111/j.1463-6409.2007.00316.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Giribet G, Okusu A, Lindgren AR, Huff SW, Schrödl M, Nishiguchi MK. Evidence for a clade composed of molluscs with serially repeated structures: monoplacophorans are related to chitons. Proc Natl Acad Sci U S A 2006; 103:7723-8. [PMID: 16675549 PMCID: PMC1472512 DOI: 10.1073/pnas.0602578103] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Indexed: 11/18/2022] Open
Abstract
Monoplacophorans are among the rarest members of the phylum Mollusca. Previously only known from fossils since the Cambrian, the first living monoplacophoran was discovered during the famous second Galathea deep-sea expedition. The anatomy of these molluscs shocked the zoological community for presenting serially repeated gills, nephridia, and eight sets of dorsoventral pedal retractor muscles. Seriality of organs in supposedly independent molluscan lineages, i.e., in chitons and the deep-sea living fossil monoplacophorans, was assumed to be a relic of ancestral molluscan segmentation and was commonly accepted to support a direct relationship with annelids. We were able to obtain one specimen of a monoplacophoran Antarctic deep-sea species for molecular study. The first molecular data on monoplacophorans, analyzed together with the largest data set of molluscs ever assembled, clearly illustrate that monoplacophorans and chitons form a clade. This "Serialia" concept may revolutionize molluscan systematics and may have important implications for metazoan evolution as it allows for new interpretations for primitive segmentation in molluscs.
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Affiliation(s)
- Gonzalo Giribet
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 16 Divinity Avenue, BioLabs 1119, Cambridge, MA 02138, USA.
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Knudsen B, Kohn AB, Nahir B, McFadden CS, Moroz LL. Complete DNA sequence of the mitochondrial genome of the sea-slug, Aplysia californica: conservation of the gene order in Euthyneura. Mol Phylogenet Evol 2005; 38:459-69. [PMID: 16230032 DOI: 10.1016/j.ympev.2005.08.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Revised: 08/08/2005] [Accepted: 08/27/2005] [Indexed: 11/28/2022]
Abstract
We have sequenced and characterized the complete mitochondrial genome of the sea slug, Aplysia californica, an important model organism in experimental biology and a representative of Anaspidea (Opisthobranchia, Gastropoda). The mitochondrial genome of Aplysia is in the small end of the observed sizes of animal mitochondrial genomes (14,117 bp, NCBI Accession No. NC_005827). The Aplysia genome, like most other mitochondrial genomes, encodes genes for 2 ribosomal subunit RNAs (small and large rRNAs), 22 tRNAs, and 13 protein subunits (cytochrome c oxidase subunits 1-3, cytochrome b apoenzyme, ATP synthase subunits 6 and 8, and NADH dehydrogenase subunits 1-6 and 4L). The gene order is virtually identical between opisthobranchs and pulmonates, with the majority of differences arising from tRNA translocations. In contrast, the gene order from representatives of basal gastropods and other molluscan classes is significantly different from opisthobranchs and pulmonates. The Aplysia genome was compared to all other published molluscan mitochondrial genomes and phylogenetic analyses were carried out using a concatenated protein alignment. Phylogenetic analyses using maximum likelihood based analyses of the well aligned regions of the protein sequences support both monophyly of Euthyneura (a group including both the pulmonates and opisthobranchs) and Opisthobranchia (as a more derived group). The Aplysia mitochondrial genome sequenced here will serve as an important platform in both comparative and neurobiological studies using this model organism.
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Affiliation(s)
- Bjarne Knudsen
- Department of Zoology, University of Florida, 223 Bartram Hall, Gainesville, 32611, USA
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26
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Passamaneck YJ, Schander C, Halanych KM. Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences. Mol Phylogenet Evol 2005; 32:25-38. [PMID: 15186794 DOI: 10.1016/j.ympev.2003.12.016] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2003] [Revised: 12/12/2003] [Indexed: 11/23/2022]
Abstract
The Mollusca represent one of the most morphologically diverse animal phyla, prompting a variety of hypotheses on relationships between the major lineages within the phylum based upon morphological, developmental, and paleontological data. Analyses of small-ribosomal RNA (SSU rRNA) gene sequence have provided limited resolution of higher-level relationships within the Mollusca. Recent analyses suggest large-subunit (LSU) rRNA gene sequences are useful in resolving deep-level metazoan relationships, particularly when combined with SSU sequence. To this end, LSU (approximately 3.5 kb in length) and SSU (approximately 2 kb) sequences were collected for 33 taxa representing the major lineages within the Mollusca to improve resolution of intraphyletic relationships. Although the LSU and combined LSU+SSU datasets appear to hold potential for resolving branching order within the recognized molluscan classes, low bootstrap support was found for relationships between the major lineages within the Mollusca. LSU+SSU sequences also showed significant levels of rate heterogeneity between molluscan lineages. The Polyplacophora, Gastropoda, and Cephalopoda were each recovered as monophyletic clades with the LSU+SSU dataset. While the Bivalvia were not recovered as monophyletic clade in analyses of the SSU, LSU, or LSU+SSU, the Shimodaira-Hasegawa test showed that likelihood scores for these results did not differ significantly from topologies where the Bivalvia were monophyletic. Analyses of LSU sequences strongly contradict the widely accepted Diasoma hypotheses that bivalves and scaphopods are closely related to one another. The data are consistent with recent morphological and SSU analyses suggesting scaphopods are more closely related to gastropods and cephalopods than to bivalves. The dataset also presents the first published DNA sequences from a neomeniomorph aplacophoran, a group considered critical to our understanding of the origin and early radiation of the Mollusca.
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Affiliation(s)
- Yale J Passamaneck
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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Affiliation(s)
- Kenneth M. Halanych
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849;
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Dreyer H, Steiner G. The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca). Mol Phylogenet Evol 2004; 31:605-17. [PMID: 15062797 DOI: 10.1016/j.ympev.2003.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2003] [Revised: 07/21/2003] [Indexed: 10/27/2022]
Abstract
Comparisons of mitochondrial gene sequences and gene arrangements can be informative for reconstructing high-level phylogenetic relationships. We determined the complete sequence of the mitochondrial genome of Siphonodentalium lobatum, (Mollusca, Scaphopoda). With only 13,932 bases, it is the shortest molluscan mitochondrial genome reported so far. The genome contains the usual 13 protein-coding genes, two rRNA and 22 tRNA genes. The ATPase subunit 8 gene is exceptionally short. Several transfer RNAs show truncated TpsiC arms or DHU arms. The gene arrangement of S. lobatum is markedly different from all other known molluscan mitochondrial genomes and shows low similarity even to an unpublished gene order of a dentaliid scaphopod. Phylogenetic analyses of all available complete molluscan mitochondrial genomes based on amino acid sequences of 11 protein-coding genes yield trees with low support for the basal branches. None of the traditionally accepted molluscan taxa and phylogenies are recovered in all analyses, except for the euthyneuran Gastropoda. S. lobatum appears as the sister taxon to two of the three bivalve species. We conclude that the deep molluscan phylogeny is probably beyond the resolution of mitochondrial protein sequences. Moreover, assessing the phylogenetic signal in gene order data requires a much larger taxon sample than is currently available, given the exceptional diversity of this character set in the Mollusca.
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Affiliation(s)
- Hermann Dreyer
- Institute of Zoology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
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DREYER HERMANN, STEINER GERHARD, HARPER ELIZABETHM. Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences. Zool J Linn Soc 2003. [DOI: 10.1046/j.1096-3642.2003.00065.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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