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González-Delgado S, Rodríguez-Flores PC, Giribet G. Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia). Mol Phylogenet Evol 2024; 198:108129. [PMID: 38878989 DOI: 10.1016/j.ympev.2024.108129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/15/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024]
Abstract
Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.
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Affiliation(s)
- Sara González-Delgado
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Santa Cruz de Tenerife, Canary Islands, Spain; Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paula C Rodríguez-Flores
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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2
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Batistão AR, Audino JA, Passos FD. Comparative anatomy of siphons in tellinoidean clams (Bivalvia, Tellinoidea). J Morphol 2024; 285:e21762. [PMID: 39129184 DOI: 10.1002/jmor.21762] [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: 06/17/2024] [Revised: 08/01/2024] [Accepted: 08/03/2024] [Indexed: 08/13/2024]
Abstract
Siphons are tubular organs formed by fusion and posterior extension of the marginal mantle folds. They are supposed to have performed key roles in the evolution of bivalves by enabling these animals to occupy several ecological niches. However, anatomical details of these organs are scarce for one of the most diverse lineages of tropical bivalves, the superfamily Tellinoidea. We investigated the siphonal morphology of 15 species, sampling five tellinoidean families, by integrating scanning electron microscopy, confocal microscopy, and histology. The siphons revealed variations in length, pigmentation, tentacles, papillae, and number of nerve cords. Due to the presence of sensorial structures, such as papillae and tentacles, we reclassify the siphons of Tellinoidea from type A to A+. Additional anatomical patterns were identified at family and genus levels. For example, the incurrent siphon shorter than the excurrent and 24 tentacles are putative synapomorphies of Donacidae. We also highlight shared siphonal traits between Donacidae and Solecurtidae as well as between Semelidae and Tellinidae. In addition, our data support the idea of Psammobiidae as a paraphyletic lineage. Overall, we provide an extensive comparative data set on siphonal traits with significant relevance for bivalve taxonomy, functional anatomy, and evolutionary investigations.
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Affiliation(s)
- Alan R Batistão
- Department of Animal Biology, State University of Campinas, Campinas, São Paulo, Brazil
| | - Jorge A Audino
- Department of Zoology, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Flávio D Passos
- Department of Animal Biology, State University of Campinas, Campinas, São Paulo, Brazil
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3
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Gao Q, Tang Y, Zhang J. A new species of the genus Yoldiella (Bivalvia, Protobranchia, Yoldiidae) from Haima Cold Seep, South China Sea, China. Zookeys 2024; 1204:223-240. [PMID: 38882561 PMCID: PMC11176815 DOI: 10.3897/zookeys.1204.121088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 05/08/2024] [Indexed: 06/18/2024] Open
Abstract
In present study, a previously unidentified but frequently encountered species of deep-sea protobranch, Yoldiellahaimaensis sp. nov., is described new to science from the Haima Cold Seep on the northwestern slope of the South China Sea. A morphological analysis confirmed that this species belongs to a previously undescribed species of the genus Yoldiella A.E. Verrill & K.J. Bush, 1897. It differs morphologically from other known species within the genus in its shell shape, degree of inflation, beaks, and number of hinge teeth. Furthermore, we sequenced three gene segments of Y.haimaensis sp. nov., comprising a nuclear ribosomal gene (18S rRNA), a nuclear protein-coding gene (histone H3), and a mitochondrial gene (cytochrome c oxidase subunit I, COI). Our phylogenetic analysis performed on the superfamily Nuculanoidea and family Yoldiidae indicates that the genus Yoldiella is non-monophyletic, and the widely recognized families within the superfamily Nuculanoidea are also not monophyletic. Our results provide molecular insights into the Protobranchia and highlight the necessity for further samples and data to revise the classification of families and genera within the superfamily using an integrative approach that combines morphological analysis and molecular data.
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Affiliation(s)
- Qi Gao
- School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China Institute of Oceanology, Chinese Academy of Sciences Qingdao China
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China Qingdao Agricultural University Qingdao China
| | - Yan Tang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China Qingdao Agricultural University Qingdao China
| | - Junlong Zhang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China Qingdao Agricultural University Qingdao China
- Marine Biological Museum, Chinese Academy of Sciences, Qingdao 266071, China Marine Biological Museum, Chinese Academy of Sciences Qingdao China
- University of Chinese Academy of Sciences, Beijing 100049, China University of Chinese Academy of Sciences Beijing China
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4
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Zhou Z, Song Y, Zheng Z, Liu Y, Yao H, Rao X, Lin G. The Complete Mitochondrial Genome and Phylogenetic Analysis of the Freshwater Shellfish Novaculina chinensis (Bivalvia: Pharidae). Int J Mol Sci 2023; 25:67. [PMID: 38203240 PMCID: PMC10778892 DOI: 10.3390/ijms25010067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Razor clams, belonging to the Pharidae and Solenidae families, are ecologically and economically important; however, very little research has been conducted on the Pharidae family. The genus Novaculina is a marine-derived freshwater lineage, and Novaculina chinensis is a rare freshwater species of the Pharidae family. In order to understand the phylogenetic relationships of N. chinensis, we sequenced the mitochondrial genome of the genus Novaculina, which is 16,262 bp in length and consists of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The phylogenetic relationships of 69 Imparidentian mitochondrial genomes (mitogenomes) indicated that N. chineisis is closely related to Sinonovacula constricta of the order Adapedonta. Our study also found that the Ka/Ks ratios of 12 protein-coding genes in the Pharidae family are lower than one, indicating the occurrence of negative purification selection. Morphological observations of the siphons of N. chinensis, Novaculina myanmarensis, and Novaculina gangetica indicate that N. chinensis may be the ancestral clade of the genus Novaculina, which has not been proposed in previous studies. Our study provides useful molecular information on the phylogenetic and evolutionary relationships of Pharidae and also contributes to the conservation and management of the germplasm resources of N. chinensis.
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Affiliation(s)
| | | | | | | | | | - Xiaozhen Rao
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (Z.Z.); (Y.S.); (Z.Z.); (Y.L.); (H.Y.)
| | - Gang Lin
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (Z.Z.); (Y.S.); (Z.Z.); (Y.L.); (H.Y.)
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5
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Simmons M, Horbelt N, Sverko T, Scoppola E, Jackson DJ, Harrington MJ. Invasive mussels fashion silk-like byssus via mechanical processing of massive horizontally acquired coiled coils. Proc Natl Acad Sci U S A 2023; 120:e2311901120. [PMID: 37983489 PMCID: PMC10691215 DOI: 10.1073/pnas.2311901120] [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: 07/12/2023] [Accepted: 10/11/2023] [Indexed: 11/22/2023] Open
Abstract
Zebra and quagga mussels (Dreissena spp.) are invasive freshwater biofoulers that perpetrate devastating economic and ecological impact. Their success depends on their ability to anchor onto substrates with protein-based fibers known as byssal threads. Yet, compared to other mussel lineages, little is understood about the proteins comprising their fibers or their evolutionary history. Here, we investigated the hierarchical protein structure of Dreissenid byssal threads and the process by which they are fabricated. Unique among bivalves, we found that threads possess a predominantly β-sheet crystalline structure reminiscent of spider silk. Further analysis revealed unexpectedly that the Dreissenid thread protein precursors are mechanoresponsive α-helical proteins that are mechanically processed into β-crystallites during thread formation. Proteomic analysis of the byssus secretory organ and byssus fibers revealed a family of ultrahigh molecular weight (354 to 467 kDa) asparagine-rich (19 to 20%) protein precursors predicted to form α-helical coiled coils. Moreover, several independent lines of evidence indicate that the ancestral predecessor of these proteins was likely acquired via horizontal gene transfer. This chance evolutionary event that transpired at least 12 Mya has endowed Dreissenids with a distinctive and effective fiber formation mechanism, contributing significantly to their success as invasive species and possibly, inspiring new materials design.
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Affiliation(s)
- Miriam Simmons
- Department of Chemistry, McGill University, Montreal, QCH3A 0B8, Canada
| | - Nils Horbelt
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam14476, Germany
| | - Tara Sverko
- Department of Chemistry, McGill University, Montreal, QCH3A 0B8, Canada
| | - Ernesto Scoppola
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam14476, Germany
| | - Daniel J. Jackson
- Department of Geobiology, Geoscience Center, University of Göttingen, Göttingen37077, Germany
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Gerdol M, Nerelli DE, Martelossi N, Ogawa Y, Fujii Y, Pallavicini A, Ozeki Y. Taxonomic Distribution and Molecular Evolution of Mytilectins. Mar Drugs 2023; 21:614. [PMID: 38132935 PMCID: PMC10744619 DOI: 10.3390/md21120614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023] Open
Abstract
R-type lectins are a widespread group of sugar-binding proteins found in nearly all domains of life, characterized by the presence of a carbohydrate-binding domain that adopts a β-trefoil fold. Mytilectins represent a recently described subgroup of β-trefoil lectins, which have been functionally characterized in a few mussel species (Mollusca, Bivalvia) and display attractive properties, which may fuel the development of artificial lectins with different biotechnological applications. The detection of different paralogous genes in mussels, together with the description of orthologous sequences in brachiopods, supports the formal description of mytilectins as a gene family. However, to date, an investigation of the taxonomic distribution of these lectins and their molecular diversification and evolution was still lacking. Here, we provide a comprehensive overview of the evolutionary history of mytilectins, revealing an ancient monophyletic evolutionary origin and a very broad but highly discontinuous taxonomic distribution, ranging from heteroscleromorphan sponges to ophiuroid and crinoid echinoderms. Moreover, the overwhelming majority of mytilectins display a chimera-like architecture, which combines the β-trefoil carbohydrate recognition domain with a C-terminal pore-forming domain, suggesting that the simpler structure of most functionally characterized mytilectins derives from a secondary domain loss.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Daniela Eugenia Nerelli
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Nicola Martelossi
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Yukiko Ogawa
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo 859-3298, Japan
| | - Yuki Fujii
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo 859-3298, Japan
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Yasuhiro Ozeki
- Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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Li Y, He X, Lin Y, Li YX, Kamenev GM, Li J, Qiu JW, Sun J. Reduced chemosymbiont genome in the methane seep thyasirid and the cooperated metabolisms in the holobiont under anaerobic sediment. Mol Ecol Resour 2023; 23:1853-1867. [PMID: 37486074 DOI: 10.1111/1755-0998.13846] [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: 04/07/2023] [Revised: 06/16/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Previous studies have deciphered the genomic basis of host-symbiont metabolic complementarity in vestimentiferans, bathymodioline mussels, vesicomyid clams and Alviniconcha snails, yet little is known about the chemosynthetic symbiosis in Thyasiridae-a family of Bivalvia regarded as an excellent model in chemosymbiosis research due to their wide distribution in both deep-sea and shallow-water habitats. We report the first circular thyasirid symbiont genome, named Candidatus Ruthturnera sp. Tsphm01, with a size of 1.53 Mb, 1521 coding genes and 100% completeness. Compared to its free-living relatives, Ca. Ruthturnera sp. Tsphm01 genome is reduced, lacking components for chemotaxis, citric acid cycle and de novo biosynthesis of small molecules (e.g. amino acids and cofactors), indicating it is likely an obligate intracellular symbiont. Nevertheless, the symbiont retains complete genomic components of sulphur oxidation and assimilation of inorganic carbon, and these systems were highly and actively expressed. Moreover, the symbiont appears well-adapted to anoxic environment, including capable of anaerobic respiration (i.e. reductions of DMSO and nitrate) and possession of a low oxygen-adapted type of cytochrome c oxidase. Analysis of the host transcriptome revealed its metabolic complementarity to the incomplete metabolic pathways of the symbiont and the acquisition of nutrients from the symbiont via phagocytosis and exosome. By providing the first complete genome of reduced size in a thyasirid symbiont, this study enhances our understanding of the diversity of symbiosis that has enabled bivalves to thrive in chemosynthetic habitats. The resources will be widely used in phylogenetic, geographic and evolutionary studies of chemosynthetic bacteria and bivalves.
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Affiliation(s)
- Yunlong Li
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Xing He
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Yuxuan Lin
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yi-Xuan Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Gennady M Kamenev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation
| | - Jiying Li
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
- Laoshan Laboratory, Qingdao, China
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8
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Wang Y, Yang Y, Kong L, Sasaki T, Li Q. Phylogenomic resolution of Imparidentia (Mollusca: Bivalvia) diversification through mitochondrial genomes. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:326-336. [PMID: 37637250 PMCID: PMC10449738 DOI: 10.1007/s42995-023-00178-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 04/25/2023] [Indexed: 08/29/2023]
Abstract
Despite significant advances in the phylogenomics of bivalves over the past decade, the higher-level phylogeny of Imparidentia (a superorder of Heterodonta) remains elusive. Here, a total of five new mitochondrial sequences (Chama asperella, Chama limbula, Chama dunkeri, Barnea manilensis and Ctena divergens) was added to provide resolution in nodes that required additional study. Although the monophyly of Lucinida remains less clear, the results revealed the overall backbone of the Imparidentia tree and the monophyly of Imparidentia. Likewise, most relationships among the five major Imparidentia lineages-Lucinida, Cardiida, Adapedonta, Myida and Venerida-were addressed with a well-supported topology. Basal relationships of Imparidentia recovered Lucinidae as the sister group to all remaining imparidentian taxa. Thyasiridae is a sister group to other imparidentian bivalves (except Lucinidae species) which is split into Cardiida, Adapedonta and the divergent clade of Neoheterodontei. Neoheterodontei was comprised of Venerida and Myida, the former of which now also contains Chamidae as the sister group to all the remaining venerid taxa. Moreover, molecular divergence times were inferred by calibrating nine nodes in the Imparidentia tree of life by extinct taxa. The origin of these major clades ranged from Ordovician to Permian with the diversification through the Palaeozoic to Mesozoic. Overall, the results obtained in this study demonstrate a better-resolved Imparidentia phylogeny based on mitochondrial genomes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00178-x.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
| | - Yi Yang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266237 China
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9
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Collins KS, Edie SM, Jablonski D. Convergence and contingency in the evolution of a specialized mode of life: multiple origins and high disparity of rock-boring bivalves. Proc Biol Sci 2023; 290:20221907. [PMID: 36750185 PMCID: PMC9904949 DOI: 10.1098/rspb.2022.1907] [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: 09/22/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Evolutionary adaptation to novel, specialized modes of life is often associated with a close mapping of form to the new function, resulting in narrow morphological disparity. For bivalve molluscs, endolithy (rock-boring) has biomechanical requirements thought to diverge strongly from those of ancestral functions. However, endolithy in bivalves has originated at least eight times. Three-dimensional morphometric data representing 75 species from approximately 94% of extant endolithic genera and families, along with 310 non-endolithic species in those families, show that endolithy is evolutionarily accessible from many different morphological starting points. Although some endoliths appear to converge on certain shell morphologies, the range of endolith shell form is as broad as that belonging to any other bivalve substrate use. Nevertheless, endolithy is a taxon-poor function in Bivalvia today. This limited richness does not derive from origination within source clades having significantly low origination or high extinction rates, and today's endoliths are not confined to low-diversity biogeographic regions. Instead, endolithy may be limited by habitat availability. Both determinism (as reflected by convergence among distantly related taxa) and contingency (as reflected by the endoliths that remain close to the disparate morphologies of their source clades) underlie the occupation of endolith morphospace.
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Affiliation(s)
| | - Stewart M. Edie
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - David Jablonski
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
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10
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Salas C, Bueno-Pérez JDD, López-Téllez JF, Checa AG. Form and function of the mantle edge in Protobranchia (Mollusca: Bivalvia). ZOOLOGY 2022; 153:126027. [PMID: 35809463 DOI: 10.1016/j.zool.2022.126027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/02/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022]
Abstract
We analyzed, by optical and transmission electron microscopy, the morphology and function of the mantle edge, including the formation of the periostracum, of ten species of protobranchs. Five species from the order Nuculida, four species from the order Nuculanida and one species from the order Solemyida were studied. A second outer fold, which seems to function as a template for the internal marginal crenulations of the valves, is present in the crenulated species of Nucula. The minute non-crenulated Ennucula aegeensis shows the glandular basal cells displaced toward the periostracal groove, resembling a minute additional fold between the outer and middle folds. Intense secretion of glycocalyx, together with active uptake of particles, have been observed in the inner epithelium of the middle mantle fold and the whole epithelium of the inner mantle fold in all the studied species. Contrary to the rest of the bivalves, all the protobranchs analyzed have two basal cells involved in the formation of the external nanometric pellicle of the periostracum, a character that would support the monophyly of protobranchs. A three-layered pattern is the general rule for the periostracum in protobranchs, like for other bivalves. The presence of pouches of translucent layer inside the tanned dark layer under periostracal folds is characteristic of the species with a folded periostracum; its function is unclear but could give flexibility to the periostracum. The non-nacreous internal shell layer and the presence of translucent pouches under periostracal folds in Sarepta speciosa resemble those found in nuculanids. However, the free periostracum is rather similar to those of N. hanleyi and E. aegeensis, with a continuous vesicular layer. All the latter supports the inclusion of Sarepta in the order Nuculanida but could indicate either a basal lineage or that the translucent vesicular layer is an adaptive trait.
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Affiliation(s)
- Carmen Salas
- Departamento de Biología Animal, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; Instituto de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Centro de Experimentación Grice-Hutchinson, 29004 Málaga, Spain.
| | | | - Juan Félix López-Téllez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Campanillas, Málaga.
| | - Antonio G Checa
- Departamento de Estratigrafía y Paleontología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, 18100 Armilla, Spain.
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11
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Shimizu K, Takeuchi T, Negishi L, Kurumizaka H, Kuriyama I, Endo K, Suzuki M. Evolution of EGF-like and Zona pellucida domains containing shell matrix proteins in mollusks. Mol Biol Evol 2022; 39:6633355. [PMID: 35796746 PMCID: PMC9290575 DOI: 10.1093/molbev/msac148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several types of shell matrix proteins (SMPs) have been identified in molluskan shells. Their diversity is the consequence of various molecular processes, including domain shuffling and gene duplication. However, the evolutionary origin of most SMPs remains unclear. In this study, we investigated the evolutionary process EGF-like and zona pellucida (ZP) domains containing SMPs. Two types of the proteins (EGF-like protein (EGFL) and EGF-like and ZP domains containing protein (EGFZP)) were found in the pearl oyster, Pinctada fucata. In contrast, only EGFZP was identified in the gastropods. Phylogenetic analysis and genomic arrangement studies showed that EGFL and EGFZP formed a clade in bivalves, and their encoding genes were localized in tandem repeats on the same scaffold. In P. fucata, EGFL genes were expressed in the outer part of mantle epithelial cells are related to the calcitic shell formation. However, in both P. fucata and the limpet Nipponacmea fuscoviridis, EGFZP genes were expressed in the inner part of the mantle epithelial cells are related to aragonitic shell formation. Furthermore, our analysis showed that in P. fucata, the ZP domain interacts with eight SMPs that have various functions in the nacreous shell mineralization. The data suggest that the ZP domain can interact with other SMPs, and EGFL evolution in pterimorph bivalves represents an example of neo-functionalization that involves the acquisition of a novel protein through gene duplication.
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Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Isao Kuriyama
- Mie Prefecture Fisheries Research Institute, 3564-3 Hamajima, Hamajima-cho, Shima-city, Mie 517-0404, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
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12
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Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks. Sci Rep 2022; 12:11040. [PMID: 35773462 PMCID: PMC9247169 DOI: 10.1038/s41598-022-15076-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Mito-nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia.
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13
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Salamanca-Díaz DA, Ritschard EA, Schmidbaur H, Wanninger A. Comparative Single-Cell Transcriptomics Reveals Novel Genes Involved in Bivalve Embryonic Shell Formation and Questions Ontogenetic Homology of Molluscan Shell Types. Front Cell Dev Biol 2022; 10:883755. [PMID: 35813198 PMCID: PMC9261976 DOI: 10.3389/fcell.2022.883755] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/19/2022] [Indexed: 12/29/2022] Open
Abstract
Mollusks are known for their highly diverse repertoire of body plans that often includes external armor in form of mineralized hardparts. Representatives of the Conchifera, one of the two major lineages that comprises taxa which originated from a uni-shelled ancestor (Monoplacophora, Gastropoda, Cephalopoda, Scaphopoda, Bivalvia), are particularly relevant regarding the evolution of mollusk shells. Previous studies have found that the shell matrix of the adult shell (teleoconch) is rapidly evolving and that the gene set involved in shell formation is highly taxon-specific. However, detailed annotation of genes expressed in tissues involved in the formation of the embryonic shell (protoconch I) or the larval shell (protoconch II) are currently lacking. Here, we analyzed the genetic toolbox involved in embryonic and larval shell formation in the quagga mussel Dreissena rostriformis using single cell RNA sequencing. We found significant differences in genes expressed during embryonic and larval shell secretion, calling into question ontogenetic homology of these transitory bivalve shell types. Further ortholog comparisons throughout Metazoa indicates that a common genetic biomineralization toolbox, that was secondarily co-opted into molluscan shell formation, was already present in the last common metazoan ancestor. Genes included are engrailed, carbonic anhydrase, and tyrosinase homologs. However, we found that 25% of the genes expressed in the embryonic shell field of D. rostriformis lack an ortholog match with any other metazoan. This indicates that not only adult but also embryonic mollusk shells may be fast-evolving structures. We raise the question as to what degree, and on which taxonomic level, the gene complement involved in conchiferan protoconch formation may be lineage-specific or conserved across taxa.
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Affiliation(s)
- David A. Salamanca-Díaz
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Elena A. Ritschard
- Division of Molecular Evolution and Development, Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Hannah Schmidbaur
- Division of Molecular Evolution and Development, Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Andreas Wanninger
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- *Correspondence: Andreas Wanninger,
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14
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Crouch NMA, Edie SM, Collins KS, Bieler R, Jablonski D. Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families. Proc Biol Sci 2021; 288:20212178. [PMID: 34847770 PMCID: PMC8634622 DOI: 10.1098/rspb.2021.2178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
Analyses of evolutionary dynamics depend on how phylogenetic data are time-scaled. Most analyses of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. This contrasts with budding, where nodes are calibrated using the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale evaluation of how branching models affect macroevolutionary analyses. We time-calibrated 91% of nodes, ranging in age from 2.59 to 485 Ma, in a phylogeny of 97 extant bivalve families. Allowing budding-based calibrations minimizes conflict between the tree and observed fossil record, and reduces the summed duration of inferred 'ghost lineages' from 6.76 billion years (Gyr; bifurcating model) to 1.00 Gyr (budding). Adding 31 extinct paraphyletic families raises ghost lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but incorporates more information to date divergences between lineages. Macroevolutionary analyses under a bifurcating model conflict with other palaeontological evidence on the magnitude of the end-Palaeozoic extinction, and strongly reduce Cenozoic diversification. Consideration of different branching models is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, a budding model appears more appropriate.
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Affiliation(s)
- Nicholas M. A. Crouch
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Stewart M. Edie
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | | | - Rüdiger Bieler
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - David Jablonski
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
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15
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Paz-Sedano S, Díaz-Agras G, Gosliner TM, Pola M. Revealing morphological characteristics of Goniodorididae genera (Mollusca: Nudibranchia). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00508-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractDetailed knowledge of the anatomy of the species is an essential element in taxonomic studies, since it allows the comparison and differentiation of separate groups of taxa. It becomes especially important when considering type species, as the subsequent identification of the species that compose the taxa is based on its characteristics, considered common in the group. However, despite its relevance, there are still numerous species without detailed descriptions, being especially significant among invertebrates. The family Goniodorididae is a little-known group of nudibranchs that includes eight recognized genera: Okenia, Goniodoris, Ancula, Lophodoris, Spahria, Trapania, Goniodoridella and Murphydoris. Several of their species are not completely described, including type species, and the systematics of the family is still unclear. Here we study in detail the external morphology and internal anatomy of the type species of five of the eight Goniodorididae genera using microcomputed tomography and scanning electron microscopy. We include the species Okenia elegans, Goniodoris nodosa, Ancula gibbosa, Goniodoridella savignyi and Murphydoris singaporensis as well as one species of Trapania, T. graeffei. We describe for the first time the detailed internal anatomy of the type species Goniodoridella savignyi. The diagnostic features of each genus are compared, and a preliminary framework is shown to clarify their systematics and identifications.
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16
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Markich SJ. Comparative embryo/larval sensitivity of Australian marine bivalves to ten metals: A disjunct between physiology and phylogeny. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147988. [PMID: 34323817 DOI: 10.1016/j.scitotenv.2021.147988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
Metal contamination within the urbanized coastal zon is one threat linked to a decline in the abundance, distribution and/or species diversity of wild marine bivalve populations. This study determined the 48-h embryo/larval sensitivity (no-effect concentration (NEC) and median-effect concentration (EC50)) of ten marine bivalve species (nine endemic to Australia) to aluminium (Al), cadmium (Cd), chromium (Cr), cobalt (Co), copper (Cu), iron (Fe), lead (Pb), manganese (Mn), nickel (Ni) and zinc (Zn), key metal contaminants impacting urbanized coastal zones in south-eastern Australia, in natural seawater (20-22 °C, 30‰ salinity, pH 7.8-7.9, 1.2 mg/L dissolved organic carbon). For all metals, except Fe, the order of sensitivity was oysters > mussels ≥ scallops ≥ cockles ≥ clams, where the economically-important oysters, Magallana gigas and Saccostrea glomerata, were 2.6 (Al) to 4.2 (Cd) times more sensitive than the least sensitive clam species. For all bivalve species, the order of metal sensitivity was Cu > Pb > Zn = Ni > Co > Cd > Al > Cr(VI) > Mn ≥ Fe(III), where Cu was eight times more toxic than Zn or Ni, 28 times more toxic than Cd, 220 times more toxic than Cr(VI) and 570 times more toxic than Fe(III). Iron, unlike the other nine soluble metals, occurred as particulate Fe(III) oxyhydroxide, where EC50 values decreased with increasing exposure time as the larval (D-veliger) stage. There was no significant (p > 0.05) effect of embryo/larval mass, or surface area/volume, on metal sensitivity. Further, there was no significant (p > 0.05) relationship between metal sensitivity and phylogeny (genetic distance). Divalent metal sensitivity was positively related (r2 = 0.87) to cell surface metal-binding affinity. The current Australian marine water quality guideline for Ni is not protective of the ten bivalve species (NECs were 2-6-fold below the guideline), while the guideline for Zn is not protective of oysters.
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Affiliation(s)
- Scott J Markich
- Aquatic Solutions International, North Narrabeen Beach, NSW 2101, Australia; Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
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17
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Passos FD, Batistão AR, Bieler R. When size matters: the first comprehensive anatomical study of a species of "Condylocardiidae", an extremely miniaturized bivalve. PeerJ 2021; 9:e12108. [PMID: 34540376 PMCID: PMC8411939 DOI: 10.7717/peerj.12108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
'Miniaturization' is a widespread phenomenon among the Metazoa. In the molluscan class Bivalvia, records of miniaturization are numerous. Among the Archiheterodonta, Warrana besnardi (Klappenbach, 1963) has attracted attention for its tiny size, which does not exceed 1.5 mm in shell length, and because it belongs to a group with limited anatomical information and often-debated status, the "Condylocardiidae" (which recent molecular studies place deeply nested within the family Carditidae). All species of Warrana Laseron, 1953 are small-bodied, and so miniaturization presumably occurred from a large-bodied ancestor within the Carditidae sensu lato. South American W. besnardi is here studied in detail. Its small size and the enlargement of the anterodorsal region during growth, reflects (and likely led) to infaunal habit, living as a burrowing bivalve that passively feeds on deposit particles entering the pallial cavity anteriorly. Mantle glands, previously reported as a common feature of other archiheterodonts, are missing in W. besnardi, but spongiform tissue in the antero-ventral portion of the mantle lobes presumably represents a blood sinus that might compensate for the great reduction of the ctenidia. Lecithotrophy is reported, with yolky oocytes bearing a thick non-cellular capsule layer; brooding was not observed, and it is here hypothesized that the extreme miniaturization, with the great reduction of ctenidia, is responsible for a shift in the reproductive mode of condylocardiids, contrasting with the commonly reported ovoviviparity of the carditids.
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Affiliation(s)
- Flávio Dias Passos
- Department of Animal Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Alan Rodrigo Batistão
- Department of Animal Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Rüdiger Bieler
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States
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18
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L. Simone LR, do Amaral VS. Phenotypic Features of Dimya cf. Japonica (Bivalvia, Dimyidae) from Niue Island (South Pacific) with Accounts on Its Phylogeny and Taxonomic Relationships. MALACOLOGIA 2021. [DOI: 10.4002/040.064.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Luiz Ricardo L. Simone
- Museu de Zoologia da Universidade de São Paulo, Cx Postal 42391; 04218-970 São Paulo, SP, Brazil
| | - Vanessa Simão do Amaral
- Universidade Federal do Espírito Santo – Centro Universitário Norte do Espírito Santo, Rodovia Governador Mario Covas, km 60 s/n, Bairro Litorâneo, 29932-540, São Mateus, ES, Brazil
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19
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Stewart DT, Robicheau BM, Youssef N, Garrido-Ramos MA, Chase EE, Breton S. Expanding the Search for Sperm Transmission Elements in the Mitochondrial Genomes of Bivalve Mollusks. Genes (Basel) 2021; 12:1211. [PMID: 34440385 PMCID: PMC8394068 DOI: 10.3390/genes12081211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA) in bivalve mollusks is one of the most notable departures from the paradigm of strict maternal inheritance of mtDNA among metazoans. Recently, work on the Mediterranean mussel Mytilus galloprovincialis suggested that a nucleotide motif in the control region of this species, known as the sperm transmission element (STE), helps protect male-transmitted mitochondria from destruction during spermatogenesis. Subsequent studies found similar, yet divergent, STE motifs in other marine mussels. Here, we extend the in silico search for mtDNA signatures resembling known STEs. This search is carried out for the large unassigned regions of 157 complete mitochondrial genomes from within the Mytiloida, Veneroida, Unionoida, and Ostreoida bivalve orders. Based on a sliding window approach, we present evidence that there are additional putative STE signatures in the large unassigned regions of several marine clams and freshwater mussels with DUI. We discuss the implications of this finding for interpreting the origin of doubly uniparental inheritance in ancestral bivalve mollusks, as well as potential future in vitro and in silico studies that could further refine our understanding of the early evolution of this unusual system of mtDNA inheritance.
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Affiliation(s)
- Donald T. Stewart
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (B.M.R.); (N.Y.)
| | - Noor Youssef
- Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (B.M.R.); (N.Y.)
| | - Manuel A. Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Emily E. Chase
- Institut Méditerranéen d’Océanologie, Aix-Marseille University, 13288 Marseille, France;
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada;
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20
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Ip JCH, Xu T, Sun J, Li R, Chen C, Lan Y, Han Z, Zhang H, Wei J, Wang H, Tao J, Cai Z, Qian PY, Qiu JW. Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam. Mol Biol Evol 2021; 38:502-518. [PMID: 32956455 PMCID: PMC7826175 DOI: 10.1093/molbev/msaa241] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Endosymbiosis with chemosynthetic bacteria has enabled many deep-sea invertebrates to thrive at hydrothermal vents and cold seeps, but most previous studies on this mutualism have focused on the bacteria only. Vesicomyid clams dominate global deep-sea chemosynthesis-based ecosystems. They differ from most deep-sea symbiotic animals in passing their symbionts from parent to offspring, enabling intricate coevolution between the host and the symbiont. Here, we sequenced the genomes of the clam Archivesica marissinica (Bivalvia: Vesicomyidae) and its bacterial symbiont to understand the genomic/metabolic integration behind this symbiosis. At 1.52 Gb, the clam genome encodes 28 genes horizontally transferred from bacteria, a large number of pseudogenes and transposable elements whose massive expansion corresponded to the timing of the rise and subsequent divergence of symbiont-bearing vesicomyids. The genome exhibits gene family expansion in cellular processes that likely facilitate chemoautotrophy, including gas delivery to support energy and carbon production, metabolite exchange with the symbiont, and regulation of the bacteriocyte population. Contraction in cellulase genes is likely adaptive to the shift from phytoplankton-derived to bacteria-based food. It also shows contraction in bacterial recognition gene families, indicative of suppressed immune response to the endosymbiont. The gammaproteobacterium endosymbiont has a reduced genome of 1.03 Mb but retains complete pathways for sulfur oxidation, carbon fixation, and biosynthesis of 20 common amino acids, indicating the host’s high dependence on the symbiont for nutrition. Overall, the host–symbiont genomes show not only tight metabolic complementarity but also distinct signatures of coevolution allowing the vesicomyids to thrive in chemosynthesis-based ecosystems.
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Affiliation(s)
- Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jin Sun
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Division of Life Science, Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa Prefecture, Japan
| | - Yi Lan
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Division of Life Science, Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhuang Han
- Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, Hainan, China
| | - Haibin Zhang
- Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, Hainan, China
| | - Jiangong Wei
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Hongbin Wang
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Jun Tao
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Pei-Yuan Qian
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Division of Life Science, Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
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21
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Hernandez AM, Ryan JF. Six-state Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses. Syst Biol 2021; 70:1200-1212. [PMID: 33837789 PMCID: PMC8513762 DOI: 10.1093/sysbio/syab027] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 01/25/2023] Open
Abstract
Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of six-state recoding approaches by comparing the performance of analyses on recoded and non-recoded data sets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches consistently outperform six-state recoding approaches. Our results suggest that six-state recoding strategies are not effective in the face of high saturation. Furthermore, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies six-state recoding outweighs its benefits. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these consistently outperform six-state recoding. Our analyses of other recoding schemes suggest that under conditions of very high compositional heterogeneity, it may be advantageous to apply recoding using more than six states, but we caution that applying any recoding should include sufficient justification. Our results have important implications for the more than 90 published papers that have incorporated six-state recoding, many of which have significant bearing on relationships across the tree of life. [Compositional heterogeneity; Dayhoff 6-state recoding; S&R 6-state recoding; six-state amino acid recoding; substitution saturation.]
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, P.O. Box 118525, Gainesville, FL, 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, P.O. Box 118525, Gainesville, FL, 32611, USA
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22
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Feng J, Guo Y, Yan C, Ye Y, Yan X, Li J, Xu K, Guo B, Lü Z. Novel gene rearrangement in the mitochondrial genome of Siliqua minima (Bivalvia, Adapedonta) and phylogenetic implications for Imparidentia. PLoS One 2021; 16:e0249446. [PMID: 33822813 PMCID: PMC8023497 DOI: 10.1371/journal.pone.0249446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/18/2021] [Indexed: 11/19/2022] Open
Abstract
Siliqua minima (Gmelin, 1791) is an important economic shellfish species belonging to the family Pharidae. To date, the complete mitochondrial genome of only one species in this family (Sinonovacula constricta) has been sequenced. Research on the Pharidae family is very limited; to improve the evolution of this bivalve family, we sequenced the complete mitochondrial genome of S. minima by next-generation sequencing. The genome is 17,064 bp in length, consisting of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA). From the rearrangement analysis of bivalves, we found that the gene sequences of bivalves greatly variable among species, and with closer genetic relationship, the more consistent of the gene arrangement is higher among the species. Moreover, according to the gene arrangement of seven species from Adapedonta, we found that gene rearrangement among families is particularly obvious, while the gene order within families is relatively conservative. The phylogenetic analysis between species of the superorder Imparidentia using 12 conserved PCGs. The S. minima mitogenome was provided and will improve the phylogenetic resolution of Pharidae species.
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Affiliation(s)
- Jiantong Feng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Yahong Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Chengrui Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Kaida Xu
- Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, MOA, Key Laboratory of Sustainable Utilization of Technology Research, Marine Fisheries Research Institute of Zhejiang, Zhoushan, China
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Zhenming Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
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23
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McCartney MA. Structure, function and parallel evolution of the bivalve byssus, with insights from proteomes and the zebra mussel genome. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200155. [PMID: 33813897 DOI: 10.1098/rstb.2020.0155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The byssus is a structure unique to bivalves. Byssal threads composed of many proteins extend like tendons from muscle cells, ending in adhesive pads that attach underwater. Crucial to settlement and metamorphosis, larvae of virtually all species are byssate. By contrast, in adults, the byssus is scattered throughout bivalves, where it has had profound effects on morphological evolution and been key to adaptive radiations of epifaunal species. I compare byssus structure and proteins in blue mussels (Mytilus), by far the best characterized, to zebra mussels (Dreissena polymorpha), in which several byssal proteins have been isolated and sequenced. By mapping the adult byssus onto a recent phylogenomic tree, I confirm its independent evolution in these and other lineages, likely parallelisms with common origins in development. While the byssus is superficially similar in Dreissena and Mytilus, in finer detail it is not, and byssal proteins are dramatically different. I used the chromosome-scale D. polymorpha genome we recently assembled to search for byssal genes and found 37 byssal loci on 10 of the 16 chromosomes. Most byssal genes are in small families, with several amino acid substitutions between paralogs. Byssal proteins of zebra mussels and related quagga mussels (D. rostriformis) are divergent, suggesting rapid evolution typical of proteins with repetitive low complexity domains. Opportunities abound for proteomic and genomic work to further our understanding of this textbook example of a marine natural material. A priority should be invasive bivalves, given the role of byssal attachment in the spread of, and ecological and economic damage caused by zebra mussels, quagga mussels and others. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Sigwart JD, Lindberg DR, Chen C, Sun J. Molluscan phylogenomics requires strategically selected genomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200161. [PMID: 33813889 DOI: 10.1098/rstb.2020.0161] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The extraordinary diversity in molluscan body plans, and the genomic mechanisms that enable it, remains one of the great questions of evolution. The eight distinct living taxonomic classes of molluscs are each unambiguously monophyletic; however, significant controversy remains about the phylogenetic relationships among those eight branches. Molluscs are the second-largest animal phylum, with over 100 000 living species with broad biological, economic and medical interest. To date, only around 53 genome assemblies have been accessioned to NCBI GenBank covering only four of the eight living molluscan classes. Furthermore, the molluscan taxa where partial or whole-genome assemblies are available are often aberrantly fast evolving or recently derived lineages. Characteristic adaptations provide interesting targets for whole-genome projects, in animals like the scaly-foot snail or octopus, but without basal-branching lineages for comparison, the context of recently derived features cannot be assessed. The currently available genomes also create a non-optimal set of taxa for resolving deeper phylogenetic branches: they are a small sample representing a large group, and those that are available come primarily from a rarefied pool. Thoughtful selection of taxa for future projects should focus on the blank areas of the molluscan tree, which are ripe with opportunities to delve into peculiarities of genome evolution, and reveal the biology and evolutionary history of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Julia D Sigwart
- Senckenberg Research Institute, 60325 Frankfurt am Main, Germany.,Queen's University Belfast Marine Laboratory, Portaferry, Newtownards BT22 1PF, UK.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong
| | - David R Lindberg
- Department of Integrative Biology, University of California, Berkeley, USA
| | - Chong Chen
- X-STAR, Japan Agency for Marine Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
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25
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Moles J, Giribet G. A polyvalent and universal tool for genomic studies in gastropod molluscs (Heterobranchia). Mol Phylogenet Evol 2020; 155:106996. [PMID: 33148425 DOI: 10.1016/j.ympev.2020.106996] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 10/23/2022]
Abstract
Molluscs are the second most diverse animal phylum and heterobranch gastropods present ~ 44,000 species. These comprise fascinating creatures with huge morphological and ecological disparity. Such great diversity comes with even larger phylogenetic uncertainty and many taxa have been largely neglected in molecular assessments. Genomic tools have provided resolution to deep cladogenic events but generating large numbers of transcriptomes/genomes is expensive and usually requires fresh material. Here we leverage a target enrichment approach to design and synthesize a probe set based on available genomes and transcriptomes across Heterobranchia. Our probe set contains 57,606 70mer baits and targets a total of 2,259 ultra-conserved elements (UCEs). Post-sequencing capture efficiency was tested against 31 marine heterobranchs from major groups, including Acochlidia, Acteonoidea, Aplysiida, Cephalaspidea, Pleurobranchida, Pteropoda, Runcinida, Sacoglossa, and Umbraculida. The combined Trinity and Velvet assemblies recovered up to 2,211 UCEs in Tectipleura, up to 1,978 in Nudipleura, and up to 1,927 in Acteonoidea, the latter two being the most distantly related taxa to our core study group. Total alignment length was 525,599 bp and contained 52% informative sites and 21% missing data. Maximum-likelihood and Bayesian inference approaches recovered the monophyly of all orders tested as well as the larger clades Nudipleura, Panpulmonata, and Euopisthobranchia. The successful enrichment of diversely preserved material and DNA concentrations demonstrate the polyvalent nature of UCEs, and the universality of the probe set designed. We believe this probe set will enable multiple, interesting lines of research, that will benefit from an inexpensive and largely informative tool that will, additionally, benefit from the access to museum collections to gather genomic data.
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Affiliation(s)
- Juan Moles
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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26
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McCulloch KJ, Koenig KM. Krüppel-like factor/specificity protein evolution in the Spiralia and the implications for cephalopod visual system novelties. Proc Biol Sci 2020; 287:20202055. [PMID: 33081641 PMCID: PMC7661307 DOI: 10.1098/rspb.2020.2055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The cephalopod visual system is an exquisite example of convergence in biological complexity. However, we have little understanding of the genetic and molecular mechanisms underpinning its elaboration. The generation of new genetic material is considered a significant contributor to the evolution of biological novelty. We sought to understand if this mechanism may be contributing to cephalopod-specific visual system novelties. Specifically, we identified duplications in the Krüppel-like factor/specificity protein (KLF/SP) sub-family of C2H2 zinc-finger transcription factors in the squid Doryteuthis pealeii. We cloned and analysed gene expression of the KLF/SP family, including two paralogs of the DpSP6-9 gene. These duplicates showed overlapping expression domains but one paralog showed unique expression in the developing squid lens, suggesting a neofunctionalization of DpSP6-9a. To better understand this neofunctionalization, we performed a thorough phylogenetic analysis of SP6-9 orthologues in the Spiralia. We find multiple duplications and losses of the SP6-9 gene throughout spiralian lineages and at least one cephalopod-specific duplication. This work supports the hypothesis that gene duplication and neofunctionalization contribute to novel traits like the cephalopod image-forming eye and to the diversity found within Spiralia.
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Affiliation(s)
- Kyle J McCulloch
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA 02138, USA.,John Harvard Distinguished Science Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Kristen M Koenig
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA 02138, USA.,John Harvard Distinguished Science Fellows, Harvard University, Cambridge, MA 02138, USA
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Ryu T, Kim JG, Lee J, Yu OH, Yum S, Kim D, Woo S. First transcriptome assembly of a newly discovered vent mussel, Gigantidas vrijenhoeki, at Onnuri Vent Field on the northern Central Indian Ridge. Mar Genomics 2020; 57:100819. [PMID: 32933864 DOI: 10.1016/j.margen.2020.100819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 11/17/2022]
Abstract
This is the first report of a transcriptome assembly of a newly discovered hydrothermal vent mussel, Gigantidas vrijenhoeki (Bivalvia: Mytilidae), on the Central Indian Ridge. Gigantidas vrijenhoeki was identified from material collected at the newly discovered Onnuri Vent Field (OVF) on the Central Indian Ridge in 2018, and was reported as a new species, distinct from another dominant hydrothermal vent mussel, Bathymodiolus marisindicus, in 2020. We sequenced the transcriptome of G. vrijenhoeki using the Illumina HiSeq X System. De novo assembly and analysis of the coding regions predicted 25,405 genes, 84.76% of which was annotated by public databases. The transcriptome of G. vrijenhoeki will be a valuable resource in studying the ecological and biological characteristics of this new species, which is distinct from other deep-sea mussels. These data should also support the investigation of the relationship between the environmental conditions of hydrothermal vents and the unique distribution of G. vrijenhoeki in the OVF of the Central Indian Ridge.
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Affiliation(s)
- Taewoo Ryu
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Jong Guk Kim
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
| | - Jimin Lee
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
| | - Ok Hwan Yu
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
| | - Seungshic Yum
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology, Geoje 53201, South Korea
| | - Dongsung Kim
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
| | - Seonock Woo
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea.
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28
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Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves. BMC Evol Biol 2020; 20:50. [PMID: 32357841 PMCID: PMC7195748 DOI: 10.1186/s12862-020-01614-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. RESULTS In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade. CONCLUSIONS The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exaptations existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.
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29
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Sato K, Kano Y, Setiamarga DHE, Watanabe HK, Sasaki T. Molecular phylogeny of protobranch bivalves and systematic implications of their shell microstructure. ZOOL SCR 2020. [DOI: 10.1111/zsc.12419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Kei Sato
- Waseda University Tokyo Japan
- The University Museum The University of Tokyo Tokyo Japan
| | - Yasunori Kano
- Atmosphere and Ocean Research Institute The University of Tokyo Chiba Japan
| | - Davin H. E. Setiamarga
- The University Museum The University of Tokyo Tokyo Japan
- National Institute of Technology Wakayama College Gobo Japan
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30
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Zelaya DG, Güller M, Ituarte C. Filling a blank in bivalve taxonomy: an integrative analysis of Cyamioidea (Mollusca: Bivalvia). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Abstract
This contribution provides the first integrative study of Cyamioidea, a group of bivalves largely neglected in the past. By combining information obtained from shell morphology, gross anatomy, histology, reproductive biology and DNA sequencing, the distinctive characters of Cyamioidea are determined, and the taxa belonging to this superfamily are revised. Gaimardioidea, previously considered as a distinct superfamily, is reduced to family level (Gaimardiidae), which, along with Cyamiidae, are assigned to Cyamioidea. All studied cyamioideans share a common reproductive character: the presence of a true follicular epithelium surrounding each developing oocyte, which persists after spawning, surrounding the developing embryos and participating in their anchorage to the gill filaments. Several morphological and anatomical characters support the distinction of Gaimardiidae and Cyamiidae. Based on that information, the placement of Gaimardia and Kidderia in Gaimardiidae, and that of Cyamiocardium, Cyamiomactra, Cyamium, Heteromactra, Pseudokelly, Ptychocardia and Reloncavia in Cyamiidae, is confirmed. Jukesena, historically placed in Veneroidea, is here allocated to Cyamiidae. Neoleptonidae, previously also attributed to Cyamioidea, are reallocated to Veneroidea.
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Affiliation(s)
- Diego G Zelaya
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Biodiversidad y Biología Experimental, Ciudad Universitaria, Piso, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marina Güller
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Biodiversidad y Biología Experimental, Ciudad Universitaria, Piso, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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31
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Thai BT, Lee YP, Gan HM, Austin CM, Croft LJ, Trieu TA, Tan MH. Whole Genome Assembly of the Snout Otter Clam, Lutraria rhynchaena, Using Nanopore and Illumina Data, Benchmarked Against Bivalve Genome Assemblies. Front Genet 2019; 10:1158. [PMID: 31824566 PMCID: PMC6880199 DOI: 10.3389/fgene.2019.01158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Laurence J Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Tuan Anh Trieu
- Faculty of Biology, Ha Noi National University of Education, Ha Noi, Vietnam.,Science and Technique Department, Hung Vuong University, Viet Tri, Vietnam
| | - Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
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32
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Collins KS, Edie SM, Gao T, Bieler R, Jablonski D. Spatial filters of function and phylogeny determine morphological disparity with latitude. PLoS One 2019; 14:e0221490. [PMID: 31465483 PMCID: PMC6715166 DOI: 10.1371/journal.pone.0221490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022] Open
Abstract
The drivers of latitudinal differences in the phylogenetic and ecological composition of communities are increasingly studied and understood, but still little is known about the factors underlying morphological differences. High-resolution, three-dimensional morphological data collected using computerized micro-tomography (micro-CT) allows comprehensive comparisons of morphological diversity across latitude. Using marine bivalves as a model system, this study combines 3D shape analysis (based on a new semi-automated procedure for placing landmarks and semilandmarks on shell surfaces) with non-shape traits: centroid size, proportion of shell to soft-tissue volume, and magnitude of shell ornamentation. Analyses conducted on the morphology of 95% of all marine bivalve species from two faunas along the Atlantic coast of North America, the tropical Florida Keys and the boreal Gulf of Maine, show that morphological shifts between these two faunas, and in phylogenetic and ecological subgroups shared between them, occur as changes in total variance with a bounded minimum rather than directional shifts. The dispersion of species in shell-shape morphospace is greater in the Gulf of Maine, which also shows a lower variance in ornamentation and size than the Florida Keys, but the faunas do not differ significantly in the ratio of shell to internal volume. Thus, regional differences conform to hypothesized effects of resource seasonality and predation intensity, but not to carbonate saturation or calcification costs. The overall morphological differences between the regional faunas is largely driven by the loss of ecological functional groups and family-level clades at high latitudes, rather than directional shifts in morphology within the shared groups with latitude. Latitudinal differences in morphology thus represent a complex integration of phylogenetic and ecological factors that are best captured in multivariate analyses across several hierarchical levels.
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Affiliation(s)
- K. S. Collins
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - S. M. Edie
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - T. Gao
- Committee on Computational and Applied Mathematics, Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - R. Bieler
- Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, United States of America
| | - D. Jablonski
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, United States of America
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Pfeiffer JM, Breinholt JW, Page LM. Unioverse: A phylogenomic resource for reconstructing the evolution of freshwater mussels (Bivalvia, Unionoida). Mol Phylogenet Evol 2019; 137:114-126. [DOI: 10.1016/j.ympev.2019.02.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/25/2019] [Accepted: 02/18/2019] [Indexed: 10/27/2022]
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