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Alqudah AA. Phylogenetic analysis and genetic similarities of Phyllidia spp. by comparing the nucleotide sequence of 16S rRNA and cytochrome c genes. BRAZ J BIOL 2023; 84:e272732. [PMID: 37493707 DOI: 10.1590/1519-6984.272732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/01/2023] [Indexed: 07/27/2023] Open
Abstract
Phyllidiid nudibranchs are brightly colored gastropod molluscs, frequently encountered in coral reefs of the tropical Indo-Pacific. This study aimed to identify the phylogenetic similarities among the Phyllidia spp. The phylogenetic similarities among all the available Phyllidia spp. were studied by comparing the nucleotide sequence of 16s rRNA and cytochrome c genes (cox I). Sequences were retrieved from NCBI databases and aligned by using Geneious software. A phylogenetic tree was constructed for the retrieved sequences of Phyllidia spp. by using the neighbor-joining method on MEGA software and the pairwise distances were also calculated. The similarities among nucleotide sequences of 16s rRNA showed that the P. elegans, and P. haegeli had the highest similarities (99.92%) and the lowest similarities (99.14%) among P. haegeli and P. picta. While nucleotide sequences of cox I showed the highest similarities (99.90%) between P. elegans and P. ocellata, and the P. varicosa had the lowest similarities 99.74% with P. koehleri and P. larryi. The molecular phylogenetic analysis based on mitochondrial marker indicated a close relation between P. elegans and P. alyta in both cox I and 16s rRNA phylogenetic tree. The phylogenetic tree of 16s rRNA gene shows the P. ocellata is closely related to the clade of species P. exquisita. The available phylogenetic analysis could be useful in further studies of Phyllidiidae within Nudibranchia.
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Affiliation(s)
- A A Alqudah
- Tafila Technical University, Department of Applied Biology, Tafila, Jordan
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2
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The smallest marine bivalves from the end of the world (Tierra del Fuego, Isla de Los Estados and Burdwood Bank). Polar Biol 2022. [DOI: 10.1007/s00300-022-03018-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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4
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Lemer S, Bieler R, Giribet G. Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life. Proc Biol Sci 2020; 286:20182684. [PMID: 30963927 PMCID: PMC6408618 DOI: 10.1098/rspb.2018.2684] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bivalvia has been the subject of extensive recent phylogenetic work to attempt resolving either the backbone of the bivalve tree using transcriptomic data, or the tips using morpho-anatomical data and up to five genetic markers. Yet the first approach lacked decisive taxon sampling and the second failed to resolve many interfamilial relationships, especially within the diverse clade Imparidentia. Here we combine dense taxon sampling with 108 deep-sequenced Illumina-based transcriptomes to provide resolution in nodes that required additional study. We designed specific data matrices to address the poorly resolved relationships within Imparidentia. Our results support the overall backbone of the bivalve tree, the monophyly of Bivalvia and all its main nodes, although the monophyly of Protobranchia remains less clear. Likewise, the inter-relationships of the six main bivalve clades were fully supported. Within Imparidentia, resolution increases when analysing Imparidentia-specific matrices. Lucinidae, Thyasiridae and Gastrochaenida represent three early branches. Gastrochaenida is sister group to all remaining imparidentians, which divide into six orders. Neoheterodontei is always fully supported, and consists of Sphaeriida, Myida and Venerida, with the latter now also containing Mactroidea, Ungulinoidea and Chamidae, a family particularly difficult to place in earlier work. Overall, our study, by using densely sampled transcriptomes, provides the best-resolved bivalve phylogeny to date.
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Affiliation(s)
- Sarah Lemer
- 1 University of Guam Marine Laboratory , 303 University Drive, UOG Station, Mangilao, GU 96923 , USA.,2 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
| | - Rüdiger Bieler
- 3 Integrative Research Center, Field Museum of Natural History , 1400 South Lake Shore Drive, Chicago, IL 60605 , USA
| | - Gonzalo Giribet
- 2 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
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5
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Lopes-Lima M, Hattori A, Kondo T, Hee Lee J, Ki Kim S, Shirai A, Hayashi H, Usui T, Sakuma K, Toriya T, Sunamura Y, Ishikawa H, Hoshino N, Kusano Y, Kumaki H, Utsugi Y, Yabe S, Yoshinari Y, Hiruma H, Tanaka A, Sao K, Ueda T, Sano I, Miyazaki JI, Gonçalves DV, Klishko OK, Konopleva ES, Vikhrev IV, Kondakov AV, Yu Gofarov M, Bolotov IN, Sayenko EM, Soroka M, Zieritz A, Bogan AE, Froufe E. Freshwater mussels (Bivalvia: Unionidae) from the rising sun (Far East Asia): phylogeny, systematics, and distribution. Mol Phylogenet Evol 2020; 146:106755. [PMID: 32028028 DOI: 10.1016/j.ympev.2020.106755] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/10/2020] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
Freshwater mussels (Bivalvia: Unionidae) is a diverse family with around 700 species being widespread in the Northern Hemisphere and Africa. These animals fulfill key ecological functions and provide important services to humans. Unfortunately, populations have declined dramatically over the last century, rendering Unionidae one of the world's most imperiled taxonomic groups. In Far East Asia (comprising Japan, Korea, and Eastern Russia), conservation actions have been hindered by a lack of basic information on the number, identity, distribution and phylogenetic relationships of species. Available knowledge is restricted to studies on national and sub-national levels. The present study aims to resolve the diversity, biogeography and evolutionary relationships of the Far East Asian Unionidae in a globally comprehensive phylogenetic and systematic context. We reassessed the systematics of all Unionidae species in the region, including newly collected specimens from across Japan, South Korea, and Russia, based on molecular (including molecular species delineation and a COI + 28S phylogeny) and comparative morphological analyses. Biogeographical patterns were then assessed based on available species distribution data from the authors and previous reference works. We revealed that Unionidae species richness in Far East Asia is 30% higher than previously assumed, counting 43 species (41 native + 2 alien) within two Unionidae subfamilies, the Unioninae (32 + 1) and Gonideinae (9 + 1). Four of these species are new to science, i.e. Beringiana gosannensissp. nov., Beringiana fukuharaisp. nov., Buldowskia kamiyaisp. nov., and Koreosolenaia sitgyensisgen. & sp. nov. We also propose a replacement name for Nodularia sinulata, i.e. Nodularia breviconchanom. nov. and describe a new tribe (Middendorffinaiini tribe nov.) within the Unioninae subfamily. Biogeographical patterns indicate that this fauna is related to that from China south to Vietnam until the Mekong River basin. The Japanese islands of Honshu, Shikoku, Kyushu, Hokkaido, and the Korean Peninsula were identified as areas of particularly high conservation value, owing to high rates of endemism, diversity and habitat loss. The genetically unique species within the genera Amuranodonta, Obovalis, Koreosolenaiagen. nov., and Middendorffinaia are of high conservation concern.
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Affiliation(s)
- Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal; SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, c/o The David Attenborough Building, Pembroke Street, CB2 3QZ Cambridge, United Kingdom
| | - Akimasa Hattori
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan
| | - Takaki Kondo
- Division of Natural Science, Osaka Kyoiku University Kashiwara, 582-8582 Osaka, Japan
| | - Jin Hee Lee
- Daegu Science High School, 42110 Daegu, South Korea
| | - Sang Ki Kim
- NNIBR - Animal & Plant Research Team, Nakdonggang National Institute of Biological Resources, 37242 Sangju, South Korea
| | - Akihisa Shirai
- Musashi High School and Junior High School, Musashi Academy of the Nezu Foudation, 1-26-1, Toyotama-kami, Nerima-ku, Tokyo 176-8535, Japan
| | - Hironori Hayashi
- Department of Urban and Environmental Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Fukuoka, Japan
| | - Taira Usui
- Sapporo Youth and Women's Activity Association, Takino Suzuran Hillside National Government Park, 247 Takino, Minami-ku, Sapporo, Hokkaido 005-0862, Japan
| | - Kanta Sakuma
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan; Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, 252-5201 Kanagawa, Japan
| | - Taishi Toriya
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan; University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Youhei Sunamura
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan; Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, 156-8502 Tokyo, Japan
| | - Haruki Ishikawa
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan; Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, 156-8502 Tokyo, Japan
| | - Naoki Hoshino
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan; Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
| | - Yushi Kusano
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan; Shinshu University, 3-1-1 Asahi, Matsumoto-shi, Nagano 390-8621, Japan
| | - Hinata Kumaki
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan
| | - Yuya Utsugi
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan
| | - Shinnosuke Yabe
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan
| | - Yuma Yoshinari
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan
| | - Hazuki Hiruma
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan
| | - Akiko Tanaka
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan
| | - Kentaro Sao
- Matsuyama High School, 1-6-10 Matsuyama-cho, Higashimatsuyama, Saitama 355-0018, Japan
| | - Takuya Ueda
- Freshwater Fisheries Research Laboratory, Chiba Prefectural Fisheries Research Center, 1390 Usuidai, Sakura, Chiba 285-0864, Japan
| | - Isao Sano
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-0862, Japan
| | - Jun-Ichi Miyazaki
- Faculty of Education, University of Yamanashi, Kofu, Yamanashi 400-8510, Japan
| | - Duarte V Gonçalves
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal
| | - Olga K Klishko
- Institute of Natural Resources, Ecology, and Cryology Siberian Branch, Russian Academy of Sciences, str. Nedoresova, 16a, Chita, Russia
| | - Ekaterina S Konopleva
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000 Arkhangelsk, Russia; Northern Arctic Federal University, Northern Dvina Emb. 17, 163000 Arkhangelsk, Russia
| | - Ilya V Vikhrev
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000 Arkhangelsk, Russia; Northern Arctic Federal University, Northern Dvina Emb. 17, 163000 Arkhangelsk, Russia; Laboratory of Macroecology & Biogeography of Invertebrates, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia
| | - Alexander V Kondakov
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000 Arkhangelsk, Russia; Northern Arctic Federal University, Northern Dvina Emb. 17, 163000 Arkhangelsk, Russia; Laboratory of Macroecology & Biogeography of Invertebrates, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia
| | - Mikhail Yu Gofarov
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000 Arkhangelsk, Russia; Northern Arctic Federal University, Northern Dvina Emb. 17, 163000 Arkhangelsk, Russia
| | - Ivan N Bolotov
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000 Arkhangelsk, Russia; Northern Arctic Federal University, Northern Dvina Emb. 17, 163000 Arkhangelsk, Russia
| | - Elena M Sayenko
- FSCEATB FEB RAS - Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, pr. 100-letiya Vladivostoka 159, 690022 Vladivostok, Russia
| | - Marianna Soroka
- Instytute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland
| | - Alexandra Zieritz
- University of Nottingham, School of Geography, Nottingham, United Kingdom
| | - Arthur E Bogan
- North Carolina State Museum of Natural Sciences, 11 West Jones St., Raleigh, NC 27601, United States
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal
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6
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Vikhrev IV, Bolotov IN, Altun A, Gofarov MY, Dvoryankin GA, Kondakov AV, Ozcan T, Ozcan G. The revenant: rediscovery of Margaritifera homsensis from Orontes drainage with remarks on its taxonomic status and conservation (Bivalvia: Margaritiferidae). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1343876] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Ilya V. Vikhrev
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Ivan N. Bolotov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Ayhan Altun
- Faculty of Marine Sciences and Technology, Iskenderun Technical University, Iskenderun 31200, Hatay, Turkey
| | - Mikhail Y. Gofarov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Gennady A. Dvoryankin
- SevPINRO – Northern Branch of the Polar Scientific-Research Institute of Fish Husbandry and Oceanography, Uritskogo 17, Arkhangelsk 163000, Russian Federation
| | - Alexander V. Kondakov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Tahir Ozcan
- Faculty of Marine Sciences and Technology, Iskenderun Technical University, Iskenderun 31200, Hatay, Turkey
| | - Gulnaz Ozcan
- Faculty of Marine Sciences and Technology, Iskenderun Technical University, Iskenderun 31200, Hatay, Turkey
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Konopleva ES, Bolotov IN, Vikhrev IV, Gofarov MY, Kondakov AV. An integrative approach underscores the taxonomic status of Lamellidens exolescens, a freshwater mussel from the Oriental tropics (Bivalvia: Unionidae). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1249530] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ekaterina S. Konopleva
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
| | - Ivan N. Bolotov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
| | - Ilya V. Vikhrev
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
| | - Mikhail Y. Gofarov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
| | - Alexander V. Kondakov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
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Combosch DJ, Collins TM, Glover EA, Graf DL, Harper EM, Healy JM, Kawauchi GY, Lemer S, McIntyre E, Strong EE, Taylor JD, Zardus JD, Mikkelsen PM, Giribet G, Bieler R. A family-level Tree of Life for bivalves based on a Sanger-sequencing approach. Mol Phylogenet Evol 2016; 107:191-208. [PMID: 27840226 DOI: 10.1016/j.ympev.2016.11.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/28/2016] [Accepted: 11/03/2016] [Indexed: 12/12/2022]
Abstract
The systematics of the molluscan class Bivalvia are explored using a 5-gene Sanger-based approach including the largest taxon sampling to date, encompassing 219 ingroup species spanning 93 (or 82%) of the 113 currently accepted bivalve families. This study was designed to populate the bivalve Tree of Life at the family level and to place many genera into a clear phylogenetic context, but also pointing to several major clades where taxonomic work is sorely needed. Despite not recovering monophyly of Bivalvia or Protobranchia-as in most previous Sanger-based approaches to bivalve phylogeny-our study provides increased resolution in many higher-level clades, and supports the monophyly of Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Heterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata, Imparidentia, and Neoheterodontei, in addition to many other lower clades. However, deep nodes within some of these clades, especially Pteriomorphia and Imparidentia, could not be resolved with confidence. In addition, many families are not supported, and several are supported as non-monophyletic, including Malletiidae, Nuculanidae, Yoldiidae, Malleidae, Pteriidae, Arcidae, Propeamussiidae, Iridinidae, Carditidae, Myochamidae, Lyonsiidae, Pandoridae, Montacutidae, Galeommatidae, Tellinidae, Semelidae, Psammobiidae, Donacidae, Mactridae, and Cyrenidae; Veneridae is paraphyletic with respect to Chamidae, although this result appears to be an artifact. The denser sampling however allowed testing specific placement of species, showing, for example, that the unusual Australian Plebidonax deltoides is not a member of Donacidae and instead nests within Psammobiidae, suggesting that major revision of Tellinoidea may be required. We also showed that Cleidothaerus is sister group to the cementing member of Myochamidae, suggesting that Cleidothaeridae may not be a valid family and that cementation in Cleidothaerus and Myochama may have had a single origin. These results highlight the need for an integrative approach including as many genera as possible, and that the monophyly and relationships of many families require detailed reassessment. NGS approaches may be able to resolve the most recalcitrant nodes in the near future.
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Affiliation(s)
- David J Combosch
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Timothy M Collins
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Emily A Glover
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Daniel L Graf
- Biology Department, University of Wisconsin-Stevens Point, 800 Reserve Street, Stevens Point, Wisconsin 54481, USA
| | - Elizabeth M Harper
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - John M Healy
- Queensland Museum, PO Box 3300, South Brisbane, Queensland 4101, Australia
| | - Gisele Y Kawauchi
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Zoology Department, Universidade Federal de Minas Gerais, Brazil
| | - Sarah Lemer
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Erin McIntyre
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Ellen E Strong
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 163, Washington, DC 20013, USA
| | - John D Taylor
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - John D Zardus
- Department of Biology, The Citadel, 171 Moultrie Street, Charleston, SC 29409, USA
| | - Paula M Mikkelsen
- Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA.
| | - Rüdiger Bieler
- Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
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9
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Bolotov IN, Vikhrev IV, Bespalaya YV, Gofarov MY, Kondakov AV, Konopleva ES, Bolotov NN, Lyubas AA. Multi-locus fossil-calibrated phylogeny, biogeography and a subgeneric revision of the Margaritiferidae (Mollusca: Bivalvia: Unionoida). Mol Phylogenet Evol 2016; 103:104-121. [DOI: 10.1016/j.ympev.2016.07.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 07/01/2016] [Accepted: 07/18/2016] [Indexed: 11/16/2022]
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10
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Amaro R, Bouza C, Pardo BG, Castro J, San Miguel E, Villalba A, Lois S, Outeiro A, Ondina P. Identification of novel gender-associated mitochondrial haplotypes in Margaritifera margaritifera(Linnaeus, 1758). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Rafaela Amaro
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Carmen Bouza
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Belén G. Pardo
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Jaime Castro
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Eduardo San Miguel
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas de Corón (CIMA); Consellería do Medio Rural e do Mar da Xunta de Galicia; Aptdo. 13 36620 Vilanova de Arousa Spain
| | - Sabela Lois
- Department of Zoology; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Adolfo Outeiro
- Department of Zoology; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Paz Ondina
- Department of Zoology; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
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González VL, Andrade SCS, Bieler R, Collins TM, Dunn CW, Mikkelsen PM, Taylor JD, Giribet G. A phylogenetic backbone for Bivalvia: an RNA-seq approach. Proc Biol Sci 2015; 282:20142332. [PMID: 25589608 PMCID: PMC4308999 DOI: 10.1098/rspb.2014.2332] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000–20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals.
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Affiliation(s)
- Vanessa L González
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sónia C S Andrade
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rüdiger Bieler
- Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Timothy M Collins
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Paula M Mikkelsen
- Paleontological Research Institution and Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14850, USA
| | - John D Taylor
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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