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Elsa Froufe - One of the best experts on this subject based on the ideXlab platform.
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Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)
Zoological Journal of the Linnean Society, 2020Co-Authors: Alexandra Zieritz, Arthur E Bogan, Elsa Froufe, Han Ming Gan, Ronaldo Sousa, Ivan Bolotov, Duarte V Gonçalves, David C Aldridge, André Gomes-dos-santos, Amilcar TeixeiraAbstract:Abstract The Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian clade Contradentini+Rectidentini. We calculate substitution rates for the mitogenome, the 13 protein-coding genes, the two ribosomal units and three commonly used fragments (co1, nd1 and 16S) of both F- and M-mtDNA, based on a fossil-calibrated, mitogenomic phylogeny of the Unionidae. Phylogenetic analyses, including an M+F concatenated dataset, consistently recovers a monophyletic Gonideinae. Subfamily-level topology is congruent with that of a previous nuclear genomic study and with patterns in mitochondrial gene order, suggesting Unionidae F-type 2 as a synapomorphy of the Gonideinae. Our phylogeny indicates that the clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini split in the early Cretaceous (~125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (~79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type co1 and 16S for certain Unionidae and Margaritiferidae species (pairs).
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Variability of mitochondrial ORFans hints at possible differences in the system of doubly uniparental inheritance of mitochondria among families of freshwater mussels (Bivalvia: Unionida)
BMC Evolutionary Biology, 2019Co-Authors: Davide Guerra, Manuel Lopes-lima, Elsa Froufe, Han Ming Gan, Paz Ondina, Rafaela Amaro, M.w. Klunzinger, Claudia Tasso Callil, Vincent Prié, Arthur E BoganAbstract:Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly uniparental inheritance (DUI) of mitochondria. DUI is a system in which distinct female-transmitted and male-transmitted mitotypes coexist in a single species. In families Unionidae and Margaritiferidae, the transition from dioecy to hermaphroditism and the loss of DUI appear to be linked, and this event seems to affect the integrity of the ORFan genes. These observations led to the hypothesis that the ORFans have a role in DUI and/or sex determination. Complete mitochondrial genome sequences are however scarce for most families of freshwater mussels, therefore hindering a clear localization of DUI in the various lineages and a comprehensive understanding of the influence of the ORFans on DUI and sexual systems. Therefore, we sequenced and characterized eleven new mitogenomes from poorly sampled freshwater mussel families to gather information on the evolution and variability of the ORFan genes and their protein products. We obtained ten complete plus one almost complete mitogenome sequence from ten representative species (gonochoric and hermaphroditic) of families Margaritiferidae, Hyriidae, Mulleriidae, and Iridinidae. ORFan genes are present only in DUI species from Margaritiferidae and Hyriidae, while non-DUI species from Hyriidae, Iridinidae, and Mulleriidae lack them completely, independently of their sexual system. Comparisons among the proteins translated from the newly characterized ORFans and already known ones provide evidence of conserved structures, as well as family-specific features. The ORFan proteins show a comparable organization of secondary structures among different families of freshwater mussels, which supports a conserved physiological role, but also have distinctive family-specific features. Given this latter observation and the fact that the ORFans can be either highly mutated or completely absent in species that secondarily lost DUI depending on their respective family, we hypothesize that some aspects of the connection among ORFans, sexual systems, and DUI may differ in the various lineages of unionids.
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diversity biogeography and conservation of freshwater mussels bivalvia unionida in east and southeast asia
Hydrobiologia, 2018Co-Authors: Alexandra Zieritz, Arthur E Bogan, Elsa Froufe, Olga K Klishko, Takaki Kondo, Uthaiwan Kovitvadhi, Satit Kovitvadhi, Manuel Lopeslima, John M Pfeiffer, Ronaldo SousaAbstract:Recent research efforts have significantly advanced our knowledge on Asian freshwater mussel (Bivalvia: Unionida) diversity and distribution. Here we provide a modern consensus of the diversity, biogeography and conservation of Unionida in the region comprising East and Southeast Asia (excluding Wallacea) and Asian Russia. A data review confirmed the presence of 228 native and 3 non-native Unionida (98% Unionidae, 2% Margaritiferidae), rendering the region a global hotspot of freshwater mussel diversity. Species richness was highest in China (particularly Yangtze basin) in absolute numbers and Cambodia when correcting for country area, and decreased gradually towards the south and steeply towards the north and east. Six of the seven unionid subfamilies are native to the region, with species richness peaking in Southeast Asia for Rectidentinae, Gonideinae, Parreysiinae and Modellnaiinae, China for Anodontinae and Unioninae, and Asian Russia for Margaritiferidae. Conservation status and data collected after 1980 were not available for 61 and 24% of species, respectively. Dams, deforestation and pollution are likely the major threats to mussels in the region, though data in this respect are scarce. The Philippines, Laos, Indonesia, Myanmar and Malaysia are among the countries with the poorest data availability and urgently require research.
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Lifting the curtain on the freshwater mussel diversity of the Italian Peninsula and Croatian Adriatic coast
Biodiversity and Conservation, 2017Co-Authors: Elsa Froufe, Manuel Lopes-lima, Vincent Prié, Amilcar Teixeira, Nicoletta Riccardi, Serena Zaccara, Isabella Vanetti, Jasna Lajtner, Simone Varandas, Alexandra ZieritzAbstract:Freshwater mussels of the order Unionida have been dramatically declining globally. Despite their ecological importance, conservation of these animals has been hindered by unresolved taxonomy and a lack of data on the distribution and status of populations, especially in southern Europe. Although the Italian Peninsula has been noted as a centre of endemism and one of the major refugia of the glacial ages for several taxa, few studies have been performed on the genetic diversity of Unionida. Most importantly, the taxonomic status of several freshwater mussel populations of the Italian Peninsula is still unresolved. Here we present the first comprehensive dataset for the Unionida of the region spanning Italy and the coastal Croatian region (west of the Dinaric Alps). In total, 191 specimens were collected (85 Anodonta, 64 Unio , 17 Microcondylaea bonellii and 25 Sinanodonta woodiana ) from 34 sites across the Italian Peninsula and coastal Croatian river basins for molecular identification (COI, 16S and 28S). Genetic analyses were performed to understand major phylogenetic and phylogeographic patterns. Seven species were detected: three Anodonta species ( A. anatina , A. cygnea and A. exulcerata ), two Unio species ( U. mancus and U. elongatulus ), Microcondylaea bonellii , and the invasive Sinanodonta woodiana . The presence of three endemic species ( A. exulcerata , U. elongatulus and M. bonellii ) confirms the importance of the region as a centre of endemism for freshwater mussels. The Apennine Mountains act as an important biogeographic barrier.
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taxonomic reassessment of the freshwater mussel genus unio bivalvia Unionidae in russia and ukraine based on morphological and molecular data
Zootaxa, 2017Co-Authors: Olga K Klishko, Arthur E Bogan, Elsa Froufe, Manuel Lopeslima, Lyudmila Vasiliev, Lyudmila YanovichAbstract:The taxonomy of species within the genus Unio (Bivalvia: Unionidae: Unioninae) in Russia and Ukraine has been contentious due to the lack of correspondence between three concurrent yet divergent classifications. In order to clarify which classification system best reflects the evolutionary relationships among these taxa, we performed detailed morphological analyses on 720 Ukrainian and Russian specimens, complemented with molecular data (COI) from a selected number of specimens. The morphological character data set shows the existence of only three widespread species with slight eco-morphological variations. Statistical analyses of shell morphometric parameters and molecular analyses based on mtDNA COI gene fragment sequences confirm the existence of the same three species within a single genus, Unio , in Russia and Ukraine, that is U. pictorum, U. tumidus and U. crassus . Results from molecular analyses suggest the existence of an additional subgroup within the U. crassus lineage, U. crassus cf. courtilieri that deserves further research. The present integrated approach confirms the validity of the classification by Zhadin (1952) and rejects the complex classifications of Starobogatov et al . (2004) and Bogatov & Kijashko (2016).
Arthur E Bogan - One of the best experts on this subject based on the ideXlab platform.
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Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)
Zoological Journal of the Linnean Society, 2020Co-Authors: Alexandra Zieritz, Arthur E Bogan, Elsa Froufe, Han Ming Gan, Ronaldo Sousa, Ivan Bolotov, Duarte V Gonçalves, David C Aldridge, André Gomes-dos-santos, Amilcar TeixeiraAbstract:Abstract The Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian clade Contradentini+Rectidentini. We calculate substitution rates for the mitogenome, the 13 protein-coding genes, the two ribosomal units and three commonly used fragments (co1, nd1 and 16S) of both F- and M-mtDNA, based on a fossil-calibrated, mitogenomic phylogeny of the Unionidae. Phylogenetic analyses, including an M+F concatenated dataset, consistently recovers a monophyletic Gonideinae. Subfamily-level topology is congruent with that of a previous nuclear genomic study and with patterns in mitochondrial gene order, suggesting Unionidae F-type 2 as a synapomorphy of the Gonideinae. Our phylogeny indicates that the clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini split in the early Cretaceous (~125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (~79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type co1 and 16S for certain Unionidae and Margaritiferidae species (pairs).
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Variability of mitochondrial ORFans hints at possible differences in the system of doubly uniparental inheritance of mitochondria among families of freshwater mussels (Bivalvia: Unionida)
BMC Evolutionary Biology, 2019Co-Authors: Davide Guerra, Manuel Lopes-lima, Elsa Froufe, Han Ming Gan, Paz Ondina, Rafaela Amaro, M.w. Klunzinger, Claudia Tasso Callil, Vincent Prié, Arthur E BoganAbstract:Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly uniparental inheritance (DUI) of mitochondria. DUI is a system in which distinct female-transmitted and male-transmitted mitotypes coexist in a single species. In families Unionidae and Margaritiferidae, the transition from dioecy to hermaphroditism and the loss of DUI appear to be linked, and this event seems to affect the integrity of the ORFan genes. These observations led to the hypothesis that the ORFans have a role in DUI and/or sex determination. Complete mitochondrial genome sequences are however scarce for most families of freshwater mussels, therefore hindering a clear localization of DUI in the various lineages and a comprehensive understanding of the influence of the ORFans on DUI and sexual systems. Therefore, we sequenced and characterized eleven new mitogenomes from poorly sampled freshwater mussel families to gather information on the evolution and variability of the ORFan genes and their protein products. We obtained ten complete plus one almost complete mitogenome sequence from ten representative species (gonochoric and hermaphroditic) of families Margaritiferidae, Hyriidae, Mulleriidae, and Iridinidae. ORFan genes are present only in DUI species from Margaritiferidae and Hyriidae, while non-DUI species from Hyriidae, Iridinidae, and Mulleriidae lack them completely, independently of their sexual system. Comparisons among the proteins translated from the newly characterized ORFans and already known ones provide evidence of conserved structures, as well as family-specific features. The ORFan proteins show a comparable organization of secondary structures among different families of freshwater mussels, which supports a conserved physiological role, but also have distinctive family-specific features. Given this latter observation and the fact that the ORFans can be either highly mutated or completely absent in species that secondarily lost DUI depending on their respective family, we hypothesize that some aspects of the connection among ORFans, sexual systems, and DUI may differ in the various lineages of unionids.
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diversity biogeography and conservation of freshwater mussels bivalvia unionida in east and southeast asia
Hydrobiologia, 2018Co-Authors: Alexandra Zieritz, Arthur E Bogan, Elsa Froufe, Olga K Klishko, Takaki Kondo, Uthaiwan Kovitvadhi, Satit Kovitvadhi, Manuel Lopeslima, John M Pfeiffer, Ronaldo SousaAbstract:Recent research efforts have significantly advanced our knowledge on Asian freshwater mussel (Bivalvia: Unionida) diversity and distribution. Here we provide a modern consensus of the diversity, biogeography and conservation of Unionida in the region comprising East and Southeast Asia (excluding Wallacea) and Asian Russia. A data review confirmed the presence of 228 native and 3 non-native Unionida (98% Unionidae, 2% Margaritiferidae), rendering the region a global hotspot of freshwater mussel diversity. Species richness was highest in China (particularly Yangtze basin) in absolute numbers and Cambodia when correcting for country area, and decreased gradually towards the south and steeply towards the north and east. Six of the seven unionid subfamilies are native to the region, with species richness peaking in Southeast Asia for Rectidentinae, Gonideinae, Parreysiinae and Modellnaiinae, China for Anodontinae and Unioninae, and Asian Russia for Margaritiferidae. Conservation status and data collected after 1980 were not available for 61 and 24% of species, respectively. Dams, deforestation and pollution are likely the major threats to mussels in the region, though data in this respect are scarce. The Philippines, Laos, Indonesia, Myanmar and Malaysia are among the countries with the poorest data availability and urgently require research.
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a revised list of the freshwater mussels mollusca bivalvia unionida of the united states and canada
Freshwater Mollusk Biology and Conservation, 2017Co-Authors: James D Williams, Arthur E Bogan, Kevin S Cummings, Jeffrey T Garner, Nathan A Johnson, John L. Harris, Robert S. Butler, Thomas G WattersAbstract:We present a revised list of freshwater mussels (order Unionida, families Margaritiferidae and Unionidae) of the United States and Canada, incorporating changes in nomenclature and systematic taxonomy since publication of the most recent checklist in 1998. We recognize a total of 298 species in 55 genera in the families Margaritiferidae (one genus, five species) and Unionidae (54 genera, 293 species). We propose one change in the Margaritiferidae: the placement of the formerly monotypic genus Cumberlandia in the synonymy of Margaritifera. In the Unionidae, we recognize three new genera, elevate four genera from synonymy, and place three previously recognized genera in synonymy. We recognize for the first time two species (one native and one nonindigenous) in the Asian genus Sinanodonta as occurring in North America. We recognize four new species and one subspecies and elevate 21 species from synonymy. We elevate 10 subspecies to species status and no longer recognize four subspecies. We change common names for five taxa, correct spelling for eight species, and correct the date of publication of original descriptions for four species.
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taxonomic reassessment of the freshwater mussel genus unio bivalvia Unionidae in russia and ukraine based on morphological and molecular data
Zootaxa, 2017Co-Authors: Olga K Klishko, Arthur E Bogan, Elsa Froufe, Manuel Lopeslima, Lyudmila Vasiliev, Lyudmila YanovichAbstract:The taxonomy of species within the genus Unio (Bivalvia: Unionidae: Unioninae) in Russia and Ukraine has been contentious due to the lack of correspondence between three concurrent yet divergent classifications. In order to clarify which classification system best reflects the evolutionary relationships among these taxa, we performed detailed morphological analyses on 720 Ukrainian and Russian specimens, complemented with molecular data (COI) from a selected number of specimens. The morphological character data set shows the existence of only three widespread species with slight eco-morphological variations. Statistical analyses of shell morphometric parameters and molecular analyses based on mtDNA COI gene fragment sequences confirm the existence of the same three species within a single genus, Unio , in Russia and Ukraine, that is U. pictorum, U. tumidus and U. crassus . Results from molecular analyses suggest the existence of an additional subgroup within the U. crassus lineage, U. crassus cf. courtilieri that deserves further research. The present integrated approach confirms the validity of the classification by Zhadin (1952) and rejects the complex classifications of Starobogatov et al . (2004) and Bogatov & Kijashko (2016).
Manuel Lopes-lima - One of the best experts on this subject based on the ideXlab platform.
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Freshwater mussels (Bivalvia: Unionidae) from the rising sun (Far East Asia): phylogeny, systematics, and distribution
Molecular phylogenetics and evolution, 2020Co-Authors: Manuel Lopes-lima, Takaki Kondo, Jin Hee Lee, Akimasa Hattori, Sang Ki Kim, Akihisa Shirai, Hironori Hayashi, Taira Usui, Kanta Sakuma, Taishi ToriyaAbstract: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 gosannensis sp. nov., Beringiana fukuharai sp. nov., Buldowskia kamiyai sp. nov., and Koreosolenaia sitgyensis gen. & sp. nov. We also propose a replacement name for Nodularia sinulata, i.e. Nodularia breviconcha nom. 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, Koreosolenaia gen. nov., and Middendorffinaia are of high conservation concern.
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Variability of mitochondrial ORFans hints at possible differences in the system of doubly uniparental inheritance of mitochondria among families of freshwater mussels (Bivalvia: Unionida)
BMC Evolutionary Biology, 2019Co-Authors: Davide Guerra, Manuel Lopes-lima, Elsa Froufe, Han Ming Gan, Paz Ondina, Rafaela Amaro, M.w. Klunzinger, Claudia Tasso Callil, Vincent Prié, Arthur E BoganAbstract:Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly uniparental inheritance (DUI) of mitochondria. DUI is a system in which distinct female-transmitted and male-transmitted mitotypes coexist in a single species. In families Unionidae and Margaritiferidae, the transition from dioecy to hermaphroditism and the loss of DUI appear to be linked, and this event seems to affect the integrity of the ORFan genes. These observations led to the hypothesis that the ORFans have a role in DUI and/or sex determination. Complete mitochondrial genome sequences are however scarce for most families of freshwater mussels, therefore hindering a clear localization of DUI in the various lineages and a comprehensive understanding of the influence of the ORFans on DUI and sexual systems. Therefore, we sequenced and characterized eleven new mitogenomes from poorly sampled freshwater mussel families to gather information on the evolution and variability of the ORFan genes and their protein products. We obtained ten complete plus one almost complete mitogenome sequence from ten representative species (gonochoric and hermaphroditic) of families Margaritiferidae, Hyriidae, Mulleriidae, and Iridinidae. ORFan genes are present only in DUI species from Margaritiferidae and Hyriidae, while non-DUI species from Hyriidae, Iridinidae, and Mulleriidae lack them completely, independently of their sexual system. Comparisons among the proteins translated from the newly characterized ORFans and already known ones provide evidence of conserved structures, as well as family-specific features. The ORFan proteins show a comparable organization of secondary structures among different families of freshwater mussels, which supports a conserved physiological role, but also have distinctive family-specific features. Given this latter observation and the fact that the ORFans can be either highly mutated or completely absent in species that secondarily lost DUI depending on their respective family, we hypothesize that some aspects of the connection among ORFans, sexual systems, and DUI may differ in the various lineages of unionids.
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Lifting the curtain on the freshwater mussel diversity of the Italian Peninsula and Croatian Adriatic coast
Biodiversity and Conservation, 2017Co-Authors: Elsa Froufe, Manuel Lopes-lima, Vincent Prié, Amilcar Teixeira, Nicoletta Riccardi, Serena Zaccara, Isabella Vanetti, Jasna Lajtner, Simone Varandas, Alexandra ZieritzAbstract:Freshwater mussels of the order Unionida have been dramatically declining globally. Despite their ecological importance, conservation of these animals has been hindered by unresolved taxonomy and a lack of data on the distribution and status of populations, especially in southern Europe. Although the Italian Peninsula has been noted as a centre of endemism and one of the major refugia of the glacial ages for several taxa, few studies have been performed on the genetic diversity of Unionida. Most importantly, the taxonomic status of several freshwater mussel populations of the Italian Peninsula is still unresolved. Here we present the first comprehensive dataset for the Unionida of the region spanning Italy and the coastal Croatian region (west of the Dinaric Alps). In total, 191 specimens were collected (85 Anodonta, 64 Unio , 17 Microcondylaea bonellii and 25 Sinanodonta woodiana ) from 34 sites across the Italian Peninsula and coastal Croatian river basins for molecular identification (COI, 16S and 28S). Genetic analyses were performed to understand major phylogenetic and phylogeographic patterns. Seven species were detected: three Anodonta species ( A. anatina , A. cygnea and A. exulcerata ), two Unio species ( U. mancus and U. elongatulus ), Microcondylaea bonellii , and the invasive Sinanodonta woodiana . The presence of three endemic species ( A. exulcerata , U. elongatulus and M. bonellii ) confirms the importance of the region as a centre of endemism for freshwater mussels. The Apennine Mountains act as an important biogeographic barrier.
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Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes.
Molecular phylogenetics and evolution, 2016Co-Authors: Manuel Lopes-lima, Elsa Froufe, Olga K Klishko, Uthaiwan Kovitvadhi, Satit Kovitvadhi, Mohamed Ghamizi, Karen E. Mock, Ümit Kebapçı, Octávio S. PauloAbstract:Abstract Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032 bp (COI + 28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.
Shan Ouyang - One of the best experts on this subject based on the ideXlab platform.
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Phylogenetic position of Aculamprotula polysticta, comb. res. (Bivalvia : Unionidae) inferred from phylogenetic relationships in Unionida
Invertebrate Systematics, 2020Co-Authors: Kyung Seok Kim, Guang-long Xie, Shan OuyangAbstract:Accurate phylogenies are important for understanding the evolutionary histories of organisms, their reproductive traits and ecological habits. The freshwater mussel order Unionida is currently thought to include six families. However, assignment of particular species to these families has been unstable, particularly for species that have been described solely on conchological characters. Unio polystictus Heude, 1877 represents such a species. Based on DNA sequence data from five genes (COI, 16S rRNA, 18S rRNA, 28S rRNA and histone H3) and complete mitochondrial genomes, we investigated the phylogenetic position and generic affinities of U. polystictus using various analytical methods. Both the five-gene and mitogenome datasets strongly supported transferring U. polystictus from Margaritiferidae to Unionidae as Aculamprotula polysticta, comb. res. Our results also supported the following intrageneric relationships: (Aculamprotula tortuosa, ((Aculamprotula polysticta, Aculamprotula scripta), (Aculamprotula fibrosa, Aculamprotula tientsinersis))). In addition, by comparing the morphological features of Aculamprotula (Unionidae, Unioninae), Lamprotula (Unionidae, Gonideinae) and Gibbosula (Margaritiferidae, Gibbosulinae) species, potential issues of relying solely on shell morphology for high-level classification of freshwater mussels are highlighted. Confirmation of classification position and genetic relationship for Aculamprotula polysticta will helpful to understand the ecological characteristics, reproductive strategies and host-fish requirements, which can be inferred from closely related taxa.
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Analysis of mitochondrial genomes resolves the phylogenetic position of Chinese freshwater mussels (Bivalvia, Unionidae).
ZooKeys, 2019Co-Authors: Xiongjun Liu, Kevin J Roe, Wang, Shan OuyangAbstract:The Yangtze River basin is one of the most species-rich regions for freshwater mussels on Earth, but is gravely threatened by anthropogenic activities. However, conservation planning and management of mussel species has been hindered by a number of taxonomic uncertainties. In order to clarify the taxonomic status and phylogenetic position of these species, mitochondrial genomes of four species (Acuticostachinensis, Schistodesmuslampreyanus, Cuneopsisheudei and Cuneopsiscapitatus) were generated and analyzed along with data from 43 other mitogenomes. The complete F-type mitogenomes of A.chinensis, S.lampreyanus, C.heudei, and C.capitatus are 15652 bp, 15855 bp, 15892 bp, and 15844 bp, respectively, and all four F-type mitogenomes have the same pattern of gene arrangement. ML and BI trees based on the mitogenome dataset are completely congruent, and indicate that the included Unionidae belong to three subfamilies with high bootstrap and posterior probabilities, i.e., Unioninae (Aculamprotula, Cuneopsis, Nodularia, and Schistodesmus), Anodontinae (Cristaria, Arconaia, Acuticosta, Lanceolaria, Anemina, and Sinoanodonta), and Gonideinae (Ptychorhynchus, Solenaia, Lamprotula, and Sinohyriopsis). Results also indicate that A.chinensis has affinities with Arconaialanceolata and Lanceolariagrayii and is a member of the subfamily Anodontinae.
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Microsatellite analysis of genetic diversity and genetic structure of the Chinese freshwater mussel Solenaia carinata (Bivalvia: Unionidae)
Aquatic Conservation: Marine and Freshwater Ecosystems, 2017Co-Authors: Tingting Sun, Chun-hua Zhou, Xiongjun Liu, David T Zanatta, Hongxiu Ding, Wenjing Yang, Shan OuyangAbstract:The freshwater mussels (Unionidae) in the Yangtze River basin of China are among the most diverse assemblages on Earth. Freshwater mussels provide valuable ecosystem services (e.g. natural water filtration) and economic value (shell, pearls, and food), but are experiencing global declines as a result of pollution, habitat alteration, and overharvest. Despite the diversity and value of freshwater mussels in the Yangtze River basin, relatively little is known about the biology of the many species endemic to the region. Solenaia carinata is an endemic and potentially imperilled freshwater mussel (Bivalvia: Unionidae) in China that is distributed in a single major tributary of the middle Yangtze; the Poyang Lake basin in Jiangxi Province. This study represents the first analyses of the genetic diversity and population genetic structure of S. carinata. Solenaia carinata specimens (n=64) were collected from three sites in large tributary rivers of Poyang Lake. Using 19 polymorphic microsatellite markers, the results showed that S. carinata had a moderate level of genetic diversity (PIC ranged from 0.464 to 0.484), limited evidence of a recent genetic bottleneck, little genetic differentiation (FST ranged from 0.021 to 0.045), high levels of gene flow (Nm ranged from 3.675 to 33.227) and limited genetic structure among the three sampling locations. Given that S. carinata inhabits a highly interconnected system of large rivers and lakes, the results of low differentiation and high gene flow among geographically proximate sampling locations (sites separated by between 8 and 20 km of water) are not surprising. The results indicate that specimens can be used and moved from anywhere across the distribution of S. carinata for the purposes of captive propogation and translocation.
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The complete maternal mitochondrial genome of rare Chinese freshwater mussel Lepidodesma languilati (Bivalvia: Unionidae: Unioninae).
Mitochondrial DNA. Part A DNA mapping sequencing and analysis, 2015Co-Authors: Chun-hua Zhou, Shan Ouyang, Mei-huang DingAbstract:Lepidodesma languilati is considered threatened because of the influence of human activities in China. The complete F-type mitochondrial genome of L. languilati was determined in this study (GenBank accession no. KT381195). It is a 15 754-bp-long circular molecule that consists of 37 genes that are typically found in other invertebrates. The overall base composition of the entire sequence is as follows: A (39.1%), T (25.7%), C (23.4%), and G (11.8%). Except for cox1 (TTG), cob (ATT), nad1 (ATT), nad6 (ATA), nad4 (TTG), and atp8 (GTG), 7 of the 13 protein-coding genes initiate with orthodox ATG start codon. All the 13 protein-coding genes have complete termination codon TAA or TAG. Phylogenetic tree indicates that L. languilati belongs to Unioninae. The newly sequenced complete mitogenome can provide basic data for comparative studies on mitochondrial genomes of Unionidae. It could also lay the important theoretical foundation for phylogenetics, population genetics, germplasm resources protection, sustainable, and reasonable utilization.
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Complete maternal mitochondrial genome of freshwater mussel Aculamprotula tientsinensis (Bivalvia: Unionidae: Unioninae).
Mitochondrial DNA. Part A DNA mapping sequencing and analysis, 2015Co-Authors: Chun-hua Zhou, Shan OuyangAbstract:AbstractAculamprotula tientsinensis is a rare and endemic species of freshwater mussel in China. This study firstly determined the complete F-type mitochondrial genome of A. tientsinensis. The circle genome (15 695 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 FORF gene. Except for cob, nad5 and nad6, the remaining protein-coding genes initiate with the orthodox start codon (ATG, ATA, ATT). There are 26 non-coding regions in the mitogenome of A. tientsinensis, ranging in size from 1 to 229 bp. The base composition of the genome is A (37.83%), G (12.69%), T (25.43%) and C (24.06%). Gene order is identical to other female species of Unionidae but for Gonideinae. The phylogenetic analyses of Unionidae indicate that A. tientsinensis is closely related to A. tortuosa and A. coreana, which belong to Unioninae. The complete mitogenome can deepen comparative and evolutionary genomics of Unionidae and be more comprehensive to parse the genetic relationship between the species and the owners...
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Microsatellite analysis of genetic diversity and genetic structure of the Chinese freshwater mussel Solenaia carinata (Bivalvia: Unionidae)
Aquatic Conservation: Marine and Freshwater Ecosystems, 2017Co-Authors: Tingting Sun, Chun-hua Zhou, Xiongjun Liu, David T Zanatta, Hongxiu Ding, Wenjing Yang, Shan OuyangAbstract:The freshwater mussels (Unionidae) in the Yangtze River basin of China are among the most diverse assemblages on Earth. Freshwater mussels provide valuable ecosystem services (e.g. natural water filtration) and economic value (shell, pearls, and food), but are experiencing global declines as a result of pollution, habitat alteration, and overharvest. Despite the diversity and value of freshwater mussels in the Yangtze River basin, relatively little is known about the biology of the many species endemic to the region. Solenaia carinata is an endemic and potentially imperilled freshwater mussel (Bivalvia: Unionidae) in China that is distributed in a single major tributary of the middle Yangtze; the Poyang Lake basin in Jiangxi Province. This study represents the first analyses of the genetic diversity and population genetic structure of S. carinata. Solenaia carinata specimens (n=64) were collected from three sites in large tributary rivers of Poyang Lake. Using 19 polymorphic microsatellite markers, the results showed that S. carinata had a moderate level of genetic diversity (PIC ranged from 0.464 to 0.484), limited evidence of a recent genetic bottleneck, little genetic differentiation (FST ranged from 0.021 to 0.045), high levels of gene flow (Nm ranged from 3.675 to 33.227) and limited genetic structure among the three sampling locations. Given that S. carinata inhabits a highly interconnected system of large rivers and lakes, the results of low differentiation and high gene flow among geographically proximate sampling locations (sites separated by between 8 and 20 km of water) are not surprising. The results indicate that specimens can be used and moved from anywhere across the distribution of S. carinata for the purposes of captive propogation and translocation.
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The complete maternal mitochondrial genome of rare Chinese freshwater mussel Lepidodesma languilati (Bivalvia: Unionidae: Unioninae).
Mitochondrial DNA. Part A DNA mapping sequencing and analysis, 2015Co-Authors: Chun-hua Zhou, Shan Ouyang, Mei-huang DingAbstract:Lepidodesma languilati is considered threatened because of the influence of human activities in China. The complete F-type mitochondrial genome of L. languilati was determined in this study (GenBank accession no. KT381195). It is a 15 754-bp-long circular molecule that consists of 37 genes that are typically found in other invertebrates. The overall base composition of the entire sequence is as follows: A (39.1%), T (25.7%), C (23.4%), and G (11.8%). Except for cox1 (TTG), cob (ATT), nad1 (ATT), nad6 (ATA), nad4 (TTG), and atp8 (GTG), 7 of the 13 protein-coding genes initiate with orthodox ATG start codon. All the 13 protein-coding genes have complete termination codon TAA or TAG. Phylogenetic tree indicates that L. languilati belongs to Unioninae. The newly sequenced complete mitogenome can provide basic data for comparative studies on mitochondrial genomes of Unionidae. It could also lay the important theoretical foundation for phylogenetics, population genetics, germplasm resources protection, sustainable, and reasonable utilization.
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Complete maternal mitochondrial genome of freshwater mussel Aculamprotula tientsinensis (Bivalvia: Unionidae: Unioninae).
Mitochondrial DNA. Part A DNA mapping sequencing and analysis, 2015Co-Authors: Chun-hua Zhou, Shan OuyangAbstract:AbstractAculamprotula tientsinensis is a rare and endemic species of freshwater mussel in China. This study firstly determined the complete F-type mitochondrial genome of A. tientsinensis. The circle genome (15 695 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 FORF gene. Except for cob, nad5 and nad6, the remaining protein-coding genes initiate with the orthodox start codon (ATG, ATA, ATT). There are 26 non-coding regions in the mitogenome of A. tientsinensis, ranging in size from 1 to 229 bp. The base composition of the genome is A (37.83%), G (12.69%), T (25.43%) and C (24.06%). Gene order is identical to other female species of Unionidae but for Gonideinae. The phylogenetic analyses of Unionidae indicate that A. tientsinensis is closely related to A. tortuosa and A. coreana, which belong to Unioninae. The complete mitogenome can deepen comparative and evolutionary genomics of Unionidae and be more comprehensive to parse the genetic relationship between the species and the owners...
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The complete F-type mitochondrial genome of Chinese Anodonta arcaeformis (Bivalvia: Unionidae: Anodontinae).
Mitochondrial DNA. Part A DNA mapping sequencing and analysis, 2014Co-Authors: Ouyang Shan, Chun-hua ZhouAbstract:AbstractAnodonta arcaeformis is a Chinese common species. The complete F-type mitochondrial genome was first determined. The complete genome is 15,672 bp in length, with AT content 64.59%. All the 37 typical animal mitochondrial genes were identified, including 13 protein coding genes, 22 tRNA genes and 2 rRNA genes. And a novel FORF (277 bp, 92aa) was found between tRNAGlu and ND2, which was considered to be involved in sex determination. The putative control region (270 bp) is located between ND5 and tRNAGln, with an A + T content of 70.07%. The gene order is identical to other species of Unionidae female mitochondrial except Gonideinae.
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The Complete Maternally and Paternally Inherited Mitochondrial Genomes of the Endangered Freshwater Mussel Solenaia carinatus (Bivalvia: Unionidae) and Implications for Unionidae Taxonomy
PloS one, 2013Co-Authors: Xiao-chen Huang, Jun Rong, Yong Liu, Ming-hua Zhang, Yuan Wan, Ouyang Shan, Chun-hua ZhouAbstract:Doubly uniparental inheritance (DUI) is an exception to the typical maternal inheritance of mitochondrial (mt) DNA in Metazoa, and found only in some bivalves. In species with DUI, there are two highly divergent gender-associated mt genomes: maternal (F) and paternal (M), which transmit independently and show different tissue localization. Solenaia carinatus is an endangered freshwater mussel species exclusive to Poyang Lake basin, China. Anthropogenic events in the watershed greatly threaten the survival of this species. Nevertheless, the taxonomy of S. carinatus based on shell morphology is confusing, and the subfamilial placement of the genus Solenaia remains unclear. In order to clarify the taxonomic status and discuss the phylogenetic implications of family Unionidae, the entire F and M mt genomes of S. carinatus were sequenced and compared with the mt genomes of diverse freshwater mussel species. The complete F and M mt genomes of S. carinatus are 16716 bp and 17102 bp in size, respectively. The F and M mt genomes of S. carinatus diverge by about 40% in nucleotide sequence and 48% in amino acid sequence. Compared to F counterparts, the M genome shows a more compact structure. Different gene arrangements are found in these two gender-associated mt genomes. Among these, the F genome cox2-rrnS gene order is considered to be a genome-level synapomorphy for female lineage of the subfamily Gonideinae. From maternal and paternal mtDNA perspectives, the phylogenetic analyses of Unionoida indicate that S. carinatus belongs to Gonideinae. The F and M clades in freshwater mussels are reciprocal monophyly. The phylogenetic trees advocate the classification of sampled Unionidae species into four subfamilies: Gonideinae, Ambleminae, Anodontinae, and Unioninae, which is supported by the morphological characteristics of glochidia.
