Percorrer por autor "Vikhrev, Ilya V."
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- Complete mitochondrial genomes of the freshwater mussels Amblema plicata (Say, 1817), Pleurobema oviforme (Conrad, 1834), and Popenaias popeii (Lea, 1857) (Bivalvia: Unionidae: Ambleminae)Publication . Teiga-Teixeira, João; Froufe, Elsa; Gomes-dos-Santos, André; Bogan, Arthur E.; Karatayev, Alexander Y.; Burlakova, Lyubov E.; Aldridge, David C.; Bolotov, Ivan N.; Vikhrev, Ilya V.; Teixeira, Amílcar; Varandas, Simone; Zanatta, David T.; Lopes-Lima, ManuelFreshwater mussels are a critically imperiled group of mollusks that play key ecological roles and provide important services to humans. The Ambleminae is the only subfamily of these mussels, endemic to North America. Complete mitogenomes have only been sequenced for two of five tribes of the subfamily. Pleurobema oviforme, Amblema plicata, and Popenaias popeii each belong to tribes Pleurobemini, Amblemini, and Popenaidini, respectively, and have not had published mitogenomes. Thus, this study aims to present the complete mitogenomes for these species, to provide a phylogeny of the Ambleminae and confirm the gene arrangements with representation from each of its tribes. The newly sequenced mitogenomes range from 15,852 to 15,993 nucleotides, are composed of 13 PCGs, 22 tRNAs, and two rRNAs and all share the same (UF1) gene order.
- Conbiomics: the missing approach for the conservation of freshwater bivalvesPublication . Froufe, Elsa; Fonseca, Miguel M.; Teixeira, Amílcar; Varandas, Simone; Gonçalves, Duarte V.; Hinzmann, Mariana; Arenas-Arenas, Francisco José; Gan, Han Ming; Breton, Sophie; Prié, Vincent; Zieritz, Alexandra; Bogan, Arthur E.; Razgour, Orly; Vikhrev, Ilya V.; Bolotov, Ivan N.; Pfeiffer, John; Lopes-Lima, ManuelThe decline of freshwater biodiversity hás reached alarming proportions. The extinction rate of freshwater biodiversity is predicted to be five times faster than ali other groups of species. The Unionidae, being the largest of the freshwater bivalve families, is among the most endangered group in the world. They are important providers of aquatic ecosystem services and are characterized by an unusual pattem of mtDNA inheritance. However, phylogeny, population genetic structure and species-level diversity remains unclear for much of the group. With an experienced and well-qualified team, the present proposal aims to define the most important freshwater mussel taxa and most criticai áreas for conservation, at European and Global leveis, to inform the most relevant policy niakers. This will be achieved by integrating a genomics approach with available distribution data, in order to determine and map global species richness, phylogenetic diversity, and weighted endemism. This complementary approach will not only help conserve this vulnerable group but will offer wider benefits to freshwater ecosystems whose billions of people depend globally. Additionally, as these animals have an extraordinary unusual pattern of mtDNA inheritance, they will be used as model-taxa to study the evolution of mtDNA and life in general.
- The crown pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)Publication . Gomes-dos-Santos, André; Lopes-Lima, Manuel; Machado, André M.; Ramos, António Marcos; Usié, Ana; Bolotov, Ivan N.; Vikhrev, Ilya V.; Breton, Sophie; Castro, L. Filipe C.; Fonseca, Rute R. da; Geist, Juergen; Österling, Martin E.; Prié, Vincent; Teixeira, Amílcar; Gan, Han Ming; Simakov, Oleg; Froufe, ElsaSince historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species' unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.
- Diversity, biogeography, evolutionary relationships, and conservation of Eastern Mediterranean freshwater mussels (Bivalvia: Unionidae)Publication . Lopes-Lima, Manuel; Gürlek, Mustafa Emre; Kebapçi, Ümit; Şereflişan, Hülya; Yanık, Telat; Mirzajani, Alireza; Neubert, Eike; Prié, Vincent; Teixeira, Amílcar; Gomes-dos-Santos, André; Barros-García, David; Bolotov, Ivan N.; Kondakov, Alexander V.; Vikhrev, Ilya V.; Tomilova, Alena A.; Özcan, Tahir; Altun, Ayhan; Gonçalves, Duarte V.; Bogan, Arthur E.; Froufe, ElsaLocated at the junction between Europe, Africa, and Asia, with distinct evolutionary origins and varied ecological and geographical settings, together with a marked history of changes in orogeny and configuration of the main river basins, turned the Eastern Mediterranean into a region of high diversity and endemism of freshwater taxa. Freshwater mussels (Bivalvia, Unionidae) from the Western Palearctic have been widely studied in their European range, but little attention has been dedicated to these taxa in the Eastern Mediterranean region and their diversity and phylogeography are still poorly understood. The present study aims to resolve the diversity, biogeography, and evolutionary relationships of the Eastern Mediterranean freshwater mussels. To that end, we performed multiple field surveys, phylogenetic analyses, and a thorough taxonomic revaluation. We reassessed the systematics of all Unionidae species in the region, including newly collected specimens across Turkey, Israel, and Iran, combining COI + 16S + 28S and COI phylogenies with molecular species delineation methods. Phylogeographical patterns were characterized based on published molecular data, newly sequenced specimens, and species distribution data, as well as ancestral range estimations. We reveal that Unionidae species richness in the Eastern Mediterranean is over 70% higher than previously assumed, counting 19 species within two subfamilies, the Unioninae (14) and Gonideinae (5). We propose two new species, Anodonta seddoni sp. nov. and Leguminaia anatolica sp. nov. Six additional taxa, Unio delicatus stat. rev., Unio eucirrus stat. rev., Unio hueti stat. rev., Unio sesirmensis stat. rev., Unio terminalis stat. rev. removed from the synonymy of Unio tigridis, as well as Unio damascensis stat. rev. removed from the synonymy of Unio crassus, are re-described. The nominal taxa Unio rothi var. komarowi O. Boettger, 1880 and Unio armeniacus Kobelt, 1911 are proposed as new synonyms of Unio bruguierianus, and Anodonta cyrea Drouët, 1881 and Anodonta cilicica Kobelt and Rolle, 1895 as new synonyms of Anodonta anatina. Also, the presence of Unio tumidus in the Maritza River is confirmed. The phylogeographic patterns described here are interpreted concerning major past geological events. Conservation needs and implications are presented, together with populations and species conservation priorities.
- Expansion and systematics redefinition of the most threatened freshwater mussel family, the MargaritiferidaePublication . Lopes-Lima, Manuel; Bolotov, Ivan N.; Do, Van Tu; Aldridge, David C.; Fonseca, Miguel M.; Gan, Han Ming; Gofarov, Mikhail Y.; Kondakov, Alexander V.; Prié, Vincent; Sousa, Ronaldo; Varandas, Simone; Vikhrev, Ilya V.; Teixeira, Amílcar; Wu, Rui Wen; Wu, Xiaoping; Zieritz, Alexandra; Froufe, Elsa; Bogan, Arthur E.Two Unionida (freshwater mussel) families are present in the Northern Hemisphere; the Margaritiferidae, representing the most threatened of unionid families, and the Unionidae, which include several genera of unresolved taxonomic placement. The recent reassignment of the poorly studied Lamprotula rochechouartii from the Unionidae to the Margaritiferidae motivated a new search for other potential species of margaritiferids from members of Gibbosula and Lamprotula. Based on molecular and morphological analyses conducted on newly collected specimens from Vietnam, we here assign Gibbosula crassa to the Margaritiferidae. Additionally, we reanalyzed all diagnostic characteristics of the Margaritiferidae and examined museum specimens of Lamprotula andGibbosula.As a result, two additional speciesarealsomovedtotheMargaritiferidae, i.e.Gibbosula confragosa and Gibbosula polysticta. We performed a robust five marker phylogeny with all available margaritiferid species and discuss the taxonomy within the family. The present phylogeny reveals the division of Margaritiferidae into four ancient clades with distinct morphological, biogeographical and ecological characteristics that justify the division of the Margaritiferidae into two subfamilies (Gibbosulinae and Margaritiferinae) and four genera (Gibbosula, Cumberlandia, Margaritifera, and Pseudunio). The systematics of the Margaritiferidae family is redefined as well as their distribution, potential origin and main biogeographic patterns.
- Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implicationsPublication . Lopes-Lima, Manuel; Geist, Juergen P.; Egg, S.; Beran, Luboš; Bikashvili, Ani; Van Bocxlaer, Bert; Bogan, Arthur E.; Bolotov, Ivan N.; Chelpanovskaya, O.A.; Douda, Karel; Fernandes, Verónica; Gomes-dos-Santos, André; Gonçalves, Duarte Vasconcelos; Gürlek, Mustafa Emre; Johnson, Nathan A.; Karaouzas, Ioannis D.; Kebapçı, Ümit; Kondakov, Duarte Vasconcelos; Kuehn, Ralf; Lajtner, Jasna; Mumladze, Levan; Nagel, Karl Otto; Neubert, Eike; Österling, Martin E.; Pfeiffer, John M.; Prié, Vincent; Riccardi, Nicoletta; Sell, Jerzy; Schneider, Lea D.; Shumka, Spase; Sîrbu, Ioan; Skujienė, Grita; Smith, Chase H.; Sousa, Ronaldo Gomes; Stöckl, K.; Taskinen, Jouni K.; Teixeira, Amílcar; Todorov, Milcho T.; Trichkova, Teodora A.; Urbańska, Maria; Välilä, Santtu; Varandas, Simone Da Graça Pinto; Veríssimo, Joana; Vikhrev, Ilya V.; Woschitz, G.; Zając, Katarzyna; Zając, Tadeusz A.; Zanatta, David Thomas; Zieritz, Alexandra; Zogaris, Stamatis; Froufe, ElsaThe global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectus stat. rev., Unio gontierii stat. rev., Unio mardinensis stat. rev., Unio nanus stat. rev., and Unio vicarius stat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.
- The male and female complete mitochondrial genomes of the threatened freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) (Bivalvia: Margaritiferidae)Publication . Gomes-dos-Santos, André; Froufe, Elsa; Amaro, Rafaela; Ondina, Paz; Breton, Sophie; Guerra, Davide; Aldridge, David C.; Bolotov, Ivan N.; Vikhrev, Ilya V.; Gan, Han Ming; Gonçalves, Duarte V.; Bogan, Arthur E.; Sousa, Ronaldo; Stewart, Donald; Teixeira, Amílcar; Varandas, Simone; Zanatta, David; Lopes-Lima, ManuelThe complete mitogenomes of one (M-)ale (North America), one Hermaphroditic (Europe), and two (F-)emale (North America and Europe) individuals of the freshwater pearl mussel Margaritifera margaritifera were sequenced. The M-type and F-type (Female and Hermaphroditic) mitogenomes have 17,421 and 16,122 nucleotides, respectively. All with the same content: 13 protein-coding genes, 22 transfer RNA, two ribosomal RNA genes, and one sex-related ORF. The M-type is highly divergent (37.6% uncorrected p-distance) from the F-type mitogenomes. North American and European F-type mitogenomes exhibit low genetic divergence (68 nt substitutions), and the Female and Hermaphroditic European mitogenomes are almost identical, and matching sex-related ORFs.
- The role of anthropogenic habitats in freshwater mussel conservationPublication . Sousa, Ronaldo; Halabowski, Dariusz; Labecka, Anna M.; Douda, Karel; Aksenova, Olga V.; Bespalaya, Yulia V.; Bolotov, Ivan N.; Geist, Juergen; Jones, Hugh A.; Konopleva, Ekaterina; Klunzinger, Michael W.; Lasso, Carlos A.; Lewin, Iga; Liu, Xiongjun; Lopes-Lima, Manuel; Mageroy, Jon; Mlambo, Musa; Nakamura, Keiko; Nakano, Mitsunori; Österling, Martin E.; Pfeiffer, John; Prié, Vincent; Paschoal, Lucas R.P.; Riccardi, Nicoletta; Santos, Rogério; Shumka, Spase; Smith, Allan K.; Son, Mikhail O.; Teixeira, Amílcar; Thielen, Frankie; Torres, Santiago; Varandas, Simone; Vikhrev, Ilya V.; Wu, Xiaoping; Zieritz, Alexandra; Nogueira, Joana GarridoAnthropogenic freshwater habitats may provide undervalued prospects for long-term conservation as part of species conservation planning. This fundamental, but overlooked, issue requires attention considering the pace that humans have been altering natural freshwater ecosystems and the accelerated levels of biodiversity decline in recent decades. We compiled 709 records of freshwater mussels (Bivalvia, Unionida) inhabiting a broad variety of anthropogenic habitat types (from small ponds to large reservoirs and canals) and reviewed their importance as refuges for this faunal group. Most records came from Europe and North America, with a clear dominance of canals and reservoirs. The dataset covered 228 species, including 34 threatened species on the IUCN Red List. We discuss the conservation importance and provide guidance on how these anthropogenic habitats could be managed to provide optimal conservation value to freshwater mussels. This review also shows that some of these habitats may function as ecological traps owing to conflicting management practices or because they act as a sink for some populations. Therefore, anthropogenic habitats should not be seen as a panacea to resolve conservation problems. More information is necessary to better understand the trade-offs between human use and the conservation of freshwater mussels (and other biota) within anthropogenic habitats, given the low number of quantitative studies and the strong biogeographic knowledge bias that persists.