Browsing by Author "Aldridge, David C."
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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.
- Conservation status of freshwater mussels in Europe: state of the art and future challengesPublication . Lopes-Lima, Manuel; Sousa, Ronaldo; Geist, Juergen; Aldridge, David C.; Araujo, Rafael; Bergengren, Jakob; Bespalaya, Yulia V.; Bódis, Erika; Burlakova, Lyubov E.; Van Damme, Dirk; Douda, Karel; Froufe, Elsa; Georgiev, Dilian; Gumpinger, Clemens; Karatayev, Alexander Y.; Kebapçi, Ümit; Killeen, Ian; Lajtner, Jasna; Larsen, Bjørn M.; Lauceri, Rosaria; Legakis, Anastasios; Lois, Sabela; Lundberg, Stefan; Moorkens, Evelyn A.; Motte, Gregory; Nagel, Karl Otto; Ondina, Paz; Outeiro, Adolfo; Paunovic, Momir; Prié, Vincent; Proschwitz, Ted von; Riccardi, Nicoletta; Rudzīte, Mudīte; Rudzītis, Māris; Scheder, Christian; Seddon, Mary; Şereflişan, Hülya; Simić, Vladica; Sokolova, Svetlana; Stoeckl, Katharina; Taskinen, Jouni; Teixeira, Amílcar; Thielen, Frankie; Trichkova, Teodora; Varandas, Simone; Vicentini, Heinrich; Zajac, Katarzyna; Zając, Tadeusz; Zogaris, StamatisFreshwater mussels of the Order Unionida provide important ecosystem functions and services, yet many of their populations are in decline. We comprehensively review the status of the 16 currently recognized species in Europe, collating for the first time their life-history traits, distribution, conservation status, habitat preferences, and main threats in order to suggest future management actions. In northern, central, and eastern Europe, a relatively homogeneous species composition is found in most basins. In southern Europe, despite the lower species richness, spatially restricted species make these basins a high conservation priority. Information on freshwater mussels in Europe is unevenly distributed with considerable differences in data quality and quantity among countries and species. To make conservation more effective in the future, we suggest greater international cooperation using standardized protocols and methods to monitor and manage European freshwater mussel diversity. Such an approach will not only help conserve this vulnerable group but also, through the protection of these important organisms, will offer wider benefits to freshwater ecosystems.
- 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.
- The first Margaritiferidae male (M-Type) mitogenome: Mitochondrial gene order as a potential character for determining higher-order phylogeny within Unionida (Bivalvia)Publication . Lopes-Lima, Manuel; Fonseca, Miguel M.; Aldridge, David C.; Bogan, Arthur E.; Gan, Han Ming; Ghamizi, Mohamed; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Zanatta, David T.; Zieritz, Alexandra; Froufe, Elsa
- Fishing for hosts: larval spurting by the endangered thick-shelled river mussel, Unio crassusPublication . Aldridge, David C.; Brian, Joshua I.; Cmiel, Adam; Lipinska, Anna; Lopes-Lima, Manuel; Sousa, Ronaldo; Teixeira, Amílcar; Zajac, Katarzyna; Zając, TadeuszUnderstanding the life-history characteristics of endangered species is crucial to their conservation, management, and predicting their responses to environmental change (Stark et al., 2004). Host specificity is central to the evolutionary diversification and conservation of the Unionida (Barnhart et al., 2008; Modesto et al., 2018). In the North American mussels of the Ambleminae subfamily, specificity toward a restricted host fish range that shares the same microhabitat as the mussel has resulted in remarkable morphologies and behaviors that dramatically increase the likelihood of attachment and successful transmission of larvae (glochidia).
- Genetic diversity of the pan-European freshwater mussel Anodonta anatina (Bivalvia: Unionoida) based on CO1: new phylogenetic insights and implications for conservationPublication . Froufe, Elsa; Sobral, Carina; Teixeira, Amílcar; Sousa, Ronaldo; Varandas, Simone; Aldridge, David C.; Lopes-Lima, Manuel1. The duck mussel, Anodonta anatina, has been described as abundant and widespread in Europe. However, it is listed as near threatened or threatened in several countries owing to severe declines in abundance and/or spatial distribution. 2. Despite its potential ecological importance and conservation status almost nothing is known regarding its genetic diversity. 3. As a preliminary analysis, variation within the cytochrome oxidase 1 mitochondrial gene was determined from European specimens from Portugal in the south west, to Ukraine in the east, and Sweden in the north. 4. Three major mtDNA clades were retrieved: clade 1 includes all the individuals from Iberia, except those from the Ebro basin; clade 2 includes all the European non-Iberian and non-Italian samples; and clade 3 includes all the individuals from Italy and from the Ebro basin. AMOVA analysis revealed significant genetic differences among the three clades. Within each of the major clades, several geographically related haplogroups were also retrieved, especially in Iberia, where four genetically distinct groups (North-West, South-Central, South-West and Ebro) were revealed. 5. Given the evidence of regional declines of A. anatina in Europe, the confirmation of geographically distinct genotypes indicates a need for the development of management strategies directed towards the conservation of localized populations.
- 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.
- Mesozoic mitogenome rearrangements and freshwater mussel (Bivalvia: Unionoidea) macroevolutionPublication . Froufe, Elsa; Bolotov, Ivan N.; Aldridge, David C.; Bogan, Arthur E.; Breton, Sophie; Gan, Han Ming; Kovitvadhi, Uthaiwan; Kovitvadhi, Satit; Riccardi, Nicoletta; Secci-Petretto, Giulia; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Zanatta, David; Zieritz, Alexandra; Fonseca, Miguel M.; Lopes-Lima, ManuelUsing a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female mitogenome (i.e., gene orders MF1 and UF1). Our results suggest that this macroevolutionary jump was completed within a relatively short time interval (95% HPD 201–226 Ma) that coincided with the Triassic–Jurassic mass extinction. Both gene orders have persisted within these clades for ~200 Ma. The monophyly of the so-called “problematic” Gonideinae taxa was supported by all the inferred phylogenies in this study using, for the first time, the M- and F-type mitogenomes either singly or combined. Within Gonideinae, two additional splits in the gene order (UF1 to UF2, UF2 to UF3) occurred in the Mesozoic and have persisted for ~150 and ~100 Ma, respectively. Finally, the mitogenomic results suggest ancient connections between freshwater basins of East Asia and Europe near the Cretaceous–Paleogene boundary, probably via a continuous paleo-river system or along the Tethys coastal line, which are well supported by at least three independent but almost synchronous divergence events.
- Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- And M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)Publication . Zieritz, Alexandra; Froufe, Elsa; Bolotov, Ivan N.; Gonçalves, Duarte V.; Aldridge, David C.; Bogan, Arthur E.; Gan, Han Ming; Gomes-dos-Santos, André; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Zanatta, David; Lopes-Lima, ManuelThe 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).
- Newly developed microsatellite markers for the pan-European duck mussel, Anodonta anatina: Revisiting the main mitochondrial lineagesPublication . Lopes-Lima, Manuel; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Riccardi, Nicoletta; Aldridge, David C.; Froufe, ElsaFreshwater mussels of the family Unionidae are one of the most threatened groups worldwide and have suffered severe decline over recent decades. Although the freshwater duck mussel, Anodonta anatina (Linnaeus, 1758), is still widespread, this species has shown evidence of recent declines and is already protected in some European countries. Informed conservation efforts must take into account patterns in genetic diversity and phylogeography. In the present study, 20 newly developed polymorphic loci were described and tested in seven populations of A. anatina, belonging to three previously detected divergent mtDNA lineages. The genetic diversity patterns, within and among A. anatina populations, were evaluated to test their congruence with those lineages. A high genetic differentiation (F ST ) was found among all populations, with the exception of those in Central Europe (Germany) and the UK, which were not strongly structured. The present study confirms the division of the species into three evolutionarily significant units corresponding to the three previously detected mtDNA lineages, which should be managed independently. Furthermore, owing to the high differentiation among southern European populations, the establishment of distinct management units for the Guadalquivir, Guadiana and Douro populations in the Iberian Peninsula is also proposed.