Inferring phylogeny, demography and adaptive evolution in Margaritiferidae from High-throughput Sequencing data

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The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Publication . Gomes-dos-Santos, André; Lopes-Lima, Manuel; Machado, André M.; Forest, Thomas; Achaz, Guillaume; Teixeira, Amílcar; Prié, Vincent; Castro, L. Filipe C.; Froufe, Elsa

Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species’ unique biological and evolutionary features, helping promote its conservation.

2023Journal article

Open access

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, Elsa

Located 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.

2021Journal article

Open access

The silent extinction of freshwater mussels in Portugal

Publication . Lopes-Lima, Manuel; Reis, Joaquim; Alvarez, Maria G.; Anastácio, Pedro M.; Banha, Filipe; Beja, Pedro; Castro, Paulo S.; Gama, Mafalda; Gil, Maria G.; Gomes-dos-Santos, André; Miranda, Fernando Jorge Veloso; Nogueira, Joana Garrido; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Froufe, Elsa

Freshwater mussels are one of the most threatened animal groups in the world. In the European Union, threatened and protected mussel species are not adequately monitored, while species considered to be common and widespread receive even less attention. This is particularly worrying in the Mediterranean region, where species endemism is high and freshwater habitats are severely affected by water scarcity. In the absence of hard data on population trends, we report here a long-term comparison of freshwater mussel assemblages at 132 sites covering 15 different hydrological basins in Portugal. This study reveals a widespread decline of 60 % in the number of sites and 67 % in the overall abundance of freshwater mussels across Portugal over the last 20 years, indicating that all species are rapidly declining and threatened with extinction. These results show that current legislation and conservation measures are largely ineffective and highlight the importance of updating the Habitats Directive to enforce standard monitoring protocols for threatened species in the European Union and to extend monitoring to other freshwater species thought to be common and widespread. Efficient water management, restrictions on irrigation expansion in important biodiversity areas, mitigation of hydrological changes and loss of aquatic habitat connectivity caused by physical alterations are urgently needed to reverse these declining population trends. For the severely endangered species Margaritifera margaritifera, Potomida littoralis, and Unio tumidiformis, where populations are now critically low, more urgent action is needed, such as ex-situ conservation, protection of remaining populations and large-scale habitat restoration.

2023Journal article

Open access

The gill transcriptome of threatened European freshwater mussels

Publication . Gomes-dos-Santos, André; Machado, André M.; Castro, L. Filipe C.; Prié, Vincent; Teixeira, Amílcar; Lopes-Lima, Manuel; Froufe, Elsa

Genomic tools applied to non-model organisms are critical to design successful conservation strategies of particularly threatened groups. Freshwater mussels of the Unionida order are among the most vulnerable taxa and yet almost no genetic resources are available. Here, we present the gill transcriptomes of five European freshwater mussels with high conservation concern: Margaritifera margaritifera, Unio crassus, Unio pictorum, Unio mancus and Unio delphinus. The final assemblies, with N50 values ranging from 1069–1895 bp and total BUSCO scores above 90% (Eukaryote and Metazoan databases), were structurally and functionally annotated, and made available. The transcriptomes here produced represent a valuable resource for future studies on these species’ biology and ultimately guide their conservation.

2022Journal article

Open access

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, Manuel

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).

2021Journal article

Open access