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

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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 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