Freshwater ecosystems are threatened by human activities and their biodiversity declines far grea... more Freshwater ecosystems are threatened by human activities and their biodiversity declines far greater than those on marine and terrestrial ecosystems. Severa! impacts such as habitat loss and fragmentation, pollution, river regulation, overexploitation, introduction ofinvasive species and envoronmental changes are responsible for increasing the extinction risk ofnative species and for the dismption of important ecosystem functions and services. Freshwater mussels (Bivalvia: Unionoida) are among the most threatened faunistic groups in these freshwater ecosystems. These mussels depend on fish to complete their life cycle, where mussel larvae use a specific range of fish hosts to metamorphose. Therefore, the persistence of freshwater mussel species will ultimately depend on the conservation oftheir físh hosts. The Iberian Península holds a high levei ofspatially restricted species and endemisms. Many native físh and mussel species oflberia are listed as vulnerable, endangered or critica...
Figure 1. Recent multi-locus phylogenetic hypotheses on Gonideinae sensu Pfeiffer et al. (2019). ... more Figure 1. Recent multi-locus phylogenetic hypotheses on Gonideinae sensu Pfeiffer et al. (2019). Vertical bars indicate subfamilies recognized in respective publications. Note that Froufe et al. (2020) adopted a new systematic framework with three instead of two family-group levels, and thus, traditional tribes (ending -ini) are considered subtribes (ending -ina) in that study.
Figure 3. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 14 concatenated indi... more Figure 3. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 14 concatenated individual mtDNA gene sequences (12 protein-coding and 2 rRNA genes). Values for branch support above each node represent Bayesian posterior probabilities percentage/maximum likelihood bootstrap support. *Supported values ≥ 95 are represented by an asterisk.
Figure 6. Relationship between (A) mean Ka/Ks and substitution rate (μ) per female-type (full cir... more Figure 6. Relationship between (A) mean Ka/Ks and substitution rate (μ) per female-type (full circles) and male-type (empty circles) mtDNA protein-coding gene; and (B) differences between male- and female-type K a /K s and μ per proteincoding mtDNA gene.
Figure 4. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 28 concatenated indi... more Figure 4. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 28 concatenated individual mtDNA gene sequences, i.e. 14 from female-type (12 protein-coding and 2 rRNA genes) and 14 (12 protein-coding and 2 rRNA genes) from male-type mitochondria. Values for branch support above each node represent Bayesian posterior probabilities percentage/ maximum likelihood bootstrap.
Figure 2. Gene maps of the F- and M-type mitochondrial genomes of Lens contradens, Physunio super... more Figure 2. Gene maps of the F- and M-type mitochondrial genomes of Lens contradens, Physunio superbus, Hyriopsis bialata and Rectidens sumatrensis. Genes positioned inside the circle are encoded on the heavy strand, and genes outside the circle are encoded on the light strand. Colour codes: small and large ribosomal RNAs (red); transfer RNAs (purple); M-orf, F-specific open reading frame (yellow); M-orf, M-specific open reading frame (yellow); protein-coding genes (green).
Figure 5. Fossil-calibrated ultrametric chronogram of the Unionidae calculated under a lognormal ... more Figure 5. Fossil-calibrated ultrametric chronogram of the Unionidae calculated under a lognormal relaxed clock model and a Yule process speciation implemented in BEAST v.1.10.1 and obtained for the complete F-type mitogenome data set. The newly sequenced tribe-level taxa are coloured red. An outgroup sample (Margaritiferidae) has been removed for better visualization (but see original BEAST tree in Supporting Information, Fig. S1A). Bars indicate 95% confidence intervals of the estimated divergence times between lineages (Mya). Black numbers near nodes are mean ages (Mya). Colour labels indicate the F-mtDNA gene order (UF1, UF2, and UF3). Stratigraphic chart according to the International Commission on Stratigraphy v.2018/08 (www.stratigraphy.org). Abbreviations: J, Jurassic; K, Cretaceous; N, Neogene; Pg, Palaeogene; Q, Quaternary.
The use of non-physical barriers, particularly based on acoustic and luminous stimuli has been hi... more The use of non-physical barriers, particularly based on acoustic and luminous stimuli has been historically used to influence the behavior of fish, mainly for fishing purposes. Nowadays, behavioral barriers and guidance systems have been developed, not only to deter movements of fish, but also to promote behavioral responses with the objective of native fish protection, in particular the potamodromous species, reducing their mortality in the hydraulic structures of dams and guiding them towards transposition systems or to replacement habitats in regularized water bodies. This review details the use of acoustic and luminous systems and their evolution in recent years (Scopus 2012–2019) for the development of selective behavioral barriers for fish. We found that recent technologies try to identify new acoustic and luminous sensory ranges. Ambient sound, sound of predators or luminous spectral bands with different wavelengths have been used to selectively stimulate target and non-targe...
Since historical times, the inherent human fascination with pearls turned the freshwater pearl mu... more Since 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’ ...
The Unionidae represent an excellent model taxon for unravelling the drivers of freshwater divers... more 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+Rectiden...
Molecular phylogenetics and evolution, Jan 3, 2018
Two Unionida (freshwater mussel) families are present in the Northern Hemisphere; the Margaritife... more 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 and Gibbosula. As a result, two additional species are also moved to the Margaritiferidae, i.e. Gibbosula confragosa and Gibbosula polysticta. We performed a robust five marker phylogeny with all available margaritiferid species and discuss the t...
Molecular phylogenetics and evolution, Jan 9, 2016
Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsi... more 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. The present study presents the most comprehensive phylogeny of the most species rich 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). Mol...
Molecular phylogenetics and evolution, Jul 23, 2016
The Potomida genus (Bivalvia, Unionida) has a Circum-Mediterranean distribution and like other fr... more The Potomida genus (Bivalvia, Unionida) has a Circum-Mediterranean distribution and like other freshwater mussel species, its populations have suffered dramatic declines. Although this genus is currently considered as monotypic, it has a long history of taxonomic revisions and presently many aspects of its systematics and evolutionary history are unclear. We sampled a total of 323 individuals from 39 different sites across the Potomida genus distribution, and sequenced two mitochondrial (16S rDNA and Cytochrome c Oxidase Subunit I) and one nuclear (28S rDNA) genes to clarify its phylogeny and phylogeographic history. Our results show that the genus includes two well-supported clades, one comprising solely the western Mediterranean species Potomida littoralis, and the other including two eastern Mediterranean species, the Greek endemic P. acarnanica and the Anatolian and Middle Eastern P. semirugata. We suggest that Potomida started radiating during the upper Miocene, and that both v...
Freshwater ecosystems are threatened by human activities and their biodiversity declines far grea... more Freshwater ecosystems are threatened by human activities and their biodiversity declines far greater than those on marine and terrestrial ecosystems. Severa! impacts such as habitat loss and fragmentation, pollution, river regulation, overexploitation, introduction ofinvasive species and envoronmental changes are responsible for increasing the extinction risk ofnative species and for the dismption of important ecosystem functions and services. Freshwater mussels (Bivalvia: Unionoida) are among the most threatened faunistic groups in these freshwater ecosystems. These mussels depend on fish to complete their life cycle, where mussel larvae use a specific range of fish hosts to metamorphose. Therefore, the persistence of freshwater mussel species will ultimately depend on the conservation oftheir físh hosts. The Iberian Península holds a high levei ofspatially restricted species and endemisms. Many native físh and mussel species oflberia are listed as vulnerable, endangered or critica...
Figure 1. Recent multi-locus phylogenetic hypotheses on Gonideinae sensu Pfeiffer et al. (2019). ... more Figure 1. Recent multi-locus phylogenetic hypotheses on Gonideinae sensu Pfeiffer et al. (2019). Vertical bars indicate subfamilies recognized in respective publications. Note that Froufe et al. (2020) adopted a new systematic framework with three instead of two family-group levels, and thus, traditional tribes (ending -ini) are considered subtribes (ending -ina) in that study.
Figure 3. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 14 concatenated indi... more Figure 3. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 14 concatenated individual mtDNA gene sequences (12 protein-coding and 2 rRNA genes). Values for branch support above each node represent Bayesian posterior probabilities percentage/maximum likelihood bootstrap support. *Supported values ≥ 95 are represented by an asterisk.
Figure 6. Relationship between (A) mean Ka/Ks and substitution rate (μ) per female-type (full cir... more Figure 6. Relationship between (A) mean Ka/Ks and substitution rate (μ) per female-type (full circles) and male-type (empty circles) mtDNA protein-coding gene; and (B) differences between male- and female-type K a /K s and μ per proteincoding mtDNA gene.
Figure 4. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 28 concatenated indi... more Figure 4. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 28 concatenated individual mtDNA gene sequences, i.e. 14 from female-type (12 protein-coding and 2 rRNA genes) and 14 (12 protein-coding and 2 rRNA genes) from male-type mitochondria. Values for branch support above each node represent Bayesian posterior probabilities percentage/ maximum likelihood bootstrap.
Figure 2. Gene maps of the F- and M-type mitochondrial genomes of Lens contradens, Physunio super... more Figure 2. Gene maps of the F- and M-type mitochondrial genomes of Lens contradens, Physunio superbus, Hyriopsis bialata and Rectidens sumatrensis. Genes positioned inside the circle are encoded on the heavy strand, and genes outside the circle are encoded on the light strand. Colour codes: small and large ribosomal RNAs (red); transfer RNAs (purple); M-orf, F-specific open reading frame (yellow); M-orf, M-specific open reading frame (yellow); protein-coding genes (green).
Figure 5. Fossil-calibrated ultrametric chronogram of the Unionidae calculated under a lognormal ... more Figure 5. Fossil-calibrated ultrametric chronogram of the Unionidae calculated under a lognormal relaxed clock model and a Yule process speciation implemented in BEAST v.1.10.1 and obtained for the complete F-type mitogenome data set. The newly sequenced tribe-level taxa are coloured red. An outgroup sample (Margaritiferidae) has been removed for better visualization (but see original BEAST tree in Supporting Information, Fig. S1A). Bars indicate 95% confidence intervals of the estimated divergence times between lineages (Mya). Black numbers near nodes are mean ages (Mya). Colour labels indicate the F-mtDNA gene order (UF1, UF2, and UF3). Stratigraphic chart according to the International Commission on Stratigraphy v.2018/08 (www.stratigraphy.org). Abbreviations: J, Jurassic; K, Cretaceous; N, Neogene; Pg, Palaeogene; Q, Quaternary.
The use of non-physical barriers, particularly based on acoustic and luminous stimuli has been hi... more The use of non-physical barriers, particularly based on acoustic and luminous stimuli has been historically used to influence the behavior of fish, mainly for fishing purposes. Nowadays, behavioral barriers and guidance systems have been developed, not only to deter movements of fish, but also to promote behavioral responses with the objective of native fish protection, in particular the potamodromous species, reducing their mortality in the hydraulic structures of dams and guiding them towards transposition systems or to replacement habitats in regularized water bodies. This review details the use of acoustic and luminous systems and their evolution in recent years (Scopus 2012–2019) for the development of selective behavioral barriers for fish. We found that recent technologies try to identify new acoustic and luminous sensory ranges. Ambient sound, sound of predators or luminous spectral bands with different wavelengths have been used to selectively stimulate target and non-targe...
Since historical times, the inherent human fascination with pearls turned the freshwater pearl mu... more Since 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’ ...
The Unionidae represent an excellent model taxon for unravelling the drivers of freshwater divers... more 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+Rectiden...
Molecular phylogenetics and evolution, Jan 3, 2018
Two Unionida (freshwater mussel) families are present in the Northern Hemisphere; the Margaritife... more 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 and Gibbosula. As a result, two additional species are also moved to the Margaritiferidae, i.e. Gibbosula confragosa and Gibbosula polysticta. We performed a robust five marker phylogeny with all available margaritiferid species and discuss the t...
Molecular phylogenetics and evolution, Jan 9, 2016
Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsi... more 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. The present study presents the most comprehensive phylogeny of the most species rich 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). Mol...
Molecular phylogenetics and evolution, Jul 23, 2016
The Potomida genus (Bivalvia, Unionida) has a Circum-Mediterranean distribution and like other fr... more The Potomida genus (Bivalvia, Unionida) has a Circum-Mediterranean distribution and like other freshwater mussel species, its populations have suffered dramatic declines. Although this genus is currently considered as monotypic, it has a long history of taxonomic revisions and presently many aspects of its systematics and evolutionary history are unclear. We sampled a total of 323 individuals from 39 different sites across the Potomida genus distribution, and sequenced two mitochondrial (16S rDNA and Cytochrome c Oxidase Subunit I) and one nuclear (28S rDNA) genes to clarify its phylogeny and phylogeographic history. Our results show that the genus includes two well-supported clades, one comprising solely the western Mediterranean species Potomida littoralis, and the other including two eastern Mediterranean species, the Greek endemic P. acarnanica and the Anatolian and Middle Eastern P. semirugata. We suggest that Potomida started radiating during the upper Miocene, and that both v...
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