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opennotspecifiedDec 2017View details →

FIGURE 4 in Taxonomic reassessment of the freshwater mussel genus Unio (Bivalvia: Unionidae) in Russia and Ukraine based on morphological and molecular data

FIGURE 4. Overview of pseudocardinal and lateral teeth: A, Unio pictorum (above INREC-UP2; below ZSU-U2); B, U. tumidus (above INREC-UT6; below INREC-UT8); C, U. crassus (above ZISP-UC199; below ZSU-U11). Features of pseudocardinal teeth morphology of left valve: d–g, U. pictorum (INREC: UP1, UP3, UP15, UP311); h–o, U. tumidus (INREC: UT3, UT4, UT11, UT19, UT172, UT296, UT297, UT698); p–s, U. crassus (INREC: UC1a, UC131, UC516). Generic names according to Zhadin's system. Scale bar 1 cm.

opennotspecifiedDec 2017View details →

FIGURE 1 in Taxonomic reassessment of the freshwater mussel genus Unio (Bivalvia: Unionidae) in Russia and Ukraine based on morphological and molecular data

FIGURE 1. Regions of study and localities of collection of Unio species. A, overview map of Eurasia. B, the Ukraine. C, European Russia. Symbols: U = Ukraine, ER = European Russia, T = Transbaikalian refuge.

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Obovaria olivaria maf filtered vcf file from: RAD-tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)

Obovaria olivaria is a species of freshwater mussel native to the Mississippi River and Laurentian Great Lakes-St. Lawrence River drainages of North America. This mussel has experienced population declines across large parts of its distribution and is imperiled in many jurisdictions. Obovaria olivaria uses the similarly imperiled Acipenser fulvescens (Lake Sturgeon) as a host for its glochidia. We employed mitochondrial DNA sequencing and Restriction-site Associated DNA sequencing (RAD-seq) to assess patterns of genetic diversity and population structure of O. olivaria from 19 collection locations including the St. Lawrence River drainage, the Great Lakes drainage, the Upper Mississippi River drainage, the Ohioan River drainage and the Mississippi Embayment. Heterozygosity was highest in Upper Mississippi and Great Lakes populations, followed by a reduction in diversity and relative effective population size in the St. Lawrence populations. Pairwise FST ranged from 0.00 to 0.20, and analyses of genetic structure revealed two major ancestral populations, one including all St. Lawrence River/Ottawa River sites and the other including remaining sites; however, significant admixture and isolation by river distance across the range were evident. The genetic diversity and structure of O. olivaria is consistent with the existing literature on Acipenser fulvescens and suggest that, although northern and southern O. olivaria populations are genetically distinct, genetic structure in O. olivaria is largely clinal rather than discrete across its range. Conservation and restoration efforts of O. olivaria should prioritize the maintenance and restoration of locations where O. olivaria remain, especially in northern rivers, and to ensure connectivity that will facilitate dispersal of Acipenser fulvescens and movement of encysted glochidia.

opencc-zeroFeb 2024View details →

opencc-by-4.0Mar 2024View details →

LD information used in MUSSEL for EUR, AFR, AMR, EAS, and SAS

Estimated LD block matrices and other LD information used in MUSSEL for EUR, AFR, AMR, EAS, and SAS for approximately 2.0 million SNPs in HapMap 3 plus MEGA. Given the limited storage space on Zenodo, we have deposited the LD information generated based on 1000 Genomes LD reference panel and provided the link to download the LD files below using: (1) 1000 Genomes LD reference panel: EUR: <a href="https://www.dropbox.com/s/wvxh4yqthm8m7uf/EUR.zip?dl=0">https://www.dropbox.com/s/wvxh4yqthm8m7uf/EUR.zip?dl=0</a> (~6.73G, unzip by: tar -zxvf EUR.tar.gz)  AFR: <a href="https://www.dropbox.com/s/iwqg65uieevfzj2/AFR.zip?dl=0">https://www.dropbox.com/s/iwqg65uieevfzj2/AFR.zip?dl=0</a> (~7.69G, unzip by: tar -zxvf AFR.tar.gz) AMR: <a href="https://www.dropbox.com/s/mev5zyf4x6m076q/AMR.zip?dl=0">https://www.dropbox.com/s/mev5zyf4x6m076q/AMR.zip?dl=0</a> (~8.80G, unzip by: tar -zxvf AMR.tar.gz) EAS: <a href="https://www.dropbox.com/s/o28mlovtakv5n7v/EAS.zip?dl=0">https://www.dropbox.com/s/o28mlovtakv5n7v/EAS.zip?dl=0</a> (~5.63G, unzip by: tar -zxvf EAS.tar.gz) SAS: <a href="https://www.dropbox.com/s/idp02rgl8xv379b/SAS.zip?dl=0">https://www.dropbox.com/s/idp02rgl8xv379b/SAS.zip?dl=0</a> (~2.60G, unzip by: tar -zxvf SAS.tar.gz)   (2) UK Biobank reference panel: EUR: <a href="https://www.dropbox.com/scl/fi/09yd12dest1tqxkt8p8ch/EUR.zip?rlkey=774vb1e5d6hfnyucilx160cyo&dl=0">https://www.dropbox.com/scl/fi/09yd12dest1tqxkt8p8ch/EUR.zip?rlkey=774vb1e5d6hfnyucilx160cyo&dl=0</a> (~13.15G, unzip by: tar -zxvf EUR.tar.gz)  AFR: <a href="https://www.dropbox.com/scl/fi/jfymih83anr2vuevmfqok/AFR.zip?rlkey=r1lxpn1fnbk98ssf8f8ji4xkk&dl=0">https://www.dropbox.com/scl/fi/jfymih83anr2vuevmfqok/AFR.zip?rlkey=r1lxpn1fnbk98ssf8f8ji4xkk&dl=0</a> (~11.59G, unzip by: tar -zxvf AFR.tar.gz) AMR: <a href="https://www.dropbox.com/s/2ba4tsbhz03rg83/AMR.zip?dl=0">https://www.dropbox.com/s/2ba4tsbhz03rg83/AMR.zip?dl=0</a> (~4.88G, unzip by: tar -zxvf AMR.tar.gz) EAS: <a href="https://www.dropbox.com/s/uofu788707dp4xv/EAS.zip?dl=0">https://www.dropbox.com/s/uofu788707dp4xv/EAS.zip?dl=0</a> (~4.27G, unzip by: tar -zxvf EAS.tar.gz) SAS: <a href="https://www.dropbox.com/scl/fi/o635c86ylthbl3omfetbu/SAS.zip?rlkey=ot396toxl0phaiae15cnpbeyn&dl=0">https://www.dropbox.com/scl/fi/o635c86ylthbl3omfetbu/SAS.zip?rlkey=ot396toxl0phaiae15cnpbeyn&dl=0</a> (~11.44G, unzip by: tar -zxvf SAS.tar.gz)

opencc-by-4.0Nov 2024View details →

Mussel attachment geometric models

The provided data includes the geometric model files (in STL format) of fouling mussel (Limnoperna fortunei) attachment. The geometric model of an individual adult mussel was generated in Blender. Considering the size of an individual adult mussel (about 20 mm), a 20 cm × 20 cm plane was selected to place a certain density of mussels. The density of the attachment model was set from 500 ind/m2 to 20,000 ind/m2. The location and orientation of each individual mussel was randomly placed on the plane, and three replicates were provided. Besides, the mussel attachment considered the mussel size distributions based on the sampling data from South China and North China.

Figure 4 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

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 3 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

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 1 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

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 6 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

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 2 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

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 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

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.

opencc-zeroNov 2021View details →

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ddRAD-seq alignment data for Unionid mussels

North American watersheds contain the world's highest diversity of freshwater mussels (Unionoida), and up to 40 species can co-occur in a single riffle. They collectively exhibit little evidence for ecological differentiation during the long-lived, benthic phase of their life cycle. In contrast, their brief parasitic larval phase involves the infection of a wide diversity of fish hosts. Gravid female mussels have evolved multiple methods for increasing the probability of infecting a host fish. Some species use a passive broadcast strategy: placing high numbers of larvae in the water column and relying on chance encounters with potential hosts for infection. Most species have a proactive strategy that entails the use of prey-mimetic lures to change the behavior of the hosts, i.e., eliciting a feeding response through which they become infected. Gravid females collectively produce two main lure types: a mantle tissue lure (on the female's body) and a brood lure, containing infective larvae, that she releases into the external environment. In this study, we used a phylogenomic approach (ddRAD-seq) to place the diversity of infection strategies used by 54 North American lampsiline mussels into an evolutionary context. Ancestral state reconstruction recovered evidence for the early evolution of mantle lures in this clade, with brood lures and broadcast infection strategies both being independently derived twice. The most common infection strategy, occurring in our largest ingroup clade, is a mixed one in which mimetic mantle lures are apparently the predominant infection mechanism, but gravid females also release simple, non-mimetic brood lures at the end of the season. This mixed infection strategy clade shows some evidence of an increase in diversification rate and most members use bass (Micropterus & Ambloplites spp.) as their predominant fish hosts. Broad linkage between infection strategies and predominant fish host genera is also seen in other lampsiline clades: worm-like mantle lures of Toxolasma spp. with sunfish (Lepomis spp.); insect larvae-like brood lures (Ptychobranchus spp.), or mantle lures (Medionidus spp., Obivariaspp.), or mantle lures combined with host capture (Epioblasma spp.) with a spectrum of darter (Etheostoma & Percinaspp.) and sculpin (Cottus spp.) hosts, and tethered brood lures (Hamiota spp.) with bass (Micropterus & Ambloplites spp.). Our phylogenetic results confirm that discrete lampsiline mussel clades exhibit considerable specialization in the primary fish host clades their larvae parasitize, and in the host infection strategies they employ to do so. They are also consistent with the hypothesis that larval resource partitioning of fish hosts is an important factor in maintaining species diversity in mussel assemblages. We conclude that taking their larval ecology and host-infection mechanisms into account, lampsiline mussels may be legitimately viewed as a cryptic adaptive radiation.

Figure 15 in Species boundaries, geographic distribution and evolutionary history of the Western Palaearctic freshwater mussels Unio (Bivalvia: Unionidae)

Figure 15. Coalescence-based species tree generated in BEAST. The x-axis scale is in millions of years. Bars indicate 95% high probability density intervals. Asterisks (*) in the tree indicate posterior probabilities pp> 0.9.

Figure 9 in Species boundaries, geographic distribution and evolutionary history of the Western Palaearctic freshwater mussels Unio (Bivalvia: Unionidae)

Figure 9. Differing shell shapes of Unio elongatulus. A, Po di Tolle River, Italy. B, Lake Candia, Italy. C, Venice, Italy. D, Lake Cestella, Italy. E, Lake Bačinska, Croatia. F, G, Mirna River, Croatia. H, Zrmanja River, Croatia. I, Lake Scutari, Albania. Scale bar 2 cm.

Figure 6 in Species boundaries, geographic distribution and evolutionary history of the Western Palaearctic freshwater mussels Unio (Bivalvia: Unionidae)

Figure 6. Differing shell shapes of Unio tigridis. A, Lake Kinneret, Israel. B, Tersakan River, Southwest Turkey.

Figure 7 in Species boundaries, geographic distribution and evolutionary history of the Western Palaearctic freshwater mussels Unio (Bivalvia: Unionidae)

Figure 7. Differing shell shapes of Unio mancus. A, Stabiacciu River, Corsica. B, Liscia River, Sardinia. C, Cedrino River, Corsica. D, River at Banyoles Lake, Spain. E, F, Araxisi River, Sardinia. Scale bar 2 cm.

Figure 4 in Species boundaries, geographic distribution and evolutionary history of the Western Palaearctic freshwater mussels Unio (Bivalvia: Unionidae)

Figure 4. Differing shell shapes of Unio foucauldianus. A, Loukos River. B, Oum Er Rbia River. C, Molouya River. D, Mda River. E, Martil River. F, Beth River (Sebou). G, Loukos River. Scale bar 2 cm.

Figure 3 in Species boundaries, geographic distribution and evolutionary history of the Western Palaearctic freshwater mussels Unio (Bivalvia: Unionidae)

Figure 3. Differing shell shapes of Unio tumidus. A, Franconian Saale, a tributary of the Main River (Rhine), Germany. B, Fulda River (Weser), Germany. C, Okna River (Danube), Slovakia. D, Danube River, Slovakia. E, Ferma Lake (Rhine), Germany. F, Thames River, UK. G, Fulda River (Weser), Germany. H, Rhine River, Germany. I, Horloff River (Rhine), Germany. Scale bar 2 cm.

Figure 2 in Species boundaries, geographic distribution and evolutionary history of the Western Palaearctic freshwater mussels Unio (Bivalvia: Unionidae)

Figure 2. Schematic distribution of the Unio species in the Western Palaearctic. Points indicate the general vicinity of sampled localities. See Supporting Information, Table S1 for details.

Figure 1 in Species boundaries, geographic distribution and evolutionary history of the Western Palaearctic freshwater mussels Unio (Bivalvia: Unionidae)

Figure 1. Bayesian tree reconstruction based on the two mitochondrial genes analysed. Values on the branches indicate Bayesian posterior probabilities, ML and MP bootstrap values. Results from the species delimitation analyses are also shown in this figure (green: M-PTP with a Bayesian tree; red: M-PTP with an ML tree; blue: bGMYC analysis). Names for the currently recognized morphospecies are also indicated in the phylogenetic tree.