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One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies
In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the "one‐locus‐several‐primer‐sets" (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey–predator interactions.
Figure 3 in Corals and reefs of Cosmoledo and Aldabra atolls: Extent of damage, assemblage shifts and recovery following the severe mortality of 1998
Figure 3. Visual estimates of coral cover at various depths on seaward slopes (diamonds) and lagoon patch reefs (open circles). The dotted curve indicates hypothetical or possible approximate maximum pre-bleaching coral cover with depth, based on maximum values found in patches here at shallow and intermediate depths. The solid curve is a third-order polynomial fit of the seaward reef cover values. Average seaward reef mortality is suggested by the gap between the two curves. The arrow marks the approximate transition depth.
Figure 2 in Corals and reefs of Cosmoledo and Aldabra atolls: Extent of damage, assemblage shifts and recovery following the severe mortality of 1998
Figure 2. (a) Seaward reef slope of West Cosmoledo. This is typical of shallow seaward slopes of south, through west to the north, showing very limited coral growth, but presence of algae. (b) Dead Millepora colonies in the lagoon are extensive, without sign of live growth and few new recruits. (c) Acropora palifera, showing recovery on shallow seaward slopes. It is growing on the side of a large dead colony of the same species. (d) Dead Acropora cytherea, eroded but still standing. Most examples in November 2002 were remnants of stumps. A new Acropora has since settled on the table. The yellow device is a newly installed temperature logger.
Figure 1 in Corals and reefs of Cosmoledo and Aldabra atolls: Extent of damage, assemblage shifts and recovery following the severe mortality of 1998
Figure 1. The Aldabra group of atolls, showing survey sites. Top left: location map, rectangle shows location of the four components of the Aldabra group; top right: World Vector Shoreline outline of the four groups; lower right: Cosmoledo Atoll (scanned image from map); lower left: Aldabra (from a Landsat MSS). On lower maps, dots indicate sample sites in lagoon and seaward sites, rectangles indicate sample sites in main channels. In Cosmoledo, lagoon sites are pooled. On seaward side of Cosmoledo, sites were West (Menai Island), North (North Island) and North-West (midway between the two). Seaward site in Aldabra was 300–500 m north of the field station (marked by ×). All sites in Cosmoledo lagoon had radii of at least 100 m, or, on seaward sites, along at least 200 m of reef between 0 and 30 m depth.
FIGURES 1–10 in RAFAŁ GOSIK & PETER SPRICK (2013) Morphology and identification of the pupae of several species of soil-dwelling broad-nosed weevils from Central Europe (Coleoptera, Curculionidae, Entiminae). Zootaxa, 3731(4): 445-472.
FIGURES 1–10. Weevils (adults, dorsal view): 1—Barypeithes pellucidus: immature; 2—Brachyderes incanus; 3—Liophloeus tessulatus; 4—Otiorhynchus dieckmanni; 5—O. tenebricosus form lugdunensis; 6—Peritelus sphaeroides; 7—Phyllobius intrusus; 8—P. pyri s. str.; 9—Strophosoma sus; 10—Tanymecus palliatus (photos: P. Sprick).
Figs. 25–30. Several glossiphoniid leeches. 25. Haementeria gracilis. 26 in Leech Collections from Chile Including Two New Species of Helobdella (Annelida: Hirudinida)
Figs. 25–30. Several glossiphoniid leeches. 25. Haementeria gracilis. 26. Theromyzon propinquium (live). 27. Helobdella duplicata. 28. Helobdella simplex. 29. Helobdella michaelseni. 30. Helobdella cordobensis.
Text-fig. 1. Location of Ivanovce Pliocene primate site in Slovakia within the wider area of the Carpathians-Pannonian Basin (white circle). The northern wall of the former limestone quarry at Ivanovce near Trenčín in western Slovakia. Several karst fillings provided a rich early Pliocene vertebrate assemblage. a: schematic sketch of the site showing the location of different karst fillings, b: photo of the same site during the palaeontological research in 1960s. in Allosorex Stenodus Fejfar, 1966 (Eulipotyphla, Soricidae): Re-Description Of Type Material And Re-Interpretation Of Its Fossil Record
Text-fig. 1. Location of Ivanovce Pliocene primate site in Slovakia within the wider area of the Carpathians-Pannonian Basin (white circle). The northern wall of the former limestone quarry at Ivanovce near Trenčín in western Slovakia. Several karst fillings provided a rich early Pliocene vertebrate assemblage. a: schematic sketch of the site showing the location of different karst fillings, b: photo of the same site during the palaeontological research in 1960s.
Text-fig. 2. Phylogeography based on mitochondrial phylogeny showing several evolutionary lineages of Arvicola and the separation of the Italian lineage of Arvicola, currently A. italicus (lineage A1), from European and Euro-Asiatic groups. From Wust-Saucy (1998: fig. 27), modified. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 2. Phylogeography based on mitochondrial phylogeny showing several evolutionary lineages of Arvicola and the separation of the Italian lineage of Arvicola, currently A. italicus (lineage A1), from European and Euro-Asiatic groups. From Wust-Saucy (1998: fig. 27), modified.
Figs. 207–210. Trichocyclus arabana. 207. Male gonopore. 208. Female palpal tarsal organ. 209. Male ALS, with several piriform gland spigots. 210. Female tarsus 1 in The Pholcids Of Australia (Araneae; Pholcidae): Taxonomy, Biogeography, And Relationships
Figs. 207–210. Trichocyclus arabana. 207. Male gonopore. 208. Female palpal tarsal organ. 209. Male ALS, with several piriform gland spigots. 210. Female tarsus 1 near tip. Scale lines: 50 µm (207, 210), 10 µm (208, 209).
FIG. 4 in On type material and the identity of several Iulus species described by Paul Gervais, in the collection of the Muséum national d'Histoire naturelle in Paris (Diplopoda, Spirostreptida, Spirobolida)
FIG. 4. — Neocricus striolatus (Gervais, 1847), holotype; A, gonopods (front view); B, anterior gonopods (caudal view); C, D, left posterior gonopod (lateral and mesal, respectively). Scale bar: 2.0 mm.
FIG. 3 in On type material and the identity of several Iulus species described by Paul Gervais, in the collection of the Muséum national d'Histoire naturelle in Paris (Diplopoda, Spirostreptida, Spirobolida)
FIG. 3. — Amastigogonus verreauxii (Gervais, 1847), holotype; A, anterior body end (lateral view); B, midbody segment (lateral view); C, telson (lateral view); D, leg-pair 1 and gnathochilarium (caudal view); E, gonopods (caudal view); F, G, anterior gonopod (front and lateral views, respectively); H, left posterior gonopod (caudal view). Scale bars: A-D, 1.0 mm; E-H, 0.5 mm.
FIG. 2 in On type material and the identity of several Iulus species described by Paul Gervais, in the collection of the Muséum national d'Histoire naturelle in Paris (Diplopoda, Spirostreptida, Spirobolida)
FIG. 2. — Gymnostreptus trimarginatus (Gervais, 1847), lectotype; A, anterior body end (lateral view); B, midbody segment (lateral view); C, telson (lateral view). Scale bar: 2.0 mm.
FIG. 1 in On type material and the identity of several Iulus species described by Paul Gervais, in the collection of the Muséum national d'Histoire naturelle in Paris (Diplopoda, Spirostreptida, Spirobolida)
FIG. 1. — Gymnostreptus sublaevis (Gervais, 1847), lectotype (A, C-H) and female paralectotype (B); A, collum (lateral view); B, telson (lateral view); C, gena (lateral view); D, leg 1 (front view); E-G, gonopods (front, lateral, and caudal views, respectively, with lateral folds of paracoxites broken off); H, tip of solenomerite (drawn not to scale). Scale bars: A-G, 2.0 mm; H, 1.0 mm.
Text-fig. 2. Synchrotron radiation X-ray tomographic microscopy volume renderings (a, b) and orthoslices (c–e) of Mugideiriflora portugallica gen. et sp. nov. from the Early Cretaceous Catefica locality, Portugal (holotype, S174254, Catefica sample 150). Yellow dots – stamens, red dots – carpels. a) Flower in lateral view showing the broad bases of the laminar tepals; b) Flower in longitudinal section showing the flat to slightly concave floral receptacle with a central conical gynoecial region (cut between orthoslices yz0800 and 1220); c) Flower in transverse section showing the numerous laminar tepals in several series and the stamens cut in the region of the poorly differentiated anthers; note cellular differences between outer (op) and inner (in) perianth parts, as well as and transverse sections of anthers, apparently with laterally to slightly dorsally placed pollen sacs (arrow heads) (cut at orthoslice xy0770); d) Flower in transverse section showing the numerous laminar tepals in several series, flattened rhomboidal stamen bases in several series, and poorly differentiated carpels (cut at orthoslice xy0820); e) Flower in transverse section showing the numerous laminar tepals in several series, flattened rhomboidal stamen bases in several series, and poorly differentiated carpels (cut at orthoslice xy0920); f) Flower in longitudinal section showing the shallowly concave floral receptacle with laminar tepals, stamens, and a central conical gynoecial region bearing poorly differentiated carpels (cut at orthoslice yz0900); g) Flower in longitudinal section perpendicular to that in (f) showing stamens and poorly differentiated carpels (cut at orthoslice xz1630). Scale bars = 1 mm (a, b), 500 µm (c–g). in Multiparted, Apocarpous Flowers From The Early Cretaceous Of Eastern North America And Portugal
Text-fig. 2. Synchrotron radiation X-ray tomographic microscopy volume renderings (a, b) and orthoslices (c–e) of Mugideiriflora portugallica gen. et sp. nov. from the Early Cretaceous Catefica locality, Portugal (holotype, S174254, Catefica sample 150). Yellow dots – stamens, red dots – carpels. a) Flower in lateral view showing the broad bases of the laminar tepals; b) Flower in longitudinal section showing the flat to slightly concave floral receptacle with a central conical gynoecial region (cut between orthoslices yz0800 and 1220); c) Flower in transverse section showing the numerous laminar tepals in several series and the stamens cut in the region of the poorly differentiated anthers; note cellular differences between outer (op) and inner (in) perianth parts, as well as and transverse sections of anthers, apparently with laterally to slightly dorsally placed pollen sacs (arrow heads) (cut at orthoslice xy0770); d) Flower in transverse section showing the numerous laminar tepals in several series, flattened rhomboidal stamen bases in several series, and poorly differentiated carpels (cut at orthoslice xy0820); e) Flower in transverse section showing the numerous laminar tepals in several series, flattened rhomboidal stamen bases in several series, and poorly differentiated carpels (cut at orthoslice xy0920); f) Flower in longitudinal section showing the shallowly concave floral receptacle with laminar tepals, stamens, and a central conical gynoecial region bearing poorly differentiated carpels (cut at orthoslice yz0900); g) Flower in longitudinal section perpendicular to that in (f) showing stamens and poorly differentiated carpels (cut at orthoslice xz1630). Scale bars = 1 mm (a, b), 500 µm (c–g).
Text-fig. 53. Scanning electron microscope (SEM) images of tricolpate pollen of Nicholsia brevicolpites gen. et sp. nov. from a coprolite containing several kinds of pollen; Torres Vedras locality, Portugal. a) Detail of the coprolite that yielded the tricolpate pollen in this Text-figure showing several different kinds of pollen grains; b–d) Tricolpate pollen grains in polar (b) and equatorial (c, d) views showing colpi, coarsely granular aperture membrane and foveolate tectum. Specimen, TV44-S137906-03 (holotype; a–d). Scale bars 30 Μm (a), 6 Μm (b–d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 53. Scanning electron microscope (SEM) images of tricolpate pollen of Nicholsia brevicolpites gen. et sp. nov. from a coprolite containing several kinds of pollen; Torres Vedras locality, Portugal. a) Detail of the coprolite that yielded the tricolpate pollen in this Text-figure showing several different kinds of pollen grains; b–d) Tricolpate pollen grains in polar (b) and equatorial (c, d) views showing colpi, coarsely granular aperture membrane and foveolate tectum. Specimen, TV44-S137906-03 (holotype; a–d). Scale bars 30 Μm (a), 6 Μm (b–d).
Text-fig. 48. Scanning electron microscope (SEM) images of monocolpate pollen from a coprolite; Torres Vedras locality, Portugal. a) Coprolite that yielded the pollen in this Text-figure as well as several other kinds of pollen; b) Reticulum of pollen grain showing the tall, sharp muri and obconical columellae; c–e) Grains of Goczania inaequalis sp. nov. intermixed with pollen grains that have a coarse, loosely attached reticulum with tall, sharp muri and sparse columellae; note the weak transverse striations on the muri and that the reticulum is much larger than the main body of the grain that it encloses. Specimen, TV44-S148023. Scale bars 300 Μm (a), 6 Μm (c–e), 3 Μm (b). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 48. Scanning electron microscope (SEM) images of monocolpate pollen from a coprolite; Torres Vedras locality, Portugal. a) Coprolite that yielded the pollen in this Text-figure as well as several other kinds of pollen; b) Reticulum of pollen grain showing the tall, sharp muri and obconical columellae; c–e) Grains of Goczania inaequalis sp. nov. intermixed with pollen grains that have a coarse, loosely attached reticulum with tall, sharp muri and sparse columellae; note the weak transverse striations on the muri and that the reticulum is much larger than the main body of the grain that it encloses. Specimen, TV44-S148023. Scale bars 300 Μm (a), 6 Μm (c–e), 3 Μm (b).
Text-fig. 2. Portuguese Early Cretaceous formations in the Torres Vedras and in the Figueira da Foz region. The Torres Vedras mesofossil flora was collected in the lower Almargem Formation. The Buarcos mesofossil flora, and several other younger mesofossil floras from Portugal, are from the lower part of the Figueira da Foz Formation. Based on information in Rey et al. (2006). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 2. Portuguese Early Cretaceous formations in the Torres Vedras and in the Figueira da Foz region. The Torres Vedras mesofossil flora was collected in the lower Almargem Formation. The Buarcos mesofossil flora, and several other younger mesofossil floras from Portugal, are from the lower part of the Figueira da Foz Formation. Based on information in Rey et al. (2006).
Text-fig. 7. Plant fossils from Primorye, Partizansk coal basin, Frentsevka Formation, Bolshoy Kuvshin locality, early – middle Albian. a, c, e – Achaenocarpites capitellatus KRASSILOV et VOLYNETS: a – spec. IBSS 320-132, c – spec. IBSS 320-132, e – spec. IBSS 320-120; b – Onychiopsis psilotoides (STOKES et WEBB) WARD, spec. – IBSS 320-165; d, g – branching infructescence with several follicular fruits: d – spec. IBSS 320-145, g – IBSS 320-145; f – Asiatifolium elegans G.SUN, S.X.GUO et SHAO L.ZHENG, spec. IBSS 320-75. Scale bar 0.5 cm. in An Angiosperm Dominated Herbaceous Community From The Early - Middle Albian Of Primorye, Far East Of Russia
Text-fig. 7. Plant fossils from Primorye, Partizansk coal basin, Frentsevka Formation, Bolshoy Kuvshin locality, early – middle Albian. a, c, e – Achaenocarpites capitellatus KRASSILOV et VOLYNETS: a – spec. IBSS 320-132, c – spec. IBSS 320-132, e – spec. IBSS 320-120; b – Onychiopsis psilotoides (STOKES et WEBB) WARD, spec. – IBSS 320-165; d, g – branching infructescence with several follicular fruits: d – spec. IBSS 320-145, g – IBSS 320-145; f – Asiatifolium elegans G.SUN, S.X.GUO et SHAO L.ZHENG, spec. IBSS 320-75. Scale bar 0.5 cm.
Text-fig. 1. Gastonispermum portugallicum gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). Note remains of mounting media on several seeds (¤). a) Seed in oblique view showing seed shape, the slightly raised raphal ridge and the position of hilum (hi) and micropyle (mi) on the raphal side of the seed (S170218). b, c) Seeds in lateral view (b, S170234; c, S175095). d–f) Holotype (S174820); seed in lateral view (d) and cut volume rendering (e, f) through the median plane of the seed showing palisade-shaped sclerenchyma cells of exotesta and remains of embryo (emb) and surrounding nutritive tissue (e, cut between yz0440-0530; f, cut between slices yz440-480). g) Hilum (hi) and micropyle (mi) of seed in (1a) showing the Y-shaped micropylar slit in the outer integument. h) Cut volume rendering through the median plane of the seed (cut at yz0492) showing seed coat mainly composed of palisade-shaped cells of the exotesta (S174435). i) Seed surface showing the raised outlines of the undulate anticlinal walls of the exotestal cells (S175045). Scale bars = 500 µm (a–e); 250 µm (g); 125 µm (f, i). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 1. Gastonispermum portugallicum gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). Note remains of mounting media on several seeds (¤). a) Seed in oblique view showing seed shape, the slightly raised raphal ridge and the position of hilum (hi) and micropyle (mi) on the raphal side of the seed (S170218). b, c) Seeds in lateral view (b, S170234; c, S175095). d–f) Holotype (S174820); seed in lateral view (d) and cut volume rendering (e, f) through the median plane of the seed showing palisade-shaped sclerenchyma cells of exotesta and remains of embryo (emb) and surrounding nutritive tissue (e, cut between yz0440-0530; f, cut between slices yz440-480). g) Hilum (hi) and micropyle (mi) of seed in (1a) showing the Y-shaped micropylar slit in the outer integument. h) Cut volume rendering through the median plane of the seed (cut at yz0492) showing seed coat mainly composed of palisade-shaped cells of the exotesta (S174435). i) Seed surface showing the raised outlines of the undulate anticlinal walls of the exotestal cells (S175045). Scale bars = 500 µm (a–e); 250 µm (g); 125 µm (f, i).
Fig. 2 in Arganiella Giusti & Pezzoli, 1980 (Caenogastropoda: Truncatelloidea: Hydrobiidae): a widespread genus or several narrow-range endemic genera?
Fig. 2. Shells, operculum and radulae of Docleiana tabanensis (Boeters, Glöer & Pešić, 2014) (UGSB 18847). A–C. Shells. D–E. Operculum (D = inner side; E = outer side). F. Protoconch. G–I. Radulae. G. Portion of radula ribbon. H. Central radular teeth. I. Inner and outer marginal teeth.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.