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Figs 18–23 in A revision of the Afrotropical hover fly genus Afroxanthandrus Kassebeer, 2000 (Diptera, Syrphidae), with the description of two new species and one new synonymy
Figs 18–23. Male genitalia of species of Afroxanthandrus Kassebeer, 2000. 18–20. Dorsal views. 18. A. comorosensis sp. nov., holotype (RMCA ENT 000056900). 19. A. congensis (Curran, 1938) (RMCA ENT 000028396). 20. A. conopeum sp. nov., paratype (NMSA-Dip 086809). 21–23. Lateral views. 21. A. comorosensis sp. nov., holotype (RMCA ENT 000056900). 22. A. congensis (RMCA ENT 000028396). 23. A. conopeum sp. nov., paratype (NMSA-Dip 086809). Scale bars = 0.5 mm.
Figs 9–10 in A revision of the Afrotropical hover fly genus Afroxanthandrus Kassebeer, 2000 (Diptera, Syrphidae), with the description of two new species and one new synonymy
Figs 9–10. Lateral view of species of Afroxanthandrus Kassebeer, 2000. 9. A. conopeum sp. nov., holotype, ♂ (NMSA-Dip 219971). 10. A. congensis (Curran, 1938), ♀ (ANHRTUK 00282352). Scale bars = 1 mm.
Fig. 7 in One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)
Fig. 7. Ancestral state reconstruction: A, Pubescence of the ovary; B, Number of ovary locules. Pie charts represent the marginal likelihood at ancestral nodes. The character matrix and support values for the inferred states are available in suppl. Table S2. Morphological traits were mapped on the dated tree topology pruned to 47 taxa. Node labels correspond to node number. — RN: Réserves Naturelles; SF: Service Forestier.
Fig. 11 in One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)
Fig. 11. Ancestral state reconstruction: A, Corolla tube length to corolla lobe length ratio; B, Total length of the corolla. Color gradients along the branches represent interpolation of state changes. Probabilities of ancestral node states, their computed variances and 95% confidence intervals are presented in suppl. Table S3. Morphological traits were mapped on the dated tree topology pruned to 47 taxa. — RN: Réserves Naturelles; SF: Service Forestier.
Fig. 1. Species tree reconstruction inferred from ASTRAL-II using 89 specimens and 787 in One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)
Fig. 1. Species tree reconstruction inferred from ASTRAL-II using 89 specimens and 787 individual gene trees obtained using RAxML. The node labels represent ASTRAL support values. Note that ASTRAL only calculates internal branch length and that tip lines are artificially fixed with the same length for all the specimens. Tip labels include the species names and the collector codes. Branch colors represent the traditional classification: Labramia (dark green), Manilkara (orange), Faucherea (yellow) and Labourdonnaisia (pink). The revised four major genetic clades are highlighted by a colored bar as follows: Labramia (dark green), Manilkara s.str. (orange), Faucherea and Labourdonnaisia (pink), and the Abebaia clade (blue). The main regions are indicated as follows: Afr: Africa; Ame: Americas; Com: Comoros; Ind: Indonesia; Mad: Madagascar; Msc: Mascarenes; Pac: Pacific Asia. RN: Réserves Naturelles; SF: Service Forestier.
Fig. 4. Maximum clade credibility and divergence time estimations from BEAST reconstruction using 89 specimens and 20 in One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)
Fig. 4. Maximum clade credibility and divergence time estimations from BEAST reconstruction using 89 specimens and 20 genes. Background colors represent the four Manilkarinae clades. Node labels are given as the mean of node age estimates for the main clades, including their 95% HPD and posterior probability (PP). The latter are only shown when PP <1. Epoch and ages in million years ago are represented at the bottom. Primary calibration points from fossils data are indicated with a red star, whereas clades constrained as monophyletic are labeled with an asterisk. RN: Réserves Naturelles; SF: Service Forestier.
Fig. 10 in One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)
Fig. 10. Ancestral state reconstruction: A, Dorsal appendage length to corolla lobe length ratio; B, Staminode length to corolla lobe length ratio. Color gradients along the branches represent interpolation of state changes. Probabilities of ancestral node states, their computed variances and 95% confidence intervals are presented in suppl. Table S3. Morphological traits were mapped on the dated tree topology pruned to 47 taxa. — RN: Réserves Naturelles; SF: Service Forestier.
Data from: A de novo chromosome-level genome assembly of Coregonus sp. "Balchen": one representative of the Swiss Alpine whitefish radiation
<p>Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild-caught <i>Coregonus sp. "Balchen" </i>from Lake Thun to ~90x coverage. PacBio reads were assembled independently using three different assemblers, Falcon, Canu and wtdbg2 and subsequently scaffolded with additional Hi-C data. All three assemblies were highly contiguous, had strong synteny to a previously published <i>Coregonus</i>linkage map, and when mapping additional short-read data to each of the assemblies, coverage was fairly even across most chromosome-scale scaffolds. Here, we present the first <i>de novo</i>genome assembly for the Salmonid subfamily Coregoninae. The final 2.2 Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb, and was 93.3% complete for BUSCOs. The assembly consisted of ~52% TEs and contained 44,525 genes.</p>
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 4 in A new species of Myrmecotypus Pickard-Cambridge spider (Araneae: Corinnidae: Castianeirinae) from the Bolivian orocline, imitating one of the world's most aggressive ants
Figure 4. Myrmecotypus rubrofemoratus new species: Paratype female (CBF). A) Dorsal. B) Lateral (Please note that most hairs are broken off due to storage in ethanol). Scale bar 1 mm.
Figure 3. Myrmecotypus rubrofemoratus new species, genitalia. A in A new species of Myrmecotypus Pickard-Cambridge spider (Araneae: Corinnidae: Castianeirinae) from the Bolivian orocline, imitating one of the world's most aggressive ants
Figure 3. Myrmecotypus rubrofemoratus new species, genitalia. A) Palp male holotype (IBSI-Ara 1507), ventral view. B–C) Epigyne female allotype (IBSI-Ara 1467). B) Ventral. C) Same, cleared.
Figure 5 in A new species of Myrmecotypus Pickard-Cambridge spider (Araneae: Corinnidae: Castianeirinae) from the Bolivian orocline, imitating one of the world's most aggressive ants
Figure 5. Comparison of ant-mimicking Myrmecotypus spider and potential ant model. A–B) Myrmecotypus rubrofemoratus new species female, habitus in life. A) Dorsal. B) Lateral. C–D) Potential ant model Camponotus femoratus (Fabricius, 1804). C) Dorsal. D) Lateral.
Figure 1 in A new species of Myrmecotypus Pickard-Cambridge spider (Araneae: Corinnidae: Castianeirinae) from the Bolivian orocline, imitating one of the world's most aggressive ants
Figure 1. Ecoregion distribution of Myrmecotypus rubrofemoratus new species, according to the regionalization by Navarro and Ferreira (2011). Collection location indicated by red circle, map produced with QGIS (version 2.14.3, http:// www.qgis.org/en/site).
PLATE IIB. Paratrigonidium Brunner, 1893. (A–E), Paratrigonidium nitidum Brunner, 1893: A, Male elytra membranous & harpvein only one; B, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; C, Lateral field of tegmina inmale blackish, presenting 3 parallel veins and the fourth incomplete; D, The hind femur with a feeble brownish band/stripe; E, The female ovipositor fulvous at base, darkened in the middle. Trigonidium Rambur, 1839. (F–I), Trigonidium humbertianum (Saussure, 1878): F, Anterior tibiae with tympanum on both sides; G, Fifth joint of maxillary palpi large and triangular; H, Female ovipositor curved, compressed, acute at apex; I, Male sub-genital plate feebly notched at apex. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IIB. Paratrigonidium Brunner, 1893. (A–E), Paratrigonidium nitidum Brunner, 1893: A, Male elytra membranous & harpvein only one; B, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; C, Lateral field of tegmina inmale blackish, presenting 3 parallel veins and the fourth incomplete; D, The hind femur with a feeble brownish band/stripe; E, The female ovipositor fulvous at base, darkened in the middle. Trigonidium Rambur, 1839. (F–I), Trigonidium humbertianum (Saussure, 1878): F, Anterior tibiae with tympanum on both sides; G, Fifth joint of maxillary palpi large and triangular; H, Female ovipositor curved, compressed, acute at apex; I, Male sub-genital plate feebly notched at apex.
PLATE IA. Natula Gorochov, 1987. (A–L), Natula matsuurai (Sugimoto, 2001): A, Male; B, Female; C, Face with a transverse dark strip near epistomal suture; D, Fifth joint of maxillary palpi hatchet shaped; E, Lateral field of tegmina deeper than lateral lobe of pronotum; F, Hind tibia with 3 pairs of dorsal spines on both sides but largest inner apical spurs as long as or half of basitarsus; G, Fore tibia with oval shaped outer and inner tympanum; H, Harp vein only one, Mirror area occupying half dorsal surface, not divided with a small concentric inner veinlet; I, Pronotum with roundly convex anterior margin; J, Female ovipositor strongly upcurved, half as long as hind femur, three fifth area from base widened and bumpy, with a dorsal groove, cerci as long as ovipositor; K, Male sub-genital plate longer than wide, hind margin narrowly truncated with a small projected median lobe, two styli present; L, Female sub-genital plate roundly triangular. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IA. Natula Gorochov, 1987. (A–L), Natula matsuurai (Sugimoto, 2001): A, Male; B, Female; C, Face with a transverse dark strip near epistomal suture; D, Fifth joint of maxillary palpi hatchet shaped; E, Lateral field of tegmina deeper than lateral lobe of pronotum; F, Hind tibia with 3 pairs of dorsal spines on both sides but largest inner apical spurs as long as or half of basitarsus; G, Fore tibia with oval shaped outer and inner tympanum; H, Harp vein only one, Mirror area occupying half dorsal surface, not divided with a small concentric inner veinlet; I, Pronotum with roundly convex anterior margin; J, Female ovipositor strongly upcurved, half as long as hind femur, three fifth area from base widened and bumpy, with a dorsal groove, cerci as long as ovipositor; K, Male sub-genital plate longer than wide, hind margin narrowly truncated with a small projected median lobe, two styli present; L, Female sub-genital plate roundly triangular.
Armature formula of P1–P4 as follows: P5 (Fig. 2B). With outer seta of BENP arising from long setophore. Endopodal lobe triangular, reaching middle of exopod; with small spinules along outer margin and at base of inner setae; with five elements – one outer subdistal, one apical and one inner subdistal normal seta, and two inner bifurcate elements. Exopod elongate, 2.8 times as long as wide; with spinules along inner margin and with few proximal outer spinules; with six elements – three outer slender, short setae, two apical elements, of which outermost one shorter, and one inner seta. in Proposal of new genera and species of the subfamily Diosaccinae (Copepoda: Harpacticoida: Miraciidae)
Armature formula of P1–P4 as follows: P5 (Fig. 2B). With outer seta of BENP arising from long setophore. Endopodal lobe triangular, reaching middle of exopod; with small spinules along outer margin and at base of inner setae; with five elements – one outer subdistal, one apical and one inner subdistal normal seta, and two inner bifurcate elements. Exopod elongate, 2.8 times as long as wide; with spinules along inner margin and with few proximal outer spinules; with six elements – three outer slender, short setae, two apical elements, of which outermost one shorter, and one inner seta.
One for all and all for one: phenotype assortment and reproductive success in masculinized females
<p>Homophily by morphological and behavioral traits has been described in several species of vertebrates, but its functional consequences remain poorly studied. Homophily by plurally breeding females may improve direct fitness by enhancing reproductive success. Female mammals may exhibit phenotypical masculinization due to exposure to androgens during early development, a condition that is associated with maternal performance during subsequent breeding. Our goal was to assess whether female composition (in terms of masculinization) of plurally breeding groups influences female fitness in a natural population of degus <i>(Octodon degus).</i> We assessed if plurally breeding female degus assort themselves by anogenital distance (AGD), an accurate measure of masculinization level. We also quantified if homophily by AGD phenotype affects female reproductive success and the reproductive output of the group. Plurally breeding groups typically included similarly masculinized (i.e., long AGD) females or similarly feminized (short AGD) females, indicating a strong degree of homophily. Females weaned more offspring in plurally breeding groups with more masculinized females. Additionally, standardized variance in the number of offspring weaned decreased in plurally breeding groups with mostly masculinized females, indicating greater reproductive equality in these groups. We conclude that female degus organize into homophilic social groups of similar AGD, and that social groups of masculinized females exhibit higher reproductive success.</p>
FIG. 11 in Review of the Lispe tentaculata-group (Diptera: Muscidae) in China, with one new synonym
FIG. 11. ─ Male phalli of Lispe tentaculata-group, lateral view: A, L. alpinicola Zhong, Wu & Fan, 1981 (adapted from Zhong, Wu & Fan 1981); B, L. sociabilis Loew, 1862 (adapted from Snyder 1954); C, L. tentaculata (De Geer, 1776) (adapted from Hennig 1960); D, L. tentaculata (De Geer, 1776) (specimen from Xinjiang, China). Scale bar: 0.50 mm.
FIG. 10 in Review of the Lispe tentaculata-group (Diptera: Muscidae) in China, with one new synonym
FIG. 10. ─ Male terminalia of Lispe fanjingshanensis Wei, 2006 (adapted from Li & Jin 2006) (L. sericipalpis Stein, 1904): A, cerci, ventral view; B, epandrium, surstyli, cerci and phallus, lateral view.
FIG. 7 in Review of the Lispe tentaculata-group (Diptera: Muscidae) in China, with one new synonym
FIG. 7. ─ SEM images of male genitals of Lispe orientalis Wiedemann, 1824 (A, B) and L. sericipalpis Stein, 1904 (C, D): A, C, genitals, lateral views; B, D, degenerated gonopods fused with hypandrium, lateral view (arrows). Scale bars: A, C, 120 μm; B, D, 40 μm.
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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.