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Data from: Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages
1. The biodiversity of mixed-species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of >2600 individuals of leaf beetles (Chrysomelidae) from 10 communities. 2. Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes generated for 156 species (89% of species in the study); (ii) mitogenomes obtained by the de novo assembly of sequence reads from the real-world communities; and (iii) a custom set of DNA barcode (cox1-5′) sequences. 3. Species detection against the custom-built reference genomes was very high (>90%). False presences were rare against mitogenomes but slightly higher against the barcode references. False absences were mainly due to the incompleteness of the reference databases and, thus, more prevalent in the de novo data set. Biomass (abundance × body length) and read numbers were strongly correlated, demonstrating the potential of mitochondrial metagenomics for studies of species abundance. 4. A phylogenetic tree from the mitogenomes showed high congruence with known relationships in Chrysomelidae. Patterns of taxonomic and phylogenetic dissimilarity between sites were highly consistent with data from morphological identifications. 5. The power of mitochondrial metagenomics results from the possibility of rapid assembly of mitogenomes from mixtures of specimens and the use of read counts for accurate estimates of key parameters of biodiversity directly from community samples.
Data from: Present conditions may mediate the legacy effect of past land-use changes on species richness and composition of above- and below-ground assemblages
1. In forest ecosystems, the influence of landscape history on contemporary biodiversity patterns has been shown to provide a convenient framework to explain shifts in plant assemblages. However, very few studies have controlled for present human-induced activities when analyzing the effect of forest continuity on community structures. By cutting and removing trees, foresters substantially change stand ecological conditions, with consequences on biodiversity patterns. Disentangling the effect of past and present human activities on biodiversity is thus crucial for ecosystem management and conservation. 2. We explored the response of plant and springtail species richness and composition to forest continuity (ancient vs recent) in montane forests, while controlling for stand maturity (mature vs overmature). We established 70 sites in landscapes dominated by unfragmented ancient forests where we surveyed plants and assessed springtails by analyzing environmental DNA. 3. Neither plant nor springtail species richness was influenced by forest continuity or by stand maturity. Instead, site-specific characteristics, especially soil properties and canopy openness, were of major importance in shaping above- and below-ground richness. 4. For plant and springtail species composition, the effect of forest continuity was mediated by stand maturity. Thus, both plants and springtails showed a convergence in assemblage patterns with the increasing availability of overmature stand attributes. Moreover, soil and stand-scale factors were evidently more important than landscape-scale factors in shaping above- and below-ground species composition. 5. Synthesis. We clearly demonstrated that biodiversity patterns are more strongly influenced by present human-induced activities than by past human-induced activities. In the Northern Alps where our study sites were located, the colonization credit of most species has been paid off and the transient biodiversity deficit usually related to forest continuity has moved toward equilibrium. These findings emphasize the necessity to better control for local-scale factors when analyzing the response of biodiversity to forest continuity; we call for more research into the effects of forest continuity in unfragmented mountain forests.
Data from: Phylogeny, traits and biodiversity of a neotropical bat assemblage: close relatives show similar responses to local deforestation
If species' evolutionary pasts predetermine their responses to evolutionarily novel stressors, then phylogeny could predict species survival in an increasingly human-dominated world. To understand the role of phylogenetic relatedness in structuring responses to rapid environmental change, we focused on assemblages of Neotropical bats, an ecologically diverse and functionally important group. We examined how taxonomic and phylogenetic diversity shift between tropical forest and farmland. We then explored the importance of evolutionary history by ascertaining whether close relatives share similar responses to environmental change and which species traits might mediate these trends. We analyzed a 5-year data set (5,011 captures) from 18 sites in a countryside landscape in southern Costa Rica using statistical models that account and correct for imperfect detection of species across sites, spatial autocorrelation, and consideration of spatial scale. Taxonomic and phylogenetic diversity decreased with deforestation, and assemblages became more phylogenetically clustered. Species' responses to deforestation were strongly phylogenetically correlated. Body mass and absolute wing loading explained a substantial portion of species variation in species' habitat preferences, likely related to these traits' influence on maneuverability in cluttered forest environments. Our findings highlight the role that evolutionary history plays in determining which species will survive human impacts and the need to consider diversity metrics, evolutionary history, and traits together when making predictions about species persistence for conservation or ecosystem functioning.
FIGURE 13 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 13. Metaphase (A) and karyotype (B) of a female Aphyosemion campomaanense from ABK 07/181 (site 20, Fig. 1) (2n=44, NF=58) showing 1 pair of metacentric (with different amounts of heterochromatin), 6 pairs of subtelocentric and 15 pairs of acrocentric chromosomes.
FIGURE 12. Aphyosemion lividum, adult male from site 6 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 12. Aphyosemion lividum, adult male from site 6 (ABC 06/94). Specimen not preserved (approximately 30 mm SL). Photo by J.-F. Agnèse.
FIGURE 11. Aphyosemion ahli, adult male from ABC 06 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 11. Aphyosemion ahli, adult male from ABC 06/79 (site 11, Fig. 1). Specimen not preserved (approximately 35 mm SL). Photo by J.-F. Agnèse.
FIGURE 10. Aphyosemion campomaanense, adult male from ABK 07 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 10. Aphyosemion campomaanense, adult male from ABK 07/181 (site 20, fig. 1). This male (estimated 12 months old, approximately 45 mm SL) still has a large yellow margin to the anal fin. Specimen not preserved. Photo by J.-F. Agnèse.
FIGURE 9. Aphyosemion campomaanense, adult female from ABK 07 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 9. Aphyosemion campomaanense, adult female from ABK 07/181 (site 20, fig. 1, identical to ABC 06/84). Specimen not preserved (approximately 30 mm SL). Photo by A. Persson.
FIGURE 7. Aphyosemion campomaanense, adult male from ABK 07 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 7. Aphyosemion campomaanense, adult male from ABK 07/181 (site 20, Fig. 1). This male (estimated 10 months old) has an incomplete anal fin margin. Specimen not preserved (approximately 40 mm SL). Photo by P. Delaroche
FIGURE 8. Aphyosemion campomaanense, adult male from ABK 07 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 8. Aphyosemion campomaanense, adult male from ABK 07/181 (site 20, Fig.1, identical to ABC 06/84). This male was captured in January 2007 when estimated to be two month old. Left and right profiles were photographed in March (estimated 4 months old, approximately 30 mm SL), May (estimated 6 months old) and September 2007 (estimated 10 months old, approximately 40 mm SL). The yellow margin of the anal fin has quite completely disappeared after 10 months. The caudal pattern also changed during this period in terms of number and shape of the vertical bars. One can also observe the asymmetrical pattern of the right and left sides (especially the pattern of bars on the posterior). Specimen not preserved. Photos by A. Persson.
FIGURE 6. Aphyosemion campomaanense, adult male from ABC 06 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 6. Aphyosemion campomaanense, adult male from ABC 06/83 (site 20, Fig. 1). This estimated 14 month old male never had any yellow margin on the anal fin, nor did any other male sampled from of this population. Specimen not preserved (approximately 40 mm SL). Photo by J.-F. Agnèse.
FIGURE 5 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 5. Paratype of Aphyosemion campomaanense, MRAC 07-30-P-2-21, adult female (34 mm SL) from type locality (site 21, Fig. 1).
FIGURE 3 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 3. Consensus tree (majority rule) based on Distance Method (Neighbor-Joining). Consensus trees obtained with the Maximum Likelihood and the Maximum Parsimony methods were congruent. Numbers above or below the branches are percentages of bootstrap values based on 1000 replicates for each method (DM, ML, MP). Values below 50% are not shown. Aphyosemion (Chromaphyosemion) lugens was used to root the tree. Numbers correspond to sites on the map (Fig. 1).
FIGURE 2 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 2. Consensus tree (majority rule) based on the Distance Method (Neighbor-Joining). Consensus trees obtained with the Maximum Likelihood and the Maximum Parsimony methods were congruent. Numbers above or below the branches are percentages of bootstrap values based on 1000 replicates for each method (DM, ML, MP). Aphyosemion cameronense and A. mimbon were used to root the tree.
FIGURE 4 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 4. Holotype of Aphyosemion campomaanense, MRAC A7-30-P-1, adult male (36 mm SL) from site 21 (Fig. 1) in the Campo-Ma'an reserve (ABC 06/86, 2.33735° N, 10.20435° E).
FIGURE 1 in Genetic characterization of the Aphyosemion calliurum species group and description of a new species from this assemblage: A. campomaanense (Cyprinodontiformes: Aplocheiloidei: Nothobranchiidae) from Southern Cameroon
FIGURE 1. Map of the Western part of Cameroon showing sampling sites. Black stars indicate a species from the A. calliurum group, white and black (type locality) circles indicate A. campomaanense. Numbers refer to sites listed in Table 1.
FIGURE 9 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 9. Selected examples of symbiotic associations between reef fishes recorded at the Laje de Santos Marine State Park. The barber goby Elacatinus figaro cleans the head of the jubauna reeffish Chromis jubauna hovering close to the goby's cleaning station (a); the same cleaner species inspects the back of the nocturnal squirrelfish Holocentrus adscensionis that approached its cleaning station (b); juvenile spotfin hogfish Bodianus pulchellus cleans the mouth of the spotted moray Gymnothorax moringa (c); adult of the same hogfish species cleans the head of the jubauna reeffish (d); the wrasse Halichoeres sp. n. follows a group of the white trevally Pseudocaranx dentex, which stir sediment clouds while feeding on the sandy bottom (e); the dusky grouper Mycteroperca marginata closely follows the goldspotted snake eel Myrichthys ocellatus that nudges its head in rocky crevices (f); the spotfin hogfish follows the flying gurnard Dactylopterus volitans moving close to the bottom (g); two diskfish Remora remora attached near the mouth of the Atlantic manta Manta birostris (h).Photos: M. Andrade (h); A. Carvalho Filho (e-f); J. P. Krajewski (a); O.J. Luiz Jr. (c-d, g); A. de Luca Jr. (b).
FIGURE 8 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 8. Cluster analysis of habitat types at the Laje de Santos Marine State Park based on the similarity of species composition. The relative distribution of trophic categories in each habitat is shown in the graphs. CAR = Carnivore; MIF = Mobile Invertebrate Feeder; OMN = Omnivore; PIS = Piscivore; PLK = Planktivore; ROVH = Roving Herbivore; SIF = Sessile Invertebrate Feeder; TERH = Territorial Herbivore.
FIGURE 10 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 10. Targeted and endangered top-predators recorded at the Laje de Santos Marine State Park. The dusky groupers Mycteroperca marginata are very common in the area, but attain unusual large size and are largely unafraid of divers, contrarily to what happens at other unprotected sites (a); the goliath grouper Epinephelus itajara (b) and the cubera snapper Lutjanus cyanopterus (c). Several individuals of these two latter species have been seen at in the Laje de Santos in the last two years, after a period of more than ten years over which they remained unrecorded at the site. Photos: A. Carvalho-Filho (c); L. Cheidde (b); A. Valente (a).
FIGURE 3 in The reef fish assemblage of the Laje de Santos Marine State Park, Southwestern Atlantic: annotated checklist with comments on abundance, distribution, trophic structure, symbiotic associations, and conservation
FIGURE 3. Some abundant fish species at the Laje de Santos Marine State Park. The tomtate grunt Haemulon aurolineatum (a); adult and juvenile sergeant major Abudefduf saxatilis (b); the brown chromis Chromis multilineata (c); juvenile dusky damselfish Stegastes fuscus (d); intermediate individual of the jubauna reeffish Chromis jubauna (e); the silver porgy Diplodus argenteus (f); juvenile porkfish Anisotremus virginicus (g); the ringneck blenny Parablennius pilicornis (h). Photos: O.J. Luiz Jr, except (e) by L.F. Cassino.
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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.