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Derived variables and coordinates to assess the ecological relevance of multiscale bathymetry for coral species distribution modelling across the Great Barrier Reef
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Data from: Species Delimitation of Endemic Atlantic Forest Inga subnuda (Leguminosae, Caesalpinioideae, mimosoid clade) Subspecies Based on Morphological, Ecological and Palaeoecological Data
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FIGURE 2 in A new genus and two new species of sea stars (Family Asterinidae) from Indonesian marine lakes, with notes on habitat and feeding ecology
FIGURE 2. Internal structures of Limnasterias gen. nov., A–B Limnasterias oinops holotype, MZB.Astr.00040: A. Ray and abactinal surface removed to show absence of superambulacral plates (arrow) B. Appressed superactinal plate at distal edge of interradius (arrow) C. Limnasterias estradivariae paratype, MZB.Astr.00047, abactinal surface and ray removed, showing interradial pillar (arrow) and absence of superambulacral plates D. L. estradivariae paratype, MZB.Astr.00048, superactinal plate (arrow). Note that residual fibers from packaging are present in Fig. 2C.
FIGURE 4 in A new genus and two new species of sea stars (Family Asterinidae) from Indonesian marine lakes, with notes on habitat and feeding ecology
FIGURE 4. Live and in situ observations of Limnasterias gen. nov. A. Limnasterias oinops, paratype, MZB.Astr.00042, live animal. B. Regurgitated remains of cannibalized L. oinops with visible furrow spines (arrow). C. Limnasterias estradivariae, paratype, MZB.Astr.00047, live animal. D. L. oinops on macroalgae. E. L. estradivariae on macroalgae.
FIGURES 38–39 in A new species of Holophloeus Jordan (Coleoptera: Anthribidae) from eastern Madagascar with ecological notes on it and H. tuberosus (Fairmaire, 1897)
FIGURES 38–39. Type locality of Holophloeus loebli Trýzna & Baňař sp. nov. in Mantadia National Park, Eulophia circuit, 2017; 38, primary forest with single huge torso of lying trunk; 39, detail of cover of bark with specimens.
FIGURES 34–35 in A new species of Holophloeus Jordan (Coleoptera: Anthribidae) from eastern Madagascar with ecological notes on it and H. tuberosus (Fairmaire, 1897)
FIGURES 34–35. Collecting site of Holophloeus loebli Trýzna & Baňař sp. nov. in Andasibe National Park, Analamazaotra forest, 2016.
FIGURES 32–33 in A new species of Holophloeus Jordan (Coleoptera: Anthribidae) from eastern Madagascar with ecological notes on it and H. tuberosus (Fairmaire, 1897)
FIGURES 32–33. Collecting site of Holophloeus tuberosus (Fairmaire, 1897) in Mt. ďAmbre National Park, Mille arbres circuit, 2016.
FIGURES 15–22 in Description of the larvae of three species of the genus Mordellistena (Coleoptera: Mordellidae) with notes on their ecology
FIGURES 15–22. Details of the larva of Mordellistena koelleri Ermisch, 1956. 15: head; 16: antenna; 17: mandible, ventral view; 18: maxillolabial complex; 19: labial palp; 20: apical process, lateral view; 21: apical processes, dorsal view; 22: apical processes, posterior view.
Supplementary material 1 from: Dickey JWE, Cuthbert RN, South J, Britton JR, Caffrey J, Chang X, Crane K, Coughlan NE, Fadaei E, Farnsworth KD, Ismar-Rebitz SMH, Joyce PWS, Julius M, Laverty C, Lucy FE, MacIsaac HJ, McCard M, McGlade CLO, Reid N, Ricciardi A, Wasserman RJ, Weyl OLF, Dick JTA (2020) On the RIP: using Relative Impact Potential to assess the ecological impacts of invasive alien species. NeoBiota 55: 27-60. https://doi.org/10.3897/neobiota.55.49547
Table S1. Outline of different numerical response proxies available, guidance for their use and the advantages and disadvantages of each
Data from: Ecological speciation in sympatric palms: 3. genetic map reveals genomic islands underlying species divergence in Howea
Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction-site associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, some of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.
Data from: Specialization and niche overlap across spatial scales: revealing ecological factors shaping species richness and coexistence in Australian songbirds
1. Ecological specialization enables the partitioning of resources and thus can facilitate the coexistence of species and promote higher species richness. Specialization and niche partitioning are expected to exert a decisive influence on local spatial scales, while species richness at regional scales should be shaped mostly by historical factors and abiotic conditions. Moreover, specialization is expected to be particularly important in communities that are exceptionally species rich for their environmental conditions. Concurrently, niche overlap in these communities should be minimized to enable species coexistence. 2. We tested these hypotheses by studying specialization-richness relationship and niche overlap in assemblages of 298 species of songbirds (Passeriformes) across Australia. We used local (2-6 ha) to regional (bioregions) spatial scales, and detailed data on habitat, diet, and foraging behaviour (method, substrate, and stratum). 3. We expected the richness-specialization relationship to be particularly strong i) on local spatial scales and ii) in communities exceptionally species rich for given environmental conditions (approximated by moisture and vegetation complexity). We also expected iii) low niche overlap in assemblages with specialized species. 4. Only the third prediction was partly supported. First, while the specialization and species richness were often positively related, the strength and the direction of the relationship changed between traits and across spatial scales. The strength of the specialization-richness relationship was consistently positive only in foraging stratum, and it increased towards smaller spatial scales only in case of habitat and diet. Simultaneously, species in local communities demonstrated high overlap in habitat and diet. Second, we did not find particularly strong specialization-richness relationships in exceptionally species rich communities. Third, we found the expected negative relationship between specialization and overlap in foraging stratum and substrate (in local communities), suggesting that species partition ecological space locally in terms of where they find food. 5. Our expectations were only weakly supported. Specialization on foraging stratum was probably important in facilitating species co-existence. Conversely, although species were often specialized on habitat and diet, high overlap in these traits did not preclude their local coexistence. Overall, specialization and overlap in foraging traits were more important for species coexistence than habitat or diet.
Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers
Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.
Data from: Species-habitat relationships and ecological correlates of butterfly abundance in a transformed tropical landscape
Tropical butterfly conservation strategies often focus on total and/or common species richness to assess the conservation value of a patch or habitat. However, such a strategy overlooks the unique dynamics of rare species. We evaluated the species-habitat relationships of 209 common, intermediate, and rare butterfly species (including morphospecies) across four habitat types (mature, degraded, or fragmented forest, and urban parks) and two patch sizes (<400 ha, ≥400 ha) in Singapore. Common species richness was consistent across habitat types. Intermediate species richness declined by more than 50 percent in urban parks (relative to all forest habitats), and rare species richness was reduced by 50 percent in degraded and fragmented forest and by 90 percent in urban parks (relative to mature forest). Large patches had comparable overall richness to small patches, but they supported more rare species and three times as many habitat-restricted species over a similar area. Importantly, a number of rare species were confined to single small patches. Mixed-effects regression models were constructed to identify habitat and ecological/life history variables associated with butterfly abundance. These models revealed that species with greater habitat specialization, rare larval host plants, few larval host plant genera, and narrow global geographic ranges were more likely to be rare species. Overall, these results demonstrate that the richness of habitat-restricted and rare species do not follow the same spatial distribution patterns as common species. Therefore, while conserving mature forests is key, effective butterfly conservation in a transformed landscape should take into account rare and habitat-restricted species.
Data from: Visualizing connectivity of ecological and evolutionary concepts – an exploration of research on plant species rarity
<p>Understanding the ecological and evolutionary factors that influence species rarity has important theoretical and applied implications, yet the reasons why some species are rare while others are common remain unresolved. As a novel exploration of scientific knowledge, we used network analysis conceptually to visualize the foci of a comprehensive base of >800 studies on plant species rarity within the context of ecology and evolution. In doing so, we highlight existing research strengths that could substantiate novel syntheses and gaps that could inspire new research. Our results reveal strong integrated foci on population dynamics with other ecological concepts. In contrast, despite the potential for ecological and evolutionary processes to interact, few studies explored the interplay of environmental factors and microevolutionary patterns. The cellular and molecular biology, physiology, and plasticity of rare plant species within both ecological and evolutionary contexts similarly provide avenues for impactful future investigations.</p>
Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments
<p><span>Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of <i>Streptococcus suis</i>, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of <i>S. suis</i>). While genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, i.e. host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of non-functional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria.</span></p>
Palma et al 2021 Plant functional traits reflect different dimensions of species invasiveness. Ecology. DATASET
<p>Dataset used in publication <em>Palma et al 2021 Plant functional traits reflect different dimensions of species invasiveness. Ecology.</em> It includes:</p> <p>(1) records of Vegetative height and Specific leaf area for 82 exotic species measured in to Victoria, Australia. The location where the plant samples were collected is also described. See tab 'Trait_field_collection'.</p> <p>(2) traits and other variables collected from the literature, including Seed mass, Longevity, Reproduction type, Seed morphology, Dispersion vector, Likely introduction pathway, Management. See tab 'Traits_literature'.</p> <p> </p>
FIGURE 3. Leptagrion dispar. a in Description of the larva of Leptagrion dispar Selys, 1876 (Odonata: Coenagrionidae) with notes on distribution and ecology of the specie
FIGURE 3. Leptagrion dispar. a—Last larval instar, dorsal view; b—Head and thorax—dorsal view; c—Prementum—dorsal view; d—Labial palp, dorsal view; e—Right mandible, inner view; f—Left mandible, inner view; g—Gonapophysis and cercus of the male, ventral view; h—lamellas—dorsal view; i—Median caudal lamella—dorsal view; j—Lateral caudal lamella, lateral view. Scales: Fig. a = 5 mm, Figs. b–d = 1 mm, Figs. e–f = 0,5 mm, Figs. g–j = 1 mm.
F I G U R E 7 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species
F I G U R E 7 Outer morphology of Microcebus jonahi. (a) Drawing of an adult individual; (b) Habitus of adult female (paratype individual BD1); (c–e) Close‐ups of adult male (holotype B34). Illustration copyright by Stephen D. Nash/IUCN SSC Primate Specialist Group; used with permission. Photos by D. Schüssler
F I G U R E 6 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species
F I G U R E 6 Reproductive records for adult males (a) and females (b) of Microcebus spp. in northeastern Madagascar and presence of juvenile individuals (c) in the population
F I G U R E 5 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species
F I G U R E 5 Linear discriminant analysis including all morphometric parameters (except third toe length). All five linages can be distinguished statistically (Wilk's lambda = 0.005; F = 10.338; p <.001) with a misclassification rate of 12.8%. dia, Mantadia NP; vala, Ambavala
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.