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Figure 6 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 6. Co-evolution of key reproductive traits in crocodile newts, based on life-history information (Supporting Information, Table S3) reported on our mitochondrial phylogeny (Fig. 1). White nodes: missing data. Ancestral states (reconstructed by the parsimony method of MESQUITE) are shown on internal nodes. Photos: amplexus of T. pseudoƲerrucosus and egg clutch of E. maxiquadratus (credits: AH).
Figure 5 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 5. Nuclear phylogeny of 27 crocodile newt species based on 3.2 kb combining four nuclear introns (POM-C, RAG1, BDNF and NCX1). Species are symbol-coded by genera and colour-coded by subclades as in the mitochondrial phylogeny (Fig. 1). Photos: E. maxiquadratus and T. pseudoƲerrucosus (credits: AH).
Figure 1 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 1. Time-calibrated phylogeny of crocodile newts built from 16.2 kb of mitochondrial sequences representative of the sampled genetic diversity of all known taxa. Major clades are distinguished by symbols (squares: Echinotriton; circles: Tylototriton) and colours to visualize their geographic distributions. Photos: E. maxiquadratus and T. pseudoƲerrucosus (credits: AH).
Figure 9 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 9. Appearance of Echinotriton (Echinotriton) raffaellii sp. nov. Top: live individual observed at the type locality (credits: AH); bottom: the holotype MVZ:Herp:232187 (credits: MVZ).
Figure 2 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 2. Phylogeography of crocodile newts part I: genus Echinotriton and subgenus Tylototriton. The phylogenetic position and geographic distribution of each lineage is detailed by coloured symbols on the tree and the corresponding maps. Type localities of described taxa are indicated by stars. For T. Ʋerrucosus, we highlighted the paraphyletic position of sequences attributed to T. shanjing, as well as its type locality with asterisks.
Figure 4 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 4. Evolution in isolation-by-distance in crocodile newts, as shown by ND2 sequence divergence vs. average geographic distances between analysed lineages.
Figure 3 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 3. Phylogeography of crocodile newts part II: subgenus Yaotriton. The phylogenetic position and geographic distribution of each lineage is detailed by coloured symbols on the tree and the corresponding maps. Type localities of described taxa are indicated by stars.
Figure 7 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 7. Simultaneous diversification (splitting events) through time in crocodile newts (blue bars) and the similarly surveyed South-East/East Asian tree frog genus Zhangixalus (green bars; Dufresnes et al., 2022), overlaid by Earth temperature (red curve). The latter is shown as the difference with the average temperature over the 1960–90 period, combining the datasets from Zachos et al. (2008), Hansen et al. (2013) and Lisiecki & Raymo (2005). In both amphibians, ancestral clades diverged in the Early Miocene and probably expanded throughout Asia during the Miocene climatic optimum; extant clades and species then appeared as the climate progressively cooled down and the South-East Asian monsoon strengthened in the Late Miocene onwards, and recently accelerated during the Pleistocene Quaternary glaciations. Photos: E. maxiquadratus (credit: AH) and Z. chenfui (credit: S. N. Litvinchuk).
Figure 8 in Towards completing the crocodile newts' puzzle with all-inclusive phylogeographic resources
Figure 8. Portrays of subgenera Sinotriton subgen. nov. and Echinotriton. Notice the shape of the vertebral ridge (segmented in Sinotriton vs. smooth in Echinotriton) and the fifth toe (normally developed in Sinotriton vs. rudimentary in Echinotriton). Photos: E. chinhaiensis, E. maxiquadratus (credits: AH); E. andersoni, E. raffaellii (credits: J. Nerz).
Effects of brood and group size on nestling provisioning and resource allocation in a communal bird
<p>Resource limitations, either due to environmental conditions or constraints on parental provisioning effort, can drive intense competition among offspring. In communal groups, resource availability may increase if parents receive assistance from other group members; however, if those caregivers also produce young, offspring demand may increase at the same time. It is possible, therefore, that the costs of intrabrood competition in large broods may outweigh the benefits of provisioning from additional caregivers. We tested the relationships between group size, brood size, and provisioning rates in the greater ani (<em>Crotophaga</em> <em>major</em>), a communally nesting cuckoo in which multiple breeding pairs and nonreproductive helpers cooperatively raise a shared brood. Crucially, brood and group size can vary independently in this species, allowing us to test changes in each variable separately. Using video footage of 2255 prey deliveries across 10 nests, we found that an increase in the number of adult caregivers within a group did not sufficiently offset a corresponding increase in the number of dependent young within a brood: prey availability per average nestling decreased with brood size, regardless of group size. In larger broods, last-hatched nestlings received significantly less prey than their broodmates, in part due to greater hatching asynchrony that exacerbated competitive asymmetries and facilitated inequality in food allocation. Our results indicate that last-hatched ani nestlings suffer a "double cost" in large broods: they must compete with more nestmates, and suffer disproportionately from asynchronous hatching. These costs may contribute to increased parent-offspring conflict and may constrain group size in communal breeders.</p>
Dataset: Resource limitation has a limited impact on the outcome of virus-fungus co-infection in an insect host
<p>Infection by pathogens is strongly affected by the diet or condition of the prospective host. Studies that examine the impact of diet have mainly focussed on single pathogens; however, co-infections within a single host are thought to be common. Different pathogen groups might respond differently to resource availability and diverse infections could increase the costs of host defence, meaning the outcome of mixed infections under varying dietary regimes is likely to be hard to predict. We used the generalist cabbage looper, <em>Trichoplusia ni</em> and two of its pathogens, the DNA virus <em>T. ni</em> nucleopolyhedrovirus (TniSNPV) and the entomopathogenic fungus, <em>Beauveria bassiana</em> to examine how nutrient reduction affected the outcome of mixed pathogen infection. We challenged insects with a low or high effective dose of virus, alone or combined with a single dose of fungus. We manipulated food availability after pathogen challenge by diluting artificial diet with cellulose, a non-nutritious bulking agent, and examined its impact on host and pathogen fitness. Reducing diet quantity did not alter overall or pathogen-specific mortality. In all cases, TniSNPV-induced mortality was negatively affected by fungus challenge. Similarly, <em>B. bassiana</em>-induced mortality was negatively affected by TniSNPV challenge, but only at the higher virus dose. Dietary dilution mainly affected <em>B. bassiana </em>speed of kill when mixed with a high dose of TniSNPV, with an increase in the duration of fungal infection when cellulose was low (high quantity). One pathogen dominated the production of transmission stages in the cadavers and co-infection did not affect the yield of either pathogen. There was no evidence that co-infections were more costly to the survivors of pathogen challenge. In conclusion, dietary dilution did not determine the outcome of mixed pathogen infection, but it had more subtle effects, that differed between the two pathogens and could potentially alter pathogen recycling and host-pathogen dynamics.</p>
Data from: Trait-based effects of plant invasion on floral resources, hoverflies and bees
<p>1. Plant invasions can lead to homogeneous communities with decreased functional diversity. However, invasive plants, with various morphological and phenological traits, may drive pollinator communities in a less predictable, more complex way. They can promote pollinators compatible with their floral traits while leaving others without foraging resources.</p> <p>2. Our observational study on 10 invasive herbaceous species applied a trait-based approach to investigate plant invasion-driven changes in floral resources, hoverfly, and bee communities. We sampled invaded and non-invaded (control) sites before and during the flowering of the invasive plants. We analysed the differences in floral traits between invasive and native plants, functional diversity, and trait distributions of flower and pollinator communities between the invaded and control sites.</p> <p>3. Five invasive plant species differed from natives in floral traits. Plant invasion caused species-specific changes in functional diversity and trait distributions of communities. For instance, invaded sites had a decreased functional diversity of hoverflies before flowering of invasive species, and larger hoverflies during flowering of invasive species compared with control sites. Smaller bees were associated with invasive plants with shallow flowers, while larger and long-tongued bees were associated with two invasive species with restricted floral access.</p> <p>4. Similar to previous studies, pollinator traits showed mixed or neutral responses to plant invasion. This is probably due to the high integration capability of invasive plants into plant-pollinator systems, or limitations in sampling, trait resolution, and unrevealed environmental factors. We provide recommendations for future studies to better understand the trait-based community composition of flowering plants and pollinators.</p>
Seemingly gliding: the power of metadata in academic resource discovery systems
<p>Creators of resource discovery systems are at a turning point in development: their systems must satisfy the users’ needs for the delivery of high-quality, academically-rigorous content, while also providing the most straightforward, Google-like interfaces possible. The role of metadata in this scenario becomes paramount as users enter a world which seems serendipitous, but which is still subject to academic rigour, relevance and comprehensiveness.<br> Ironically, such a system, necessarily supported by high-quality metadata, increasingly conceals them, thus lowering their profile in the user’s mind, and their importance becomes even more camouflaged to the user community. Without them, however, there is no system.<br> This paper explores this dichotomy, describing a vision for resource discovery which creates a seamless journey between related, yet disparate, resources. It moves on to look at a case study of a single tool: the HASSET thesaurus, developed at the UK Data Archive. This tool’s journey from an inhouse-developed thesaurus to the lynch-pin of many online services is described in detail. Lastly, the paper takes the theory of achieving focused results from a simple interface and, using HASSET, applies it to an existing service: the Economic and Social Data Service (ESDS). Metadata is shown to be the essential – and yet increasingly<br> invisible – force at work in effective resource discovery systems.</p>
Burden and resources in caregivers of people with multiple sclerosis: a qualitative study
<p><strong><em>Background: </em></strong><em>Caregivers of people with Multiple Sclerosis are required to provide ongoing assistance especially during the advanced stages of the disease. They have to manage interventions and assume responsibilities which significantly impact both their personal quality </em>of life and family’s dynamics. </p> <p><strong><em>Objective: </em></strong><em>A qualitative phenomenological study was carried out to understand the experience of burden in caregivers and their resources to manage it. The study also explores how healthcare services involved in the Multiple Sclerosis Clinical Pathway respond to the needs of well-being of patients and family members.</em></p> <p><strong><em>Methods: </em></strong><em>17 caregivers were involved in focus groups and in semi-structured individual interviews.</em></p> <p><strong><em>Results: </em></strong><em>Fatigue is experienced by all respondents and it starts when physical disabilities increase or when people become aware of them. Many caregivers declare that they refer to intrinsic (love towards their relatives, patience and dedication) or extrinsic (family members, hobbies) resources to cope with the burden of assistance. Patient associations and the Multiple Sclerosis Clinical Pathway play a significant role in supporting caregivers. </em></p> <p><strong><em>Conclusions:</em></strong></p> <p><em>Fatigue, loneliness, and isolation are experienced by caregivers and strongly affect their quality of life and health status. The study highlights caregivers’ need to reconcile working times with care times, to give more space to self-care and to have moments to share their experiences with someone else. These needs should be at the core of health policies in order to avoid physical and emotional breakdowns which could lead to the rupture of the relational balance on which home care is based. </em></p>
Dataset for Energy Resource Management Considering Participation in the Wholesale Day-Ahead Market
<p>This release is associated with a paper entitled "A Novel Bilevel Programming Formulation for Optimizing the Interaction of Distribution System Operators and GENCOs in Day-Ahead Markets".</p> <p>In this document, we provide the mathematical manipulation employed to linearize an MPEC problem that models the market-clearing process considering the participation of generation companies and distribution operators in the day-ahead market. Additionally, we provide a numerical example of the pricing mechanism designed for solving the optimization problem. </p> <p>Finally, we include information regarding the transmission and distribution power systems adopted to present the results shown in the paper. These systems are modified versions of the IEEE <a href="https://icseg.iti.illinois.edu/ieee-14-bus-system/">14-bus</a> and the IEEE <a href="https://cmte.ieee.org/pes-testfeeders/resources/">34-bus</a>, respectively. Three renewable non-dispatchable generators were added to the original 14-bus system, while 5 dispatchable generators and 3 non-dispatchable generators were added to the distribution system. 13 load shapes were considered as well as 5 scenarios for each uncertain variable (wind velocity, solar irradiance, distribution load oscillation, and transmission load oscillation). The data regarding the costs and physical parameters of each of the power system's elements are provided in this document.</p>
Figure 3 in The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae
Figure 3. An analysis of selective pressure in the protein coding genes (PCGs) of Lontra longicaudis indicates that the Ka/Ks value can show whether a gene is undergoing selection, and based on the magnitude of the value, what type of selection is taking place. Ka/Ks values <1 indicate purifying selection, whereas values equal to 1 indicate neutral selection. The Ka/Ks ratios (vertical axis) were calculated for each of the 13 PCGs (horizontal axis) by performing pairwise comparisons with L. lutra. Photo credit: John Tomsett.
Figure 6 in The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae
Figure 6. Phylomitogenomic analysis of Lontra longicaudis and related species in the family Mustelidae. Total-evidence phylogenetic tree obtained from ML analysis based on a concatenated alignment of amino acids of the 13 protein-coding genes present in the mitochondrial genome of representatives of the family Mustelidae. The branches are colour coded to represent their respective bootstrap values. Photo credit: John Tomsett.
Figure 2 in The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae
Figure 2. Codon usage analysis of PCGs in the mitochondrial genome of Lontra longicaudis. All 20 amino acids [adenine (A), cysteine (C), aspartic acid (D), glutamic acid (E), phenylalanine (F), glycine (G), histidine (H), isoleucine (I), lysine (K), leucine (L), methionine (M), asparagine (N), proline (P), glutamine (Q), arginine (R), serine (S), threonine (T), valine (V), tryptophan (W), tyrosine (Y)] are listed by their one-letter abbreviations along the horizontal axis. Each amino acid comprises several codons that are listed and colour coded below their respective amino acid. The length of the coloured regions indicates the frequency of the respective codon within that amino acid. The vertical axis represents the RSCU values for the amino acids.
Figure 5 in The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae
Figure 5. Characteristics of the domains found in the D-Loop/CR of the Lontra longicaudis mitochondrial genome. Top: Features observed in all three well-conserved domains. Centre: Secondary structure of long tandem repeat observed in the CSB region, between CSB1 and CSB2. Bottom: D-Loop/CR sequence in which the different features have been highlighted with different colours.
Figure 1 in The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae
Figure 1. Circular DNA mitochondrial genome map of Lontra longicaudis. The annotated map depicts 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS: 12S ribosomal RNA and rrnL: 16S ribosomal RNA), 22 transfer RNA (tRNA) genes, and the putative control region. Photo credit: John Tomsett.
ScienceDex guides
Understand access before you commit
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.