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Supporting Data for: The genome of the pygmy right whale illuminates the evolution of rorquals
<p class="MsoNormal"><a name="_Hlk108424880"></a><em><u><span>Background</span></u></em></p> <p class="MsoNormal"><span><span>Baleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells. The pygmy right whale is the smallest and most elusive among the baleen whales. It reaches only a fraction of the body length compared to its relatives and it is the only living member of an otherwise extinct family. This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. Apart from that, genomic data of this species might help to investigate cancer resistance in large whales, since these mechanisms are not as important for the pygmy right whale as in other giant rorquals and right whales. </span></span></p> <p class="MsoNormal"><span><em><u><span>Results</span></u></em></span></p> <p class="MsoNormal"><span><span>Here, we present a first <em>de novo</em> genome of the species and test its potential in phylogenomics and cancer research. To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. Furthermore, a genome wide comparison of selection rates between large and small bodied baleen whales revealed a small set of conserved candidate genes with potential connections to cancer resistance. </span></span></p> <p class="MsoNormal"><span><em><u><span>Conclusions</span></u></em></span></p> <p class="MsoNormal"><span><span>Our results suggest that the evolution of rorquals is best described as a hard polytomy with a rapid radiation and high levels of introgression. The lack of shared positive selected genes between different large-bodied whale species supports a previously proposed convergent evolution of gigantism and hence cancer resistance in baleen whales. </span></span></p>
Fig. 1. Dorsal habitus, right half denuded. A in A new species of the xanthid crab genus Banareia A. Milne-Edwards, 1869 (Crustacea: Brachyura: Xanthidae) from the Bay of Bengal, southeastern India
Fig. 1. Dorsal habitus, right half denuded. A, Banareia metiguinotae, new species, holotype, female (40.5 × 27.8 mm) (CASAU CR 2020- 1020), Tamil Nadu, India; B, Banareia serenei Guinot, 1976, holotype, male (52.0 × 35.0 mm) (MNHN-IU-2014-22606 (= MNHN-B7224)), Nha Trang Bay, Vietnam. Scale bars = 10.0 mm.
Data from the Knowledge Rights 21 Project Retain Institutional Survey 2022
<p>Project Retain is a one-year project led by SPARC Europe as part of The Knowledge Rights 21 (KR21) Programme, funded by Arcadia fund (https://www.arcadiafund.org.uk/) which aims to promote change in European copyright, in this case, to support Open Access. Research on rights retention and open licensing in Europe aims to underpin a campaign to develop copyright policy amongst publishers, funders and institutions to support authors.</p> <p>The results of the project Retain are published in the "Opening Knowledge: Retaining Rights and Licensing in Europe 2023" report - <a href="https://doi.org/10.5281/zenodo.8084051">https://doi.org/10.5281/zenodo.8084051</a>.</p> <p>Within the project, the survey was conducted with the aim to understand the policies and support research institutions have put in place in a number of areas affecting their researchers.<br> The survey asks about the following topics:</p> <p>1. Copyright of scientific publications - how intellectual property that protects original works of authorship applies to the written outputs of research.<br> Specifically:</p> <ul> <li>Whether the initial ownership of copyright is with authors or their</li> <li>employing organisation</li> <li>What rights are transfered from authors to publisher</li> </ul> <p>2. Author rights retention - the extent to which researchers retain rather than transferring control of their published research</p> <p>3. Reuse of scientific publications - ensuring that the written outputs of research can be reused, by the community as a whole but also by the original author in new contexts</p> <p>4. Open licensing - the promotion of licenses which grant permission to access, re-use and redistribute.</p> <p>The full survey questionnaire file is included in appended to the dataset.</p> <p>The survey was disseminated widely across Europe by SPARC Europe and its partner organisations through newsletters, email lists and social media channels in the autumn of 2022. The survey received 238 unique responses with a completion rate of 71%. </p> <p>A total of 92 responses were excluded from the final analysis because:</p> <ul> <li>they provided extremely limited or no detail in their responses</li> <li>they answered ‘no’ when asked if they agreed to take part in the survey</li> <li>their response was identifiably a duplicate </li> </ul> <p>A total of 146 unique responses were included in the final dataset and analysed.</p> <p>The deposited dataset is anonymised: the personal data and the names and URLs of the institutions are removed or redacted.<br> </p>
FIGS. 392–396. Typhloleleupius. 392. T. doryloides, right proleg omitted. 393–396. T in Generic Revisions Of The Scopaeina And The Sphaeronina (Coleoptera: Staphylinidae: Paederinae: Lathrobiini)
FIGS. 392–396. Typhloleleupius. 392. T. doryloides, right proleg omitted. 393–396. T. nr. minutus. 393. Prothorax. 394. Procoxa, anteromesial. 395. Labrum. 396. Maxillary palpus, fourth palpomere missing.
Fig. 4. Scelolabes bivittatus Philippi, 1865. A–F. Male terminalia. A. Ventral view. B. Dorsal view. C. Left lateral view. D. Right lateral view. E–F in Revision of Neotropical Scelolabes Philippi (Diptera, Hybotidae, Ocydromiinae): two new species and a proposal of delimitation
Fig. 4. Scelolabes bivittatus Philippi, 1865. A–F. Male terminalia. A. Ventral view. B. Dorsal view. C. Left lateral view. D. Right lateral view. E–F. Surstyli in frontal view. E. Left. F. Right. G. Female terminalia in ventral view. Scale bars = 0.1 mm.
Forestation at the right time with the right species can generate persistent carbon benefits in China
<p>This collection contains the datasets used in our study ‘<strong>Forestation at the right time with the right species can generate persistent carbon benefits in China</strong>’.</p> <p><em><strong>Part A: Data</strong></em></p> <p>Most of the data presented here are after pre-processing, such as transforming the projection, extracting variables, clipping to the study region (70<sup>o</sup>E-140<sup>o</sup>E,15<sup>o</sup>N-55<sup>o</sup>N), and resampling to 1-km.</p> <p>The original source of these data sets (usually global, at different resolutions) is given in 'data_original.txt' as well as in the 'Data availability' of the main text.</p> <p>1. potential_china_forest_1km.rar: contains the potential forest distributions for China at 1-km resolution from multiple source (Random Forest, WRI and ORCHIDEE). Note: the forest distribution is in the form of logical variables in the .mat file, where a value of 1 or true means that the grid point is potentially forestable, and a value of 0 or false means this grid is not suitable for forest.</p> <p>2. ori_carbon_all_grid_1km.mat: Living biomass carbon densities in 2010 for China at 1-km (unit: Mg C ha-1). Both aboveground and belowground biomass carbon are included. The original biomass map is from Spawn et al. 2020.</p> <p>3. Forest_inventory_data_5th_9th.xlsx: 1) The forest area reported in 5th to 9th national forest inventory 2) The forest area of different age classes derived form the 9th national forest inventory.</p> <p>4. data_original.txt: the original source of these data sets</p> <p><strong>Part B: MATLAB Code</strong></p> <p>This file (Matlab_code.rar) contains the code, functions and parameters for our analysis of the data, mainly MATLAB files (.m or mat)</p> <p><strong>Part C: Demo/Example data and code</strong></p> <p>This file (Demo.rar) contains the demo of our code running, which includes the demo code along with code comments, input data for the demo, and the expected output results.</p> <p><strong>Part D: Docs</strong></p> <p>Reference and guidelines (Docs.rar).</p> <p>If you have any questions or suggestions, please contact xuhaotony@pku.edu.cn</p>
Data from: Nutrigonometry I: using right-angle triangles to quantify nutritional trade-offs in performance landscapes
<p>Animals regulate their food intake to maximise the expression of fitness traits but are forced to trade-off optimal expression of some fitness traits due to differences in nutrient requirements of each trait ('nutritional trade-offs'). Nutritional trade-offs have been experimentally uncovered using the Geometric Framework for Nutrition (GF). However, current analytical methods to measure such responses rely on either visual inspection or complex models of vector calculations applied to multidimensional performance landscapes, making these approaches subjective, or conceptually difficult, computationally expensive, and in some cases inaccurate. Here, we present a simple trigonometric model to measure nutritional trade-offs in multidimensional landscapes (Nutrigonometry), which relies on the trigonometric relationships of right-angle triangles and thus, is both conceptually and computationally easier to understand and use than previous quantitative approaches. We apply Nutrigonometry to a landmark GF dataset for the comparison of several standard statistical models to assess model performance in finding regions in the performance landscapes. This revealed that polynomial (Bayesian) regressions can be used for precise and accurate predictions of peaks and valleys in performance landscapes, irrespective of the underlying structure of the data (i.e., individual food intakes vs fixed diet ratios). We then identified the known nutritional trade-off between lifespan and reproductive rate both in terms of nutrient balance and concentration for validation of the model. This shows Nutrigonometry enables a fast, reliable, and reproducible quantification of nutritional trade-offs in multidimensional performance landscapes, thereby broadening the potential for future developments in comparative research on the evolution of animal nutrition.</p>
"I'm something of an untrained, unofficial cultural anthropologist myself. Ihave a business interviewing people to capture their personal histories. I'm always interested how people fit into their world and how they affect their world. I'm a graphic designer who works in the same building as the printing presses that I recorded. Iwalk past the presses every day on my way to talk to the folks in the prepress department. I'm on friendly but not drinking terms with the pressmen. I'm a friend with the prepress manager. Three Heidelberg presses are installed side by side in an open warehouse-like room. The presses are about twenty feet long and about five feet high. With their series of four humps or mounds where each printing cylinder is located, the presses remind one of giant, gray, mechanical caterpillars. Each press has a cyan cylinder, a magenta cylinder, a yellow cylinder and a black cylinder – so the humps are brightly colored. The presses are well lit by banks of fluorescent lights hanging from the ceiling over each press. When you walk into the press room you hear the sound of rock music blaring from a boom box radio mixed with the general din of the presses. It is only when you walk up to a press like Idid for the recordings that you really start to hear the individual strains of clicking, clacking and mechanical, syncopated chattering. When I made my recordings I was intrigued by the subtle variations in the sounds produced by these machines that aren't apparent when you first walk through the door. The pressmen were kind enough to allow me to walk right up to the presses and poke my microphone quite close to the rotating press cylinders. Iuse a Danish Pro Audio microphone about the size of a pencil eraser. An extremely sensitive mic with the capacity for capturing loud sounds such as the presses up close. Rotating the mic to one side or the other focused on the unique sounds coming from one cylinder or the other." [Kevin/KMerrell]18 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice
"I'm something of an untrained, unofficial cultural anthropologist myself. Ihave a business interviewing people to capture their personal histories. I'm always interested how people fit into their world and how they affect their world. I'm a graphic designer who works in the same building as the printing presses that I recorded. Iwalk past the presses every day on my way to talk to the folks in the prepress department. I'm on friendly but not drinking terms with the pressmen. I'm a friend with the prepress manager. Three Heidelberg presses are installed side by side in an open warehouse-like room. The presses are about twenty feet long and about five feet high. With their series of four humps or mounds where each printing cylinder is located, the presses remind one of giant, gray, mechanical caterpillars. Each press has a cyan cylinder, a magenta cylinder, a yellow cylinder and a black cylinder – so the humps are brightly colored. The presses are well lit by banks of fluorescent lights hanging from the ceiling over each press. When you walk into the press room you hear the sound of rock music blaring from a boom box radio mixed with the general din of the presses. It is only when you walk up to a press like Idid for the recordings that you really start to hear the individual strains of clicking, clacking and mechanical, syncopated chattering. When I made my recordings I was intrigued by the subtle variations in the sounds produced by these machines that aren't apparent when you first walk through the door. The pressmen were kind enough to allow me to walk right up to the presses and poke my microphone quite close to the rotating press cylinders. Iuse a Danish Pro Audio microphone about the size of a pencil eraser. An extremely sensitive mic with the capacity for capturing loud sounds such as the presses up close. Rotating the mic to one side or the other focused on the unique sounds coming from one cylinder or the other." [Kevin/KMerrell]18
Estimation of reinforced urn processes under left-truncation and right-censoring
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Data from: Nutrigonometry I: using right-angle triangles to quantify nutritional trade-offs in performance landscapes
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Supporting Data for: The genome of the pygmy right whale illuminates the evolution of rorquals
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Data from: Unobserved individual and population level impacts of fishing gear entanglements on North Atlantic right whales
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Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile–Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground
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Comparative analysis of a geometric and an adhesive righting strategy against toppling in inclined hexapedal locomotion
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Linking variation in water democracy to system performance on the human right to water
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Pl. 16. — Male anal appendages of Malaysian species of Amphicnemis, dorsal view and right side in Descriptions and records of South-East Asiatic Odonata (II)
Pl. 16. — Male anal appendages of Malaysian species of Amphicnemis, dorsal view and right side
Data from: Siring success in kangaroos: size matters for those in the right place at the right time
In polygynous species, male reproductive success is predicted to be monopolized by a few dominant males. This prediction is often not supported, suggesting that ecological and alternative mating tactics influence siring success. The spatiotemporal distribution of individuals and the number of males competing for each receptive female are often overlooked, because they are difficult to monitor in wild animals. We examined how spatial overlap of female-male pairs, the time spent by a male on the breeding site, number of competitors and morphological traits influence siring probability in eastern grey kangaroos (<i>Macropus giganteus</i>). We compared home range overlap for 12,208 dam-male pairs and 295 known dam-sire pairs to define local competitive groups and to estimate every male's opportunity to sire the young of each female. We compared models considering morphological traits relative to the entire population or to local competitive groups. Including local competition improved model performance because it estimated the intensity of competition and compared each male's morphological traits to those of its competitive group. Regardless of size, males can increase their probability to sire a young by increasing their <i>mating opportunity</i> relative to the mother. We underline the importance of considering spatial structure to assess the intensity of competition in species where males cannot equally access all females in a population. The estimation of mating opportunity and intensity of local competition improves our understanding of how morphological traits affect siring success when each mating event involves a different set of competing males, a characteristic of most wild species.
Something is not quite right: effects of two land uses on anuran diversity in subtropical grasslands
Although habitat modification is considered one of the main causes of biodiversity loss, the relative contribution of different rural land uses to biodiversity conservation are far less known. Additionally, the realization of the multidimensionality of biodiversity demands studies integrating variation of functional traits and phylogenetic information as complements to address the effects of land use on the structure of animal communities. Herein, we investigated the effects of land use (i.e., intensive agricultural and extensive livestock rearing) on functional and phylogenetic diversity of anuran communities in farmland ponds from the Uruguayan savanna ecoregion, while considering the effects of local factors (i.e., water depth) on species composition. We surveyed adults and tadpoles in 22 ponds and quantified five traits related to tadpole feeding, habitat use, and predator avoidance. Tadpole identification was corroborated by DNA barcoding based on a fragment of the mitochondrial 16S rRNA gene. We observed a decline in phylogenetic mean nearest taxon distance associated with increase of surrounding agricultural land use. While land use intensification did not affect richness (functional or phylogenetic), ponds in livestock ranches hosted about four times more tadpoles than agricultural ponds. Functional evenness decreased with water depth, although such relationship disappeared when considering phylogenetic non-independence. Our results indicated that specific anuran clades were more sensitive to intensification in land use, reinforcing a recent view of phylogenetic homogenization following habitat conversion. Additionally, our study suggests that extensive cattle grazing over wide native pastures may provide an alternative more compatible with conservation than short-term crops in subtropical grasslands.
Figure 2. Iporangaia pustulosa male rubbing the right metatarsus IV in Mode of use of sexually dimorphic glands in a Neotropical harvestman (Arachnida: Opiliones) with paternal care
Figure 2. Iporangaia pustulosa male rubbing the right metatarsus IV against the substrate (seta).
Data from: Plant-soil feedbacks mediate shrub expansion in declining forests, but only in the right light
1. Contemporary global change, including the widespread mortality of foundation tree species, is altering ecosystems and plant communities at unprecedented rates. Plant-soil interactions drive myriad community dynamics, and we hypothesized such interactions may be an important driver of succession following the loss of foundation tree species. 2. We examined whether plant-soil biota interactions, in the context of a putatively important light gradient associated with foundation tree decline, mediate the expansion of Rhododendron maximum in southeastern US forests where Tsuga canadensis (eastern hemlock), a dominant foundation tree species, is in decline. Using an 11-month, controlled inoculation experiment paired with Illumina sequencing, we tested the following hypotheses: (1) Relative to conspecific (R. maximum-conditioned) soils, R. maximum seedlings have higher performance in soils conditioned by T. canadensis and lower performance in interspace soils (conditioned by neither T. canadensis nor R. maximum) due to variation in soil fungal biota, and (2) seedling performance is greater in high light versus low light environments (matching environments under infested versus uninfested T. canadensis crowns, respectively). 3. In partial support of the first hypothesis, we found that R. maximum seedling performance was highest in T. canadensis-conditioned and R. maximum-conditioned soils and lowest in interspace soils. Mechanistically, soils conditioned by T. canadensis and R. maximum had more ericoid and ectomycorrhizal fungi, less saprotrophic fungi, and were less species-rich than interspace soils, and variation in these community traits predicted substantial variation in R. maximum seedling biomass. However, in support of our second hypothesis, soil effects on plant performance were evident in high light only; in low light, soil inoculation did not affect plant performance and plants performed worse. 4. Synthesis. Our findings suggest interactions with soil biota act synergistically with altered abiotic environments to mediate species responses to widespread foundation tree mortality, providing evidence for a novel mechanism of plant response to large-scale disturbance. Examining plant-soil interactions in the context of relevant abiotic gradients can therefore enhance our understanding, predictions, and management of community development processes following forest disturbance.
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.