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Data from: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes
BACKGROUND: Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species. METHODOLOGY/PRINCIPAL FINDINGS: We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences. CONCLUSIONS/SIGNIFICANCE: Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.
Data from: Concerted versus independent evolution and the search for multiple refugia: comparative phylogeography of four forest beetles
Phylogeographic structure and its underlying causes are not necessarily shared among community members, with important implications for using individual organisms as indicators for ecosystem evolution, such as the identification of forest refugia. We used mitochondrial DNA (COI), Bayesian coalescent ancestral state reconstruction (implemented in BEAST) and ecological niche models (ENMs) to construct geo-spatial histories for four co-distributed New Zealand forest beetles (Leiodidae, Nitidulidae, Staphylinidae, Zopheridae) to examine the extent to which they have tracked environmental changes together through time. Hindcast ENMs identified potential forest refugia during the Last Glacial Maximum, while ancestral state reconstruction identified key geographic connections for each species, facilitating direct comparison of dispersal patterns supported by the data and the time frame in which they occurred. Well-supported geographic state transitions for each species were mostly between neighboring regions, favoring a historical scenario of stepping stone colonization of newly-suitable habitat rather than long distance dispersal. No geographic state transitions were shared by all four species, but three shared multiple projected South Island refugia and recent dispersal from the southernmost refugium. In contrast, strongly supported dispersal patterns in the refugia-rich northern South Island suggest more individualistic responses to environmental change in these ecologically similar forest species.
Data from: How common road salts and organic additives alter freshwater food webs: in search of safer alternatives
The application of deicing road salts began in the 1940s and has increased drastically in regions where snow and ice removal is critical for transportation safety. The most commonly applied road salt is sodium chloride (NaCl). However, the increased costs of NaCl, its negative effects on human health, and the degradation of roadside habitats has driven transportation agencies to seek alternative road salts and organic additives to reduce the application rate of NaCl or increase its effectiveness. Few studies have examined the effects of NaCl in aquatic ecosystems, but none have explored the potential impacts of road salt alternatives or additives on aquatic food webs. We assessed the effects of three road salts (NaCl, MgCl2 and ClearLane™) and two road salts mixed with organic additives (GeoMelt™ and Magic Salt™) on food webs in experimental aquatic communities, with environmentally relevant concentrations, standardized by chloride concentration. We found that NaCl had few effects on aquatic communities. However, the microbial breakdown of organic additives initially reduced dissolved oxygen. Additionally, microbial activity likely transformed unusable phosphorus from the organic additives to usable phosphorus for algae, which increased algal growth. The increase in algal growth led to an increase in zooplankton abundance. Finally, MgCl2 – a common alternative to NaCl – reduced compositional differences of zooplankton, and at low concentrations increased the abundance of amphipods. Synthesis and applications. Our results indicate that alternative road salts (to NaCl), and road salt additives can alter the abundance and composition of organisms in freshwater food webs at multiple trophic levels, even at low concentrations. Consequently, road salt alternatives and additives might alter ecosystem function and ecosystem services. Therefore, transportation agencies should use caution in applying road salt alternatives and additives. A comprehensive investigation of road salt alternatives and road salt additives should be conducted before wide-scale use is implemented. Further research is also needed to determine the impacts of salt additives and alternatives on higher trophic levels, such as amphibians and fish.
Data from: Tidal drift removes the need for area restricted search in foraging Atlantic puffins
Understanding how animals forage is a central objective in ecology. Theory suggests that where food is uniformly distributed, Brownian movement ensures maximum prey encounter rate, but when prey is patchy, the optimal strategy resembles a Lévy walk where Area Restricted Search (ARS) is interspersed with commuting between prey patches. Such movement appears ubiquitous in high trophic level marine predators. Here we report foraging and diving behaviour in a seabird with a high cost of flight, the Atlantic puffin (Fratercula arctica), and report a clear lack of Brownian or Levy flight and associated ARS. Instead, puffins foraged using tides to transport them through their feeding grounds. Energetic models suggest the cost of foraging trips using the drift strategy is 28-46% less than flying between patches. We suggest such alternative movement strategies are habitat-specific, but likely to be far more widespread than currently thought.
Data from: Adaptive nowcasting of influenza outbreaks using Google searches
Seasonal influenza outbreaks and pandemics of new strains of the influenza virus affect humans around the globe. However, traditional systems for measuring the spread of flu infections deliver results with one or two weeks delay. Recent research suggests that data on queries made to the search engine Google can be used to address this problem, providing real-time estimates of levels of influenza-like illness in a population. Others have however argued that equally good estimates of current flu levels can be forecast using historic flu measurements. Here, we build dynamic 'nowcasting' models; in other words, forecasting models that estimate current levels of influenza, before the release of official data one week later. We find that when using Google Flu Trends data in combination with historic flu levels, the mean absolute error (MAE) of in-sample 'nowcasts' can be significantly reduced by 14.4%, compared with a baseline model that uses historic data on flu levels only. We further demonstrate that the MAE of out-of-sample nowcasts can also be significantly reduced by between 16.0% and 52.7%, depending on the length of the sliding training interval. We conclude that, using adaptive models, Google Flu Trends data can indeed be used to improve real-time influenza monitoring, even when official reports of flu infections are available with only one week's delay.
Data from: The search for loci under selection: trends, biases and progress
Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAA) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analyzed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographic coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP-based selection studies and help to progress landscape and evolutionary genomics.
Data from: A genome‐wide search for local adaptation in a terrestrial‐breeding frog reveals vulnerability to climate change
Terrestrial‐breeding amphibians are likely to be vulnerable to warming and drying climates, as their embryos require consistent moisture for successful development. Adaptation to environmental change will depend on sufficient genetic variation existing within or between connected populations. Here, we use Single Nucleotide Polymorphism (SNP) data to investigate genome‐wide patterns in genetic diversity, gene flow and local adaptation in a terrestrial‐breeding frog (Pseudophryne guentheri) subject to a rapidly drying climate and recent habitat fragmentation. The species was sampled across 12 central and range‐edge populations (192 samples), and strong genetic structure was apparent, as were high inbreeding coefficients. Populations showed differences in genetic diversity, and one population lost significant genetic diversity in a decade. More than 500 SNP loci were putatively under directional selection, and 413 of these loci were correlated with environmental variables such as temperature, rainfall, evaporation and soil moisture. One locus showed homology to a gene involved in the activation of maturation in Xenopus oocytes, which may facilitate rapid development of embryos in drier climates. The low genetic diversity, strong population structuring and presence of local adaptation revealed in this study shows why management strategies such as targeted gene flow may be necessary to assist isolated populations to adapt to future climates.
Data from: Searching for diamonds in the apomictic rough: a case study involving Boechera lignifera (Brassicaceae)
The genus Boechera is one of the most difficult species complexes in North America, with about 70 sexual diploids and hundreds of apomictic taxa representing diverse combinations of nearly every known sexual genome. In this study, we set out to clarify the taxonomy of Boechera lignifera, which currently includes a small number of sexual diploid populations in addition to the widespread apomictic diploid upon which the name is based. Using data from cytological studies, microsatellite DNA analyses, geography, and morphology, we demonstrate that the apomictic populations are genetically quite divergent from the sexual diploids. We propose the name Boechera kelseyana to accommodate the sexual diploid taxon, which occurs entirely south of the geographic range of B. lignifera. Boechera kelseyana is consistently separable from B. lignifera based on pollen and seed morphology, the length and proximal orientation of fruiting pedicels, differences in the branching and orientation of trichomes on the lowers stems, and the number of flowers and cauline leaves on unbranched fertile stems.
Data from: Males, but not females, perform strategic mate searching movements between host plants in a leaf beetle with scramble competition polygyny
1. Mate searching is assumed to be performed mostly by males, but when females benefit from multiple mating or are under risk of failing to mate, they may also perform mate searching. This is especially important in scramble competition polygynies, in which mate searching is the main mechanism of mate competition. Typically, more mobile individuals are expected to achieve higher mating success because mobility increases their probability of finding mates. 2. If we assume individual movements are mainly explained by mate searching in scramble competition polygynies, we can investigate searching strategies by asking when individuals should leave their location and where they should go. We hypothesize that individuals will leave their locations when mating opportunities are scarce and will seek spatially close sites with better mating opportunities. 3. We tested these hypotheses for males and females of Leptinotarsa undecimlineata, a leaf beetle with scramble competition polygyny in which both sexes are promiscuous. Individuals mate and feed exclusively on Solanum plants, thus individual movements can be described as switches between plants. 4. Females were less likely than males to leave isolated plants, and both males and females moved preferentially to neighbouring plants. Males were more likely to leave when the local number of females was low, and the number of males was high. They moved to plants with more females, a behaviour consistent with a mate searching strategy. Females were more likely to move to plants with fewer males and many females, a behaviour consistent with male harassment avoidance. 5. Strategic movement is widely considered in foraging context, but seldom in a mate searching context. Considering that selection to minimize searching costs, maximize mating success, and minimize harassment may be ubiquitous in nature, we argue that strategic movements by mate searching individuals are likely to occur in many species.
Data from: Reproductive effort and success of males in scramble competition polygyny: evidence for trade-offs between foraging and mate-search
1. Patterns of male reproductive allocation provide insight into life-history characteristics. The trade-offs associated with resource and female group defense are well-defined. However, less is understood about trade-offs in species that practice scramble-competition polygyny, where successful strategies may favor competitive mate-searching rather than contest competition and fighting. 2. White-tailed deer (Odocoileus virginianus) practice scramble-competition polygyny where solitary males search for and assess receptivity of females scattered across the landscape. Physically mature males are expected to do most of the breeding because of the high energetic costs of reproduction and high social status. However, young males may collectively sire one-third of offspring. To gain a better understanding of trade-offs associated with scramble-competition polygyny, we quantified metrics associated with reproductive effort and success. 3. We quantified changes in body mass of harvested males, energetic costs of locomotion based on movements of GPS radio-collared males, and timing of reproduction via temporal genetic parentage assignments. 4. Young males (1.5 and 2.5 years old) sired offspring, but their mating success was mainly limited to peak rut, when most females were in estrus. Furthermore, multiple paternity was common, indicating opportunistic reproduction. Reproductive effort, indexed by body mass loss, was highest in prime-age males (5.5-6.5 years old). Surprisingly, young and post-prime males also exhibited significant body mass loss, indicative of investment in reproductive effort. Movement rates increased 2 to 4-fold during rut as a function of mate-search activities, but cost of locomotion would cause only about one-third of observed body mass loss. Because males are capital breeders, we infer most of body mass loss is due to reduced foraging. 5. In scramble-competition polygyny, the repeated location of potential mates and assessment of their estrous status appear to be important constituents of male mating strategies. Therefore mating success may be influenced by time management and spatial memory, and not based solely on social dominance. Thus, reproductive effort should be greater for individuals capable of reducing time foraging. For those that cannot, opportunistic mating opportunities may arise when operative adult sex ratios are low. Our analyses reveal valuable insight into the trade-offs associated with scramble-competition polygyny.
Characterizing long-range search behavior in Diptera using complex 3D virtual environments
<p>The exemplary search capabilities of flying insects have established them as one of the most diverse taxa on Earth. However, we still lack the fundamental ability to quantify, represent, and predict trajectories under natural contexts to understand search and its applications. For example, flying insects have evolved in complex multimodal 3D environments, but we do not yet understand which features of the natural world are used to locate distant objects. Here, we independently and dynamically manipulate 3D objects, airflow fields, and odor plumes in virtual reality over large spatial and temporal scales. We demonstrate that that flies make use of features such as foreground segmentation, perspective, motion parallax, and integration of multiple modalities to navigate to objects in a complex 3D landscape while in flight. We first show that tethered flying insects of multiple species navigate to virtual 3D objects. Using the apple fly, <i>Rhagoletis pomonella</i>, we then measure their reactive distance to objects and show that these flies<i> </i>use perspective and local parallax cues to distinguish and navigate to virtual objects of different sizes and distances. We also show that apple flies can orient in the absence of optic flow by using only directional airflow cues, and require simultaneous odor and directional airflow input for plume following to a host volatile blend. The elucidation of these features unlocks the opportunity to quantify parameters underlying insect behavior such as reactive space, optimal foraging, and dispersal, as well as develop strategies for pest management, pollination, robotics and search algorithms.</p>
Could Google Trends be used to predict methamphetamine-related crime? An analysis of search volume data in Switzerland, Germany, and Austria
<p>Data for paper submitted to PLoS One on 2016-07-08. Title: Could Google Trends be used to predict methamphetamine-related crime? An analysis of search volume data in Switzerland, Germany, and Austria</p> <p>Authors: Alex Gamma, Roman Schleifer, Wolfgang Weinmann, Anna Buadze, Michael Liebrenz</p> <p>Format: ZIP-file</p> <p>Contains:<br /> - Two datafiles, each as .csv and .dta (Stata version 11) file.<br /> - README file with instructions</p> <p> </p> <p> </p>
FIGURE 3. Maximum parsimony phylogenetic relationships with the taxon Pituna poranga removed. Heuristic search with 50 in Description of a new annual rivulid killifish genus from Venezuela
FIGURE 3. Maximum parsimony phylogenetic relationships with the taxon Pituna poranga removed. Heuristic search with 50 random additions and TBR branch swapping resulted in a single most parsimonious topology of 5706 steps. Numbers above nodes are bootstrap values based on 2000 pseudoreplicates (25 random additions each); only values over 50 are reported. Numbers below branches are Bremer support indices which are equivalent to unreversed synapomorphies.
FIGURE 2. Maximum parsimony phylogenetic hypothesis. Heuristic search with 50 in Description of a new annual rivulid killifish genus from Venezuela
FIGURE 2. Maximum parsimony phylogenetic hypothesis. Heuristic search with 50 random additions and TBR branch swapping resulted in a single most parsimonious topology of 6206 steps. Numbers above nodes are bootstrap values based on 2000 pseudoreplicates (25 random additions each); only values over 50 are reported. Numbers below branches are Bremer support indices which are equivalent to unreversed synapomorphies.
FIGURES 82–83. Fig. 82 in External egg structure of the Pentatomidae (Hemiptera: Heteroptera) and the search for characters with phylogenetic importance
FIGURES 82–83. Fig. 82. Most parsimonious tree (L = 63) in the analysis of the genus Nezara resulting from analysis under equal weighting of characters with 40 characters, six of which were egg characters. Fig. 83. Stric consensus of 10 most parsimonious trees (L = 104.493) of the Chinavia obstinata group resulting from analysis under equal weighting of characters with 45 characters, five of which were egg characters.
FIGURES 73–81 in External egg structure of the Pentatomidae (Hemiptera: Heteroptera) and the search for characters with phylogenetic importance
FIGURES 73–81. Eggs of the Pentatomidae viewed with SEM. Fig. 73. Serdia apicicornis Stål, detail of AMP. Figs. 74–76. Thoreyella maracaja Bernardes, Schwertner & Grazia. Fig. 74. Lateral view. Fig. 75. Anterior view. Fig. 76. Magnification of anterior pole, showing the AMP. Figs. 77–81. Capivaccius bufo Distant. Fig. 77. Anterior view. Fig. 78. Magnification of the lateral wall. Fig. 79. Magnification of anterior pole, showing the eclosion line and the AMP. Fig. 80. Detail of anterior pole. Fig. 81. Detail of AMP. Abbreviations: amp—aero-micropylar process, ec–eclosion line.
FIGURES 37–48 in External egg structure of the Pentatomidae (Hemiptera: Heteroptera) and the search for characters with phylogenetic importance
FIGURES 37–48. Eggs of the Pentatomidae viewed with SEM. Figs. 37 and 38. Euschistus (Lycipta) riograndensis Weiler & Grazia. Fig. 37. Magnification of the lateral wall. Fig. 38. Detail of the lateral wall, showing the AMP. Figs. 39–42. Euschistus (Mitripus) paranticus Grazia. Fig. 39. Lateral view. Fig. 40. Anterior view. Fig. 41. Magnification of anterior pole, showing the AMP. Fig. 42. Detail of AMP. Figs. 43–46. Mormidea cornicollis Stål. Fig. 43. Lateral view. Fig. 44. Anterior view. Fig. 45. Magnification of anterior pole. Fig. 46. Detail of AMP. Figs. 47 and 48. Chinavia armigera (Stål). Fig 47. Lateral view. Fig. 48. Anterior view. Abbreviations: amp–aero-micropylar process, lw–lateral wall.
FIGURES 1–12 in External egg structure of the Pentatomidae (Hemiptera: Heteroptera) and the search for characters with phylogenetic importance
FIGURES 1–12. Eggs of the Pentatomidae viewed with stereomicroscopy. Fig. 1. Podisus nigrispinus (Dallas), egg mass, anterior view. Fig. 2. Euschistus (Lycipta) riograndensis Weiler & Grazia, lateral view. Fig. 3. Euschistus (Mitripus) paranticus Grazia, lateral view. Figs. 4 and 5. Mormidea cornicollis Stål. Fig. 4. Newly laid eggs, anterior view. Fig. 5. Fertile eggs, anterior view. Fig. 6. Chinavia armigera (Stål), fertile eggs, anterior view. Fig. 7. Chinavia aseada (Rolston), lateral view. Fig. 8. Chinavia brasicola (Rolston), anterior view. Fig. 9. Chinavia runaspis (Dallas), anterior view. Fig. 10. Banasa induta Stål, lateral view. Fig. 11. Serdia apicicornis Stål, anterior view. Fig. 12. Thoreyella maracaja Bernardes, Schwertner & Grazia, lateral view. Scale bar = 1 mm.
FIGURES 25–36 in External egg structure of the Pentatomidae (Hemiptera: Heteroptera) and the search for characters with phylogenetic importance
FIGURES 25–36. Eggs of the Pentatomidae viewed with SEM. Fig. 25. Catulona pensa Rolston, detail of anterior pole, showing the AMP and the granulated area. Figs. 26–30. Dichelops (Diceraeus) furcatus (Fabricius). Fig. 26. Lateral view. Fig. 27. Anterior view. Fig. 28. Magnification of the lateral wall. Fig. 29. Magnification of anterior pole, showing the eclosion line and the AMP. Fig. 30. Detail of AMP. Figs. 31–35. Euschistus (Euschistus) heros (Fabricius). Fig. 31. Lateral view. Fig. 32. Anterior view. Fig. 33. Magnification of the lateral wall, showing the AMP. Fig. 34. Magnification of AMP, showing connector sheets (asterisks). Fig. 35. Detail of AMP surface. Fig. 36. Euschistus (Lycipta) riograndensis Weiler & Grazia, anterior view. Abbreviations: amp–aero-micropylar process, ec–eclosion line, ga–granulated area, lw–lateral wall.
FIGURES 49–60 in External egg structure of the Pentatomidae (Hemiptera: Heteroptera) and the search for characters with phylogenetic importance
FIGURES 49–60. Eggs of Chinavia spp. viewed with SEM. Figs. 49–51. Chinavia armigera (Stål). Fig. 49. Magnification of the lateral wall, showing the polygonal cells projected inward in a funnel. Fig. 50. Detail of the anterior pole. Fig. 51. Detail of the anterior pole, showing the eclosion line, the AMP, and the connector sheets (asterisks). Figs. 52–55. Chinavia aseada (Rolston). Fig. 52. Lateral view. Fig. 53. Anterior view. Fig. 54. Magnification of the lateral wall, showing the AMP and the connector sheets (asterisks). Fig. 55. Magnification of anterior pole, showing the eclosion line, the AMP, and the connector sheets (asterisks). Figs. 56–59. Chinavia brasicola (Rolston). Fig. 56. Lateral view. Fig. 57. Anterior view. Fig. 58. Magnification of the lateral wall, showing the AMP and the connector sheets (asterisks). Fig. 59. Magnification of anterior pole, showing the eclosion line and the AMP. Fig 60. Chinavia runaspis (Dallas), lateral view. Abbreviations: amp—aeromicropylar process, ec—eclosion line, lw—lateral wall.
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.