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45 results for “rate shifts”
The Data Related to Interfacial Shift Keying Allows a High Information Rate in Molecular Communication
<p>This dataset is related to a method for molecular communication in fluids described on "Fluorescent nanoparticles for reliable communication among implantable medical devices," Carbon, vol. 190, pp. 262-275, Apr. 2022, by Federico Calì, Luca Fichera, Giuseppe Trusso Sfrazzetto, Giuseppe Nicotra, Gianfranco Sfuncia, Elena Bruno, Luca Lanzanò, Ignazio Barbagallo, Giovanni Li-Destri, Nunzio Tuccitto; doi: 10.1016/J.CARBON.2022.01.016. <br> The dataset is linked to the manuscript entitled "Interfacial Shift Keying Allows a High Information Rate in Molecular Communication: Methods and Data" by F. Calì, G. Li-Destri, and N. Tuccitto submitted to IEEE Transactions on Molecular, Biological, and Multi-Scale Communications (T-MBMC).<br> The data, including elapsed time (s), starting from the injection and fluorescence intensity (a.u.), is given in tab-separated values format as .txt files. When present, a column includes the intensity subtracted for the baseline and the subtracted and normalized intensity. In all cases, the baseline was obtained by performing a linear fit between 10 and 110 s and subtracting the line obtained from the entire dataset.<br> </p>
Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
<p>As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suit of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study we show that asymmetric rates of sequence evolution rates lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.</p>
Data from: Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives
Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.Results The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa (e.g., the bombycid, Arotros Schaus) were misplaced and here formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).Conclusions Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth "arms race". Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
F I G U R E 3 Mass specific growth rates among locations, 2016–2017 in Movement and habitat shift responses of juvenile Atlantic Salmon (Salmo salar) to annually permanent stream flooding
F I G U R E 3 Mass specific growth rates among locations, 2016–2017.
High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms
<p>Differences between males and females are usually more subtle in dioecious plants than animals, but strong sexual dimorphism has evolved convergently in the South African Cape plant genus <i>Leucadendron</i>. Such sexual dimorphism in leaf size is expected largely to be due to differential gene expression between the sexes. We compared patterns of gene expression in leaves among ten <i>Leucadendron </i>species across the genus. Surprisingly, we found no positive association between sexual dimorphism in morphology and the number or the percentage of sex-biased genes. Sex bias in most sex-biased genes evolved recently and was species-specific. We compared rates of evolutionary change in expression for genes that were sex-biased in one species but unbiased in others and found that sex-biased genes evolved faster in expression than un-biased genes. This greater rate of expression evolution of sex-biased genes, also documented in animals, might suggest the possible role of sexual selection in the evolution of gene expression. However, our comparative analysis clearly indicates that the more rapid rate of expression evolution of sex-biased genes predated the origin of bias, and shifts towards bias were depleted in signatures of adaptation. Our results are thus more consistent with the view that sex bias is simply freer to evolve in genes less subject to constraints in expression level.</p>
Data From: Shifts in morphological covariation and evolutionary rates across multiple acquisitions of the trap-jaw mechanism in Strumigenys
<p class="MsoNormal">A long-standing question in comparative biology is how the evolution of biomechanical systems influence morphological evolution. The need for functional fidelity implies that the evolution of such systems should be associated with tighter morphological covariation, which may promote or dampen rates of morphological evolution. I examine this question across multiple evolutionary origins of the trap-jaw mechanism in the genus <em>Strumigenys</em>. Trap-jaw ants have latch-mediated, spring actuated systems that amplify the power output of their mandibles. I use Bayesian estimates of covariation and evolutionary rates to test the hypotheses that the evolution of this high-performance system is associated with tighter morphological covariation in the head and mandibles relative to non-trap-jaw forms and that this leads to shifts in rates of morphological evolution. Contrary to these hypotheses, there is no evidence of a large-scale shift to higher covariation in trap-jaw forms while different traits show both increased and decreased evolutionary rates between forms. These patterns may be indicative of many-to-one mapping and/or mechanical sensitivity in the trap-jaw LaMSA system. Overall, it appears that the evolution of trap-jaw forms in <em>Strumigenys</em> did not require a correlated increase in morphological covariation, partly explaining the proclivity with which the system has evolved.</p>
Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)
<p><strong>Background and Aims</strong> <em>Rhododendron </em>is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of <em>Rhododendron </em>in the Himalaya–Hengduan Mountains where the genus is most diverse.</p> <p><strong>Methods </strong>We reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the <em>Rhododendron </em>species native to the Himalaya–Hengduan Mountains. We compared this phylogeny with nuclear phylogenies to elucidate reticulate evolutionary events and clarify relationships at all levels within the genus. We also estimated the timing and diversification history of <em>Rhododendron</em>, especially the two species-rich subgenera <em>Rhododendron</em> and <em>Hymenanthes </em>that comprise >90 % of <em>Rhododendron </em>species in the Himalaya–Hengduan Mountains.</p> <p><strong>Key Results </strong>The full plastid dataset produced a well-resolved and supported phylogeny of <em>Rhododendron</em>. We identified 13 clades that were almost always monophyletic across all published phylogenies. The conflicts between nuclear and plastid phylogenies strongly suggested that reticulation events may have occurred in the deep lineage history of the genus. Within <em>Rhododendron</em>, subgenus <em>Therorhodion </em>diverged first at 56 Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya, generating ten lineages among the component 12 clades of core <em>Rhododendron</em>. Diversification in subgenus <em>Rhododendron </em>accelerated c. 16.6 Mya and then became fairly continuous. Conversely, <em>Hymenanthes </em>diversification was slow at first, then accelerated very rapidly around 5 Mya. In the Himalaya–Hengduan Mountains, subgenus <em>Rhododendron </em>contained one major clade adapted to high altitudes and another to low altitudes, whereas most clades in <em>Hymenanthes </em>contained both low- and high-altitude species, indicating greater ecological plasticity during its diversification.</p> <p><strong>Conclusions </strong>The 13 clades proposed here may help to identify specific ancient hybridization events. This study will help to establish a stable and reliable taxonomic framework for <em>Rhododendron</em>, and provides insight into what drove its diversification and ecological adaption. Denser sampling of taxa, examining both organelle and nuclear genomes, is needed to better understand the divergence and diversification history of <em>Rhododendron</em>.</p>
Data From: Shifts in morphological covariation and evolutionary rates across multiple acquisitions of the trap-jaw mechanism in Strumigenys
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Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
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Data from: Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory
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Data from: Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives
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Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)
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High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms
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Data from: Decreasing predation rates and shifting predator compositions along a land-use gradient in Madagascar's vanilla landscapes
<p>1. Land-use change is the main driver of deforestation and land degradation resulting in the loss of biodiversity and ecosystem functioning in north-eastern Madagascar. Vanilla, the region's main cash crop, is grown in agroforestry systems and may provide an opportunity for the conservation of biodiversity and ecosystem functioning.</p> <p>2. We used dummy caterpillars to assess predation rates and predator communities along a land-use gradient including unburned old-growth and forest fragments, herbaceous and woody fallows after shifting cultivation with fire usage, as well as rice paddies. The studied vanilla agroforests were either forest-derived or fallow-derived. Besides land-use type, we considered the effects of land-use history (unburned/burned), plot-level parameters and the landscape composition to conclude on management recommendations.</p> <p>3. Old-growth forest and forest fragments exhibited highest predation rates, which decreased with land-use intensity. Overall, predation was higher in unburned land-use types than in more open, previously burned habitats and rice paddies. High stem and vegetation densities were positively related to predation rates, but decreased with land-use intensity. High forest cover in the surrounding landscape led to higher predation rates, while local structural parameters remained more important.</p> <p>4. The predator community was arthropod-dominated across all land-use types with ants responsible for between 33 % and 69 % of all predation events. Overall predator composition in old-growth and forest fragments differed from all other land-use types. Predation by Gryllacrididae (Orthoptera) was lower in all land-use types, including forest-derived vanilla, than in old-growth forest and forest fragments, where they were important contributors to total predation. Vertebrate predation was low throughout.</p> Synthesis and applications: Forested habitats feature higher predation rates and different predator compositions than other land-use systems. Maintaining or restoring tree- and understory-rich vanilla agroforestry represents a viable tool in landscape conservation programmes as it has the potential to contribute to the conservation of predation as an important ecosystem function in both forest- and fallow-derived agroforests. However, vanilla agroforestry has limited value in conserving forest-specialised predator communities. While the establishment of tree-rich agroforests on former fallow land is favourable for conservation ecosystem functioning, further forest transformation should be <a>avoided</a>.
Data from: Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens
The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.
Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)
The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous–Paleogene (K–Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K–Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10,000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1–3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K–Pg mass extinction, in the Paleocene–Eocene (65.5–33.9 Ma) or in association with the Eocene–Oligocene transition (33.9 Ma).
Data from: Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae)
Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus Hypericum is one of these. Results:To investigate the effect of macroecological niche shifts on evolutionary success we combine historical biogeography with analyses of diversification dynamics and climatic niche shifts in a phylogenetic framework. Hypericum evolved cold tolerance c. 30 million years ago, and successfully colonized all ice-free continents, where today ~500 species exist. The other members of Hypericaceae stayed in their tropical habitats and evolved into ~120 species. We identified a 15–20 million year lag between the initial change in temperature preference in Hypericum and subsequent diversification rate shifts in the Miocene. Conclusions:Contrary to the dramatic niche shift early in the evolution of Hypericum most extant species occur in temperate climates including high elevations in the tropics. These cold/temperate niches are a distinctive characteristic of Hypericum. We conclude that the initial release from an evolutionary constraint (from tropical to temperate climates) is an important novelty in Hypericum. However, the initial shift in the adaptive landscape into colder climates appears to be a precondition, and may not be directly related to increased diversification rates. Instead, subsequent events of mountain formation and further climate cooling may better explain distribution patterns and species-richness in Hypericum. These findings exemplify important macroevolutionary patterns of plant diversification during large-scale global climate change.
A specialist bee and its host plants experience phenological shifts at different rates in response to climate change
<p>Changes in climate can alter the phenology of organisms, potentially decoupling partners within mutualisms. Previous studies have shown that plant and pollinator phenologies are shifting over time, but these shifts have primarily been documented for generalists and within small geographic regions, and the specific climatic cues regulating these shifts are not well-understood. We examined phenological shifts in a specialist pollinator and its host plant species over a 117-year study period using a digitized dataset of over 4,000 unique collection records. We assess how climatic cues regulate these organisms' phenologies using PRISM weather data associated with each record. We tested the hypothesis that rates of phenological change would be greater at northern latitudes. We found that the phenology of the specialist bee pollinator Habropoda laboriosa is changing over time, but at different rates across its range. Specifically, phenology is advancing to a greater degree in more northern populations, with increasing phenological advances of 0.04 days/year with each degree of latitude, and with a delay in phenology in more southern populations. In contrast, only one species in the host plant genus Vaccinium is experiencing phenological change over time. For this plant, rates of change are also variable across latitudes, but in a pattern opposite that of the bee; while phenology is advancing across its range, rates of advance are highest in more southern populations, with decreasing phenological advances of 0.01 days/year with each degree of latitude. The phenologies of both the bee and three of four Vaccinium spp. were regulated primarily by spring temperature, with phenologies overall advancing with increasing temperature, and with the strongest responses shown by the bee in northern populations. Our study provides partial support for the hypothesis that phenologies advance most at northern latitudes, but demonstrates that pollinators and plants do not adhere similarly to this prediction. Additionally, we illustrate the potential for phenological mismatch between a specialist pollinator and its host plants by showing that plants and pollinators are advancing their phenologies at different rates across space and time and with differing responses to changing climatic cues.</p>
Data from: A new method for testing evolutionary rate variation and shifts in phenotypic evolution
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Data from: Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae)
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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.