Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
853
datasets available to search
ShareScore release 0.7.1
Dataset results
853 results for “evolutionary history”
From Gondwana to GAARlandia: Evolutionary history and biogeography of ogre‐faced spiders (Deinopis)
Aim <p>We explore the evolutionary history of the ogre‐faced spiders (<i>Deinopis</i>) from their Early Cretaceous origins to present day. Specifically, we investigate how vicariance and dispersal have shaped distribution patterns of this lineage. Within the Caribbean, we test the role of GAARlandia, a hypothesized land bridge that connected South America to the Greater Antilles during the Eocene–Oligocene transition (~35–33 Ma), in the biogeography of <i>Deinopis</i>.</p> Taxon <p>Araneae: Deinopidae: <i>Deinopis</i>.</p> Location <p>Caribbean islands, with additional global exemplars.</p> Methods <p>Combining standard Sanger sequence data with an Anchored Hybrid Enrichment (AHE) phylogenomic dataset, we use Bayesian inference to estimate the phylogenetic relationships of <i>Deinopis</i>. "BioGeoBEARS" is used to test the GAARlandia hypothesis, and to pinpoint major dispersal events in the biogeographic history of <i>Deinopis</i>.</p> Results <p>The phylogeny supports the nesting of a Caribbean clade within a continental grade. Model comparisons indicate GAARlandia as the best fitting model, and the biogeographic analyses reflect the geologic history within the Caribbean. Ancient and recent overwater dispersal events are also indicated within this lineage. There is also an ancient 113 Ma split into Old and New World clades.</p> Main Conclusions <p>The <i>Deinopis</i> phylogeny corresponds well with geography. This is reflected in the support for the GAARlandia land bridge hypothesis and the phylogenetic relationships within and among Caribbean islands mirroring nuances of Caribbean geologic history. Overwater dispersal also plays an important role in the biogeographic history of this lineage as implicated in the colonization of the volcanic and sedimentary Lesser Antilles and in a "reverse" colonization of North America. The spider family Deinopidae is an ancient lineage with origins dating back to Gondwana. While overwater dispersal has clearly played a role in the biogeography of the genus, the <i>Deinopis</i> phylogeny bears a strong signature of ancient geological events.</p>
Data from: A multilocus analysis of Epicopeiidae (Lepidoptera, Geometroidea) provides new insights into their relationships and the evolutionary history of mimicry
<p>The family Epicopeiidae is a small group of day-flying moths, known for mimicking many different groups of butterflies and moths. So far, there still lacks a reliable phylogenetic framework of Epicopeiidae that is necessary to our understanding of the evolutionary process of their mimicry. In this study, we sequenced 94 nuclear protein-coding markers for 56 epicopeiid samples and 11 outgroups, covering all ten genera of Epicopeiidae. We used homemade PCR-generated baits to capture target sequences, which allowed us to utilize old and dried specimens that were difficult to handle by conventional PCR + Sanger sequencing. Maximum likelihood and Bayesian analyses of the newly obtained dataset (86,388 bp) at both DNA and protein levels produced identical phylogenies with strong support. The non-mimicry genus <em>Deuveia</em> is the sister group of other epicopeiid genera. <em>Epicopeia</em> and <em>Nossa</em> are not monophyletic, and these two genera nest together to form a clade. We also estimated divergence times of Epicopeiidae and found that their initial diversification happened in Eocene about 41 million years ago. The ancestral state reconstruction of mimicry type for this family suggested that the last common ancestor of epicopeiid moths is non-mimetic, and the Riodinidae-mimicry type evolved first. In summary, our work provides a comprehensive and robust time-calibrated phylogeny of Epicopeiidae that provides a sound framework for revising their classification and interpreting character evolution.</p>
Datasets - Evolutionary history, not ecogeographic rules, explains size variation of tropical insects along elevational gradients
<p>One of the best-known biogeographic rules for ectotherms is the temperature-size rule, which asserts that ectotherms produce smaller adults at warmer temperatures. Although this is often true, it has become clear that there is no single process behind the pattern and many exceptions to the rule. To disentangle such complex temperature-size relationships, individual clades must be examined at ecological and evolutionary scales.</p> <p>We examined temperature-size relationships for 2106 individuals from 64 populations and 40 species of <i>Cephaloleia</i> rolled-leaf beetles (Chrysomelidae; Cassidinae)<b> </b>occurring along two tropical elevational gradientss: Barva and the Talamanca Cordillera in Costa Rica, Central America. We tested whether the temperature-size rule applied to interspecific elevational assemblages, intraspecific elevational populations, or different rearing temperatures for individual populations.</p> <p>At the interspecific scale, evolutionary history, rather than elevation, explains body size. At the intraspecific scale, only one of seven species followed the temperature-size rule across elevations. When larvae were reared at different temperatures, only one of five populations followed the temperature-size rule. Most populations grew to a fixed size regardless of temperature.</p> <p>Size in <i>Cephaloleia</i> beetles is constrained by their evolutionary history and responds to factors that rarely correlate with temperature. As temperature increases, ectotherms will not universally shrink, but determining if and why their size will change will require further investigation.</p> <p>Here we provide the following datasets used to determine effects of temperature on insect body size at population and community levels: <i>Supplement S1.</i> Body length for 2106 individuals representing 64 populations from 40 species of <i>Cephaloleia </i>rolled-leaf beetle along the Barva and Talamanca elevational gradients, Costa Rica<i>. Supplement S2.</i> Intraspecific differences in length for 798 individuals from seven <i>Cephaloleia </i>species present at multiple life zone<i>.</i><i> Supplement S3.</i> Effects of developmental temperatures on <i>Cephaloleia </i>adult size in 968 individuals from four species and five populations reared in the laboratory at temperatures between 10 and 35 °C.</p>
data sets and trees for the Rasplus et al paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)" Cladistics (2020)
<p>Data sets and trees for the Rasplus <em>et al</em>. paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus <em>Ficus</em> (Moraceae)" Cladistics (2020). Preprint = https://www.biorxiv.org/content/10.1101/2020.04.15.042259v1</p> <p><strong>*.phy = Data sets (phylip format) [see Table 2 of the paper for more details].</strong></p> <p>- <strong>mergeR1R2.phy</strong> : complete data set (530 RAD loci shared by 75% of the samples + assembly of forward & reverse reads)<br> - <strong>mergeR1R2_GCinfmean.phy</strong> : loci with GC content inferior or equal to mean GC content<br> - <strong>mergeR1R2_GCsupmean.phy</strong> : loci with GC content strictly superior to mean GC content<br> - <strong>mergeR1R2_LS3.phy</strong> : loci that evolve at a homogeneous rate across clades of interest (Clade1= sect. Pharmacosycea; Clade2=subg. Urostigma, Clade3=sect. Oreosycea, Clade4= "gynodioecious clade")<br> - <strong>mergeR1R2_PCA.phy</strong> : loci for which difference between Long Branch (LB) scores for sect. Pharmacosycea and other ingroups was not significant according to our custom iterative PCA approach</p> <p> <br> <strong>Fig*.nwk : Trees (newick format) that were obtained for the different data sets.</strong></p> <p>Trees are also included as Figures or Supplementary Figures of the paper. Note that you may visualize these nwk trees in FigTree (open FigTree. Upload the FigS1A_RAxML_mergeR1R2_inclfigtreeannot.nex first and then open the other trees - do not close FigTree in between !- Annotations included in the first file will be automatically used to annotate other trees). </p> <p><strong>Appendix S2 : Morphological matrix + morphological tree + 4 competing molecular trees. </strong></p> <p>This file can be opened in Mesquite to get reconstruction of ancestral character states</p>
Data from: Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism
<p><i>Ficus</i> (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of <i>Ficus</i>. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout <i>Ficus</i> evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.</p>
Data from: Eco-evolutionary feedbacks predict the time course of rapid life history evolution
Organisms can change their environment and, in so doing, change the selection they experience and how they evolve. Population density is one potential mediator of such interactions because high population densities can impact the ecosystem and reduce resource availability. At present, such interactions are best known from theory and laboratory experiments. Here we quantify the importance of such interactions in nature by transplanting guppies from a stream where they co-occur with predators into tributaries that previously lacked both guppies and predators. If guppies evolve solely because of the immediate reduction in mortality rate, the strength of selection and rate of evolution should be greatest at the outset then decline as the population adapts to its new environment. If indirect effects caused by the increase in guppy population density in the absence of predation prevail, then there should be a lag in guppy evolution because time is required for them to modify their environment. The duration of this lag is predicted to be associated with the environmental modification caused by guppies. We observed a lag in life history evolution associated with increases in population density and altered ecology. How guppies evolved matched predictions derived from evolutionary theory that incorporates such density effects.
Two leaves that cannot die: the genome sequence of Welwitschia mirabilis reveals its unique biology and evolutionary history
<p>Welwitschia mirabilis (hereafter Welwitschia), the sole species in Welwitschiales, belongs to gnetophytes, an ancient, enigmatic gymnosperm lineage. It is a strikingly bizarre plant with distinctive morphology of just two large ever-elongating leaves and is remarkable in being able to survive extreme environmental stresses of the Namibian and Angolan deserts. Here, we provide a chromosome-level assembly of its genome (6.8 Gb/1C) and extensive methylome and transcriptome data to reveal the genetics underpinning its intriguing biology. The Welwitschia genome has been shaped by a lineage-specific ancient whole genome duplication ~ 86 million years ago, and more recently (within 10 million years) by bursts of retrotransposon activity. In addition, high levels of cytosine methylation, extremely so for CHH motifs, are associated with retrotransposons, whilst their long-term deamination has resulted in an exceptionally GC-poor genome. High levels of methylation are likely to be responses to maintain genomic integrity in the face of stress-induced retroelement mobility while reduced GC content will confer a genomic advantage under nutrient limitation. Changes in the copy number and/or expression of key gene families and specific transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant's extreme longevity under increasing temperature, nutrient and water stress. The Welwitschia chromosome level assembly here, along with a new high-quality assembly for Gnetum montanum, enhances our understanding of genome evolution in gnetophytes. It also provides critical new insights into the extraordinary development of Welwitschia's ever-growing leaves, enabling its survival in such hostile conditions.</p>
Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains
<p><span><span><span><span><span><span><span><span><span><span><span>Mountains are among the most biodiverse areas on the globe. In young mountain ranges, exceptional plant species-richness is often associated to recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species-richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analyzing plant diversification dynamicsin the<i>campo rupestre</i>, an ecosystem associated to pre-Cambrian mountaintops and highlands of eastern South America, areas where plant species-richness and endemism are among the highest in the world. Analyses of 15 angiosperm clades show that radiations of endemics present fastest rates of diversification during the climatically unstable period of the last 5 million years. However, results from ancestral range estimations using different models disagree on the age of the earliest <i>in situ</i>speciation events and point to a complex floristic assembly. There is a general trend for higher diversification rates associated to these areas, but endemism may also increase or reduce extinction rates, depending on the group. Montane habitats, no matter their geological age, may lead to boosts in speciation rates by accelerating population isolation in archipelago-like systems, circumstances that can also result in higher extinction rates and fast species turnover, misleading age estimates of endemic lineages. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: The molecular phylogenetics of Trachymyrmex ants and their fungal cultivars provide insights into the origin and co-evolutionary history of 'higher-attine' ant agriculture
The fungus‐growing ants and their fungal cultivars constitute a classic example of a mutualism that has led to complex coevolutionary dynamics spanning c. 55–65 Ma. Of the five agricultural systems practised by fungus‐growing ants, higher‐attine agriculture, of which leaf‐cutter agriculture is a derived subset, remains poorly understood despite its relevance to ecosystem function and human agriculture across the Neotropics and parts of North America. Among the ants practising higher‐attine agriculture, the genus Trachymyrmex Forel, as currently defined, shares most‐recent common ancestors with both the leaf‐cutter ants and the higher‐attine genera Sericomyrmex Mayr and Xerolitor Sosa‐Calvo et al. Although previous molecular‐phylogenetic studies have suggested that Trachymyrmex is a paraphyletic grade, until now insufficient taxon sampling has prevented a full investigation of the evolutionary history of this group and limited the possibility of resolving its taxonomy. Here we describe the results of phylogenetic analyses of 38 Trachymyrmex species, including 27 of the 49 described species and at least 11 new species, using four nuclear markers, as well as phylogenetic analyses of the fungi cultivated by 23 species of Trachymyrmex using two markers. We generated new genetic data for 112 ants (402 new gene sequences) and 95 fungi (153 new gene sequences). Our results corroborate previous findings that Trachymyrmex, as currently defined, is paraphyletic. We propose recognizing two new genera, Mycetomoellerius gen.n. and Paratrachymyrmex gen.n., and restricting the continued use of Trachymyrmex to the clade of nine largely North American species that contains the type species [Trachymyrmex septentrionalis (McCook)] and that is the sister group of the leaf‐cutting ants. Our fungal cultivar phylogeny generally corroborates previously observed broad patterns of ant–fungus association, but it also reveals further violations of those patterns. Higher‐attine fungi are divided into two groups: (i) the single species Leucoagaricus gongylophorus (Möller); and (ii) its sister clade, consisting of multiple species, recently referred to as Leucoagaricus Singer 'clade B'. Our phylogeny indicates that, although most non‐leaf‐cutting higher‐attine ants typically cultivate species in clade B, some species cultivate L. gongylophorus, whereas still others cultivate fungi typically associated with lower‐attine agriculture. This indicates that the attine agricultural systems, which are currently defined by associations between ants and fungi, are not entirely congruent with ant and fungal phylogenies. They may, however, be correlated with as yet poorly understood biological traits of the ants and/or of their microbiomes.
Evolutionary history of Neotropical savannas geographically concentrates species, phylogenetic and functional diversity of lizards
<p>Supporting information (scripts) to compute diversity and endemism indices copied and available by Dan Rosauer (https ://github.com/DanRosauer/phylospatial).</p> <p>Aim: Understanding where and why species diversity is geographically concentrated remains a challenge in biogeography and macroevolution. This is true for the Cerrado, the most biodiverse tropical savanna in the world, which has experienced profound biodiversity loss. Previous studies have focused on a single metric (species composition), neglecting the fact that 'species' within the biome are often composed of cryptic species. In order to identify biodiversity hotspots more robustly and across multiple dimensions we integrate functional, spatial and new phylogeographic data for the Cerrado lizard fauna by (a) mapping the spatial patterns of species and phylogenetic diversity; and (b) using endemism measures to identify areas of unique diversity. We then quantify the extent to which existing protected areas represent the diversity.</p> <p>Location: Brazilian savanna (Cerrado).</p> <p>Methods: We generated species distribution models using distribution records for all Cerrado lizard species. These, combined with mitochondrial DNA phylogenies and natural history data, allowed us to map species richness, phylogenetic and functional diversity and phylogenetic and weighted endemism. Phylogenetic endemism maps were then cross-referenced against protected areas to calculate the amount of evolutionary history preserved within these areas.</p> <p>Results: The central region of the Cerrado, a vast and climatically stable plateau, stands out as important under all biodiversity metrics. Including evolutionary relationships in biodiversity assessment, we detected four regional hotspots with high concentration of spatially restricted evolutionary diversity. Protected areas cover only 10% of the Cerrado area and hold 11.64% of the summed phylogenetic endemism of all lizards in the biome.</p> <p>Main Conclusions: We highlighted both stable (Chapada dos Veadeiros and Serra do Espinhaço plateaus) and environmentally heterogenous regions (Araguaia and Tocantins valleys) as hotspots of evolutionary diversity. The creation and/or manipulation of areas for conservation are essential for the conservation and survival of the rich and endemic lizard fauna of the Cerrado.</p>
Supplemental 3D Model Data - New insights into the evolutionary history of Fungi from a 407 million year old blastocladiomycota-like fossil showing multiple sporangia and an extensive hyphal network (SPIERSView and VAXML format)
<p>Three-dimensional reconstruction models of Fungi from a 407 million year old blastocladiomycota-like fossil showing multiple sporangia and an extensive hyphal network in SPIERSView and VAXML format. 2D and 3D (Red/Cyan) images also provided as a PDF.</p> <p>Notes:</p> <ol> <li>SPIERSView file (.SPV) models can conveniently be viewed using the SPIERSView software, freely available in both Windows and Mac versions from http://www.spiers‐software.org. However, note that low-performance computers may not possess a sufficiently powerful graphics card to render and rotate the model.</li> <li>VAXML file format models are saved as a ZIP-compressed VAXML datasets. VAXML uses one or more .STL files to define the geometry of objects that comprise the dataset, together with one .VAXML file that provides metadata on the dataset as a whole, and specifies how the .STL files should be put together. We recommend using the free SPIERS software to view this model format (http://spiers-software.org/). However, .STL files can be opened independently in several freely available software programs (e.g. MeshLab, Blender). Additional information on the VAXML format can be found here: http://spiers-software.org/VAXML.htm.</li> </ol>
Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahe and moho
<p>Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction, and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahe (<em>Porphyrio hochstetteri</em>) and the moho (North Island takahe; <em>P. mantelli</em>), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahe and moho subfossils (12 takahe and four moho) and retrieved comparable sequence data from takahemuseum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahepopulations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahe have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister-species relationship between takahe and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted <em>Porphyrio </em>ancestor approximately four million year ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.</p>
Evolutionary history and environmental variability structure contemporary tropical vertebrate communities
<p>Tropical regions harbor over half of the world's mammals and birds, but how their communities have assembled over evolutionary timescales remains unclear. To compare eco-evolutionary assembly processes between tropical mammals and birds, we tested how hypotheses concerning niche conservatism, environmental stability, environmental heterogeneity, and time-for-speciation relate to tropical vertebrate community phylogenetic and functional structure. We used in-situ observations of species identified from systematic camera trap sampling as realized communities from 15 protected tropical rainforests in four tropical regions worldwide. We quantified standardized phylogenetic and functional structure for each community and estimated the multi-trait phylogenetic signal (PS) in ecological strategies for the four regional species pools of mammals and birds. Using linear regression models, we test three non-mutually exclusive hypotheses by comparing the relative importance of colonization time, paleo-environmental changes in temperature and land cover since 3.3 Mya, contemporary seasonality in temperature and productivity, and environmental heterogeneity for predicting community phylogenetic and functional structure. The phylogenetic and functional structure showed non-significant yet varying tendencies toward clustering or dispersion in all communities. Mammals had stronger multi-trait PS in ecological strategies than birds (mean PS: mammal = 0.62, bird = 0.43). Distinct dominant processes were identified for mammal and bird communities. For mammals, colonization time and elevation range significantly predicted phylogenetic clustering and functional dispersion tendencies, respectively. For birds, elevation range and contemporary temperature seasonality significantly predicted phylogenetic and functional clustering tendencies, respectively, while habitat diversity significantly predicted functional dispersion tendencies. Our results reveal different eco-evolutionary assembly processes structuring contemporary tropical mammal and bird communities over evolutionary timescales that have shaped tropical diversity. Our study identified marked differences among taxonomic groups in the relative importance of historical colonization and sensitivity to environmental change. </p>
Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History
<p>This repository contains the supplementary files associated with the study 'Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History'.</p>
The evolutionary history of sedges (Cyperaceae) in Madagascar
<p><span><span><span><span><span><span><span><span><span><span><span><b>Aim:</b> Madagascar is renowned for its unparalleled biodiversity and endemism. With many ecosystems under threat, research is urgently needed on its unique plant diversity. This applies both to Madagascar's forests and treeless vegetation types. Sedges (Cyperaceae) are among the top ten species-richest angiosperm families in Madagascar (310 native species, 38% endemic), of which two thirds occur in open habitats. We aimed to infer the evolutionary history of sedges in Madagascar, by estimating the number, age and origins of endemic lineages, and how they diversified on the island. We tested contrasting hypotheses of (i) few colonisations but important <i>in situ</i> radiations against (ii) a high number of anagenetic colonisations.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Location:</b> Madagascar and the surrounding Indian Ocean islands, integrated within a global dataset.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Taxon:</b> Sedge family Cyperaceae.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods: </b>We estimated time-calibrated molecular phylogenies encompassing a large proportion of Madagascar's known sedge flora (incl. 55% of native species), integrating sequence data for 1382 accessions representing almost 25% of the c. 5600 sedge species worldwide, combined with ancestral area reconstruction, diversification analyses and Bayesian stochastic mapping.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results: </b>Cyperaceae lineages arrived in Madagascar from c. 40 mya with many arriving more recently. About 20 endemic lineages of Cyperaceae occur on the island, of which only six encompass more than five species. All except one of the endemic lineages that diversified in Madagascar use the C<sub>3</sub> photosynthetic pathway. The main biogeographical links of Madagascar's sedge flora are to Southern and Tropical Africa.</span></span></span></span></span></span></span></span></span></span></span></p> <p><b>Main conclusions:</b><span><span><span><span><span><span><span><span><span><span> The biogeographical history of Cyperaceae in Madagascar is a chronicle of relatively recent multiple in and out processes of long-distance dispersal colonisations constrained by distance. Also, the Madagascar region is not only a "sink" for immigrant taxa, <i>in situ</i> diversification and dispersal to other regions also occurred. Some of the most diverse endemic lineages show clear adaptation to local environments.</span></span></span></span></span></span></span></span></span></span></p>
A meta-analysis of the effects of habitat aridity, evolutionary history of grazing, and grazing intensity on bee and butterfly communities worldwide
<p>A variety of habitat-associated factors moderate effects of grazing on insect biodiversity. Here, we examine how aridity, evolutionary history of grazing, and grazing intensity individually and interactively mediate the effect of livestock grazing on pollinator diversity (native bees and butterflies).</p> <p>Using a meta-analysis of 59 studies published in the primary literature we characterized the response of pollinator communities to grazing across several continents.</p> <p>In very humid habitats high grazing intensities generally had negative impacts on pollinator abundance and richness, but these effects were not found in semi-arid habitats, where livestock grazing intensity did not interact with aridity to impact pollinator abundance or richness. However, within semi-arid habitats livestock grazing was associated with reduced pollinator richness in areas with short evolutionary histories grazing.</p> <p>Pollinator life history mediated effects of livestock grazing on pollinator communities: livestock grazing had negative impacts on richness of social bees and butterflies but not solitary bees, though abundances of all three pollinator categories were consistently reduced under livestock grazing.</p> <p>Our synthesis suggests that effects of cattle on pollinators may be driven by impacts on nesting habitats (e.g., soil compaction), rather than consumption or alteration of forb cover. Our collective findings have importance for coordinating grazing management and pollinator conservation efforts and help to distinguish how grazing practices could impact pollinator biodiversity across ecoclimatic regions.</p>
Unraveling the evolutionary history of the snakefly family Inocelliidae (Insecta: Raphidioptera) through integrative phylogenetics
<p>Inocelliidae is one of the two extant families of the holometabolan order Raphidioptera (snakeflies), with the modern fauna represented by seven genera and 44 species. The evolutionary history of the family is little known. Here we present the first phylogenetic and biogeographic analyses based on a worldwide sampling of taxa and datasets combined with morphological characters and mitochondrial genomes, aiming to investigate the intergeneric phylogeny and historical biogeography of Inocelliidae. The phylogenetic inference from the combined analysis of morphological and molecular data recovered the sister-group relationship between a clade of (<em>Negha</em> + <em>Indianoinocellia</em>) + <em>Sininocellia</em> and a clade of <em>Fibla</em> + the <em>Inocellia</em> clade (interiorly nested by <em>Amurinocellia</em> and <em>Parainocellia</em>). <em>Amurinocellia</em> <strong>stat. rev.</strong> and <em>Parainocellia</em><strong> stat. rev. et emend. nov.</strong> are relegated to subgeneric status within Inocellia, while a newly erected subgenus of <em>Inocellia</em>, <em>Epinocellia</em> <strong>subgen. nov.</strong>, accommodates the former <em>Parainocellia</em> <em>burmana</em> (U. Aspöck and H. Aspöck, 1968) plus a new species <em>Inocellia</em> (<em>Epinocellia</em>) weii sp. nov. Further, the <em>Inocellia</em> crassicornis group constitutes the nominate subgenus <em>Inocellia</em> <strong>stat. nov</strong>., but the <em>Inocellia</em> <em>fulvostigmata</em> group is paraphyletic. Diversification within Inocelliidae is distinguished by an Eocene divergence leading to extant genera and a Miocene radiation of species. A biogeographic scenario depicts how the diverse inocelliid fauna from East Asia could have originated from western North America via dispersal across the Beringia during the early Tertiary, and how the Miocene ancestors of <em>Inocellia</em> could have accomplished long-distance dispersals via the Tibet‐Himalayan corridor or eastern Palaearctic to western Palaearctic. Our results shed new light specifically on the evolution of Inocelliidae and, in general, the Raphidioptera.</p>
Backward Population Synthesis: Mapping the Evolutionary History of Gravitational-Wave Progenitors dataset
<p>Dataset release accompanying Backward Population Synthesis: Mapping the Evolutionary History of Gravitational-Wave Progenitors.</p> <p>Note that A22_02_rerun.hdf, A22_5_rerun.hdf, A22_rerun.hdf, KW_rerun.h5 are not directly used in generating the plots in the paper.</p>
Impact of host demography and evolutionary history on endosymbiont molecular evolution: a test in carpenter ants (Genus Camponotus) and their Blochmannia endosymbionts
Obligate endosymbioses are tight associations between symbionts and the hosts they live inside. Hosts and their associated obligate endosymbionts generally exhibit codiversification, which has been documented in taxonomically diverse insect lineages. Host demography (e.g., effective population sizes) may impact the demography of endosymbionts, which may lead to an association between host demography and the patterns and processes of endosymbiont molecular evolution. Here, we used whole-genome sequencing data for carpenter ants (Genus Camponotus; subgenera Camponotus and Tanaemyrmex) and their Blochmannia endosymbionts as our study system to address whether Camponotus demography shapes Blochmannia molecular evolution. Using whole-genome phylogenomics, we confirmed previous work identifying codiversification between carpenter ants and their Blochmannia endosymbionts. We found that Blochmannia genes have evolved at a pace ~30× faster than that of their hosts' molecular evolution and that these rates are positively associated with host rates of molecular evolution. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. Host demography was associated with Blochmannia shifts toward increased selection strengths, but not associated with Blochmannia selection relaxation, positive selection, genetic drift rates, or genome size evolution. Mixed support for relationships between host effective population sizes and Blochmannia molecular evolution suggests weak or uncoupled relationships between host demography and Blochmannia population genomic processes. Finally, we found that Blochmannia genome size evolution was associated with genome-wide estimates of genetic drift and number of genes with relaxed selection pressures. --
A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)
<p>Whole genome duplication events are notably widespread in plants and this poses particular challenges for phylogenetic inference in allopolyploid lineages, i.e. lineages that result from the merging of two or more diverged genomes after interspecific hybridization. The nuclear genomes resulting from allopolyploidization contain homologous gene copies from different evolutionary origins called homoeologs, whose orthologs must be sorted out in order to reconstruct the evolutionary history of polyploid clades. In this study, we propose a methodological approach to resolve the phylogeny of allopolyploid clades focusing on mesopolyploid genomes, which experienced some level of genome reshuffling and gene fractionation across their subgenomes. To illustrate our methodological framework, we applied it to a clade belonging to the model Brassicaceae plant family, the Brassiceae tribe, that experienced a mesohexaploidy event. The dataset analysed consists of both publically available genomic sequences and new transcriptomic data according to taxa. The present methodology requires a well-annotated reference genome, for which the identification of the parental subgenome fragments has been performed (e.g. Brassica rapa and Brassica oleracea). Focusing on fully retained genes (i.e., genes for which all homoeologous gene copies inherited from the parental lineages are still present in the reference genome), the method constructs multilabelled gene trees that allow subsequent assignment of each gene copy to its diploid parental lineage. Once the orthologous copies are identified, genes from the same parental origin are concatenated and tree-building methods are used to reconstruct the species tree. This method allows resolving the phylogenetic relationships (i) among extant species within a mesopolyploid clade, (ii) among the parental lineages of a mesopolyploid lineage, and (iii) between the parental lineages and closely related extant species. We report here the first well-resolved nuclear-based phylogeny of the Brassiceae tribe.</p>
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.