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.
591
datasets available to search
ShareScore release 0.9.0
Dataset results
591 results for “phylogenomic data”
Data from: Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae
<p>In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that, while ILS could by itself explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are with few exceptions highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.</p>
Supplementary data for: Phylogenomics, male internal genitalia, a new species, and other notes on new world Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)
<p>Based on past and expanded DNA sampling, the orthopteran families Stenopelmatidae and Anostostomatidae, as currently structured, are shown to be non-monophyletic. The splay-footed cricket genus <em>Comicus</em>, is confirmed to be genetically distinct from all Stenopelmatidae. We add two specimens to our previously published phylogenetic tree for New World <em>Stenopelmatus </em>Jerusalem cricket species and report the first multilocus DNA recovery for <em>S. ater </em>from Costa Rica. Male internal genitalia may be of systematic value in Jerusalem crickets, but we believe they should be analyzed when in their unfolded, "physiologically functional" state, where morphological characters can be seen in more detail when compared to their preserved, folded state. We describe <em>Stenopelmatus nuevoguatemalae </em>n. sp. from Guatemala.</p>
Data from: Phylogenomic perspectives on speciation in a North American biodiversity hotspot: An example using the California sages (Salvia subgenus Audibertia; Lamiaceae)
<p>The California Floristic Province (CA-FP) is the most species-rich region of North American north of Mexico. Several hypotheses have been proposed to explain why this region is exceptionally diverse, including that it harbors many recently diverged clades with weak or no barriers to reproduction.</p> <p><em>Salvia</em> subgenus <em>Audibertia</em> is a conspicuous element of the CA-FP, with multiple species often occurring in sympatry. Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyze contemporaneous patterns of geneflow and mechanical reproductive isolation.</p> <p>Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades and species are generally not mechanically isolated.</p> <p>Rapid, recent speciation with some horizontal geneflow during the rise of Mediterranean climate is the underlying cause of extant diversity in subgenus <em>Audibertia</em>. Geneflow has largely not facilitated speciation. Its signal in the nuclear genome seems to mostly be erased by backcrossing, but organellar genomes each capture different events of historical geneflow, perhaps characteristic of many lineages in the CA-FP. Mechanical reproductive isolation is likely only part of a mosaic of factors limiting geneflow.</p>
Data from: The influence of the number of tree searches on maximum likelihood inference in phylogenomics
<p>Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., ten) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥ 10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6 /15 phylogenomic datasets. Lastly, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.</p>
Data from: Phylogenomic loci define the generic boundaries of Gochnatieae and improve resolution at the species level in Moquiniastrum (Compositae)
<p>Understanding the evolution of the tribe Gochnatieae (Compositae) has been the subject of considerable effort in the past decade. This is due to the key position of this tribe in the phylogeny of the sunflower family and the corresponding implications for biogeographic and morphological evolution of Compositae. Previous studies have confirmed the monophyly of this tribe as well as most of the genera that belong to it. However, phylogenetic resolution of Gochnatieae at both the genus- and species-level has remained poor. A subset of new phylogenomic loci used in this study has proven effective and has improved phylogenetic resolution in this group. The results of this work demonstrate Gochnatieae is a well-supported clade comprised of nine genera (<em>Anastraphia</em>, <em>Cnicothamnus</em>, <em>Cyclolepis</em>, <em>Gochnatia</em>, <em>Moquiniastrum</em>, <em>Nahuatlea</em>, <em>Pentaphorus</em>, <em>Richterago</em>, <em>Tehuasca</em>). One recently described genus, <em>Vickia</em>, was not included in this study; but its placement in Gochnatieae as a tenth genus in the tribe is well-justified. The monospecific <em>Cyclolepis</em>, which had been circumscribed within the tribe since its inception but was subsequently removed and designated as <em>incertae sedis</em> since 2014, is also shown to belong to Gochnatieae. We confirmed the monophyletic <em>Moquiniastrum</em> with two well-supported subclades. Ancestral area reconstruction analyses show that Gochnatieae originated in Eastern South America about 53 my. Apparently, except for <em>Cyclolepis</em> and <em>Richterago</em>, the ancestors of the other genera of Gochnatieae originated about 44 my from an area that now corresponds to the central Andes. The presence of the genera in the Chaco phytogeographic province, central Chile, and Mexico-United States-Caribbean is a result of dispersal from the central Andes. The ancestral distribution of <em>Moquiniastrum</em> corresponds to a large area comprising Eastern South America and the current central Andes, about 32 my. Ancestral character state reconstruction that included four characters indicates several states associated with complex plant reproductive biology such as gynodioecy, gynomonoecy, and polygamodioecy are derived in Gochnatieae as are heterogamous capitula (in <em>Moquiniastrum</em> and <em>Richterago</em>), dimorphic and subdimorphic corollas (in <em>Cnicothamnus</em>, <em>Moquiniastrum</em>, and <em>Richterago</em>), and the presence of marginal female corollas (in <em>Moquiniastrum</em> and <em>Richterago</em>). Within <em>Moquiniastrum</em>, two subclades (Densicephalum and Polymorphum) exhibit divergent patterns of trait evolution associated with these reproductive characters which suggests this genus can serve as a model to understand the sexual system evolution in plants.</p>
Data from: Plastid phylogenomic analysis of Podostemaceae with an emphasis on Neotropical podostemoideae
<p>Podostemaceae are a clade of aquatic flowering plants that form important components of tropical river ecosystems. Species in the family exhibit highly derived growth forms and high vegetative phenotypic plasticity, both of which contribute to taxonomic confusion. The backbone phylogeny of the family remains poorly resolved, many species remain to be included in a molecular phylogenetic analysis, and the monophyly of many taxa remains to be tested. To address these issues, we assembled sequence data for 73 protein-coding plastid genes from 132 samples representing 68 species (~23% of described species) that span the breadth of most major taxonomic, morphological, and biogeographic groups of Podostemaceae. With these data, we conducted the first plastid phylogenomic analysis of the family with broad taxon sampling. These analyses resolved most nodes with high support, including relationships not recovered in previous analyses. No evidence of widespread, well-supported conflict among individual plastid genes and the concatenated phylogeny was observed. We present new evidence that four genera (<em>Apinagia</em>, <em>Marathrum</em>, <em>Oserya</em>, and <em>Podostemum</em>), as well as four species, are not monophyletic. In particular, we show that <em>Podostemum flagelliforme</em> should not be included in <em>Podostemum and is better recognized as Devillea flagelliformis, </em>and that <em>Marathrum capillaceum</em> is embedded within <em>Lophogyne </em>s.l.<em> </em>and should be recognized as <em>Lophogyne capillacea</em>. We also place a previously unsampled and undescribed species that likely represents a new genus. In contrast to previous studies, the neotropical genera <em>Diamantina</em>, <em>Ceratolacis</em>, <em>Cipoia,</em> and <em>Podostemum</em> are resolved as successive sister groups to a clade of all paleotropical Podostemoideae taxa sampled, suggesting a single dispersal event from the neotropics to the paleotropics in the history of the subfamily. These results provide a strong basis for improving the classification of Podostemaceae and a framework for future phylogenomic studies of the clade employing data from the nuclear genome.</p>
Data from: Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)
Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence. We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches. All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera. Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.
Data for Concordance-based approaches in phylogenomics
<p>Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.</p>
Data from: Museum specimens provide phylogenomic data to resolve relationships of sack-bearer moths (Lepidoptera, Mimallonoidea, Mimallonidae)
Mimallonidae, the sack‐bearer moths, are a family of predominantly Neotropical moths containing nearly 300 described species. Mimallonidae feed on over 40 host plant families and are found in a variety of environments, but phylogenetic relationships of species within the family have never been investigated. We sequenced 515 loci using anchored hybrid enrichment target capture on ethanol‐preserved and dried museum specimens, with dates of collection ranging from 1985 to 2017. We sampled 47 species, representing 32 of the 36 described mimallonid genera. By incorporating 19 dry museum specimens, and recovering an average of over 400 loci for each, we illustrate the utility of natural history collections in anchored hybrid enrichment‐based phylogenomics. Maximum likelihood and multi‐species coalescent analyses provide robust support for the recognition of six higher‐level groups within Mimallonidae, which we designate as subfamilies: Zaphantinae St Laurent & Kawahara subfam.n., Aurorianinae St Laurent & Kawahara subfam.n., Mimalloninae Burmeister, Lacosominae Dyar, Druenticinae St Laurent & Kawahara subfam.n. and Cicinninae Schaus stat.n. Our phylogenetic results also robustly support eight new tribes: Lacosominae: Trogopterini St Laurent & Kawahara tribe n., Lacosomini Dyar stat.n., Alheitini St Laurent & Kawahara tribe n.; Druenticinae: Luramini St Laurent & Kawahara tribe n., Druenticini St Laurent & Kawahara tribe n.; Cicinninae: Bedosiini St Laurent & Kawahara tribe n., Psychocampini St Laurent & Kawahara tribe n., Cicinnini Schaus stat.n. Three new genera are also described based on our phylogenetic results: Herbinalla St Laurent & Kawahara, gen.n., Ulaluma St Laurent & Kawahara, gen.n., Bedosiallo St Laurent & Kawahara, gen.n. Naniteta Franclemont, syn.n. is a synonym of Lacosoma Grote. Six genera are paraphyletic, and in total 19 new combinations are proposed: Macessoga laxa comb.n., Lacosoma elassa comb.n., Thaelia anysia comb.n., Thaelia subrubiginosa comb.n., Herbinalla caudina comb.n., Druentica brosica comb.n., Ulaluma valva comb.n., Cicinnus eminens comb.n., Roelmana pluridiscata comb.n., Roelmana laguerrei comb.n., Psychocampa joanna comb.n., Psychocampa unalca comb.n., Psychocampa hamata comb.n., Psychocampa marona comb.n., Bedosiallo eugenia comb.n., Bedosiallo forbesi comb.n., Bedosiallo moengus comb.n., Bedosiallo styx comb.n. and Bedosiallo sylvia comb.n. This study is the first to implement the LEP1 probe set on a comprehensive taxonomic dataset that includes many museum specimens, and our results demonstrate that museum specimens can be used in anchored hybrid enrichment studies. Importantly, these data produce a robust phylogeny that will serve as a foundation for future studies on mimallonid evolution, such as host plant relationships and biogeography.
Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data
<p>Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data</p>
Data from: Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation
<p>The genus <i>Phytophthora</i> comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. <i>Phytophthora</i> hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 <i>Phytophthora</i> isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid <i>Phytophthora</i> isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.</p>
Data from: Phylogenomics of superrosids and core rosids based on nuclear sequences and synteny
<p class="MsoListParagraph">Superrosids form one of the largest clades of angiosperms, including 18 orders (Vitales, Saxifragales and core rosids) which exhibits remarkable morphological and ecological diversity. However, phylogenetic relationships within superrosids remain unclear.</p> <p class="MsoListParagraph">To resolve the phylogeny of superrosids, we screened 122 single copy nuclear genes from 37 species, representing all 18 orders.</p> <p class="MsoListParagraph">Vitales was revealed as sister to all other superrosids. Within core rosids, the fabids should be restricted only to the nitrogen-fixing clade, while Picramniales, the CM clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales composed an "expanded" malvids. The COM clade (sensu APG IV) did not form a monophyletic group. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either malvids or fabids. The difficult phylogeny of superrosids is likely due to the combined effects of ancient reticulation and incomplete lineage sorting.</p> <p class="MsoListParagraph">To provide broader genomic representation of Saxifragales, we constructed a high-quality chromosome-level genome assembly for <em>Tiarella polyphylla</em> (Saxifragaceae). Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, which also indicated that Saxifragales has a closer relationship with core rosids.</p> <p class="MsoListParagraph">Our findings contribute to a better understanding of the phylogeny and evolution of angiosperms.</p>
Data for: Phylogenomics of Aralia sect. Aralia (Araliaceae)
<p><span>Genome-scale data have significantly increased the number of informative characters for phylogenetic analyses and recent studies have also revealed widespread phylogenomic discordance in many plant lineages. <em>Aralia</em> sect. <em>Aralia</em> is a small plant lineage (14 spp.) of the ginseng family Araliaceae with a disjunct distribution between eastern Asia (11 spp.) and North America (3 spp.). We herein employ sequences of hundreds of nuclear loci and the complete plastomes using targeted sequence capture and genome skimming to reconstruct the phylogenetic and biogeographic history of this section. We detected substantial </span><span>conflicts among nuclear genes, yet </span><span>different analytical strategies generated largely congruent topologies from the nuclear data. Significant cytonuclear discordance was detected, especially concerning the positions of the three North American species. The phylogenomic results support two intercontinental disjunctions: (1) <em>Aralia</em> <em>californica</em> of western North America is sister to the eastern Asian clade consisting of <em>A</em>. <em>cordata</em> and <em>A</em>. <em>continentalis</em> in the nuclear tree, and (2) the eastern North American <em>A</em>. <em>racemosa</em> forms a clade with <em>A</em>. <em>bicrenata</em> from southwestern North America, and the North American <em>A</em>. <em>racemosa</em> - <em>A</em>. <em>bicrenata</em> clade is then sister </span><span>to </span><span>the eastern Asian clade consisting of <em>A</em>. <em>glabra</em> (Japan), <em>A</em>. <em>fargesii</em> (C China), and <em>A</em>. <em>apioides</em> and <em>A</em>. <em>atropurpurea</em> (the Hengduan Mountains). <em>Aralia</em> <em>cordata</em> is supported to be disjunctly distributed in Japan, Taiwan, the Ulleung island of Korea, and in Central, Southwest and South China, and <em>Aralia</em> <em>continentalis</em> is redefined with a narrower distribution in N</span><span>or</span><span>theast China, eastern Russia and peninsular Korea. </span></p>
Data from: Morphometrics and phylogenomics reveal a new species of Heuchera (Saxifragaceae) in northeastern México
<p><span>Here I describe a new species narrowly endemic to high-altitude limestone outcrops of the Sierra Madre Oriental, Coahuila, Mexico, together with a phylogenomic and morphometric evaluation of the <em>Heuchera</em> species of northeastern Mexico. Originally thought to be a disjunct population of <em>Heuchera</em> <em>sanguinea</em>, the new species is phylogenetically and morphologically most similar to <em>Heuchera</em> <em>lakelae</em>; from which it is distinguished based on morphometric characters and other morphological attributes, phylogenetic placement, geographic range, phenology, and ecological preferences.</span></p>
Data from: A phylogenomic analysis of Lonicera and its bearing on the evolution of organ fusion
<p class="MsoNormal"><strong><span>PREMISE: </span></strong><span>The ~140 species of <em>Lonicera</em> are characterized by variously fused leaves, bracteoles, and ovaries, making it a model system for studying the evolution and development of organ fusion. However, </span><span>previous phylogenetic analyses, based mainly on chloroplast DNA markers, have yielded uncertain and conflicting results. A well-supported phylogeny of <em>Lonicera</em> will allow us to trace the evolutionary history of organ fusion.</span></p> <p class="MsoNormal"><strong><span>METHODS:</span></strong><span> We inferred the phylogeny of <em>Lonicera</em> using Restriction-site Associated DNA Sequencing (RADSeq), sampling all major clades and 18 of the 23 subsections. This provided the basis for inferring the evolution of five fusion-related traits. </span></p> <p class="MsoNormal"><strong><span>RESULTS: </span></strong><span>RADSeq data yielded a well-resolved and well-supported phylogeny. The two traditionally recognized subgenera (<em>Periclymenum</em> and <em>Chamaecerasus</em>), three of the four sections (<em>Isoxylosteum</em>, <em>Coeloxylosteum</em>, and <em>Nintooa</em>), and half of the subsections sampled were recovered as monophyletic. However, the large and heterogeneous section <em>Isika</em> was strongly supported as paraphyletic. <em>Nintooa</em>, a clade of ~22 mostly vine-forming species, including <em>L. japonica</em>, was recovered in a novel position, raising the possibility of cytonuclear discordance. We document the parallel evolution of fused leaves, bracteoles, and ovaries, with rare reversals. Most strikingly, complete cupules, in which four fused bracteoles completely enclose two unfused ovaries, arose at least three times. Surprisingly, these appear to have evolved directly from ancestors with free bracteoles instead of partial cupules. </span></p> <p class="MsoNormal"><strong><span>CONCLUSIONS: </span></strong><span>We provide the most comprehensive and well-supported phylogeny of <em>Lonicera</em> to date. Our inference of multiple evolutionary shifts in organ fusion provides a solid foundation for in-depth developmental and functional analyses.</span></p>
Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera)
<p>Genomes, alignments and tree files of the study "Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera). Molecular Phylogenetics and Evolution, https://doi.org/10.1016/j.ympev.2024.108113".</p>
Data for: Preliminary phylogenomic analyses reveal multiple reversions to nocturnal behavior and morphology within the primarily diurnal tribe Adesmiini (Coleoptera: Tenebrionidae)
<p>The darkling beetle tribe Adesmiini (Tenebrionidae: Pimeliinae) is a prominent part of the African and western Palearctic desert faunas, with most species being day-active fast-running detritivores. Taxonomic diversity within the tribe is highest in the southern part of the Afrotropical realm (all genera present), while only the species-rich genus Adesmia occurs north of the Sahara. Despite containing conspicuous diurnal species, such as the fog-basking beetle Onymacrisunguicularis (a focal taxon in ecological research for decades), Adesmiini has undergone few modern taxonomic or phylogenetic studies. Hence, generic concepts and the evolution of diurnal behaviors and morphologies, rare in the primarily nocturnal family Tenebrionidae, remain poorly explored. To investigate evolutionary relationships and the origin of diurnal activity within the tribe, a genomic dataset of 529 protein-coding genes across 43 species spanning 10 of 11 Adesmiini genera was assembled and analyzed. The resulting phylogeny for the tribe does not support the monophyly of many current Adesmiini genera (i.e. Adesmia, Metriopus, Onymacris, Physadesmia, and Stenocara). Ancestral state reconstruction of diurnal activity, using eye shape as a proxy and supplemented by literature and collection records, supports the hypothesis that Adesmiini were primitively diurnal, followed by at least four shifts to nocturnal or crepuscular activity.</p>
Data for: Phylogenomic analyses of the Neotropical Artocarpeae (Moraceae) reveal a history of introgression and support the reinstatement of Acanthinophyllum
<p>This molecular study of the Neotropical Artocarpeae, the closest living allies of the Asia-Pacific breadfruit genus, uses phylogenetic and network analyses to untangle the evolutionary history of this difficult group. Results paint a picture of a rapid radiation, with introgression between sympatric species confounding attempts to reconstruct a well-supported bifurcating tree. While bifurcating trees were markedly at odds with morphology, multifurcating phylogenetic network analyses recovered multiple histories, with clearer traces of morphological alliances. The sole unambiguous finding is the sister relationship between <em>Clarisia</em> sect. <em>Acanthinophyllum</em> and the rest of the Neotropical Artocarpeae; as a result, the genus <em>Acanthinophyllum</em> is reinstated.</p>
Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data
<p>Cryptic species diversity is a major challenge for the species-rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size, and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, including the morphology of the galls they induce, has evolved in response to selection imposed by the parasitoid community, with reciprocal selection driving diversification of the parasitoids. Using a rare, continental-scale data set of <em>Sycophila</em> parasitoid wasps reared from 44 species of cynipid galls from 18 species of oak across the US, we combined mitochondrial DNA barcodes, Ultraconserved Elements (UCEs), morphological, and natural history data to delimit putative species. Using these results, we generate the first large-scale assessment of ecological specialization and host association in this species-rich group, with implications for evolutionary ecology and biocontrol. We find most <em>Sycophila</em> target specific subsets of available cynipid host galls with similar morphologies, and generally attack larger galls. Our results suggest that parasitoid wasps such as <em>Sycophila</em> have adaptations allowing them to exploit particular host trait combinations, while hosts with contrasting traits are resistant to attack. These findings support the tritrophic niche concept for the structuring of plant-herbivore-parasitoid communities.</p>
Data from: Populating a continent: Phylogenomics reveal the timing of Australian frog diversification
<p><span>The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups which vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of</span><span></span><span>, </span><span>and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas.</span></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.