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.
2,620
datasets available to search
ShareScore release 0.9.0
Dataset results
2,620 results for “Molecular Phylogeny”
Figure 1 in Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers
Figure 1. Maximum likelihood (ML) tree of Dipsadidae estimated using RAxML. Summary tree with collapsed terminals showing higher-level relationships. Numbers above and below branches indicate bootstrap and posterior probability support values, respectively. Bootstrap values below 70% and posterior probabilities below 85% are not shown. Abbreviations: CA = central Andean; SAE = southern and cis-Andean.
Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)
Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (∼2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75–218 loci across 74 taxa, with ∼50% matrix completeness across datasets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.
Data from: A worldwide molecular phylogeny provides new insight on cryptic diversity within the moonworts (Botrychium s. s., Ophioglossaceae)
The moonwort genus, Botrychium s. s., includes diploid and polyploid taxa that occur primarily in the northern hemisphere. Their evolutionary history, morphologically cryptic taxa and deep divergence of the family in the phylogeny of ferns has long fascinated pteridologists. Previous molecular studies did not include a complete taxonomic sampling of the taxa in the genus, nor multiple specimens from throughout the known geographical range of each taxon. Therefore, to investigate evolutionary relationships of the major clades of Botrychium s. s., we increased both taxonomic representativeness (multiple accessions per taxa), as well as phylogenetic resolution by including additional new chloroplast markers. To confirm identification and provide evidence from both maternal and paternal parentage of allopolyploids, we also included specimens that have been characterized by allozyme profiles determined by electrophoretic analysis of 20 nuclear enzyme loci for each taxon. We analyzed four chloroplast regions (matK intron, trnHGUG —psbA, andtrnLUAA —trnFGAA intergenic spacers, and rpL16 intron region) of 365 specimens fromAsia, Europe, North America, Oceania, and South America, sampling the geographical range of 34 of 35 accepted Botrychium s. s. taxa and thirteen putatively new taxa. We conducted a phylogenetic analysis of maternal lineages based on 2,385 aligned nucleotides using maximum likelihood and Bayesian inference to explore genetic diversity and phylogenetic relationships among taxa. We found strong support for themonophyly of three major clades: Lanceolatum, Lunaria, and Simplex-Campestre, and resolved 15 subclades. Our results suggest multiple origins for at least four polyploid taxa (B. boreale, B. michiganense, B. yaaxudakeit, and B. watertonense). The Simplex-Campestre clade had the largest number of species, despite having a similar total number of haplotypes as the Lunaria clade (62 and 59, respectively), which has the broadest worldwide distribution. In total, our new molecular phylogeny comprises 47 taxa, of which thirteen are discussed for possible taxonomic recognition.
FIGURE 5. Cyt b in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 5. Cyt b tree for Monitilorinae and Lucininae, expanded from Figure 4.
FIGURE 3. Combined gene tree for Lucininae, expanded from Figure 1 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 3. Combined gene tree for Lucininae, expanded from Figure 1.
FIGURE 2. Combined gene tree for Codakiinae, expanded from Figure 1 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 2. Combined gene tree for Codakiinae, expanded from Figure 1.
Figure 26 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figure 26. Neighbor-joining tree based on the concatenated DNA sequences.
Figure 29 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figure 29. Bayesian tree based on the concatenated DNA sequences.
Figure 28 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figure 28. Maximum likelihood tree based on the concatenated DNA sequences (-lnL = 7386.85).
Molecular phylogeny and morphological perianth evolution in Corymbia (Myrtaceae), and the implications for generic delimitation: data and tree files
<p><strong>Premise:</strong> Eucalypts (Myrtaceae tribe Eucalypteae) are currently placed in seven genera. Traditionally,<em> Eucalyptus</em> was defined by its operculum but when phylogenies placed <em>Angophora</em>, with free sepals and petals, as sister to the operculate bloodwood eucalypts, the latter were segregated into a new genus, <em>Corymbia</em>. Yet generic delimitation in the tribe Eucalypteae remains uncertain. Here we address these problems using phylogenetic analysis with the largest molecular dataset to date.</p> <p><strong>Methods: </strong>We captured 101 low-copy nuclear exons from 392 samples representing 266 species. Our phylogenetic analysis used maximum likelihood (IQtree) and multi-species coalescent (Astral). At two nodes critical to generic delimitation, we tested alternative relationships among <em>Arillastrum</em>, <em>Angophora</em>, <em>Eucalyptus</em> and <em>Corymbia</em> using Shimodaira's AU test. Phylogenetic mapping was used to explore the evolution of perianth traits.</p> <p><strong>Results: </strong>Monophyly of <em>Corymbia</em> relative to <em>Angophora</em> was decisively rejected. All alternative relationships among the seven currently recognised Eucalypteae genera imply homoplasy in evolutionary origins of the operculum. Inferred evolutionary transitions in perianth traits are congruent with divergences between major clades except that expression of separate sepals and petals in <em>Angophora</em>, which is nested within the operculate genus <em>Corymbia</em>, appears to be a reversal to the plesiomorphic perianth structure.</p> <p><strong>Conclusions:</strong> Here we formally raise <em>Corymbia</em> subg. <em>Blakella</em> to genus rank and make the relevant new combinations. We also define and name three sections within <em>Blakella</em> (<em>B.</em> sect. <em>Blakella</em>, <em>B.</em> sect. <em>Naviculares</em> and <em>B.</em> sect. <em>Maculatae</em>), and two series within <em>Blakella</em> sect. <em>Maculatae</em> (<em>B.</em> ser. <em>Maculatae</em> and <em>B.</em> ser. <em>Torellianae</em>). <em>Corymbia</em> is reduced to the red bloodwoods.</p>
Fossil calibrated molecular phylogenies of Southern cave weta
<p>Aim: The biota of continents and islands are commonly considered to have a source-sink relationship, but small islands can harbour distinctive taxa. The distribution of four monotypic genera within the southern subfamily Macropathinae on young oceanic islands indicates a role for long-distance dispersal and extinction. We used molecular dating to estimate the timing of the southern radiation and infer potential processes involved.</p> <p>Location: Subantarctic islands, South Africa, South America, Australia, Aotearoa/New Zealand.</p> <p>Taxon: Southern hemisphere camel crickets subfamily Macropathinae within the Orthopteran family Rhaphidophoridae (Cave crickets/camel crickets/cave weta/tokoriro).</p> <p>Methods: Phylogenetic relationships were inferred from whole mtDNA genomes and nuclear sequences (45S cassette; four histones). We used a fossil and one palaeogeographic event to calibrate a molecular clock analysis.</p> <p>Results: We confirm that neither the Australian nor Aotearoa/New Zealand Rhaphidophoridae fauna are monophyletic. The Macropathinae radiation may have begun in the late Jurassic but trans-oceanic dispersal is required to explain the distribution of some lineages within the subfamily Macropathinae. Dating the most recent common ancestor of seven island endemic species with their nearest mainland relative suggests that each existed long before land surface on their island home was available.</p> <p>Main conclusions: If our molecular clock analysis is a good time estimate, then our data from the island endemic species suggest a failure to sample mainland species (New Zealand, Australia, or elsewhere) due to either extinction or lack of investment into taxonomy and species discovery.</p>
Molecular phylogeny reveals the past transoceanic voyages of drywood termites (Isoptera, Kalotermitidae)
<p><span>Termites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes of ~120 species, about 27% of kalotermitid diversity, including representatives of 21 of the 23 kalotermitid genera. Our mitochondrial genome phylogenetic trees were corroborated by phylogenies inferred from nuclear ultraconserved elements derived from a subset of 28 species. We found that extant kalotermitids shared a common ancestor 84 Mya (75–93 Mya 95% HPD), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ~40 disjunctions among biogeographic realms were dated at less than 50 Mya, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for critical taxonomic revision and future comparative analyses of Kalotermitidae.</span></p>
On the computational reproducibility of molecular phylogenies
<p>Reports on the lack of computational reproducibility of molecular phylogenies, produced in multiple runs of the same program or by different programs, cast a long shadow on downstream research using these phylogenies and on efforts to build the tree of life. We show that this irreproducibility does not decrease the accuracy of the reconstructed evolutionary relationships. Also, we find inferred molecular phylogenies to have log-likelihoods comparable to or better than the true phylogeny. Therefore, the lack of computational reproducibility of molecular phylogenies is not a problem for evolutionary studies.</p>
Data for a preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): exploring the combination of targeted enrichment data and legacy Sanger sequence data
<p><span>The purpose of this study is to provide a proof-of-concept that the use of molecular data, particularly targeted enrichment data, and statistically supported methods of analysis can result in the construction of a stable phylogenetic framework for the microcaddisflies (Trichoptera: Hydroptilidae). Here, we use a combination of targeted enrichment data for ca. 300 nuclear protein-coding genes and legacy (Sanger-based) sequence data for the mitochondrial COI gene and partial sequence from the 28S rRNA gene.</span></p>
Molecular phylogeny of Dermestidae (Coleoptera) reveals the polyphyletic nature of Trogoderma Latreille, and the taxonomic placement of the Khapra Beetle Trogoderma granarium Everts
<p>The hide, larder and carpet beetles (Coleoptera: Dermestidae) are a family of mainly scavenger beetles, with numerous species such as the khapra beetle (<em>Trogoderma</em> <em>granarium</em> Everts, 1898), the black carpet beetle (<em>Attagenus</em> <em>unicolor</em> (Brahm, 1791)) and the hide beetle (<em>Dermestes</em> <em>maculatus</em> De Geer, 1774) being widely recognised as serious economic pests of stored products and museum collections (Fig. 1). A stable classification and reliable identification of genera and species of these pests and their 1,700 relatives are of great relevance for trade restrictions, biosecurity, pest management, forensics and biodiversity surveys.</p> <p>In this study, we examined and sequenced mitochondrial genomes of 477 dermestid specimens, representing all subfamilies and 90% of the globally recognised tribes and subtribes. Our study provides the most comprehensive, taxonomically verified and vouchered resource of mitochondrial reference sequences linked to specimen images and occurrence records of pests and their relatives, enabling eDNA surveys, metabarcoding and molecular species identification. It also reconstructs the phylogeny of Dermestidae based on molecular and morphological data for the first time, thereby providing robust phylogenetic hypotheses for a stable classification system from family to genus-level.</p> <p>Accordingly, a revised classification of Dermestidae with formal nomenclatural changes is proposed, recognising six subfamilies: Orphilinae, Trinodinae, Trogoparvinae subfam. nov. (type genus <em>Trogoparvus</em> Háva, 2001), Dermestinae, Attageninae and Megatominae. Trinodinae is recovered towards the base of Dermestidae with three tribes: Trinodini (=Trinoparvini syn. nov.), Thylodriini and Trichelodini. Dermestinae is the only subfamily with adults lacking a median ocellus, and it includes the tribes Thorictini stat. nov. (that is downgraded from Thorictinae), Marioutini and Dermestini. The endemic Australian genus <em>Derbyana</em> Lawrence and Ślipiński, was recovered within Holarctic <em>Dermestes</em> Linnaeus. Attageninae is strongly supported and includes the monogeneric Adelaidiini and polygenic Attagenini. Former subgenera of <em>Attagenus</em> Latreille, i.e., <em>Lanorus</em> Mulsant and Rey (= Paranovelsis Casey syn. nov.), <em>Telopes</em> Redtenbacher, and <em>Aethriostoma</em> Motschulsky, are elevated to generic level. The largest clade, Megatominae, is confirmed as monophyletic and is divided into three tribes: Anthrenini, Ctesiini and Megatomini. Megatomini is divided into three subtribes: Megatomina, Orphinina subtribe nov. (type genus <em>Orphinus</em> Motschulsky) and Trogodermina. Within the economically important lineage Trogodermina, <em>Trogoderma</em> Latreille, is delimited to contain only Holarctic species including the Khapra beetle <em>T</em>. <em>granarium</em> Everts, while a Southern Hemisphere clade is here recognised as <em>Eurhopalus</em> Solier in Gay, 1849 (= <em>Anthrenocerus</em> Arrow, 1915; <em>Myrmeanthrenus</em> Armstrong, 1945; <em>Neoanthrenus</em> Armstrong, 1941; <em>Sodaliatoma</em> Háva, 2013; <em>Reesa</em> Beal, 1967 syn. nov.). A revised classification of the extant genera of Dermestidae is also provided.</p>
Fig. 2 in Molecular phylogeny of Indonesian Lymantria Tussock Moths (Lepidoptera: Erebidae) based on CO I gene sequences
Fig. 2. Pairwise sequences divergence based on K2P model versus Transition/Transversion (Ts/Tv).
Fig. 1 in Haemoprotozoa: Making biological sense of molecular phylogenies
Fig. 1. Key characteristics of the five haemoprotozoan assemblages.
Fig. 2 in Molecular phylogeny of Indonesian Zeuzera (Lepidoptera: Cossidae) wood borer moths based on CO I gene sequence
Fig. 2. Scatter plots of K2P model distance for Transition (Ts) versus Transversion (Tv).
Processed data supporting the manuscript "Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution"
<div><strong>Processed data supporting the manuscript: </strong>Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution</div> <div> </div> <div><strong>By:</strong> Diego de S. Souza 1, 2, Rowan L. K. French 3, José O. Silva Júnior 4, Eugenio H. Nearns 5, Luciane Marinoni 4, Ian P. Swift 6, Kelly B. Miller 7, Felix A. H. Sperling 2 & Marcela L. Monné 1</div> <div> </div> <div>1 Department of Entomology, National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.</div> <div>2 Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.</div> <div>3 Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.</div> <div>4 Department of Zoology, Federal University of Paraná, Curitiba, Paraná, Brazil.</div> <div>5 National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.</div> <div>6 California State Collection of Arthropods, Sacramento, California, USA.</div> <div>7 Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA.</div> <div> </div> <div>Corresponding author: Diego de S. Souza, dsouza@fieldmuseum.org. Current affiliation: Field Museum of Natural History, Chicago, Illinois, USA.</div> <div> </div> <div> </div> <div><strong>List of Contents: </strong></div> <div> </div> <div><strong>Onciderini_concat_matrix.phy</strong></div> <div>Concatenated matrix (cox1, Wg and CPS) used for the phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini). </div> <div> </div> <div><strong>PartitionFinder_AICc_best_scheme.txt</strong></div> <div>Results from PartitionFinder v2.1.1, containing the best partitioning scheme for the concatenated matrix of Onciderini, identified using the corrected Akaike Information Criterion (AICc), with model definitions for use in the phylogenetic analyses.</div> <div> </div> <div><strong>RAxML_Onciderini_concat_matrix (zip file)</strong></div> <div>- Onciderini_concat_matrix.phy: concatenated matrix (cox1, Wg and CPS) used in the RAxML phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini).</div> <div>- Partitions_AICc_RAxML.txt: partitioning scheme used in the RAxML analysis as predefined by PartitionFinder v2.1.1 using the corrected Akaike Information Criterion (AICc).</div> <div>- RAxML_bestTree.Onciderini_concat_matrix_ML: best-scoring maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini.</div> <div>- RAxML_bipartitions.Onciderini_concat_matrix_final: bipartitions (clades) of the maximum likelihood tree inferred by RAxML with support values estimated from 1,000 pseudoreplicates.</div> <div>- RAxML_bipartitionsBranchLabels.Onciderini_concat_matrix_final: final maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini, with labeled branches showing bootstrap support values.</div> <div>- RAxML_bootstrap.Onciderini_concat_matrix_bootstrap: bootstrap trees generated from a non-parametric bootstrap analysis in RAxML based on 1,000 pseudoreplicates.</div> <div>- RAxML_info.Onciderini_concat_matrix_bootstrap: log file containing details of the bootstrap analysis, including the settings and parameters used in the non-parametric bootstrap runs in RAxML.</div> <div>- RAxML_info.Onciderini_concat_matrix_final: log file summarizing the RAxML analysis, including settings and convergence statistics for the final maximum likelihood tree.</div> <div>- RAxML_info.Onciderini_concat_matrix_ML: log file containing details of the maximum likelihood tree search, including the parameters and models applied during the maximum likelihood analysis conducted by RAxML.</div> <div>- RAxML_log.Onciderini_concat_matrix_ML: log file of the maximum likelihood tree search for the concatenated matrix of Onciderini.</div> <div>- RAxML_parsimonyTree.Onciderini_concat_matrix_ML: parsimony starting tree used by RAxML during the maximum likelihood analysis for the concatenated matrix of Onciderini.</div> <div>- RAxML_result.Onciderini_concat_matrix_ML: maximum likelihood tree inferred by RAxML from the concatenated matrix of Onciderini, summarizing the tree topology and likelihood score for the best tree obtained.</div> <div> </div> <div><strong>BI_AICc_Onciderini_concat_matrix (zip file)</strong></div> <div>- BI_AICc_Onciderini_concat_matrix.nex: nexus file containing the concatenated matrix of Onciderini used for Bayesian Inference (BI), including the best-fit model scheme identified by PartitionFinder and MCMC parameters for running the analysis in MrBayes.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex_r1_r2_combined_consensus.tree: consensus tree from two combined independent Bayesian Inference (BI) runs based on the concatenated matrix of Onciderini, after discarding the first 25% of initial generations as burn-in.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run1.p: log file containing parameter values and likelihood scores from the first run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run2.p: log file containing parameter values and likelihood scores from the second run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_lognormal (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_lognormal.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- BEAST2_Onciderini_BD_lognormal_run[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_exponential (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_exponential.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- BEAST2_Onciderini_BD_exponential_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_uniform (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_uniform.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- BEAST2_Onciderini_BD_uniform_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>Comparative_analyses (zip file)</strong></div> <div><strong>RawData (folder):</strong> raw morphometric and girdling data, plus tree that was later pruned for downstream comparative analyses; these data were used as input for the OncidHeadDimorphism-DatasetPREP-FINAL.R data cleaning script. </div> <div>- Onciderini_BD_lognormal_run1-run8_consensus.nwk: newick version of TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre (outputted as a newick file by importing the .tre file into FigTree and exporting in newick format).</div> <div>- Measurements_Onciderini_Raw_Final.csv: individual-level raw morphometric data for Onciderini.</div> <div>- Behav_Matrix_2_states_trimmed_2022-12-15.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as girdlers (2 behavioral states across Onciderini species). </div> <div>- Matrix_3_states_trimmed_final.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as facultative girdlers (3 behavioral states across Onciderini species). </div> <div>- Matrix_2_states_trimmed_1LochGirdler_Final.csv: species-level data on girdling status for Onciderini species, with only one Lochmaeocles species (L. tessellatus) classified as a girdler (2 behavioral states across Onciderini species). </div> <div> </div> <div><strong>ProcessedData (folder): </strong>filtered data and pruned trees outputted by the OncidHeadDimorphism-DatasetPREP-FINAL.R script</div> <div>- oncid_f_36spp_clean.csv: dataset of species means and log-ratios for morphometric traits in females, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_m_42spp_clean.csv: dataset of species means and log-ratios for morphometric traits in males, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_sd_35spp_clean.csv: dataset of species means for sexual dimorphism in morphometric traits, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_girdlingbehav_allingroupspp_clean.csv: full dataset of girdling behavior for 56 Onciderini species that are in the phylogenetic tree; includes separate columns for the three alternative girdling classification schemes</div> <div>- oncid_tree_behavfull_56spp.nwk: pruned phylogenetic tree for the full girdling dataset (56 species)</div> <div>- oncid_tree_f_36spp.nwk: pruned phylogenetic tree for the female morphometric dataset (36 species)</div> <div>- oncid_tree_m_42spp.nwk: pruned phylogenetic tree for the male morphometric dataset (42 species)</div> <div>- oncid_tree_mf_43spp.nwk: pruned phylogenetic tree for all species with morphometric data for males or females; used for the stochastic character map next to the heatmap plot (Fig 4)</div> <div>- oncid_tree_sd_35spp.nwk: pruned phylogenetic tree for the sexual dimorphism dataset (35 species)</div> <div> </div> <div><strong>FittedModels (folder): </strong>fitted models (mvgls, model comparison analyses, OUM models, simmaps) outputted by the OncidHeadDimorphism-Analysis-FINAL.R script </div> <div>- MacroModelFits_logRtraits_f_36spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to female morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits_logRtraits_m_42spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to male morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits-SDDI-35spp_2024-10-11.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to sexual dimorphism data across 100 stochastic character maps of girdling behavior</div> <div>- mvgls-results-headsize-mf-2024-10-12.Rdata: fitted mvgls regression models for male and female traits (analyzed separately)</div> <div>- mvgls-results-sddi-2024-10-12.Rdata: fitted mvgls regression models for sexual dimorphism</div> <div>- OUM_headtraits_f_36spp-2024-10-12.Rdata: fitted OUM models and summary statistics for female head traits</div> <div>- OUM_headtraits_m_42spp-2024-10-12.Rdata: fitted OUM models and summary statistics for male head traits</div> <div>- OUM-SDDI-35spp-2024-10-12.Rdata: fitted OUM models and summary statistics for sexual dimorphism in head traits</div> <div>- simmaps_ard_full_2state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - all Lochmaeocles species are classified as girdlers</div> <div>- simmaps_ard_full_3state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with three behavioral states (girdling, non-girdling, or facultative girdling)</div> <div>- simmaps_ard_full_1Loch.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - only one Lochmaeocles species (L. tessellatus) is classified as a girdler</div> <div>- simmaps_ard_m.RDS: stochastic character map for the 42 species used in the analyses of male morphometric traits</div> <div>- simmaps_ard_f.RDS: stochastic character map for the 36 species used in the analyses of female morphometric traits</div> <div>- simmaps_ard.RDS: stochastic character map for the 35 species used in the sexual dimorphism analyses; 2 behavioral states.</div> <div> </div> <div><strong>Rscripts (folder): </strong>R scripts used to process data and run phylogenetic comparative analyses of head size and girdling behavior.</div> <div>- OncidHeadDimorphism-DatasetPREP-FINAL.R: R script used to filter data and prune trees from the RawData folder for downstream phylogenetic comparative analyses; outputs of this script are in the ProcessedData folder.</div> <div>- OncidHeadDimorphism-Analysis-FINAL.R: R script used to analyze data in the ProcessedData folder to answer questions about the origin and evolution of girdling behavior and the relationship between girdling and head size or head size sexual dimorphism; fitted models outputted by this script are in the FittedModels folder</div> <div>- OncidHeadDimorphism-Plots-FINAL.R: R script used to generate plots for the manuscript<br><br></div>
Fig. 2 in A preliminary molecular phylogeny of shield-bearer moths (Lepidoptera: Adeloidea: Heliozelidae) highlights rich undescribed diversity
Fig. 2. Previous hypotheses regarding Heliozelidae. (a) Cladogram of Heliozelidae (after Nielsen 1980). Liozela, Chaetozela and Neospila are unpublished manuscript names for genera proposed by Nielsen. Diacopia is a synonym of Antispila that Nielsen regarded as separate genus. (b) Cladogram of Incurvarioidea (Adeloidea) including Heliozelidae (after Nielsen and Davis, 1985). Crinopterigidae has been subsumed into Incurvariidae by van Nieukerken et al. (2011). (c) Cladogram, 50% majority rule consensus tree from maximum parsimony analysis of COI sequences after van Nieukerken et al. (2012). (d) Cladogram based on phylogeny of Lepidoptera showing the position of Heliozelidae in relation to other families in Adeloidea after Wahlberg et al. (2013). (e) Cladogram based on phylogeny of non-dytrisian lineages after Regier et al. (2015) showing the split of Nematopogon from the rest of Adelidae seen in some analyses. (f) Cladogram based on maximum likelihood (ML) tree for COI data after Bernardo et al. (2015).
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.