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157 results for “Evolutionary Studies”
ActDES – a Curated Actinobacterial Database for Evolutionary Studies
<p>ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies - facilitated by reliable orthologs identification across a set of defined, phylogenetically representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These studies can then act as a springboard for the study of the evolution of virulence genes, studying the evolution of metabolism and metabolic engineering target identification.</p>
Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation
<p>Target capture emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family, however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.</p>
Data from: Methodological artefacts cause counter-intuitive evolutionary conclusions in a simulation study
<p>In their simulation study, Garcia-Costoya et al. (2023) conclude that evolutionary constraints might aid populations facing climate change. However, we are concerned that this conclusion is largely a consequence of the simulated temperature variation being too small, and, most importantly, that uneven limitations to standing variation disadvantage unconstrained populations.</p>
Secondary metabolites from nectar and pollen: a resource for ecological and evolutionary studies
<p>Floral chemistry mediates plant interactions with herbivores, pathogens, and pollinators. The chemistry of floral nectar and pollen—the primary food rewards for pollinators—can affect both plant reproduction and pollinator health. Although the existence and functional significance of nectar and pollen secondary metabolites has long been known, comprehensive quantitative characterizations of secondary chemistry exist for only a few species. Moreover, little is known about intraspecific variation in nectar and pollen chemical profiles. Because the ecological effects of secondary chemicals are dose-dependent, heterogeneity across genotypes and populations could influence floral trait evolution and pollinator foraging ecology. To better understand within- and across-species heterogeneity in nectar and pollen secondary chemistry, we undertook exhaustive LC-MS and LC-UV-based chemical characterizations of nectar and pollen methanol extracts from 31 cultivated and wild plant species. </p> <p>Nectar and pollen were collected from farms and natural areas in Massachusetts, Vermont, and California, USA, in 2013 and 2014. For wild species, we aimed to collect 10 samples from each of 3 sites. For agricultural and horticultural species, we aimed for 10 samples from each of 3 cultivars. Our dataset (1535 samples, 102 identified compounds) identifies and quantifies each compound recorded in methanolic extracts, and includes chemical metadata that describe the molecular mass, retention time, and chemical classification of each compound. A reference phylogeny is included for comparative analyses.</p> <p>We found that each species possessed a distinct chemical profile; moreover, within species, few compounds were found in both nectar and pollen. The most common secondary chemical classes were flavonoids, terpenoids, alkaloids and amines, and chlorogenic acids. The most common compounds were quercetin and kaempferol glycosides. Pollens contained high concentrations of hydroxycinnamoyl-spermidine conjugates, mainly triscoumaroyl and trisferuloyl spermidine, found in 71% of species. When present, pollen alkaloids and spermidines had median nonzero concentrations of 23,000 µM (median 52% of recorded micromolar composition). Although secondary chemistry was qualitatively consistent within each species and sample type, we found significant quantitative heterogeneity across cultivars and sites. These data provide a standard reference for future ecological and evolutionary research on nectar and pollen secondary chemistry, including its role in pollinator health and plant reproduction.</p>
Figures 53–58 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 53–58. Stereoscan photographs of Pimplinae. Figs 53, 54, mesopleuron; 53, Dolichomitus annulicornis; 54, Pimpla azteca. Figs 55–58, propodeum, dorsal; 55, Xanthopimpla aurita; 56, Echthromorpha atrata; 57, Lissopimpla excelsa; 58, Zatypota percontatoria.
Figures 87–90 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 87–90. Hind end of mesosoma with hind legs and metasoma dis-articulated; 87, Neotheronia mellosa; 88, Pimpla sumichrasti; 89, Scambus annulatus; 90, Dolichomitus annuicornis.
Figures 41–46 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 41–46. Stereoscan photographs of Pimplinae. Fig. 41, Sinarachna pallipes, head, posterior. Fig. 42, Dreisbachia avivae, mandible. Figs 43–46, Head, lateral; 43, Dolichomitus irritator, 44, Zaglyptus simonis; 45, Echthromorpha atrata; 46, Hymenoepimecis bicolor.
Figures 71–76 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 71–76. Stereoscan photographs of Pimplinae. Figs 71, 72, tergites II—IV, dorsal; 71, Polysphincta tuberosa; 72, Zatypota petronae. Figs 73–75, apex of ovipositor; 73, Liotryphon crassiseta; 74, Endromopoda detrita; 75, Dolichomitus imperator. Fig. 76, Zatypota petronae, ovipositor entire.
Figures 23–28 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 23–28. Stereoscan photographs of Pimplinae, head, anterior; 23, Ephialtes manifestator; 24, Paraperithous gnathaulax; 25, Xanthephialtes oculatus; 26, Schizopyga frigida; 27, Theronia melanocera ♀; 28, Theronia melanocera ♂.
Figures 47–52 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 47–52. Stereoscan photographs of Pimplinae, pronotum, lateral; 47, Dolichomitus irritator; 48, Pimpla azteca; 49, Schizopyga frigida; 50, Clistopyga calixtoi; 51, Hymenoepimecis bicolor; 52, Acrodactyla degener.
Figure 22 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 22. Cladogram resulting from secondary analysis: section 9 (of 9), the Polysphincta genus-complex. Although there are some similarities in topology with the primary analysis (Figs 11–13) – such as the basal position of Piogaster and the composition of two more derived clades – all genera are apparently monophyletic.
Figures 29–34 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 29–34. Stereoscan photographs of Pimplinae. Figs 29–32,head, anterior; 29, Acropimpla didyma; 30, Sericopimpla australis; 31, Dolichomitus irritator ♂; 32, Xanthopimpla aurita; Figs 33, 34, base of antennae; 33, Pimpla azteca; 34, Acrodactyla degener.
Figures 94–97 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 94–97. Posterior end of metasoma of female, showing position and shape of tergites VII−IX and associated apodemes, slightly diagrammatic; 94, Pimpla sumichrasti; 95, Neotheronia mellosa; 96, Scambus brevicornis; 97, Acrotaphus tibialis. Note the great enlargement of the apodeme on tergite VIII in Pimpla.
Figures 35–40 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 35–40. Stereoscan photographs of Pimplinae, head, posterior; 35, Dolichomitus annulicornis; 36, Pseudopimpla pygidiator; 37, Camptotypus stigmaticus; 38, Dreisbachia avivae; 39, Eruga yehi; 40, Schizopyga frigida.
Figure 20 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 20. Cladogram resulting from secondary analysis: section 7 (of 9), the Ephialtes genus-group. The topology of this cladogram broadly resembles that of the primary analysis, but note that Dolichomitus is apparently monophyletic. The results support the primary analysis in that Endromopoda (excluding Fredegunda) and Holcopimpla are not demonstrably monophyletic.
Figure 17 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 17. Cladogram resulting from secondary analysis: section 4 (of 9), the interrelationships of Xanthopimpla, Lissopimpla and Echthromorpha.
Figures 77–82 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figures 77–82. Stereoscan photographs of Pimplinae. Fig. 77, Polysphincta tuberosa, ovipositor entire. Figs 78–82, apex of metasoma, ♂, lateroventral; 78, Scambus buolianae; 79, Delomerista laevifrons; 80, Perithous scurra, 81, Xanthopimpla aurita; 82, Pimpla caeruleata.
Figure 14 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 14. Cladogram resulting from secondary analysis: section 1 (of 9), outgroups and tribes of Pimplini, showing characters supporting both the monophyly of the subfamily and the several tribes. Note that the topology of this cladogram is essentially the same as that in Fig. 1 except for the re-arrangement of the three tribes of Pimplinae: the Delomeristini is the sister-lineage to Pimplini + Ephialtini, rather than the Pimplini being the sister-group to the Delomeristini + Ephialtini.
Figure 18 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 18. Cladogram resulting from secondary analysis: section 5 (of 9), the basal Ephialtini. Note that the topology is very similar to the primary analysis (Fig. 6) except that the Ephialtes, Camptotypus and Sericopimpla genus-groups form an unresolved trichotomy.
Figure 10 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 10. Cladogram resulting from primary analysis: section 10 (of 13), the basal members of the Sericopimpla genusgroup. Note the demonstrably monophyletic nature of most genera (Sericopimpla, Tromatobia, Zaglyptus and Clistopyga) and their basal relationship to the Polysphincta genus-complex (the Polysphinctini of authors). Gregopimpla is apparently paraphyletic with respect to Iseropus.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.