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389 results for “ancestral”
Data from: Resegmentation is an ancestral feature of the gnathostome vertebral skeleton
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Data from: Population structure, ancestral admixture, gene flow, and landscape association of blacklegged ticks during range expansion in the Midwestern U.S.
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Determinate growth is predominant and likely ancestral in squamate reptiles
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Data from: Evidence for diurnal bee pollination in the ancestrally hawkmoth-pollinated genus Crinum (Amaryllidaceae)
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Archaeology demonstrates sustainable Ancestral Coast Salish salmon stewardship over thousands of years pre-contact
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Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral
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Data from: A fish-focused menu: An interdisciplinary reconstruction of Ancestral Tsleil-Waututh diets
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Data from: Ancestral area analyses reveal Pleistocene-influenced evolution in a clade of Coastal Plain endemic plants
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Data from: Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species
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Data from: The endocast of Euparkeria sheds light on the ancestral archosaur nervous system
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ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process
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Bayesian inference of ancestral host-parasite interactions under a phylogenetic model of host repertoire evolution
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Input files and setup for simulations of ancestral and modern glycosidases
<p>Input files, heme parameters, and representative structures from simulations of ancestral glycosidases and the modern glycosidase from the thermophilic <em>Halothermothrix orenii</em>. For details please see the README file provided.</p>
Ancestral state reconstruction for regeneration and autotomy in arthopods and reptiles
<p>Some form of regeneration occurs in all lifeforms and extends from single-cell organisms to humans. The degree to which regenerative ability is distributed across different taxa, however, is harder to ascertain given the potential for phylogenetic constraint or inertia, and adaptive processes to shape this pattern. Here, we examine the phylogenetic history of regeneration in two groups where the trait has been well-studied: arthropods and reptiles. Because autotomy is often present alongside regeneration in these groups, we performed ancestral state reconstructions for both traits to more precisely assess the timing of their origins and the degree to which these traits coevolve. Using an ancestral trait reconstruction, we find that autotomy and regeneration were present at the base of the arthropod and reptile trees. We also find that when autotomy is lost it does not re-evolve easily. Lastly, we find that the distribution of regeneration is intimately connected to autotomy with the association being stronger in reptiles than in arthropods. While these patterns suggest that decoupling autotomy and regeneration at a broad phylogenetic scale may be difficult, the available data provides useful insight into their entanglement. Ultimately, our reconstructions provide important groundwork to explore how selection may have played a role during the loss of regeneration in specific lineages.</p>
Post-embryonic development of Fritzolenellus suggests the ancestral morphology of the early developmental stages in Trilobita
<p>Trilobite development has been intensively explored during past decades, but information about ancestral character combinations in the early developmental stages of trilobites remains virtually unknown. Trilobites of the superfamily Olenelloidea are one of the earliest diverging groups. Study of their development coupled with the development of other early diverging trilobite groups can provide crucial information about the ancestral morphology of trilobite early stages. Herein we describe numerous well-preserved specimens of the olenelloid trilobite <em>Fritzolenellus lapworthi</em>. The earliest stages have circular cephala bearing intergenal spines and lacking genal spines. During subsequent development, morphological changes comprise the modification of the cephalic shape from circular to semi-circular, expansion of LA, gradual shortening of intergenal spines and origin and prolongation of genal spines. Trunk development of <em>Fritzolenellus</em> suggest that the development of macropleurae and macrospines are two independent processes and that origin of the opistotrunk is linked with the onset of phase 5 of cephalic development. The morphology of the early developmental stages of <em>Fritzolenellus</em> and some related taxa differs in many aspects from the morphology of equivalent stages of some other members of Olenelloidea. Consequently, two basic morphotypes are recognized during the early development of Olenelloidea – the <em>Fritzolenellus</em> and the <em>Olenellus</em> morphotypes. Comparison with Fallotaspidoidea and Redlichiina reveals that early developmental stages of these taxa share character combinations that are typical for <em>Fritzolenellus</em> morphotype. Such a comparison suggests that characters defining <em>Fritzolenellus</em> morphotype are ancestral for Trilobita. The <em>Olenellus</em> morphotype is likely a derived condition within Olenelloidea and might be related to predator deterrence.</p>
Preference, performance, and chemical defense in an endangered butterfly using novel and ancestral host plants
<p>Adoption of novel host plants by herbivorous insects can require new adaptations and may entail loss of adaptation to ancestral hosts. We examined relationships between an endangered subspecies of the butterfly <i>Euphydryas editha </i>(Taylor's checkerspot) and three host plant species. Two of the hosts (<i>Castilleja hispida, Castilleja levisecta</i>) were used ancestrally while the other, <i>Plantago lanceolata</i>, is exotic and was adopted more recently. We measured oviposition preference, neonate preference, larval growth, and secondary chemical uptake on all three hosts. Adult females readily laid eggs on all hosts but favored <i>Plantago </i>and tended to avoid <i>C. levisecta. </i>Oviposition preference changed over time.<i> </i>Neonates had no preference among host species, but consistently chose bracts over leaves within both <i>Castilleja </i>species. Larvae developed successfully on all species and grew to similar size on all of them unless they ate only <i>Castilleja </i>leaves (rather than bracts) which limited their growth. Diet strongly influenced secondary chemical uptake by larvae. Larvae that ate <i>Plantago </i>or <i>C. hispida </i>leaves contained the highest concentrations of iridoid glycosides, and iridoid glycoside composition varied with host species and tissue type. Despite having largely switched to a novel exotic host and generally performing better on it, this population has retained breadth in preference and ability to use other hosts.</p>
Human genome ancestral state files
<p>Files containing ancestral states at all positions of the human genome, inferred based on consensus support among three ape species; Gorilla, Chimpanzee and Orangutan.</p>
Data from: Ancestral plasticity and allometry in threespine stickleback reveal phenotypes associated with derived, freshwater ecotypes
For over a century, evolutionary biologists have debated whether and how phenotypic plasticity impacts the processes of adaptation and diversification. The empirical tests required to resolve these issues have proven elusive, mainly because it requires documentation of ancestral reaction norms, a difficult prospect where many ancestors are either extinct or have evolved. The threespine stickleback radiation is not limited in this regard, making it an ideal system in which to address general questions regarding the role of plasticity in adaptive evolution. As retreating ice sheets have exposed new habitats, oceanic stickleback founded innumerable freshwater populations, many of which have evolved parallel adaptations to their new environments. Because the founding oceanic population is extant, we can directly evaluate whether specific patterns of ancestral phenotypic expression in the context of novel environments (plasticity), or over ontogeny, predisposed the repeated evolution of "benthic" and "limnetic" ecotypes in shallow and deep lakes, respectively. Consistent with this hypothesis, we found that oceanic stickleback raised in a complex habitat and fed a macroinvertebrate diet expressed traits resembling derived, benthic fish. Alternatively, when reared in a simple environment on a diet of zooplankton, oceanic stickleback developed phenotypes resembling derived, limnetic fish. As fish in both treatments grew, their body depths increased allometrically, as did the size of their mouths, while their eyes became relatively smaller. Allometric trajectories were subtly but significantly impacted by rearing environment. Thus, both environmental and allometric influences on development, along with their interactive effects, produced variation in phenotypes consistent with derived benthic and limnetic fish, which may have predisposed the repeated genetic accommodation of this specific suite of traits. We also found significant shape differences between marine and anadromous stickleback, which has implications for evaluating the ancestral state of stickleback traits.
Data from: Genetic diversity, population structure and ancestral origin of Australian wheat
Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian Sstates, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with maintaining genetic diversity for long-term selection gains and to plan future breeding programs.
Data from: Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome
Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding and active pharyngeal filter feeding. The results demonstrate that an orientation with the mouth facing downstream of the current was optimal for drag and lift reduction. Moreover, they show that there was almost no flow to the mouth and associated marginal groove under simulations of passive feeding, whereas considerable flow towards the animal was observed for active feeding, which would have enhanced the transport of suspended particles to the mouth. This strongly suggests that cinctans were active pharyngeal filter feeders, like modern enteropneust hemichordates and urochordates, indicating that the ancestral deuterostome employed a similar feeding strategy.
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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.