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389 results for “ancestral”
Data from: Calculating structural complexity in phylogenies using ancestral ontologies
Complexity is an important aspect of evolutionary biology, but there are many reasonable concepts of complexity, and its objective measurement is an elusive matter. Here we develop a simple measure of complexity based on counts of elements, incorporating the hierarchical information as represented in anatomical ontologies. Neomorphic and transformational characters are used to identify novelties and individuated morphological regions, respectively. By linking the characters to terms in an anatomical ontology a node-driven approach is implemented, where a node ontology and a complexity score are inferred from the optimization of individual characters on each ancestral or terminal node. From the atomized vector of character scorings, the anatomical ontology is used to integrate the hierarchical structure of morphology in terminals and ancestors. These node ontologies are used to calculate a measure of complexity that can be traced on phylogenetic trees and is harmonious with usual phylogenetic operations. This strategy is compared with a terminal-driven approach, where the complexity scores are calculated only for terminals, and optimized as a continuous character on the internal nodes. These ideas are applied to a real dataset of 166 araneomorph spider species scored for 393 characters, using the Spider Ontology (SPD); complexity scores and transitions are calculated for each node and branch, respectively. This result in a distribution of transitions skewed towards simplification; the transitions in complexity have no apparent correlation with character branch lengths. The node-driven and terminal-driven estimations are generally correlated in the complexity scores, but have higher divergence in the transition values. The structure of the ontology is used to provide complexity scores for organ systems and body parts of the focal groups.
Data from: A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels
Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they have diversified rapidly. Here, we compare signals from DNA sequences with morphological signals using pictures of skulls and computational simulations. Phylogenetic analyses reveal step-wise geographic divergence across the Northern Hemisphere. In Central and South America, tree squirrels form two separate clades, which split from a common ancestor. Simulations of ancestral distributions show western Amazonia as the epicenter of speciation in South America. This finding suggests that wet tropical forests on the foothills of Andes possibly served as refugia of squirrel diversification during Pleistocene climatic oscillations. Comparison of phylogeny and morphology reveals one major discrepancy: Microsciurus species are a single clade morphologically but are polyphyletic genetically. Modeling of morphology–diet relationships shows that the only group of species with a direct link between skull shape and diet are the bark-gleaning insectivorous species of Microsciurus. This finding suggests that the current designation of Microsciurus as a genus is based on convergent ecologically driven changes in morphology.
Data from: Ancestral whole genome duplication in the marine chelicerate horseshoe crabs
Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs—Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.
Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies
<p>Introgression is arguably one of the most important biological processes in the evolution of groups of related species, affecting at least 10% of the extant species in the animal kingdom. Introgression reduces genetic divergence between species, and in some cases can be highly beneficial, facilitating rapid adaptation to ever-changing environmental pressures. Introgression also significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.</p>
Figure 4 from: Roxo FF, Ochoa LE, Silva GSC, Oliveira C (2015) Rhinolekos capetinga: a new cascudinho species (Loricariidae, Otothyrinae) from the rio Tocantins basin and comments on its ancestral dispersal route. ZooKeys 481: 109-130. https://doi.org/10.3897/zookeys.481.8755
Figure 4 - a Map showing the distribution of Rhinolekos capetinga. Type locality at córrego da Branca, green star – 14°53'47.2"S, 47°34'58.4"W. Paratype localities at córrego da Branca, red star – 14°57'01.6"S, 47°35'57.0"W, and at córrego Roncador, pink star – 14°43'51.3"S, 47°32'34.0"W b Habitat and submerged vegetation where the specimens were found in type locality of córrego da Branca, 14°53'47.2"S, 47°34'58.4"W. Photo: LH Roxo.
Figure 3 from: Roxo FF, Ochoa LE, Silva GSC, Oliveira C (2015) Rhinolekos capetinga: a new cascudinho species (Loricariidae, Otothyrinae) from the rio Tocantins basin and comments on its ancestral dispersal route. ZooKeys 481: 109-130. https://doi.org/10.3897/zookeys.481.8755
Figure 3 - Rhinolekos capetinga, live specimen, MZUSP 116102, holotype, male, 37.5 mm SL, rio Tocantins basin, Goiás State, Brazil. Photo: FF Roxo.
Figure 5 from: Roxo FF, Ochoa LE, Silva GSC, Oliveira C (2015) Rhinolekos capetinga: a new cascudinho species (Loricariidae, Otothyrinae) from the rio Tocantins basin and comments on its ancestral dispersal route. ZooKeys 481: 109-130. https://doi.org/10.3897/zookeys.481.8755
Figure 5 - Biogeographic distribution and time-calibrated phylogenetic tree of Microlepidogaster and Rhinolekos species, based on three mitochondrial (16SrRNA, COI, Cytb) and one nuclear marker (F-reticulon 4), modified from figure 7 of Roxo et al. (2014a). The map colorations indicate distinct biogeographic regions according to classification available in Roxo et al. (2014a): Green – Coastal drainages (A); Red – upper rio Paraná basin (B); Purple – Paraguay, Lower Paraná and Uruguay basins (C); Blue – Amazon basin (D); Yellow – São Francisco basin (E).
Figure 2 from: Roxo FF, Ochoa LE, Silva GSC, Oliveira C (2015) Rhinolekos capetinga: a new cascudinho species (Loricariidae, Otothyrinae) from the rio Tocantins basin and comments on its ancestral dispersal route. ZooKeys 481: 109-130. https://doi.org/10.3897/zookeys.481.8755
Figure 2 - Rhinolekos capetinga, LBP 19001, paratype, 34.5 mm SL. a Anterior portion of axial skeleton and dorsal-fin supports (left side, lateral view). Vertebrae counts included five vertebrae of the Weberian apparatus. np nucal plate; rv6 rib of sixth vertebrae; px2 compound proximal and medial radial 2; sn+px1 compound supraneural first dorsal-fin proximal radial; sp1 first dorsal-fin spinelet; sp2 second dorsal-fin spine; v6−12 vertebrae 6−12 b Skull of Rhinolekos capetinga; f frontal; soc supraoccipital; cpt parieto-supraoccipital; op opercle; io1−5 infraorbitals; pop preopercle; cp 1−2 cheek plates; pr 1−3 postrostral plates; pf prefrontal plates; le lateral ethmoid; n nasal; lpn lateronasal plate; r rostral plate; pn prenasal; sp sphenotic.
Figure 1 from: Roxo FF, Ochoa LE, Silva GSC, Oliveira C (2015) Rhinolekos capetinga: a new cascudinho species (Loricariidae, Otothyrinae) from the rio Tocantins basin and comments on its ancestral dispersal route. ZooKeys 481: 109-130. https://doi.org/10.3897/zookeys.481.8755
Figure 1 - Rhinolekos capetinga MZUSP 116102, holotype, male, 37.5 mm SL, Goiás State, rio Tocantins basin, Brazil.
Supplementary material 2 from: Royzenblat S, Kulacic J, Friedrich M (2023) Evidence of ancestral nocturnality, locomotor clock regression, and cave zone-adjusted sleep duration modes in a cave beetle. Subterranean Biology 45: 79-94. https://doi.org/10.3897/subtbiol.45.100717
Activity logs of the two long-term adjusted DD animals
Supplementary material 1 from: Royzenblat S, Kulacic J, Friedrich M (2023) Evidence of ancestral nocturnality, locomotor clock regression, and cave zone-adjusted sleep duration modes in a cave beetle. Subterranean Biology 45: 79-94. https://doi.org/10.3897/subtbiol.45.100717
Activity logs of select non-adjusting DD animals
Supplementary material 3 from: Royzenblat S, Kulacic J, Friedrich M (2023) Evidence of ancestral nocturnality, locomotor clock regression, and cave zone-adjusted sleep duration modes in a cave beetle. Subterranean Biology 45: 79-94. https://doi.org/10.3897/subtbiol.45.100717
Actograms of the long-term adjusted LD animals
Supplementary material 4 from: Royzenblat S, Kulacic J, Friedrich M (2023) Evidence of ancestral nocturnality, locomotor clock regression, and cave zone-adjusted sleep duration modes in a cave beetle. Subterranean Biology 45: 79-94. https://doi.org/10.3897/subtbiol.45.100717
Activity logs of the long-term adjusted LD animals
Data from: Sexually antagonistic genetic variance for fitness in an ancestral and a novel environment
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Data from: The return to water in ancestral Xenopus was accompanied by a novel mechanism for producing and shaping vocal signals
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Data from: Replicated evolutionary inhibition of a complex ancestral behaviour in an adaptive radiation
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Data from: Palaeohistological evidence for ancestral high metabolic rate in archosaurs
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Data from: Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes
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Data from: Calculating structural complexity in phylogenies using ancestral ontologies
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Data from: Parallel genome-wide fixation of ancestral alleles in partially outcrossing experimental populations of Caenorhabditis elegans
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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.