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477 results for “Evolution: molecular”
Molecular evolution of the sex peptide network in Drosophila
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Data from: Dissecting molecular evolution of class 1 integron gene cassettes and identifying their bacterial hosts in suburban creeks via epicPCR
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Data from: Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas
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Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)
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Data from: Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution
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Data for: The pace of mitochondrial molecular evolution varies with seasonal migration distance
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Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve
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Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism
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Molecular phylogeny and morphological perianth evolution in Corymbia (Myrtaceae), and the implications for generic delimitation: data and tree files
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Data from: Molecular evolution of sour tolerance in birds
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Impact of host demography and evolutionary history on endosymbiont molecular evolution: a test in carpenter ants (Genus Camponotus) and their Blochmannia endosymbionts
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Data from: Parallel molecular evolution in pathways, genes, and sites in high-elevation hummingbirds revealed by comparative transcriptomics
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Data from: A molecular phylogeny of Eumorpha (Lepidoptera: Sphingidae) and the evolution of anti-predator larval eyespots
Many insects possess conspicuous external circular ring markings that resemble the eye of a vertebrate. These 'eyespots' typically function to startle or otherwise deter predators, but few studies have examined how eyespots have evolved. We study the evolution of the posterior larval eyespot in the charismatic New World hawkmoth genus Eumorpha. While Eumorpha has a range of posterior larval eyespot shapes and sizes, little is known of how this trait has evolved because phylogenetic relationships of Eumorpha remain largely unknown. In this study, we included 62 individuals from 23 of 26 described Eumorpha species, and sequenced four genes (CAD, EF-1α, Wingless and COI), totaling 3773 base pairs. Maximum likelihood and Bayesian phylogenetic methods produced largely congruent trees with well-supported relationships. Our analyses reveal that Eumorpha probably had an ancestor with a posterior larval eyespot and that the eyespot was subsequently lost in at least three lineages. Eumorpha appears to have originated in Central and South America and expanded its distribution to North America.
Data from: The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth. Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record. The limited number of genes and species explored and pervasive variations in evolutionary rates are the most likely sources of such discrepancies. Here we compared concatenated amino acid sequences of 129 proteins from 36 eukaryotes to determine the divergence times of several major clades, including animals, fungi, plants, and various protists. Due to significant variations in their evolutionary rates, and to handle the uncertainty of the fossil record, we used a Bayesian relaxed molecular clock simultaneously calibrated by six paleontological constraints. We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950–1,259 million years ago (Mya), animals diverged from choanoflagellates 761–957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642–761 Mya. The divergence times appeared to be robust with respect to prior assumptions and paleontological calibrations. Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be ≈100 million years more ancient than the Cambrian boundary.
Data from: Molecular cytogenetic and genomic insights to chromosomal evolution
This review summarizes aspects of the extensive literature on the patterns and processes underpinning chromosomal evolution in vertebrates and especially placental mammals. It highlights the growing synergy between molecular cytogenetics and comparative genomics, particularly with respect to fully or partially sequenced genomes, and provides novel insights into changes in chromosome number and structure across deep division of the vertebrate tree of life. The examination of basal numbers in the deeper branches of the vertebrate tree suggest a haploid (n) chromosome number of 10–13 in an ancestral vertebrate, with modest increases in tetrapods and amniotes most probably by chromosomal fissioning. Information drawn largely from cross-species chromosome painting in the data-dense Placentalia permits the confident reconstruction of an ancestral karyotype comprising n=23 chromosomes that is similarly retained in Boreoeutheria. Using in silico genome-wide scans that include the newly released frog genome we show that of the nine ancient syntenies detected in conserved karyotypes of extant placentals (thought likely to reflect the structure of ancestral chromosomes), the human syntenic segmental associations 3p/21, 4pq/8p, 7a/16p, 14/15, 12qt/22q and 12pq/22qt predate the divergence of tetrapods. These findings underscore the enhanced quality of ancestral reconstructions based on the integrative molecular cytogenetic and comparative genomic approaches that collectively highlight a pattern of conserved syntenic associations that extends back ~360 million years ago.
Data from: Molecular phylogenetics and the evolution of fruit and leaf morphology of Dichaea (Orchidaceae: Zygopetalinae)
BACKGROUND AND AIMS: The orchid genus Dichaea, with over 100 species found throughout the neotropics, is easily recognized by distichous leaves on long stems without pseudobulbs and flowers with infrastigmatic ligules. The genus has previously been divided into four sections based primarily on presence of ovary bristles and a foliar abscission layer. The aim of this work is to use DNA sequence data to estimate phylogenetic relationships within Dichaea and map the distribution of major morphological characters that have been used to delimit subgenera/sections. METHODS: Sequence data for the nuclear ribosomal internal transcribed spacers and plastid matK, trnL intron, trnL-F spacer and ycf1 for 67 ingroup and seven outgroup operational taxonomic units were used to estimate phylogenetic relationships within Dichaea. Taxa from each of the four sections were sampled, with the greatest representation from section Dichaea, the most diverse and taxonomically puzzling group. KEY RESULTS: Molecular data and morphology support monophyly of Dichaea. Results indicate that section Dichaeopsis is polyphyletic and based on symplesiomorphies, including deciduous leaves and smooth ovaries that are widespread in Zygopetalinae. There are at least three well-supported clades within section Dichaeopsis. Section Pseudodichaea is monophyletic and defined by setose ovaries and leaves with an abscission layer. Sections Dichaea and Dichaeastrum are monophyletic and defined by pendent habit and persistent leaves. Section Dichaeastrum, distinguished from section Dichaea primarily by a glabrous ovary, is potentially polyphyletic. CONCLUSIONS: The leaf abscission layer was lost once, occurring only in the derived sections Dichaea and Dichaeastrum. The setose fruit is a more homoplasious character with several losses and gains within the genus. We propose an informal division of the genus based upon five well-supported clades.
Data from: Molecular evolution of anthocyanin pigmentation genes following losses of flower color
Background: Phenotypic transitions, such as trait gain or loss, are predicted to carry evolutionary consequences for the genes that control their development. For example, trait losses can result in molecular decay of the pathways underlying the trait. Focusing on the Iochrominae clade (Solanaceae), we examine how repeated losses of floral anthocyanin pigmentation associated with flower color transitions have affected the molecular evolution of three anthocyanin pathway genes (Chi, F3h, and Dfr). Results: We recovered intact coding regions for the three genes in all of the lineages that have lost floral pigmentation, suggesting that molecular decay is not associated with these flower color transitions. However, two of the three genes (Chi, F3h) show significantly elevated dN/dS ratios in lineages without floral pigmentation. Maximum likelihood analyses suggest that this increase is due to relaxed constraint on anthocyanin genes in the unpigmented lineages as opposed to positive selection. Despite the increase, the values for dN/dS in both pigmented and unpigmented lineages were consistent overall with purifying selection acting on these loci. Conclusions: The broad conservation of anthocyanin pathway genes across lineages with and without floral anthocyanins is consistent with the growing consensus that losses of pigmentation are largely achieved by changes in gene expression as opposed to structural mutations. Moreover, this conservation maintains the potential for regain of flower color, and indicates that evolutionary losses of floral pigmentation may be readily reversible.
Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing
Many phylogenomic studies based on transcriptomes have been limited to "single-copy" genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups.
Data from: Major radiations in the evolution of caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks
BACKGROUND: Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America ("eocardiids"). RESULTS: A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. CONCLUSIONS: The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone.
Data from: Morphological and molecular evolution and their consequences for conservation and taxonomy in the Le Conte's Thrasher (Toxostoma lecontei)
We evaluated geographic variation and subspecific taxonomy in the Le Conte's Thrasher (Toxostoma lecontei) by analyzing DNA sequences from 16 nuclear loci, one mitochondrial DNA locus, and four study skin characters, and compared these data sets with previously published data on plumage coloration and different mtDNA genes. Morphological support for the southernmost taxon, T. l. arenicola, is relatively weak: multivariate analyses of morphometrics or back coloration do not provide diagnostic support, although one color character differs statistically. However, combined DNA analyses indicate that T. l. arenicola is diagnosable and reciprocally monophyletic, diverging from T. l. lecontei at least 140,000 years ago. Little to no past introgression across a very short geographic distance despite the long period of isolation is strong evidence of independently evolving taxa. We suggest that the lack of morphological divergence in traits related to niche use has prevented the two taxa from invading each other's range. Despite relatively weak morphological differences we suggest that these two deeply divergent lineages merit species status, and we suggest Vizcaino Thrasher for the common name corresponding to T. l. arenicola. The population size of T. l. arenicola is small and the taxon is in need of preservation attention.
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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.