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477 results for “Molecular evolution”
FIGURE 3 in Evolution of species diversity in the genus Chamaecostus (Costaceae): molecular phylogenetics and morphometric approaches
FIGURE 3. Box and whisker plots of three significantly different morphometric variables between Chamaecostus cuspidatus (n=14), Chamaecostus subsessilis s.str. (n=51) and Chamaecostus acaulis comb. nov. (n=83), showing means, quartiles and ranges. A—Leaf length (cm); B—Leaf Maximum Width (cm); C—Leaf Area (cm2).
FIGURE 4. Chamaecostus acaulis comb. nov. and Chamaecostus subsessilis s in Evolution of species diversity in the genus Chamaecostus (Costaceae): molecular phylogenetics and morphometric approaches
FIGURE 4. Chamaecostus acaulis comb. nov. and Chamaecostus subsessilis s.str.. (B) photo by W.W.Thomas. (D) photo by D.Skinner.
FIGURE 1 in Evolution of species diversity in the genus Chamaecostus (Costaceae): molecular phylogenetics and morphometric approaches
FIGURE 1. Schematic representation of measured morphometric variables; LL—Leaf Length, LW—Leaf Maximum Width, AA—Apex Angle, BA—Base Angle.
Evolution of the conformational dynamics of the molecular chaperone Hsp90
<p>MD snapshots from: "Evolution of the conformational dynamics of the molecular chaperone Hsp90"</p> <p> </p>
Data from: Molecular evolution of the nuclear factor (erythroid-derived 2)-like 2 gene Nrf2 in Old World fruit bats (Chiroptera: Pteropodidae)
Mammals developed antioxidant systems to defend against oxidative damage in their daily life. Enzymatic antioxidants and low molecular weight antioxidants (LMWAs) constitute major parts of the antioxidant systems. Nuclear factor (erythroid-derived 2)-like 2 (Nrf2, encoded by the Nrf2 gene) is a central transcriptional regulator, regulating transcription, of many antioxidant enzymes. Frugivorous bats eat large amounts of fruits that contain high levels of LMWAs such as vitamin C, thus, a reliance on LMWAs might greatly reduce the need for antioxidant enzymes in comparison to insectivorous bats. Therefore, it is possible that frugivorous bats have a reduced need for Nrf2 function due to their substantial intake of diet-antioxidants. To test whether the Nrf2 gene has undergone relaxed evolution in fruit-eating bats, we obtained Nrf2 sequences from 16 species of bats, including four Old World fruit bats (Pteropodidae) and one New World fruit bat (Phyllostomidae). Our molecular evolutionary analyses revealed changes in the selection pressure acting on Nrf2 gene and identified seven specific amino acid substitutions that occurred on the ancestral lineage leading to Old World fruit bats. Biochemical experiments were conducted to examine Nrf2 in Old World fruit bats and showed that the amount of catalase, which is regulated by Nrf2, was significantly lower in the brain, heart and liver of Old World fruit bats despite higher levels of Nrf2 protein in Old World fruit bats. Computational predictions suggest that three of these seven amino acid replacements might be deleterious to Nrf2 function. Therefore, the results suggest that Nrf2 gene might have experienced relaxed constraint in Old World fruit bats, however, we cannot rule out the possibility of positive selection. Our study provides the first data on the molecular adaptation of Nrf2 gene in frugivorous bats in compensation to the increased levels of LWMAs from their fruit-diet.
Data from: Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles
Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.
FIGURE 3 in Spatiotemporal evolution of Reaumuria (Tamaricaceae) in Central Asia: insights from molecular biogeography
FIGURE 3. Reconstructions of ancestral areas performed with S-DIVA on the left, Lagrange on the right, for several nodes, and the most similar states (areas) with largest frequencies calculated by RASP, are illustrated on the right. Pie charts at the internal nodes represent the calculated probabilities (relative frequencies) of alternative ancestral area reconstructions. In the right figure, several dispersals are indicated by arrows on the branches. Node numbers (1~9) are in italics at the right of the node, the same as in Fig. 2. Area letters as stated in the text: A: Tianshan Mountains; B: Pamir-Alai mountains; C: eastern Central Asia; D: western Central Asia; E: Iran-Turkey; and F: Mediterranean. A detailed description is in the text.
FIGURE 2 in Spatiotemporal evolution of Reaumuria (Tamaricaceae) in Central Asia: insights from molecular biogeography
FIGURE 2. Phylogenetic tree and chronogram using BEAST Bayesian inference. Values at left of nodes on the tree are bootstrap support above, and posterior probability below. At the right of nodes are the estimated dating values and their 95% HPD from BEAST. Node numbers (1~9) are in italic at the right of nodes. The classification system derived from tree construction, including two sections and five series, is shown on the right of figure, and detailed in the Appendix.
FIGURE 1 in Spatiotemporal evolution of Reaumuria (Tamaricaceae) in Central Asia: insights from molecular biogeography
FIGURE 1. Distribution of Reaumuria, modified from Hao et al. (2013). Three species of series Kaschgaricae are detailed in Fig. 1c, six distribution areas, and westward and eastward idspersals conducted from biogeographical history reconstruction are illustrated in Fig. 1d.
FIGURE 4. For S in Spatiotemporal evolution of Reaumuria (Tamaricaceae) in Central Asia: insights from molecular biogeography
FIGURE 4. For S-DIVA results, the calculations of its biogeographical events including dispersal, vicariance and extinction, produced in RASP, are shown.
Molecular evolution of phototransduction pathway genes in nocturnal and diurnal fireflies (Coleoptera: Lampyridae)
<p>Most organisms are dependent on sensory cues from their environment for survival and reproduction. Fireflies (Coleoptera: Lampyridae) represent an ideal system for studying sensory niche adaptation due to many species relying on bioluminescent communication, as well as a diversity of ecology. Here we examine the phototransduction pathway in this non-model organism, and provide some of the first evidence for positive selection in the PT pathway in insects. Duplications are found in calmodulin, inactivation no afterpotential C, inactivation no afterpotential D, and transient receptor potential. We also find strong support for positive selection in arrestin-2, inactivation no afterpotential D, and transient receptor potential, with weak support for positive selection in guanine nucleotide-binding protein G(q) subunit alpha and neither inactivation nor afterpotential C. This represents an exciting new avenue of study as we seek to further understand these molecular players.</p>
Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks
<p>Temperature differences over time and space has been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning a large latitudinal gradient. The association between temperature (and other species traits) and long-term substitution rate was assessed based on 1268 sequenced exons of 44 species pairs from the Eugongylinae subfamily using regression analyses. Temperature is the strongest, positively-correlated predictor of variation in substitution rate across the Australian Eugongylinae. It explains 45% of variation in synonymous substitution rate, and 11% after controlling for all the other factors. Synonymous substitution rate is also negatively associated with body size, with 6% variation explained by body size after controlling for the effects of temperature. Other factors are not associated with synonymous substitution rate after controlling for temperature. Overall, this study points to temperature as a strong predictor of the molecular evolution rate in the Eugongylinae subfamily, and demonstrates the power of large-scale exonic data to identify correlates of the rate of molecular evolution.</p>
Figure 3 in A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanic Daphnia populations in the Alps
Figure 3. Map of the Alps showing European Daphnia pulicaria populations (1–12) and haplotypes (A1–A10) considered in this study. Different colours and patterns identify haplotypes found in more than one population or together with other haplotypes. See Table 1 for details of populations.
Figure 1 in A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanic Daphnia populations in the Alps
Figure 1. Map showing the distribution of European Daphnia pulicaria, including melanic populations specifically sampled in alpine lakes in the Western Italian Alps for this study. Within the enlarged box, the dashed grey line delimits river catchments where melanic populations were found (Orco and Dora di Savaranche). On the right, one melanic specimen from lake Nivolet. Abbreviations: GPNP, Gran Paradiso National Park. Abbreviations: SJM, Svalbard; RUS, Russia; ISL, Island; NOR, Norway; SWE, Sweden; GBR, Great Britain; DEU, Germany; POL, Poland; CZE, Czech Republic; CHE, Switzerland; ESP, Spain; HUN, Hungary; MNE, Montenegro; ALB, Albania; MKD, Macedonia; TRI, Trebecchi Inferiore; TRS, Trebecchi Superiore; NIV, Nivolet; LIL, Lillet.
Figure 1 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 1. Sampling localities of Mesocarabus specimens used in this study and identified by voucher number, as listed in Table 1. Colour code: brown, Carabus riffensis; red, Carabus macrocephalus; orange, Carabus macrocephalus barcelecoanus; purple, Carabus dufourii; yellow, Carabus lusitanicus; pink, Carabus lusitanicus baguenai; blue, Carabus problematicus; and green, Carabus problematicus, from Ochagavía.
Figure 5 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 5. Ultrametric time-calibrated tree for combined DNA markers (ALL-B data set) in Carabus. Numbers above nodes represent posterior probabilities. Grey bars on nodes represent the 95% confidence intervals for node ages (Myr), with mean ages indicated inside the bars. Labels A–D indicate the cladogenetic events for Mesocarabus and Iberian Oreocarabus referred to in the main text; labels G1 and G2 indicate nodes used as calibration priors. Specimen illustrated: Carabus (Mesocarabus) lusitanicus from Albacete, Spain.
Figure 4. Bayesian 50 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 4. Bayesian 50% majority rule consensus tree for the total evidence data set (ALL-B). Numbers besides nodes represent posterior probabilities and bootstrap values for maximum-likelihood and maximum-parsimony analyses, respectively. Labels A–D indicate the cladogenetic events for Mesocarabus and Iberian Oreocarabus referred to in the text. The species colour codes are as described in Figure 1. Voucher numbers are indicated in brackets. Vertical bars represent the main lineages, as proposed by Imura (1996) and Deuve (2004). Specimens illustrated: 1, Carabus (Mesocarabus) lusitanicus from Tarragona, Spain; 2, Carabus (Mesocarabus) macrocephalus from León, Spain; 3, Carabus (Mesocarabus) riffensis from El Biutz, Morocco; 4, Carabus (Oreocarabus) guadarramus from Madrid, Spain; 5, Carabus (Oreocarabus) amplipennis from León, Spain; 6, Carabus (Orinocarabus) concolor from Bex, Switzerland; 7, Carabus (Nesaeocarabus) abbreviatus from Tenerife, Spain; 8, Carabus (Eurycarabus) faminii from Rif Massif, Morocco.
Figure 2 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 2. Distribution map of some Carabus lineages within the Metacarabi in the western Palaearctic region.
Figure 3. Bayesian 50 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 3. Bayesian 50% majority rule consensus trees from (a) nuclear (NUC) and (b) mitochondrial (MIT) data sets. The numbers beside nodes represent posterior probabilities and bootstrap values for maximum-likelihood and maximumparsimony analyses, respectively. Labels A–D indicate cladogenetic events referred to in the text for Mesocarabus (in blue) and Iberian Oreocarabus (in red). Asterisks indicate incongruent nodes between MIT and NUC data sets. The species colour codes are as described in Figure 1. Voucher numbers are indicated in brackets. Specimens illustrated: 1, Carabus (Mesocarabus) lusitanicus from Salamanca, Spain; 2, Carabus (Oreocarabus) ghiliani from Segovia, Spain.
Figure 6 in Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA
Figure 6. Ultrametric time-calibrated tree for combined DNA markers (ALL-B data set) in Carabus showing ancestral area inferences (A, Iberian Peninsula; B, Eurasia; C, North Africa and Canary Islands). Pie charts represent the probability for each area reconstruction. The grey bars on nodes represent the 95% confidence intervals for node ages (Myr), with mean ages indicated inside bars. The palaeogeographic reconstructions are taken from Andeweg (2002).
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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.