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37 results for “Evolutionary Mapping”
RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" in Journal of Evolutionary Biology
<p>This a data set from the paper RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" to be published in Journal of Evolutionary Biology</p>
Text-fig. 1. Locality map and Keshin Formation section at Cape Tsvetkov, East Taimyr (after Kazakov et al. 2002). 1 – tuff conglomerate, 2 – sandstone, 3 – grained siltstone, 4 – siltstone, 5 – mudstone, 6 – foraminifers, 7 – conchostracans, 8 – plant megafossils, 9 – locality of described plants, 10 – Tsvetkov Cape (East Taimyr). in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 1. Locality map and Keshin Formation section at Cape Tsvetkov, East Taimyr (after Kazakov et al. 2002). 1 – tuff conglomerate, 2 – sandstone, 3 – grained siltstone, 4 – siltstone, 5 – mudstone, 6 – foraminifers, 7 – conchostracans, 8 – plant megafossils, 9 – locality of described plants, 10 – Tsvetkov Cape (East Taimyr).
Data for "Rapid mapping of alloy surface phase diagrams via Bayesian evolutionary multitasking"
<p>For the ORR study, the final datasets of the DFT-relaxed adsorbate-alloy configurations for the Pd-Ag(111) surface are stored in <strong>ads_PdAg_111_dft.db. </strong>For the SMR study, the final datasets of the DFT-relaxed adsorbate-alloy configurations for the Pt-Ni(111), (100) and (311) surfaces are stored in <strong>ads_PtNi_111_dft.db</strong>, <strong>ads_PtNi_100_dft.db</strong> and <strong>ads_PtNi_311_dft.db</strong>, respectively.</p> <p>The 76,265 tasks (combining 15,253 SMR conditions with 5 exploration parameters) used for the BEM runs in the SMR study can be found in <strong>bem_smr_tasks.csv</strong>.</p> <p>All the input files and scripts for BEM high-throughput screening (for both ORR and SMR studies), DFT calculations, EMT benchmarks, SGCMC simulations, structure generation and plotting (e.g. surface free energy diagrams and 2D phase diagrams) are all provided in <strong>inputs_and_scripts.zip</strong>.</p>
A comprehensive map of evolutionary constraints across the enterovirus A genome
Open the record for dataset details and reuse information.
Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models
<p>Modern phylogenetic comparative methods allow estimating evolutionary rates of phenotypic change, how these rates differ across clades, and assessing whether the rate remained constant over time. Unfortunately, currently available phylogenetic comparative tools express the rate in terms of a scalar dimension, hence they do not allow us to determine rate variations among different parts of a single, complex phenotype, or charting of realized rate variation directly onto the phenotype. Herein, we present a new method which allows the mapping of evolutionary rate variation directly on three-dimensional phenotypes, informing on the direction and magnitude of trait change automatically.</p> <p>This new method, implemented by the function rate.map embedded in the R package 'RRphylo', is based on phylogenetic ridge regression rate estimates. Since the latter represent ridge regression slopes, they possess sign and magnitude. In 'RRphylo', different rates are calculated for different districts of the phenotype, which can then be visualized directly onto the phenotype itself. We present the application of rate.map to the evolution of facial skeleton in Hominoidea (the clade including living and fossil apes), the primate clade inclusive of Homo and the greater apes. We found that the highly derived, unique shape of the face in modern humans evolved through rapid phenotypic changes affecting the nasal bones, the brow ridge and the maxillary region. The canine fossa, a facial feature unique to Homo sapiens, did not belong to a region of rapid phenotypic change, and could be seen as the by-product of midface evolution as suggested by previous studies.</p>
Evolutionary Map of the Universe (EMU): discovering 18-cm OH maser sources in ASKAP continuum images of the SCORPIO field
<p>Data cubes and spectra from the ATCA C3414 project.</p> <p>Data cubes are in fits format.</p> <p>Spectra were extracted from the data cubes following what described in the text. The format is the standard output of the CASA profile tools. Each spectrum contains an header with the column description.</p>
Backward Population Synthesis: Mapping the Evolutionary History of Gravitational-Wave Progenitors dataset
<p>Dataset release accompanying Backward Population Synthesis: Mapping the Evolutionary History of Gravitational-Wave Progenitors.</p> <p>Note that A22_02_rerun.hdf, A22_5_rerun.hdf, A22_rerun.hdf, KW_rerun.h5 are not directly used in generating the plots in the paper.</p>
Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models
Open the record for dataset details and reuse information.
"The evolutionary history of Neandertal and Denisovan Y chromosomes" - hg20 mapping of the capture data
<p>This archive contains the alignments of all individuals captured with the 6.9 Mb array mapped to GRCh38/hg20. See the project's GitHub repository for more information: <a href="https://www.github.com/bodkan/archaic-ychr">https://www.github.com/bodkan/archaic-ychr</a>.</p>
Map 11 in The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines
Map 11. Distribution map of Dissonulichen (Dissonulichen) simplicipes simplicipes and D. (D.) simplicipes meridionalis in Colombia and Ecuador.
Data from: A comment on the use of stochastic character maps to estimate evolutionary rate variation in a continuously valued trait
Phylogenetic comparative biology has progressed considerably in recent years. One of the most important developments has been the application of likelihood-based methods to fit alternative models for trait evolution in a phylogenetic tree with branch lengths proportional to time. An important example of this type of method is O'Meara et al.'s (2006) "noncensored" test for variation in the evolutionary rate for a continuously valued character trait through time or across the branches of a phylogenetic tree. According to this method, we first hypothesize evolutionary rate regimes on the tree (called "painting" in Butler and King, 2004); and then we fit an evolutionary model, specifically the popular Brownian model, in which the instantaneous variance of the Brownian random diffusion process has different values in different parts of the phylogeny. The authors suggest that to test a hypothesis that the state of a discrete character influenced the rate of a continuous character, one could use the approach of Neilsen (2002) to first stochastically map the discretely valued trait, and then "test to see whether the portions of the tree with one state for the discrete character have a different rate of evolution for the continuous character than portions of the tree to which the other discrete state has been mapped" (O'Meara et al., 2006, p. 931). Indeed, this has become common practice for this and other closely related methods. Here, I examine this practice. In particular, I show that evolutionary rates estimated this way (i.e., by using maximum likelihood [ML] to fit a multirate model on each stochastically mapped tree; and then averaging across trees) are systematically biased to be more similar to each other than are the underlying generating parameters. My analysis also reveals that this effect is dependent on the rate of evolution for the discrete trait. Specifically, if the rate of evolution for the discrete character is low then the difference between the true history and any stochastically mapped 1 history is generally small. This results in evolutionary rates for the continuous trait that are estimated with little bias. Conversely, if the rate of evolution for the discrete character is very high, then the true and hypothesized character histories are often extremely dissimilar, evolutionary rate estimates are biased to be more similar to each other than their underlying generating values, and we lose power to distinguish evolutionary rates on the tree.
Data from: Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible Onagraceae lineages
A major goal of evolutionary biology is to identify key evolutionary transitions that correspond with shifts in speciation and extinction rates. Stochastic character mapping has become the primary method used to infer the timing, nature, and number of character state transitions along the branches of a phylogeny. The method is widely employed for standard substitution models of character evolution. However, current approaches cannot be used for models that specifically test the association of character state transitions with shifts in diversification rates such as state-dependent speciation and extinction (SSE) models. Here we introduce a new stochastic character mapping algorithm that overcomes these limitations, and apply it to study mating system evolution over a time-calibrated phylogeny of the plant family Onagraceae. Utilizing a hidden state SSE model we tested the association of the loss of self-incompatibility with shifts in diversification rates. Confirming long standing theory, we found that self-compatible lineages have higher extinction rates and lower net diversification rates compared to self-incompatible lineages. Furthermore, these results provide empirical evidence for the "senescing" diversification rates predicted in highly selfing lineages: our mapped character histories show that the loss of self-incompatibility is followed by a short-term spike in speciation rates, which declines after a time lag of several million years resulting in negative net diversification. Lineages that have long been self-compatible such as Fuchsia and Clarkia are in a previously unrecognized and ongoing evolutionary decline. Our results demonstrate that stochastic character mapping of SSE models is a powerful tool for examining the timing and nature of both character state transitions and shifts in diversification rates over the phylogeny.
Map 13 in The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines
Map 13. Distribution map of Paraphidnia species.
Map 15 in The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines
Map 15. Distribution map of Anaphidna species in South America.
Map 12 in The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines
Map 12. Distribution map of Dissonulichospinus n. gen. species.
Map 18 in The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines
Map 18. Distribution map of Lichenomorphus species in Southeast Brazil and Argentina.
Map 14 in The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines
Map 14. Distribution map of Anaphidna species in Central America.
Map 16 in The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines
Map 16. Distribution map of Dysonia species.
Map 19 in The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines
Map 19. Distribution map of Lichenodentix dentatithorax.
Map 17 in The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines
Map 17. Distribution map of Lichenomorphus species.
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