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182 results for “Combined analyses”
FIGURE 3 in Apios chendezhaoana (Fabaceae), an overlooked species and a new combination from China: evidence from morphological and molecular analyses
FIGURE 3. Apios chendezhaoana. (A) Habit; (B) Flowering branch; (C) Flower; (D) Standard; (E) Wings; (F) Keel; (G) Flower with petals removed; (H) Stamens; (I) Calyx; (J) Stipule; (K) Fruiting branch; (L) Tuber; (M) Young fruit; (N) Stigma. Photographed by Fan Zhang.
FIGURE 1. The 50 in Apios chendezhaoana (Fabaceae), an overlooked species and a new combination from China: evidence from morphological and molecular analyses
FIGURE 1. The 50% majority rule consensus tree resulting from Bayesian analysis of the combination of ITS and matK. Numbers near the nodes are posterior probabilities and bootstrap percentage (PP, BP) from Bayesian analysis and Maximum likelihood, respectively. A dash (--) indicates a node is inconsistent between the topology of the BI and ML trees. The new combination (species) in this study is shown in bold type.
FIGURE 2 in Iris tibetica, a new combination in I. ser. Lacteae (Iridaceae) from China: evidence from morphological and chloroplast DNA analyses
FIGURE 2. Median-joining network based on combined sequences of four cpDNA regions, depicting the relationships among haplotypes of 136 individuals from 59 localities across the geographic range of Iris ser. Lacteae. Each white circle represents a haplotype and the size of the circle is proportional to the number of individuals with that haplotype. Haplotype codes correspond to those in Table 1. Black dots indicate missing haplotypes (extinct or not sampled). Haplotypes of A, B, and C haplogroups are encircled with thin lines.
FIGURE 4 in Iris tibetica, a new combination in I. ser. Lacteae (Iridaceae) from China: evidence from morphological and chloroplast DNA analyses
FIGURE 4. Phylogenetic analysis of Iris ser. Lacteae based on psbA–trnH/rps4–trnS/trnS–trnG/trnL–trnF sequences. Neighbour-joining tree is shown with bootstrap values in 1000 replicates for NJ/MP/ML analyses (shown only when> 50%) above the branches and Bayesian posterior probabilities more than PP = 0.90 below the branches. Clades I and II within I. ser. Lacteae are indicated. Haplotypes and locality codes are given in Table 1.
FIGURE 1 in Iris tibetica, a new combination in I. ser. Lacteae (Iridaceae) from China: evidence from morphological and chloroplast DNA analyses
FIGURE 1. Map showing the locations of Iris ser. Lacteae samples analyzed in the present study (created with http://www. spatialepidemiology.net). The locality codes are given in Table 1.
FIGURE 3 in Iris tibetica, a new combination in I. ser. Lacteae (Iridaceae) from China: evidence from morphological and chloroplast DNA analyses
FIGURE 3. Genetic clustering of Iris ser. Lacteae haplotypes from 136 individuals inferred with the program BAPS. Each vertical column corresponds to one haplotype, and black vertical lines separate haplotypes from the different localities. Locality codes are given in Table 1. Different colours represent the different genetic cluster (blue-cluster 1, red-cluster 2, green-cluster 3). (a) Mixture clustering results revealing three clusters with a posterior marginal probability of 0.80; (b) Bar plot from the admixture results. The vertical bars are split into several colours when there is evidence for the admixture (P <0.05). Localities are ordered according to latitude, from south to north.
Data from: Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene flow populations
We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites (FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (Dest_Chao, R2 = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R2 = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low FST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site.
Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards
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Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species
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Data from: Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species
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Data from: Combining stable isotopes, morphological, and molecular analyses to reconstruct the diet of free-ranging consumers
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Data from: Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene flow populations
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Data from: Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM).
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Tensor image enhancement and optimal multichannel receiver combination analyses for human hyperpolarized 13C MRSI
<p>Repository of an anonymized sample patient dataset for paper "Tensor image enhancement and optimal multichannel receiver combination analyses for human hyperpolarized 13C MRSI"</p> <p>https://doi.org/10.1002/mrm.28328.</p>
Data from: Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data
Proportional and separate models able to apply different combination of substitution rate matrix and among-site rate variation model to each locus are frequently used in phylogenetic studies of multilocus data. However, the selection from among nonpartitioned (i.e., a common combination of models is applied to all-loci concatenated sequences), proportional, and separate models is usually based on the researcher's preference rather than on any information criteria. The present study describes two programs, "Kakusan4" (for DNA sequences) and "Aminosan" (for amino-acid sequences), that allow the selection of evolutionary models based on several types of information criteria. The programs can handle both multilocus and single-locus data, in addition to providing an easy-to-use wizard interface and a non-interactive command line interface. In the case of multilocus data, substitution rate matrices and among-site rate variation models are compared at each locus and at all-loci concatenated sequences, after which nonpartitioned, proportional, and separate models are compared based on information criteria. The programs also provide model configuration files for MrBayes, PAUP*, PHYML, RAxML, and Treefinder to support further phylogenetic analysis using a selected model. The best-fit models were found to differ depending on the data set. Furthermore, differences in the information criteria among nonpartitioned, proportional, and separate models were much larger than those among the nonpartitioned models. These findings suggest that selecting from nonpartitioned, proportional, and separate models results in a better phylogenetic tree. Kakusan4 and Aminosan are available at http://www.fifthdimension.jp/. They are licensed under GNU GPL Ver.2, and are able to run on Windows, MacOS X, and Linux.
Data from: PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic timeframes, and so permit the objective selection of partitioning schemes even for large multi-locus DNA datasets. We demonstrate that these methods significantly outperform previous approaches, including the ad hoc selection of partitioning schemes (e.g. partitioning by gene or codon position), and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g. the BIC, AIC, and AICc). We hope that PartitionFinder will encourage the objective selection of partitioning schemes, and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from .
Data from: More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera)
A central question concerning data collection strategy for molecular phylogenies has been, is it better to increase the number of characters or the number of taxa sampled to improve the robustness of a phylogeny estimate? A recent simulation study concluded that increasing the number of taxa sampled is preferable to increasing the number of nucleotide characters, if taxa are chosen specifically to break up long branches. We explore this hypothesis by using empirical data from noctuoid moths, one of the largest superfamilies of insects. Separate studies of two nuclear genes, elongation factor-1α (EF-1α) and dopa decarboxylase (DDC), have yielded similar gene trees and high concordance with morphological groupings for 49 exemplar species. However, support levels were quite low for nodes deeper than the subfamily level. We tested the effects on phylogenetic signal of (1) increasing the taxon sampling by nearly 60%, to 77 species, and (2) combining data from the two genes in a single analysis. Surprisingly, the increased taxon sampling, although designed to break up long branches, generated greater disagreement between the two gene data sets and decreased support levels for deeper nodes. We appear to have inadvertently introduced new long branches, and breaking these up may require a yet larger taxon sample. Sampling additional characters (combining data) greatly increased the phylogenetic signal. To contrast the potential effect of combining data from independent genes with collection of the same total number of characters from a single gene, we simulated the latter by bootstrap augmentation of the single-gene data sets. Support levels for combined data were at least as high as those for the bootstrap-augmented data set for DDC and were much higher than those for the augmented EF-1α data set. This supports the view that in obtaining additional sequence data to solve a refractory systematic problem, it is prudent to take them from an independent gene.
Fits and plot data for the paper: "Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants"
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Raw data for "Accuracy in cement hydration investigations: combined X-ray microtomography and powder diffraction analyses" paper
<p>Raw data for "Accuracy in cement hydration investigations: combined X-ray microtomography and powder diffraction analyses" paper, including:</p> <p>- TG-DTA</p> <p>- X-ray diffraction data.</p> <p>- micro-CT data.</p>
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OpenNeuro
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