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13 results for “Historical source”
Source Code Accompanying the Paper "More on network approaches in Historical Chinese Phonology (音韻學)"
<p>First version of the source code and data accompanying the paper "More on Network Approaches in Historical Chinese Phonology".</p> <p>This paper is available here:</p> <ul> <li>List, Johann-Mattis (2018): <strong>More on network approaches in Historical Chinese Phonology (音韻學)</strong>. Paper prepared for the <em>LFK Society Young Scholars Symposium</em>. Taibei: Li Fang-Kuei Society ofr Chinese Linguistics. URL: <a href="https://hal.archives-ouvertes.fr/hal-01706927">https://hal.archives-ouvertes.fr/hal-01706927</a>.</li> </ul> <pre><code>@InProceedings{List2018a, author = {List, Johann-Mattis}, title = {{More on Network Approaches in Historical Chinese Phonology (音韻學)}}, booktitle = {{LFK Society Young Scholars Symposium}}, year = {2018}, publisher = {Li Fang-Kuei Society for Chinese Linguistics}, pdf = {https://hal.archives-ouvertes.fr/hal-01706927/file/main.pdf}, url = {https://hal.archives-ouvertes.fr/hal-01706927}, address = {Taipei}, hal_id = {hal-01706927}, } </code></pre> <p>See the README.md for mor information.</p> <ul> <li> </li> </ul>
Confronting sources of systematic error to resolve historically contentious relationships: a case study using gadiform fishes (Teleostei, Paracanthopterygii, Gadiformes)
<p>Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large datasets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically important fishes in the world (e.g., Cods, Hakes, and Rattails). Despite many attempts, a robust higher-level phylogenetic framework was lacking due to limited character and taxonomic sampling, particularly from several species-poor families that have been recalcitrant to phylogenetic placement. We compiled the first phylogenomic dataset, including <span>14,208 loci (>2.8 M bp) from 58 species representing all recognized gadiform families, to infer a time-calibrated phylogeny for the group. </span>Data were generated with a gene-capture approach targeting coding DNA sequences from single-copy protein-coding genes. Species-tree and concatenated maximum-likelihood analyses resolved all family-level relationships within Gadiformes. While there were a few differences between topologies produced by the DNA and the amino acid datasets, most of the historically unresolved relationships among gadiform lineages were consistently well resolved with high support in our analyses regardless of the methodological and biological approaches used. However, at deeper levels, we observed inconsistency in branch support estimates between bootstrap and gene and site coefficient factors (gCF, sCF). Despite numerous short internodes, all relationships received unequivocal bootstrap support while gCF and sCF had very little support, reflecting hidden conflict across loci. Most of the gene-tree and species-tree discordance in our study is a result of short divergence times, and consequent lack of informative characters at deep levels, rather than incomplete lineage sorting (ILS). We use this phylogeny to establish a new<span> higher-level classification of Gadiformes as a way of clarifying the evolutionary diversification of the order.</span> We recognize 17 families in five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei, and Macrouroidei (including two subclades). A time-calibrated analysis using 15 fossil taxa suggests that Gadiformes evolved ~79.5 million years ago (Ma) in the late Cretaceous, but that most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass extinction (66 Ma)<span>. </span>Our results reiterate the importance of examining phylogenomic analyses for evidence of systematic error that can emerge as a result of unsuitable modeling of biological factors and/or methodological issues, even when datasets are large and yield high support for phylogenetic relationships.</p>
Metal(loid)s in urban soil from historical municipal solid waste landfill: Geochemistry, source apportionment, bioaccessibility testing and human health risks - Supplementary data
<p>This is a supplementary dataset to the paper:</p> <p>Hiller E., Faragó T., Kolesár M., Filová L., Mihaljevič M., Jurovič L., Demko R., Mchlica A., Štefánek J., Vítková M. (2024): Metal(loid)s in urban soil from historical municipal solid waste landfill: Geochemistry, source apportionment, bioaccessibility and human health risks. <em>Chemosphere</em> <strong>362</strong>, 142677. DOI: 10.1016/j.chemosphere.2024.142677</p> <p>This research was supported by the Johannes Amos Comenius Programme (OP JAC), project No. CZ.02.01.01/00/22_008/0004605, Natural and anthropogenic georisks. The dataset is published under the Creative Commons Attribution 4.0 International License (CC-BY-4.0). This license allows others to distribute, remix, adapt, and build upon the dataset for any purpose, even commercially, as long as they give appropriate credit to the original creator(s).</p>
Data from: Estimating potential global sources and secondary spread of freshwater invasions under historical and future climates
<p>Aim: We employ a climate-matching method to evaluate potential source regions of freshwater invasive species to an introduced region and their potential secondary spread under historical and future climates.</p> <p>Location: Global source regions, with primary introductions to the Laurentian Great Lakes and secondary introductions throughout North America</p> <p>Methods: We conducted a climate-match analysis using the CLIMATE algorithm to estimate global source freshwater ecoregions under historical and future climates with an ensemble of general circulation models for climate change scenario SSP5-8.5. Given existing research, we use a climate match of ≥ 71.7% between ecoregions to indicate climatic conditions that will not inhibit the survival of introduced freshwater organisms. Further, we estimate the secondary spread of freshwater invaders to the ecoregions of North America under historical and future climates.</p> <p>Results: We identified 54 global freshwater ecoregions with a climate match ≥ 71.7% to the recipient Laurentian Great Lakes under historical climatic conditions and 11 additional ecoregions were predicted to exceed the threshold under climate change. Three of the 11 ecoregions were located in South America, a continent where no matches existed under historical climates and eight were located in the southern United States, southern Europe, Japan, and New Zealand. Further, we identify 34 North American ecoregions of potential secondary spread of freshwater invasions from the Great Lakes under historical climatic conditions, and five ecoregions were predicted to exceed the threshold under climate change.</p> <p>Main conclusion: We provide a climate-match method that can be employed to assess the sources and spread of freshwater invasions under historical and future climate scenarios. Our climate-match method predicted increases in climate match between the recipient region and several potential source regions, and changes in areas of potential spread under climate change. The identified ecoregions are candidates for detailed biosecurity risk assessments and related management actions. The identified ecoregions are candidates for detailed biosecurity risk assessments and related management actions.</p>
Confronting sources of systematic error to resolve historically contentious relationships: a case study using gadiform fishes (Teleostei, Paracanthopterygii, Gadiformes)
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Data from: Estimating potential global sources and secondary spread of freshwater invasions under historical and future climates
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Historical biogeography and character-mapping of Hiptage (Malpighiaceae) corroborate Indochina's rainforests as one of the main sources of plant diversity in Southeastern Asia
<p>In Malpighiaceae,<b> </b><i>Hiptage</i> represents one of the seven past dispersal events from the Neotropics to the Paleotropical region, being by far the most widely diversified and distributed genus of Paleotropical Malpighiaceae. In this study, we tested the monophyly of the current infrageneric classification of <i>Hiptage</i> with a dated and calibrated molecular phylogeny. We also reconstructed ancestral areas to elucidate which route led to the colonization of Southeast Asia by the most recent common ancestor (MRCA) of this genus (Mainland or Indian routes). The pre-existing infrageneric classification of <i>Hiptage</i> was recovered as non-monophyletic due to being solely based on homoplasic morphological characters, such as the presence and number of sepal nectar glands. Regarding its biogeography, the MRCA of <i>Hiptage</i> arose in the rainforests of southeast Asia ca. 24.0 Mya and greatly diversified in this region. Few lineages have dispersed eastward to the pacific islands or westwards to India. Based on our results, we hypothesize that the MRCA of <i>Hiptage</i> did not take the Indian route to reach Southeastern Asia. Instead, it reached this region by past mainland forest connections between North America-Europe (Boreotropical hypothesis) and southeast Asia. Nonetheless, distribution ranges for the species of <i>Hiptage</i> must be carefully revised, and the five species of <i>Hiptage</i> endemic to India must also be sampled so we can properly test which route led the MRCA of <i>Hiptage</i> to reach Southeast Asia in the early Miocene.</p>
Historic version of the Environments - EOL project: updated source files from partner
The version we had been using is "eol_env_annotations_noParentTerms.tar.gz"
Historical biogeography and character-mapping of Hiptage (Malpighiaceae) corroborate Indochina's rainforests as one of the main sources of plant diversity in Southeastern Asia
Open the record for dataset details and reuse information.
Supplementary material 1 from: Miyazaki Y, Murase A (2019) Fish rubbings, 'gyotaku', as a source of historical biodiversity data. ZooKeys 904: 89-101. https://doi.org/10.3897/zookeys.904.47721
: Data type: species data
Figure 2 from: Miyazaki Y, Murase A (2019) Fish rubbings, 'gyotaku', as a source of historical biodiversity data. ZooKeys 904: 89-101. https://doi.org/10.3897/zookeys.904.47721
Figure 2 Three species targeted in leisure fishing and listed as threatened species in the Japanese national Red List. AHucho perryi (Brevoort, 1856) from a shop in Hokkaido BSillago parvisquamis Gill, 1861 from a shop facing Tokyo Bay CLates japonicus Katayama & Taki, 1984 from a shop in Miyazaki Prefecture.
Figure 3 from: Miyazaki Y, Murase A (2019) Fish rubbings, 'gyotaku', as a source of historical biodiversity data. ZooKeys 904: 89-101. https://doi.org/10.3897/zookeys.904.47721
Figure 3 The number of 'gyotaku' rubbings stocked at the 16 fishing shops targeted by the present study based on the year of creation. The bold and dotted lines indicate the estimation and the 95% CI (upper and lower limits) based on the statistical analysis using a state space model.
Figure 1 from: Miyazaki Y, Murase A (2019) Fish rubbings, 'gyotaku', as a source of historical biodiversity data. ZooKeys 904: 89-101. https://doi.org/10.3897/zookeys.904.47721
Figure 1 An explanation of fish rubbing ('gyotaku', in Japanese). A 1st step – the fish specimen is painted using ink B 2nd step – the specimen is covered with a sheet of paper C the finished image of the fish specimen on the paper. This is known as the direct method of 'gyotaku'; there is also an indirect method whereby a sheet of paper is placed on the fish specimen, then the sheet is painted by hand using ink. See also Hiyama (1964a, b) and Shimizu (1972, 1975).
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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