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Data for paper on the evolution of Chinese characters
<p>This dataset contains all image, complexity and distinctiveness data that was used for:</p> <p>Han, S. J, Kelly, P., Winters, J., & Kemp, C. (2022). Simplification is not dominant in the evolution of Chinese characters. <em>Open Mind</em>.</p> <p>The code for this project can be found <a href="https://github.com/cskemp/chinesecharacters">here</a>. The file uploaded here is intended to replace the sample data folder that is available in the code repository.</p> <p>Our dataset includes data scraped from hanziyuan.net, as well as data from the following sources:</p> <p>Sun, C. C., Hendrix, P., Ma, J., & Baayen, R. H. (2018). Chinese lexical database (CLD): A large-scale lexical database for simplified Mandarin Chinese. Behavior Research Methods, 50(6), 2606–2629.</p> <p>Wikimedia Commons. (2021). Chinese characters decomposition. <a href="https://commons.wikimedia.org/wiki/Commons:Chinese_characters_decomposition">https://commons.wikimedia.org/wiki/Commons:Chinese_characters_decomposition</a></p> <p>Liu, C.-L., Yin, F., Wang, D.-H., & Wang, Q.-F. (2011). CASIA online and offline Chinese handwriting databases. In 2011 international conference on document analysis and recognition (pp. 37–41). <a href="https://doi.org/10.1109/ICDAR.2011.17">https://doi.org/10.1109/ICDAR.2011.17</a></p> <p>Chen, P.-C. (2020). Traditional Chinese handwriting dataset. GitHub. <a href="https://github.com/AI-FREE-Team/Traditional-Chinese-Handwriting-Dataset">https://github.com/AI-FREE-Team/Traditional-Chinese-Handwriting-Dataset</a></p>
Fig. 7. Vertebral character trait evolution across phocoenids and related delphinoids. A. Character 2, thoracic vertebral counts. B. Character 8 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises
Fig. 7. Vertebral character trait evolution across phocoenids and related delphinoids. A. Character 2, thoracic vertebral counts. B. Character 8, ratio of centrum length/centrum height of lumbar vertebrae. C. Character 12, height of neural spine. D. Character 14, regional anterior inclination of neural arches. See Table 2 for detailed character descriptions.
Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character's evolution: R scripts and simulated trees
<p>All R scripts used in this study, and the set of simulated phylogenetic trees used in the study.</p> <p>1. Modern methods of ancestral state estimation (ASE) incorporate branch length information, and it has been demonstrated that ASEs are more accurate when conducted on the branch lengths most correlated with a character's evolution; however, a reliable method for choosing between alternate branch length sets for discrete characters has not yet been proposed.<br><br>2. In this study, we simulate paired chronograms and phylograms, and generate binary characters that evolve in correlation with one of these. We then investigate (1) the effect of alternate branch lengths on ASE error, and (2) whether phylogenetic signal statistics and/or model-fit statistic can be used to select the branch lengths most correlated with a binary character.<br><br>3. In agreement with previous studies, we find that ASEs are more accurate when conducted on the branch lengths most correlated with the character. Phylogenetic signal statistics show limited utility for selecting the correct branch lengths, but model-fit statistics are found to be more accurate, with the correct branch lengths generally returning greater model-fit (lower AICc and BIC values). Using this method to choose between alternate branch length sets is more accurate when tree and character properties are more favorable for model optimization, and when shape differences between alternate phylogenies are greater.<br><br>4. Our results indicate that researchers conducting ASEs on discrete characters should carefully consider which branch lengths are appropriate, and, in the absence of other evidence, we suggest estimating model-fit values over alternate branch length sets and evolutionary models and choosing the branch length/model combination that returns better model fit.</p>
Data from: Stochastic character mapping, Bayesian model selection, and biosynthetic pathways shed new light on the evolution of habitat preference in cyanobacteria
<p>Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis paving the way for complex life. Studying the evolution and ecological niche of cyanobacteria and their ancestors is crucial for understanding the intricate dynamics of biosphere evolution. These organisms frequently deal with environmental stressors such as salinity and drought, and they employ compatible solutes as a mechanism to cope with these challenges. Compatible solutes are small molecules that help maintain cellular osmotic balance in high-salinity environments, such as marine waters. Their production plays a crucial role in salt tolerance, which, in turn, influences habitat preference. Among the five known compatible solutes produced by cyanobacteria (sucrose, trehalose, glucosylglycerol, glucosylglycerate, and glycine betaine), their synthesis varies between individual strains. In this study, we work in a Bayesian stochastic mapping framework, integrating multiple sources of information about compatible solute biosynthesis in order to predict the ancestral habitat preference of Cyanobacteria. Through extensive model selection analyses and statistical tests for correlation, we identify glucosylglycerol and glucosylglycerate as the most significantly correlated with habitat preference, while trehalose exhibits the weakest correlation. Additionally, glucosylglycerol, glucosylglycerate, and glycine betaine show high loss/gain rate ratios, indicating their potential role in adaptability, while sucrose and trehalose are less likely to be lost due to their additional cellular functions. Contrary to previous findings, our analyses predict that the last common ancestor of Cyanobacteria (living at around 3180 Ma) had a 97% probability of a high salinity habitat preference and was likely able to synthesize glucosylglycerol and glucosylglycerate. Nevertheless, cyanobacteria likely colonized low-salinity environments shortly after their origin, with an 89% probability of the first cyanobacterium with low-salinity habitat preference arising prior to the Great Oxygenation Event (2460 Ma). Stochastic mapping analyses provide evidence of cyanobacteria inhabiting early marine habitats, aiding in the interpretation of the geological record. Our age estimate of ~2590 Ma for the divergence of two major cyanobacterial clades (Macro- and Microcyanobacteria) suggests that these were likely significant contributors to primary productivity in marine habitats in the lead-up to the Great Oxygenation Event, and thus played a pivotal role in triggering the sudden increase in atmospheric oxygen.</p>
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales.
Phylogeny and floral character evolution of Mentzelia section Bicuspidaria (Loasaceae)
<p><i>Mentzelia</i> section <i>Bicuspidaria</i> (Loasaceae) is a monophyletic group of desert ephemerals that inhabit the complex, heterogeneous landscapes of the southwestern United States and northwestern Mexico. To investigate species circumscriptions and evolutionary relationships in <i>Bicuspidaria</i>, we employed phylogeny reconstructions based on DNA sequences from the plastid <i>trnL-trnF</i>, <i>trnS-trnfM</i>, <i>ndhF-rpl32</i>, and <i>rpl32-trnL</i> regions and the nuclear ribosomal ITS and ETS regions. Due to evidence of discordant relationships reconstructed from the plastid and nuclear partitions, we used coalescent-based methods in addition to concatenated data sets to estimate the species tree. Maximum likelihood reconstructions based on the combined plastid and nuclear data and coalescent-based reconstructions inferred congruent, fully-resolved species-level phylogenies of section <i>Bicuspidaria</i>. A monophyletic section <i>Bicuspidaria</i> was composed of two main clades, which corresponded to a clade of species endemic to the United States composed of <i>M. reflexa</i>, <i>M. tricuspis</i>,<i> </i>and <i>M. tridentata</i> that was sister to a clade of species at least partially distributed in Mexico, composed of <i>M. hirsutissima</i> and <i>M. involucrata</i>. Despite the unusual floral morphology of <i>M. reflexa</i>, molecular reconstructions placed <i>M. reflexa</i> sister to <i>M. tridentata</i>. All species of <i>Bicuspidaria</i> were monophyletic, except for <i>M. hirsutissima</i>, which was composed of two distinct lineages and paraphyletic with respect to <i>M. involucrata</i>. The northern clade of <i>M. hirsutissima</i> from California and Baja California was sister to <i>M. involucrata</i>, and both, in turn, were sister to a geographically disjunct southern clade of <i>M. hirsutissima</i> from Baja California Sur and Cedros Island. These phylogeny reconstructions provide evidence for the inclusion of five species in section <i>Bicuspidaria</i> and have uncovered cryptic diversity that has been largely unrecognized. Character state reconstructions based on the phylogeny of section <i>Bicuspidaria</i> suggest innovative and, at times, homoplasious floral evolution.</p>
Figs. 9–14 in Cranial Anatomy in Tenrecid Insectivorans: Character Evolution Across Competing Phylogenies
Figs. 9–14. Coronal sections through middle ear of tenrecid genera, as follows. 9. Potamogale velox (ZIUT HL17 mm), anterior to jugular foramen, slice 43.3.4. 10. Potamogale velox (ZIUT HL 17 mm), posterior to anterior carotid foramen, slice 37.2.5. 11. Micropotamogale lamottei (IZEA 939), anterior to jugular foramen, slice 181.2.2. 12. Micropotamogale lamottei (IZEA 939), posterior to anterior carotid foramen, slice 177.2.1. 13. Geogale aurita (MCZ 45504), anterior to jugular foramen, slice 105.3.1. 14. Geogale aurita (MCZ 45504), anterior to anterior carotid foramen, slice 96.1.2.
Fig. 39 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 39. Cladogram of phylogenetic relationships within Mammaliaformes based on analyses by Rougier et al. (1996a) and Hu et al. (1997).
Fig. 38 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 38. Cladogram of phylogenetic relationships within Multituberculata (a), based on the analysis in Rougier et al. (1997), with an enlargement of the tree section containing Kryptobaatar and its nearest relatives, all of which are Mongolian Late Cretaceous taxa with the exception of Pentacosmodon from the North American Paleocene (b). A similar Mongolian Late Cretaceous grouping was called Djadochtatheria by KielanJaworowska and Hurum (1997). In their phylogeny, Kryptobaatar is in a clade Djadochtatheriidae, with Djadochtatherium, Catopsbaatar, and Tombaatar.
Fig. 35 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 35. Reconstruction of the skull of Kryptobaatar dashzevegi in posterior view. Abbreviations bo basioccipital; exoc exoccipital; fr frontal; lac lacrimal; man mandible; pa parietal; pet petrosal; sq squamosal; sup supraoccipital.
Fig. 36 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 36. Reconstruction of the skull of Kryptobaatar dashzevegi in left lateral view (A) with the major cranial arteries (white outline) and veins (black) added (B). Zygomatic arch is cut to show vessels in the floor of the orbit. Vessels in shadow pass through intramural canals, with the exception of the part of the ramus superior immediately rostral to the dorsalmost ramus temporalis branch which is endocranial. Abbreviations: adm arteria diploëtica magna (and accompanying vein); ea ethmoidal artery (and accompanying vein); ef ethmoidal foramen; fbu foramen buccinatorium; fdac foramen of dorsal ascending canal; fdv foramen for frontal diploic vein; fma foramen masticatorium; frt foramen for ramus temporalis; ioa infraorbital artery (and accompanying vein); iof infraorbital foramen; lhv lateral head vein; mef metoptic foramen (which transmitted pituitoorbital vein); oa ophthalmic artery; oca occipital artery (and accompanying vein); ompf orbital opening of minor palatine foramen; opf optic foramen; otc orbitotemporal canal; psa proximal stapedial artery; ptc posttemporal canal; ptv posttrigeminal vein; ri ramus inferior; rio ramus infraorbitalis (and accompanying vein); rm ramus mandibularis (and accompanying vein); rs ramus superior (and accompanying vein); rso ramus supraorbitalis (and accompanying vein); rt ramus temporalis (and accompanying vein); sgf supraglenoid foramen; son supraorbital notch; spa sphenopalatine artery (and accompanying vein); spf sphenopalatine foramen sphf sphenorbital fissure; tc transverse canal; tcv transverse canal vein.
Fig. 32 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 32. Reconstruction of the skull of Kryptobaatar dashzevegi in dorsal view. Abbreviations: al anterior lamina; exoc exoccipital; fr frontal; ju jugal; lac lacrimal; mx maxilla; na nasal; pa parietal pmx premaxilla; sq squamosal; sup supraoccipital.
Fig. 34 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 34. Reconstruction of the skull of Kryptobaatar dashzevegi in ventral view. Abbreviations: al anterior lamina; ali alisphenoid; bo basioccipital; bs basisphenoid; exoc exoccipital; fr frontal; mx maxilla; pal palatine; pet petrosal; pmx premaxilla; pt pterygoid; sq squamosal; vo vomer.
Fig. 37 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 37. Reconstruction of the right basicranium of Kryptobaatar dashzevegi in ventral view (A) with the major cranial arteries (white outline) and veins (black) added (B). Abbreviations: adm arteria diploëtica magna (and accompanying vein); ali alisphenoid; aptca artery of pterygoid canal; cp crista parotica; ctpp caudal tympanic process of petrosal; er epitympanic recess; fma foramen masticatorium; foi foramen ovale inferium; fv fenestra vestibuli; gica groove for internal carotid artery; gl glenoid fossa; gpsa groove for proximal stapedial artery; ica internal carotid artery; jf jugular fossa; jfo jugular foramen; lhv lateral head vein; lpt lateral pterygopalatine trough;
Fig. 31 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 31. Reconstruction of the skull of Kryptobaatar dashzevegi in anterior view. Abbreviations: fr frontal; lac lacrimal; man mandible; mx maxilla; na nasal; pmx premaxilla; sq squamosal.
Fig. 27 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 27. Reconstruction of the floor of the endocranium of Kryptobaatar dashzevegi. Parallel lines represent the cut edge of the braincase. Abbreviations: al anterior lamina; bo basioccipital; ce cavum epiptericum; ds dorsum sellae; exoc exoccipital; fica foramen for internal carotid artery; fpv foramen for pituitoorbital vein; fr frontal; hf hypophyseal fossa; iam internal acoustic meatus; jfo jugular foramen; jsp jugum sphenoidale; mef metoptic foramen; ocon occipital condyle; opf optic foramen; or orbitosphenoid; pa parietal; pan pila antotica; pet petrosal; pm pila metoptica; pop postorbital process prc prootic canal; sf subarcuate fossa; son supraorbital notch; sphf sphenorbital fissure; sq squamosal sup supraoccipital.
Fig. 29 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 29. Stereophotograph of the left lower jaw of Kryptobaatar dashzevegi PSSMAE 113 in lateral view.
Fig. 25 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 25. Stereophotograph of the floor of the endocranium of Kryptobaatar dashzevegi PSSMAE 123 in dorsal (A) and oblique dorsal (B) views, with accompanying line drawings. Gray pattern represents matrix; parallel lines denote breakage. Abbreviations: al anterior lamina; bo basioccipital; ce cavum epiptericum; ds dorsum sellae; exoc exoccipital; ff facial foramen; fica foramen for internal carotid artery; fpv foramen for pituitoorbital vein; fr frontal; fV3 foramen for mandibular nerve; hf hypophyseal fossa; iam internal acoustic meatus; jn jugular notch; jsp jugum sphenoidale; mef metoptic foramen mx maxilla; na nasal; opf optic foramen; or orbitosphenoid; ow orbital wing (pila preoptica); pan pila antotica; prc prootic canal; pm pila metoptica; sf subarcuate fossa; sphf sphenorbital fissure; tus tuberculum sellae.
Fig. 24 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 24. Schematic drawings of embryonic chondrocrania in left lateral view. A, generalized sauropsid; B, generalized multituberculate, as reconstructed from here; C, generalized monotreme D, generalized marsupial; E, generalized placental. Abbreviations: ais anterior intercavernous sinus; cev capsuloparietal emissary vein; ea ethmoidal artery; en ethmoidal nerve; ev ethmoidal vein; ips inferior petrosal sinus; nc nasal capsule oa ophthalmic artery; oc otic capsule; pan pila antotica; pis posterior intercavernous sinus; pm pila metoptica; pp pila preoptica; ps prootic sinus pv pituitoorbital vein; II optic nerve; III oculomotor nerve; IV trochlear nerve; V trigeminal nerve; VI abducens nerve, VII facial nerve.
Fig. 23 in Cranial Anatomy Of Kryptobaatar Dashzevegi (Mammalia, Multituberculata), And Its Bearing On The Evolution Of Mammalian Characters
Fig. 23. Pencil drawing of the left zygomatic arch of Kryptobaatar dashzevegi PSSMAE 113 in dorsal view, with accompanying line drawing. Abbreviations: fr frontal; ju jugal; lac lacrimal; mx maxilla; pa parietal; sq squamosal; tr temporal ridge.
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