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915 results for “morphological evolution”
Data set: Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes
<h1>Repository for "Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes"</h1> <p>---</p> <p>These data scripts were used to perform analyses included in the research paper "Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes" </p> <p>Main questions for the study:</p> <p>1. What are the main axes of morphological variation?<br>2. Does variation in morphology among species correlate with their current environments? <br>3. Are lineages that occupy ecologically similar habitats morphologically convergent? <br>4. Is speciation predominantly allopatric or sympatric? <br>5. Do sister species have greater morphological and ecological niche overlap than expected relative to non-sister species pairs?</p> <h2>## Data structure</h2> <p>Contents in the data folder is archived as a zip and can be downloaded from Zenodo (for all versions see https://zenodo.org/doi/10.5281/zenodo.10397830). Once you unzip the zipped files, you will see three folders and some files that are no in any folders. </p> <p>/data/ - files that were manually created and the phylogeny</p> <p>/data/script_generated_data/ - A combination of processed data needed to run the analyses </p> <p>/data/dorsal/ - photographs of the head from the dorsal view. These photos were used for digitising landmarks and semilandmarks. </p> <p>/data/worldclim2_30s/ - cropped and merged annual temperature from WorldClim2 (Fick and Hijmans 2017), soil bulk density from <a href="https://esoil.io/TERNLandscapes/Public/Pages/SLGA/GetData.html">Soil and Landscape Grid of Australia</a>, and Global Aridity Index from Zomer et al. (2022). <br><br>/DREaD/ - contains some files required to replicate DREaD analysis</p> <h2>## Code/Software</h2> <p>All scripts can be run using open source software. Scripts should be run in order to create necessary files that will be saved in /data/script_generated_data/ for further scripts. R is required to run R scripts (.R).</p> <h3>### /Code</h3> <p> - utility/*.R - scripts for custom functions. These are sourced in other scripts.<br> - DREaD/*.R - scripts associated with DREaD analyses<br> - 00_linear_measurement_shaperatio.R - script used to account for sexual dimorphism and calculate conventional PCA. Addresses Q1.<br> - 01_model_fitting.R - script used to address Q2 and plot visualisations.<br> - 02_convergence.R - this script calculates Ct1-4 and C5 scores. Addresses Q3.<br> - 02_convergence_model_fitting.R - this script evaluates fit of different evolutionary models to traits. Addresses Q3.<br> - 02_convergence_test_simulations.R - simulation studies to show that our phylogeny has sufficient power to detect convergence.<br> - 03_niche_enmtools_bias_account.R - calculates ecological niche models (ENMs) for each species using MAXENT. Runs Age-Overlap Correlation tests for geography and ENMs. Partially addresses Q4.<br> - 03_DREaD_Blindsnakes_AS.R - script to run DREaD analysis. <br> - 03_morpho_niche_overlap_plots.R - Runs Age-Overlap Correlation tests for body shape and snout shape. Plots AOCs. Partially addresses Q4. <br> - 04_pairwise_distance_test.R - Binomial tests between sister and non-sister pairs for ENMs and Geographic Range. Partially addresses Q5<br> - 04_morpho_pairwise.R - Binomial tests between sister and non-sister pairs for body shape and snout shape. Partially addresses Q5</p> <h2>## Contact</h2> <p>Should you have questions about these scripts or would like to request raw data, please do not hesitate to contact Sarin Tiatragul (contact information can be found in the paper) or on Github (https://github.com/stiatragul/blindsnakemorphoevo)</p> <h2>## References</h2> <p><a name="ref-fickWorldClim2017"></a>Fick, S. E., and R. J. Hijmans. 2017. <a href="https://doi.org/10.1002/joc.5086">WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas</a>. International Journal of Climatology 37:4302–4315.</p> <p><a name="ref-zomerVersion2022"></a>Zomer, R. J., J. Xu, and A. Trabucco. 2022. <a href="https://doi.org/10.1038/s41597-022-01493-1">Version 3 of the global aridity index and potential evapotranspiration database</a>. Scientific Data 9:409.</p>
Neogene–Quaternary uplift and landscape evolution in northern Greenland recorded by subglacial valley morphology: Datasets
<p>This dataset contains a csv file of subglacial valley morphology derived from radio-echo sounding datasets in northern Greenland, and an ESRI shapefile of the interpreted channel network. For further documentation of the data please view the README.txt file.</p> <p>RADAR-DERIVED VALLEY MORPHOLOGY</p> <ul> <li><strong>northern_Greenland_valley_morphology.csv</strong>: location and morphology of subglacial valleys in northern Greenland, as imaged by airborne radio-echo sounding datasets.</li> </ul> <p>SUBGLACIAL VALLEY NETWORK</p> <ul> <li><strong>northern_Greenland_valley_network.shp (and ancillary files: .cpg, .dbf, .prj, .qpj, .shx)</strong>: ESRI shapefile of the interpreted valley network in the northern Greenland subglacial drainage catchment.</li> </ul>
Morphological cladogenesis and terminal dwarfing in extinct Late Miocene through Pliocene menardiform globorotalids: New complementary data to «Evolutionary prospection in the Neogene planktic foraminifer Globorotalia menardii and related forms from ODP Hole 925B (Céara Rise, western tropical Atlantic): evidence for gradual evolution superimposed by long distance dispersal ?, Swiss J. Palaeontology, 135:205-248»
<p>A complementary morphometric data set is provided to the study of Knappertsbusch (2016) about the shell evolution of menardiform globorotalids (Neogene planktic foraminifera) at ODP Hole 925B from Céara Rise in the the western tropical Atlantic. The new measurements confirm splitting of extinct <em>Globorotalia multicamerata</em> from the <em>G. menardii</em> stock via the intermediate form <em>G. limbata</em> between about 6 Ma to 5 Ma ago. After splitting both <em>G. limbata</em> and <em>G. multicamerata</em> show gradual divergence from <em>G. menardii</em> in several shell parameters illustrating morphological cladogenesis. Between 2.88 Ma and 2.59 Ma the same parameters show a concerted trend towards reduced values indicating pre-extinction dwarfing. A comparison with published literature data of Delta<sup>18</sup>O trends between species, that populated the mixed layer (<em>Globigerinoides sacculifer</em>) and the thermocline layer (<em>Neogloboquadrina dutertrei</em>) at this location during those times suggests, that both divergence and subsequent dwarfing trends were probably the results of changes in upper watermass stratification.</p> <p>The complementary data set is provided in six zipped archives APPENDIX A, B, C, D, E and F (zipped with free software 7-Zip 22.00 (x64), 2022-06-15 from 1999-2022 Igor Pawlow), together with a description of the data in file Report_925B_suppl_1.pdf.</p>
Data for: Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies
<p>This repository contains a record of analysis scripts and sequence alignments used for the analyses presented in the manuscript.</p> <p>Some of the R scripts depend on supplementary tables associated with the manuscript.</p>
Novelty and emergent patterns in sperm: morphological diversity and evolution of spermatozoa and sperm conjugation in ground beetles (Coleoptera: Carabidae)
<p>The beetle family Carabidae, with about 40,000 species, exhibits enough diversity in sperm structure and behavior to be an excellent model system for studying patterns and processes of sperm evolution. We explore their potential, documenting<b> </b>sperm form in 177 species of ground beetles using light microscopy and collecting data on 1 qualitative and 7 quantitative sperm phenotypic traits. Our sampling captures 61% of the tribal-level diversity of ground beetles. These data highlight the notable morphological diversity of sperm in ground beetles and suggest that sperm in the group have dynamic evolutionary histories with much morphological innovation and convergence. Sperm vary among species in total length (48–3,400mm), head length (0.5–270mm), and head width (0.2–6.3mm). Most ground beetles make sperm with heads that are indistinct from the flagella at the gross morphological level. However, some or all <i>Omophron</i>,<i>Trachypachus</i>, and Dyschiriini make broad-headed sperm that show morphological differences between species. Most ground beetles package their sperm into groups of sperm, termed conjugates, and ground beetles show variation in conjugate form and in the number and arrangement of sperm in a conjugate. Most ground beetles make sperm conjugates by embedding their sperm in a hyaline rod or spermatostyle. The spermatostyle is remarkably variable among species and varies in length from 17–41,000mm. Several unrelated groups of ground beetles make only singleton sperm, including Nebriinae, Cicindelinae, many Trechinae, and the tribe Paussini. In order to study patterns in sperm evolution, we combine these data with a low-resolution phylogeny of ground beetles. Results from modern comparative analyses suggest the following: sperm differ from conjugates in some aspect of their underlying evolutionary process, sperm have influenced conjugate evolution and vice versa, and conjugation with a spermatostyle likely evolved early within the history of Carabidae and it has been lost independently at least three times.</p>
Supporting voucher images for Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales
<p>A compressed directory of images of voucher specimens used for sequencing and phylogenetic analysis.</p>
TEMNOS (Temnospondyl Evolution, Morphology, Nomenclature, and Other Stuff) v1.1.0
<p>This is the second release of the TEMNOS database, which contains three metadata files, four data files, an overarching README, a README for each data file, and a contributing document. Refer to the linked GitHub repository and associated preprint for additional details. Changes to this version:</p> <ul> <li>Minor bug fixes</li> <li>Updating all files based on recent literature (current as of 2025/08/02)</li> <li>Surveying previously unsampled clades for specimen listing (D2)</li> <li>Documentation updated</li> </ul>
FIG. 12 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 12. Optimizations of selected sesamoids that were apparently lost independently in at least two bat lineages; red indicates presence of the sesamoid in a taxon or clade, blue indicates absence, and gray indicates ambiguity. The topology corresponds to the tree shown in figure 3.
FIG. 10 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 10. Optimizations of selected sesamoids found to be present in just one terminal taxon; red indicates presence of the sesamoid in a taxon, blue indicates absence, and gray indicates ambiguity. The topology corresponds to the tree shown in figure 3.
FIG. 6 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 6. Selected sesamoids in the hind limb and tail of various extant species. A. Left joint between pelvic girdle and femur of Carollia perspicillata (dorsal view). B. Right knee of Eptesicus furinalis (tibial). C. Left knee of Tadarida brasiliensis (fibular). D. Left knee of Sturnira lilium (tibial).
FIG. 4 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 4. Selected sesamoids in the forelimb of various extant species. A. Left shoulder of Dasypterus ega (dorsal view). B. Left elbow of Molossops temminkii (dorsal). C. Left elbow of Tadarida brasiliensis (ventral). D. Right carpus of Eptesicus furinalis (dorsal).
FIG. 3 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 3. Phylogeny used in the optimization analysis of sesamoid characters follows relationships proposed by Simmons et al. (2008; extinct taxa indicated with a dagger) and Amador et al. (2018; extant taxa). Species represented in our dataset exclusively by data from autopodial sesamoids compiled from prior studies are indicated with an asterisk (*).
FIG. 2 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 2. Eocene bat fossils: Icaronycteris index YPM-PU 18150 showing some of the preserved sesamoids, highlighted with red lines. A. Left elbow (dorsal view). B. Left carpus (dorsal). C. Right tarsus (ventral-preaxial). D. Left knee (fibular). E. Right foot (ventral). F. Sequence of caudal vertebrae (dorsal).
FIG. 7 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 7. Selected sesamoids in the hind limb and tail of various extant species. A. Right tarsus of Dasypterus ega (dorsal). B. Right autopodium of Artibeus planirostris (dorsal). C. Right autopodium of Eptesicus furinalis (ventral). D. Caudal vertebrae of E. furinalis (dorsal).
FIG. 1 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 1. Eocene bat fossils: Onychonycteris finneyi AMNH 142467 showing some of the preserved sesamoids, highlighted with red lines. A. Left elbow (dorsal view). B. Left carpus (ventral-preaxial). C. Left knee (tibial). D. Right foot (dorsal).
FIG. 13 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 13. Comparison between the elbow of bats (A, left elbow of Dasypterus ega; B, left elbow of Molossops temminkii) and humans (C, D, modified from Mittal et al., 2014), including either an olecranon (A, C) or an ulnar patella (B, D). The possible homology between the ulnar patella in bats and the anomalous "patella cubiti" in humans is shown.
FIG. 5 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 5. Selected sesamoids in the forelimb of various extant species. A. Right carpus of Tadarida brasiliensis (ventral). B. Right carpus of Eptesicus furinalis (ventral). C. Metacarpo-phalangeal joint of wing digits II, III, and V of E. furinalis (ventral). D. Interphalangeal joints of wing digits III (lateral) and I (dorsolateral) of Artibeus planirostris.
FIG. 8 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 8. Optimizations of selected sesamoids that characterize particular clades and which may represent synapomorphies; red indicates presence of the sesamoid in a taxon or clade, blue indicates absence, and gray indicates ambiguity. The topology corresponds to the tree shown in figure 3.
FIG. 9 in Morphology and Evolution of Sesamoid Elements in Bats (Mammalia: Chiroptera)
FIG. 9. Optimizations of selected sesamoids interpreted in this study as probable plesiomorphic features of crown Chiroptera; red indicates presence of the sesamoid, and gray indicates ambiguity. The topology corresponds to the tree shown in figure 3.
Fig. 2 in What Morphology and Molecules Tell Us about the Evolution of Oligotrichea (Alveolata, Ciliophora)
Fig. 2. Maximum Likelihood tree of the Oligotrichida inferred from small subunit ribosomal RNA (SSU rRNA) gene sequences (66 taxa and 1823 nucleotide positions) aligned with the Muscle algorithm (Edgar 2004) implemented in MEGA ver. 5.1 (Tamura et al. 2011). The alignment is available upon request. The tree was computed with RAxML (Stamatakis et al. 2008) and the datasets were bootstrap re-sampled 100 times. Support values are listed at the nodes. The second values at the nodes represent the posterior probability values of a Bayesian Inference analysis performed with MrBayes (Ronquist and Huelsenbeck 2003). Values below 50% and 0.5, respectively, are represented by a dash. * – initially published as Spirostrombidium sp.; ** – initially published as Parallelostrombidium sp.
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