skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Fast mvSLOUCH: Model comparison for multivariate Ornstein--Uhlenbeck-based models of trait evolution on large phylogenies
These are the Supplementary Material, R scripts and numerical results accompanying Bartoszek, Fuentes Gonzalez, Mitov, Pienaar, Piwczyński, Puchałka, Spalik and Voje "Model Selection Performance in Phylogenetic Comparative Methods under multivariate Ornstein–Uhlenbeck Models of Trait Evolution". The four data files concern two datasets. Ungulates: measurements of muzzle width, unworn lower third molar crown height, unworn lower third molar crown width and feeding style and their phylogeny; Ferula: measurements of ratio of canals, periderm thickness, wing area, wing thickness,  and fruit mass, and their phylogeny.  more » « less
Award ID(s):
2225683
PAR ID:
10487317
Author(s) / Creator(s):
; ; ; ; ; ; ;
Publisher / Repository:
Dryad
Date Published:
Subject(s) / Keyword(s):
FOS: Natural sciences model selection model selection adaptation model selection multivariate Ornstein-Uhlenbeck process multivariate phylogenetic comparative methods adaptation model selection multivariate Ornstein-Uhlenbeck process multivariate phylogenetic comparative methods Biological Scaling Feeding styles Food comminution food selectivity hypsodonty Mammalia Oral morphology Ungulata
Format(s):
Medium: X Size: 24120 bytes
Size(s):
24120 bytes
Sponsoring Org:
National Science Foundation
More Like this
  1. ‘Small-bodied faunivore’ is the dominant ancestral ecomorphotype early in crown mammalian radiations, but it is unknown how far back this trend extends within Synapsida (the mammalian total group). To examine synapsid macroevolutionary patterns in a phylogenetic context, we built a time-calibrated meta-phylogeny of 2,128 synapsid species from the Carboniferous through Eocene (305–34 Ma), based on 211 published character matrices, each weighted according to their dependence on ‘parent’ matrices. All published character matrices focusing on non-mammalian synapsids were included, making the meta-phylogeny comprehensive for non-mammaliaform synapsids. Further, we used the most comprehensive early mammaliaform matrices. We then collected jaw length measurements (as a proxy for body size) and dietary information for 408 synapsid species (37 non-therapsid pelycosaurs, 134 non-cynodont therapsids, 46 non-mammaliaform cynodonts, 80 non-therian mammaliaforms, and 178 therians). We used the meta-phylogeny in conjunction with jaw length measurements to investigate patterns of body-size and dietary evolution during radiations of synapsid subclades. The results show that faunivory is the typical ancestral diet of each major radiation within Synapsida, but the small-to-large trend in body-size within radiations does not become established until the end-Triassic size bottleneck near the base of Mammaliaformes. Instead, ‘pelycosaur’, ‘therapsid’, and ‘cynodont’ subclades have ancestral jaw lengths that are considerably larger than non-therian mammaliaforms and therians. The shift to small ancestral body sizes is one of several aspects of the mammalian phenotype to emerge in the Late Triassic. Furthermore, by placing ‘mammaliaforms’ and mammals near their likely lower size limit, this change forced most subsequent body-size diversification to consist of trends toward larger sizes, altering macroevolutionary dynamics for the remainder of synapsid history. 
    more » « less
  2. Abstract Trees can differ enormously in their crown architectural traits, such as the scaling relationships between tree height, crown width and stem diameter. Yet despite the importance of crown architecture in shaping the structure and function of terrestrial ecosystems, we lack a complete picture of what drives this incredible diversity in crown shapes. Using data from 374,888 globally distributed trees, we explore how climate, disturbance, competition, functional traits, and evolutionary history constrain the height and crown width scaling relationships of 1914 tree species. We find that variation in height–diameter scaling relationships is primarily controlled by water availability and light competition. Conversely, crown width is predominantly shaped by exposure to wind and fire, while also covarying with functional traits related to mechanical stability and photosynthesis. Additionally, we identify several plant lineages with highly distinctive stem and crown forms, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legume trees in African savannas. Our study charts the global spectrum of tree crown architecture and pinpoints the processes that shape the 3D structure of woody ecosystems. 
    more » « less
  3. With most ungulates absent from Africa until the Miocene, the morphologically diverse hyraxes were a major component of the Eocene-Oligocene community at Quarry L-41 (~34 Ma) in the Fayum Depression, Egypt. However, their foraging strategies are poorly understood. This study focuses on four extinct hyraxes: Thyrohyrax meyeri, Thyrohyrax litholagus, and Megalohyrax eocaneus, all expected to be grazers; and Saghatherium bowni, previously described as a browser. Mesowear can place extinct herbivores on a spectrum from grazer to browser based on the abrasiveness oftheir lifetime diets. Crown height, tooth length, and cusp angle were measured for the first lower molars (M1) in these four hyrax species. Specimens were categorized into Wear Classes (WC), which correspond with developmental age. WC ranged from 1, first adult molar fully erupted, to 8, all molars extremely worn with significant dentin exposure. Change in mean crown height and cusp angle across different wear classes was not significantly different. Nonetheless, apparent trends suggest compositional differences in diet. Change in mean crown height for Saghertherium indicates that it incorporated more graze than browse because M1 wear occurred in earlier WCs and increased throughout life. In contrast, less wear for WC 1 through 4 in Thyrohyrax indicates that it incorporated more browse. This agrees with recently collected carbon isotope data, which suggests that Saghatherium’s diet included more graze than Thyrohyrax’s. These data are consistent with the description ofThyrohyrax as an arboreal browser. The change in mean crown height for Megalohyrax also suggests a less abrasive diet, although sample size for Megalohyrax was smaller. The browse-biased diet for Megalohyrax is surprising, as isotope values suggest a more open environment. Browsing in salt-stressed environments, forest canopies or forest edges could explain these combined data. Megalohyrax could have foraged in a wider variety of environments than the other taxa because its larger size enabled a wider range. By reconstructing the diets and niche partitioning among morphologically diverse hyraxes at L-41, we hope to gain insights about the ecosystem represented by L-41 near the Eocene-Oligocene Boundary (EOB). This locality represents a time of ecological dynamism when many mammalian communities were dramatically restructured, though the impact of the EOB on African mammal communities remains poorly understood. 
    more » « less
  4. {"Abstract":["Abstract<\/strong><\/p>\n\nThe NeonTreeCrowns dataset is a set of individual level crown estimates for 100 million trees at 37 geographic sites across the United States surveyed by the National Ecological Observation Network\u2019s Airborne Observation Platform. Each rectangular bounding box crown prediction includes height, crown area, and spatial location. <\/p>\n\nHow can I see the data?<\/strong><\/p>\n\nA web server to look through predictions is available through idtrees.org<\/p>\n\nDataset Organization<\/strong><\/p>\n\nThe shapefiles.zip contains 11,000 shapefiles, each corresponding to a 1km^2 RGB tile from NEON (ID: DP3.30010.001). For example "2019_SOAP_4_302000_4100000_image.shp" are the predictions from "2019_SOAP_4_302000_4100000_image.tif" available from the NEON data portal: https://data.neonscience.org/data-products/explore?search=camera. NEON's file convention refers to the year of data collection (2019), the four letter site code (SOAP), the sampling event (4), and the utm coordinate of the top left corner (302000_4100000). For NEON site abbreviations and utm zones see https://www.neonscience.org/field-sites/field-sites-map. <\/p>\n\nThe predictions are also available as a single csv for each file. All available tiles for that site and year are combined into one large site. These data are not projected, but contain the utm coordinates for each bounding box (left, bottom, right, top). For both file types the following fields are available:<\/p>\n\nHeight: The crown height measured in meters. Crown height is defined as the 99th quartile of all canopy height pixels from a LiDAR height model (ID: DP3.30015.001)<\/p>\n\nArea: The crown area in m2<\/sup> of the rectangular bounding box.<\/p>\n\nLabel: All data in this release are "Tree".<\/p>\n\nScore: The confidence score from the DeepForest deep learning algorithm. The score ranges from 0 (low confidence) to 1 (high confidence)<\/p>\n\nHow were predictions made?<\/strong><\/p>\n\nThe DeepForest algorithm is available as a python package: https://deepforest.readthedocs.io/. Predictions were overlaid on the LiDAR-derived canopy height model. Predictions with heights less than 3m were removed.<\/p>\n\nHow were predictions validated?<\/strong><\/p>\n\nPlease see<\/p>\n\nWeinstein, B. G., Marconi, S., Bohlman, S. A., Zare, A., & White, E. P. (2020). Cross-site learning in deep learning RGB tree crown detection. Ecological Informatics<\/em>, 56<\/em>, 101061.<\/p>\n\nWeinstein, B., Marconi, S., Aubry-Kientz, M., Vincent, G., Senyondo, H., & White, E. (2020). DeepForest: A Python package for RGB deep learning tree crown delineation. bioRxiv<\/em>.<\/p>\n\nWeinstein, Ben G., et al. "Individual tree-crown detection in RGB imagery using semi-supervised deep learning neural networks." Remote Sensing<\/em> 11.11 (2019): 1309.<\/p>\n\nWere any sites removed?<\/strong><\/p>\n\nSeveral sites were removed due to poor NEON data quality. GRSM and PUUM both had lower quality RGB data that made them unsuitable for prediction. NEON surveys are updated annually and we expect future flights to correct these errors. We removed the GUIL puerto rico site due to its very steep topography and poor sunangle during data collection. The DeepForest algorithm responded poorly to predicting crowns in intensely shaded areas where there was very little sun penetration. We are happy to make these data are available upon request.<\/p>\n\n# Contact<\/p>\n\nWe welcome questions, ideas and general inquiries. The data can be used for many applications and we look forward to hearing from you. Contact ben.weinstein@weecology.org. <\/p>"],"Other":["Gordon and Betty Moore Foundation: GBMF4563"]} 
    more » « less