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Junco hyemalis Bone Microstructure

Cite this dataset

Louis, Leeann; Bowie, Rauri; Dudley, Robert (2021). Junco hyemalis Bone Microstructure [Dataset]. Dryad.


Migration is the primary strategy that temperate birds use to avoid overwintering under harsh conditions. As a consequence, migratory birds have evolved specific morphological features in their wings and skeleton. However, in addition to varying in overall shape and size, bone can also change at the microstructural level by, for example, increasing its thickness. Such changes are critical to preventing fracture and damage under repeated loading (fatigue), yet it is not known whether migratory behaviour influences bone microstructure. To address this gap in the literature, we performed micro-computed tomography on skeletons of resident and migrant subspecies of the Dark-eyed Junco Junco hyemalis. We investigated the differences in the major wing bone, the humerus, and the major leg bone, the femur. In each bone, we studied the microarchitecture of the two types of bone tissue: cortical bone, the thick outer layer of bone; and trabecular bone, which is the porous network of bone tissue at the ends of long bones. We used linear models to quantify morphological features with respect to body mass and migratory behaviour. Humeri from migratory birds were thinner, wider, and had higher overall geometric stiffness, that is, a higher polar moment of inertia, relative to humeri from resident birds. These features may help keep their bones stiff to maintain their increased body mass during migration. In contrast, migrant femora were shorter, thinner, and had lower geometric stiffness than femora of residents, potentially to reduce total body mass. Tissue mineral density was lower in in both the humerus and femur of migratory birds. In addition, migratory subspecies had less trabecular bone (lower bone volume fraction) due primarily to a loss in trabecular thickness. Migratory behaviour may thus select for improved stiffness and fatigue resistance in the wing bones and reduced mass of leg bones. Our work demonstrates how important insights about morphological adaptation can be obtained by investigating bone microstructure.  


Specimen data (specimen name, date collected, altitude, etc.) were recorded during collection and obtained by querying the AMNH ornithological collections database. Length was measured during the "scout-view" preview scan for each bone. Micro-computed tomography data were collected for each bone using a high-resolution micro-computed tomography scanner (μCT 35, Scanco Medical, Brüttisellen, Switzerland) operated at an X-ray energy of 70 kVP, an integration time of 300 ms, and a spatial resolution of 6 μm isotropic voxel size. To assess morphological features, regions of interest were first defined using semi-automated region-drawing scripts, and then a threshold of 540 mg cm-3 was applied to differentiate bone from air. Finally, an automatic script (IPL, Scanco Medical, Brüttisellen, Switzerland) employing distance transformation methods was used to measure various morphological features (trabecular number, cortical thickness, etc.).

Usage notes

General notes:

  • All specimens are included twice in the spreadsheet: once for data on the humerus, and once for data on the femur.
  • There are some missing values for elevation of collection (11 out of 87 specimens).

Full definitions for all data fields:

  • Museum: Institution from which the specimen was loaned. Here it is always the American Museum of Natural History (AMNH) in New York, NY, US
  • SpecNum: Specimen number of the skeleteon in the museum
  • Name: Full species name of the specimen (Genus species subspecies)
  • Subspp: Subspecies name
  • Sex: Specimen sex
  • Location: Details on where the specimen was collected
  • Elev: Altitude (in m) at which the specimen was collected, if available.
  • Date: Month, day, and year at which the specimen was collected
  • Day: Julian date: the integer day of the year where 1 corresponds to January 1st and 365 corresponds to December 31st (in a non-leap year)
  • Mass: Weight at collection in grams
  • Side: Right or left wing / leg from which the bone was taken
  • Bone: Femur or humerus
  • CtDOI: DOI number for cortical computed tomography data available at MorphoSource (
  • TbDOI: DOI number for trabecular computed tomography data available at MorphoSource (
  • Length: Bone length in mm, taken during the scout-view
  • TbBV: Trabecular bone volume (mm^3): Volume of mineralized trabecular bone tissue within the total volume analyzed
  • BVTV: Trabecular bone volume fraction (%): Ratio of trabecular bone divided by the total volume of tissue analyzed
  • ConnDens: Connectivity density (mm^-3): The degree of connectivity between trabecular, normalized by the total volume assessed
  • SMI: Structure model index (SMI): Trabecular structure assessed from 0 to 3, where 0 is plate-like and 3 is rod-like
  • TbN: Trabecular number (mm^-1): Average number of trabeculae per unit length. Calculated as the inverse of the mean distance between the mid-axes of the trabeculae
  • TbTh: Trabecular thickness (mm): Average thickness of a trabecula. Determined by fitting a sphere to the trabecula and averaging the diameter of the sphere for all trabeculae
  • TbSp: Trabecular separation (mm): Average distance between trabeculae. Found using the same process as trabecular thickness but spheres are fit to the empty space rather than the trabeculae
  • CtAr: Cortical bone area (mm^2): Average cross-sectional area within the tissue that is mineralized bone
  • TAr: Tissue area (mm^2): Cross-sectional area within the outer edge of the diaphysis (e.g. the whole bone cross section), including both mineralized bone and interior bone marrow. Averaged across all cross-sections in the analyzed volume
  • MaAr: Marrow area (mm^2): Average cross-sectional area of marrow tissue, equal to T.Ar – Bn.Ar
  • CtArTAr: Cortical bone area fraction (%): Fraction of total tissue area occupied by mineralized bone
  • CtTh: Cortical thickness (mm): Thickness of the cortical bone averaged across all cross-sections
  • J: Polar area moment of inertia (mm^4) Geometric resistance of the cortical bone to twisting. For a hollow cylinder, this is , J = π(D4 – d4)/32, where D is the outer diameter of the circle, and d is the inner diameter
  • CtTMD: Cortical tissue mineral density (mg cm^-3): Average amount of mineralized tissue within a volume of cortical bone, calculated from the grayscale value and converted to a physical density using a calibration phantom. This includes small (5 μm) pores containing cells and their dendrites, but not larger pores containing blood vessels


National Science Foundation, Award: NSF DGE 1752814

National Science Foundation, Award: NSF DGE 1106400

National Science Foundation Graduate Education and Research Traineeship, Award: NSF DGE 0903711

American Society of Bone and Mineral Research 2018 Adele L. Boskey Young Investigator Award

American Ornithologists' Union/American Ornithological Society

University of California (UC) Berkeley Museum of Vertebrate Zoology Karl Koford Fund

University of California, Berkeley Museum of Vertebrate Zoology Wihelm Martens Fund

University of California, Berkeley Museum of Vertebrate Zoology Karl Koford Fund

University of California, Berkeley Museum of Vertebrate Zoology Karl Koford Fund

University of California, Berkeley Museum of Vertebrate Zoology Albert Preston Hendrickson Fund

University of California, Berkeley Museum of Vertebrate Zoology David and Marvalee Wake Fund

University of California, Berkeley Department of Integrative Biology Graduate Research Funds

Berkeley Chapter of Sigma Xi Grants in Aid of Research