Leaf geometric morphometric analyses of Callicarpa and Geunsia (Lamiaceae) in the Malesian region

Danila JS, Alejandro GJD. 2021. Leaf geometric morphometric analyses of Callicarpa and Geunsia (Lamiaceae) in the Malesian region. Biodiversitas 22: 4379-4390. Leaves are one of the most substantial organs of plants for it serves as a basis of species identification. Leaf morphology provides distinguishing features that help in the discrimination of plant species as well as investigation of leaf features among populations. This study aimed to investigate leaf shape variations between the two genera Geunsia Blume group and its closely related taxon, Callicarpa L. (Lamiaceae) using a landmark-based geometric morphometric method. The differences in the leaf shape among former members of Geunsia, namely C. apoensis, C. basilanensis, C. flavida, C. paloensis, C. pentandra, C. ramiflora, and C. surigaensis are also evaluated. Two primary landmarks and 14 semilandmarks were assigned in all samples to represent changes around the leaf margin. The Procrustes fit was generated using MorphoJ software which displays the mean and landmark position for individual configurations. Canonical Variate Analysis (CVA) and Mahalanobis Distance (MD) were able to discriminate all samples of Geunsia species using a scatter plot. Furthermore, Procrustes ANOVA showed a significant difference (P = 0.0082) among the seven species of the Geunsia group. Based on the results obtained, geometric morphometrics of leaf shape is effective in interspecific discrimination within members of Geunsia. However, the result of Discriminant Analysis (DA) showed that Geunsia and Callicarpa groups made leaf shape differences inefficient in discriminating the two genera. Therefore, further morphological studies on landmark-based geometric morphometrics of leaf shape involving a larger number of samples especially in the study of intergeneric classification are suggested.

MeshMonk: Open-source large-scale intensive 3D phenotyping

In the post-genomics era, an emphasis has been placed on disentangling ‘genotype-phenotype’ connections so that the biological basis of complex phenotypes can be understood. However, our ability to efficiently and comprehensively characterize phenotypes lags behind our ability to characterize genomes. Here, we report a toolbox for fast and reproducible high-throughput dense phenotyping of 3D images. Given a target image, a rigid registration is first used to orient a template to the target surface, then the template is transformed further to fit the specific shape of the target using a non-rigid transformation model. As validation, we used N = 41 3D facial images registered with MeshMonk and manually landmarked at 19 locations. We demonstrate that the MeshMonk registration is accurate, with 0.62 mm as the average root mean squared error between the manual and automatic placements and no variation in landmark position or centroid size significantly attributable to landmarking method used. Though validated using 19 landmarks for comparison with traditional methods, MeshMonk allows for automatic dense phenotyping, thus facilitating more comprehensive investigations of 3D shape variation. This expansion opens up an exciting avenue of study in assessing genomic and phenomic data to better understand the genetic contributions to complex morphological traits.

Kinematic Analysis of a Six-Degrees-of-Freedom Model Based on ISB Recommendation: A Repeatability Analysis and Comparison with Conventional Gait Model

Objective. The purpose of the present work was to assess the validity of a six-degrees-of-freedom gait analysis model based on the ISB recommendation on definitions of joint coordinate systems (ISB 6DOF) through a quantitative comparison with the Helen Hays model (HH) and repeatability assessment.Methods. Four healthy subjects were analysed with both marker sets: an HH marker set and four marker clusters in ISB 6DOF. A navigated pointer was used to indicate the anatomical landmark position in the cluster reference system according to the ISB recommendation. Three gait cycles were selected from the data collected simultaneously for the two marker sets.Results. Two protocols showed good intertrial repeatability, which apart from pelvic rotation did not exceed 2°. The greatest differences between protocols were observed in the transverse plane as well as for knee angles. Knee internal/external rotation revealed the lowest subject-to-subject and interprotocol repeatability and inconsistent patterns for both protocols. Knee range of movement in transverse plane was overestimated for the HH set (the mean is 34°), which could indicate the cross-talk effect.Conclusions. The ISB 6DOF anatomically based protocol enabled full 3D kinematic description of joints according to the current standard with clinically acceptable intertrial repeatability and minimal equipment requirements.