Browsing by Subject "Morphometrics"
Item Computer Vision Methods to Characterize the Morphology of Mouse Skulls for Neuroscience Applications(2023-02) Gulner, BeatriceComputer vision is a powerful tool for automating the characterization of biological specimen morphology. Classical morphometric studies have provided crucial insights into the skull anatomy of commonly used wildtype (WT) laboratory mice strains such as the C57BL/6. With the increasing use of transgenic (TG) animals in neuroscience research, it is important to determine whether the results from morphometric studies performed on WT strains can be extended to TG strains derived from these WT strains. In this thesis, we first report a new computer vision-based analysis pipeline for surveying mouse skull morphology using Microcomputed Tomography (µCT) scans. We applied this pipeline to study and compare eight cohorts of adult mice from two strains, including both male and female mice at two age points. We found that the overall skull morphology was generally conserved between cohorts, with only 13% of landmark distance differences reaching statistical significance. In addition, we surveyed the dorsal skull bone thickness differences between cohorts. We observed significantly thicker dorsal, parietal, and/or interparietal bones in WT, male, or older mice for 53% of thickness comparisons. Many neuroscience experiments require penetrating the mouse skull to record or modulate neural activity in the brain. Craniotomy procedures on sub-millimeter thick skull tissue are time-consuming to perform manually and require substantial training to attain an acceptable success rate. Previous researchers have used automation to reduce the training needed, increase speed, and minimize variability, but insufficient knowledge of the dorsal skull thickness limits their performance. We thus present a fast, non-invasive method which employs preoperative Optical Coherence Tomography (OCT) imaging to guide a robot to perform single-pass craniotomies in mice. The mouse skull is scanned with an OCT scanner immediately prior to surgery, then a custom computer vision-based analysis pipeline extracts an approximately 10 µm axial by 20 µm lateral resolution 3D profile of the dorsal and ventral surfaces of the mouse calvaria within the Field of View (FOV). A cutting path is generated based on the depth of the ventral surface along the desired craniotomy path. Comparison with µCT skull thickness data and preliminary surgery results indicates that this method provides an acceptable profile across most of the mouse dorsal skull, though more iteration is required to ensure accurate measurement of the area around the lambdoid sinus.Item Molecules & morphology reveal ‘new’ divergent, widespread Lampsiline species (Bivalvia: Unionidae)(2018-06) Keogh, SeanThe recognition of biodiversity in imperiled groups of organisms is fundamental to their conservation. In the Family Unionidae, the greatest radiation of freshwater mussels, species descriptions have been misled by extreme intraspecific shell variation and conversely interspecific conchological stasis. Lampsilis teres (Rafinesque, 1820) a polymorphic, widespread species has historically been split into as many as three subspecies that correlate to phenotypic variants. Recently, one subspecies was elevated to species level based on unique morphology and molecular differences. However, other subspecies designations are no longer recognized and no study has investigated these phenotypes with molecular characters. In this study I characterize the morphology of two phenotypes of L. teres using geometric and traditional morphometrics and use molecular phylogenetics to test the hypothesis that phenotypes represent separate species. Results from my molecular analyses unanimously indicate that L. teres as it is currently recognized is made up of two divergent, non-sister species. Herein I redescribe Lampsilis anodontoides (Lea, 1831) and use morphometrics and machine-learning algorithms to characterize shell morphology variation in each taxon.Item The Roles of Ecological Opportunity and Incumbency Effects in the Macroevolution of the Luzon Island, Philippines “Old Endemic” Murine Rodents(2019-05) Rowsey, DakotaThe evolutionary theory of adaptive radiation posits that lineages that experience a breadth of available resources in the absence of competition, known as ecological opportunity, should diversify to specialize on aspects of these available resources. The rapid evolution decelerates as niches fill in a static, spatially limited system, resulting in an assemblage of ecologically distinct species. Despite evidence to support this mode of diversification, little attention has been given to how this process unfolds in systems with multiple, ecologically similar colonizing lineages. The primary-colonizing, or incumbent, lineage, through exploiting niches in the absence of competitors, may serve to depress the rates and patterns of species and ecological diversity of subsequent colonists. In this dissertation, I explored four aims that seek to test whether the evolution of two clades of rodents endemic to Luzon Island, Philippines, Chrotomyini and Phloeomyini, exhibited evolution consistent with incumbency effects held by Phloeomyini and placed on secondary-colonizing Chrotomyini. First, I determined whether the rates of lineage diversification of the two Luzon Old Endemic (LOE) clades were consistent with reduced ecological opportunity in secondarily-colonizing Chrotomyini, resulting in lower rates of species accumulation. My results instead indicate that Chrotomyini has experienced a faster rate of diversification inconsistent with incumbency effects. Second, I tested whether the mandible of the LOE rodents, as a proxy for diet, exhibits rates of evolution consistent with lower ecological opportunity for Chrotomyini as well as patterns of diversity consistent with clade-specific partitioning of morphological variation. I found that both LOE clades evolved disparate mandible shapes at a similar rate, apart from outlying genus Rhynchomys, but that the two clades occupy nearly discrete areas of morphospace. Third, I tested whether the shape of the humerus can be used to approximate locomotory niche in a similar way to linear measurements of the ulna, metacarpal, and phalanx, to determine whether the morphology associated with locomotory strategy in the two LOE clades is convergent on shared locomotory mode. I found that although the humerus predicts some aspects of locomotory strategy, a substantial proportion of shape variation is reflected by different adaptations within shared locomotory category, thus providing a complement to, rather than replacement for, distal forelimb measurements. Finally, I tested whether the observed lack of mandibular shape overlap between the two LOE clades is consistent Chrotomyini being limited by Phloeomyini in terms of the area of morphospace it could diversify into and whether the ancestral chrotomyine lineage may have exhibited morphology disparate from Phloeomyini, thus facilitating its colonization and subsequent diversification. I found that the patterns of mandibular shape variation in the two LOE clades are consistent with the establishment of a biotic filter, meaning that Chrotomyini’s success on Luzon was facilitated by persistent ecological distinction from incumbent Phloeomyini. This dissertation illustrates that subfamily-related clades can experience substantial ecological distinction both within and between each clade. This distinction can permit repeated colonization of spatially constrained systems: as long as each colonizing clade remains ecologically distinct, evolution may proceed uninhibited by inter-clade competitive effects. Incumbency effects may thus more strongly influence the community assembly of species in a system than their evolutionary rates.