Efficient and robust reconstruction of botanical branching structure from laser scanned points

This paper presents a reconstruction pipeline for recovering branching structure of trees from laser scanned data points. The process is made up of two main blocks: segmentation and reconstruction. Based on a variational k-means clustering algorithm, cylindrical components and ramified regions of data points are identified and located. An adjacency graph is then built from neighborhood information of components. Simple heuristics allow us to extract a skeleton structure and identify branches from the graph. Finally, a B-spline model is computed to give a compact and accurate reconstruction of the branching system. © 2009 IEEE.published_or_final_versionThe 11th IEEE International Conference on Computer-Aided Design and Computer Graphics (CAD/Graphics '09), Huangshan, China, 19-21 August 2009. In Proceedings of 11th CAD/Graphics, 2009, p. 572-57

Footprints on water: The genetic wake of dispersal among reefs

Analysis of genetic data can reveal past and ongoing demographic connections between reef populations. The history, extent, and geography of isolation and exchange help to determine which populations are evolutionarily distinct and how to manage threatened reefs. Here the genetic approaches undertaken to understand connectivity among reefs are reviewed, ranging from early allozyme studies on genetic subdivision, through the use of sequence data to infer population histories, to emerging analyses that pull the influences of the past connections away from the effects of ongoing dispersal. Critically, some of these new approaches can infer migration and isolation over recent generations, thus offering the opportunity to answer many questions about reef connectivity and to better collaborate with ecologists and oceanographers to address problems that remain. © 2007 Springer-Verlag

Historical and Contemporary DNA Indicate Fisher Decline and Isolation Occurred Prior to the European Settlement of California

Establishing if species contractions were the result of natural phenomena or human induced landscape changes is essential for managing natural populations. Fishers (Martes pennanti) in California occur in two geographically and genetically isolated populations in the northwestern mountains and southern Sierra Nevada. Their isolation is hypothesized to have resulted from a decline in abundance and distribution associated with European settlement in the 1800s. However, there is little evidence to establish that fisher occupied the area between the two extant populations at that time. We analyzed 10 microsatelliteloci from 275 contemporary and 21 historical fisher samples (1880-1920) to evaluate the demographic history of fisher in California. We did not find any evidence of a recent (post-European) bottleneck in the northwestern population. In the southern Sierra Nevada, genetic subdivision within the population strongly influenced bottleneck tests. After accounting for genetic subdivision, we found a bottleneck signal only in the northern and central portions of the southern Sierra Nevada, indicating that the southernmost tip of these mountains may have acted as a refugium for fisher during the anthropogenic changes of the late 19th and early 20th centuries. Using a coalescent-based Bayesian analysis, we detected a 90% decline in effective population size and dated the time of decline to over a thousand years ago. We hypothesize that fisher distribution in California contracted to the two current population areas pre-European settlement, and that portions of the southern Sierra Nevada subsequently experienced another more recent bottleneck post-European settlement

Reconstruction of Weakly Simple Polygons from their Edges

Given n line segments in the plane, do they form the edge set of a weakly simple polygon; that is, can the segment endpoints be perturbed by at most epsilon, for any epsilon > 0, to obtain a simple polygon? While the analogous question for simple polygons can easily be answered in O(n log n) time, we show that it is NP-complete for weakly simple polygons. We give O(n)-time algorithms in two special cases: when all segments are collinear, or the segment endpoints are in general position. These results extend to the variant in which the segments are directed, and the counterclockwise traversal of a polygon should follow the orientation. We study related problems for the case that the union of the n input segments is connected. (i) If each segment can be subdivided into several segments, find the minimum number of subdivision points to form a weakly simple polygon. (ii) If new line segments can be added, find the minimum total length of new segments that creates a weakly simple polygon. We give worst-case upper and lower bounds for both problems

Assessing changes in connectivity and abundance through time for fisher in the southern Sierra Nevada

Small populations are at increased risk of extinction due to their vulnerability to stochastic events. The population of fisher (Pekania pennanti, formerly Martes pennanti) in the southern Sierra Nevada Mountains of California is small and completely genetically isolated. My dissertation research investigates the timing and cause of this population\u27s isolation, the degree of genetic subdivision within the population, the landscape features shaping gene flow, and the detection of population declines. I detected a 90% decline in effective population size and dated the time of decline to over a thousand years ago. Analyzing historical and contemporary genetic samples, I also found a recent bottleneck signal in the northern portion of the southern Sierra Nevada, indicating the southernmost tip of these mountains may have acted as a refugium for fisher in the late 19th century. I conclude that this population became isolated pre-European settlement, and that portions of the southern Sierra Nevada subsequently experienced another more recent bottleneck post-European settlement. I found that the southern Sierra Nevada fisher population is not highly genetically subdivided as previously thought. This population follows a pattern of isolation by distance with additional structuring that corresponds to geographic features and management boundaries. It can be characterized as having areas that are resistant to gene flow but without major barriers. I show that both sex-biased dispersal and spatial landscape heterogeneity can affect the determination of what landscape features structure gene flow, and that the landscape features influencing gene flow are different for each sex and within different geographic regions. Using a spatially-based simulation approach, I investigated the power of the Sierra Nevada fisher monitoring program to detect population trend, and illustrate the relationship between occupancy and abundance in this population. I show that a simulated 43% decline in abundance over an 8-year period only resulted in a 23% decline in occupancy. I also found that increasing the effective sampling area, implementing biennial instead of annual sampling, and increasing the type I error rate all increase statistical power to detect trend. Overall this research provides a better understanding of the historical and contemporary connectivity of this population and our ability to monitor population trends over time that will contribute to the conservation of fisher populations in the future

Representing space for practical reasoning

This paper describes a new approach to representing space and time for practical reasoning, based on space-filling cells. Unlike R n, the new models can represent a bounded region of space using only finitely many cells, so they can be manipulated directly. Unlike Z n, they have useful notions of function continuity and region connectedness. The topology of space is allowed to depend on the situation being represented, accounting for sharp changes in function values and lack of connectedness across object boundaries. Algorithms based on this model of space are neither purely region-based nor purely boundary-based, but a blend of the two. This new style of algorithm design is illustrated by a new program for finding edges in grey-scale images. Although the program is based on a relatively conventional second directional difference operator, it can detect fine texture in the presence of camera noise, produce connected boundaries around sharp corners, and return thin boundaries without "feathering. " New algorithms are presented for combining directional differences, suppressing the effects of camera noise, reconstructing image intensities from the second difference values and merging results from different scales (including suppression of spurious boundaries in staircase patterns).