Australian Sphingidae – DNA Barcodes Challenge Current Species Boundaries and Distributions

© 2014 Rougerie et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

Joining Inventory by Parataxonomists with DNA Barcoding of a Large Complex Tropical Conserved Wildland in Northwestern Costa Rica

BACKGROUND: The many components of conservation through biodiversity development of a large complex tropical wildland, Area de Conservacion Guanacaste (ACG), thrive on knowing what is its biodiversity and natural history. For 32 years a growing team of Costa Rican parataxonomists has conducted biodiversity inventory of ACG caterpillars, their food plants, and their parasitoids. In 2003, DNA barcoding was added to the inventory process. METHODOLOGY/PRINCIPAL FINDINGS: We describe some of the salient consequences for the parataxonomists of barcoding becoming part of a field biodiversity inventory process that has centuries of tradition. From the barcoding results, the parataxonomists, as well as other downstream users, gain a more fine-scale and greater understanding of the specimens they find, rear, photograph, database and deliver. The parataxonomists also need to adjust to collecting more specimens of what appear to be the "same species"--cryptic species that cannot be distinguished by eye or even food plant alone--while having to work with the name changes and taxonomic uncertainty that comes with discovering that what looked like one species may be many. CONCLUSIONS/SIGNIFICANCE: These career parataxonomists, despite their lack of formal higher education, have proven very capable of absorbing and working around the additional complexity and requirements for accuracy and detail that are generated by adding barcoding to the field base of the ACG inventory. In the process, they have also gained a greater understanding of the fine details of phylogeny, relatedness, evolution, and species-packing in their own tropical complex ecosytems. There is no reason to view DNA barcoding as incompatible in any way with tropical biodiversity inventory as conducted by parataxonomists. Their year-round on-site inventory effort lends itself well to the sampling patterns and sample sizes needed to build a thorough barcode library. Furthermore, the biological understanding that comes with barcoding increases the scientific penetrance of biodiversity information, DNA understanding, evolution, and ecology into the communities in which the parataxonomists and their families are resident

A variational Bayesian method for inverse problems with impulsive noise

We propose a novel numerical method for solving inverse problems subject to impulsive noises which possibly contain a large number of outliers. The approach is of Bayesian type, and it exploits a heavy-tailed t distribution for data noise to achieve robustness with respect to outliers. A hierarchical model with all hyper-parameters automatically determined from the given data is described. An algorithm of variational type by minimizing the Kullback-Leibler divergence between the true posteriori distribution and a separable approximation is developed. The numerical method is illustrated on several one- and two-dimensional linear and nonlinear inverse problems arising from heat conduction, including estimating boundary temperature, heat flux and heat transfer coefficient. The results show its robustness to outliers and the fast and steady convergence of the algorithm.Comment: 20 pages, to appear in J. Comput. Phy

Trajectory of Substance Use Disorders and Collegiate Recovery in Emerging Adults

Abstract Collegiate Recovery Programs (CRPs) provide services to support emerging adults achieve academic success, while maintaining substance use disorder recovery. College and university campuses can often be considered abstinence-hostile environments, giving rise to the need of support services for students in recovery. A nationwide survey to understand the efficacy of services provided by CRPs was conducted to assess the demographics and academic profiles of students involved with CRPs. Co-occurring disorders including mental health issues, criminal histories, utilizations of recovery services and 12-step groups, and work histories of students were also assessed. CRPs can provide services and an environment to students that increase recovery capital domains. Recovery capital domains such as spirituality, health and wellness, academics, critical thinking and discernment, personal achievement, and service opportunities may be related to metrics of academic success such as grade point average. However, measuring success for those in substance use disorder recovery through academics metrics alone could present a barrier to improving recovery services. Assessing the effectiveness of CRP programs through the lens of recovery capital offers a strengths-based, wholistic approach to improving services for students in recovery. Future directions include administering comprehensive measurements for recovery success, in addition to academic metrics, for students that are members of CRP. Keywords: Substance Use Recovery; Emerging Adults; Collegiate Recovery Program

Wolbachia and DNA barcoding insects: patterns, potential and problems

Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region

Surrogate: A Body-Dexterous Mobile Manipulation Robot with a Tracked Base

Robotics platforms in accordance with various embodiments of the invention can be utilized to implement highly dexterous robots capable of whole body motion. Robotics platforms in accordance with one embodiment of the invention include: a memory containing a whole body motion application; a spine, where the spine has seven degrees of freedom and comprises a spine actuator and three spine elbow joints that each include two spine joint actuators; at least one limb, where the at least one limb comprises a limb actuator and three limb elbow joints that each include two limb joint actuators; a tracked base; a connecting structure that connects the at least one limb to the spine; a second connecting structure that connects the spine to the tracked base; wherein the processor is configured by the whole body motion application to move the at least one limb and the spine to perform whole body motion

Supervised Remote Robot with Guided Autonomy and Teleoperation (SURROGATE): A Framework for Whole-Body Manipulation

The use of the cognitive capabilities of humans to help guide the autonomy of robotics platforms in what is typically called “supervised-autonomy” is becoming more commonplace in robotics research. The work discussed in this paper presents an approach to a human-in-the-loop mode of robot operation that integrates high level human cognition and commanding with the intelligence and processing power of autonomous systems. Our framework for a “Supervised Remote Robot with Guided Autonomy and Teleoperation” (SURROGATE) is demonstrated on a robotic platform consisting of a pan-tilt perception head, two 7-DOF arms connected by a single 7-DOF torso, mounted on a tracked-wheel base. We present an architecture that allows high-level supervisory commands and intents to be specified by a user that are then interpreted by the robotic system to perform whole body manipulation tasks autonomously. We use a concept of “behaviors” to chain together sequences of “actions” for the robot to perform which is then executed real time

Inter-specific hybridization underlies phenotypic variability in Daphnia populations

In the glacial lakes of the Palaearctic three species of Cladocera commonly coexist: Daphnia hyalina, D. galeata , and D. cucullata . Frequently these populations contain not only animals which are morphologically typical for the species but also individuals of an intermediate phenotype. Electrophoretic investigations of allozyme-patterns in morphologically typical individuals reveal that each species is fixed for a different allele at the GOT locus. Morphologically intermediate animals are heterozygous for the alleles of the two species which they resemble. The allelic pattern at other loci is also consistent with the assumption that morphological intermediates are formed via interspecific hybridization. Very few backcrosses between galeata-hyalina hybrids and their parent species are found, and there is no indication of gene flow between D. cucullata and the other species.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47761/1/442_2004_Article_BF00378763.pd