POPULATION GENETIC STRUCTURE OF MOOSE (ALCES ALCES) OF SOUTH-CENTRAL ALASKA

The location of a population can influence its genetic structure and diversity by impacting the degree of isolation and connectivity to other populations. Populations at range margins are often thought to have less genetic variation and increased genetic structure, and a reduction in genetic diversity can have negative impacts on the health of a population. We explored the genetic diversity and connectivity between 3 peripheral populations of moose (Alces alces) with differing potential for connectivity to other areas within interior Alaska. Populations on the Kenai Peninsula and from the Anchorage region were found to be significantly differentiated (FST = 0.071, P < 0.0001) with lower levels of genetic diversity observed within the Kenai population. Bayesian analyses employing assignment methodologies uncovered little evidence of contemporary gene flow between Anchorage and Kenai, suggesting regional isolation. Although gene flow outside the peninsula is restricted, high levels of gene flow were detected within the Kenai that is explained by male-biased dispersal. Furthermore, gene flow estimates differed across time scales on the Kenai Peninsula which may have been influenced by demographic fluctuations correlated, at least in part, with habitat change.

Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska

During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged \u3e100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre-and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak

Insights into bear evolution from a Pleistocene polar bear genome

The polar bear (Ursus maritimus) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears (Ursus arctos). Here, we extend our earlier studies of a 130,000- to 115,000-y-old polar bear from the Svalbard Archipelago using a 10x coverage genome sequence and 10 new genomes of polar and brown bears from contemporary zones of overlap in northern Alaska. We demonstrate a dramatic decline in effective population size for this ancient polar bear's lineage, followed by a modest increase just before its demise. A slightly higher genetic diversity in the ancient polar bear suggests a severe genetic erosion over a prolonged bottleneck in modern polar bears. Statistical fitting of data to alternative admixture graph scenarios favors at least one ancient introgression event from brown bears into the ancestor of polar bears, possibly dating back over 150,000 y. Gene flow was likely bidirectional, but allelic transfer from brown into polar bear is the strongest detected signal, which contrasts with other published work. These findings may have implications for our understanding of climate change impacts: Polar bears, a specialist Arctic lineage, may not only have undergone severe genetic bottlenecks but also been the recipient of generalist, boreal genetic variants from brown bears during critical phases of Northern Hemisphere glacial oscillations.Peer reviewe

Exhumation of the central Wasatch Mountains, Utah: 2. Thermokinematic model of exhumation, erosion, and thermochronometer interpretation

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95279/1/jgrb13381.pd

Quaking Regulates Hnrnpa1 Expression through Its 3′ UTR in Oligodendrocyte Precursor Cells

In mice, Quaking (Qk) is required for myelin formation; in humans, it has been associated with psychiatric disease. QK regulates the stability, subcellular localization, and alternative splicing of several myelin-related transcripts, yet little is known about how QK governs these activities. Here, we show that QK enhances Hnrnpa1 mRNA stability by binding a conserved 3′ UTR sequence with high affinity and specificity. A single nucleotide mutation in the binding site eliminates QK-dependent regulation, as does reduction of QK by RNAi. Analysis of exon expression across the transcriptome reveals that QK and hnRNP A1 regulate an overlapping subset of transcripts. Thus, a simple interpretation is that QK regulates a large set of oligodendrocyte precursor genes indirectly by increasing the intracellular concentration of hnRNP A1. Together, the data show that hnRNP A1 is an important QK target that contributes to its control of myelin gene expression

Can direct manipulation lower the barriers to programming and promote positive transfer to textual programming? An experimental study

Novices face many barriers when learning to program, including the need to learn both a new syntax and a model of computation. By constraining syntax and providing concrete visual representations on which to operate, direct manipulation programming environments can potentially lower these barriers. However, what if the learning goal of the novice is to be able ultimately to program in conventional textual languages, as is the case for introductory computer science students? Can direct manipulation programming environments lower the barriers to programming, and, at the same time, promote positive transfer to textual programming? To address this question, we designed a new direct manipulation programming interface for ALVIS Live!, a novice programming environment. We then conducted an experimental study that compared the programming outcomes promoted by the new direct manipulation interface to those promoted by ALVIS Live!’s textual programming interface. We found that the direct manipulation interface not only led to significantly better initial programming outcomes, but also to significant positive transfer to the textual interface. Our results show that direct manipulation interfaces can provide novices with a “way in ” to traditional textual programming. 1

A methodology for analyzing the temporal evolution of novice programs based on semantic components

Empirical studies of novice programming typically rely on code solutions or test responses as the basis of their analyses. While such data can provide insight into novice programming knowledge, they say little about the programming processes in which novices engage. For those interested in improving novice programming environments, a key research question arises: How can we collect and analyze data on novice programming that will enable us (a) to analyze and compare the programming processes promoted by alternative novice programming environments, and (b) ultimately to build better novice programming environments? To address this question, we have collected a large video corpus of novices as they construct code solutions in various versions of ALVIS Live! [14], a novice programming environment. Through detailed post-hoc analyses of our video corpus, we have developed a methodology for compiling the moment-by-moment evolution of novice code solutions. Based on an analysis of an ideal code solution’s key semantic components, our methodology enables one to document, on a second-by-second basis, (a) what part of a code solution a programmer is focusing on, and (b) where the semantic feedback provided by the programming environment is helping. Although it is time and labor intensive, our methodology provides researchers with a standard set of data and representations for comparing the programming processes promoted by alternative programming environments