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Citations since 2017
6 Research Items
Balancing the competing, and often conflicting, needs of people and wildlife in shared landscapes is a major challenge for conservation science and policy worldwide. Connectivity is critical for wildlife persistence, but dispersing animals may come into conflict with people, leading to severe costs for humans and animals and impeding connectivity....
Genetic connectivity lies at the heart of evolutionary theory, and landscape genetics has rapidly advanced to understand how gene flow can be impacted by the environment. Isolation by landscape resistance, often inferred through the use of circuit theory, is increasingly identified as being critical for predicting genetic connectivity across comple...
Global land use change has resulted in the loss and fragmentation of habitats and amplified the pace of species extinction. With carnivores being disproportionately at risk of range contraction, restoration is an important strategy to counter the impacts of habitat loss and fragmentation. While protection of public lands has been the cornerstone of...
Quantifying landscape connectivity is fundamental to better understand and predict how populations respond to environmental change. Currently, popular methods to quantify landscape connectivity emphasize how landscape features provide resistance to movement. While many tools are available to quantify landscape resistance, these do not discern betwe...
I recently read a couple different papers that use similar techniques for capturing target sequences from degraded DNA and DNA that is contaminated with DNA from other sources. One paper generates a library of biotinylated RNA probes/baits  using high quality DNA. Another paper does a very similar thing, but creates biotinylated DNA probes/baits instead . Obviously, the procedure for generating RNA and DNA probes is different, but what I'm wondering is, once the probes have been created, are there any advantages or disadvantages in terms of reliability or accuracy (not cost or time) of using a RNA probe vs a DNA probe when trying to capture short (100-500 bp) target DNA fragments for SNP genotyping of individuals?
- Carpenter, M. L., Buenrostro, J. D., Valdiosera, C., Schroeder, H., Allentoft, M. E., Sikora, M., … Bustamante, C. D. (2013). Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries. The American Journal of Human Genetics, 93(5), 852–864. https://doi.org/10.1016/j.ajhg.2013.10.002
- Suchan, T., Pitteloud, C., Gerasimova, N. S., Kostikova, A., Schmid, S., Arrigo, N., … Alvarez, N. (2016). Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on collection specimens. PLoS ONE, 11(3), 1–22. https://doi.org/10.1371/journal.pone.0151651
I'm doing fecal DNA extractions from herbivores and suspect that polysaccharides are carrying over to the final product (low quality nanodrop scores, evidence of some form of carryover on gel images). I'd like to confirm that polysaccharides are present, and was thinking that applying the starch test using Lugol's iodine solution would be a cheap and elegant way of doing so. The question is, will Lugol's solution (iodine + potassium iodide + water) work correctly in 1X TE buffer (also has a small amount of Tween)?
I'm a graduate student at a US institution currently doing population genetics research using the genotyping-by-sequencing (GBS) protocol. In the process of my lab work, I've identified several potential methods for modifying the protocol that could reduce costs and improve results. Now, I would like to try and create some inexpensive experiments to test these ideas. We have all the equipment necessary to do the work in house, and it's just a matter of covering the cost of the consumables (extraction, ligation, and pcr materials, as well as a MiSeq flowcell kit). Does anyone have any recommendations for small grants ($2000-$5000) that would be suitable for running these types of experiments? Thank you.
Basically, I'm exploring new methods for analyzing genetic data of individuals and populations across landscapes, but before applying them to real world data, I'd like to see how they work when applied to simulated data in certain idealized scenarios to help ensure that they work as expected. To that end, I'm interested in finding any software that can be used to generate genetic data (microsatellites and/or SNPs) for individuals across a landscape. Thanks.