Here you find information on research projects that I have previously participated in, but am no longer actively pursuing. Publications relating to these projects are also listed here. If you would like a PDF reprint, please e-mail me or check my publications page.
Genomic Methods Development
As a technician in the Tung lab, I primarily worked on projects developing new genomic methods. Specifically, the enrichment of host genomic DNA from fecal samples, the development of a high throughput function assay for DNA methylation in enhancer regions, and the influence of storage condition on 16S ribosomal DNA sequencing for microbiome studies. The collection of invasive samples containing high quality genomic DNA (e.g. blood, tissue) from animals is often expensive, labor-intensive, and logistically difficult. This is particularly true for natural populations and relatively large bodied animals. Ideally, we would be able to gather high quality genomic DNA from noninvasive sampling techniques such as collection of feces. Unfortunately, host fecal DNA makes up only a tiny fraction of the total DNA extracted from feces (~1%). Most DNA is environmental or bacterial in origin. In the Tung lab we are currently developing protocols in order to enrich fecal extracted samples for endogenous host DNA allowing us to conduct genomic studies without the use of invasive sampling.
- Snyder-Mackler N, Majoros WH, Yuan ML, Shaver AO, Gordon J, Kopp G, Schlebusch S, Wall JD, Alberts SC, Mukherjee S, Zhou X, Tung J (2016) Efficient genome-wide sequencing and low coverage pedigree analysis from non-invasively collected samples. Genetics. In Press.
- Blekhman R, Tang K, Archie EA, Barreiro LB, Johnson ZP, Wilson ME, Kohn J, Yuan ML, Gesquiere L, Grieneisen L, Tung J (2016) Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. bioRxiv. doi: http://dx.doi.org/10.1101/038844
I maintain an active interest in the evolution of gut microbial communities in reptiles. As a group, reptilian gut microbiomes are poorly studied, despite the wide range of dietary modes and specializations, including the repeated evolution of obligate herbivory, a highly specialized dietary mode that requires cellulolytic microbial mutualists. Thus far surveys of reptilian gut microbiomes are too sparse to draw broad conclusions about their evolution. Questions regarding broad evolutionary patterns of reptilian gut microbiota are just waiting to be answered! I have previousy characterized the gut microbiome of the gopher tortoise, Gopherus polyphemus (Yuan et al. 2015). Our study showed broad homogeniety across individuals, but also an influence of host kinship, inbreeding, fine-scale spatial structure, and possibly age in shaping gut microbial communities.
- Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR (2015) Kinship, inbreeding, and fine-spatial structure influence gut communities of a hindgut-fermenting tortoise. Molecular Ecology 24: 2521–2536. DOI: 10.1111/mec.13169
While at Cornell University, I had the opportunity to work with Joaquin Goyret studying the sensory ecology of foraging by the nocturnal hawkmoth, Manduca sexta. Given the ability to rear laboratory colonies, M. sexta, make an excellent study species for controlled laboratory experiments examining sensory ecology and foraging behavior. We studied the effects of olfactory stimulation and varying illuminance on the close range foraging behavior of these hawkmoths using mock flowers. We found that in the absence of olfactory signals, the ability of M. sexta to successfully identify and forage from our artificial flowers was impaired under low light conditions. However, foraging efficiency was recovered by the inclusion of an oflactory signal. Our results suggest that odor can act as a compensatory signal in the absence of adequate visual stimulation (i.e. low light availability), however, when light levels were high, olfaction was redundant to vision during foraging (Goyret and Yuan 2015).
Photo Credit: Joaquin Goyret (Full disclosure: the photo is of Macroglossum stellatarum)
- Goyret J, Yuan ML (2015) Influence of ambient illumination on the use of olfactory and visual signals by a nocturnal hawkmoth during close-range foraging. Integrative and Comparative Biology. DOI: 10.1093/icb/icv009