Graduate Research Symposium 2010
Saturday, March 27, 2010
Biology/Physics Building Room 130, 9:00am to ~ 4:00pm
The EEB Graduate Student Symposium is an all day event where graduate students present their research to other graduate students and faculty. Any EEB graduate student can present: BSMS, masters, PhD, old and new students. New graduate students usually present research ideas or preliminary data, while those more ‘seasoned’ students present their most recent results, often in preparation for upcoming spring and summer meetings.
|8:30-9:00||Coffee & Tea (drinks only)|
|9:00-9:15||Debra Kendall||Welcome address by the associate dean for life sciences and for research and graduate education|
|9:15-9:30||Alejandro Rico||Hummingbird feeding mechanics|
|9:30-9:45||Elizabeth Wade||Microsatellite and gene discovery using 454 sequencing in the cicada genus Kikihia|
|9:45-10:00||Jessica Budke||Examining the gametophytic calyptra and its role in sporophyte development using the cord moss (Funaria hygrometrica).|
|10:00-10:15||Kerri Mocko||"Service to the plant": Solar tracking and leaf shape in Pelargonium|
|10:15-10:30||Chris Owen||Systematics and diversification of the Australian cicada genus Pauropsalta|
|10:30-11:00||Morning Break - Drinks and Fruit|
|11:00-11:15||Susan Herrick||Temporal patterns in calling behavior of syntopic anurans.|
|11:15-11:30||Tobias Landberg||Something something salamanders|
|11:30-11:45||Brian Klingbeil||Season-specific responses of bats to landscape structure in Amazonia|
|11:45-12:00||Kristiina Hurme||Antipredator behavior in schooling tadpoles|
|12:00-1:30||Lunch - Sandwiches and Salad|
|1:30-2:00||Lori Hosaka LaPlante||Keynote Address: TBA|
|2:00-2:15||Geert Goemans||The cicada tribe Zammarini: trying to untangle the taxonomic mess|
|2:15-2:30||Karolina Fučíková||Cryptic diversity of tiny green thingies: To barcode or not to barcode?|
|2:30-2:45||Yu Fan||Are you over-partitioning?|
|2:45-3:00||Nic Tippery||It's Greek to me, but Latin to you: Notes on nomenclature|
|3:00-3:15||Frank Smith||The evolutionary developmental genetics of wing number in insects.|
|3:15-3:30||Diego Sustaita||The beak of the shrike: variation in form and a story about function...|
|3:55-4:00||Nic Tippery||Best Grad/Postdoc Webpage - 2010|
Temporal patterns in calling behavior of syntopic anurans
Phenotypically similar species are hypothesized to adjust their behavior when they coexist to decrease competition. Pond-breeding frogs constitute an ideal system to address this hypothesis because multiple species may compete for noise-free periods to call for mates. American bullfrogs (Rana catesbeiana) and green frogs (R. clamitans) commonly co-occur in breeding ponds. Males of both species vocalize to defend territories and attract females. However, bullfrogs call more aggressively than green frogs and are expected to control access to the limiting acoustic resources. I predicted that green frogs increase chorusing activity in periods of bullfrog inactivity and that these patterns can be detected at both diel and seasonal scales. I used automated acoustic software to identify bullfrog and green frog vocalizations through two breeding seasons. Temporal partitioning occurs on a seasonal time scale. Bullfrog and green frog calling rates are both high early in the season in late May but then diverge. Bullfrog calling rate peaks in mid-June and drops sharply thereafter. In contrast, green frog calling falls to low levels in June but then rebounds when bullfrog calling declines, so that green frog calling reaches a second peak in late June and tapers off thereafter, ceasing in early August. There is no evident temporal partitioning on shorter time scales. Both species call most from midnight until 0600. However, the diel timing of bullfrog calling is predictable, whereas green frog calling is more variable. These results suggest green frogs are responding to reduced bullfrog activity by adjusting their calling effort.
Hummingbird feeding mechanics
Modulation of feeding behavior in hummingbirds, the most important vertebrate pollinators, has been demonstrated to affect the persistence of many kinds and number of plants, and subsequently the interactions and services provided by entire ecosystems. Similarly, composition and concentration of floral nectars has been shown to influence which flowers hummingbirds feed at, and their rate of movement among flowers. To date, our understanding of feeding behavior in hummingbirds is based on the theory that they use capillarity in order to feed on nectar. It is widely accepted as fact that hummingbirds feed by moving nectar up their tongues in the same way that water moves up a tiny capillary glass tube. Our entire understanding of the nature of the interaction of hummingbirds and plants has been based on this concept of the mechanics of feeding. My previous work on the structure of the hummingbird tongue suggests that the capillarity model of feeding in hummingbirds may be wrong. Preliminary results point to a novel and radically different nectar trapping mechanism; if true, our ideas about how external factors affect the rate at which hummingbirds gain nectar from flowers would change. In this presentation I document the process of nectar uptake using high-speed video and microscopy capabilities describing the fluid mechanics of tongue loading, discussing the implications of this new perspective at several different levels ranging from biophysics to ecology and evolution.
Examining the gametophytic calyptra and its role in sporophyte development using the cord moss (Funaria hygrometrica).
In bryophytes (mosses, liverworts and hornworts) the diploid sporophyte is small, unbranched, and physically attached to the maternal haploid gametophyte. One of the major maternal influences in moss plants is a cap of gametophyte tissue (the calyptra) that covers the sporophyte’s apex during early developmental stages. Previous studies indicate that the calyptra functions mechanically to influence sporophyte development and is necessary for spore formation. Sporophytes without their calyptra wilt at the apex; they survive only when placed in a high humidity chamber. These observations stimulated the hypothesis that the maternally derived calyptra functions as a waterproof cap, preventing desiccation of the developing sporophyte’s apex. In plants the cuticle, an external layer of lipids and waxes, maintains internal hydration. To explore this hypothesis, I am using scanning and transmission electron microscopy to examine cuticle morphology and development of both the calyptra and sporophyte in the moss Funaria hygrometrica. Results for this species indicate that the calyptra’s cuticle is thicker and more complex than other gametophyte tissues; the cuticle is also present on the calyptra throughout sporophyte development. These observations support the calyptra as a specialized maternal gametophyte structure and provide a mechanism by which the calyptra prevents harmful water loss during critical sporophyte developmental stages. Sporophyte development is directly related to reproductive output and thus evolutionary fitness in mosses. The maternal care provided by the calyptra and its cuticle may have been a critical innovation for the evolutionary success of the ~12,500 moss species worldwide.
Cryptic diversity of tiny green thingies: To barcode or not to barcode?
The taxonomy of green coccoid algae traditionally has been limited by their character-poor morphology when solely using light microscopy. Alternative methods, especially the use of molecular sequence data, often reveal cryptic diversity and help clarify phylogenetic affiliations of green coccoids. The present study focuses on the genus Pseudomuriella Hanagata and its phylogenetic relationships to morphologically similar genera. Newly-discovered, morphologically cryptic diversity of the genus Pseudomuriella is reported here and examined using molecular markers – barcodes – from the three cellular compartments: the plastid rbcL gene, the nuclear ribosomal internal transcribed spacer 2, and the mitochondrial cox1 gene. The utility of the three markers is discussed using a comparison of their performance in species-level resolution within the Pseudomuriella clade, while also considering the ease of their use. All three genes examined were found to contain variation usable for species-level resolution, and provided largely consistent phylogenies. A joint use of the three markers may be the ideal tool for barcoding cryptic green algal species, but rbcL appears to be the most practical combination of good phylogenetic signal and ease of use.
Microsatellite and gene discovery using 454 sequencing in the cicada genus Kikihia
Genomic information for non-model organisms is becoming increasingly easier to obtain. Next generation sequencing is revolutionizing whole genome and transcriptome sequencing by providing large amounts of data relatively cheap. Traditional techniques for obtaining nuclear loci for population genetics studies, such as microsatellites and SNPs (single nucleotide polymorphisms) are labor intensive and expensive. In addition, nuclear loci for phylogenetic analyses tend to be limited to a few loci with conserved primers that are used on a wide range of taxa. I have used 454 Life Sciences technology to whole genome sequence nine species of the New Zealand genus Kikihia in an attempt to isolate microsatellites and SNPs for population genetics analyses for this genus and protein-coding genes for systematic studies in the cicada family. In this presentation, I will briefly overview next generation sequencing technology and present my preliminary findings on the cicada genome.
It's Greek to me, but Latin to you: Notes on nomenclature
The classical languages of Latin and Greek have trickled down to us through a variety of historical uses, from simple transmission of ancient texts to entirely new uses of the languages by speakers of modern languages. Although as scientists we all embrace the necessity of a certain familiarity with Latin and Greek, ever fewer people are actually familiar with the origins and meanings of the words they use. I will present a brief overview of these classical languages as they are used by scientists today, including the different grammatical forms of words, derivation of some popular names, and the ever-important and often-overlooked question of how to tell if a word construct is of Latin or Greek origin (yes, they are different languages!).
"Service to the plant": Solar tracking and leaf shape in Pelargonium
Solar tracking in plants describes the temporary and reversible movement of leaves in response to light. Darwin recognized that this phenomenon provided a “service to the plant” that has since been studied by ecophysiologists, most extensively in arid environments. Under cool temperatures and non-water stressed conditions, plants display diaheliotropic movements that maintain leaves perpendicular to incident light, maximizing photon flux density to achieve high photosynthetic rates throughout the day. Under hot, dry conditions, paraheliotropic movements parallel to solar incidence reduce photon flux density to prevent thermal damage and enhance water use efficiency. Examined mostly in species with pulvini and pinnate leaves, there has been little direct attention to the effect of leaf shape on the extent of solar tracking. Leaf energy exchange with the environment depends on the physical properties of a given leaf shape such that an entire leaf has a thicker boundary layer and less heat transfer with the environment than a highly dissected leaf. Therefore, dissected leaves are predicted to maintain temperatures closer to ambient. However, energy budgets for any shape of leaf can be influenced by changes in leaf angle. We measured diurnal changes in leaf inclination and azimuth of two closely related co-occurring geophytic Pelargonium species of contrasting leaf shape. While both species tracked the sun during the course of the day, there was more movement in highly dissected leaves. Under winter growing conditions, leaves of the dissected species moved to intercept more solar radiation and heat up more quickly than the non-dissected species. Between species, differences in leaf shape and solar tracking combined to result in similar maximum leaf temperatures. Thus the full extent of Darwin’s “service to the plant” results from the synergistic effects of leaf movement and morphology.
Are you over-partitioning?
Partitioned analyses have been routine in recent Bayesian phylogenetics because of three reasons. First, automated sequencing has made it feasible to sequence large amounts of nucleotide data. Second, genes or codon positions may endure different selective pressures, and models need to account for the resulting differences in substitution rates and/or pattern of substitution. Third, it is necessary to partition the data due to intrinsic differences; for example, molecular and morphological data can only be reasonably combined if a different models can applied to each separately. It is always a challenge, however, to avoid unnecessarily complex partitioning schemes. The Bayes Factor (BF) has been demonstrated to be a good model selection criterion, but its usage relies on the accurate estimation of the marginal likelihood of each model. The Harmonic Mean (HM) estimator of marginal likelihood is a computationally fast approach, and has been widely used in Bayesian phylogenetic research. However, it is known to be biased, which causes it to favor more complex (e.g. more highly partitioned) models. Here, we propose a new method of marginal likelihood estimation, the Stabilized Stepping-Stone () method, and apply it to a simulation study. 200 nucleotide data sets of various sizes (number of taxa and sites) were simulated from an unpartitioned General Time Reversible (GTR) model, and later analyzed by both unpartitioned and partitioned (with 2 equal subsets) models.The BF calculated from HM (HM-BF) and (-BF) showed very different results, not only in magnitude but also in repeatability, despite the fact that both HM and analyses were based on samples of equal size. The HM-BF method chose the more complex partitioned model 21.5% of the time, compared with 0.5% for the -BF method. The method was strikingly better than HM in terms of repeatability. Pairs of independent analyses had regression 0.9991, whereas for pairs of HM analyses was only 0.1636.