Graduate Research Symposium 2010 - Revision history

TobiasLandberg at 02:52, 27 March 2010

2010-03-27T02:52:12Z

JessicaBudke at 19:56, 26 March 2010

2010-03-26T19:56:45Z

ChrisOwen at 17:14, 26 March 2010

2010-03-26T17:14:30Z

MariaPickering at 22:02, 24 March 2010

2010-03-24T22:02:44Z

AdamWilson at 15:37, 24 March 2010

2010-03-24T15:37:49Z

JessicaBudke at 22:37, 22 March 2010

2010-03-22T22:37:13Z

DanielFan at 18:38, 22 March 2010

2010-03-22T18:38:47Z

KristiinaHurme at 18:33, 22 March 2010

2010-03-22T18:33:12Z

KerriMocko at 18:31, 22 March 2010

2010-03-22T18:31:59Z

ChrisOwen at 18:31, 22 March 2010

2010-03-22T18:31:35Z

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 | 11:00-11:15  ||Alejandro Rico || Hummingbird feeding mechanics
 |-
-| 11:15-11:30  || [[Tobias Landberg]]  || Something something salamanders
+| 11:15-11:30  || [[Tobias Landberg]]  || Ontogeny of escape swimming performance in spotted salamanders and survival with fish predators
 |-
 | 11:30-11:45  ||Brian Klingbeil  || Season-specific responses of bats to landscape structure in Amazonia
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 <br> Anti-predator Behavior in Schooling and Non-schooling Tadpoles (Anura, Leptodactylidae) <br>
 Tadpoles developing in temporary ponds must grow quickly to reach metamorphosis before the pond dries; these tadpoles must be more active and spend more time foraging than tadpoles of species developing in permanent ponds, but are also more susceptible to predation. Tadpole schooling may allow individuals to reduce predation risk by finding safety in numbers, and achieve foraging rates that would be too risky for individual tadpoles. While maximizing growth rates, schooling tadpoles might sacrifice their ability to escape from predators since individuals cannot maximize both growth rate and burst swimming speed. If tadpoles are unable to escape from predators, they may avoid capture by remaining inconspicuous within the selfish herd and avoiding detection. This strong selection for not being an “odd” individual can minimize variation in growth and behavior among individuals, and may result in stereotyped anti-predator behaviors. To determine if schooling tadpoles experience depressed anti-predator behavior, I performed predation trials with both schooling (Leptodactylus insularum) and non-schooling (Physalaemus pustulosus) Leptodactylid tadpoles. For each predation trial, I recorded the activity levels of 10 tadpoles before and after the addition of a lethal insect predator. I found that schooling tadpoles exhibited significantly higher activity levels and were more vulnerable to predation than non-schooling tadpoles were. I will also test to see if schooling tadpoles experience a higher encounter rate with predators.
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 [[Category:Graduate Research Symposium]]
 [[Category:Graduate Student Resources]]
 __NOTOC__

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 | 3:15-3:30  ||Diego Sustaita || The beak of the shrike: variation in form and a story about function...
 |-
-| 3:30-3:45  || ||
+!style="background:#efefef;" | 3:30-3:45  || || '''Speed Talks'''
 |-
-!style="background:#efefef;" | 3:45-4:00  || || '''Speed Talks'''
+| 3:30-3:35 || Lori Benoit ||  Hydrilla highlights
 |-
-| 3:45-3:50 || Lori Benoit ||  Hydrilla highlights
+| 3:35-3:40  || Maria Pickering  || Highlights from a Collecting Trip in Vietnam
 |-
-| 3:50-3:55  || Maria Pickering  || Highlights from a Collecting Trip in Vietnam
+| 3:40-3:45  || [[Nic Tippery]] || Best Grad/Postdoc Webpage - 2010
-|-
-| 3:55-4:00  || [[Nic Tippery]] || Best Grad/Postdoc Webpage - 2010
 |-
 |}

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 | 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''
+| 10:15-10:30  || Chris Owen || Diversification of the Australian cicada genus ''Pauropsalta''
 |-
 !style="background:#efefef;"| 10:30-11:00  ||  || '''Morning Break - Drinks and Fruit'''

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 | 3:45-3:50 || Lori Benoit ||  Hydrilla highlights
 |-
-| 3:50-3:55  ||  ||
+| 3:50-3:55  || Maria Pickering  || Highlights from a Collecting Trip in Vietnam
 |-
 | 3:55-4:00  || [[Nic Tippery]] || Best Grad/Postdoc Webpage - 2010

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 | 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
+| 9:15-9:30  || Susan Herrick || Temporal patterns in calling behavior of syntopic anurans.
 |-
 | 9:30-9:45  ||Elizabeth Wade || Microsatellite and gene discovery using 454 sequencing in the cicada genus Kikihia
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 !style="background:#efefef;"| 10:30-11:00  ||  || '''Morning Break - Drinks and Fruit'''
 |-
-| 11:00-11:15  ||Susan Herrick || Temporal patterns in calling behavior of syntopic anurans.
+| 11:00-11:15  ||Alejandro Rico || Hummingbird feeding mechanics
 |-
 | 11:15-11:30  || [[Tobias Landberg]]  || Something something salamanders
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 !style="background:#efefef;" | 3:45-4:00  || || '''Speed Talks'''
 |-
-| 3:45-3:50 ||  ||
+| 3:45-3:50 || Lori Benoit ||  Hydrilla highlights
 |-
 | 3:50-3:55  ||  ||

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 !style="background:#efefef;"| 12:00-1:30 ||  ||   Lunch - Sandwiches and Salad
 |-
-| 1:30-2:00  || Lori Hosaka LaPlante || Keynote Address: TBA
+| 1:30-2:00  || Lori Hosaka LaPlante || Keynote Address: Seals, Saints and Salamanders
 |-
 | 2:00-2:15  || Geert Goemans || The cicada tribe Zammarini: trying to untangle the taxonomic mess

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 <span id="NAME">'''[[Yu Fan]]''' </span>
 <br> Are you over-partitioning? <br>
-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 (<math>\rm{S}^3</math>) 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 <math>\rm{S}^3</math> (<math>\rm{S}^3</math>-BF) showed very different results, not only in magnitude but also in repeatability, despite the fact that both HM and <math>\rm{S}^3</math> 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 <math>\rm{S}^3</math>-BF method. The <math>\rm{S}^3</math> method was strikingly better than HM in terms of repeatability. Pairs of independent <math>\rm{S}^3</math> analyses had regression <math>R^2</math> 0.9991, whereas <math>R^2</math> for pairs of HM analyses was only 0.1636.
+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 (<math>\rm{S}^3</math>) 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 model with Gamma rate heterogeneity (GTR+G), and later analyzed by both unpartitioned and partitioned (with 2 equal subsets) models.The BF calculated from HM (HM-BF) and <math>\rm{S}^3</math> (<math>\rm{S}^3</math>-BF) showed very different results, not only in magnitude but also in repeatability, despite the fact that both HM and <math>\rm{S}^3</math> 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 <math>\rm{S}^3</math>-BF method. The <math>\rm{S}^3</math> method was strikingly better than HM in terms of repeatability. Pairs of independent <math>\rm{S}^3</math> analyses had regression <math>R^2</math> 0.9991, whereas <math>R^2</math> for pairs of HM analyses was only 0.1636.
 <span id="NAME">'''Kristiina Hurme'''</span>

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 <span id="NAME">'''Kerri Mocko </span>
 <br> "Service to the plant": Solar tracking and leaf shape in ''Pelargonium'' <br>
-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.
+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.
 <span id="NAME">'''[[Yu Fan]]''' </span>