RAPID: Ecological Resistance of Multiply Stressed Populations: The Response of Tidal Marsh Birds and Plants to Hurricane Sandy

All animal and plant populations can weather change. However, the amount of environmental change a population can absorb is likely to depend upon other, past and ongoing stresses that the population experiences. This project will test whether the ability of populations of native plants and animals in coastal marshes to withstand the recent, extreme storm Hurricane Sandy was greater or less in marshes more subject to past stresses. Researchers will compare the abundances of marsh plants and animals before and after the storm and test whether vulnerability was greater in more specialized species or in marshes surrounded by development, invaded by introduced plants, or challenged by high rates of sea-level rise, and whether previous protection of areas from different kinds of development or use helped reduce vulnerability. By addressing these questions using current theories of ecosystem disturbance, the research will provide general insights on the effects of disturbance and stress on native species and habitats. This research also will provide a specific assessment of Hurricane Sandy\u27s impact on tidal marshes, a vital buffer against storm damage. This will help managers target specific marshes for conservation and restoration and improve the efficiency of planned federal restoration efforts. The work will also inform future coastal management planning by identifying which types of marshes are most vulnerable to future disturbances. Findings will be disseminated to local, state, and federal partners through the Saltmarsh Habitat and Avian Research Program, a cooperative consortium of universities, non-governmental organizations, and state and Federal agency partners working together to conserve tidal marsh habitats and the species they support (www.tidalmarshbirds.org). The project will also help train 20 field technicians

Comparison of measures of marker informativeness for ancestry and admixture mapping

<p>Abstract</p> <p>Background</p> <p>Admixture mapping is a powerful gene mapping approach for an admixed population formed from ancestral populations with different allele frequencies. The power of this method relies on the ability of ancestry informative markers (AIMs) to infer ancestry along the chromosomes of admixed individuals. In this study, more than one million SNPs from HapMap databases and simulated data have been interrogated in admixed populations using various measures of ancestry informativeness: Fisher Information Content (FIC), Shannon Information Content (SIC), F statistics (F_ST), Informativeness for Assignment Measure (I_n), and the Absolute Allele Frequency Differences (delta, δ). The objectives are to compare these measures of informativeness to select SNP markers for ancestry inference, and to determine the accuracy of AIM panels selected by each measure in estimating the contributions of the ancestors to the admixed population.</p> <p>Results</p> <p>F_STand I_nhad the highest Spearman correlation and the best agreement as measured by Kappa statistics based on deciles. Although the different measures of marker informativeness performed comparably well, analyses based on the top 1 to 10% ranked informative markers of simulated data showed that I_nwas better in estimating ancestry for an admixed population.</p> <p>Conclusions</p> <p>Although millions of SNPs have been identified, only a small subset needs to be genotyped in order to accurately predict ancestry with a minimal error rate in a cost-effective manner. In this article, we compared various methods for selecting ancestry informative SNPs using simulations as well as SNP genotype data from samples of admixed populations and showed that the I_nmeasure estimates ancestry proportion (in an admixed population) with lower bias and mean square error.</p

Using admixture mapping to identify genetic linkages with variation in human facial shape

Liberton D.K., Claes P., Beleza S., Barsh G., Tang H., Shriver M.D., ''Using admixture mapping to identify genetic linkages with variation in human facial shape'', American journal of physical anthropology, pp. 180, 2013 (82nd annual meeting of the American Association of Physical Anthropologists (AAPA), April 9-13, 2013, Knoxville, Tennessee, USA).status: publishe

Using automated high density quasi-landmarks to test for associations between normal facial feature variation, genetic ancestry and candidate gene variation in Cape Verdeans

Liberton D.K., Claes P., Mcevoy B., Beleza S., Barsh G., Tang H., Absher D., Shriver M.D., ''Using automated high density quasi-landmarks to test for associations between normal facial feature variation, genetic ancestry and candidate gene variation in Cape Verdeans'', American journal of physical anthropology, pp. 198, 2011 (80th annual meeting of the American Association of Physical Anthropologists (AAPA), April 12-16, 2011, Minneapolis, Minnesota, USA).status: publishe

Sexual dimorphism in multiple aspects of 3D facial symmetry & asymmetry defined by spatially-dense geometric morphometrics

Accurate measurement of facial sexual dimorphism is useful to understanding facial anatomy and specifically how faces influence, and have been influenced by, sexual selection. An important facial aspect is the display of bilateral symmetry, invoking the need to investigate aspects of symmetry and asymmetry separately when examining facial shape. Previous studies typically employed landmarks that provided only a sparse facial representation, where different landmark choices could lead to contrasting outcomes. Furthermore, sexual dimorphism is only tested as a difference of sample means, which is statistically the same as a difference in population location only. Within the framework of geometric morphometrics, we partition facial shape, represented in a spatially dense way, into patterns of symmetry and asymmetry, following a two-factor anova design. Subsequently, we investigate sexual dimorphism in symmetry and asymmetry patterns separately, and on multiple aspects, by examining (i) population location differences as well as differences in population variance-covariance; (ii) scale; and (iii) orientation. One important challenge in this approach is the proportionally high number of variables to observations necessitating the implementation of permutational and computationally feasible statistics. In a sample of gender-matched young adults (18-25 years) with self-reported European ancestry, we found greater variation in male faces than in women for all measurements. Statistically significant sexual dimorphism was found for the aspect of location in both symmetry and asymmetry (directional asymmetry), for the aspect of scale only in asymmetry (magnitude of fluctuating asymmetry) and, in contrast, for the aspect of orientation only in symmetry. Interesting interplays with hypotheses in evolutionary and developmental biology were observed, such as the selective nature of the force underpinning sexual dimorphism and the genetic independence of the structural patterns of fluctuating asymmetry. Additionally, insights into growth patterns of the soft tissue envelope of the face and underlying skull structure can also be obtained from the results.Claes P., Walters M., Shriver M.D., Puts D., Gibson G., Clement J., Baynam G., Verbeke G., Vandermeulen D., Suetens P., ''Sexual dimorphism in multiple aspects of 3D facial symmetry & asymmetry defined by spatially-dense geometric morphometrics'', Journal of anatomy, vol. 221, no. 2, pp. 97-114, August 2012 (Journal of anatomy cover illustration: Sexual dimorphism in 3D facial symmetry and directional asymmetry. Faces on the left display average symmetry females/males while faces on the right show amplified directional asymmetry females/males. See article by Claes et al., 'Sexual dimorphism in multiple aspects of 3D facial symmetry and asymmetry defined by spatially dense geometric morphometrics', in this issue of Journal of Anatomy (2012) 221, pp. 97–114.).status: publishe

Nelson's Sparrow - Genomic Data

Filtered VCF containing approximately 2.5 million SNPs. This file contains data for 17 individuals (c = coastal, u = upland). See extended data table 1 for sample informatio

Savannah Sparrows - Genomic Data

Filtered VCF containing approximately 13 million SNPs. This file contains data for 20 individuals (c = coastal, u = upland). See extended data table 1 for sample information

Swamp Sparrow - Genomic Data

Filtered VCF containing approximately 12.3 million SNPs. This file contains data for 22 individuals (c = coastal, u = upland). Se extended data table 1 for sample information

Colloid-facilitated metal transport in peat filters

The effect of colloids on metal retention in peat columns was studied, with the focus on colloids from two sources - organic matter leached from peat, and introduced organic and hydrous ferric oxide (HFO) colloids. A significant fraction of metals was found to be associated with peat-produced organic colloids; however the concentrations of organic colloids leached are low (trace concentrations) and temporal and have a limited effect on the efficiency of peat filters. In contrast, the presence of organic and HFO colloids in the input water causes a significant decrease in the performance of peat filters. Organic colloids were identified as the main vector of cadmium, copper, nickel, and zinc, while lead is transported by both organic and HFO colloids. The colloidal distribution of metals obtained in this study has important implications for the mobility of trace metals in porous media. The occurrence of colloids in the input waters and their characteristics must be considered when designing water treatment facilities