9 Works

Data from: Reproductive aging patterns in primates reveal that humans are distinct

Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Marina Cords, Linda M. Fedigan, Anne Pusey, Tara S. Stoinski, Karen B. Strier, William F. Morris & Anne M. Bronikowski
Women rarely give birth after approximately 45 years of age, and they experience the cessation of reproductive cycles – menopause – at approximately 50 years of age, after a fertility decline lasting almost two decades. Such reproductive senescence in mid-lifespan is an evolutionary puzzle of enduring interest because it should be inherently disadvantageous. Further, comparative data on reproductive senescence from other primates, or indeed other mammals, remains relatively rare. Here we carried out the first...

Data from: Quantifying and comparing phylogenetic evolutionary rates for shape and other high-dimensional phenotypic data

Dean C. Adams
Many questions in evolutionary biology require the quantification and comparison of rates of phenotypic evolution. Recently, phylogenetic comparative methods have been developed for comparing evolutionary rates on a phylogeny for single, univariate traits (σ2), and evolutionary rate matrices (R) for sets of traits treated simultaneously. However, high-dimensional traits like shape remain under-examined with this framework, because methods suited for such data have not been fully developed. In this article, I describe a method to quantify...

Data from: Genomic BLUP decoded: a look into the black box of genomic prediction

David Habier, Rohan L. Fernando & Dorian J. Garrick
Genomic best linear unbiased prediction (BLUP) is a statistical method that uses relationships between individuals calculated from single-nucleotide polymorphisms (SNPs) to capture relationships at quantitative trait loci (QTL). We show that genomic BLUP exploits not only linkage disequilibrium (LD) and additive-genetic relationships, but also cosegregation to capture relationships at QTL. Simulations were used to study the contributions of those types of information to accuracy of genomic estimated breeding values (GEBVs), their persistence over generations without...

Data from: Predator perception of Batesian mimicry and conspicuousness in a salamander

Andrew C. Kraemer & Dean C. Adams
In Batesian mimicry a palatable mimic deceives predators by resembling an unpalatable model. The evolution of Batesian mimicry relies on the visual capabilities of the potential predators, as prey detection provides the selective force driving evolutionary change. We compared the visual capabilities of several potential predators to test predictions stemming from the hypothesis of Batesian mimicry between two salamanders: the model species Notophthalmus viridescens, and polymorphic mimic, Plethodon cinereus. First, we found mimicry to be...

Data from: Ecological co-associations influence species’ responses to past climatic change: an example from a Sonoran Desert bark beetle

Ryan C. Garrick, John D. Nason, Rodney J. Dyer & Juan F. Fernández-Manjarrés
Ecologically interacting species may have phylogeographic histories that are shaped both by features of their abiotic landscape, and by biotic constraints imposed by their co-association. The Baja California peninsula provides an excellent opportunity to examine the influence of abiotic vs. biotic factors on patterns of diversity in plant-insect species. This is because past climatic and geological changes impacted the genetic structure of plants quite differently to that of co-distributed free-living animals (e.g., herpetofauna and small...

Data from: Extent and variability of interstitial telomeric sequences and their effects on estimates of telomere length

Christopher G. Foote, David Vleck & Carol M. Vleck
Telomeres often shorten with time, although this varies between tissues, individuals and species, and their length and/or rate of change may reflect fitness and rate of senescence. Measurement of telomeres is increasingly important to ecologists, yet the relative merits of different methods for estimating telomere length are not clear. In particular the extent to which interstitial telomere sequences (ITSs), telomere repeats located away from chromosomes ends, confound estimates of telomere length is unknown. Here we...

Data from: Evidence of lasting impact of the Deepwater Horizon oil spill on a deep Gulf of Mexico coral community

Pen-Yuan Hsing, Bo Fu, Elizabeth A. Larcom, Samantha P. Berlet, Timothy M. Shank, Annette Frese Govindarajan, Alexandra Julia Lukasiewicz, Philip M. Dixon & Charles R. Fisher
A coral community 11 km southwest of the site of the Deepwater Horizon blowout at 1,370 m water depth was discovered 3.5 months after the well was capped on 3 November 2010. Gorgonian corals at the site were partially covered by a brown flocculent material (floc) that contained hydrocarbons fingerprinted to the oil spill. Here we quantify the visible changes to the corals at this site during five visits over 17 months by digitizing images...

Data from: Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits

Geoffrey P. Morris, Davina H. Rhodes, Zachary Brenton, Punna Ramu, Vinayan Madhumal Thayil, Santosh Deshpande, C. Thomas Hash, Charlotte Acharya, Sharon E. Mitchell, Edward S. Buckler, Jianming Yu & Stephen Kresovich
Genome-wide association studies (GWAS) are a powerful method to dissect the genetic basis of traits, though in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissect the genetic control of flavonoid pigmentation traits in the cereal grass sorghum using high-resolution genotyping-by-sequencing (GBS) SNP markers. Studying the grain tannin trait, we find that General Linear Models (GLM) are not able to precisely map tan1-a, a known...

Data from: Genome-wide discovery and characterization of maize long non-coding RNAs

Lin Li, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng-Ting Yeh, Wei Wu, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C. P. Timmermans, Nathan M. Springer & Gary J. Muehlbauer
Background: Long noncoding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown. Results: By exploiting available public ESTs, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNA. Of these lncRNAs, more than 90% are predicted to be...

Registration Year

  • 2013
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Affiliations

  • Iowa State University
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  • Columbia University
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  • Duke University
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  • Department of Plant Biology
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  • University of North Carolina
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  • University of Minnesota
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  • Institute of Primate Research
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  • University of Wisconsin-Madison
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  • University of Paris-Sud
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  • University of South Carolina
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