Biology subjects

Susan C Alberts

Publications and source records attributed to Susan C Alberts.

3 recordsLinked to original sources

bioRxiv2015

Efficient genome-wide sequencing and low coverage pedigree analysis from non-invasively collected samples

Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping non-invasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from non-invasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA, and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only non-invasive samples are available. The lab protocol and software (\"WHODAD\") are freely available at www.tung-lab.org/protocols and www.xzlab.org/software, respectively.

Genomics↗

bioRxiv2014

The Genetic Architecture of Gene Expression Levels in Wild Baboons

Gene expression variation is well documented in human populations and its genetic architecture has been extensively explored. However, we still know little about the genetic architecture of gene expression variation in other species, particularly our closest living relatives, the nonhuman primates. To address this gap, we performed an RNA sequencing (RNA-seq)-based study of 63 wild baboons, members of the intensively studied Amboseli baboon population in Kenya. Our study design allowed us to measure gene expression levels and identify genetic variants using the same data set, enabling us to perform complementary mapping of putative cis-acting expression quantitative trait loci (eQTL) and measurements of allele-specific expression (ASE) levels. We discovered substantial evidence for genetic effects on gene expression levels in this population. Surprisingly, we found more power to detect individual eQTL in the baboons relative to a HapMap human data set of comparable size, probably as a result of greater genetic variation, enrichment of SNPs with high minor allele frequencies, and longer-range linkage disequilibrium in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes. Interestingly, genes with eQTL significantly overlapped between the baboon and human data sets, suggesting that some genes may tolerate more genetic perturbation than others, and that this property may be conserved across species. Finally, we used a Bayesian sparse linear mixed model to partition genetic, demographic, and early environmental contributions to variation in gene expression levels. We found a strong genetic contribution to gene expression levels for almost all genes, while individual demographic and environmental effects tended to be more modest. Together, our results establish the feasibility of eQTL mapping using RNA-seq data alone, and act as an important first step towards understanding the genetic architecture of gene expression variation in nonhuman primates.

Genomics↗

bioRxiv2014

Exaggerated estrous swellings and male mate choice in primates: testing the reliable indicator hypothesis in the Amboseli baboons.

INTRODUCTION INTRODUCTION METHODS RESULTS DISCUSSION LITERATURE CITED The evolution of male mate choice in sex-role reversed species can easily be understood according to the general principles of sexual selection. That is, when females are mate-limited they are expected to compete for access to males and those males, in turn, are expected to be choosy. This phenomenon is well described in some sex-role reversed species of pipefish (Berglund et al. 1989; Vincent et al. 1992) and shorebirds (Szekely & Reynolds 1995). In contrast, when the sex roles are conventional, choosy males will be at a competitive disadvantage and, therefore, male mate choice should be selected against. Of course, exceptions to this prediction have been demonstrated, most notably in those cases where fe ...

Animal Behavior and Cognition↗