Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models

Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document micro-evolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have causal effects on fitness, but few valid tests of this exist. Here we show, using a quantitative genetic framework and six decades of life-history data on two free-living populations of great tits Parus major, that selection estimates for egg-laying date and clutch size are relatively unbiased. Predicted responses to selection based on the Robertson-Price Identity were similar to those based on the multivariate breeder’s equation, indicating that unmeasured covarying traits were not missing from the analysis. Changing patterns of phenotypic selection on these traits (for laying date, linked to climate change) therefore reflect changing selection on breeding values, and genetic constraints appear not to limit their independent evolution. Quantitative genetic analysis of correlational data from pedigreed populations can be a valuable complement to experimental approaches to help identify whether apparent associations between traits and fitness are biased by missing traits, and to parse the roles of direct versus indirect selection across a range of environments.

Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in Condylostoma magnum

mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3' end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state.mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3' end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state.

Prevalence and genetic diversity of Blastocystis in family units living in the United States

The human gut is host to a diversity of microorganisms including the single-celled microbial eukaryote Blastocystis. Although Blastocystis has a global distribution, there is dearth of information relating to its prevalence and diversity in many human populations. The mode of Blastocystis transmission to humans is also insufficiently characterised, however, it is speculated to vary between different populations. Here we investigated the incidence and genetic diversity of Blastocystis in a US population and also the possibility of Blastocystis human-human transmission between healthy individuals using family units (N = 50) living in Boulder, Colorado as our sample-set. Ten of the 139 (~ 7%) individuals in our dataset were positive for Blastocystis, nine of whom were adults and one individual belonging to the children/adolescents group. All positive cases were present in different family units. A number of different Blastocystis subtypes (species) were detected with no evidence of mixed infections. The prevalence of Blastocystis in this subset of the US population is comparatively low relative to other industrialised populations investigated to date; however, subtype diversity was largely consistent with that previously reported in studies of European populations. The distribution of Blastocystis within family units indicates that human-human transmission is unlikely to have occurred within families that participated in this study. It is not unexpected that given the world-wide variation in human living conditions and lifestyles between different populations, both the prevalence of Blastocystis and its mode of transmission to humans may vary considerably.