Marin, K. | Search bioRxiv

bioRxiv2023

SurvBal: Compositional Microbiome Balances for Survival Outcomes

Identification of balances of bacterial taxa in relation to continuous and dichotomous outcomes is an increasingly frequent analytic objective in microbiome profiling experiments. SurvBal enables the selection of balances in relation to censored survival or time-to-event outcomes which are of considerable interest in many biomedical studies. The most commonly used survival models - the Cox proportional hazards and parametric survival models are included in the package, which are used in combination with step-wise selection procedures to identify the optimal associated balance of microbiome, i.e., the ratio of the geometric means of two groups of taxas relative abundances. Availability and implementationSurvBal is available as an R package and a Shiny app: https://github.com/yinglia/SurvBal, https://yinglistats.shinyapps.io/shinyapp-survbal/.

bioinformatics↗

bioRxiv2019

Size reductions and genomic changes associated with harvesting within two generations in wild walleye populations

The extent and rate of harvest-induced genetic changes in natural populations may impact population productivity, recovery and persistence. While there is substantial evidence for phenotypic changes in harvested fishes, knowledge of genetic change in the wild remains limited, as phenotypic and genetic data are seldom considered in tandem, and the number of generations needed for genetic changes to occur is not well understood. We quantified changes in size-at-age, sex-specific changes in body size, and genomic metrics in three harvested walleye (Sander vitreus) populations and a fourth reference population with low harvest levels over a 15-year period in Mistassini Lake, Quebec. We also collected Traditional Ecological Knowledge (TEK) surrounding concerns about these populations over time. Using [~]9000 SNPs, genomic metrics included changes in population structure, neutral genomic diversity, effective population size and signatures of selection. TEK revealed concerns about overall reductions in body size and number of fish caught. Smaller body size, smaller size-at-age, changing population structure (population differentiation within one river and homogenization between two others), and signatures of selection between historical and contemporary samples reflected coupled phenotypic and genomic change in the three harvested populations in both sexes, while no change occurred in the reference population. Sex-specific analyses revealed differences in both body size and genomic metrics but were inconclusive about whether one sex was disproportionately affected. Our results support that harvest-induced genetic changes can arise within 1-2.5 generations in long-lived wild fishes, demonstrating the need to investigate concerns about harvest-induced evolution quickly once they have been raised.

ecology↗