Biology subjects

Baird, S. E.

Publications and source records attributed to Baird, S. E..

3 recordsLinked to original sources

bioRxiv2026

A gap-free, telomere-to-telomere genome assembly for the Caenorhabditis briggsae reference strain AF16

The nematode Caenorhabditis elegans was the first metazoan to have its genome completely sequenced and assembled. Since that time, researchers have continuously updated the reference genome and manually curated its approximately 20,000 genes. The closely related species, Caenorhabditis briggsae, has served as a comparative model because of its similar morphology, mode of reproduction, and patterns of intra-species genetic variation. However, the genomic resources for C. briggsae lag behind C. elegans, hindering comparative genomics studies between the species. Decades of experimentation have been performed in the AF16 reference strain genetic background, so we obtained high-coverage long-read sequencing and high-throughput chromosome conformation capture data to create an updated reference genome for an isogenic derivative of AF16, named CGC2. The CGC2 genome is vastly improved relative to the existing AF16 assemblies, with no unplaced sequence, no gaps, and telomere-to-telomere contiguity. To provide genomic resources for CGC2, we exploited deep RNA-seq libraries from all developmental stages to predict protein-coding gene annotations comparable in accuracy and completeness to the existing AF16 gene models. We also performed lift-over of 108 validated insertion-deletion variants to the updated coordinate system of the CGC2 genome to facilitate future mappings of mutations. In summary, we present an updated reference genome for the canonical AF16 reference strain with improved genomic resources to enable high-quality intra- and inter-species comparative studies.

genomics↗

bioRxiv2024

Air Pocket for a Non-Air-Breathing Fish: Developing Respirometry Methodology for the critically endangered Delta Smelt

Respirometry quantifies O2 consumption to estimate metabolic activity across stressor(s), and the resulting data is central for devising conservation strategies for fishes. Due to its rapid adoption and widespread utility, protocols have been established to foster quality control and increase consistency. However, the application of established respirometry protocols on the Delta Smelt (Hypomesus transpacificus) have been largely unsuccessful, with reports over the past 12 years documenting high mortality rates that can only be circumvented with very short measurement duration ([~]4 h). This prevents the measurement of standard metabolic rate (SMR) and critical O2 tension (Pcrit), and ultimately obstructed physiological research, management actions and conservation tools development. In this study, we detailed the anecdotal, behavioral and empirical evidence that culminated in successful measurements of Delta Smelt SMR and Pcrit at 10, 12, 15, 17 and 19{degrees}C. We discovered the Delta Smelt is physotomous and requires frequent refilling of its air bladder to maintain buoyancy. Inspired by air-breathing fish respirometry, the inclusion of an air pocket within their chamber led to considerably more robust respirometry measurements compared to past attempts. The influence of fasting and time of day on O2 consumption were also examined. Altogether, this methodology paves the way for acquiring critical knowledge needed to inform Delta Smelt research and conservation (e.g. the development of metabolic index). The lessons learned may also have implications for other aspects of Delta Smelt conservation such as decreasing conservation aquaculture operating costs and improving survival during fish transport and supplementation.

physiology↗

bioRxiv2019

Genetically distinct behavioral modules underlie natural variation in thermal performance curves

Thermal reaction norms pervade organismal traits as stereotyped responses to temperature, a fundamental environmental input into sensory and physiological systems. Locomotory behavior represents an especially plastic read-out of animal response, with its dynamic dependence on environmental stimuli presenting a challenge for analysis and for understanding the genomic architecture of heritable variation. Here we characterize behavioral reaction norms as thermal performance curves for the nematode Caenorhabditis briggsae, using a collection of 23 wild isolate genotypes and 153 recombinant inbred lines to quantify the extent of genetic and plastic variation in locomotory behavior to temperature changes. By reducing the dimensionality of the multivariate phenotypic response with a function-valued trait framework, we identified genetically distinct behavioral modules that contribute to the heritable variation in the emergent overall behavioral thermal performance curve. Quantitative trait locus mapping isolated regions on Chromosome II associated with locomotory activity at benign temperatures and Chromosome V loci related to distinct aspects of sensitivity to high temperatures, with each quantitative trait locus explaining up to 28% of trait variation. These findings highlight how behavioral responses to environmental inputs as thermal reaction norms can evolve through independent changes to genetically distinct modular components of such complex phenotypes.\n\nArticle SummaryPlastic responses to environmental inputs, reaction norm phenotypes that can be summarized with parameters of fits to a mathematical function, are pervasive across diverse organismal traits and crucial to organismal fitness. We quantified the nematode Caenorhabditis briggsaes behavioral thermal performance curves as function-valued traits for 23 wild isolate genotypes and 153 recombinant inbred lines. We identified quantitative trait loci on multiple chromosomes that define genetically distinct behavioral modules contributing to the emergent overall behavioral thermal performance curve. These findings highlight how dynamic behavioral responses to environmental inputs can evolve through independent changes to genetically distinct modular components of such complex phenotypes.

evolutionary biology↗