Biology subjects

Dolby, G. A.

Publications and source records attributed to Dolby, G. A..

3 recordsLinked to original sources

bioRxiv2023

Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly

Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z-chromosome scaffolds. These putative Z-chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.

evolutionary biology↗

bioRxiv2022

Social determinants of health and disease in companion dogs: A cohort study from the Dog Aging Project

Exposure to social environmental adversity is associated with health and survival in many social species, including humans. However, little is known about if and how these health and mortality effects vary across the lifespan, largely due to the difficulty of studying long-lived organisms across much of their lifespan. Here, we leveraged a relatively new and powerful model for human aging, the companion dog, to investigate which components of the social environment are associated with dog health and how these associations vary across the lifespan. We drew on comprehensive survey data collected on 21,410 dogs from the Dog Aging Project and identified five factors that together explained 33.7% of the variation in a dogs social environment. Factors capturing financial and household adversity were associated with poorer health and lower physical mobility in companion dogs, while factors that captured social support, such as living with other dogs, were associated with better health when controlling for dog age and weight. Some of these associations differed across a dogs lifespan, including a stronger relationship between owner age and health in younger (as compared to older) dogs. Taken together, these findings suggest the importance of income, stability, and owner age on owner-reported health outcomes in companion dogs and point to potential behavioral and/or environmental modifiers that can be used to promote healthy aging across species.

evolutionary biology↗

bioRxiv2021

The information signature of diverging lineages

Divergence and speciation are the generators of biodiversity on Earth. Yet, we still seek to understand why species are unevenly distributed across taxa and geographic settings. This is partly because we lack a way to directly compare aspects of population divergence across unrelated species and an integrative quantitative framework for how geographical setting relates to genetic divergence. Here we postulate that, based on communications theory, there is a communications channel between Earths surface and the structuring of genomic information among populations. Each species is a separate receiver of this message. Organism traits determine the clarity of that channel. Calculating the partial information decomposition (PID) of genetic metrics under different evolutionary scenarios can measure the signature of this communication. We show in silico how the informational decomposition of 97,200 genetic lattices varies as lineages diverge. The decomposed nodes of Tajimas D, {theta}W, and {pi} show strong context-dependent information signatures, while FST was least informative. Specific decompositions detected whether lineages divergence with or without gene flow better than current SFS-based tools. The study of information in an evolutionary genomic and landscape context suggests it may be a helpful framework and for understanding the diversity of life across Earth and their coevolution.

evolutionary biology↗