Biology subjects

Cheek, R. G.

Publications and source records attributed to Cheek, R. G..

3 recordsLinked to original sources

bioRxiv2025

Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including [~]100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.

evolutionary biology↗

bioRxiv2023

ONeSAMP 3.0: Effective Population Size via SNP Data for One Population Sample

O_LIThe genetic effective size (Ne) is arguably one of the most important characteristics of a population as it impacts the rate of loss of genetic diversity. Genetic estimators of (Ne) increasingly popular tools in population and conservation genetic studies. Yet there are very few methods that can estimate the Ne from data from a single population and without extensive information about the genetics of the population, such as a linkage map, or a reference genome of the species of interest. C_LIO_LIWe present ONeSAMP 3.0, an algorithm for estimating Ne from single nucleotide polymorphism (SNP) data collected from a single population sample using Approximate Bayesian Computation and local linear regression. C_LIO_LIWe demonstrate the utility of this approach using simulated Wright-Fisher populations, and empirical data from five endangered Channel Island fox (Urocyon littoralis) populations to evaluate the performance of ONeSAMP 3.0 compared to a commonly used Ne estimator. Our results show that ONeSAMP 3.0 is robust to the number of individual samples and number of loci included in and appears accurate even if the range of true Ne values is large. C_LIO_LIThis method is broadly applicable to natural populations and is flexible enough that future versions could easily include summary statistics appropriate for a suite of biological and sampling conditions. ONeSAMP 3.0 is publicly available under the GNU license at https://github.com/AaronHong1024/ONeSAMP_3 and also available with Bioconda (https://bioconda.github.io/index.html). C_LI

bioinformatics↗

bioRxiv2017

Down Feather Structure Varies Between High And Low Elevation Male Andean Torrent Ducks (Merganetta armata)

Feathers are one of the defining characteristics of birds and serve a critical role in thermal insulation and physical protection against the environment. Feather structure is known to vary among individuals, and it has been suggested that populations exposed to different environmental conditions may exhibit different patterns in feather structure. We examined both down and contour feathers from two populations of male Torrent Ducks (Merganetta armata) from Lima, Peru, including one high-altitude population from the Chancay-Huaral River at approximately 3500 meters (m) elevation and one low-altitude population from the Chillon River at approximately 1500 m. Down feather structure differed significantly between the two populations. Ducks from the high-altitude population had longer, denser down compared with low-altitude individuals. Contour feather structure varied greatly among individuals but showed no significant difference between populations. These results suggest that the innermost, insulative layer of plumage (the down), may have developed in response to lower ambient temperatures at high elevations. The lack of observable differences in the contour feathers may be due to the general constraints of the waterproofing capability of this outer plumage layer.\n\nResumenEl plumaje es una caracteristica que define a las aves y cumple roles criticos en el aislamiento termico y proteccion fisica del ambiente. Se sabe que la estructura de las plumas varia ente individuos, y se ha sugerido que poblaciones expuestas a diferentes condiciones ambientales pueden exhibir diferentes patrones en la estructura de las plumas. En este estudio se examinaron tanto el plumon como las plumas de contorno de machos adultos del Pato de los Torrentes (Merganetta armata) de dos poblaciones, una en el rio Chancay-Huaral a 3,500 msnm y otra en el rio Chillon a 1,500 msnm, ubicadas en Lima, Peru. La estructura de los plumones difiere significativamente entre las dos poblaciones. Los patos de la poblacion a grandes elevaciones tienen plumones largos, y densos comparados con los individuos de las partes bajas. La estructura de las plumas de contorno varia ampliamente entre individuos pero no muestra diferencias significativas entre poblaciones. Estos resultados sugieren que las diferencias entre las capas interiores de aislamiento del plumaje (plumon), haberse desarrollado como respuesta en ambientes de bajas temperaturas a grandes elevaciones. En cambio la falta de detectables diferencias en las plumas de contorno puede ser debido a la constante seleccion en la capacidad impermeable de la capa de plumas exteriores.

zoology↗