Biology subjects

Puckett, E. E.

Publications and source records attributed to Puckett, E. E..

6 recordsLinked to original sources

bioRxiv2026

Measuring American black bear genetic load in fixed structural variants and runs of homozygosity

Populations living in geographically isolated regions are expected to have reduced gene flow, increased genetic drift, and elevated levels of inbreeding, influencing both genetic load and possibly the distribution of structural variants. The American black bear (Ursus americanus) is widely found across Ontario, Canada, where populations inhabit diverse landscapes ranging from relatively intact contiguous forested landscapes to isolated regions such as the Saugeen Peninsula. Here, we investigated the population genomic history across five Ontario black bear populations using a combination of short-read (SR) and long-read (LR) sequencing data. We compared population genetic metrics including nucleotide diversity ({pi}), Tajimas D, runs of homozygosity (ROH), and genome-wide structural variants (SVs) to assess population health and identify signatures of isolation. Our results showed that the isolated Saugeen Peninsula population is genetically distinct and exhibited reduced nucleotide diversity, greater ROH and SV abundance compared with mainland populations. The population also showed elevated genetic load in all genomic features, suggesting increased exposure of deleterious variation that are expressed in ROH and population specific SVs. We further discuss the integration of ROH, SVs and genetic load in conservation assessments.

genomics↗

bioRxiv2026

Population specific bottlenecks inflated differentiation measures of Louisiana black bear and negate subspecific status

Significant debate has revolved around the delimitation of subspecific boundaries relative to conservation policy, and specifically how best to maximize limited resources. The conservation of subspecies captures intraspecific genetic diversity and aids in the long-term preservation of adaptive potential. Here, we evaluate patterns of neutral and adaptive genomic variation across the eastern lineage of the American black bear. We specifically assess the relative impact of phylogeographic history and local adaptation on differentiation of subpopulations in Louisiana, which were federally protected as a subspecies from 1992-2016. Despite high values of genetic differentiation (Fst >0.127) of these focal populations, we show that serial founder events during range expansion into eastern North America and multiple bottlenecks drove patterns of diversity within Louisiana. While we attribute initial population divergence between Louisiana subpopulations to east-west shifts of the Mississippi River between 6.2 - 2.7kya, drift accelerated following bottlenecks that were likely due to indigenous societies cultural and land-use changes and later to impacts of European fur traders. We further show that local adaptation has had a smaller impact (4.6%) than phylogeography (30.1%) on the distribution of genomic variation across this lineage. The strongest drivers of adaptive variation include mean annual temperature and monthly precipitation variation, where northern populations have substantial derived variation. Our genomic assessment, in conjunction with weak phenotypic data, does not support the continued recognition of Ursus americanus luteolus as a subspecies of American black bear. Continued genetic conservation efforts should focus on maintaining or increasing diversity, while supporting ongoing successes of demographic recovery.

evolutionary biology↗

bioRxiv2023

Convergent molecular constraint in mammalian carnivores: Selection on liver and kidney functions during the evolution of more carnivorous diets

Mammalia comprises a great diversity of diet types and associated adaptations. An understanding of the genomic mechanisms underlying these adaptations may offer insights for improving human health. Comparative genomic studies of diet that employ taxonomically restricted analyses or simplified diet classifications may suffer reduced power to detect molecular convergence associated with diet evolution. Here, we used a quantitative carnivory score--indicative of the amount of animal protein in the diet--for 80 mammalian species to detect significant correlations between the relative evolutionary rates of genes and changes in diet. We identified six genes--ACADSB, CLDN16, CPB1, PNLIP, SLC13A2, and SLC14A2--that experienced significant changes in evolutionary constraint alongside changes in carnivory score, becoming less constrained in lineages evolving more herbivorous diets. We further considered the biological functions associated with diet evolution and observed that pathways related to amino acid and lipid metabolism, biological oxidation, and small molecule transport experienced reduced purifying selection as lineages became more herbivorous. Liver and kidney functions showed similar patterns of constraint with dietary change. Our results indicate that, in highly carnivorous lineages, selection acts on the liver and kidneys to maintain sufficient metabolism and excretion of substances found in excess in carnivorous diets. These biological functions become less important with the evolution of increasing herbivory, so experience a relaxation of constraint in more herbivorous lineages.

genomics↗

bioRxiv2022

Genetic architecture and evolution of color variation in American black bears

Color variation is a frequent evolutionary substrate for camouflage in small mammals but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus, exhibits a range of colors including the cinnamon morph which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (P < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that impaired protein localization and decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos, but is not fixed across the range. HIGHLIGHTSO_LIThe cinnamon morph of American black bears and brown bears have different missense mutations in TYRP1 that account for their similar coloration C_LIO_LITYRP1 variants in American black bears and brown bears are loss-of-function alleles associated with impaired protein localization to melanosomes C_LIO_LIIn American black bears, the variant causing the cinnamon morph arose 9,360 years ago in the western lineage where it provides an adaptive advantage, and has spread northwards and eastwards by migration C_LI

evolutionary biology↗

bioRxiv2021

Evolution of degrees of carnivory and dietary specialization across Mammalia and their effects on speciation

AO_SCPLOWBSTRACTC_SCPLOWConflation between omnivory and dietary generalism limits ecological and evolutionary analyses of diet, including estimating contributions to speciation and diversification. Additionally, categorizing species into qualitative dietary classes leads to information loss in these analyses. Here, we constructed two continuous variables - degree of carnivory (i.e., the position along the continuum from complete herbivory to complete carnivory) and degree of dietary specialization (i.e., the number and variety of food resources utilized) - to elucidate their histories across Mammalia, and to tease out their independent contributions to mammalian speciation. We observed that degree of carnivory significantly affected speciation rate across Mammalia, whereas dietary specialization did not. We further considered phylogenetic level in diet-dependent speciation and saw that degree of carnivory significantly affected speciation in ungulates, carnivorans, bats, eulipotyphlans, and marsupials, while the effect of dietary specialization was only significant in carnivorans. Across Mammalia, omnivores had the lowest speciation rates. Our analyses using two different categorical diet variables led to contrasting signals of diet-dependent diversification, and subsequently different conclusions regarding diets macroevolutionary role. We argue that treating variables such as diet as continuous instead of categorical reduces information loss and avoids the problem of contrasting macroevolutionary signals caused by differential discretization of biologically continuous traits.

evolutionary biology↗

bioRxiv2018

Brown rat demography reveals pre-commensal structure in eastern Asia prior to expansion into Southeast Asia during the Song dynasty

Fossil evidence indicates that the globally-distributed brown rat (Rattus norvegicus) originated in northern China and Mongolia. Historical records report the human-mediated invasion of rats into Europe in the 1500s, followed by global spread due to European imperialist activity during the1600s-1800s. We analyzed 14 genomes representing seven previously identified evolutionary clusters and tested alternative demographic models to infer patterns of range expansion, divergence times, and changes in effective population (Ne) size for this globally important pest species. We observed three range expansions from the ancestral population that produced the Pacific (~4.8kya), eastern China (diverged ~0.55kya), and Southeast (SE) Asia (~0.53kya) lineages. Our model shows a rapid range expansion from SE Asia into the Middle East then continued expansion into central Europe 537 years ago (1478 AD). We observed declining Ne within all brown rat lineages from 150-1kya, reflecting population contractions during glacial cycles. Ne increased since 1kya in Asian and European, but not Pacific, evolutionary clusters. Our results support the hypothesis that northern Asia was the ancestral range for brown rats. We suggest that southward human migration across China between 800-1550s AD resulted in the introduction of rats to SE Asia, from which they rapidly expanded via existing maritime trade routes. Finally, we discovered that North America was colonized separately on both the Atlantic and Pacific seaboards, yet by evolutionary clusters of vastly different ages and genomic diversity levels. Our results should stimulate discussions among historians and zooarcheologists regarding the relationship between humans and rats.

evolutionary biology↗