Biology subjects

Pollard, M. D.

Publications and source records attributed to Pollard, M. D..

4 recordsLinked to original sources

bioRxiv2025

Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae

The flowering plant order Asterales exhibits a striking disparity in species richness, with >30,000 species in Asteraceae compared to <50 in its sister family Calyceraceae. To investigate the genomic basis of this imbalance, we assembled three new chromosome-level genomes, including the first for Calyceraceae, and re-annotated five additional genomes. Comparative analyses revealed exceptionally high repeat content in both Asteraceae and Calyceraceae, pervasive chromosomal rearrangements, and evidence for shared and lineage-specific WGDs. In Asteraceae, tandem and dispersed duplications disproportionately drove expansions of gene families linked to secondary metabolism and stress response, while segmental duplicates bore signatures of adaptive selection for the regulation of biosynthetic and metabolic processes. Selective pressures on flowering time regulators suggest an evolved balance between regulatory flexibility and developmental constraint in floral diversification. These patterns reveal that, beyond ancient polyploidy, small-scale duplications and selective fine-tuning of regulatory networks underpinned the ecological versatility in Asteraceae, fueling its extraordinary diversification.

genomics↗

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↗