skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


  • NSF Public Access
  • Search Results
  • Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
Title: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian 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 use 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 have identified six genes—ACADSB,CLDN16,CPB1,PNLIP,SLC13A2, andSLC14A2—that experienced significant changes in evolutionary constraint alongside changes in carnivory score, becoming less constrained in lineages evolving more herbivorous diets. We further consider the biological functions associated with diet evolution and observe 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 show similar patterns of constraint with dietary change. Our results indicate that these functions are important for the consumption of animal matter and become less important with the evolution of increasing herbivory. So, genes expressed in these tissues experience a relaxation of evolutionary constraint in more herbivorous lineages.  more » « less
Award ID(s):
2233124
PAR ID:
10560865
Author(s) / Creator(s):
; ;
Publisher / Repository:
Genome Research
Date Published:
Journal Name:
Genome Research
ISSN:
1088-9051
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; ; ; ; et al (, Molecular Ecology)
    null (Ed.)
    Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored. 
    more » « less
  2. ; ; ; ; ; ; ; ; ; ; et al (, Molecular ecology)
    Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defence receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defence response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance antiviral immune response while dampening inflammatory signalling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored. 
    more » « less
  3. ; ; ; ; ; ; ; ; ; (, Molecular Ecology)
    ABSTRACT Herbivorous insects tolerate chemical and metabolic variation in their host plant diet by modulating physiological traits. Insect immune response is one such trait that plays a crucial role in maintaining fitness but can be heavily influenced by variation in host plant quality. An important question is how the use of different host plants affects the ability of herbivorous insects to resist viral pathogens. Furthermore, the transcriptional changes associated with this interaction of diet and viral pathogens remain understudied. The Melissa blue butterfly (Lycaeides melissa) has colonised the exotic legumeMedicago sativaas a larval host within the past 200 years. We used this system to study the interplay between the effects of host plant variation and viral infection on physiological responses and global gene expression. We measured immune strength in response to infection by the Junonia coenia densovirus (JcDV) in two ways: (1) direct measurement of phenoloxidase activity and melanisation, and (2) transcriptional sequencing of individuals exposed to different viral and host plant treatments. Our results demonstrate that viral infection caused total phenoloxidase (total PO) to increase and viral infection and host plant interactively affected total PO such that for infected larvae, total PO was significantly higher for larvae consuming the native host plant. Additionally,L. melissalarvae differentially expressed several hundred genes in response to host plant treatment, but with minimal changes in gene expression in response to viral infection. Not only immune genes, but several detoxification, transporter, and oxidase genes were differentially expressed in response to host plant treatments. These results demonstrate that in herbivorous insects, consumption of a novel host plant can alter both physiological and transcriptional responses relevant to viral infection, emphasising the importance of considering immune and detoxification mechanisms into models of evolution of host range in herbivorous insects. 
    more » « less
  4. ; (, The Anatomical Record)
    Abstract Despite documented ecomorphological shifts toward an herbivorous diet in several coelurosaurian lineages, the evolutionary tempo and mode of these changes remain poorly understood, hampered by sparse cranial materials for early representatives of major clades. This is particularly true for Therizinosauria, with representative crania best known for the late‐divergingErlikosaurus andrewsiand the early taxonJianchangosaurus yixianensis. Here we describe a series of new cranial bones ofFalcarius utahensis, the geologically oldest therizinosaurian from the Early Cretaceous Cedar Mountain Formation, Utah, United States. This new material provides the most complete understanding of the skull to date forFalcariusand frames the pattern and timing of cranial evolution in therizinosaurians and early coelurosaurians. Previously unknown elements include a well‐preserved maxilla, jugal, parietals, squamosal, laterosphenoids, and pterygoid. Computed tomography data differentiate the incisiform rostral dentary dentition from possible premaxillary teeth, the first in a therizinosaurian. Notable features include a primitive morphology of the jugal and frontoparietal complex shared with other early diverging taxa (e.g., tyrannosauroids,Incisivosaurus,Ornitholestes, Fukuivenator), and a large maxillary fenestra, convergent with troodontids. Additional specimens of previously known elements confirm their taxonomic utility and provide insight into intraspecific variation. Following patterns of other archosaurs, variable traits relate to the prominence of ridges and contours (likely associated with musculature) and the proportions of pneumatic features, whereas invariant traits correspond to the topology of bony contacts and major cranial nerves. Early, integrated evolution of the rostrum and adductor complex characterized early therizinosaurians, which was further modified alongside reduced paranasal complexity in later therizinosaurids. 
    more » « less
  5. ; ; ; ; ; ; ; ; (, Genome Biology and Evolution)
    Graham, Allie (Ed.)
    Abstract Adaptation to extreme environments often involves the evolution of dramatic physiological changes. To better understand how organisms evolve these complex phenotypic changes, the repeatability and predictability of evolution, and possible constraints on adapting to an extreme environment, it is important to understand how adaptive variation has evolved. Poeciliid fishes represent a particularly fruitful study system for investigations of adaptation to extreme environments due to their repeated colonization of toxic hydrogen sulfide–rich springs across multiple species within the clade. Previous investigations have highlighted changes in the physiology and gene expression in specific species that are thought to facilitate adaptation to hydrogen sulfide–rich springs. However, the presence of adaptive nucleotide variation in coding and regulatory regions and the degree to which convergent evolution has shaped the genomic regions underpinning sulfide tolerance across taxa are unknown. By sampling across seven independent lineages in which nonsulfidic lineages have colonized and adapted to sulfide springs, we reveal signatures of shared evolutionary rate shifts across the genome. We found evidence of genes, promoters, and putative enhancer regions associated with both increased and decreased convergent evolutionary rate shifts in hydrogen sulfide–adapted lineages. Our analysis highlights convergent evolutionary rate shifts in sulfidic lineages associated with the modulation of endogenous hydrogen sulfide production and hydrogen sulfide detoxification. We also found that regions with shifted evolutionary rates in sulfide spring fishes more often exhibited convergent shifts in either the coding region or the regulatory sequence of a given gene, rather than both. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email