1
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Telizhenko V, Kosiol C, McGowen MR, Gol'din P. Relaxed selection in evolution of genes regulating limb development gives clue to variation in forelimb morphology of cetaceans and other mammals. Proc Biol Sci 2024; 291:20241106. [PMID: 39378996 DOI: 10.1098/rspb.2024.1106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/29/2024] [Accepted: 09/02/2024] [Indexed: 10/10/2024] Open
Abstract
Cetaceans have evolved unique limb structures, such as flippers, due to genetic changes during their transition to aquatic life. However, the full understanding of the genetic and evolutionary mechanisms behind these changes is still developing. By examining 25 limb-related protein-coding genes across various mammalian species, we compared genetic changes between aquatic mammals, like whales, and other mammals with unique limb structures such as bats, rodents and elephants. Our findings revealed significant modifications in limb-related genes, including variations in the Hox, GDF5 and Evx genes. Notably, a relaxed selection in several key genes was observed, suggesting a lifting of developmental constraints, which might have facilitated the emergence of morphological innovations in cetacean limb morphology. We also uncovered non-synonymous changes, insertions and deletions in these genes, particularly in the polyalanine tract of HOXD13, which are distinctive to cetaceans or convergent with other aquatic mammals. These genetic variations correlated with the diverse and specialized limb structures observed in cetaceans, indicating a complex interplay of relaxed selection and specific mutations in mammalian limb evolution.
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Affiliation(s)
| | - Carolin Kosiol
- University of St Andrews , St Andrews, Fife KY16 9TF, UK
| | - Michael R McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History , Washington, DC 20560, USA
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2
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Ewart KM, Ho SYW, Chowdhury AA, Jaya FR, Kinjo Y, Bennett J, Bourguignon T, Rose HA, Lo N. Pervasive relaxed selection in termite genomes. Proc Biol Sci 2024; 291:20232439. [PMID: 38772424 DOI: 10.1098/rspb.2023.2439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 05/02/2024] [Indexed: 05/23/2024] Open
Abstract
Genetic changes that enabled the evolution of eusociality have long captivated biologists. More recently, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequences of eusociality in termites, we analysed nine genomes, including newly sequenced genomes from three non-eusocial cockroaches. Using a phylogenomic approach, we found that termite genomes have experienced lower rates of synonymous substitutions than those of cockroaches, possibly as a result of longer generation times. We identified higher rates of non-synonymous substitutions in termite genomes than in cockroach genomes, and identified pervasive relaxed selection in the former (24-31% of the genes analysed) compared with the latter (2-4%). We infer that this is due to reductions in effective population size, rather than gene-specific effects (e.g. indirect selection of caste-biased genes). We found no obvious signature of increased genetic load in termites, and postulate efficient purging of deleterious alleles at the colony level. Additionally, we identified genomic adaptations that may underpin caste differentiation, such as genes involved in post-translational modifications. Our results provide insights into the evolution of termites and the genomic consequences of eusociality more broadly.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Al-Aabid Chowdhury
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Frederick R Jaya
- Ecology & Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Yukihiro Kinjo
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Okinawa International University, Okinawa, Japan
| | - Juno Bennett
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Harley A Rose
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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3
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Barkdull M, Moreau CS. Worker Reproduction and Caste Polymorphism Impact Genome Evolution and Social Genes Across the Ants. Genome Biol Evol 2023; 15:evad095. [PMID: 37243539 PMCID: PMC10287540 DOI: 10.1093/gbe/evad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Eusocial insects are characterized by several traits, including reproductive division of labor and caste polymorphisms, which likely modulate genome evolution. Concomitantly, evolution may act on specific genes and pathways underlying these novel, sociality-associated phenotypes. Reproductive division of labor should increase the magnitude of genetic drift and reduce the efficacy of selection by reducing effective population size. Caste polymorphism has been associated with relaxed selection and may facilitate directional selection on caste-specific genes. Here, we use comparative analyses of 22 ant genomes to test how reproductive division of labor and worker polymorphism influence positive selection and selection intensity across the genome. Our results demonstrate that worker reproductive capacity is associated with a reduction in the degree of relaxed selection but is not associated with any significant change to positive selection. We find decreases in positive selection in species with polymorphic workers, but no increase in the degree of relaxed selection. Finally, we explore evolutionary patterns in specific candidate genes associated with our focal traits in eusocial insects. Two oocyte patterning genes previously implicated in worker sterility evolve under intensified selection in species with reproductive workers. Behavioral caste genes generally experience relaxed selection associated with worker polymorphism, whereas vestigial and spalt, both associated with soldier development in Pheidole ants, experience intensified selection in worker polymorphic species. These findings expand our understanding of the genetic mechanisms underlying elaborations of sociality. The impacts of reproductive division of labor and caste polymorphisms on specific genes illuminate those genes' roles in generating complex eusocial phenotypes.
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Affiliation(s)
- Megan Barkdull
- Department of Ecology & Evolutionary Biology, Cornell University
| | - Corrie S Moreau
- Department of Ecology & Evolutionary Biology, Cornell University
- Department of Entomology, Cornell University
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Gu H, Wang L, Lv X, Yang W, Zhang L, Zhang Z, Zhu T, Jia Y, Chen Y, Qu L. Domestication affects sex-biased gene expression evolution in the duck. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221313. [PMID: 37035296 PMCID: PMC10073915 DOI: 10.1098/rsos.221313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Genes with sex-biased expression are thought to underlie sexually dimorphic phenotypes and are therefore subject to different selection pressures in males and females. Many authors have proposed that sexual conflict leads to the evolution of sex-biased expression, which allows males and females to reach separate phenotypic and fitness optima. The selection pressures associated with domestication may cause changes in population architectures and mating systems, which in turn can alter their direction and strength. We compared sex-biased expression and genetic signatures in wild and domestic ducks (Anas platyrhynchos), and observed changes of sexual selection and identified the genomic divergence affected by selection forces. The extent of sex-biased expression in both sexes is positively correlated with the level of both d N /d S and nucleotide diversity. This observed changing pattern may mainly be owing to relaxed genetic constraints. We also demonstrate a clear link between domestication and sex-biased evolutionary rate in a comparative framework. Decreased polymorphism and evolutionary rate in domesticated populations generally matched life-history phenotypes known to experience artificial selection. Taken together, our work suggests the important implications of domestication in sex-biased evolution and the roles of artificial selection and sexual selection for shaping the diversity and evolutionary rate of the genome.
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Affiliation(s)
- Hongchang Gu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Li Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Zebin Zhang
- Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tao Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
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5
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Chen Y, Tan S, Fu J. Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans). J Mol Evol 2022; 90:389-399. [PMID: 36029325 DOI: 10.1007/s00239-022-10070-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
High-elevation adaptation provides an excellent system for examining adaptive evolution, and adaptive variations may manifest at gene expression or any other phenotypic levels. We examined gene expression profiles of Asiatic toads (Bufo gargarizans) along an elevational gradient from both wild and common-garden acclimated populations. Asiatic toads originated from high altitudes have distinctive gene expression patterns. We identified 18 fixed differentially expressed genes (DEGs), which are different in both wild and acclimated samples, and 1217 plastic DEGs, which are different among wild samples. The expression levels of most genes were linearly correlated with altitude gradient and down-regulated in high-altitude populations. Expression variations of several genes associated with metabolic process are fixed, and we also identified a co-expression module that is significantly different between acclimated populations and has functions related to DNA repair. The differential expression of the vast majority genes, however, are due to phenotypic plasticity, revealing the highly plastic nature of gene expression variations. Expression modification of some specific genes related to metabolism and response to UV radiation play crucial role in adaptation to high altitude for Asiatic toads. Common-garden experiments are essential for evaluating adaptive evolution of natural populations.
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Affiliation(s)
- Ying Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
- The University of Chinese Academy of Science, Beijing, China.
| | - Song Tan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- The University of Chinese Academy of Science, Beijing, China
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
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6
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Villacastin AJ, Adams KS, Boonjue R, Rushton PJ, Han M, Shen JQ. Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice. Sci Rep 2021; 11:14887. [PMID: 34290268 PMCID: PMC8295372 DOI: 10.1038/s41598-021-94109-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/05/2021] [Indexed: 01/30/2023] Open
Abstract
WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identified prevalence of Group III WRKYs despite differences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that finely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversification of an important gene family under strong selective pressure for biotechnological improvements of the world's most valued food crop.
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Affiliation(s)
- Anne J Villacastin
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Keeley S Adams
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Rin Boonjue
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Paul J Rushton
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Mira Han
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Jeffery Q Shen
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA.
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7
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de la Serna Buzon SM, Martin RA, Pfennig DW. Carryover effects and the evolution of polyphenism. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractAn individual’s early-life environment and phenotype often influence its traits and performance as an adult. We investigated whether such ‘carryover effects’ are associated with alternative, environmentally-induced phenotypes (‘polyphenism’), and, if so, whether they influence the evolution of polyphenism. To do so, we studied Mexican spadefoot toads, Spea multiplicata, which have evolved a polyphenism consisting of two, dramatically different forms: a carnivore morph and an omnivore morph. We sampled both morphs from a fast-drying and a slow-drying pond and reared them to sexual maturity. Larval environment (pond) strongly influenced survival as well as age and size at metamorphosis and sexual maturity; i.e. environment-dependent carryover effects were present. By contrast, larval phenotype (morph) did not affect life-history traits at sexual maturity; i.e. phenotype-dependent carryover effects were absent. These results are consistent with theory, which suggests that by amplifying selective trade-offs in heterogenous environments, environment-dependent carryover effects might foster the evolution of polyphenism. At the same time, by freeing selection to refine a novel phenotype without altering the existing form, the absence of phenotype-dependent carryover effects might enable polyphenism to evolve in the first place. Generally, carryover effects might play an underappreciated role in the evolution of polyphenism.
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Affiliation(s)
| | - Ryan A Martin
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA
| | - David W Pfennig
- Department of Biology, CB#3280, University of North Carolina, Chapel Hill, NC, USA
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8
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Draghi J. Phenotypic variability can promote the evolution of adaptive plasticity by reducing the stringency of natural selection. J Evol Biol 2019; 32:1274-1289. [DOI: 10.1111/jeb.13527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Jeremy Draghi
- Department of Biological Sciences Virginia Tech Blacksburg VA USA
- Department of Biology Brooklyn College CUNY Brooklyn NY USA
- The Graduate Center of the City University of New York New York NY USA
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9
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Bui LT, Ragsdale EJ. Multiple plasticity regulators reveal targets specifying an induced predatory form in nematodes. Mol Biol Evol 2019; 36:2387-2399. [PMID: 31364718 DOI: 10.1093/molbev/msz171] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/19/2019] [Accepted: 07/17/2019] [Indexed: 12/19/2022] Open
Abstract
The ability to translate a single genome into multiple phenotypes, or developmental plasticity, defines how phenotype derives from more than just genes. However, to study the evolutionary targets of plasticity and their evolutionary fates, we need to understand how genetic regulators of plasticity control downstream gene expression. Here, we have identified a transcriptional response specific to polyphenism (i.e., discrete plasticity) in the nematode Pristionchus pacificus. This species produces alternative resource-use morphs - microbivorous and predatory forms, differing in the form of their teeth, a morphological novelty - as influenced by resource availability. Transcriptional profiles common to multiple polyphenism-controlling genes in P. pacificus reveal a suite of environmentally sensitive loci, or ultimate target genes, that make up an induced developmental response. Additionally, in vitro assays show that one polyphenism regulator, the nuclear receptor (NR) NHR-40, physically binds to promoters with putative HNF4⍺ (the NR class including NHR-40) binding sites, suggesting this receptor may directly regulate genes that describe alternative morphs. Among differentially expressed genes were morph-limited genes, highlighting factors with putative "on-off" function in plasticity regulation. Further, predatory morph-biased genes included candidates - namely, all four P. pacificus homologs of Hsp70, which have HNF4⍺ motifs - whose natural variation in expression matches phenotypic differences among P. pacificus wild isolates. In summary, our study links polyphenism regulatory loci to the transcription producing alternative forms of a morphological novelty. Consequently, our findings establish a platform for determining how specific regulators of morph-biased genes may influence selection on plastic phenotypes.
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Affiliation(s)
- Linh T Bui
- Department of Biology, Indiana University, Bloomington, IN
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10
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Warner MR, Mikheyev AS, Linksvayer TA. Transcriptomic basis and evolution of the ant nurse-larval social interactome. PLoS Genet 2019; 15:e1008156. [PMID: 31107868 DOI: 10.1101/514356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/31/2019] [Accepted: 04/24/2019] [Indexed: 05/20/2023] Open
Abstract
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant larval development by collecting and sequencing the transcriptomes of interacting nurses and larvae across time. We find that the majority of nurse and larval transcriptomes exhibit parallel expression dynamics across larval development. We leverage this widespread nurse-larva gene co-expression to infer putative social gene regulatory networks acting between nurses and larvae. Genes with the strongest inferred social effects tend to be peripheral elements of within-tissue regulatory networks and are often known to encode secreted proteins. This includes interesting candidates such as the nurse-expressed giant-lens, which may influence larval epidermal growth factor signaling, a pathway known to influence various aspects of insect development. Finally, we find that genes with the strongest signatures of social regulation tend to experience relaxed selective constraint and are evolutionarily young. Overall, our study provides a first glimpse into the molecular and evolutionary features of the social mechanisms that regulate all aspects of social life.
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Affiliation(s)
- Michael R Warner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Timothy A Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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11
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Warner MR, Mikheyev AS, Linksvayer TA. Transcriptomic basis and evolution of the ant nurse-larval social interactome. PLoS Genet 2019; 15:e1008156. [PMID: 31107868 PMCID: PMC6544314 DOI: 10.1371/journal.pgen.1008156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/31/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant larval development by collecting and sequencing the transcriptomes of interacting nurses and larvae across time. We find that the majority of nurse and larval transcriptomes exhibit parallel expression dynamics across larval development. We leverage this widespread nurse-larva gene co-expression to infer putative social gene regulatory networks acting between nurses and larvae. Genes with the strongest inferred social effects tend to be peripheral elements of within-tissue regulatory networks and are often known to encode secreted proteins. This includes interesting candidates such as the nurse-expressed giant-lens, which may influence larval epidermal growth factor signaling, a pathway known to influence various aspects of insect development. Finally, we find that genes with the strongest signatures of social regulation tend to experience relaxed selective constraint and are evolutionarily young. Overall, our study provides a first glimpse into the molecular and evolutionary features of the social mechanisms that regulate all aspects of social life.
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Affiliation(s)
- Michael R. Warner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Timothy A. Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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12
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Touchon JC, Robertson JM. You cannot have it all: Heritability and constraints of predator‐induced developmental plasticity in a Neotropical treefrog. Evolution 2018; 72:2758-2772. [DOI: 10.1111/evo.13632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 10/10/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Justin Charles Touchon
- Biology Department Boston University Boston Massachusetts 02215
- Current Address: Biology Department Vassar College Poughkeepsie New York 12604
| | - Jeanne Marie Robertson
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York 14853
- Current Address: Department of Biology California State University Northridge California 91330
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13
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Morphological novelty emerges from pre-existing phenotypic plasticity. Nat Ecol Evol 2018; 2:1289-1297. [PMID: 29988161 DOI: 10.1038/s41559-018-0601-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/08/2018] [Indexed: 02/01/2023]
Abstract
Plasticity-first evolution (PFE) posits that novel features arise when selection refines pre-existing phenotypic plasticity into an adaptive phenotype. However, PFE is controversial because few tests have been conducted in natural populations. Here we present evidence that PFE fostered the origin of an evolutionary novelty that allowed certain amphibians to invade a new niche-a distinctive carnivore morph. We compared morphology, gene expression and growth of three species of spadefoot toad tadpoles when reared on alternative diets: Scaphiopus holbrookii, which (like most frogs) never produce carnivores; Spea multiplicata, which sometimes produce carnivores, but only through diet-induced plasticity; and Spea bombifrons, which often produce carnivores regardless of diet. Consistent with PFE, we found diet-induced plasticity-in morphology and gene expression-in Sc. holbrookii, adaptive refinement of this plasticity in Sp. multiplicata, and further refinement of the carnivore phenotype in Sp. bombifrons. Generally, phenotypic plasticity might play a significant, if underappreciated, role in evolutionary innovation.
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14
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Renn SCP, O'Rourke CF, Aubin-Horth N, Fraser EJ, Hofmann HA. Dissecting the Transcriptional Patterns of Social Dominance across Teleosts. Integr Comp Biol 2018; 56:1250-1265. [PMID: 27940616 DOI: 10.1093/icb/icw118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In many species, under varying ecological conditions, social interactions among individuals result in the formation of dominance hierarchies. Despite general similarities, there are robust differences among dominance hierarchies across species, populations, environments, life stages, sexes, and individuals. Understanding the proximate mechanisms underlying the variation is an important step toward understanding the evolution of social behavior. However, physiological changes associated with dominance, such as gonadal maturation and somatic growth, often complicate efforts to identify the specific underlying mechanisms. Traditional gene expression analyses are useful for generating candidate gene lists, but are biased by choice of significance cut-offs and difficult to use for between-study comparisons. In contrast, complementary analysis tools allow one to both test a priori hypotheses and generate new hypotheses. Here we employ a meta-analysis of high-throughput expression profiling experiments to investigate the gene expression patterns that underlie mechanisms and evolution of behavioral social phenotypes. Specifically, we use a collection of datasets on social dominance in fish across social contexts, sex, and species. Using experimental manipulation to produce female dominance hierarchies in the cichlid Astatotilapia burtoni, heralded as a genomic model of social dominance, we generate gene lists, and assess molecular gene modules. In the dominant female gene expression profile, we demonstrate a strong pattern of up-regulation of genes previously identified as having male-biased expression and furthermore, compare expression biases between male and female dominance phenotypes. Using a threshold-free approach to identify correlation throughout ranked gene lists, we query previously published datasets associated with maternal behavior, alternative reproductive tactics, cooperative breeding, and sex-role reversal to describe correlations among these various neural gene expression profiles associated with different instances of social dominance. These complementary approaches capitalize on the high-throughput gene expression profiling from similar behavioral phenotypes in order to address the mechanisms associated with social dominance behavioral phenotypes.
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Affiliation(s)
- Suzy C P Renn
- *Department of Biology, Reed College, 3203 SE Woodstock blvd, Portland, OR 97202, USA
| | - Cynthia F O'Rourke
- *Department of Biology, Reed College, 3203 SE Woodstock blvd, Portland, OR 97202, USA
| | - Nadia Aubin-Horth
- Département de Biologie & Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Avenue de la Médecine - Local 1242 Québec G1V 0A6, QC Canada
| | - Eleanor J Fraser
- UCSF School of Medicine, 513 Parnassus Ave, Med Sci, San Francisco, CA 94122, USA
| | - Hans A Hofmann
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, 2415 Speedway - C0990, Austin, TX 78705, USA
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15
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Langenhof MR, Komdeur J. Why and how the early-life environment affects development of coping behaviours. Behav Ecol Sociobiol 2018; 72:34. [PMID: 29449757 PMCID: PMC5805793 DOI: 10.1007/s00265-018-2452-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 01/19/2018] [Accepted: 01/25/2018] [Indexed: 01/02/2023]
Abstract
Understanding the ways in which individuals cope with threats, respond to challenges, make use of opportunities and mediate the harmful effects of their surroundings is important for predicting their ability to function in a rapidly changing world. Perhaps one of the most essential drivers of coping behaviour of adults is the environment experienced during their early-life development. Although the study of coping, defined as behaviours displayed in response to environmental challenges, has a long and rich research history in biology, recent literature has repeatedly pointed out that the processes through which coping behaviours develop in individuals are still largely unknown. In this review, we make a move towards integrating ultimate and proximate lines of coping behaviour research. After broadly defining coping behaviours (1), we review why, from an evolutionary perspective, the development of coping has become tightly linked to the early-life environment (2), which relevant developmental processes are most important in creating coping behaviours adjusted to the early-life environment (3), which influences have been shown to impact those developmental processes (4) and what the adaptive significance of intergenerational transmission of coping behaviours is, in the context of behavioural adaptations to a fast changing world (5). Important concepts such as effects of parents, habitat, nutrition, social group and stress are discussed using examples from empirical studies on mammals, fish, birds and other animals. In the discussion, we address important problems that arise when studying the development of coping behaviours and suggest solutions.
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Affiliation(s)
- M. Rohaa Langenhof
- Behavioural Physiology and Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Jan Komdeur
- Behavioural Physiology and Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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16
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Warner MR, Mikheyev AS, Linksvayer TA. Genomic Signature of Kin Selection in an Ant with Obligately Sterile Workers. Mol Biol Evol 2017; 34:1780-1787. [PMID: 28419349 PMCID: PMC5455959 DOI: 10.1093/molbev/msx123] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Kin selection is thought to drive the evolution of cooperation and conflict, but the specific genes and genome-wide patterns shaped by kin selection are unknown. We identified thousands of genes associated with the sterile ant worker caste, the archetype of an altruistic phenotype shaped by kin selection, and then used population and comparative genomic approaches to study patterns of molecular evolution at these genes. Consistent with population genetic theoretical predictions, worker-upregulated genes experienced reduced selection compared with genes upregulated in reproductive castes. Worker-upregulated genes included more taxonomically restricted genes, indicating that the worker caste has recruited more novel genes, yet these genes also experienced reduced selection. Our study identifies a putative genomic signature of kin selection and helps to integrate emerging sociogenomic data with longstanding social evolution theory.
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Affiliation(s)
- Michael R Warner
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan
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17
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Chau LM, Goodisman MAD. Gene duplication and the evolution of phenotypic diversity in insect societies. Evolution 2017; 71:2871-2884. [PMID: 28875541 DOI: 10.1111/evo.13356] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 12/16/2022]
Abstract
Gene duplication is an important evolutionary process thought to facilitate the evolution of phenotypic diversity. We investigated if gene duplication was associated with the evolution of phenotypic differences in a highly social insect, the honeybee Apis mellifera. We hypothesized that the genetic redundancy provided by gene duplication could promote the evolution of social and sexual phenotypes associated with advanced societies. We found a positive correlation between sociality and rate of gene duplications across the Apoidea, indicating that gene duplication may be associated with sociality. We also discovered that genes showing biased expression between A. mellifera alternative phenotypes tended to be found more frequently than expected among duplicated genes than singletons. Moreover, duplicated genes had higher levels of caste-, sex-, behavior-, and tissue-biased expression compared to singletons, as expected if gene duplication facilitated phenotypic differentiation. We also found that duplicated genes were maintained in the A. mellifera genome through the processes of conservation, neofunctionalization, and specialization, but not subfunctionalization. Overall, we conclude that gene duplication may have facilitated the evolution of social and sexual phenotypes, as well as tissue differentiation. Thus this study further supports the idea that gene duplication allows species to evolve an increased range of phenotypic diversity.
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Affiliation(s)
- Linh M Chau
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
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18
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Projecto-Garcia J, Biddle JF, Ragsdale EJ. Decoding the architecture and origins of mechanisms for developmental polyphenism. Curr Opin Genet Dev 2017; 47:1-8. [PMID: 28810163 DOI: 10.1016/j.gde.2017.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 01/09/2023]
Abstract
Developmental polyphenism affords a single genotype multiple solutions to match an organism to its environment. Because polyphenism is the extreme example of how development deviates from a linear genetic blueprint, it demands a genetic explanation for how environmental cues shunt development to hypothetically alternative modules. We highlight several recent advances that have begun to illuminate genetic mechanisms for polyphenism and how this recurring developmental novelty may arise. An emerging genetic knowledge of polyphenism is providing precise targets for testing hypotheses of how switch mechanisms are built-out of olfactory, nutrient-sensing, hormone-reception, and developmental and genetic buffering systems-to accommodate plasticity. Moreover, classic and new model systems are testing the genetic basis of polyphenism's proposed causal roles in evolutionary change.
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Affiliation(s)
- Joana Projecto-Garcia
- Department of Biology, Indiana University, 915 E. 3rd St., Bloomington, IN 47405, United States
| | - Joseph F Biddle
- Department of Biology, Indiana University, 915 E. 3rd St., Bloomington, IN 47405, United States
| | - Erik J Ragsdale
- Department of Biology, Indiana University, 915 E. 3rd St., Bloomington, IN 47405, United States.
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19
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Schrader L, Helanterä H, Oettler J. Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior. Mol Biol Evol 2017; 34:535-544. [PMID: 27999112 PMCID: PMC5400372 DOI: 10.1093/molbev/msw240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Plastic gene expression underlies phenotypic plasticity and plastically expressed genes evolve under different selection regimes compared with ubiquitously expressed genes. Social insects are well-suited models to elucidate the evolutionary dynamics of plastic genes for their genetically and environmentally induced discrete polymorphisms. Here, we study the evolution of plastically expressed genes in the ant Cardiocondyla obscurior—a species that produces two discrete male morphs in addition to the typical female polymorphism of workers and queens. Based on individual-level gene expression data from 28 early third instar larvae, we test whether the same evolutionary dynamics that pertain to plastically expressed genes in adults also pertain to genes with plastic expression during development. In order to quantify plasticity of gene expression over multiple contrasts, we develop a novel geometric measure. For genes expressed during development, we show that plasticity of expression is positively correlated with evolutionary rates. We furthermore find a strong correlation between expression plasticity and expression variation within morphs, suggesting a close link between active and passive plasticity of gene expression. Our results support the notion of relaxed selection and neutral processes as important drivers in the evolution of adaptive plasticity.
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Affiliation(s)
- Lukas Schrader
- Institut für Zoologie, Universität Regensburg, Regensburg, Germany.,Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jan Oettler
- Institut für Zoologie, Universität Regensburg, Regensburg, Germany
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20
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Levis NA, Serrato‐Capuchina A, Pfennig DW. Genetic accommodation in the wild: evolution of gene expression plasticity during character displacement. J Evol Biol 2017; 30:1712-1723. [DOI: 10.1111/jeb.13133] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 12/14/2022]
Affiliation(s)
- N. A. Levis
- Department of Biology University of North Carolina Chapel Hill NC USA
| | | | - D. W. Pfennig
- Department of Biology University of North Carolina Chapel Hill NC USA
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21
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Pespeni MH, Ladner JT, Moczek AP. Signals of selection in conditionally expressed genes in the diversification of three horned beetle species. J Evol Biol 2017; 30:1644-1657. [PMID: 28379613 DOI: 10.1111/jeb.13079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 03/05/2017] [Indexed: 01/20/2023]
Abstract
Species radiations may be facilitated by phenotypic differences already present within populations, such as those arising through sex-specific development or developmental processes biased towards particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among- and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the genus: horn location, polarity of sexual dimorphism and degree of nutritional sensitivity. Our approach combined de novo transcript assembly, assessment of amino acid substitutions (dN/dS) across orthologous gene pairs and integration of gene function and conditional gene expression data. We identified 17 genes across the three species pairs related to axis patterning, development and metabolism with dN/dS > 1 and detected elevated dN/dS in genes related to metabolism and biosynthesis in the most closely related species pair, which is characterized by a loss of nutritional polyphenism and a reversal of sexual dimorphism. Further, we found that genes that are conditionally expressed (i.e. as a function of sex, nutrition or body region) within one of our focal species also showed significantly stronger signals of positive or relaxed purifying selection between species divergent along the same morphological axis (i.e. polarity of sexual dimorphism, degree of nutritional sensitivity or location of horns). Our findings thus reveal a positive relationship between intraspecific differentiation due to condition-specific development and genetic divergences among species.
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Affiliation(s)
- M H Pespeni
- Department of Biology, Indiana University, Bloomington, IN, USA.,Department of Biology, University of Vermont, Burlington, VT, USA
| | - J T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - A P Moczek
- Department of Biology, Indiana University, Bloomington, IN, USA
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22
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Morandin C, Mikheyev AS, Pedersen JS, Helanterä H. Evolutionary constraints shape caste-specific gene expression across 15 ant species. Evolution 2017; 71:1273-1284. [PMID: 28262920 DOI: 10.1111/evo.13220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/16/2017] [Indexed: 12/22/2022]
Abstract
Development of polymorphic phenotypes from similar genomes requires gene expression differences. However, little is known about how morph-specific gene expression patterns vary on a broad phylogenetic scale. We hypothesize that evolution of morph-specific gene expression, and consequently morph-specific phenotypic evolution, may be constrained by gene essentiality and the amount of pleiotropic constraints. Here, we use comparative transcriptomics of queen and worker morphs, that is, castes, from 15 ant species to understand the constraints of morph-biased gene expression. In particular, we investigate how measures of evolutionary constraints at the sequence level (expression level, connectivity, and number of gene ontology [GO] terms) correlate with morph-biased expression. Our results show that genes indeed vary in their potential to become morph-biased. The existence of genes that are constrained in becoming caste-biased potentially limits the evolutionary decoupling of the caste phenotypes, that is, it might result in "caste load" occasioning from antagonistic fitness variation, similarly to sexually antagonistic fitness variation between males and females. On the other hand, we suggest that genes under low constraints are released from antagonistic variation and thus more likely to be co-opted for morph specific use. Overall, our results suggest that the factors that affect sequence evolutionary rates and evolution of plastic expression may largely overlap.
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Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan.,Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia
| | - Jes Søe Pedersen
- Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
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23
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Jones BM, Kingwell CJ, Wcislo WT, Robinson GE. Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality. Proc Biol Sci 2017; 284:20162228. [PMID: 28053060 PMCID: PMC5247497 DOI: 10.1098/rspb.2016.2228] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022] Open
Abstract
Developmental plasticity may accelerate the evolution of phenotypic novelty through genetic accommodation, but studies of genetic accommodation often lack knowledge of the ancestral state to place selected traits in an evolutionary context. A promising approach for assessing genetic accommodation involves using a comparative framework to ask whether ancestral plasticity is related to the evolution of a particular trait. Bees are an excellent group for such comparisons because caste-based societies (eusociality) have evolved multiple times independently and extant species exhibit different modes of eusociality. We measured brain and abdominal gene expression in a facultatively eusocial bee, Megalopta genalis, and assessed whether plasticity in this species is functionally linked to eusocial traits in other bee lineages. Caste-biased abdominal genes in M. genalis overlapped significantly with caste-biased genes in obligately eusocial bees. Moreover, caste-biased genes in M. genalis overlapped significantly with genes shown to be rapidly evolving in multiple studies of 10 bee species, particularly for genes in the glycolysis pathway and other genes involved in metabolism. These results provide support for the idea that eusociality can evolve via genetic accommodation, with plasticity in facultatively eusocial species like M. genalis providing a substrate for selection during the evolution of caste in obligately eusocial lineages.
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Affiliation(s)
- Beryl M Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Smithsonian Tropical Research Institute, Panama City 20521-9100, Panama
| | - Callum J Kingwell
- Smithsonian Tropical Research Institute, Panama City 20521-9100, Panama
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - William T Wcislo
- Smithsonian Tropical Research Institute, Panama City 20521-9100, Panama
| | - Gene E Robinson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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24
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Schneider RF, Meyer A. How plasticity, genetic assimilation and cryptic genetic variation may contribute to adaptive radiations. Mol Ecol 2016; 26:330-350. [PMID: 27747962 DOI: 10.1111/mec.13880] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/30/2016] [Accepted: 10/07/2016] [Indexed: 12/13/2022]
Abstract
There is increasing evidence that phenotypic plasticity can promote population divergence by facilitating phenotypic diversification and, eventually, genetic divergence. When a 'plastic' population colonizes a new habitat, it has the possibility to occupy multiple niches by expressing several distinct phenotypes. These initially reflect the population's plastic range but may later become genetically fixed by selection via the process of 'genetic assimilation' (GA). Through this process multiple specialized sister lineages can arise that share a common plastic ancestor - the 'flexible stem'. Here, we review possible molecular mechanisms through which natural selection could fix an initially plastic trait during GA. These mechanisms could also explain how GA may contribute to cryptic genetic variation that can subsequently be coopted into other phenotypes or traits, but also lead to nonadaptive responses. We outline the predicted patterns of genetic and transcriptional divergence accompanying flexible stem radiations. The analysis of such patterns of (retained) adaptive and nonadaptive plastic responses within and across radiating lineages can inform on the state of ongoing GA. We conclude that, depending on the stability of the environment, the molecular architecture underlying plastic traits can facilitate diversification, followed by fixation and consolidation of an adaptive phenotype and degeneration of nonadaptive ones. Additionally, the process of GA may increase the cryptic genetic variation of populations, which on one hand may serve as substrate for evolution, but on another may be responsible for nonadaptive responses that consolidate local allopatry and thus reproductive isolation.
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Affiliation(s)
- Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitaetstrasse 10, 78457, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitaetstrasse 10, 78457, Konstanz, Germany
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25
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Ehrenreich IM, Pfennig DW. Genetic assimilation: a review of its potential proximate causes and evolutionary consequences. ANNALS OF BOTANY 2016; 117:769-79. [PMID: 26359425 PMCID: PMC4845796 DOI: 10.1093/aob/mcv130] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 06/29/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Most, if not all, organisms possess the ability to alter their phenotype in direct response to changes in their environment, a phenomenon known as phenotypic plasticity. Selection can break this environmental sensitivity, however, and cause a formerly environmentally induced trait to evolve to become fixed through a process called genetic assimilation. Essentially, genetic assimilation can be viewed as the evolution of environmental robustness in what was formerly an environmentally sensitive trait. Because genetic assimilation has long been suggested to play a key role in the origins of phenotypic novelty and possibly even new species, identifying and characterizing the proximate mechanisms that underlie genetic assimilation may advance our basic understanding of how novel traits and species evolve. SCOPE This review begins by discussing how the evolution of phenotypic plasticity, followed by genetic assimilation, might promote the origins of new traits and possibly fuel speciation and adaptive radiation. The evidence implicating genetic assimilation in evolutionary innovation and diversification is then briefly considered. Next, the potential causes of phenotypic plasticity generally and genetic assimilation specifically are examined at the genetic, molecular and physiological levels and approaches that can improve our understanding of these mechanisms are described. The review concludes by outlining major challenges for future work. CONCLUSIONS Identifying and characterizing the proximate mechanisms involved in phenotypic plasticity and genetic assimilation promises to help advance our basic understanding of evolutionary innovation and diversification.
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Affiliation(s)
- Ian M Ehrenreich
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA and
| | - David W Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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26
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Murren CJ, Auld JR, Callahan H, Ghalambor CK, Handelsman CA, Heskel MA, Kingsolver JG, Maclean HJ, Masel J, Maughan H, Pfennig DW, Relyea RA, Seiter S, Snell-Rood E, Steiner UK, Schlichting CD. Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity. Heredity (Edinb) 2015; 115:293-301. [PMID: 25690179 PMCID: PMC4815460 DOI: 10.1038/hdy.2015.8] [Citation(s) in RCA: 313] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/21/2014] [Accepted: 12/15/2014] [Indexed: 12/13/2022] Open
Abstract
Phenotypic plasticity is ubiquitous and generally regarded as a key mechanism for enabling organisms to survive in the face of environmental change. Because no organism is infinitely or ideally plastic, theory suggests that there must be limits (for example, the lack of ability to produce an optimal trait) to the evolution of phenotypic plasticity, or that plasticity may have inherent significant costs. Yet numerous experimental studies have not detected widespread costs. Explicitly differentiating plasticity costs from phenotype costs, we re-evaluate fundamental questions of the limits to the evolution of plasticity and of generalists vs specialists. We advocate for the view that relaxed selection and variable selection intensities are likely more important constraints to the evolution of plasticity than the costs of plasticity. Some forms of plasticity, such as learning, may be inherently costly. In addition, we examine opportunities to offset costs of phenotypes through ontogeny, amelioration of phenotypic costs across environments, and the condition-dependent hypothesis. We propose avenues of further inquiry in the limits of plasticity using new and classic methods of ecological parameterization, phylogenetics and omics in the context of answering questions on the constraints of plasticity. Given plasticity's key role in coping with environmental change, approaches spanning the spectrum from applied to basic will greatly enrich our understanding of the evolution of plasticity and resolve our understanding of limits.
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Affiliation(s)
- C J Murren
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - J R Auld
- Department of Biology, West Chester University, West Chester, PA, USA
| | - H Callahan
- Barnard College, Columbia University, New York, NY, USA
| | - C K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - C A Handelsman
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - M A Heskel
- Research School of Biology, Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - J G Kingsolver
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - H J Maclean
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - J Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - D W Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - R A Relyea
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - S Seiter
- Department of Ecology and Evolution, University of Colorado Boulder, Boulder, CO, USA
| | - E Snell-Rood
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, USA
| | - U K Steiner
- Department of Biology, University of Southern Denmark, Max-Planck Odense Centre on the Biodemography of Aging, Odense, Denmark
| | - C D Schlichting
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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27
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Smith CR, Helms Cahan S, Kemena C, Brady SG, Yang W, Bornberg-Bauer E, Eriksson T, Gadau J, Helmkampf M, Gotzek D, Okamoto Miyakawa M, Suarez AV, Mikheyev A. How Do Genomes Create Novel Phenotypes? Insights from the Loss of the Worker Caste in Ant Social Parasites. Mol Biol Evol 2015; 32:2919-31. [PMID: 26226984 PMCID: PMC4651238 DOI: 10.1093/molbev/msv165] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A central goal of biology is to uncover the genetic basis for the origin of new
phenotypes. A particularly effective approach is to examine the genomic
architecture of species that have secondarily lost a phenotype with respect to
their close relatives. In the eusocial Hymenoptera, queens and workers have
divergent phenotypes that may be produced via either expression of alternative
sets of caste-specific genes and pathways or differences in expression patterns
of a shared set of multifunctional genes. To distinguish between these two
hypotheses, we investigated how secondary loss of the worker phenotype in
workerless ant social parasites impacted genome evolution across two independent
origins of social parasitism in the ant genera Pogonomyrmex and
Vollenhovia. We sequenced the genomes of three social
parasites and their most-closely related eusocial host species and compared gene
losses in social parasites with gene expression differences between host queens
and workers. Virtually all annotated genes were expressed to some degree in both
castes of the host, with most shifting in queen-worker bias across developmental
stages. As a result, despite >1 My of divergence from the last common
ancestor that had workers, the social parasites showed strikingly little
evidence of gene loss, damaging mutations, or shifts in selection regime
resulting from loss of the worker caste. This suggests that regulatory changes
within a multifunctional genome, rather than sequence differences, have played a
predominant role in the evolution of social parasitism, and perhaps also in the
many gains and losses of phenotypes in the social insects.
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Affiliation(s)
| | | | - Carsten Kemena
- Institute for Evolution and Biodiversity, Westfälische Wilhems-Universität Münster, Münster, Germany
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington DC
| | - Wei Yang
- Department of Computer Science, University of Illinois Urbana-Champaign
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfälische Wilhems-Universität Münster, Münster, Germany
| | - Ti Eriksson
- School of Life Sciences, Arizona State University
| | | | | | - Dietrich Gotzek
- Department of Entomology, University of Georgia Department of Animal Biology, University of Illinois Urbana-Champaign
| | - Misato Okamoto Miyakawa
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - Andrew V Suarez
- Department of Animal Biology, University of Illinois Urbana-Champaign Department of Entomology, University of Illinois Urbana-Champaign
| | - Alexander Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
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28
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Morandin C, Dhaygude K, Paviala J, Trontti K, Wheat C, Helanterä H. Caste-biases in gene expression are specific to developmental stage in the ant Formica exsecta. J Evol Biol 2015; 28:1705-18. [PMID: 26172873 DOI: 10.1111/jeb.12691] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 02/02/2023]
Abstract
Understanding how a single genome creates and maintains distinct phenotypes is a central goal in evolutionary biology. Social insects are a striking example of co-opted genetic backgrounds giving rise to dramatically different phenotypes, such as queen and worker castes. A conserved set of molecular pathways, previously envisioned as a set of 'toolkit' genes, has been hypothesized to underlie queen and worker phenotypes in independently evolved social insect lineages. Here, we investigated the toolkit from a developmental point of view, using RNA-Seq to compare caste-biased gene expression patterns across three life stages (pupae, emerging adult and old adult) and two female castes (queens and workers) in the ant Formica exsecta. We found that the number of genes with caste-biased expression increases dramatically from pupal to old adult stages. This result suggests that phenotypic differences between queens and workers at the pupal stage may derive from a relatively low number of caste-biased genes, compared to higher number of genes required to maintain caste differences at the adult stage. Gene expression patterns were more similar among castes within developmental stages than within castes despite the extensive phenotypic differences between queens and workers. Caste-biased expression was highly variable among life stages at the level of single genes, but more consistent when gene functions (gene ontology terms) were investigated. Finally, we found that a large part of putative toolkit genes were caste-biased at least in some life stages in F. exsecta, and the caste-biases, but not their direction, were more often shared between F. exsecta and other ant species than between F. exsecta and bees. Our results indicate that gene expression should be examined across several developmental stages to fully reveal the genetic basis of polyphenisms.
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Affiliation(s)
- C Morandin
- Centre of Excellence in Biological Interactions, Department of Biosciences, Helsinki University, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - K Dhaygude
- Centre of Excellence in Biological Interactions, Department of Biosciences, Helsinki University, Helsinki, Finland
| | - J Paviala
- Centre of Excellence in Biological Interactions, Department of Biosciences, Helsinki University, Helsinki, Finland
| | - K Trontti
- Centre of Excellence in Biological Interactions, Department of Biosciences, Helsinki University, Helsinki, Finland
| | - C Wheat
- Department of Zoology, Population Genetics, Stockholm University, Stockholm, Sweden
| | - H Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, Helsinki University, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
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Mikheyev AS, Linksvayer TA. Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns. eLife 2015; 4:e04775. [PMID: 25621766 PMCID: PMC4383337 DOI: 10.7554/elife.04775] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/23/2015] [Indexed: 11/24/2022] Open
Abstract
Studies of the genetic basis and evolution of complex social behavior emphasize
either conserved or novel genes. To begin to reconcile these perspectives, we studied
how the evolutionary conservation of genes associated with social behavior depends on
regulatory context, and whether genes associated with social behavior exist in
distinct regulatory and evolutionary contexts. We identified modules of co-expressed
genes associated with age-based division of labor between nurses and foragers in the
ant Monomorium pharaonis, and we studied the relationship between
molecular evolution, connectivity, and expression. Highly connected and expressed
genes were more evolutionarily conserved, as expected. However, compared to the rest
of the genome, forager-upregulated genes were much more highly connected and
conserved, while nurse-upregulated genes were less connected and more evolutionarily
labile. Our results indicate that the genetic architecture of social behavior
includes both highly connected and conserved components as well as loosely connected
and evolutionarily labile components. DOI:http://dx.doi.org/10.7554/eLife.04775.001 Animal species vary widely in their degree of social behavior. Some species live
solitarily, and others, such as ants and humans, form large societies. Many
researchers have tried to understand the genetic changes underlying the evolution of
social behavior. Some researchers suggest that it involves recycling existing genes
that also have other conserved functions. Others propose that the evolution of social
behavior involves completely new genes that are not found in related but solitary
species. Ants are one of the best-studied social animals. An established colony can contain
many 1000s of individuals that live and work together and perform different roles.
The queen's job is to lay eggs, while the worker ants do everything else,
including collecting food, caring for the young, and protecting the colony. In some
species of ant—including the pharaoh ant—a worker's role changes
as it ages. Younger workers tend to stay in the nest and nurse the brood, while older
workers tend to leave the nest and forage for food. Mikheyev and Linksvayer asked: which genes are responsible for this age-based
division of labor? And how did this aspect of social behavior evolve? First, after
observing pharaoh ants from two colonies set up in the laboratory, they confirmed
that workers nursing the brood were on average almost a week younger than those seen
collecting food. Next Mikheyev and Linksvayer identified which genes were expressed
in ants of different ages, or ants engaged in different tasks. Specific sets of genes
were expressed more (or ‘up-regulated’) in nurse workers, while others
were up-regulated in foraging workers. Mikheyev and Linksvayer then investigated how rapidly these genes had evolved by
comparing them to related genes found in other social insects (fire ants and honey
bees). They also determined the ‘connectivity’ of these genes by asking
how many other genes showed similar expression patterns. In many organisms, how
rapidly a gene evolves depends on how tightly connected its expression is to the
expression of other genes; highly connected genes evolve more slowly. The genes that were expressed more in the older foraging workers were both more
highly connected and more evolutionarily conserved in the other social insects. Genes
that were up-regulated in the younger nurse workers were more loosely connected and
rapidly evolving. Mikheyev and Linksvayer's findings show that the evolution of social behavior
in animals involves both new genes, which tend to be loosely connected, and conserved
genes, which tend to be more highly connected. DOI:http://dx.doi.org/10.7554/eLife.04775.002
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Affiliation(s)
- Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
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Plasticity-mediated persistence in new and changing environments. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2014; 2014:416497. [PMID: 25386380 PMCID: PMC4216699 DOI: 10.1155/2014/416497] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/18/2022]
Abstract
Baldwin's synthesis of the Organicist position, first published in 1896 and elaborated in 1902, sought to rescue environmentally induced phenotypes from disrepute by showing their Darwinian significance. Of particular interest to Baldwin was plasticity's mediating role during environmental change or colonization—plastic individuals were more likely to successfully survive and reproduce in new environments than were nonplastic individuals. Once a population of plastic individuals had become established, plasticity could further mediate the future course of evolution. The evidence for plasticity-mediated persistence (PMP) is reviewed here with a particular focus on evolutionary rescue experiments, studies on invasive success, and the role of learning in survival. Many PMP studies are methodologically limited, showing that preexistent plasticity has utility in new environments (soft PMP) rather than directly demonstrating that plasticity is responsible for persistence (hard PMP). An ideal PMP study would be able to demonstrate that (1) plasticity preexisted environmental change, (2) plasticity was fortuitously beneficial in the new environment, (3) plasticity was responsible for individual persistence in the new environment, and (4) plasticity was responsible for population persistence in succeeding generations. Although PMP is not ubiquitous, Baldwin's hypotheses have been largely vindicated in theoretical and empirical studies, but much work remains.
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Helanterä H, Uller T. Neutral and adaptive explanations for an association between caste-biased gene expression and rate of sequence evolution. Front Genet 2014; 5:297. [PMID: 25221570 PMCID: PMC4148897 DOI: 10.3389/fgene.2014.00297] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/08/2014] [Indexed: 12/30/2022] Open
Abstract
The castes of social insects provide outstanding opportunities to address the causes and consequences of evolution of discrete phenotypes, i.e., polymorphisms. Here we focus on recently described patterns of a positive association between the degree of caste-specific gene expression and the rate of sequence evolution. We outline how neutral and adaptive evolution can cause genes that are morph-biased in their expression profiles to exhibit historical signatures of faster or slower sequence evolution compared to unbiased genes. We conclude that evaluation of different hypotheses will benefit from (i) reconstruction of the phylogenetic origin of biased expression and changes in rates of sequence evolution, and (ii) replicated data on gene expression variation within versus between morphs. Although the data are limited at present, we suggest that the observed phylogenetic and intra-population variation in gene expression lends support to the hypothesis that the association between caste-biased expression and rate of sequence evolution largely is a result of neutral processes.
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Affiliation(s)
- Heikki Helanterä
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of HelsinkiHelsinki, Finland
| | - Tobias Uller
- Department of Zoology, Edward Grey Institute, University of OxfordOxford, UK
- Department of Biology, University of LundSölvegatan, Lund, Sweden
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Ledon-Rettig CC, Pfennig DW, Chunco AJ, Dworkin I. Cryptic Genetic Variation in Natural Populations: A Predictive Framework. Integr Comp Biol 2014; 54:783-93. [DOI: 10.1093/icb/icu077] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Morandin C, Havukainen H, Kulmuni J, Dhaygude K, Trontti K, Helanterä H. Not only for egg yolk--functional and evolutionary insights from expression, selection, and structural analyses of Formica ant vitellogenins. Mol Biol Evol 2014; 31:2181-93. [PMID: 24895411 DOI: 10.1093/molbev/msu171] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Vitellogenin (Vg), a storage protein, has been extensively studied for its egg-yolk precursor role, and it has been suggested to be fundamentally involved in caste differences in social insects. More than one Vg copy has been reported in several oviparous species, including ants. However, the number and function of different Vgs, their phylogenetic relatedness, and their role in reproductive queens and nonreproductive workers have been studied in few species only. We studied caste-biased expression of Vgs in seven Formica ant species. Only one copy of conventional Vg was identified in Formica species, and three Vg homologs, derived from ancient duplications, which represent yet undiscovered Vg-like genes. We show that each of these Vg-like genes is present in all studied Hymenoptera and some of them in other insects as well. We show that after each major duplication event, at least one of the Vg-like genes has experienced a period of positive selection. This, combined with the observation that the Vg-like genes have acquired or lost specific protein domains suggests sub- or neofunctionalization between Vg and the duplicated genes. In contrast to earlier studies, Vg was not consistently queen biased in its expression, and the caste bias of the three Vg-like genes was highly variable among species. Furthermore, a truncated and Hymenoptera-specific Vg-like gene, Vg-like-C, was consistently worker biased. Multispecies comparisons are essential for Vg expression studies, and for gene expression studies in general, as we show that expression and also, putative functions cannot be generalized even among closely related species.
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Affiliation(s)
- Claire Morandin
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Helsinki, FinlandTvärminne Zoological Station, University of Helsinki, Helsinki, Finland
| | - Heli Havukainen
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Helsinki, FinlandDepartment of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Jonna Kulmuni
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Helsinki, FinlandDepartment of Biology and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Kishor Dhaygude
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Helsinki, Finland
| | - Kalevi Trontti
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Helsinki, FinlandDepartment of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Heikki Helanterä
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Helsinki, FinlandTvärminne Zoological Station, University of Helsinki, Helsinki, Finland
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34
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Purandare SR, Bickel RD, Jaquiery J, Rispe C, Brisson JA. Accelerated evolution of morph-biased genes in pea aphids. Mol Biol Evol 2014; 31:2073-83. [PMID: 24770714 DOI: 10.1093/molbev/msu149] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Phenotypic plasticity, the production of alternative phenotypes (or morphs) from the same genotype due to environmental factors, results in some genes being expressed in a morph-biased manner. Theoretically, these morph-biased genes experience relaxed selection, the consequence of which is the buildup of slightly deleterious mutations at these genes. Over time, this is expected to result in increased protein divergence at these genes between species and a signature of relaxed purifying selection within species. Here we test these theoretical expectations using morph-biased genes in the pea aphid, a species that produces multiple morphs via polyphenism. We find that morph-biased genes exhibit faster rates of evolution (in terms of dN/dS) relative to unbiased genes and that divergence generally increases with increasing morph bias. Further, genes with expression biased toward rarer morphs (sexual females and males) show faster rates of evolution than genes expressed in the more common morph (asexual females), demonstrating that the amount of time a gene spends being expressed in a morph is associated with its rate of evolution. And finally, we show that genes expressed in the rarer morphs experience decreased purifying selection relative to unbiased genes, suggesting that it is a relaxation of purifying selection that contributes to their faster rates of evolution. Our results provide an important empirical look at the impact of phenotypic plasticity on gene evolution.
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Affiliation(s)
| | | | - Julie Jaquiery
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Claude Rispe
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, FranceINRA, UMR1300 Biology, Epidemiology and Risk Analysis in Animal Health, Nantes, France
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Morris M, Rogers SM. Integrating phenotypic plasticity within an Ecological Genomics framework: recent insights from the genomics, evolution, ecology, and fitness of plasticity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:73-105. [PMID: 24277296 DOI: 10.1007/978-94-007-7347-9_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
E.B. Ford's 1964 book Ecological Genetics was a call for biologists to engage in multidisciplinary work in order to elucidate the link between genotype, phenotype, and fitness for ecologically relevant traits. In this review, we argue that the integration of an ecological genomics framework in studies of phenotypic plasticity is a promising approach to elucidate the causal links between genes and the environment, particularly during colonization of novel environments, environmental change, and speciation. This review highlights some of the questions and hypotheses generated from a mechanistic, evolutionary, and ecological perspective, in order to direct the continued and future use of genomic tools in the study of phenotypic plasticity.
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Affiliation(s)
- Matthew Morris
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada,
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36
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Holman L, Kokko H. The evolution of genomic imprinting: costs, benefits and long-term consequences. Biol Rev Camb Philos Soc 2013; 89:568-87. [DOI: 10.1111/brv.12069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 09/15/2013] [Accepted: 09/26/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Luke Holman
- Centre of Excellence in Biological Interactions, Division of Ecology, Evolution & Genetics; Research School of Biology, Australian National University; Daley Road, Canberra Australian Capital Territory 0200 Australia
| | - Hanna Kokko
- Centre of Excellence in Biological Interactions, Division of Ecology, Evolution & Genetics; Research School of Biology, Australian National University; Daley Road, Canberra Australian Capital Territory 0200 Australia
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37
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Renn SC, Schumer ME. Genetic accommodation and behavioural evolution: insights from genomic studies. Anim Behav 2013. [DOI: 10.1016/j.anbehav.2013.02.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Extinction or Survival? Behavioral Flexibility in Response to Environmental Change in the African Striped Mouse Rhabdomys. SUSTAINABILITY 2013. [DOI: 10.3390/su5010163] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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de Sá RO, Streicher JW, Sekonyela R, Forlani MC, Loader SP, Greenbaum E, Richards S, Haddad CFB. Molecular phylogeny of microhylid frogs (Anura: Microhylidae) with emphasis on relationships among New World genera. BMC Evol Biol 2012; 12:241. [PMID: 23228209 PMCID: PMC3561245 DOI: 10.1186/1471-2148-12-241] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/28/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis). RESULTS One mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an unprecedented sampling of 200 microhylid taxa representing 91% of currently recognized subfamilies and 95% of New World genera. Our analyses do not fully resolve relationships among subfamilies supporting previous studies that have suggested a rapid early diversification of this clade. We observed a close relationship between Synapturanus and Otophryne of the subfamily Otophryninae. Within the subfamily Gastrophryninae relationships between genera were well resolved. CONCLUSION Otophryninae is distantly related to all other New World microhylids that were recovered as a monophyletic group, Gastrophryninae. Within Gastrophryninae, five genera were recovered as non-monophyletic; we propose taxonomic re-arrangements to render all genera monophyletic. This hypothesis of relationships and updated classification for New World microhylids may serve as a guide to better understand the evolutionary history of this group that is apparently subject to convergent morphological evolution and chromosome reduction. Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to mid Miocene.
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Affiliation(s)
- Rafael O de Sá
- Department of Biology, University of Richmond, Richmond, VA 23173, USA
| | - Jeffrey W Streicher
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas at Arlington, Arlington, TX, 76010, USA
| | | | | | - Simon P Loader
- Department of Environmental Sciences, University of Basel, Basel, CH-4056, Switzerland
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Avenue, El Paso, TX, 79968, USA
| | - Stephen Richards
- Herpetology Department, South Australian Museum, North Terrace, Adelaide, 5000, South Australia
- Department of Terrestrial Vertebrates, Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin, NT, 0801, Australia
| | - Célio F B Haddad
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Caixa Postal 199, Rio Claro, São Paulo, 13506-900, Brazil
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40
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Hunt BG, Ometto L, Keller L, Goodisman MAD. Evolution at two levels in fire ants: the relationship between patterns of gene expression and protein sequence evolution. Mol Biol Evol 2012; 30:263-71. [PMID: 23051842 DOI: 10.1093/molbev/mss234] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Variation in protein sequence and gene expression each contribute to phenotypic diversity, and may be subject to similar selective pressures. Eusocial insects are particularly useful for investigating the evolutionary link between protein sequence and condition-dependent patterns of gene expression because gene expression plays a central role in determining differences between eusocial insect sexes and castes. We investigated the relationship between protein coding sequence evolution and gene expression patterns in the fire ants Solenopsis invicta, S. richteri, and their hybrids to gain greater insight into how selection jointly operates on gene expression and coding sequence. We found that genes with high expression variability within castes and sexes were frequently differentially expressed between castes and sexes, as well as between species and hybrids. These results indicate that genes showing high variation in expression in one context also tend to show high variation in expression in other contexts. Our analyses further revealed that variation in both intra- and interspecific gene expression was positively associated with rate of protein sequence evolution in Solenopsis. This suggests that selective constraints on a gene operate both at the level of protein sequence and at the level of gene expression regulation. Overall, our study provides one of the strongest demonstrations that selective constraints mediate both protein sequence evolution and gene expression variability across different biological contexts and timescales.
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Affiliation(s)
- Brendan G Hunt
- School of Biology, Georgia Institute of Technology, USA.
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Abstract
In the past decade, there has been a resurgent interest in whether and how phenotypic plasticity might impact evolutionary processes. Of fundamental importance is how the environment influences individual phenotypic development while simultaneously selecting among phenotypic variants in a population. Conceptual and theoretical treatments of the evolutionary implications of plasticity are numerous, as are criticisms of the conclusions. As such, the time is ripe for empirical evidence to catch up with theoretical predictions. To this end, I provide a summary of eight hypotheses at the core of this issue, highlighting various approaches by which they can be tested. My goal is to provide practical guidance to those seeking to understand the complex ways by which phenotypic plasticity can influence evolutionary innovation and diversification.
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Affiliation(s)
- Matthew A Wund
- Department of Biology, The College of New Jersey, PO Box 7718, Ewing, NJ, USA.
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42
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Valena S, Moczek AP. Epigenetic mechanisms underlying developmental plasticity in horned beetles. GENETICS RESEARCH INTERNATIONAL 2012; 2012:576303. [PMID: 22567393 PMCID: PMC3335661 DOI: 10.1155/2012/576303] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/05/2011] [Indexed: 11/18/2022]
Abstract
All developmental plasticity arises through epigenetic mechanisms. In this paper we focus on the nature, origins, and consequences of these mechanisms with a focus on horned beetles, an emerging model system in evolutionary developmental genetics. Specifically, we introduce the biological significance of developmental plasticity and summarize the most important facets of horned beetle biology. We then compare and contrast the epigenetic regulation of plasticity in horned beetles to that of other organisms and discuss how epigenetic mechanisms have facilitated innovation and diversification within and among taxa. We close by highlighting opportunities for future studies on the epigenetic regulation of plastic development in these and other organisms.
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Affiliation(s)
- Sophie Valena
- Department of Biology, Indiana University, 915 E Third Street, Myers Hall 150, Bloomington, IN 47405-7107, USA
| | - Armin P. Moczek
- Department of Biology, Indiana University, 915 E Third Street, Myers Hall 150, Bloomington, IN 47405-7107, USA
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