1
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Hoge C, de Manuel M, Mahgoub M, Okami N, Fuller Z, Banerjee S, Baker Z, McNulty M, Andolfatto P, Macfarlan TS, Schumer M, Tzika AC, Przeworski M. Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features. Science 2024; 383:eadj7026. [PMID: 38386752 DOI: 10.1126/science.adj7026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/04/2024] [Indexed: 02/24/2024]
Abstract
In some mammals, notably humans, recombination occurs almost exclusively where the protein PRDM9 binds, whereas in vertebrates lacking an intact PRDM9, such as birds and canids, recombination rates are elevated near promoter-like features. To determine whether PRDM9 directs recombination in nonmammalian vertebrates, we focused on an exemplar species with a single, intact PRDM9 ortholog, the corn snake (Pantherophis guttatus). Analyzing historical recombination rates along the genome and crossovers in pedigrees, we found evidence that PRDM9 specifies the location of recombination events, but we also detected a separable effect of promoter-like features. These findings reveal that the uses of PRDM9 and promoter-like features need not be mutually exclusive and instead reflect a tug-of-war that is more even in some species than others.
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Affiliation(s)
- Carla Hoge
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Marc de Manuel
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Mohamed Mahgoub
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Naima Okami
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Zachary Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Shreya Banerjee
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Zachary Baker
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Morgan McNulty
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Athanasia C Tzika
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
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2
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Yang L, Borne F, Betz A, Aardema ML, Zhen Y, Peng J, Visconti R, Wu M, Roland BP, Talsma AD, Palladino MJ, Petschenka G, Andolfatto P. Predatory fireflies and their toxic firefly prey have evolved distinct toxin resistance strategies. Curr Biol 2023; 33:5160-5168.e7. [PMID: 37989309 PMCID: PMC10872512 DOI: 10.1016/j.cub.2023.10.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/04/2023] [Accepted: 10/27/2023] [Indexed: 11/23/2023]
Abstract
Toxic cardiotonic steroids (CTSs) act as a defense mechanism in many firefly species (Lampyridae) by inhibiting a crucial enzyme called Na+,K+-ATPase (NKA). Although most fireflies produce these toxins internally, species of the genus Photuris acquire them from a surprising source: predation on other fireflies. The contrasting physiology of toxin exposure and sequestration between Photuris and other firefly genera suggests that distinct strategies may be required to prevent self-intoxication. Our study demonstrates that both Photuris and their firefly prey have evolved highly resistant NKAs. Using an evolutionary analysis of the specific target of CTS (ATPα) in fireflies and gene editing in Drosophila, we find that the initial steps toward resistance were shared among Photuris and other firefly lineages. However, the Photuris lineage subsequently underwent multiple rounds of gene duplication and neofunctionalization, resulting in the development of ATPα paralogs that are differentially expressed and exhibit increasing resistance to CTS. By contrast, other firefly species have maintained a single copy. Our results implicate gene duplication as a facilitator in the transition of Photuris to its distinct ecological role as a predator of toxic firefly prey.
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Affiliation(s)
- Lu Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Flora Borne
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Anja Betz
- Department of Applied Entomology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Matthew L Aardema
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA; Department of Biology, Montclair State University, Montclair, NJ 07043, USA
| | - Ying Zhen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Julie Peng
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Regina Visconti
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Mariana Wu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Bartholomew P Roland
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Aaron D Talsma
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Michael J Palladino
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Georg Petschenka
- Department of Applied Entomology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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3
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Yang L, Borne F, Betz A, Aardema ML, Zhen Y, Peng J, Visconti R, Wu M, Roland BP, Talsma AD, Palladino MJ, Petschenka G, Andolfatto P. Predatory fireflies and their toxic firefly prey have evolved distinct toxin resistance strategies. bioRxiv 2023:2023.03.08.531760. [PMID: 36945443 PMCID: PMC10028858 DOI: 10.1101/2023.03.08.531760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Toxic cardiotonic steroids (CTS) act as a defense mechanism in many firefly species (Lampyridae) by inhibiting a crucial enzyme called Na+,K+-ATPase (NKA). While most fireflies produce these toxins internally, species of the genus Photuris acquire them from a surprising source: predation on other fireflies. The contrasting physiology of toxin exposure and sequestration between Photuris and other firefly genera suggests that distinct strategies may be required to prevent self-intoxication. Our study demonstrates that both Photuris and their firefly prey have evolved highly-resistant NKAs. Using an evolutionary analysis of the specific target of CTS (ATPα) in fireflies, and gene-editing in Drosophila, we find that the initial steps towards resistance were shared among Photuris and other firefly lineages. However, the Photuris lineage subsequently underwent multiple rounds of gene duplication and neofunctionalization, resulting in the development of ATPα paralogs that are differentially expressed and exhibit increasing resistance to CTS. In contrast, other firefly species have maintained a single copy. Our results implicate gene duplication as a facilitator in the transition of Photuris to its distinct ecological role as predator of toxic firefly prey.
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Affiliation(s)
- Lu Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA
| | - Flora Borne
- Department of Biological Sciences, Columbia University, New York, USA
| | - Anja Betz
- Department of Applied Entomology, University of Hohenheim, Stuttgart, Germany
| | - Matthew L Aardema
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA
- Department of Biology, Montclair State University, Montclair, USA
| | - Ying Zhen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Julie Peng
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA
| | - Regina Visconti
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA
| | - Mariana Wu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA
| | - Bartholomew P Roland
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Aaron D Talsma
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Mike J Palladino
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Georg Petschenka
- Department of Applied Entomology, University of Hohenheim, Stuttgart, Germany
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, USA
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4
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Hoge C, de Manuel M, Mahgoub M, Okami N, Fuller Z, Banerjee S, Baker Z, McNulty M, Andolfatto P, Macfarlan TS, Schumer M, Tzika AC, Przeworski M. Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features. bioRxiv 2023:2023.07.11.548536. [PMID: 37502971 PMCID: PMC10369914 DOI: 10.1101/2023.07.11.548536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In vertebrates, there are two known mechanisms by which meiotic recombination is directed to the genome: in humans, mice, and other mammals, recombination occurs almost exclusively where the protein PRDM9 binds, while in species lacking an intact PRDM9, such as birds and canids, recombination rates are elevated near promoter-like features. To test if PRDM9 also directs recombination in non-mammalian vertebrates, we focused on an exemplar species, the corn snake (Pantherophis guttatus). Unlike birds, this species possesses a single, intact PRDM9 ortholog. By inferring historical recombination rates along the genome from patterns of linkage disequilibrium and identifying crossovers in pedigrees, we found that PRDM9 specifies the location of recombination events outside of mammals. However, we also detected an independent effect of promoter-like features on recombination, which is more pronounced on macro- than microchromosomes. Thus, our findings reveal that the uses of PRDM9 and promoter-like features are not mutually-exclusive, and instead reflect a tug of war, which varies in strength along the genome and is more lopsided in some species than others.
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Affiliation(s)
- Carla Hoge
- Dept. of Biological Sciences, Columbia University
| | | | - Mohamed Mahgoub
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - Naima Okami
- Dept. of Biological Sciences, Columbia University
| | | | | | | | | | | | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - Molly Schumer
- Dept. of Biology, Stanford University
- Howard Hughes Medical Institute, Stanford, CA
| | - Athanasia C Tzika
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva
| | - Molly Przeworski
- Dept. of Biological Sciences, Columbia University
- Howard Hughes Medical Institute, Stanford, CA
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5
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Pallares LF, Lea AJ, Han C, Filippova EV, Andolfatto P, Ayroles JF. Dietary stress remodels the genetic architecture of lifespan variation in outbred Drosophila. Nat Genet 2023; 55:123-129. [PMID: 36550361 DOI: 10.1038/s41588-022-01246-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
Evolutionary theory suggests that lifespan-reducing alleles should be purged from the gene pool, and yet decades of genome-wide association and model organism studies have shown that they persist. One potential explanation is that alleles that regulate lifespan do so only in certain environmental contexts. We exposed outbred Drosophila to control and high-sugar diets and genotyped more than 10,000 adult flies to track allele frequency changes over the course of a single adult lifespan. We identified thousands of lifespan-associated alleles associated with early versus late-life trade-offs, late-onset effects and genotype-by-environment interactions. Remarkably, a third of lifespan-associated genetic variation had environmentally dependent effects on lifespan. We find that lifespan-reducing alleles are often recently derived, have stronger effects on a high-sugar diet and show signatures of selection in wild Drosophila populations, consistent with the evolutionary mismatch hypothesis. Our results provide insight into the highly polygenic and context-dependent genetic architecture of lifespan variation and the evolutionary processes that shape this key trait.
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Affiliation(s)
- Luisa F Pallares
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Amanda J Lea
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Clair Han
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Elena V Filippova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | - Julien F Ayroles
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA.
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6
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Mohammadi S, Özdemir Hİ, Ozbek P, Sumbul F, Stiller J, Deng Y, Crawford AJ, Rowland HM, Storz JF, Andolfatto P, Dobler S. Epistatic Effects Between Amino Acid Insertions and Substitutions Mediate Toxin resistance of Vertebrate Na+,K+-ATPases. Mol Biol Evol 2022; 39:6874786. [PMID: 36472530 PMCID: PMC9778839 DOI: 10.1093/molbev/msac258] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
The recurrent evolution of resistance to cardiotonic steroids (CTS) across diverse animals most frequently involves convergent amino acid substitutions in the H1-H2 extracellular loop of Na+,K+-ATPase (NKA). Previous work revealed that hystricognath rodents (e.g., chinchilla) and pterocliform birds (sandgrouse) have convergently evolved amino acid insertions in the H1-H2 loop, but their functional significance was not known. Using protein engineering, we show that these insertions have distinct effects on CTS resistance in homologs of each of the two species that strongly depend on intramolecular interactions with other residues. Removing the insertion in the chinchilla NKA unexpectedly increases CTS resistance and decreases NKA activity. In the sandgrouse NKA, the amino acid insertion and substitution Q111R both contribute to an augmented CTS resistance without compromising ATPase activity levels. Molecular docking simulations provide additional insight into the biophysical mechanisms responsible for the context-specific mutational effects on CTS insensitivity of the enzyme. Our results highlight the diversity of genetic substrates that underlie CTS insensitivity in vertebrate NKA and reveal how amino acid insertions can alter the phenotypic effects of point mutations at key sites in the same protein domain.
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Affiliation(s)
- Shabnam Mohammadi
- Molecular Evolutionary Biology, Institute of Cell and Systems Biology of Animals, Universität Hamburg, Hamburg 20146, Germany.,Max Planck Institute for Chemical Ecology, Research Group Predators and Toxic Prey, Jena 07745, Germany
| | | | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Göztepe, İstanbul 34722, Turkey
| | - Fidan Sumbul
- INSERM, Aix-Marseille Université, Inserm, CNRS, Marseille 13009, France
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, University of Copenhagen, Copenhagen 2100, Denmark
| | - Yuan Deng
- Villum Centre for Biodiversity Genomics, University of Copenhagen, Copenhagen 2100, Denmark.,BGI-Shenzhen, Shenzhen 518083, China
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Hannah M Rowland
- Max Planck Institute for Chemical Ecology, Research Group Predators and Toxic Prey, Jena 07745, Germany
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY
| | - Susanne Dobler
- Molecular Evolutionary Biology, Institute of Cell and Systems Biology of Animals, Universität Hamburg, Hamburg 20146, Germany
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7
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Tomihara K, Andolfatto P, Kiuchi T. Allele-specific knockouts reveal a role for apontic-like in the evolutionary loss of larval melanin pigmentation in the domesticated silkworm, Bombyx mori. Insect Mol Biol 2022; 31:701-710. [PMID: 35752945 PMCID: PMC9633403 DOI: 10.1111/imb.12797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/22/2022] [Indexed: 05/25/2023]
Abstract
The domesticated silkworm, Bombyx mori, and its wild progenitor, B. mandarina, are extensively studied as a model case of the evolutionary process of domestication. A conspicuous difference between these species is the dramatic reduction in melanin pigmentation in both larval and adult B. mori. Here we evaluate the efficiency of CRISPR/Cas9-targeted knockouts of pigment-related genes as a tool to understand their potential contributions to domestication-associated melanin pigmentation loss in B. mori. To demonstrate the efficacy of targeted knockouts in B. mandarina, we generated a homozygous CRISPR/Cas9-targeted knockout of yellow-y. In yellow-y knockout mutants, black body colour became lighter throughout the larval, pupal and adult stages, confirming a role for this gene in melanin pigment formation. Further, we performed allele-specific CRISPR/Cas9-targeted knockouts of the pigment-related transcription factor, apontic-like (apt-like) in B. mori × B. mandarina F1 hybrid individuals which exhibit B. mandarina-like larval pigmentation. Knockout of the B. mandarina allele of apt-like in F1 embryos results in white patches on the dorsal integument of larvae, whereas corresponding knockouts of the B. mori allele consistently exhibit normal F1 larval pigmentation. These results demonstrate a contribution of apt-like to the evolution of reduced melanin pigmentation in B. mori. Together, our results demonstrate the feasibility of CRISPR/Cas9-targeted knockouts as a tool for understanding the genetic basis of traits associated with B. mori domestication.
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Affiliation(s)
- Kenta Tomihara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10026, USA
| | - Takashi Kiuchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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8
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Mohammadi S, Herrera-Álvarez S, Yang L, Rodríguez-Ordoñez MDP, Zhang K, Storz JF, Dobler S, Crawford AJ, Andolfatto P. Constraints on the evolution of toxin-resistant Na,K-ATPases have limited dependence on sequence divergence. PLoS Genet 2022; 18:e1010323. [PMID: 35972957 DOI: 10.1101/2021.11.29.470343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/09/2022] [Accepted: 07/04/2022] [Indexed: 05/25/2023] Open
Abstract
A growing body of theoretical and experimental evidence suggests that intramolecular epistasis is a major determinant of rates and patterns of protein evolution and imposes a substantial constraint on the evolution of novel protein functions. Here, we examine the role of intramolecular epistasis in the recurrent evolution of resistance to cardiotonic steroids (CTS) across tetrapods, which occurs via specific amino acid substitutions to the α-subunit family of Na,K-ATPases (ATP1A). After identifying a series of recurrent substitutions at two key sites of ATP1A that are predicted to confer CTS resistance in diverse tetrapods, we then performed protein engineering experiments to test the functional consequences of introducing these substitutions onto divergent species backgrounds. In line with previous results, we find that substitutions at these sites can have substantial background-dependent effects on CTS resistance. Globally, however, these substitutions also have pleiotropic effects that are consistent with additive rather than background-dependent effects. Moreover, the magnitude of a substitution's effect on activity does not depend on the overall extent of ATP1A sequence divergence between species. Our results suggest that epistatic constraints on the evolution of CTS-resistant forms of Na,K-ATPase likely depend on a small number of sites, with little dependence on overall levels of protein divergence. We propose that dependence on a limited number sites may account for the observation of convergent CTS resistance substitutions observed among taxa with highly divergent Na,K-ATPases (See S1 Text for Spanish translation).
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Affiliation(s)
- Shabnam Mohammadi
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
- Molecular Evolutionary Biology, Institut für Zell- und Systembiologie der Tiere, Universität Hamburg, Hamburg, Germany
| | - Santiago Herrera-Álvarez
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Lu Yang
- Department of Ecology and Evolution, Princeton University, Princeton, New Jersey, United States of America
| | | | - Karen Zhang
- Department of Ecology and Evolution, Princeton University, Princeton, New Jersey, United States of America
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Susanne Dobler
- Molecular Evolutionary Biology, Institut für Zell- und Systembiologie der Tiere, Universität Hamburg, Hamburg, Germany
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York city, New York, United States of America
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9
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Mohammadi S, Herrera-Álvarez S, Yang L, Rodríguez-Ordoñez MDP, Zhang K, Storz JF, Dobler S, Crawford AJ, Andolfatto P. Constraints on the evolution of toxin-resistant Na,K-ATPases have limited dependence on sequence divergence. PLoS Genet 2022; 18:e1010323. [PMID: 35972957 PMCID: PMC9462791 DOI: 10.1371/journal.pgen.1010323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/09/2022] [Accepted: 07/04/2022] [Indexed: 11/19/2022] Open
Abstract
A growing body of theoretical and experimental evidence suggests that intramolecular epistasis is a major determinant of rates and patterns of protein evolution and imposes a substantial constraint on the evolution of novel protein functions. Here, we examine the role of intramolecular epistasis in the recurrent evolution of resistance to cardiotonic steroids (CTS) across tetrapods, which occurs via specific amino acid substitutions to the α-subunit family of Na,K-ATPases (ATP1A). After identifying a series of recurrent substitutions at two key sites of ATP1A that are predicted to confer CTS resistance in diverse tetrapods, we then performed protein engineering experiments to test the functional consequences of introducing these substitutions onto divergent species backgrounds. In line with previous results, we find that substitutions at these sites can have substantial background-dependent effects on CTS resistance. Globally, however, these substitutions also have pleiotropic effects that are consistent with additive rather than background-dependent effects. Moreover, the magnitude of a substitution’s effect on activity does not depend on the overall extent of ATP1A sequence divergence between species. Our results suggest that epistatic constraints on the evolution of CTS-resistant forms of Na,K-ATPase likely depend on a small number of sites, with little dependence on overall levels of protein divergence. We propose that dependence on a limited number sites may account for the observation of convergent CTS resistance substitutions observed among taxa with highly divergent Na,K-ATPases (See S1 Text for Spanish translation). Individual amino acids within a protein work in concert to produce a functionally coherent structure that must be maintained as a protein diverges over time. Given this structure-function relationship, we expect the effects of new mutations to depend on amino acid states at other sites throughout the protein (i.e., background dependence) and that identical mutations will have more similar effects in more closely-related species, for which orthologous proteins will be less diverged. We tested this hypothesis by performing protein-engineering experiments on ATP1A, a protein that mediates resistance to toxins known as cardiotonic steroids (CTS), to reveal the extent of background-dependence across representative tetrapods. We find that, while the effects of mutations at two key sites implicated in CTS-resistance are indeed often background-dependent, the magnitude of these effects does not correlate with overall levels of ATP1A divergence. Our results instead suggest that background-dependent effects are determined by amino acid states at a small number of sites throughout the protein. Evolutionary constraints imposed by relatively few sites may explain the frequent occurrence of identical or similar CTS-resistance substitutions among ATP1A proteins of highly divergent animals (See S1 Text for Spanish translation).
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Affiliation(s)
- Shabnam Mohammadi
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
- Molecular Evolutionary Biology, Institut für Zell- und Systembiologie der Tiere, Universität Hamburg, Hamburg, Germany
| | - Santiago Herrera-Álvarez
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Lu Yang
- Department of Ecology and Evolution, Princeton University, Princeton, New Jersey, United States of America
| | | | - Karen Zhang
- Department of Ecology and Evolution, Princeton University, Princeton, New Jersey, United States of America
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Susanne Dobler
- Molecular Evolutionary Biology, Institut für Zell- und Systembiologie der Tiere, Universität Hamburg, Hamburg, Germany
| | - Andrew J. Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York city, New York, United States of America
- * E-mail:
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10
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Ng D, Pinharanda A, Vogt MC, Litwin-Kumar A, Stearns K, Thopte U, Cannavo E, Enikolopov A, Fiederling F, Kosmidis S, Noro B, Rodrigues-Vaz I, Shayya H, Andolfatto P, Peterka DS, Tabachnik T, D’Armiento J, Goldklang M, Bendesky A. WHotLAMP: A simple, inexpensive, and sensitive molecular test for the detection of SARS-CoV-2 in saliva. PLoS One 2021; 16:e0257464. [PMID: 34529736 PMCID: PMC8445428 DOI: 10.1371/journal.pone.0257464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/01/2021] [Indexed: 12/23/2022] Open
Abstract
Despite the development of effective vaccines against SARS-CoV-2, epidemiological control of the virus is still challenging due to slow vaccine rollouts, incomplete vaccine protection to current and emerging variants, and unwillingness to get vaccinated. Therefore, frequent testing of individuals to identify early SARS-CoV-2 infections, contact-tracing and isolation strategies remain crucial to mitigate viral spread. Here, we describe WHotLAMP, a rapid molecular test to detect SARS-CoV-2 in saliva. WHotLAMP is simple to use, highly sensitive (~4 viral particles per microliter of saliva) and specific, as well as inexpensive, making it ideal for frequent screening. Moreover, WHotLAMP does not require toxic chemicals or specialized equipment and thus can be performed in point-of-care settings, and may also be adapted for resource-limited environments or home use. While applied here to SARS-CoV-2, WHotLAMP can be modified to detect other pathogens, making it adaptable for other diagnostic assays, including for use in future outbreaks.
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Affiliation(s)
- David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Merly C. Vogt
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- Howard Hughes Medical Institute, Columbia University, New York, NY, United States of America
| | - Ashok Litwin-Kumar
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Kyle Stearns
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Urvashi Thopte
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Enrico Cannavo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | | | - Felix Fiederling
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Stylianos Kosmidis
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Barbara Noro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Ines Rodrigues-Vaz
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Hani Shayya
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Darcy S. Peterka
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Tanya Tabachnik
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Jeanine D’Armiento
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, United States of America
- Center for LAM and Rare Lung Diseases, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Monica Goldklang
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, United States of America
- Center for LAM and Rare Lung Diseases, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States of America
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11
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Mohammadi S, Yang L, Harpak A, Herrera-Álvarez S, Del Pilar Rodríguez-Ordoñez M, Peng J, Zhang K, Storz JF, Dobler S, Crawford AJ, Andolfatto P. Concerted evolution reveals co-adapted amino acid substitutions in Na +K +-ATPase of frogs that prey on toxic toads. Curr Biol 2021; 31:2530-2538.e10. [PMID: 33887183 DOI: 10.1016/j.cub.2021.03.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/12/2021] [Accepted: 03/26/2021] [Indexed: 11/18/2022]
Abstract
Although gene duplication is an important source of evolutionary innovation, the functional divergence of duplicates can be opposed by ongoing gene conversion between them. Here, we report on the evolution of a tandem duplication of Na+,K+-ATPase subunit α1 (ATP1A1) shared by frogs in the genus Leptodactylus, a group of species that feeds on toxic toads. One ATP1A1 paralog evolved resistance to toad toxins although the other retained ancestral susceptibility. Within species, frequent non-allelic gene conversion homogenized most of the sequence between the two copies but was counteracted by strong selection on 12 amino acid substitutions that distinguish the two paralogs. Protein-engineering experiments show that two of these substitutions substantially increase toxin resistance, whereas the additional 10 mitigate their deleterious effects on ATPase activity. Our results reveal how examination of neo-functionalized gene duplicate evolution can help pinpoint key functional substitutions and interactions with the genetic backgrounds on which they arise.
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Affiliation(s)
- Shabnam Mohammadi
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Lu Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Arbel Harpak
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | | | - Julie Peng
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Karen Zhang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Susanne Dobler
- Molecular Evolutionary Biology, Zoological Institute, Universität Hamburg, Hamburg, Germany
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia.
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA.
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12
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Clark RD, Aardema ML, Andolfatto P, Barber PH, Hattori A, Hoey JA, Montes HR, Pinsky ML. Genomic signatures of spatially divergent selection at clownfish range margins. Proc Biol Sci 2021; 288:20210407. [PMID: 34102891 PMCID: PMC8187997 DOI: 10.1098/rspb.2021.0407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/11/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.
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Affiliation(s)
- René D. Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
| | - Matthew L. Aardema
- Department of Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5102, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10026, USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Akihisa Hattori
- Faculty of Liberal Arts and Education, Shiga University, 2-5-1 Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Jennifer A. Hoey
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | | | - Malin L. Pinsky
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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13
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Korgaonkar A, Han C, Lemire AL, Siwanowicz I, Bennouna D, Kopec RE, Andolfatto P, Shigenobu S, Stern DL. A novel family of secreted insect proteins linked to plant gall development. Curr Biol 2021; 31:1836-1849.e12. [PMID: 33657407 PMCID: PMC8119383 DOI: 10.1016/j.cub.2021.01.104] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022]
Abstract
In an elaborate form of inter-species exploitation, many insects hijack plant development to induce novel plant organs called galls that provide the insect with a source of nutrition and a temporary home. Galls result from dramatic reprogramming of plant cell biology driven by insect molecules, but the roles of specific insect molecules in gall development have not yet been determined. Here, we study the aphid Hormaphis cornu, which makes distinctive "cone" galls on leaves of witch hazel Hamamelis virginiana. We found that derived genetic variants in the aphid gene determinant of gall color (dgc) are associated with strong downregulation of dgc transcription in aphid salivary glands, upregulation in galls of seven genes involved in anthocyanin synthesis, and deposition of two red anthocyanins in galls. We hypothesize that aphids inject DGC protein into galls and that this results in differential expression of a small number of plant genes. dgc is a member of a large, diverse family of novel predicted secreted proteins characterized by a pair of widely spaced cysteine-tyrosine-cysteine (CYC) residues, which we named BICYCLE proteins. bicycle genes are most strongly expressed in the salivary glands specifically of galling aphid generations, suggesting that they may regulate many aspects of gall development. bicycle genes have experienced unusually frequent diversifying selection, consistent with their potential role controlling gall development in a molecular arms race between aphids and their host plants.
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Affiliation(s)
- Aishwarya Korgaonkar
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Clair Han
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Andrew L Lemire
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Igor Siwanowicz
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Djawed Bennouna
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, 262G Campbell Hall, 1787 Neil Avenue, Columbus, OH 43210, USA
| | - Rachel E Kopec
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, 262G Campbell Hall, 1787 Neil Avenue, Columbus, OH 43210, USA; Ohio State University's Foods for Health Discovery Theme, The Ohio State University, 262G Campbell Hall, 1787 Neil Avenue, Columbus, OH 43210, USA
| | - Peter Andolfatto
- Department of Biology, Columbia University, 600 Fairchild Center, New York, NY 10027, USA
| | - Shuji Shigenobu
- Laboratory of Evolutionary Genomics, Center for the Development of New Model Organism, National Institute for Basic Biology, Okazaki 444-8585, Japan; NIBB Research Core Facilities, National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - David L Stern
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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14
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Korgaonkar A, Han C, Lemire AL, Siwanowicz I, Bennouna D, Kopec RE, Andolfatto P, Shigenobu S, Stern DL. A novel family of secreted insect proteins linked to plant gall development. Curr Biol 2021. [PMID: 33974861 DOI: 10.1101/2020.10.28.359562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
AbstractIn an elaborate form of inter-species exploitation, many insects hijack plant development to induce novel plant organs called galls that provide the insect with a source of nutrition and a temporary home. Galls result from dramatic reprogramming of plant cell biology driven by insect molecules, but the roles of specific insect molecules in gall development have not yet been determined. Here we study the aphidHormaphis cornu, which makes distinctive “cone” galls on leaves of witch hazelHamamelis virginiana. We found that derived genetic variants in the aphid genedeterminant of gall color(dgc) are associated with strong downregulation ofdgctranscription in aphid salivary glands, upregulation in galls of seven genes involved in anthocyanin synthesis, and deposition of two red anthocyanins in galls. We hypothesize that aphids inject DGC protein into galls, and that this results in differential expression of a small number of plant genes.Dgcis a member of a large, diverse family of novel predicted secreted proteins characterized by a pair of widely spaced cysteine-tyrosine-cysteine (CYC) residues, which we named BICYCLE proteins.Bicyclegenes are most strongly expressed in the salivary glands specifically of galling aphid generations, suggesting that they may regulate many aspects of gall development.Bicyclegenes have experienced unusually frequent diversifying selection, consistent with their potential role controlling gall development in a molecular arms race between aphids and their host plants.One Sentence SummaryAphidbicyclegenes, which encode diverse secreted proteins, contribute to plant gall development.
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15
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Korgaonkar A, Han C, Lemire AL, Siwanowicz I, Bennouna D, Kopec RE, Andolfatto P, Shigenobu S, Stern DL. A novel family of secreted insect proteins linked to plant gall development. Curr Biol 2021; 31:2038. [PMID: 33974861 DOI: 10.1016/j.cub.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Powell DL, Payne C, Banerjee SM, Keegan M, Bashkirova E, Cui R, Andolfatto P, Rosenthal GG, Schumer M. The Genetic Architecture of Variation in the Sexually Selected Sword Ornament and Its Evolution in Hybrid Populations. Curr Biol 2021; 31:923-935.e11. [PMID: 33513352 DOI: 10.1016/j.cub.2020.12.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
Biologists since Darwin have been fascinated by the evolution of sexually selected ornaments, particularly those that reduce viability. Uncovering the genetic architecture of these traits is key to understanding how they evolve and are maintained. Here, we investigate the genetic architecture and evolutionary loss of a sexually selected ornament, the "sword" fin extension that characterizes many species of swordtail fish (Xiphophorus). Using sworded and swordless sister species of Xiphophorus, we generated a mapping population and show that the sword ornament is polygenic-with ancestry across the genome explaining substantial variation in the trait. After accounting for the impacts of genome-wide ancestry, we identify one major-effect quantitative trait locus (QTL) that explains ~5% of the overall variation in the trait. Using a series of approaches, we narrow this large QTL interval to several likely candidate genes, including genes involved in fin regeneration and growth. Furthermore, we find evidence of selection on ancestry at one of these candidates in four natural hybrid populations, consistent with selection against the sword in these populations.
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Affiliation(s)
- Daniel L Powell
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA.
| | - Cheyenne Payne
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Shreya M Banerjee
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Mackenzie Keegan
- Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Elizaveta Bashkirova
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, New York, NY 10032, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY 10032, USA
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA; Max Planck Institute for the Biology of Aging, Postfach 41 06 23, 50931 Cologne, Germany; School of Ecology, Sun Yat-sen University, 135 Xingang West Road, Binjiang Road, Haizhu District, Guangdong Province, China
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA
| | - Molly Schumer
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Howard Hughes Medical Institute, 327 Campus Drive, Stanford, CA 94305, USA.
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17
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Fuller ZL, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L, Peng J, Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M. Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science 2020; 369:369/6501/eaba4674. [PMID: 32675347 DOI: 10.1126/science.aba4674] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.
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Affiliation(s)
- Zachary L Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | | | - Luke A Morris
- Australian Institute of Marine Science, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Neal Cantin
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Jihanne Shepherd
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Luke Sarre
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Julie Peng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yi Liao
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | | | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Mikhail Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia.
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA.,Program for Mathematical Genomics, Columbia University, New York, NY, USA
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18
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Powell DL, García-Olazábal M, Keegan M, Reilly P, Du K, Díaz-Loyo AP, Banerjee S, Blakkan D, Reich D, Andolfatto P, Rosenthal GG, Schartl M, Schumer M. Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish. Science 2020; 368:731-736. [PMID: 32409469 DOI: 10.1126/science.aba5216] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/27/2020] [Indexed: 12/21/2022]
Abstract
The establishment of reproductive barriers between populations can fuel the evolution of new species. A genetic framework for this process posits that "incompatible" interactions between genes can evolve that result in reduced survival or reproduction in hybrids. However, progress has been slow in identifying individual genes that underlie hybrid incompatibilities. We used a combination of approaches to map the genes that drive the development of an incompatibility that causes melanoma in swordtail fish hybrids. One of the genes involved in this incompatibility also causes melanoma in hybrids between distantly related species. Moreover, this melanoma reduces survival in the wild, likely because of progressive degradation of the fin. This work identifies genes underlying a vertebrate hybrid incompatibility and provides a glimpse into the action of these genes in natural hybrid populations.
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Affiliation(s)
- Daniel L Powell
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA. .,Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, College Station, TX, USA
| | - Mateo García-Olazábal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, College Station, TX, USA
| | | | - Patrick Reilly
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bavaria, Germany
| | - Alejandra P Díaz-Loyo
- Laboratorio de Ecología de la Conducta, Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Shreya Banerjee
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA
| | - Danielle Blakkan
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, and the Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, College Station, TX, USA
| | - Manfred Schartl
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, College Station, TX, USA.,Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bavaria, Germany.,Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA.,Xiphophorus Genetic Stock Center, Texas State University San Marcos, San Marcos, TX, USA
| | - Molly Schumer
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.
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19
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Gu L, Reilly PF, Lewis JJ, Reed RD, Andolfatto P, Walters JR. Dichotomy of Dosage Compensation along the Neo Z Chromosome of the Monarch Butterfly. Curr Biol 2019; 29:4071-4077.e3. [PMID: 31735674 DOI: 10.1016/j.cub.2019.09.056] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
Abstract
Mechanisms of sex chromosome dosage compensation (SCDC) differ strikingly among animals. In Drosophila flies, chromosome-wide transcription is doubled from the single X chromosome in hemizygous (XY) males, whereas in Caenorhabditis nematodes, expression is halved for both X copies in homozygous (XX) females [1, 2]. Unlike other female-heterogametic (WZ female and ZZ male) animals, moths and butterflies exhibit sex chromosome dosage compensation patterns typically seen only in male-heterogametic species [3]. The monarch butterfly carries a newly derived Z chromosome segment that arose from an autosomal fusion with the ancestral Z [4]. Using a highly contiguous genome assembly, we show that gene expression is balanced between sexes along the entire Z chromosome but with distinct modes of compensation on the two segments. On the ancestral Z segment, depletion of H4K16ac corresponds to nearly halving of biallelic transcription in males, a pattern convergent to nematodes. Conversely, the newly derived Z segment shows a Drosophila-like mode of compensation, with enriched H4K16ac levels corresponding to doubled monoallelic transcription in females. Our work reveals that, contrary to the expectation of co-opting regulatory mechanisms readily in place, the evolution of plural modes of dosage compensation is also possible along a single sex chromosome within a species.
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Affiliation(s)
- Liuqi Gu
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA.
| | - Patrick F Reilly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - James R Walters
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA.
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20
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Taverner AM, Yang L, Barile ZJ, Lin B, Peng J, Pinharanda AP, Rao AS, Roland BP, Talsma AD, Wei D, Petschenka G, Palladino MJ, Andolfatto P. Adaptive substitutions underlying cardiac glycoside insensitivity in insects exhibit epistasis in vivo. eLife 2019; 8:48224. [PMID: 31453806 PMCID: PMC6733596 DOI: 10.7554/elife.48224] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/24/2019] [Indexed: 01/20/2023] Open
Abstract
Predicting how species will respond to selection pressures requires understanding the factors that constrain their evolution. We use genome engineering of Drosophila to investigate constraints on the repeated evolution of unrelated herbivorous insects to toxic cardiac glycosides, which primarily occurs via a small subset of possible functionally-relevant substitutions to Na+,K+-ATPase. Surprisingly, we find that frequently observed adaptive substitutions at two sites, 111 and 122, are lethal when homozygous and adult heterozygotes exhibit dominant neural dysfunction. We identify a phylogenetically correlated substitution, A119S, that partially ameliorates the deleterious effects of substitutions at 111 and 122. Despite contributing little to cardiac glycoside-insensitivity in vitro, A119S, like substitutions at 111 and 122, substantially increases adult survivorship upon cardiac glycoside exposure. Our results demonstrate the importance of epistasis in constraining adaptive paths. Moreover, by revealing distinct effects of substitutions in vitro and in vivo, our results underscore the importance of evaluating the fitness of adaptive substitutions and their interactions in whole organisms.
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Affiliation(s)
- Andrew M Taverner
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Lu Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
| | - Zachary J Barile
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, United States.,Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Becky Lin
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, United States.,Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Julie Peng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Ana P Pinharanda
- Department of Biological Sciences, Columbia University, New York, United States
| | - Arya S Rao
- Department of Biological Sciences, Columbia University, New York, United States
| | - Bartholomew P Roland
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, United States.,Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Aaron D Talsma
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, United States.,Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Daniel Wei
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, United States.,Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Georg Petschenka
- Institute for Insect Biotechnology, Justus-Liebig-Universität Gießen, Hesse, Germany
| | - Michael J Palladino
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, United States.,Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, United States
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21
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Liu Y, Ramos-Womack M, Han C, Reilly P, Brackett KL, Rogers W, Williams TM, Andolfatto P, Stern DL, Rebeiz M. Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution. Curr Biol 2019; 29:2157-2166.e6. [PMID: 31257142 DOI: 10.1016/j.cub.2019.05.074] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/10/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023]
Abstract
Hox genes pattern the anterior-posterior axis of animals and are posited to drive animal body plan evolution, yet their precise role in evolution has been difficult to determine. Here, we identified evolutionary modifications in the Hox gene Abd-B that dramatically altered its expression along the body plan of Drosophila santomea. Abd-B is required for pigmentation in Drosophila yakuba, the sister species of D. santomea, and changes to Abd-B expression would be predicted to make large contributions to the loss of body pigmentation in D. santomea. However, manipulating Abd-B expression in current-day D. santomea does not affect pigmentation. We attribute this epistatic interaction to four other genes within the D. santomea pigmentation network, three of which have evolved expression patterns that do not respond to Abd-B. Our results demonstrate how body plans may evolve through small evolutionary steps distributed throughout Hox-regulated networks. Polygenicity and epistasis may hinder efforts to identify genes and mechanisms underlying macroevolutionary traits.
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Affiliation(s)
- Yang Liu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Margarita Ramos-Womack
- Department of Ecology Evolution and Behavior, Princeton University, Princeton, NJ 08544, USA
| | - Clair Han
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Patrick Reilly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | | | - William Rogers
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Thomas M Williams
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, Sherman Fairchild Center for Life Sciences, 1212 Amsterdam Avenue, New York, NY 10027, USA
| | - David L Stern
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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22
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Yang L, Ravikanthachari N, Mariño-Pérez R, Deshmukh R, Wu M, Rosenstein A, Kunte K, Song H, Andolfatto P. Predictability in the evolution of Orthopteran cardenolide insensitivity. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180246. [PMID: 31154978 DOI: 10.1098/rstb.2018.0246] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The repeated evolutionary specialization of distantly related insects to cardenolide-containing host plants provides a stunning example of parallel adaptation. Hundreds of herbivorous insect species have independently evolved insensitivity to cardenolides, which are potent inhibitors of the alpha-subunit of Na+,K+-ATPase (ATPα). Previous studies investigating ATPα-mediated cardenolide insensitivity in five insect orders have revealed remarkably high levels of parallelism in the evolution of this trait, including the frequent occurrence of parallel amino acid substitutions at two sites and recurrent episodes of duplication followed by neo-functionalization. Here we add data for a sixth insect order, Orthoptera, which includes an ancient group of highly aposematic cardenolide-sequestering grasshoppers in the family Pyrgomorphidae. We find that Orthopterans exhibit largely predictable patterns of evolution of insensitivity established by sampling other insect orders. Taken together the data lend further support to the proposal that negative pleiotropic constraints are a key determinant in the evolution of cardenolide insensitivity in insects. Furthermore, analysis of our expanded taxonomic survey implicates positive selection acting on site 111 of cardenolide-sequestering species with a single-copy of ATPα, and sites 115, 118 and 122 in lineages with neo-functionalized duplicate copies, all of which are sites of frequent parallel amino acid substitution. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Lu Yang
- 1 Department of Ecology and Evolutionary Biology, Princeton University , Princeton, NJ 08544 , USA
| | - Nitin Ravikanthachari
- 2 National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bengaluru , India
| | - Ricardo Mariño-Pérez
- 3 Department of Entomology, Texas A&M University , College Station, TX 77843 , USA
| | - Riddhi Deshmukh
- 2 National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bengaluru , India
| | - Mariana Wu
- 1 Department of Ecology and Evolutionary Biology, Princeton University , Princeton, NJ 08544 , USA
| | - Adam Rosenstein
- 1 Department of Ecology and Evolutionary Biology, Princeton University , Princeton, NJ 08544 , USA
| | - Krushnamegh Kunte
- 2 National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bengaluru , India
| | - Hojun Song
- 3 Department of Entomology, Texas A&M University , College Station, TX 77843 , USA
| | - Peter Andolfatto
- 4 Department of Biological Sciences, Columbia University , New York, NY 10027 , USA
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23
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Schumer M, Xu C, Powell DL, Durvasula A, Skov L, Holland C, Blazier JC, Sankararaman S, Andolfatto P, Rosenthal GG, Przeworski M. Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science 2018; 360:656-660. [PMID: 29674434 PMCID: PMC6069607 DOI: 10.1126/science.aar3684] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/23/2018] [Indexed: 12/29/2022]
Abstract
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the "minor" parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture. These results support models in which ancestry from the minor parental species is more likely to persist when rapidly uncoupled from alleles that are deleterious in hybrids. Our analyses further indicate that selection on swordtail hybrids stems predominantly from deleterious combinations of epistatically interacting alleles.
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Affiliation(s)
- Molly Schumer
- Howard Hughes Medical Institute (HHMI), Boston, MA, USA.
- Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico
| | - Chenling Xu
- Center for Computational Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Daniel L Powell
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Chris Holland
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - John C Blazier
- Department of Biology, Texas A&M University, College Station, TX, USA
- Texas A&M Institute for Genome Sciences and Society, College Station, TX, USA
| | - Sriram Sankararaman
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA
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24
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Schumer M, Rosenthal GG, Andolfatto P. What do we mean when we talk about hybrid speciation? Heredity (Edinb) 2018; 120:379-382. [PMID: 29302049 PMCID: PMC5842215 DOI: 10.1038/s41437-017-0036-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/10/2017] [Accepted: 11/11/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- Molly Schumer
- Hanna Gray Fellow, Howard Hughes Medical Institute, Cambridge, MA, USA.
- Harvard Society of Fellows, Harvard University, Boston, MA, USA.
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico.
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico
- Department of Biology and Interdisciplinary Faculty of Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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25
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Crowley-Gall A, Date P, Han C, Rhodes N, Andolfatto P, Layne JE, Rollmann SM. Population differences in olfaction accompany host shift in Drosophila mojavensis. Proc Biol Sci 2017; 283:rspb.2016.1562. [PMID: 27581882 DOI: 10.1098/rspb.2016.1562] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/09/2016] [Indexed: 11/12/2022] Open
Abstract
Evolutionary shifts in plant-herbivore interactions provide a model for understanding the link among the evolution of behaviour, ecological specialization and incipient speciation. Drosophila mojavensis uses different host cacti across its range, and volatile chemicals emitted by the host are the primary cue for host plant identification. In this study, we show that changes in host plant use between distinct D. mojavensis populations are accompanied by changes in the olfactory system. Specifically, we observe differences in olfactory receptor neuron specificity and sensitivity, as well as changes in sensillar subtype abundance, between populations. Additionally, RNA-seq analyses reveal differential gene expression between populations for members of the odorant receptor gene family. Hence, alterations in host preference are associated with changes in development, regulation and function at the olfactory periphery.
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Affiliation(s)
- Amber Crowley-Gall
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Priya Date
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Clair Han
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Nicole Rhodes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Peter Andolfatto
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - John E Layne
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Stephanie M Rollmann
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
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26
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Crowley-Gall A, Date P, Han C, Rhodes N, Andolfatto P, Layne JE, Rollmann SM. Correction to ‘Population differences in olfaction accompany host shift in
Drosophila mojavensis
’. Proc Biol Sci 2017; 284:rspb.2017.1260. [DOI: 10.1098/rspb.2017.1260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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27
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McCulloch KJ, Yuan F, Zhen Y, Aardema ML, Smith G, Llorente-Bousquets J, Andolfatto P, Briscoe AD. Sexual Dimorphism and Retinal Mosaic Diversification following the Evolution of a Violet Receptor in Butterflies. Mol Biol Evol 2017; 34:2271-2284. [DOI: 10.1093/molbev/msx163] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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28
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Tate AT, Andolfatto P, Demuth JP, Graham AL. The within-host dynamics of infection in trans-generationally primed flour beetles. Mol Ecol 2017; 26:3794-3807. [PMID: 28277618 DOI: 10.1111/mec.14088] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 12/19/2022]
Abstract
Many taxa exhibit plastic immune responses initiated after primary microbial exposure that provide increased protection against disease-induced mortality and the fitness costs of infection. In several arthropod species, this protection can even be passed from parents to offspring through a phenomenon called trans-generational immune priming. Here, we first demonstrate that trans-generational priming is a repeatable phenomenon in flour beetles (Tribolium castaneum) primed and infected with Bacillus thuringiensis (Bt). We then quantify the within-host dynamics of microbes and host physiological responses in infected offspring from primed and unprimed mothers by monitoring bacterial density and using mRNA-seq to profile host gene expression, respectively, over the acute infection period. We find that priming increases inducible resistance against Bt around a critical temporal juncture where host septicaemic trajectories, and consequently survival, may be determined in unprimed individuals. Our results identify a highly differentially expressed biomarker of priming, containing an EIF4-e domain, in uninfected individuals, as well as several other candidate genes. Moreover, the induction and decay dynamics of gene expression over time suggest a metabolic shift in primed individuals. The identified bacterial and gene expression dynamics are likely to influence patterns of bacterial fitness and disease transmission in natural populations.
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Affiliation(s)
- Ann T Tate
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jeffery P Demuth
- Department of Biology, University of Texas, Arlington, TX, 76010, USA
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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29
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Aardema ML, Andolfatto P. Phylogenetic incongruence and the evolutionary origins of cardenolide-resistant forms of Na(+) ,K(+) -ATPase in Danaus butterflies. Evolution 2016; 70:1913-21. [PMID: 27405795 PMCID: PMC4980202 DOI: 10.1111/evo.12999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/19/2016] [Indexed: 12/27/2022]
Abstract
Many distantly related insect species are specialized feeders of cardenolide-containing host plants such as milkweed (Asclepias spp.). Previous studies have revealed frequent, parallel substitution of a functionally important amino acid substitution (N122H) in the alpha subunit of Na(+) ,K(+) -ATPase in a number of these species. This substitution facilitates the ability of these insects to feed on their toxic hosts and sequester cardenolides for their own use in defense. Among milkweed butterflies of the genus Danaus, the previously established phylogeny for this group suggests that N122H arose independently and fixed in two distinct lineages. We reevaluate this conclusion by examining Danaus phylogenetic relationships using >400 orthologous gene sequences assembled from transcriptome data. Our results indicate that the three Danaus species known to harbor the N122H substitution are more closely related than previously thought, consistent with a single, common origin for N122H. However, we also find evidence of both incomplete lineage sorting and post-speciation genetic exchange among these butterfly species, raising the possibility of collateral evolution of cardenolide-insensitivity in this species group.
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Affiliation(s)
- Matthew L Aardema
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, 08544.
- Current Address: American Museum of Natural History, New York, New York, 10024.
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, 08544
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, 08544
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30
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Elyashiv E, Sattath S, Hu TT, Strutsovsky A, McVicker G, Andolfatto P, Coop G, Sella G. A Genomic Map of the Effects of Linked Selection in Drosophila. PLoS Genet 2016; 12:e1006130. [PMID: 27536991 PMCID: PMC4990265 DOI: 10.1371/journal.pgen.1006130] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/26/2016] [Indexed: 01/23/2023] Open
Abstract
Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of "linked selection" on levels of genetic diversity is key to making reliable inference about demography, building a null model in scans for targets of adaptation, and learning about the dynamics of natural selection. Here, we introduce the first method that jointly infers parameters of distinct modes of linked selection, notably background selection and selective sweeps, from genome-wide diversity data, functional annotations and genetic maps. The central idea is to calculate the probability that a neutral site is polymorphic given local annotations, substitution patterns, and recombination rates. Information is then combined across sites and samples using composite likelihood in order to estimate genome-wide parameters of distinct modes of selection. In addition to parameter estimation, this approach yields a map of the expected neutral diversity levels along the genome. To illustrate the utility of our approach, we apply it to genome-wide resequencing data from 125 lines in Drosophila melanogaster and reliably predict diversity levels at the 1Mb scale. Our results corroborate estimates of a high fraction of beneficial substitutions in proteins and untranslated regions (UTR). They allow us to distinguish between the contribution of sweeps and other modes of selection around amino acid substitutions and to uncover evidence for pervasive sweeps in untranslated regions (UTRs). Our inference further suggests a substantial effect of other modes of linked selection and of adaptation in particular. More generally, we demonstrate that linked selection has had a larger effect in reducing diversity levels and increasing their variance in D. melanogaster than previously appreciated.
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Affiliation(s)
- Eyal Elyashiv
- Department of Ecology, Evolution, and Behavior, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Shmuel Sattath
- Department of Ecology, Evolution, and Behavior, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tina T. Hu
- Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Alon Strutsovsky
- Department of Ecology, Evolution, and Behavior, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Graham McVicker
- The Laboratory of Genetics and The Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Graham Coop
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
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31
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Schumer M, Cui R, Powell DL, Rosenthal GG, Andolfatto P. Ancient hybridization and genomic stabilization in a swordtail fish. Mol Ecol 2016; 25:2661-79. [DOI: 10.1111/mec.13602] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/06/2016] [Accepted: 01/06/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology Princeton University Princeton NJ 08544 USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
- Max Planck Institute for the Biology of Aging D‐50931 Cologne Germany
| | - Daniel L. Powell
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
| | - Gil G. Rosenthal
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology Princeton University Princeton NJ 08544 USA
- Lewis‐Sigler Institute for Integrative Genomics Princeton University Princeton NJ 08544 USA
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32
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Schumer M, Cui R, Rosenthal GG, Andolfatto P. simMSG: an experimental design tool for high-throughput genotyping of hybrids. Mol Ecol Resour 2015; 16:183-92. [PMID: 26032857 DOI: 10.1111/1755-0998.12434] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 11/30/2022]
Abstract
Hybridization between closely related species, whether naturally occurring or laboratory generated, is a useful tool for mapping the genetic basis of the phenotypic traits that distinguish species. The development of next-generation sequencing techniques has greatly improved our ability to assign ancestry to hybrid genomes. One such next-generation sequencing technique, multiplexed shotgun genotyping (or MSG), can be a powerful tool for genotyping hybrids. However, it is difficult a priori to predict the accuracy of MSG in natural hybrids because accuracy depends on ancestry tract length and number of ancestry informative markers. Here, we present a simulator, 'simMSG', that will allow researchers to design MSG experiments and show that in many cases MSG can accurately assign ancestry to hundreds of thousands of sites in the genomes of natural hybrids. The simMSG tool can be used to design experiments for diverse applications including QTL mapping, genotyping introgressed lines or admixture mapping.
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.,Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', Calnali, Hidalgo, Mexico
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, TAMU, College Station, TX, USA.,Max Planck Institute for the Biology of Aging, Cologne, Germany
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, TAMU, College Station, TX, USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
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Schumer M, Cui R, Rosenthal GG, Andolfatto P. Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genet 2015; 11:e1005041. [PMID: 25768654 PMCID: PMC4359097 DOI: 10.1371/journal.pgen.1005041] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/29/2015] [Indexed: 12/25/2022] Open
Abstract
Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against genetic incompatibilities. Unlike previous models of hybrid speciation, our model does not incorporate inbreeding, or assume that hybrids have an ecological or reproductive fitness advantage relative to parental populations. We show that reproductive isolation between hybrids and parental species can evolve frequently and rapidly under this model, even in the presence of substantial ongoing immigration from parental species and strong selection against hybrids. An interesting prediction of our model is that replicate hybrid populations formed from the same pair of parental species can evolve reproductive isolation from each other. This non-adaptive process can therefore generate patterns of species diversity and relatedness that resemble an adaptive radiation. Intriguingly, several known hybrid species exhibit patterns of reproductive isolation consistent with the predictions of our model.
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rongfeng Cui
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, Calnali, Hidalgo, Mexico
- Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Gil G. Rosenthal
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, Calnali, Hidalgo, Mexico
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
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Schumer M, Cui R, Powell DL, Dresner R, Rosenthal GG, Andolfatto P. High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species. eLife 2014; 3. [PMID: 24898754 PMCID: PMC4080447 DOI: 10.7554/elife.02535] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/02/2014] [Indexed: 12/18/2022] Open
Abstract
Hybridization is increasingly being recognized as a common process in both animal and plant species. Negative epistatic interactions between genes from different parental genomes decrease the fitness of hybrids and can limit gene flow between species. However, little is known about the number and genome-wide distribution of genetic incompatibilities separating species. To detect interacting genes, we perform a high-resolution genome scan for linkage disequilibrium between unlinked genomic regions in naturally occurring hybrid populations of swordtail fish. We estimate that hundreds of pairs of genomic regions contribute to reproductive isolation between these species, despite them being recently diverged. Many of these incompatibilities are likely the result of natural or sexual selection on hybrids, since intrinsic isolation is known to be weak. Patterns of genomic divergence at these regions imply that genetic incompatibilities play a significant role in limiting gene flow even in young species.
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
| | - Rongfeng Cui
- Department of Biology, Texas A&M University, College Station, United States
| | - Daniel L Powell
- Department of Biology, Texas A&M University, College Station, United States
| | - Rebecca Dresner
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
| | - Gil G Rosenthal
- Department of Biology, Texas A&M University, College Station, United States
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
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35
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey 08544
| | - Gil G. Rosenthal
- Department of Biology; Texas A&M University (TAMU); College Station Texas 77843
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca,” Calnali; Hidalgo 43230 Mexico
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey 08544
- Lewis-Sigler Institute for Integrative Genomics, Princeton University; Princeton New Jersey 08544
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Rogers RL, Cridland JM, Shao L, Hu TT, Andolfatto P, Thornton KR. Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Mol Biol Evol 2014; 31:1750-66. [PMID: 24710518 PMCID: PMC4069613 DOI: 10.1093/molbev/msu124] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of Drosophila yakuba and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,415 tandem duplications that are segregating in D. yakuba as well as 975 duplications in D. simulans, indicating greater variation in D. yakuba. Additionally, we observe high rates of secondary deletions at duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites in D. yakuba modified with deletions. These secondary deletions are consistent with the action of the large loop mismatch repair system acting to remove polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in duplicated alleles and a richer substrate of genetic novelty than has been previously reported. Most duplications are present in only single strains, suggesting that deleterious impacts are common. Drosophila simulans shows larger numbers of whole gene duplications in comparison to larger proportions of gene fragments in D. yakuba. Drosophila simulans displays an excess of high-frequency variants on the X chromosome, consistent with adaptive evolution through duplications on the D. simulans X or demographic forces driving duplicates to high frequency. We identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans, as well as 143 cases of recruited noncoding sequence in D. yakuba and 96 in D. simulans, in agreement with rates of chimeric gene origination in D. melanogaster. Together, these results suggest that tandem duplications often result in complex variation beyond whole gene duplications that offers a rich substrate of standing variation that is likely to contribute both to detrimental phenotypes and disease, as well as to adaptive evolutionary change.
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Affiliation(s)
- Rebekah L Rogers
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | - Julie M Cridland
- Department of Ecology and Evolutionary Biology, University of California, IrvineDepartment of Ecology and Evolutionary Biology, University of California, Davis
| | - Ling Shao
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | - Tina T Hu
- Department of Ecology and Evolutionary Biology and the Lewis Sigler Institute for Integrative Genomics, Princeton University
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and the Lewis Sigler Institute for Integrative Genomics, Princeton University
| | - Kevin R Thornton
- Department of Ecology and Evolutionary Biology, University of California, Irvine
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37
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Cui R, Schumer M, Kruesi K, Walter R, Andolfatto P, Rosenthal GG. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution 2013; 67:2166-79. [PMID: 23888843 DOI: 10.1111/evo.12099] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 02/26/2013] [Indexed: 01/25/2023]
Abstract
Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high-confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long-standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus.
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Affiliation(s)
- Rongfeng Cui
- Department of Biology, Texas A&M University, TAMU, College Station, Texas, 77843, USA.
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38
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Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P. An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution 2013; 67:1155-68. [PMID: 23550763 PMCID: PMC3621027 DOI: 10.1111/evo.12009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Once thought rare in animal taxa, hybridization has been increasingly recognized as an important and common force in animal evolution. In the past decade, a number of studies have suggested that hybridization has driven speciation in some animal groups. We investigate the signature of hybridization in the genome of a putative hybrid species, Xiphophorus clemenciae, through whole genome sequencing of this species and its hypothesized progenitors. Based on analysis of this data, we find that X. clemenciae is unlikely to have been derived from admixture between its proposed parental species. However, we find significant evidence for recent gene flow between Xiphophorus species. Although we detect genetic exchange in two pairs of species analyzed, the proportion of genomic regions that can be attributed to hybrid origin is small, suggesting that strong behavioral premating isolation prevents frequent hybridization in Xiphophorus. The direction of gene flow between species is potentially consistent with a role for sexual selection in mediating hybridization.
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA.
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39
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Abstract
Numerous insects have independently evolved the ability to feed on plants that produce toxic secondary compounds called cardenolides and can sequester these compounds for use in their defense. We surveyed the protein target for cardenolides, the alpha subunit of the sodium pump, Na(+),K(+)-ATPase (ATPα), in 14 species that feed on cardenolide-producing plants and 15 outgroups spanning three insect orders. Despite the large number of potential targets for modulating cardenolide sensitivity, amino acid substitutions associated with host-plant specialization are highly clustered, with many parallel substitutions. Additionally, we document four independent duplications of ATPα with convergent tissue-specific expression patterns. We find that unique substitutions are disproportionately associated with recent duplications relative to parallel substitutions. Together, these findings support the hypothesis that adaptation tends to take evolutionary paths that minimize negative pleiotropy.
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Affiliation(s)
- Ying Zhen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Matthew L. Aardema
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Edgar M. Medina
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá 11001, Colombia
| | - Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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40
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Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, Venkat A, Andolfatto P, Przeworski M. Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol 2012; 10:e1001388. [PMID: 22984349 PMCID: PMC3439417 DOI: 10.1371/journal.pbio.1001388] [Citation(s) in RCA: 317] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.
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Affiliation(s)
- Ellen M. Leffler
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (EML); (MP)
| | - Kevin Bullaughey
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Daniel R. Matute
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Wynn K. Meyer
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Laure Ségurel
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Aarti Venkat
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Molly Przeworski
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (EML); (MP)
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41
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Hu TT, Eisen MB, Thornton KR, Andolfatto P. A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res 2012; 23:89-98. [PMID: 22936249 PMCID: PMC3530686 DOI: 10.1101/gr.141689.112] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We create a new assembly of the Drosophila simulans genome using 142 million paired short-read sequences and previously published data for strain w501. Our assembly represents a higher-quality genomic sequence with greater coverage, fewer misassemblies, and, by several indexes, fewer sequence errors. Evolutionary analysis of this genome reference sequence reveals interesting patterns of lineage-specific divergence that are different from those previously reported. Specifically, we find that Drosophila melanogaster evolves faster than D. simulans at all annotated classes of sites, including putatively neutrally evolving sites found in minimal introns. While this may be partly explained by a higher mutation rate in D. melanogaster, we also find significant heterogeneity in rates of evolution across classes of sites, consistent with historical differences in the effective population size for the two species. Also contrary to previous findings, we find that the X chromosome is evolving significantly faster than autosomes for nonsynonymous and most noncoding DNA sites and significantly slower for synonymous sites. The absence of a X/A difference for putatively neutral sites and the robustness of the pattern to Gene Ontology and sex-biased expression suggest that partly recessive beneficial mutations may comprise a substantial fraction of noncoding DNA divergence observed between species. Our results have more general implications for the interpretation of evolutionary analyses of genomes of different quality.
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Affiliation(s)
- Tina T Hu
- Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.
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42
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Cande J, Andolfatto P, Prud'homme B, Stern DL, Gompel N. Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship. PLoS One 2012; 7:e43888. [PMID: 22952802 PMCID: PMC3431401 DOI: 10.1371/journal.pone.0043888] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 07/26/2012] [Indexed: 01/06/2023] Open
Abstract
In Drosophila, male flies perform innate, stereotyped courtship behavior. This innate behavior evolves rapidly between fly species, and is likely to have contributed to reproductive isolation and species divergence. We currently understand little about the neurobiological and genetic mechanisms that contributed to the evolution of courtship behavior. Here we describe a novel behavioral difference between the two closely related species D. yakuba and D. santomea: the frequency of wing rowing during courtship. During courtship, D. santomea males repeatedly rotate their wing blades to face forward and then back (rowing), while D. yakuba males rarely row their wings. We found little intraspecific variation in the frequency of wing rowing for both species. We exploited multiplexed shotgun genotyping (MSG) to genotype two backcross populations with a single lane of Illumina sequencing. We performed quantitative trait locus (QTL) mapping using the ancestry information estimated by MSG and found that the species difference in wing rowing mapped to four or five genetically separable regions. We found no evidence that these loci display epistasis. The identified loci all act in the same direction and can account for most of the species difference.
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Affiliation(s)
- Jessica Cande
- Institut de Biologie du Developpement de Marseille-Luminy, Aix-Marseille Université, Marseille, France
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and the Lewis Sigler Institute for Integrative Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Benjamin Prud'homme
- Institut de Biologie du Developpement de Marseille-Luminy, Aix-Marseille Université, Marseille, France
- * E-mail: (BP); (DS); (NG)
| | - David L. Stern
- Howard Hughes Medical Institute and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (BP); (DS); (NG)
| | - Nicolas Gompel
- Institut de Biologie du Developpement de Marseille-Luminy, Aix-Marseille Université, Marseille, France
- * E-mail: (BP); (DS); (NG)
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43
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Garrigan D, Kingan SB, Geneva AJ, Andolfatto P, Clark AG, Thornton KR, Presgraves DC. Genome sequencing reveals complex speciation in the Drosophila simulans clade. Genome Res 2012; 22:1499-511. [PMID: 22534282 PMCID: PMC3409263 DOI: 10.1101/gr.130922.111] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The three species of the Drosophila simulans clade—the cosmopolitan species, D. simulans, and the two island endemic species, D. mauritiana and D. sechellia—are important models in speciation genetics, but some details of their phylogenetic and speciation history remain unresolved. The order and timing of speciation are disputed, and the existence, magnitude, and timing of gene flow among the three species remain unclear. Here we report on the analysis of a whole-genome four-species sequence alignment that includes all three D. simulans clade species as well as the D. melanogaster reference sequence. The alignment comprises novel, paired short-read sequence data from a single highly inbred line each from D. simulans, D. mauritiana, and D. sechellia. We are unable to reject a species phylogeny with a basal polytomy; the estimated age of the polytomy is 242,000 yr before the present. However, we also find that up to 4.6% of autosomal and 2.2% of X-linked regions have evolutionary histories consistent with recent gene flow between the mainland species (D. simulans) and the two island endemic species (D. mauritiana and D. sechellia). Our findings thus show that gene flow has occurred throughout the genomes of the D. simulans clade species despite considerable geographic, ecological, and intrinsic reproductive isolation. Last, our analysis of lineage-specific changes confirms that the D. sechellia genome has experienced a significant excess of slightly deleterious changes and a dearth of presumed favorable changes. The relatively reduced efficacy of natural selection in D. sechellia is consistent with its derived, persistently reduced historical effective population size.
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Affiliation(s)
- Daniel Garrigan
- Department of Biology, University of Rochester, Rochester, New York 14627, USA.
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44
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Abstract
The transition from outcrossing to predominant self-fertilization is one of the most common evolutionary transitions in flowering plants. This shift is often accompanied by a suite of changes in floral and reproductive characters termed the selfing syndrome. Here, we characterize the genetic architecture and evolutionary forces underlying evolution of the selfing syndrome in Capsella rubella following its recent divergence from the outcrossing ancestor C. grandiflora. We conduct genotyping by multiplexed shotgun sequencing and map floral and reproductive traits in a large (N= 550) F2 population. Our results suggest that in contrast to previous studies of the selfing syndrome, changes at a few loci, some with major effects, have shaped the evolution of the selfing syndrome in Capsella. The directionality of QTL effects, as well as population genetic patterns of polymorphism and divergence at 318 loci, is consistent with a history of directional selection on the selfing syndrome. Our study is an important step toward characterizing the genetic basis and evolutionary forces underlying the evolution of the selfing syndrome in a genetically accessible model system.
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Affiliation(s)
- Tanja Slotte
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden.
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45
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Abstract
Vast tracts of noncoding DNA contain elements that regulate gene expression in higher eukaryotes. Describing these regulatory elements and understanding how they evolve represent major challenges for biologists. Advances in the ability to survey genome-scale DNA sequence data are providing unprecedented opportunities to use evolutionary models and computational tools to identify functionally important elements and the mode of selection acting on them in multiple species. This chapter reviews some of the current methods that have been developed and applied on noncoding DNA, what they have shown us, and how they are limited. Results of several recent studies reveal that a significantly larger fraction of noncoding DNA in eukaryotic organisms is likely to be functional than previously believed, implying that the functional annotation of most noncoding DNA in these organisms is largely incomplete. In Drosophila, recent studies have further suggested that a large fraction of noncoding DNA divergence observed between species may be the product of recurrent adaptive substitution. Similar studies in humans have revealed a more complex pattern, with signatures of recurrent positive selection being largely concentrated in conserved noncoding DNA elements. Understanding these patterns and the extent to which they generalize to other organisms awaits the analysis of forthcoming genome-scale polymorphism and divergence data from more species.
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Affiliation(s)
- Ying Zhen
- Department of Ecology and Evolutionary Biology, The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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46
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Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M. A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genet 2011; 7:e1002395. [PMID: 22144911 PMCID: PMC3228810 DOI: 10.1371/journal.pgen.1002395] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 10/08/2011] [Indexed: 01/23/2023] Open
Abstract
Through an analysis of polymorphism within and divergence between species, we can hope to learn about the distribution of selective effects of mutations in the genome, changes in the fitness landscape that occur over time, and the location of sites involved in key adaptations that distinguish modern-day species. We introduce a novel method for the analysis of variation in selection pressures within and between species, spatially along the genome and temporally between lineages. We model codon evolution explicitly using a joint population genetics-phylogenetics approach that we developed for the construction of multiallelic models with mutation, selection, and drift. Our approach has the advantage of performing direct inference on coding sequences, inferring ancestral states probabilistically, utilizing allele frequency information, and generalizing to multiple species. We use a Bayesian sliding window model for intragenic variation in selection coefficients that efficiently combines information across sites and captures spatial clustering within the genome. To demonstrate the utility of the method, we infer selective pressures acting in Drosophila melanogaster and D. simulans from polymorphism and divergence data for 100 X-linked coding regions.
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Affiliation(s)
- Daniel J Wilson
- Department of Human Genetics and Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.
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47
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Abstract
Cardenolides are a class of plant secondary compounds that inhibit the proper functioning of the Na(+) , K(+) -ATPase enzyme in susceptible animals. Nonetheless, many insect species are able to sequester cardenolides for their own defence. These include butterflies in the subfamily Danainae (Family: Nymphalidae) such as the monarch (Danaus plexippus). Previous studies demonstrated that monarchs harbour an asparagine (N) to histidine (H) substitution (N122H) in the α subunit of Na(+) , K(+) -ATPase (ATPα) that reduces this enzyme's sensitivity to cardenolides. More recently, it has been suggested that at ATPα position 111, monarchs may also harbour a leucine (L)/glutamine (Q) polymorphism. This later amino acid could also contribute to cardenolide insensitivity. However, here we find that incorrect annotation of the initially reported DNA sequence for ATPα has led to several erroneous conclusions. Using a population genetic and phylogenetic analysis of monarchs and their close relatives, we show that an ancient Q111L substitution occurred prior to the radiation of all Danainae, followed by a second substitution at the same site to valine (V), which arose before the diversification of the Danaus genus. In contrast, N122H appears to be a recent substitution specific to monarchs. Surprisingly, examination of a broader insect phylogeny reveals that the same progression of amino acid substitutions (Q111L → L111V + N122H) has also occurred in Chyrsochus beetles (Family: Chrysomelidae, Subfamily: Eumolpinae) that feed on cardenolide-containing host plants. The parallel pattern of amino acid substitution in these two distantly related lineages is consistent with an adaptive role for these substitutions in reducing cardenolide sensitivity and suggests that their temporal order may be limited by epistatic interactions.
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Affiliation(s)
- Matthew L Aardema
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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48
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Abstract
Structurama is a program for inferring population structure. Specifically, the program calculates the posterior probability of assigning individuals to different populations. The program takes as input a file containing the allelic information at some number of loci sampled from a collection of individuals. After reading a data file into computer memory, Structurama uses a Gibbs algorithm to sample assignments of individuals to populations. The program implements four different models: The number of populations can be considered fixed or a random variable with a Dirichlet process prior; moreover, the genotypes of the individuals in the analysis can be considered to come from a single population (no admixture) or as coming from several different populations (admixture). The output is a file of partitions of individuals to populations that were sampled by the Markov chain Monte Carlo algorithm. The partitions are sampled in proportion to their posterior probabilities. The program implements a number of ways to summarize the sampled partitions, including calculation of the ‘mean’ partition—a partition of the individuals to populations that minimizes the squared distance to the sampled partitions.
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Affiliation(s)
- John P Huelsenbeck
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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49
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Callahan B, Neher RA, Bachtrog D, Andolfatto P, Shraiman BI. Correlated evolution of nearby residues in Drosophilid proteins. PLoS Genet 2011; 7:e1001315. [PMID: 21383965 PMCID: PMC3044683 DOI: 10.1371/journal.pgen.1001315] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 01/19/2011] [Indexed: 11/19/2022] Open
Abstract
Here we investigate the correlations between coding sequence substitutions as a function of their separation along the protein sequence. We consider both substitutions between the reference genomes of several Drosophilids as well as polymorphisms in a population sample of Zimbabwean Drosophila melanogaster. We find that amino acid substitutions are “clustered” along the protein sequence, that is, the frequency of additional substitutions is strongly enhanced within ≈10 residues of a first such substitution. No such clustering is observed for synonymous substitutions, supporting a “correlation length” associated with selection on proteins as the causative mechanism. Clustering is stronger between substitutions that arose in the same lineage than it is between substitutions that arose in different lineages. We consider several possible origins of clustering, concluding that epistasis (interactions between amino acids within a protein that affect function) and positional heterogeneity in the strength of purifying selection are primarily responsible. The role of epistasis is directly supported by the tendency of nearby substitutions that arose on the same lineage to preserve the total charge of the residues within the correlation length and by the preferential cosegregation of neighboring derived alleles in our population sample. We interpret the observed length scale of clustering as a statistical reflection of the functional locality (or modularity) of proteins: amino acids that are near each other on the protein backbone are more likely to contribute to, and collaborate toward, a common subfunction. Genes are templates for proteins, yet evolutionary studies of genes and proteins often bear little resemblance. Analyses of gene evolution typically treat each codon independently, quantifying gene evolution by summing over the constituent codons. In contrast, studies of protein evolution generally incorporate protein structure and interactions between amino acids explicitly. We investigate correlations in the evolution of codons as a function of their distance from each other along the protein coding sequence. This approach is motivated by the expectation that codons near each other in sequence often encode amino acids belonging to the same functional unit. Consequently, these amino acids are more likely to interact and/or experience similar selective regimes, introducing correlation between the evolution of the underlying codons. We find codon evolution in Drosophilids to be correlated over a characteristic length scale of ≈10 codons. Specifically, the presence of a non-synonymous substitution substantially increases the probability of further such substitutions nearby, particularly within that lineage. Further analysis suggests both functional interactions between amino acids and correlation in the strength of selection contribute to this effect. These findings are relevant for understanding the relative importance of different modes of selection, and particularly the role of epistasis, in gene and protein evolution.
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Affiliation(s)
- Benjamin Callahan
- Department of Applied Physics, Stanford University, Stanford, California, United States of America.
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Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 2011; 21:610-7. [PMID: 21233398 DOI: 10.1101/gr.115402.110] [Citation(s) in RCA: 273] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a new approach to genotyping based on multiplexed shotgun sequencing that can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. We first describe a simple library construction protocol that uses just 10 ng of genomic DNA per individual and makes the approach accessible to any laboratory with standard molecular biology equipment. Sequencing this library results in a large number of sequence reads widely distributed across the genomes of multiplexed bar-coded individuals. We develop a Hidden Markov Model to estimate ancestry at all genomic locations in all individuals using these data. We demonstrate the utility of the approach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using 96 F1-backcross individuals genotyped in a single lane on an Illumina Genome Analyzer. We further demonstrate the utility of our method by genetically mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating the quality of targeted introgression lines. At this level of multiplexing and divergence between strains, our method allows estimation of recombination breakpoints to a median of 38-kb intervals. Our analysis suggests that higher levels of multiplexing and/or use of strains with lower levels of divergence are practicable.
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Affiliation(s)
- Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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