101
|
Hohenlohe PA, Magalhaes IS. The Population Genomics of Parallel Adaptation: Lessons from Threespine Stickleback. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2019_67] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
102
|
Gotanda KM, Pack A, LeBlond C, Hendry AP. Do replicates of independent guppy lineages evolve similarly in a predator-free laboratory environment? Ecol Evol 2019; 9:36-51. [PMID: 30680094 PMCID: PMC6342246 DOI: 10.1002/ece3.4585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 12/02/2022] Open
Abstract
The Trinidadian guppy is emblematic of parallel and convergent evolution, with repeated demonstrations that predation regime is a driver of adaptive trait evolution. A classic and foundational experiment in this system was conducted by John Endler 40 years ago, where male guppies placed into low-predation environments in the laboratory evolved increased color in a few generations. However, Endler's experiment did not employ the now typical design for a parallel/convergent evolution study, which would employ replicates of different ancestral lineages. We therefore implemented an experiment that seeded replicate mesocosms with small founding populations of guppies originating from high-predation populations of two very different lineages. The different mesocosms were maintained identically, and male guppy color was quantified every four months. After one year, we tested whether male color had increased, whether replicates within a lineage had parallel phenotypic trajectories, and whether the different lineages converged on a common phenotype. Results showed that male guppy color generally increased through time, primarily due to changes in melanic color, whereas the other colors showed inconsistent and highly variable trajectories. Most of the nonparallelism in phenotypic trajectories was among mesocosms containing different lineages. In addition to this mixture of parallelism and nonparallelism, convergence was not evident in that the variance in color among the mesocosms actually increased through time. We suggest that our results reflect the potential importance of high variation in female preference and stochastic processes such as drift and founder effects, both of which could be important in nature.
Collapse
Affiliation(s)
- Kiyoko M. Gotanda
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
- Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Amy Pack
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
- Global ProgramsHealth Standards OrganizationOttawaOntarioCanada
| | - Caroline LeBlond
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
| | - Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
| |
Collapse
|
103
|
Abstract
Convergent evolution provides key evidence for the action of natural selection. The process of convergence is often inferred because the same trait appears in multiple species that are not closely related. However, different parts of the genome can reveal different relationships among species, with some genes or regions uniting lineages that appear unrelated in the species tree. If changes in traits occur in these discordant regions, a false pattern of convergence can be produced (known as “hemiplasy”). Here, we provide a way to quantify the probability that hemiplasy occurs and contrast it with the probability of convergence. We find that hemiplasy is likely to explain many apparent cases of convergent evolution, even when the fraction of discordant regions is low. Convergent evolution—the appearance of the same character state in apparently unrelated organisms—is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely—or more likely—than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a method to calculate the ratio of these two probabilities (the “hemiplasy risk factor”) along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree to identify when and where incongruent traits may be due to hemiplasy.
Collapse
|
104
|
Cassin-Sackett L, Callicrate TE, Fleischer RC. Parallel evolution of gene classes, but not genes: Evidence from Hawai'ian honeycreeper populations exposed to avian malaria. Mol Ecol 2018; 28:568-583. [PMID: 30298567 DOI: 10.1111/mec.14891] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 10/14/2018] [Accepted: 10/19/2018] [Indexed: 12/29/2022]
Abstract
Adaptation in nature is ubiquitous, yet characterizing its genomic basis is difficult because population demographics cause correlations with nonadaptive loci. Introduction events provide opportunities to observe adaptation over known spatial and temporal scales, facilitating the identification of genes involved in adaptation. The pathogen causing avian malaria, Plasmodium relictum, was introduced to Hawai'i in the 1930s and elicited extinctions and precipitous population declines in native honeycreepers. After a sharp initial population decline, the Hawai'i 'amakihi (Chlorodrepanis virens) has evolved tolerance to the parasite at low elevations where P. relictum exists, and can sustain infection without major fitness consequences. High-elevation, unexposed populations of 'amakihi display little to no tolerance. To explore the genomic basis of adaptation to P. relictum in low-elevation 'amakihi, we genotyped 125 'amakihi from the island of Hawai'i via hybridization capture to 40,000 oligonucleotide baits containing SNPs and used the reference 'amakihi genome to identify genes potentially under selection from malaria. We tested for outlier loci between low- and high-elevation population pairs and identified loci with signatures of selection within low-elevation populations. In some cases, genes commonly involved in the immune response (e.g., major histocompatibility complex) were associated with malaria presence in the population. We also detected several novel candidate loci that may be implicated in surviving malaria infection (e.g., beta-defensin, glycoproteins and interleukin-related genes). Our results suggest that rapid adaptation to pathogens may occur through changes in different immune genes, but in the same classes of genes, across populations.
Collapse
Affiliation(s)
- Loren Cassin-Sackett
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia.,Department of Integrative Biology, University of South Florida, Tampa, Florida
| | - Taylor E Callicrate
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia.,Species Conservation Toolkit Initiative, Department of Conservation Science, Chicago Zoological Society, Brookfield, Illinois
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| |
Collapse
|
105
|
Kitano J, Ishikawa A, Kusakabe M. Parallel transcriptome evolution in stream threespine sticklebacks. Dev Growth Differ 2018; 61:104-113. [DOI: 10.1111/dgd.12576] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Jun Kitano
- Division of Ecological Genetics; National Institute of Genetics; Mishima, Shizuoka Japan
| | - Asano Ishikawa
- Division of Ecological Genetics; National Institute of Genetics; Mishima, Shizuoka Japan
| | - Makoto Kusakabe
- Department of Biological Science; Faculty of Science; Shizuoka University; Surugaku, Shizuoka Japan
| |
Collapse
|
106
|
Mandic M, Ramon ML, Gerstein AC, Gracey AY, Richards JG. Variable gene transcription underlies phenotypic convergence of hypoxia tolerance in sculpins. BMC Evol Biol 2018; 18:163. [PMID: 30390629 PMCID: PMC6215679 DOI: 10.1186/s12862-018-1275-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 10/18/2018] [Indexed: 01/03/2023] Open
Abstract
Background The degree by which mechanisms underlying phenotypic convergence are similar among taxa depends on the number of evolutionary paths available for selection to act upon. Likelihood of convergence will be influenced by an interplay of factors such as genetic architecture, phylogenetic history and population demography. To determine if there is convergence or divergence in mechanisms underlying phenotypic similarity, we assessed whether gene transcription patterns differed among species with similar levels of hypoxia tolerance. Results Three species of marine fish from the superfamily Cottoidea (smoothhead sculpin [Artedius lateralis], sailfin sculpin [Nautichthys oculofasciatus] and Pacific staghorn sculpin [Leptocottus armatus]), all of which have previously been shown to share the same level of hypoxia tolerance, were exposed to short-(8 h) and longer-term (72 h) hypoxia and mRNA transcripts were assessed using a custom microarray. We examined hypoxia-induced transcription patterns in metabolic and protein production pathways and found that a high proportion of genes associated with these biological processes showed significant differences among the species. Specifically, the data suggest that the smoothhead sculpin, unlike the sailfin sculpin and the Pacific staghorn sculpin, relied on amino acid degradation rather than glycolysis or fatty acid oxidation to generate ATP during hypoxia exposure. There was also variation across the species in the transcription of genes involved in protein production (e.g. mRNA processing and protein translation), such that it increased in the smoothhead sculpin, decreased in the sailfin sculpin and was variable in the Pacific staghorn sculpin. Conclusions Changes in metabolic and protein production pathways are part of the key responses of fishes to exposures to environmental hypoxia. Yet, species with similar overall hypoxia tolerance exhibited different transcriptional responses in these pathways, indicating flexibility and complexity of interactions in the evolution of the mechanisms underlying the hypoxia tolerance phenotype. The variation in the hypoxia-induced transcription of genes across species with similar hypoxia tolerance suggests that similar whole-animal phenotypes can emerge from divergent evolutionary paths that may affect metabolically important functions. Electronic supplementary material The online version of this article (10.1186/s12862-018-1275-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Milica Mandic
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada. .,Bamfield Marine Sciences Centre, 100 Pachena Dr, Bamfield, BC, V0R 1B0, Canada.
| | - Marina L Ramon
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Aleeza C Gerstein
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church Street, Minneapolis, MN, 55455, USA
| | - Andrew Y Gracey
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Jeffrey G Richards
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.,Bamfield Marine Sciences Centre, 100 Pachena Dr, Bamfield, BC, V0R 1B0, Canada
| |
Collapse
|
107
|
Bolnick DI, Barrett RD, Oke KB, Rennison DJ, Stuart YE. (Non)Parallel Evolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062240] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parallel evolution across replicate populations has provided evolutionary biologists with iconic examples of adaptation. When multiple populations colonize seemingly similar habitats, they may evolve similar genes, traits, or functions. Yet, replicated evolution in nature or in the laboratory often yields inconsistent outcomes: Some replicate populations evolve along highly similar trajectories, whereas other replicate populations evolve to different extents or in distinct directions. To understand these heterogeneous outcomes, biologists are increasingly treating parallel evolution not as a binary phenomenon but rather as a quantitative continuum ranging from parallel to nonparallel. By measuring replicate populations’ positions along this (non)parallel continuum, we can test hypotheses about evolutionary and ecological factors that influence the extent of repeatable evolution. We review evidence regarding the manifestation of (non)parallel evolution in the laboratory, in natural populations, and in applied contexts such as cancer. We enumerate the many genetic, ecological, and evolutionary processes that contribute to variation in the extent of parallel evolution.
Collapse
Affiliation(s)
- Daniel I. Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
- Current affiliation: Department of Ecology and Evolution, University of Connecticut, Storrs, Connecticut 06268, USA
| | | | - Krista B. Oke
- Redpath Museum, McGill University, Montreal, Quebec H3A 2K6, Canada
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95060, USA
| | - Diana J. Rennison
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Yoel E. Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
108
|
Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandžija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-García CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE. The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus. Mol Ecol 2018; 27:4397-4416. [PMID: 30252986 PMCID: PMC6261294 DOI: 10.1111/mec.14877] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/08/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022]
Abstract
Understanding the molecular basis of repeatedly evolved phenotypes can yield key insights into the evolutionary process. Quantifying gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture occurs more frequently between diverging lineages than previously thought. In this study, we resequenced 47 whole genomes of the Mexican tetra from three cave populations, two surface populations and outgroup samples. We confirmed that cave populations are polyphyletic and two Astyanax mexicanus lineages are present in our data set. The two lineages likely diverged much more recently than previous mitochondrial estimates of 5-7 mya. Divergence of cave populations from their phylogenetically closest surface population likely occurred between ~161 and 191 k generations ago. The favoured demographic model for most population pairs accounts for divergence with secondary contact and heterogeneous gene flow across the genome, and we rigorously identified gene flow among all lineages sampled. Therefore, the evolution of cave-related traits occurred more rapidly than previously thought, and trogolomorphic traits are maintained despite gene flow with surface populations. The recency of these estimated divergence events suggests that selection may drive the evolution of cave-derived traits, as opposed to disuse and drift. Finally, we show that a key trogolomorphic phenotype QTL is enriched for genomic regions with low divergence between caves, suggesting that regions important for cave phenotypes may be transferred between caves via gene flow. Our study shows that gene flow must be considered in studies of independent, repeated trait evolution.
Collapse
Affiliation(s)
- Adam Herman
- Plant and Microbial Biology, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Yaniv Brandvain
- Plant and Microbial Biology, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
| | - James Weagley
- Ecology, Evolution, and Behavior, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, Maryland
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Helena Bilandžija
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
- Department of Biology, University of Maryland, College Park, Maryland
| | | | - Luis Espinasa
- School of Science, Marist College, Poughkeepsie, New York
| | - Kelly O'Quin
- Department of Biology, Centre College, Danville, Kentucky
| | - Claudia P Ornelas-García
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Mexico
| | - Masato Yoshizawa
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawaii
| | - Brian Carlson
- Department of Biology, College of Wooster, Wooster, Ohio
| | - Ernesto Maldonado
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St Louis, Missouri
| | - Suzanne E McGaugh
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
| |
Collapse
|
109
|
Van Belleghem SM, Vangestel C, De Wolf K, De Corte Z, Möst M, Rastas P, De Meester L, Hendrickx F. Evolution at two time frames: Polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution. PLoS Genet 2018; 14:e1007796. [PMID: 30422983 PMCID: PMC6258555 DOI: 10.1371/journal.pgen.1007796] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 11/27/2018] [Accepted: 10/30/2018] [Indexed: 01/12/2023] Open
Abstract
When environments change, populations may adapt surprisingly fast, repeatedly and even at microgeographic scales. There is increasing evidence that such cases of rapid parallel evolution are fueled by standing genetic variation, but the source of this genetic variation remains poorly understood. In the saltmarsh beetle Pogonus chalceus, short-winged 'tidal' and long-winged 'seasonal' ecotypes have diverged in response to contrasting hydrological regimes and can be repeatedly found along the Atlantic European coast. By analyzing genomic variation across the beetles' distribution, we reveal that alleles selected in the tidal ecotype are spread across the genome and evolved during a singular and, likely, geographically isolated divergence event, within the last 190 Kya. Due to subsequent admixture, the ancient and differentially selected alleles are currently polymorphic in most populations across its range, which could potentially allow for the fast evolution of one ecotype from a small number of random individuals, as low as 5 to 15, from a population of the other ecotype. Our results suggest that cases of fast parallel ecological divergence can be the result of evolution at two different time frames: divergence in the past, followed by repeated selection on the same divergently evolved alleles after admixture. These findings highlight the importance of an ancient and, likely, allopatric divergence event for driving the rate and direction of contemporary fast evolution under gene flow. This mechanism is potentially driven by periods of geographic isolation imposed by large-scale environmental changes such as glacial cycles.
Collapse
Affiliation(s)
- Steven M. Van Belleghem
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Carl Vangestel
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Katrien De Wolf
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Zoë De Corte
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Markus Möst
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Pasi Rastas
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Frederik Hendrickx
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| |
Collapse
|
110
|
Mandic M, Regan MD. Can variation among hypoxic environments explain why different fish species use different hypoxic survival strategies? ACTA ACUST UNITED AC 2018; 221:221/21/jeb161349. [PMID: 30381477 DOI: 10.1242/jeb.161349] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In aquatic environments, hypoxia is a multi-dimensional stressor that can vary in O2 level (partial pressure of O2 in water, PwO2 ), rate of induction and duration. Natural hypoxic environments can therefore be very different from one another. For the many fish species that have evolved to cope with these different hypoxic environments, survival requires adjusting energy supply and demand pathways to maintain energy balance. The literature describes innumerable ways that fishes combine aerobic metabolism, anaerobic metabolism and metabolic rate depression (MRD) to accomplish this, but it is unknown whether the evolutionary paths leading to these different strategies are determined primarily by species' phylogenetic histories, genetic constraint or their native hypoxic environments. We explored this idea by devising a four-quadrant matrix that bins different aquatic hypoxic environments according to their duration and PwO2 characteristics. We then systematically mined the literature for well-studied species native to environments within each quadrant, and, for each of 10 case studies, described the species' total hypoxic response (THR), defined as its hypoxia-induced combination of sustained aerobic metabolism, enhanced anaerobic metabolism and MRD, encompassing also the mechanisms underlying these metabolic modes. Our analysis revealed that fishes use a wide range of THRs, but that distantly related species from environments within the same matrix quadrant have converged on similar THRs. For example, environments of moderately hypoxic PwO2 favoured predominantly aerobic THRs, whereas environments of severely hypoxic PwO2 favoured MRD. Capacity for aerial emergence as well as predation pressure (aquatic and aerial) also contributed to these responses, in addition to other biotic and abiotic factors. Generally, it appears that the particular type of hypoxia experienced by a fish plays a major role in shaping its particular THR.
Collapse
Affiliation(s)
- Milica Mandic
- Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
| | - Matthew D Regan
- Comparative Biosciences Department, University of Wisconsin-Madison, Madison, WI 35706, USA
| |
Collapse
|
111
|
Yeaman S, Gerstein AC, Hodgins KA, Whitlock MC. Quantifying how constraints limit the diversity of viable routes to adaptation. PLoS Genet 2018; 14:e1007717. [PMID: 30296265 PMCID: PMC6193742 DOI: 10.1371/journal.pgen.1007717] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/18/2018] [Accepted: 09/26/2018] [Indexed: 12/25/2022] Open
Abstract
Convergent adaptation occurs at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns of genetic repeatability provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel index to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This index is explicitly based on the probability of observing a given amount of repeatability by chance under a given null hypothesis and is readily compared among different species and types of trait. We also formulate an index to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these indices can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to stress in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution. How many ways can evolution solve the same adaptive problem? While convergent adaptation is evident in many organisms at the phenotypic level, we are only beginning to understand how commonly this convergence extends to the genome scale. Quantifying the repeatability of adaptation at the genome scale is therefore critical for assessing how constraints affect the diversity of viable genetic responses. Here, we develop probability-based indices to quantify the deviation between observed repeatability and expectations under a range of null hypotheses, and an estimator of the proportion of loci in the genome that can contribute to adaptation. We demonstrate the usage of these indices with individual-based simulations and example datasets from yeast and conifers and discuss how they differ from previously developed approaches to studying repeatability. Because these indices are unitless, they provide a general approach to quantifying and comparing how constraints drive convergence at the genome scale across a wide range of traits and taxa.
Collapse
Affiliation(s)
- Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
| | - Aleeza C. Gerstein
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kathryn A. Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael C. Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
112
|
Cordero GA, Liu H, Wimalanathan K, Weber R, Quinteros K, Janzen FJ. Gene network variation and alternative paths to convergent evolution in turtles. Evol Dev 2018; 20:172-185. [DOI: 10.1111/ede.12264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gerardo A. Cordero
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowa
| | - Haibo Liu
- Program in Bioinformatics and Computational BiologyIowa State UniversityAmesIowa
| | | | - Rachel Weber
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowa
| | - Kevin Quinteros
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowa
| | - Fredric J. Janzen
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowa
| |
Collapse
|
113
|
Kess T, Galindo J, Boulding EG. Genomic divergence between Spanish Littorina saxatilis ecotypes unravels limited admixture and extensive parallelism associated with population history. Ecol Evol 2018; 8:8311-8327. [PMID: 30250705 PMCID: PMC6145028 DOI: 10.1002/ece3.4304] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/23/2022] Open
Abstract
The rough periwinkle, Littorina saxatilis, is a model system for studying parallel ecological speciation in microparapatry. Phenotypically parallel wave-adapted and crab-adapted ecotypes that hybridize within the middle shore are replicated along the northwestern coast of Spain and have likely arisen from two separate glacial refugia. We tested whether greater geographic separation corresponding to reduced opportunity for contemporary or historical gene flow between parallel ecotypes resulted in less parallel genomic divergence. We sequenced double-digested restriction-associated DNA (ddRAD) libraries from individual snails from upper, mid, and low intertidal levels of three separate sites colonized from two separate refugia. Outlier analysis of 4256 SNP markers identified 34.4% sharing of divergent loci between two geographically close sites; however, these sites each shared only 9.9%-15.1% of their divergent loci with a third more-distant site. STRUCTURE analysis revealed that genotypes from only three of 166 phenotypically intermediate mid-shore individuals appeared to result from recent hybridization, suggesting that hybrids cannot be reliably identified using shell traits. Hierarchical AMOVA indicated that the primary source of genomic differentiation was geographic separation, but also revealed greater similarity of the same ecotype across the two geographically close sites than previously estimated with dominant markers. These results from a model system for ecological speciation suggest that genomic parallelism is affected by the opportunity for historical or contemporary gene flow between populations.
Collapse
Affiliation(s)
- Tony Kess
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Juan Galindo
- Departamento de BioquímicaGenética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- Centro de Investigación Mariña da Universidade de Vigo (CIM‐UVIGO)VigoSpain
| | | |
Collapse
|
114
|
Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD. Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 2018; 7:e34803. [PMID: 30014848 PMCID: PMC6050045 DOI: 10.7554/elife.34803] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/05/2018] [Indexed: 12/17/2022] Open
Abstract
Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified NDP as a candidate gene for this variation. Allele-specific expression differences in NDP indicate cis-regulatory divergence between ancestral and melanistic alleles. Sequence comparisons suggest that derived alleles originated in the speckled pigeon (Columba guinea), providing a striking example of introgression. In contrast, barless rock pigeons have an increased incidence of vision defects and, like human families with hereditary blindness, carry start-codon mutations in NDP. In summary, we find that both coding and regulatory variation in the same gene drives wing pattern diversity, and post-domestication introgression supplied potentially advantageous melanistic alleles to feral populations of this ubiquitous urban bird.
Collapse
Affiliation(s)
- Anna I Vickrey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Rebecca Bruders
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Zev Kronenberg
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Emma Mackey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Ryan J Bohlender
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Emily T Maclary
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Raquel Maynez
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Edward J Osborne
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research InstituteUniversity of Illinois Urbana-ChampaignChampaignUnited States
| | - Chad D Huff
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Mark Yandell
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Michael D Shapiro
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| |
Collapse
|
115
|
Different trends in phylogenetic and functional structure of plant communities along an elevation gradient. Ecol Res 2018. [DOI: 10.1007/s11284-018-1638-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
116
|
Barts N, Greenway R, Passow CN, Arias-Rodriguez L, Kelley JL, Tobler M. Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs. Genome 2018; 61:273-286. [DOI: 10.1139/gen-2017-0051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen sulfide (H2S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H2S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H2S—along with related lineages from non-sulfidic environments—to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H2S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H2S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H2S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H2S-rich environments are not necessarily repeatable across replicated lineages.
Collapse
Affiliation(s)
- Nicholas Barts
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Ryan Greenway
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Courtney N. Passow
- Ecology, Evolution and Behavior, University of Minnesota St. Paul, 205 Cargill Building, St. Paul, MN 55108, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150, Villahermosa, Tabasco, México
| | - Joanna L. Kelley
- Department of Biological Sciences, Washington State University, 431 Heald Hall, Pullman, WA 99164, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| |
Collapse
|
117
|
McGirr JA, Martin CH. Parallel evolution of gene expression between trophic specialists despite divergent genotypes and morphologies. Evol Lett 2018; 2:62-75. [PMID: 30283665 PMCID: PMC6089502 DOI: 10.1002/evl3.41] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/20/2022] Open
Abstract
Parallel evolution of gene expression commonly underlies convergent niche specialization, but parallel changes in expression could also underlie divergent specialization. We investigated divergence in gene expression and whole-genome genetic variation across three sympatric Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist and two derived specialists adapted to novel niches: a scale-eating and a snail-eating pupfish. We sampled total mRNA from all three species at two early developmental stages and compared gene expression with whole-genome genetic differentiation among all three species in 42 resequenced genomes. Eighty percent of genes that were differentially expressed between snail-eaters and generalists were up or down regulated in the same direction between scale-eaters and generalists; however, there were no fixed variants shared between species underlying these parallel changes in expression. Genes showing parallel evolution of expression were enriched for effects on metabolic processes, whereas genes showing divergent expression were enriched for effects on cranial skeleton development and pigment biosynthesis, reflecting the most divergent phenotypes observed between specialist species. Our findings reveal that even divergent niche specialists may exhibit convergent adaptation to higher trophic levels through shared genetic pathways. This counterintuitive result suggests that parallel evolution in gene expression can accompany divergent ecological speciation during adaptive radiation.
Collapse
Affiliation(s)
- Joseph A. McGirr
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27514
| | - Christopher H. Martin
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27514
| |
Collapse
|
118
|
Genetic Dissection of a Supergene Implicates Tfap2a in Craniofacial Evolution of Threespine Sticklebacks. Genetics 2018; 209:591-605. [PMID: 29593029 DOI: 10.1534/genetics.118.300760] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/26/2018] [Indexed: 02/07/2023] Open
Abstract
In nature, multiple adaptive phenotypes often coevolve and can be controlled by tightly linked genetic loci known as supergenes. Dissecting the genetic basis of these linked phenotypes is a major challenge in evolutionary genetics. Multiple freshwater populations of threespine stickleback fish (Gasterosteus aculeatus) have convergently evolved two constructive craniofacial traits, longer branchial bones and increased pharyngeal tooth number, likely as adaptations to dietary differences between marine and freshwater environments. Prior QTL mapping showed that both traits are partially controlled by overlapping genomic regions on chromosome 21 and that a regulatory change in Bmp6 likely underlies the tooth number QTL. Here, we mapped the branchial bone length QTL to a 155 kb, eight-gene interval tightly linked to, but excluding the coding regions of Bmp6 and containing the candidate gene Tfap2a Further recombinant mapping revealed this bone length QTL is separable into at least two loci. During embryonic and larval development, Tfap2a was expressed in the branchial bone primordia, where allele specific expression assays revealed the freshwater allele of Tfap2a was expressed at lower levels relative to the marine allele in hybrid fish. Induced loss-of-function mutations in Tfap2a revealed an essential role in stickleback craniofacial development and show that bone length is sensitive to Tfap2a dosage in heterozygotes. Combined, these results suggest that closely linked but genetically separable changes in Bmp6 and Tfap2a contribute to a supergene underlying evolved skeletal gain in multiple freshwater stickleback populations.
Collapse
|
119
|
González-González A, Hug SM, Rodríguez-Verdugo A, Patel JS, Gaut BS. Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression. Mol Biol Evol 2018; 34:2839-2855. [PMID: 28961910 PMCID: PMC5815632 DOI: 10.1093/molbev/msx216] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Modifications to transcriptional regulators play a major role in adaptation. Here, we
compared the effects of multiple beneficial mutations within and between
Escherichia coli rpoB, the gene encoding the RNA polymerase β subunit,
and rho, which encodes a transcriptional terminator. These two genes have
harbored adaptive mutations in numerous E. coli evolution experiments but
particularly in our previous large-scale thermal stress experiment, where the two genes
characterized alternative adaptive pathways. To compare the effects of beneficial
mutations, we engineered four advantageous mutations into each of the two genes and
measured their effects on fitness, growth, gene expression and transcriptional termination
at 42.2 °C. Among the eight mutations, two rho mutations had
no detectable effect on relative fitness, suggesting they were beneficial only in the
context of epistatic interactions. The remaining six mutations had an average relative
fitness benefit of ∼20%. The rpoB mutations affected the expression of
∼1,700 genes; rho mutations affected the expression of fewer genes but
most (83%) were a subset of those altered by rpoB mutants. Across the
eight mutants, relative fitness correlated with the degree to which a mutation restored
gene expression back to the unstressed, 37.0 °C state. The beneficial
mutations in the two genes did not have identical effects on fitness, growth or gene
expression, but they caused parallel phenotypic effects on gene expression and genome-wide
transcriptional termination.
Collapse
Affiliation(s)
- Andrea González-González
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA.,Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Shaun M Hug
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Alejandra Rodríguez-Verdugo
- Department of Environmental Systems Sciences, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
| | | | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| |
Collapse
|
120
|
Genetic Basis of Body Color and Spotting Pattern in Redheaded Pine Sawfly Larvae ( Neodiprion lecontei). Genetics 2018; 209:291-305. [PMID: 29496749 DOI: 10.1534/genetics.118.300793] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/22/2018] [Indexed: 11/18/2022] Open
Abstract
Pigmentation has emerged as a premier model for understanding the genetic basis of phenotypic evolution, and a growing catalog of color loci is starting to reveal biases in the mutations, genes, and genetic architectures underlying color variation in the wild. However, existing studies have sampled a limited subset of taxa, color traits, and developmental stages. To expand the existing sample of color loci, we performed QTL mapping analyses on two types of larval pigmentation traits that vary among populations of the redheaded pine sawfly (Neodiprion lecontei): carotenoid-based yellow body color and melanin-based spotting pattern. For both traits, our QTL models explained a substantial proportion of phenotypic variation and suggested a genetic architecture that is neither monogenic nor highly polygenic. Additionally, we used our linkage map to anchor the current N. lecontei genome assembly. With these data, we identified promising candidate genes underlying (1) a loss of yellow pigmentation in populations in the mid-Atlantic/northeastern United States [C locus-associated membrane protein homologous to a mammalian HDL receptor-2 gene (Cameo2) and lipid transfer particle apolipoproteins II and I gene (apoLTP-II/I)], and (2) a pronounced reduction in black spotting in Great Lakes populations [members of the yellow gene family, tyrosine hydroxylase gene (pale), and dopamine N-acetyltransferase gene (Dat)]. Several of these genes also contribute to color variation in other wild and domesticated taxa. Overall, our findings are consistent with the hypothesis that predictable genes of large effect contribute to color evolution in nature.
Collapse
|
121
|
Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Mol Ecol 2018; 27:843-859. [DOI: 10.1111/mec.14497] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA USA
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and Technology Northwest A&F University Yangling Shaanxi China
| | - Rüdiger Riesch
- School of Biological Sciences Centre for Ecology, Evolution and Behaviour Royal Holloway University of London Egham Surrey UK
| |
Collapse
|
122
|
Alleman A, Feldmeyer B, Foitzik S. Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes. Sci Rep 2018; 8:1951. [PMID: 29386535 PMCID: PMC5792630 DOI: 10.1038/s41598-018-20262-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 01/15/2018] [Indexed: 01/08/2023] Open
Abstract
The transition to parasitism is a drastic shift in lifestyle, involving rapid changes in gene structure, function, and expression. After the establishment of antagonistic relationships, parasites and hosts co-evolve through reciprocal adaptations, often resulting in evolutionary arms-races. Repeated evolution of social parasitism and slavery among Temnothorax ants allows us to examine those gene expression patterns that characterize slavemaker raiding and reciprocal host defensive phenotypes. Previous behavioural studies have established that raiding strategies between Temnothorax slavemakers diverge, while host defense portfolios shift similarly under parasite pressure. We are the first to confirm this at the molecular level, revealing that slavemaking species exhibit a wider variety of genes with species-specific patterns of expression within their raiding phenotypes, whereas expression similarity is commonly found during the non-raiding phenotype. Host species response to slavemaker aggression, however, is indicated by strong changes in the expression of a relatively few number genes. Additionally, the expression of individual genes such as Acyl-CoA-Delta(11) desaturase and Trypsin-7 is strongly associated with the raiding phenotype of all three slavemaking species. Here, we provide novel insight into the gene expression patterns associated with raiding and nest defense behavior in Temnothorax ants, suggesting lineage-specific evolutionary patterns among both slavemakers and hosts.
Collapse
Affiliation(s)
- Austin Alleman
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Johannes von Müller Weg 6, Mainz, 55128, Germany.
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
| | - Susanne Foitzik
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Johannes von Müller Weg 6, Mainz, 55128, Germany
| |
Collapse
|
123
|
Bukhari G, Zhang J, Stevens PF, Zhang W. Evolution of the process underlying floral zygomorphy development in pentapetalous angiosperms. AMERICAN JOURNAL OF BOTANY 2017; 104:1846-1856. [PMID: 29247025 DOI: 10.3732/ajb.1700229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Observations of floral ontogeny indicated that floral organ initiation in pentapetalous flowers most commonly results in a median-abaxial (MAB) petal during early development, a median-adaxial (MAD) petal being less common. Such different patterns of floral organ initiation might be linked with different morphologies of floral zygomorphy that have evolved in Asteridae. Here, we provide the first study of zygomorphy in pentapetalous angiosperms placed in a phylogenetic framework, the goal being to find if the different patterns of floral organ initiation are connected with particular patterns of zygomorphy. METHODS We analyzed patterns of floral organ initiation and displays of zygomorphy, extracted from floral diagrams representing 405 taxa in 330 genera, covering 83% of orders (30 out of 36) and 37% of families (116 out of 313) in core eudicots in the context of a phylogeny using ancestral state reconstructions. KEY RESULTS The MAB petal initiation is the ancestral state of the pattern of floral organ initiation in pentapetalous angiosperms. Taxa with MAD petal initiation represent ∼30 independent origins from the ancestral MAB initiation. There are distinct developmental processes that give rise to zygomorphy in different lineages of pentapetalous angiosperms, closely related lineages being likely to share similar developmental processes. CONCLUSIONS We have demonstrated that development indeed constrains the processes that give rise to floral zygomorphy, while phylogenetic distance allows relaxation of these constraints, which provides novel insights on the role that development plays in the evolution of floral zygomorphy.
Collapse
Affiliation(s)
- Ghadeer Bukhari
- Department of Biology, Virginia Commonwealth University, 1000 West Cary Street, Richmond, Virginia 23284 USA
| | - Jingbo Zhang
- Department of Biology, Virginia Commonwealth University, 1000 West Cary Street, Richmond, Virginia 23284 USA
| | - Peter F Stevens
- Department of Biology, University of Missouri-St. Louis, One University Boulevard, St. Louis, Missouri 63121 USA
| | - Wenheng Zhang
- Department of Biology, Virginia Commonwealth University, 1000 West Cary Street, Richmond, Virginia 23284 USA
| |
Collapse
|
124
|
Partha R, Chauhan BK, Ferreira Z, Robinson JD, Lathrop K, Nischal KK, Chikina M, Clark NL. Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling. eLife 2017; 6:e25884. [PMID: 29035697 PMCID: PMC5643096 DOI: 10.7554/elife.25884] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/22/2017] [Indexed: 12/22/2022] Open
Abstract
The underground environment imposes unique demands on life that have led subterranean species to evolve specialized traits, many of which evolved convergently. We studied convergence in evolutionary rate in subterranean mammals in order to associate phenotypic evolution with specific genetic regions. We identified a strong excess of vision- and skin-related genes that changed at accelerated rates in the subterranean environment due to relaxed constraint and adaptive evolution. We also demonstrate that ocular-specific transcriptional enhancers were convergently accelerated, whereas enhancers active outside the eye were not. Furthermore, several uncharacterized genes and regulatory sequences demonstrated convergence and thus constitute novel candidate sequences for congenital ocular disorders. The strong evidence of convergence in these species indicates that evolution in this environment is recurrent and predictable and can be used to gain insights into phenotype-genotype relationships.
Collapse
Affiliation(s)
- Raghavendran Partha
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghUnited States
| | - Bharesh K Chauhan
- UPMC Eye CenterChildren’s Hospital of PittsburghPittsburghUnited States
- Department of OphthalmologyUniversity of Pittsburgh School of MedicinePittsburghUnited States
| | - Zelia Ferreira
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghUnited States
| | - Joseph D Robinson
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyUnited States
| | - Kira Lathrop
- UPMC Eye CenterChildren’s Hospital of PittsburghPittsburghUnited States
- Department of OphthalmologyUniversity of Pittsburgh School of MedicinePittsburghUnited States
| | - Ken K Nischal
- UPMC Eye CenterChildren’s Hospital of PittsburghPittsburghUnited States
- Department of OphthalmologyUniversity of Pittsburgh School of MedicinePittsburghUnited States
| | - Maria Chikina
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghUnited States
| | - Nathan L Clark
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghUnited States
| |
Collapse
|
125
|
Functional convergence and phenotypic divergence in two specialist species of pine-associated ladybirds. Evol Ecol 2017. [DOI: 10.1007/s10682-017-9918-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
126
|
Turissini DA, Gomez OM, Teixeira MM, McEwen JG, Matute DR. Species boundaries in the human pathogen Paracoccidioides. Fungal Genet Biol 2017; 106:9-25. [PMID: 28602831 PMCID: PMC8335726 DOI: 10.1016/j.fgb.2017.05.007] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/12/2017] [Accepted: 05/31/2017] [Indexed: 12/29/2022]
Abstract
The use of molecular taxonomy for identifying recently diverged species has transformed the study of speciation in fungi. The pathogenic fungus Paracoccidioides spp has been hypothesized to be composed of five phylogenetic species, four of which compose the brasiliensis species complex. Nuclear gene genealogies support this divergence scenario, but mitochondrial loci do not; while all species from the brasiliensis complex are differentiated at nuclear coding loci, they are not at mitochondrial loci. We addressed the source of this incongruity using 11 previously published gene fragments, 10 newly-sequenced nuclear non-coding loci, and 10 microsatellites. We hypothesized and further demonstrated that the mito-nuclear incongruence in the brasiliensis species complex results from interspecific hybridization and mitochondrial introgression, a common phenomenon in eukaryotes. Additional population genetic analyses revealed possible nuclear introgression but much less than that seen in the mitochondrion. Our results are consistent with a divergence scenario of secondary contact and subsequent mitochondrial introgression despite the continued persistence of species boundaries. We also suggest that yeast morphology slightly-but significantly-differs across all five Paracoccidioides species and propose to elevate four of these phylogenetic species to formally described taxonomic species.
Collapse
Affiliation(s)
- David A Turissini
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Oscar M Gomez
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia; Biology Institute, Universidad de Antioquia, Medellín, Colombia
| | - Marcus M Teixeira
- Northern Arizona Center for Valley Fever Research, Flagstaff, AZ, USA
| | - Juan G McEwen
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA.
| |
Collapse
|
127
|
Rosenblum EB, Parent CE, Diepeveen ET, Noss C, Bi K. Convergent Phenotypic Evolution despite Contrasting Demographic Histories in the Fauna of White Sands. Am Nat 2017; 190:S44-S56. [DOI: 10.1086/692138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
128
|
Mahler DL, Weber MG, Wagner CE, Ingram T. Pattern and Process in the Comparative Study of Convergent Evolution. Am Nat 2017; 190:S13-S28. [DOI: 10.1086/692648] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
129
|
Passow CN, Brown AP, Arias-Rodriguez L, Yee MC, Sockell A, Schartl M, Warren WC, Bustamante C, Kelley JL, Tobler M. Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Mol Ecol 2017; 26:4211-4225. [PMID: 28598519 PMCID: PMC5731456 DOI: 10.1111/mec.14198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 12/31/2022]
Abstract
Variation in gene expression can provide insights into organismal responses to environmental stress and physiological mechanisms mediating adaptation to habitats with contrasting environmental conditions. We performed an RNA-sequencing experiment to quantify gene expression patterns in fish adapted to habitats with different combinations of environmental stressors, including the presence of toxic hydrogen sulphide (H2 S) and the absence of light in caves. We specifically asked how gene expression varies among populations living in different habitats, whether population differences were consistent among organs, and whether there is evidence for shared expression responses in populations exposed to the same stressors. We analysed organ-specific transcriptome-wide data from four ecotypes of Poecilia mexicana (nonsulphidic surface, sulphidic surface, nonsulphidic cave and sulphidic cave). The majority of variation in gene expression was correlated with organ type, and the presence of specific environmental stressors elicited unique expression differences among organs. Shared patterns of gene expression between populations exposed to the same environmental stressors increased with levels of organismal organization (from transcript to gene to physiological pathway). In addition, shared patterns of gene expression were more common between populations from sulphidic than populations from cave habitats, potentially indicating that physiochemical stressors with clear biochemical consequences can constrain the diversity of adaptive solutions that mitigate their adverse effects. Overall, our analyses provided insights into transcriptional variation in a unique system, in which adaptation to H2 S and darkness coincide. Functional annotations of differentially expressed genes provide a springboard for investigating physiological mechanisms putatively underlying adaptation to extreme environments.
Collapse
Affiliation(s)
| | - Anthony P. Brown
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | - Muh-Ching Yee
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
- Texas A&M Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, USA
| | - Wesley C. Warren
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Joanna L. Kelley
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
| |
Collapse
|
130
|
Comeault AA, Serrato-Capuchina A, Turissini DA, McLaughlin PJ, David JR, Matute DR. A nonrandom subset of olfactory genes is associated with host preference in the fruit fly Drosophila orena. Evol Lett 2017; 1:73-85. [PMID: 30283640 PMCID: PMC6121841 DOI: 10.1002/evl3.7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/27/2017] [Indexed: 12/18/2022] Open
Abstract
Specialization onto different host plants has been hypothesized to be a major driver of diversification in insects, and traits controlling olfaction have been shown to play a fundamental role in host preferences. A diverse set of olfactory genes control olfactory traits in insects, and it remains unclear whether specialization onto different hosts is likely to involve a nonrandom subset of these genes. Here, we test the role of olfactory genes in a novel case of specialization in Drosophila orena. We report the first population‐level sample of D. orena on the West African island of Bioko, since its initial collection in Cameroon in 1975, and use field experiments and behavioral assays to show that D. orena has evolved a strong preference for waterberry (Syzygium staudtii). We then show that a nonrandom subset of genes controlling olfaction‐–those controlling odorant‐binding and chemosensory proteins–‐have an enriched signature of positive selection relative to the rest of the D. orena genome. By comparing signatures of positive selection on olfactory genes between D. orena and its sister species, D. erecta we show that odorant‐binding and chemosensory have evidence of positive selection in both species; however, overlap in the specific genes with evidence of selection in these two classes is not greater than expected by chance. Finally, we use quantitative complementation tests to confirm a role for seven olfactory loci in D. orena’s preference for waterberry fruit. Together, our results suggest that D. orena and D. erecta have specialized onto different host plants through convergent evolution at the level of olfactory gene family, but not at specific olfactory genes.
Collapse
Affiliation(s)
- Aaron A Comeault
- Department of Biology University of North Carolina Chapel Hill North Carolina 27599
| | | | - David A Turissini
- Department of Biology University of North Carolina Chapel Hill North Carolina 27599
| | - Patrick J McLaughlin
- Department of Biology Drexel University Philadelphia Pennsylvania 19104.,Bioko Biodiversity Protection Program Bioko Island Equatorial Guinea
| | - Jean R David
- Laboratoire Evolution, Genomes, Speciation (LEGS) CNRS Gif sur Yvette Cedex France.,Université Paris-Sud Orsay Cedex France.,Département Systématique et Evolution Museum National d'Histoire Naturelle (MNHN) UMR 7205 (OSEB) Paris France
| | - Daniel R Matute
- Department of Biology University of North Carolina Chapel Hill North Carolina 27599
| |
Collapse
|
131
|
Speed MP, Arbuckle K. Quantification provides a conceptual basis for convergent evolution. Biol Rev Camb Philos Soc 2017; 92:815-829. [PMID: 26932796 PMCID: PMC6849873 DOI: 10.1111/brv.12257] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 01/28/2016] [Accepted: 02/02/2016] [Indexed: 12/26/2022]
Abstract
While much of evolutionary biology attempts to explain the processes of diversification, there is an important place for the study of phenotypic similarity across life forms. When similar phenotypes evolve independently in different lineages this is referred to as convergent evolution. Although long recognised, evolutionary convergence is receiving a resurgence of interest. This is in part because new genomic data sets allow detailed and tractable analysis of the genetic underpinnings of convergent phenotypes, and in part because of renewed recognition that convergence may reflect limitations in the diversification of life. In this review we propose that although convergent evolution itself does not require a new evolutionary framework, none the less there is room to generate a more systematic approach which will enable evaluation of the importance of convergent phenotypes in limiting the diversity of life's forms. We therefore propose that quantification of the frequency and strength of convergence, rather than simply identifying cases of convergence, should be considered central to its systematic comprehension. We provide a non-technical review of existing methods that could be used to measure evolutionary convergence, bringing together a wide range of methods. We then argue that quantification also requires clear specification of the level at which the phenotype is being considered, and argue that the most constrained examples of convergence show similarity both in function and in several layers of underlying form. Finally, we argue that the most important and impressive examples of convergence are those that pertain, in form and function, across a wide diversity of selective contexts as these persist in the likely presence of different selection pressures within the environment.
Collapse
Affiliation(s)
- Michael P. Speed
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, Faculty of Health & Life SciencesUniversity of LiverpoolLiverpoolL69 7ZBU.K.
| | - Kevin Arbuckle
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, Faculty of Health & Life SciencesUniversity of LiverpoolLiverpoolL69 7ZBU.K.
| |
Collapse
|
132
|
Mazel F, Wüest RO, Gueguen M, Renaud J, Ficetola GF, Lavergne S, Thuiller W. The Geography of Ecological Niche Evolution in Mammals. Curr Biol 2017; 27:1369-1374. [PMID: 28457870 DOI: 10.1016/j.cub.2017.03.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 11/19/2022]
Abstract
Convergent adaptive evolution of species' ecological niches-i.e., the appearance of similar niches in independent lineages-is the result of natural selection acting on niche-related species traits ("traits" hereafter) and contrasts with neutral evolution [1-4]. Although trait convergences are recognized as being of importance at the species scale, we still know little about the impact of species convergence on the overall trait and niche structure of entire biotas at large spatial scales [5]. Here, we map the convergent evolution of four traits (diet, body mass, activity cycle, and foraging strata) for mammal species and assemblages (defined at 200 × 200 km resolution) at a global scale. Using data on the geographic distributions, traits, and phylogenetic relationships of species and by comparing observed patterns of trait β-diversity to evolutionary neutral expectations, we show that trait convergence is not restricted to particular lineages but scales up to entire assemblages (i.e., whole species communities). We find region-wide biota convergence in traits between regions with similar climates, particularly between Australia and other continents. Pairs of assemblages that show trait divergence often involves Arctic regions where rapid evolutionary changes occurred in response to extreme climatic constraints. By integrating both macroecological and macroevolutionary approaches into a single framework, our study quantifies the crucial role of evolutionary processes such as natural selection in the spatial distribution and structure of large-scale species assemblages.
Collapse
Affiliation(s)
- Florent Mazel
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France.
| | - Rafael O Wüest
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France; Swiss Federal Research Institute WSL, Landscape Dynamics, 8903 Birmensdorf, Switzerland
| | - Maya Gueguen
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France
| | - Julien Renaud
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France
| | - Gentile Francesco Ficetola
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Sébastien Lavergne
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France
| | - Wilfried Thuiller
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France
| |
Collapse
|
133
|
Torres-Dowdall J, Pierotti ME, Härer A, Karagic N, Woltering JM, Henning F, Elmer KR, Meyer A. Rapid and Parallel Adaptive Evolution of the Visual System of Neotropical Midas Cichlid Fishes. Mol Biol Evol 2017; 34:2469-2485. [DOI: 10.1093/molbev/msx143] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
134
|
Vertacnik KL, Linnen CR. Evolutionary genetics of host shifts in herbivorous insects: insights from the age of genomics. Ann N Y Acad Sci 2017; 1389:186-212. [DOI: 10.1111/nyas.13311] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/16/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022]
|
135
|
Kingsley EP, Kozak KM, Pfeifer SP, Yang DS, Hoekstra HE. The ultimate and proximate mechanisms driving the evolution of long tails in forest deer mice. Evolution 2016; 71:261-273. [PMID: 27958661 PMCID: PMC5324611 DOI: 10.1111/evo.13150] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 11/15/2016] [Accepted: 12/02/2016] [Indexed: 12/21/2022]
Abstract
Understanding both the role of selection in driving phenotypic change and its underlying genetic basis remain major challenges in evolutionary biology. Here, we use modern tools to revisit a classic system of local adaptation in the North American deer mouse, Peromyscus maniculatus, which occupies two main habitat types: prairie and forest. Using historical collections, we find that forest‐dwelling mice have longer tails than those from nonforested habitat, even when we account for individual and population relatedness. Using genome‐wide SNP data, we show that mice from forested habitats in the eastern and western parts of their range form separate clades, suggesting that increased tail length evolved independently. We find that forest mice in the east and west have both more and longer caudal vertebrae, but not trunk vertebrae, than nearby prairie forms. By intercrossing prairie and forest mice, we show that the number and length of caudal vertebrae are not correlated in this recombinant population, indicating that variation in these traits is controlled by separate genetic loci. Together, these results demonstrate convergent evolution of the long‐tailed forest phenotype through two distinct genetic mechanisms, affecting number and length of vertebrae, and suggest that these morphological changes—either independently or together—are adaptive.
Collapse
Affiliation(s)
- Evan P Kingsley
- Howard Hughes Medical Institute, Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138
| | - Krzysztof M Kozak
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom.,Current Address: Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá
| | - Susanne P Pfeifer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland and School of Life Sciences, Arizona State University, Tempe, Arizona, 85287
| | - Dou-Shuan Yang
- Burke Museum and Department of Biology, University of Washington, Seattle, Washington, 98195.,Current Address: US Fish and Wildlife Service, Ventura Field Office, 2493 Portola Road #B, Ventura, California, 93003
| | - Hopi E Hoekstra
- Howard Hughes Medical Institute, Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138
| |
Collapse
|
136
|
Moreno E, McGaughran A, Rödelsperger C, Zimmer M, Sommer RJ. Oxygen-induced social behaviours in Pristionchus pacificus have a distinct evolutionary history and genetic regulation from Caenorhabditis elegans. Proc Biol Sci 2016; 283:20152263. [PMID: 26888028 DOI: 10.1098/rspb.2015.2263] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Wild isolates of the nematode Caenorhabditis elegans perform social behaviours, namely clumping and bordering, to avoid hyperoxia under laboratory conditions. In contrast, the laboratory reference strain N2 has acquired a solitary behaviour in the laboratory, related to a gain-of-function variant in the neuropeptide Y-like receptor NPR-1. Here, we study the evolution and natural variation of clumping and bordering behaviours in Pristionchus pacificus nematodes in a natural context, using strains collected from 22 to 2400 metres above sea level on La Réunion Island. Through the analysis of 106 wild isolates, we show that the majority of strains display a solitary behaviour similar to C. elegans N2, whereas social behaviours are predominantly seen in strains that inhabit high-altitude locations. We show experimentally that P. pacificus social strains perform clumping and bordering to avoid hyperoxic conditions in the laboratory, suggesting that social strains may have adapted to or evolved a preference for the lower relative oxygen levels available at high altitude in nature. In contrast to C. elegans, clumping and bordering in P. pacificus do not correlate with locomotive behaviours in response to changes in oxygen conditions. Furthermore, QTL analysis indicates clumping and bordering to represent complex quantitative traits. Thus, clumping and bordering behaviours represent an example of phenotypic convergence with a different evolutionary history and distinct genetic control in both nematode species.
Collapse
Affiliation(s)
- Eduardo Moreno
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Angela McGaughran
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany CSIRO Land and Water, Black Mountain Laboratories, Clunies Ross Street, Canberra, Australian Capital Territory 2601, Australia School of Biosciences, University of Melbourne, 30 Flemington Road, Melbourne, Victoria 3010, Australia
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Manuel Zimmer
- Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| |
Collapse
|
137
|
Domyan ET, Shapiro MD. Pigeonetics takes flight: Evolution, development, and genetics of intraspecific variation. Dev Biol 2016; 427:241-250. [PMID: 27847323 DOI: 10.1016/j.ydbio.2016.11.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/28/2016] [Accepted: 11/10/2016] [Indexed: 11/26/2022]
Abstract
Intensive artificial selection over thousands of years has produced hundreds of varieties of domestic pigeon. As Charles Darwin observed, the morphological differences among breeds can rise to the magnitude of variation typically observed among different species. Nevertheless, different pigeon varieties are interfertile, thereby enabling forward genetic and genomic approaches to identify genes that underlie derived traits. Building on classical genetic studies of pigeon variation, recent molecular investigations find a spectrum of coding and regulatory alleles controlling derived traits, including plumage color, feather growth polarity, and limb identity. Developmental and genetic analyses of pigeons are revealing the molecular basis of variation in a classic example of extreme intraspecific diversity, and have the potential to nominate genes that control variation among other birds and vertebrates in general.
Collapse
Affiliation(s)
- Eric T Domyan
- Department of Biology, Utah Valley University, Orem, UT, United States.
| | - Michael D Shapiro
- Department of Biology, University of Utah, Salt Lake City, UT, United States.
| |
Collapse
|
138
|
Dalziel AC, Laporte M, Rougeux C, Guderley H, Bernatchez L. Convergence in organ size but not energy metabolism enzyme activities among wild Lake Whitefish (Coregonus clupeaformis) species pairs. Mol Ecol 2016; 26:225-244. [DOI: 10.1111/mec.13847] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/31/2016] [Accepted: 09/06/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Anne C. Dalziel
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
- Department of Biology; Saint Mary's University; 923 Robie Street Halifax Nova Scotia Canada B3H 3C3
| | - Martin Laporte
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| | - Clément Rougeux
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| | - Helga Guderley
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| | - Louis Bernatchez
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| |
Collapse
|
139
|
Corso J, Mundy NI, Fagundes NJR, de Freitas TRO. Evolution of dark colour in toucans (Ramphastidae): a case of molecular adaptation? J Evol Biol 2016; 29:2530-2538. [PMID: 27654325 DOI: 10.1111/jeb.12982] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 08/08/2016] [Accepted: 09/16/2016] [Indexed: 11/28/2022]
Abstract
In the last decades, researchers have been able to determine the molecular basis of some phenotypes, to test for evidence of natural selection upon them, and to demonstrate that the same genes or genetic pathways can be associated with convergent traits. Colour traits are often subject to natural selection because even small changes in these traits can have a large effect on fitness via camouflage, sexual selection or other mechanisms. The melanocortin-1 receptor locus (MC1R) is frequently associated with intraspecific coat colour variation in vertebrates, but it has been far harder to demonstrate that this locus is involved in adaptive interspecific colour differences. Here, we investigate the contribution of the MC1R gene to the colour diversity found in toucans (Ramphastidae). We found divergent selection on MC1R in the clade represented by the genus Ramphastos and that this coincided with the evolution of darker plumage in members of this genus. Using phylogenetically corrected correlations, we show significant and specific relationships between the rate of nonsynonymous change in MC1R (dN) and plumage darkness across Ramphastidae, and also between the rate of functionally significant amino acid changes in MC1R and plumage darkness. Furthermore, three of the seven amino acid changes in MC1R that occurred in the ancestral Ramphastos branch are associated with melanism in other birds. Taken together, our results suggest that the dark colour of Ramphastos toucans was related to nonsynonymous substitutions in MC1R that may have been subject to positive selection or to a relaxation of selective pressure. These results also demonstrate a quantitative relationship between gene and phenotype evolution, representing an example of how MC1R molecular evolution may affect macroevolution of plumage phenotypes.
Collapse
Affiliation(s)
- J Corso
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - N I Mundy
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - N J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - T R O de Freitas
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| |
Collapse
|
140
|
Meier JI, Sousa VC, Marques DA, Selz OM, Wagner CE, Excoffier L, Seehausen O. Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization. Mol Ecol 2016; 26:123-141. [PMID: 27613570 DOI: 10.1111/mec.13838] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/15/2016] [Accepted: 08/22/2016] [Indexed: 01/15/2023]
Abstract
Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.
Collapse
Affiliation(s)
- Joana I Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Vitor C Sousa
- CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Oliver M Selz
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Catherine E Wagner
- Biodiversity Institute & Department of Botany, University of Wyoming, Berry Center, 1000 E. University Ave, Laramie, WY, 82071, USA
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| |
Collapse
|
141
|
Road Map to Study Convergent Evolution: A Proposition for Evolutionary Systems Biology Approaches. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
|
142
|
Mendes FK, Hahn Y, Hahn MW. Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time. Mol Biol Evol 2016; 33:3299-3307. [PMID: 27634870 DOI: 10.1093/molbev/msw197] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is repeatable and predictable. Many recent genome-wide studies have uncovered a striking pattern of diminishing convergence over time, ascribing this pattern to the presence of intramolecular epistatic interactions. Here, we consider gene tree discordance as an alternative cause of changes in convergence levels over time in a primate dataset. We demonstrate that gene tree discordance can produce patterns of diminishing convergence by itself, and that controlling for discordance as a cause of apparent convergence makes the pattern disappear. We also show that synonymous substitutions, where neither selection nor epistasis should be prevalent, have the same diminishing pattern of molecular convergence in primates. Finally, we demonstrate that even in situations where biological discordance is not possible, discordance due to errors in species tree inference can drive similar patterns. Though intramolecular epistasis could in principle create a pattern of declining convergence over time, our results suggest a possible alternative explanation for this widespread pattern. These results contribute to a growing appreciation not just of the presence of gene tree discordance, but of the unpredictable effects this discordance can have on analyses of molecular evolution.
Collapse
Affiliation(s)
- Fábio K Mendes
- Department of Biology, Indiana University, Bloomington, IN
| | - Yoonsoo Hahn
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN.,School of Informatics and Computing, Indiana University, Bloomington, IN
| |
Collapse
|
143
|
Evolutionary Genetics: Reuse, Recycle, Converge. Curr Biol 2016; 26:R838-R840. [DOI: 10.1016/j.cub.2016.07.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
144
|
Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila. Curr Biol 2016; 26:2423-2433. [DOI: 10.1016/j.cub.2016.07.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/10/2016] [Accepted: 07/13/2016] [Indexed: 11/23/2022]
|
145
|
Selection on different genes with equivalent functions: the convergence story told by Hox genes along the evolution of aquatic mammalian lineages. BMC Evol Biol 2016; 16:113. [PMID: 27209096 PMCID: PMC4875654 DOI: 10.1186/s12862-016-0682-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/10/2016] [Indexed: 11/24/2022] Open
Abstract
Background Convergent evolution has been a challenging topic for decades, being cetaceans, pinnipeds and sirenians textbook examples of three independent origins of equivalent phenotypes. These mammalian lineages acquired similar anatomical features correlated to an aquatic life, and remarkably differ from their terrestrial counterparts. Whether their molecular evolutionary history also involved similar genetic mechanisms underlying such morphological convergence nevertheless remained unknown. To test for the existence of convergent molecular signatures, we studied the molecular evolution of Hox genes in these three aquatic mammalian lineages, comparing their patterns to terrestrial mammals. Hox genes are transcription factors that play a pivotal role in specifying embryonic regional identity of nearly any bilateral animal, and are recognized major agents for diversification of body plans. Results We detected few signatures of positive selection on Hox genes across the three aquatic mammalian lineages and verified that purifying selection prevails in these sequences, as expected for pleiotropic genes. Genes found as being positively selected differ across the aquatic mammalian lineages, but we identified a substantial overlap of their developmental functions. Such pattern likely resides on the duplication history of Hox genes, which probably provided different possible evolutionary routes for achieving the same phenotypic solution. Conclusions Our results indicate that convergence occurred at a functional level of Hox genes along three independent origins of aquatic mammals. This conclusion reinforces the idea that different changes in developmental genes may lead to similar phenotypes, probably due to the redundancy provided by the participation of Hox paralogous genes in several developmental functions. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0682-4) contains supplementary material, which is available to authorized users.
Collapse
|
146
|
|
147
|
Abstract
To what extent is the convergent evolution of protein function attributable to convergent or parallel changes at the amino acid level? The mutations that contribute to adaptive protein evolution may represent a biased subset of all possible beneficial mutations owing to mutation bias and/or variation in the magnitude of deleterious pleiotropy. A key finding is that the fitness effects of amino acid mutations are often conditional on genetic background. This context dependence (epistasis) can reduce the probability of convergence and parallelism because it reduces the number of possible mutations that are unconditionally acceptable in divergent genetic backgrounds. Here, I review factors that influence the probability of replicated evolution at the molecular level.
Collapse
Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
| |
Collapse
|
148
|
Erickson PA, Glazer AM, Killingbeck EE, Agoglia RM, Baek J, Carsanaro SM, Lee AM, Cleves PA, Schluter D, Miller CT. Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks. Evolution 2016; 70:887-902. [PMID: 26947264 DOI: 10.1111/evo.12897] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 02/10/2016] [Accepted: 02/23/2016] [Indexed: 12/13/2022]
Abstract
The extent to which convergent adaptation to similar ecological niches occurs by a predictable genetic basis remains a fundamental question in biology. Threespine stickleback fish have undergone an adaptive radiation in which ancestral oceanic populations repeatedly colonized and adapted to freshwater habitats. In multiple lakes in British Columbia, two different freshwater ecotypes have evolved: a deep-bodied benthic form adapted to forage near the lake substrate, and a narrow-bodied limnetic form adapted to forage in open water. Here, we use genome-wide linkage mapping in marine × benthic F2 genetic crosses to test the extent of shared genomic regions underlying benthic adaptation in three benthic populations. We identify at least 100 Quantitative Trait Loci (QTL) harboring genes influencing skeletal morphology. The majority of QTL (57%) are unique to one cross. However, four genomic regions affecting eight craniofacial and armor phenotypes are found in all three benthic populations. We find that QTL are clustered in the genome and overlapping QTL regions are enriched for genomic signatures of natural selection. These findings suggest that benthic adaptation has occurred via both parallel and nonparallel genetic changes.
Collapse
Affiliation(s)
- Priscilla A Erickson
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Andrew M Glazer
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Emily E Killingbeck
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Rachel M Agoglia
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Jiyeon Baek
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Sara M Carsanaro
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Anthony M Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Phillip A Cleves
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Dolph Schluter
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720.
| |
Collapse
|
149
|
Guo X, Xie L, Zhang X, Ji Y, Chen J, Pang B, Xu Y, Qi D, Guo S. Signatures of functional constraint at Fgfr1a Genes in schizothoracine fishes (Pisces: Cypriniformes): The dermal skeleton variation adapted to high-altitude environments. Integr Zool 2016; 11:86-97. [PMID: 26767459 DOI: 10.1111/1749-4877.12178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fishes harbor a huge resource of phenotypic diversity and are useful for understanding the genetic basis of morphological variation. However, it is difficult to transfer classical genetic mapping to most non-model species. In this study, we performed a comparative sequence analysis of Fgfr1a to first interpret the evolution of this candidate scale-loss gene in 15 schizothoracine fishes with various scale phenotypes. While considerable amino acid (AA) substitutions were observed, molecular evolution analysis indicates that the overall coding regions were subject to functional constraint. We also identified extra copies of Fgfr1a in 4 scale-loss fishes and detected accelerated evolution in one AA substitution specific to these duplicates. We speculate that Fgfr1a had accumulated mutations in the ancestral lineage of scale-loss schizothoracine fishes before experiencing duplication events, which was further followed by the diversification of species. In silico mutation analysis predicted deleterious effects of the mutations while no disruptive molecular mechanism was detected. Collectively, our results highlight the important role of Fgfr1a gene in the adaptive evolution of schizothoracine fishes during their radiation in the Qinghai-Tibetan Plateau.
Collapse
Affiliation(s)
- Xinyi Guo
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ling Xie
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuze Zhang
- Qinghai University for Nationalities, Xining, China
| | - Yinfa Ji
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China
| | - Juan Chen
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bo Pang
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongtao Xu
- Qinghai Normal University, Xining, China
| | - Delin Qi
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, China
| | - Songchang Guo
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China
| |
Collapse
|
150
|
Ng J, Smith SD. Widespread flower color convergence in Solanaceae via alternate biochemical pathways. THE NEW PHYTOLOGIST 2016. [PMID: 26224118 DOI: 10.1111/nph.13576] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Phenotypic convergence is rampant throughout the tree of life. While recent studies have made significant progress in ascertaining the proximate mechanisms underlying convergent phenotypes, less is known about the frequency and predictability with which convergent phenotypes arise via the same or multiple pathways at the macroevolutionary scale. We investigated the proximate causes and evolutionary patterns of red flower color in the tomato family, Solanaceae, using large-scale data mining and new sequence data to reconstruct a megaphylogeny of 1341 species. We then combined spectral and anatomical data to assess how many times red flowers have evolved, the relative contribution of different pathways to independent origins of red, and whether the underlying pathway is predicted by phylogenetic relatedness. We estimated at least 30 relatively recent origins of red flowers using anthocyanins, carotenoids, or a dual production of both pigments, with significant phylogenetic signal in the use of anthocyanins and dual production, indicating that closely related red-flowered species tend to employ the same mechanism for coloration. Our study is the first to test whether developmental pathways exhibit phylogenetic signal and implies that historical contingency strongly influences the evolution of new phenotypes.
Collapse
Affiliation(s)
- Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| |
Collapse
|