201
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Monteiro A, Gupta M. Identifying Coopted Networks and Causative Mutations in the Origin of Novel Complex Traits. Curr Top Dev Biol 2016; 119:205-26. [DOI: 10.1016/bs.ctdb.2016.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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202
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Hoyal Cuthill JF, Charleston M. Wing patterning genes and coevolution of Müllerian mimicry inHeliconiusbutterflies: Support from phylogeography, cophylogeny, and divergence times. Evolution 2015; 69:3082-96. [DOI: 10.1111/evo.12812] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 10/09/2015] [Accepted: 10/26/2015] [Indexed: 11/30/2022]
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203
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Hoyal Cuthill JF. The morphological state space revisited: what do phylogenetic patterns in homoplasy tell us about the number of possible character states? Interface Focus 2015; 5:20150049. [PMID: 26640650 PMCID: PMC4633860 DOI: 10.1098/rsfs.2015.0049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Biological variety and major evolutionary transitions suggest that the space of possible morphologies may have varied among lineages and through time. However, most models of phylogenetic character evolution assume that the potential state space is finite. Here, I explore what the morphological state space might be like, by analysing trends in homoplasy (repeated derivation of the same character state). Analyses of ten published character matrices are compared against computer simulations with different state space models: infinite states, finite states, ordered states and an 'inertial' model, simulating phylogenetic constraints. Of these, only the infinite states model results in evolution without homoplasy, a prediction which is not generally met by real phylogenies. Many authors have interpreted the ubiquity of homoplasy as evidence that the number of evolutionary alternatives is finite. However, homoplasy is also predicted by phylogenetic constraints on the morphological distance that can be traversed between ancestor and descendent. Phylogenetic rarefaction (sub-sampling) shows that finite and inertial state spaces do produce contrasting trends in the distribution of homoplasy. Two clades show trends characteristic of phylogenetic inertia, with decreasing homoplasy (increasing consistency index) as we sub-sample more distantly related taxa. One clade shows increasing homoplasy, suggesting exhaustion of finite states. Different clades may, therefore, show different patterns of character evolution. However, when parsimony uninformative characters are excluded (which may occur without documentation in cladistic studies), it may no longer be possible to distinguish inertial and finite state spaces. Interestingly, inertial models predict that homoplasy should be clustered among comparatively close relatives (parallel evolution), whereas finite state models do not. If morphological evolution is often inertial in nature, then homoplasy (false homology) may primarily occur between close relatives, perhaps being replaced by functional analogy at higher taxonomic scales.
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204
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Thurman TJ, Seymoure BM. A bird's eye view of two mimetic tropical butterflies: coloration matches predator's sensitivity. J Zool (1987) 2015. [DOI: 10.1111/jzo.12305] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- T. J. Thurman
- Redpath Museum and Department of Biology; McGill University; Montreal QC
- The Smithsonian Tropical Research Institute; Panamá Panama
| | - B. M. Seymoure
- School of Life Sciences; Arizona State University; Tempe AZ USA
- The Smithsonian Tropical Research Institute; Panamá Panama
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205
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Llaurens V, Joron M, Billiard S. Molecular mechanisms of dominance evolution in Müllerian mimicry. Evolution 2015; 69:3097-108. [DOI: 10.1111/evo.12810] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 10/02/2015] [Accepted: 10/22/2015] [Indexed: 11/29/2022]
Affiliation(s)
- V. Llaurens
- Institut de Systématique Evolution et Biodiversité, UMR7205, CNRS, EPHE, UPMC; Museum National d'Histoire Naturelle; Bâtiment d'entomologie, CP50, 45 rue Buffon 75005 Paris France
| | - M. Joron
- Institut de Systématique Evolution et Biodiversité, UMR7205, CNRS, EPHE, UPMC; Museum National d'Histoire Naturelle; Bâtiment d'entomologie, CP50, 45 rue Buffon 75005 Paris France
- Centre d'Ecologie Fonctionnelle et Evolutive; UMR 5175, CNRS-Universite de Montpellier-Universite Paul Valery Montpellier - EPHE; 1919 Route de Mende 34293 Montpellier Cedex 05 France
| | - S. Billiard
- Unité Evo-Eco-Paléo; UMR CNRS 8198, Université des Sciences et Technologies de Lille 1; Bâtiment SN2 59655 Villeneuve d'Ascq Cedex France
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206
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Wang K, Yang Y, Wang L, Ma T, Shang H, Ding L, Han J, Qiu Q. Different gene expressions between cattle and yak provide insights into high-altitude adaptation. Anim Genet 2015; 47:28-35. [PMID: 26538003 DOI: 10.1111/age.12377] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2015] [Indexed: 01/03/2023]
Abstract
DNA sequence variation has been widely reported as the genetic basis for adaptation, in both humans and other animals, to the hypoxic environment experienced at high altitudes. However, little is known about the patterns of gene expression underlying such hypoxic adaptations. In this study, we examined the differences in the transcriptomes of four organs (heart, kidney, liver and lung) between yak and cattle, a pair of closely related species distributed at high and low altitudes respectively. Of the four organs examined, heart shows the greatest differentiation between the two species in terms of gene expression profiles. Detailed analyses demonstrated that some genes associated with the oxygen supply system and the defense systems that respond to threats of hypoxia are differentially expressed. In addition, genes with significantly differentiated patterns of expression in all organs exhibited an unexpected uniformity of regulation along with an elevated frequency of nonsynonymous substitutions. This co-evolution of protein sequences and gene expression patterns is likely to be correlated with the optimization of the yak metabolic system to resist hypoxia.
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Affiliation(s)
- K Wang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Y Yang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - L Wang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - T Ma
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - H Shang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - L Ding
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Han
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Q Qiu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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207
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Abstract
Darwin's theory of evolution by natural selection is the foundation of modern biology. However, it has proven remarkably difficult to demonstrate at the genetic, genomic, and population level exactly how wild species adapt to their natural environments. We discuss how one can use large sets of multiple genome sequences from wild populations to understand adaptation, with an emphasis on the small herbaceous plant Arabidopsis thaliana. We present motivation for such studies; summarize progress in describing whole-genome, species-wide sequence variation; and then discuss what insights have emerged from these resources, either based on sequence information alone or in combination with phenotypic data. We conclude with thoughts on opportunities with other plant species and the impact of expected progress in sequencing technology and genome engineering for studying adaptation in nature.
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Affiliation(s)
- Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria;
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208
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Supple MA, Papa R, Hines HM, McMillan WO, Counterman BA. Divergence with gene flow across a speciation continuum of Heliconius butterflies. BMC Evol Biol 2015; 15:204. [PMID: 26403600 PMCID: PMC4582928 DOI: 10.1186/s12862-015-0486-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 09/14/2015] [Indexed: 12/30/2022] Open
Abstract
Background A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. Methods We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Results Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. Discussion We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Conclusions Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0486-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Megan A Supple
- Smithsonian Tropical Research Institute, Panamá City, Panamá. .,Biomathematics Program, North Carolina State University, Raleigh, NC, 27695, USA. .,Research School of Biology, The Australian National University, 134 Linnaeus Way, Canberra, ACT, 2601, Australia.
| | - Riccardo Papa
- Department of Biology and Center for Applied Tropical Ecology and Conservation, University of Puerto Rico-Rio Piedras, 00931, San Juan, Puerto Rico.
| | - Heather M Hines
- Department of Biology, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panamá City, Panamá.
| | - Brian A Counterman
- Department of Biological Sciences, Mississippi State University, 295 Lee Boulevard, Mississippi State, MS, 39762, USA.
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209
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Berner D, Salzburger W. The genomics of organismal diversification illuminated by adaptive radiations. Trends Genet 2015; 31:491-9. [DOI: 10.1016/j.tig.2015.07.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/09/2015] [Accepted: 07/15/2015] [Indexed: 02/07/2023]
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210
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Merrill RM, Dasmahapatra KK, Davey JW, Dell'Aglio DD, Hanly JJ, Huber B, Jiggins CD, Joron M, Kozak KM, Llaurens V, Martin SH, Montgomery SH, Morris J, Nadeau NJ, Pinharanda AL, Rosser N, Thompson MJ, Vanjari S, Wallbank RWR, Yu Q. The diversification of Heliconius butterflies: what have we learned in 150 years? J Evol Biol 2015; 28:1417-38. [PMID: 26079599 DOI: 10.1111/jeb.12672] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 11/27/2022]
Abstract
Research into Heliconius butterflies has made a significant contribution to evolutionary biology. Here, we review our understanding of the diversification of these butterflies, covering recent advances and a vast foundation of earlier work. Whereas no single group of organisms can be sufficient for understanding life's diversity, after years of intensive study, research into Heliconius has addressed a wide variety of evolutionary questions. We first discuss evidence for widespread gene flow between Heliconius species and what this reveals about the nature of species. We then address the evolution and diversity of warning patterns, both as the target of selection and with respect to their underlying genetic basis. The identification of major genes involved in mimetic shifts, and homology at these loci between distantly related taxa, has revealed a surprising predictability in the genetic basis of evolution. In the final sections, we consider the evolution of warning patterns, and Heliconius diversity more generally, within a broader context of ecological and sexual selection. We consider how different traits and modes of selection can interact and influence the evolution of reproductive isolation.
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Affiliation(s)
- R M Merrill
- Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | | | - J W Davey
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - D D Dell'Aglio
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - J J Hanly
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - B Huber
- Department of Biology, University of York, York, UK.,Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - C D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - M Joron
- Smithsonian Tropical Research Institute, Panama City, Panama.,Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France.,Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, Montpellier 5, France
| | - K M Kozak
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - V Llaurens
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - S H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - S H Montgomery
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - J Morris
- Department of Biology, University of York, York, UK
| | - N J Nadeau
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - A L Pinharanda
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - N Rosser
- Department of Biology, University of York, York, UK
| | - M J Thompson
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - S Vanjari
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - R W R Wallbank
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Q Yu
- Department of Zoology, University of Cambridge, Cambridge, UK.,School of Life Sciences, Chongqing University, Shapingba District, Chongqing, China
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211
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Johnson WC, Ordway AJ, Watada M, Pruitt JN, Williams TM, Rebeiz M. Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity within and between Drosophila Species. PLoS Genet 2015; 11:e1005279. [PMID: 26115430 PMCID: PMC4483262 DOI: 10.1371/journal.pgen.1005279] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/13/2015] [Indexed: 11/23/2022] Open
Abstract
The modification of transcriptional regulation has become increasingly appreciated as a major contributor to morphological evolution. However, the role of negative-acting control elements (e.g. silencers) in generating morphological diversity has been generally overlooked relative to positive-acting “enhancer” elements. The highly variable body coloration patterns among Drosophilid insects represents a powerful model system in which the molecular alterations that underlie phenotypic diversity can be defined. In a survey of pigment phenotypes among geographically disparate Japanese populations of Drosophila auraria, we discovered a remarkable degree of variation in male-specific abdominal coloration. In testing the expression patterns of the major pigment-producing enzymes, we found that phenotypes uniquely correlated with differences in the expression of ebony, a gene required for yellow-colored cuticle. Assays of ebony’s transcriptional control region indicated that a lightly pigmented strain harbored cis-regulatory mutations that caused correlated changes in its expression. Through a series of chimeric reporter constructs between light and dark strain alleles, we localized function-altering mutations to a conserved silencer that mediates a male-specific pattern of ebony repression. This suggests that the light allele was derived through the loss of this silencer’s activity. Furthermore, examination of the ebony gene of D. serrata, a close relative of D. auraria which secondarily lost male-specific pigmentation revealed the parallel loss of this silencer element. These results demonstrate how loss-of-function mutations in a silencer element resulted in increased gene expression. We propose that the mutational inactivation of silencer elements may represent a favored path to evolve gene expression, impacting morphological traits. One of the greatest challenges in understanding the relationship between genotype and phenotype is to discern how changes in DNA affect the normal functioning of genes. Mutations may generate a new function for a gene, yet it is frequently observed that they inactivate some aspect of a gene’s normal capacity. Investigations focused on understanding the developmental basis for the evolution of anatomical structures has found a prevalent role for mutations that alter developmental gene regulation. In animals, genes are transcriptionally activated in specific tissues during development by regulatory sequences distributed across their expansive non-protein coding regions. Regulatory elements known as silencers act to prevent genes from being expressed in certain tissues, providing a mechanism for precise control. Here, we show how a silencer that prevents expression of a pigment-producing enzyme in certain Drosophila species has repeatedly been subject to inactivating mutations that increased this gene’s expression. This example illustrates how such negative-acting regulatory sequences can represent a convenient target for increasing gene expression through the loss of a genetic element.
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Affiliation(s)
- Winslow C. Johnson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alison J. Ordway
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Masayoshi Watada
- Department of Biology, Faculty of Science, Ehime University, Matsuyama, Japan
| | - Jonathan N. Pruitt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Thomas M. Williams
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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212
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Elias M, Joron M. Mimicry inHeliconiusand Ithomiini butterflies: The profound consequences of an adaptation. BIO WEB OF CONFERENCES 2015. [DOI: 10.1051/bioconf/20150400008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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213
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Gain of cis-regulatory activities underlies novel domains of wingless gene expression in Drosophila. Proc Natl Acad Sci U S A 2015; 112:7524-9. [PMID: 26034272 DOI: 10.1073/pnas.1509022112] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Changes in gene expression during animal development are largely responsible for the evolution of morphological diversity. However, the genetic and molecular mechanisms responsible for the origins of new gene-expression domains have been difficult to elucidate. Here, we sought to identify molecular events underlying the origins of three novel features of wingless (wg) gene expression that are associated with distinct pigmentation patterns in Drosophila guttifera. We compared the activity of cis-regulatory sequences (enhancers) across the wg locus in D. guttifera and Drosophila melanogaster and found strong functional conservation among the enhancers that control similar patterns of wg expression in larval imaginal discs that are essential for appendage development. For pupal tissues, however, we found three novel wg enhancer activities in D. guttifera associated with novel domains of wg expression, including two enhancers located surprisingly far away in an intron of the distant Wnt10 gene. Detailed analysis of one enhancer (the vein-tip enhancer) revealed that it overlapped with a region controlling wg expression in wing crossveins (crossvein enhancer) in D. guttifera and other species. Our results indicate that one novel domain of wg expression in D. guttifera wings evolved by co-opting pre-existing regulatory sequences governing gene activity in the developing wing. We suggest that the modification of existing enhancers is a common path to the evolution of new gene-expression domains and enhancers.
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214
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Gaut BS. Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution. Mol Biol Evol 2015; 32:1661-71. [DOI: 10.1093/molbev/msv105] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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215
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Abstract
For over 100 years, it has been known that polymorphic mimicry is often switched by simple mendelian factors, yet the physical nature of these loci had escaped characterization. Now, the genome sequences of two swallowtail butterfly (Papilio) species have enabled the precise identification of a locus underlying mimicry, adding to unprecedented recent discoveries in mimicry genetics.
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Affiliation(s)
- James Mallet
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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216
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Rebeiz M, Patel NH, Hinman VF. Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development. Annu Rev Genomics Hum Genet 2015; 16:103-31. [PMID: 26079281 DOI: 10.1146/annurev-genom-091212-153423] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The molecular and genetic basis for the evolution of anatomical diversity is a major question that has inspired evolutionary and developmental biologists for decades. Because morphology takes form during development, a true comprehension of how anatomical structures evolve requires an understanding of the evolutionary events that alter developmental genetic programs. Vast gene regulatory networks (GRNs) that connect transcription factors to their target regulatory sequences control gene expression in time and space and therefore determine the tissue-specific genetic programs that shape morphological structures. In recent years, many new examples have greatly advanced our understanding of the genetic alterations that modify GRNs to generate newly evolved morphologies. Here, we review several aspects of GRN evolution, including their deep preservation, their mechanisms of alteration, and how they originate to generate novel developmental programs.
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Affiliation(s)
- Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260;
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217
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Pardo-Diaz C, Salazar C, Jiggins CD. Towards the identification of the loci of adaptive evolution. Methods Ecol Evol 2015; 6:445-464. [PMID: 25937885 PMCID: PMC4409029 DOI: 10.1111/2041-210x.12324] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022]
Abstract
1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature.
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Affiliation(s)
- Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Chris D Jiggins
- Department of Zoology, University of CambridgeDowning Street, Cambridge, CB2 3EJ, UK
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218
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Mason NA, Taylor SA. Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird. Mol Ecol 2015; 24:3009-25. [DOI: 10.1111/mec.13140] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/27/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology; Cornell University; 215 Tower Rd. Ithaca NY 14853 USA
- Fuller Evolutionary Biology Program; Laboratory of Ornithology; Cornell University; 159 Sapsucker Woods Road Ithaca NY 14850 USA
| | - Scott A. Taylor
- Department of Ecology and Evolutionary Biology; Cornell University; 215 Tower Rd. Ithaca NY 14853 USA
- Fuller Evolutionary Biology Program; Laboratory of Ornithology; Cornell University; 159 Sapsucker Woods Road Ithaca NY 14850 USA
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219
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Huber B, Whibley A, Poul YL, Navarro N, Martin A, Baxter S, Shah A, Gilles B, Wirth T, McMillan WO, Joron M. Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies. Heredity (Edinb) 2015; 114:515-24. [PMID: 25806542 PMCID: PMC4815517 DOI: 10.1038/hdy.2015.22] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 02/01/2015] [Accepted: 02/04/2015] [Indexed: 12/26/2022] Open
Abstract
Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have undergone an adaptive radiation for wing-pattern mimicry and are influenced by distinct selection regimes. Using crosses between natural wing-pattern variants, we used genome-wide restriction site-associated DNA (RAD) genotyping, traditional linkage mapping and multivariate image analysis to study the evolution of the architecture of adaptive variation in two closely related species: Heliconius hecale and H. ismenius. We implemented a new morphometric procedure for the analysis of whole-wing pattern variation, which allows visualising spatial heatmaps of genotype-to-phenotype association for each quantitative trait locus separately. We used the H. melpomene reference genome to fine-map variation for each major wing-patterning region uncovered, evaluated the role of candidate genes and compared genetic architectures across the genus. Our results show that, although the loci responding to mimicry selection are highly conserved between species, their effect size and phenotypic action vary throughout the clade. Multilocus architecture is ancestral and maintained across species under directional selection, whereas the single-locus (supergene) inheritance controlling polymorphism in H. numata appears to have evolved only once. Nevertheless, the conservatism in the wing-patterning toolkit found throughout the genus does not appear to constrain phenotypic evolution towards local adaptive optima.
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Affiliation(s)
- B Huber
- 1] Institut de Systématique, Evolution, et Biodiversité, UMR 7205 CNRS, Muséum National d'Histoire Naturelle, Paris, France [2] Laboratoire Biologie Intégrative des Populations, Ecole Pratique des Hautes Etudes (EPHE), Paris, France [3] The Smithsonian Tropical Research Institute, Balboa, República de Panamá
| | - A Whibley
- Institut de Systématique, Evolution, et Biodiversité, UMR 7205 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Y L Poul
- Institut de Systématique, Evolution, et Biodiversité, UMR 7205 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - N Navarro
- 1] Laboratoire PALEVO, Ecole Pratique des Hautes Etudes, Dijon, France [2] UMR uB/CNRS 6282-Biogéosciences, Université de Bourgogne, Dijon, France
| | - A Martin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - S Baxter
- 1] School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia [2] Department of Zoology, University of Cambridge, Cambridge, UK
| | - A Shah
- 1] Institut de Systématique, Evolution, et Biodiversité, UMR 7205 CNRS, Muséum National d'Histoire Naturelle, Paris, France [2] Department of Animal Behaviour, Universität Bielefeld, Bielefeld, Germany
| | - B Gilles
- 1] Institut de Systématique, Evolution, et Biodiversité, UMR 7205 CNRS, Muséum National d'Histoire Naturelle, Paris, France [2] The Smithsonian Tropical Research Institute, Balboa, República de Panamá
| | - T Wirth
- 1] Institut de Systématique, Evolution, et Biodiversité, UMR 7205 CNRS, Muséum National d'Histoire Naturelle, Paris, France [2] Laboratoire Biologie Intégrative des Populations, Ecole Pratique des Hautes Etudes (EPHE), Paris, France
| | - W O McMillan
- The Smithsonian Tropical Research Institute, Balboa, República de Panamá
| | - M Joron
- 1] Institut de Systématique, Evolution, et Biodiversité, UMR 7205 CNRS, Muséum National d'Histoire Naturelle, Paris, France [2] The Smithsonian Tropical Research Institute, Balboa, República de Panamá
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220
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How do regulatory networks evolve and expand throughout evolution? Curr Opin Biotechnol 2015; 34:180-8. [PMID: 25723843 DOI: 10.1016/j.copbio.2015.02.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 02/04/2015] [Accepted: 02/04/2015] [Indexed: 11/23/2022]
Abstract
Throughout evolution, regulatory networks need to expand and adapt to accommodate novel genes and gene functions. However, the molecular details explaining how gene networks evolve remain largely unknown. Recent studies demonstrate that changes in transcription factors contribute to the evolution of regulatory networks. In particular, duplication of transcription factors followed by specific mutations in their DNA-binding or interaction domains propels the divergence and emergence of new networks. The innate promiscuity and modularity of regulatory networks contributes to their evolvability: duplicated promiscuous regulators and their target promoters can acquire mutations that lead to gradual increases in specificity, allowing neofunctionalization or subfunctionalization.
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221
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De Busschere C, Van Belleghem SM, Hendrickx F. Inter and intra island introgression in a wolf spider radiation from the Galápagos, and its implications for parallel evolution. Mol Phylogenet Evol 2015; 84:73-84. [PMID: 25573742 DOI: 10.1016/j.ympev.2014.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 11/30/2022]
Abstract
Parallel radiations within island systems are often assumed to follow a simple scenario in which single colonization events are followed by in situ adaptive divergence. However, subsequent gene exchange after the initial colonization and during the divergence process might have important evolutionary impacts on species radiations. Gene exchange among ecologically similar species from different islands may lead to introgression of adaptive genetic variation and influence the parallel divergence process. In this study, we estimate levels of gene exchange within a wolf spider radiation of the genus Hogna Simon, 1885, from the Galápagos, wherein habitat specialization into 'high elevation' and 'coastal dry' species apparently evolved repeatedly on two islands. By using a multilocus approach we show that low levels of inter-island and relatively higher levels of intra island introgression shaped genetic variation in this species complex. Using these estimates, we demonstrate by means of a coalescence simulation that under these inter- and intra-island migration rates parallel evolution most likely evolves by introgression of adaptive alleles among islands, rather than through independent mutations despite the close genetic relationship of species within islands. As species phylogenies within radiations are frequently used to infer the divergence pattern, even relatively low levels of interspecific gene flow should not be neglected when interpreting parallel trait evolution.
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Affiliation(s)
- Charlotte De Busschere
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy & Phylogeny, Vautierstraat 29, 1000 Brussels, Belgium; Terrestrial Ecology Unit, Biology Department, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | - Steven Marcel Van Belleghem
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy & Phylogeny, Vautierstraat 29, 1000 Brussels, Belgium; Terrestrial Ecology Unit, Biology Department, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy & Phylogeny, Vautierstraat 29, 1000 Brussels, Belgium; Terrestrial Ecology Unit, Biology Department, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
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222
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Abstract
Genetic mutations are the main fuel of evolution. In each generation, they produce new variations, which may be sorted out by natural or sexual selection. Mutations are generated by chance; yet which are the mutations actually sorted out by evolution, and why? This review presents some recent advances regarding this question. First, we gather results obtained at molecular and cellular levels, through synthetic experiments and under artificial selection paradigms. Next, we highlight studies at the multi-cellular level, especially studies of repeated evolution, whereby independent lineages acquire similar traits. Recent meta-analysis and quantifications are being presented; together they suggest that evolutionary relevant mutations accumulate around hotspots, spanning different levels of genetic organization. Pioneering work suggests that many causes, corresponding to many biological contexts, may explain the existence of these genetic hotspots. We finally discuss methodological limits, empirical challenges and a few future potential directions for this domain of research dedicated to the genetic path of evolution.
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223
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Suzuki TK, Tomita S, Sezutsu H. Gradual and contingent evolutionary emergence of leaf mimicry in butterfly wing patterns. BMC Evol Biol 2014; 14:229. [PMID: 25421067 PMCID: PMC4261531 DOI: 10.1186/s12862-014-0229-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/27/2014] [Indexed: 12/02/2022] Open
Abstract
Background Special resemblance of animals to natural objects such as leaves provides a representative example of evolutionary adaptation. The existence of such sophisticated features challenges our understanding of how complex adaptive phenotypes evolved. Leaf mimicry typically consists of several pattern elements, the spatial arrangement of which generates the leaf venation-like appearance. However, the process by which leaf patterns evolved remains unclear. Results In this study we show the evolutionary origin and process for the leaf pattern in Kallima (Nymphalidae) butterflies. Using comparative morphological analyses, we reveal that the wing patterns of Kallima and 45 closely related species share the same ground plan, suggesting that the pattern elements of leaf mimicry have been inherited across species with lineage-specific changes of their character states. On the basis of these analyses, phylogenetic comparative methods estimated past states of the pattern elements and enabled reconstruction of the wing patterns of the most recent common ancestor. This analysis shows that the leaf pattern has evolved through several intermediate patterns. Further, we use Bayesian statistical methods to estimate the temporal order of character-state changes in the pattern elements by which leaf mimesis evolved, and show that the pattern elements changed their spatial arrangement (e.g., from a curved line to a straight line) in a stepwise manner and finally establish a close resemblance to a leaf venation-like appearance. Conclusions Our study provides the first evidence for stepwise and contingent evolution of leaf mimicry. Leaf mimicry patterns evolved in a gradual, rather than a sudden, manner from a non-mimetic ancestor. Through a lineage of Kallima butterflies, the leaf patterns evolutionarily originated through temporal accumulation of orchestrated changes in multiple pattern elements. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0229-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takao K Suzuki
- Transgenic Silkworm Research Unit, Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 1-2 Oowashi, 305-8634, Tsukuba, Ibaraki, Japan.
| | - Shuichiro Tomita
- Transgenic Silkworm Research Unit, Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 1-2 Oowashi, 305-8634, Tsukuba, Ibaraki, Japan.
| | - Hideki Sezutsu
- Transgenic Silkworm Research Unit, Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 1-2 Oowashi, 305-8634, Tsukuba, Ibaraki, Japan.
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224
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Rosser N, Dasmahapatra KK, Mallet J. Stable Heliconius butterfly hybrid zones are correlated with a local rainfall peak at the edge of the Amazon basin. Evolution 2014; 68:3470-84. [PMID: 25311415 DOI: 10.1111/evo.12539] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 09/29/2014] [Indexed: 11/28/2022]
Abstract
Multilocus clines between Müllerian mimetic races of Heliconius butterflies provide a classic example of the maintenance of hybrid zones and their importance in speciation. Concordant hybrid zones in the mimics Heliconius erato and H. melpomene in northern Peru were carefully documented in the 1980s, and this prior work now permits a historical analysis of the movement or stasis of the zones. Previous work predicted that these zones might be moving toward the Andes due to selective asymmetry. Extensive deforestation and climate change might also be expected to affect the positions and widths of the hybrid zones. We show that the positions and shapes of these hybrid zones have instead remained remarkably stable between 1985 and 2012. The stability of this interaction strongly implicates continued selection, rather than neutral mixing following secondary contact. The stability of cline widths and strong linkage disequilibria (gametic correlation coefficients Rmax = 0.35-0.56 among unlinked loci) over 25 years suggest that mimetic selection pressures on each color pattern locus have remained approximately constant (s ≈ 0.13-0.40 per locus in both species). Exceptionally high levels of precipitation at the edge of the easternmost Andes may act as a population density trough for butterflies, trapping the hybrid zones at the foot of the mountains, and preventing movement. As such, our results falsify one prediction of the Pleistocene Refugium theory: That the ranges of divergent species or subspecies should be centered on regions characterized by maxima of rainfall, with hybrid zones falling in more arid regions between them.
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Affiliation(s)
- Neil Rosser
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom; Department of Biology, University of York, Wentworth Way, York, YO10 5DD, United Kingdom.
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225
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Rosenblum EB, Parent CE, Brandt EE. The Molecular Basis of Phenotypic Convergence. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091851] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; ,
| | - Christine E. Parent
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; ,
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844;
| | - Erin E. Brandt
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; ,
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226
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Rodriguez J, Pitts JP, von Dohlen CD, Wilson JS. Müllerian mimicry as a result of codivergence between velvet ants and spider wasps. PLoS One 2014; 9:e112942. [PMID: 25396424 PMCID: PMC4232588 DOI: 10.1371/journal.pone.0112942] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/11/2014] [Indexed: 11/19/2022] Open
Abstract
Recent studies have delineated a large Nearctic Müllerian mimicry complex in Dasymutilla velvet ants. Psorthaspis spider wasps live in areas where this mimicry complex is found and are phenotypically similar to Dasymutilla. We tested the idea that Psorthaspis spider wasps are participating in the Dasymutilla mimicry complex and that they codiverged with Dasymutilla. We performed morphometric analyses and human perception tests, and tabulated distributional records to determine the fit of Psorthaspis to the Dasymutilla mimicry complex. We inferred a dated phylogeny using nuclear molecular markers (28S, elongation factor 1-alpha, long-wavelength rhodopsin and wingless) for Psorthaspis species and compared it to a dated phylogeny of Dasymutilla. We tested for codivergence between the two groups using two statistical analyses. Our results show that Psorthaspis spider wasps are morphologically similar to the Dasymutilla mimicry rings. In addition, our tests indicate that Psorthaspis and Dasymutilla codiverged to produce similar color patterns. This study expands the breadth of the Dasymutilla Müllerian mimicry complex and provides insights about how codivergence influenced the evolution of mimicry in these groups.
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Affiliation(s)
- Juanita Rodriguez
- Department of Biology, Utah State University, Logan, Utah, United States of America
| | - James P. Pitts
- Department of Biology, Utah State University, Logan, Utah, United States of America
| | - Carol D. von Dohlen
- Department of Biology, Utah State University, Logan, Utah, United States of America
| | - Joseph S. Wilson
- Department of Biology, Utah State University - Tooele, Tooele, Utah, United States of America
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227
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Abstract
Selection is predicted to drive diversification within species and lead to local adaptation, but understanding the mechanistic details underlying this process and thus the genetic basis of adaptive evolution requires the mapping of genotype to phenotype. Venom is complex and involves many genes, but the specialization of the venom gland toward toxin production allows specific transcripts to be correlated with specific toxic proteins, establishing a direct link from genotype to phenotype. To determine the extent of expression variation and identify the processes driving patterns of phenotypic diversity, we constructed genotype-phenotype maps and compared range-wide toxin-protein expression variation for two species of snake with nearly identical ranges: the eastern diamondback rattlesnake (Crotalus adamanteus) and the eastern coral snake (Micrurus fulvius). We detected significant expression variation in C. adamanteus, identified the specific loci associated with population differentiation, and found that loci expressed at all levels contributed to this divergence. Contrary to expectations, we found no expression variation in M. fulvius, suggesting that M. fulvius populations are not locally adapted. Our results not only linked expression variation at specific loci to divergence in a polygenic, complex trait but also have extensive conservation and biomedical implications. C. adamanteus is currently a candidate for federal listing under the Endangered Species Act, and the loss of any major population would result in the irrevocable loss of a unique venom phenotype. The lack of variation in M. fulvius has significant biomedical application because our data will assist in the development of effective antivenom for this species.
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228
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Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. Proc Natl Acad Sci U S A 2014; 111:E4736-42. [PMID: 25336755 DOI: 10.1073/pnas.1416574111] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Despite contingency in life's history, the similarity of evolutionarily convergent traits may represent predictable solutions to common conditions. However, the extent to which overall gene expression levels (transcriptomes) underlying convergent traits are themselves convergent remains largely unexplored. Here, we show strong statistical support for convergent evolutionary origins and massively parallel evolution of the entire transcriptomes in symbiotic bioluminescent organs (bacterial photophores) from two divergent squid species. The gene expression similarities are so strong that regression models of one species' photophore can predict organ identity of a distantly related photophore from gene expression levels alone. Our results point to widespread parallel changes in gene expression evolution associated with convergent origins of complex organs. Therefore, predictable solutions may drive not only the evolution of novel, complex organs but also the evolution of overall gene expression levels that underlie them.
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229
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Wellenreuther M, Svensson EI, Hansson B. Sexual selection and genetic colour polymorphisms in animals. Mol Ecol 2014; 23:5398-414. [DOI: 10.1111/mec.12935] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Maren Wellenreuther
- Evolutionary Ecology; Department of Biology; Lund University; SE-223 62 Lund Sweden
| | - Erik I. Svensson
- Evolutionary Ecology; Department of Biology; Lund University; SE-223 62 Lund Sweden
| | - Bengt Hansson
- Molecular Ecology; Department of Biology; Lund University; SE-223 62 Lund Sweden
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230
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Powder KE, Cousin H, McLinden GP, Craig Albertson R. A nonsynonymous mutation in the transcriptional regulator lbh is associated with cichlid craniofacial adaptation and neural crest cell development. Mol Biol Evol 2014; 31:3113-24. [PMID: 25234704 DOI: 10.1093/molbev/msu267] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Since the time of Darwin, biologists have sought to understand the origins and maintenance of life's diversity of form. However, the nature of the exact DNA mutations and molecular mechanisms that result in morphological differences between species remains unclear. Here, we characterize a nonsynonymous mutation in a transcriptional coactivator, limb bud and heart homolog (lbh), which is associated with adaptive variation in the lower jaw of cichlid fishes. Using both zebrafish and Xenopus, we demonstrate that lbh mediates migration of cranial neural crest cells, the cellular source of the craniofacial skeleton. A single amino acid change that is alternatively fixed in cichlids with differing facial morphologies results in discrete shifts in migration patterns of this multipotent cell type that are consistent with both embryological and adult craniofacial phenotypes. Among animals, this polymorphism in lbh represents a rare example of a coding change that is associated with continuous morphological variation. This work offers novel insights into the development and evolution of the craniofacial skeleton, underscores the evolutionary potential of neural crest cells, and extends our understanding of the genetic nature of mutations that underlie divergence in complex phenotypes.
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Affiliation(s)
- Kara E Powder
- Department of Biology, University of Massachusetts, Amherst
| | - Hélène Cousin
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst
| | - Gretchen P McLinden
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst
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231
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The transcription factor Apontic-like controls diverse colouration pattern in caterpillars. Nat Commun 2014; 5:4936. [DOI: 10.1038/ncomms5936] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/08/2014] [Indexed: 11/08/2022] Open
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232
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Pougach K, Voet A, Kondrashov FA, Voordeckers K, Christiaens JF, Baying B, Benes V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen KJ. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nat Commun 2014; 5:4868. [PMID: 25204769 PMCID: PMC4172970 DOI: 10.1038/ncomms5868] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/31/2014] [Indexed: 11/08/2022] Open
Abstract
The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network.
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Affiliation(s)
- Ksenia Pougach
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Arnout Voet
- Structural Bioinformatics, Center for Life Science Technologies (CLST), RIKEN, 230-0045 Yokohama, Japan
| | - Fyodor A. Kondrashov
- Laboratory of Evolutionary Genomics, Centre for genomic regulation (CRG), 08003 Barcelona, Spain
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Joaquin F. Christiaens
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Bianka Baying
- Genomics Core Facility, European Molecular Biology Laboratory Heidelberg (EMBL), 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory Heidelberg (EMBL), 69117 Heidelberg, Germany
| | - Ryo Sakai
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, B-3001 Leuven, Belgium
- iMinds Medical Information Technologies Department, KU Leuven, B-3001 Leuven, Belgium
| | - Jan Aerts
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, B-3001 Leuven, Belgium
- iMinds Medical Information Technologies Department, KU Leuven, B-3001 Leuven, Belgium
| | - Bo Zhu
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
| | - Patrick Van Dijck
- Molecular Microbiology and Biotechnology Section, KU Leuven, B-3001 Leuven, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Department M2S, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, B-3001 Leuven, Belgium
- Laboratory for Systems biology, Vlaams Instituut voor Biotechnologie (VIB), B-3001 Leuven, Belgium
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233
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Ancient homology underlies adaptive mimetic diversity across butterflies. Nat Commun 2014; 5:4817. [PMID: 25198507 PMCID: PMC4183220 DOI: 10.1038/ncomms5817] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 07/28/2014] [Indexed: 12/30/2022] Open
Abstract
Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time. Little is known about the genetic basis of convergent evolution in deeply diverged species. Here, the authors show that variation in the WntA gene is associated with parallel wing pattern variation in two butterflies that diverged more than 65 million years ago.
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234
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Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems. Dev Biol 2014; 395:367-78. [PMID: 25196151 DOI: 10.1016/j.ydbio.2014.08.031] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/22/2014] [Accepted: 08/27/2014] [Indexed: 11/23/2022]
Abstract
Most butterfly wing patterns are proposed to be derived from a set of conserved pattern elements known as symmetry systems. Symmetry systems are so-named because they are often associated with parallel color stripes mirrored around linear organizing centers that run between the anterior and posterior wing margins. Even though the symmetry systems are the most prominent and diverse wing pattern elements, their study has been confounded by a lack of knowledge regarding the molecular basis of their development, as well as the difficulty of drawing pattern homologies across species with highly derived wing patterns. Here we present the first molecular characterization of symmetry system development by showing that WntA expression is consistently associated with the major basal, discal, central, and external symmetry system patterns of nymphalid butterflies. Pharmacological manipulations of signaling gradients using heparin and dextran sulfate showed that pattern organizing centers correspond precisely with WntA, wingless, Wnt6, and Wnt10 expression patterns, thus suggesting a role for Wnt signaling in color pattern induction. Importantly, this model is supported by recent genetic and population genomic work identifying WntA as the causative locus underlying wing pattern variation within several butterfly species. By comparing the expression of WntA between nymphalid butterflies representing a range of prototypical symmetry systems, slightly deviated symmetry systems, and highly derived wing patterns, we were able to infer symmetry system homologies in several challenging cases. Our work illustrates how highly divergent morphologies can be derived from modifications to a common ground plan across both micro- and macro-evolutionary time scales.
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235
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Rapti Z, Duennes MA, Cameron SA. Defining the colour pattern phenotype in bumble bees (Bombus): a new model for evo devo. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12356] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zoi Rapti
- Department of Mathematics; University of Illinois; 1409 West Green Street Urbana IL 61801 USA
| | - Michelle A. Duennes
- Department of Entomology; University of Illinois; 320 Morrill Hall Urbana IL 61801 USA
| | - Sydney A. Cameron
- Department of Entomology; University of Illinois; 320 Morrill Hall Urbana IL 61801 USA
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236
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Henning F, Lee HJ, Franchini P, Meyer A. Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping. Mol Ecol 2014; 23:5224-40. [PMID: 25039588 DOI: 10.1111/mec.12860] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/02/2014] [Accepted: 07/12/2014] [Indexed: 01/25/2023]
Abstract
The genetic dissection of naturally occurring phenotypes sheds light on many fundamental and longstanding questions in speciation and adaptation and is a central research topic in evolutionary biology. Until recently, forward-genetic approaches were virtually impossible to apply to nonmodel organisms, but the development of next-generation sequencing techniques eases this difficulty. Here, we use the ddRAD-seq method to map a colour trait with a known adaptive function in cichlid fishes, well-known textbook examples for rapid rates of speciation and astonishing phenotypic diversification. A suite of phenotypic key innovations is related to speciation and adaptation in cichlids, among which body coloration features prominently. The focal trait of this study, horizontal stripes, evolved in parallel in several cichlid radiations and is associated with piscivorous foraging behaviour. We conducted interspecific crosses between Haplochromis sauvagei and H. nyererei and constructed a linkage map with 867 SNP markers distributed on 22 linkage groups and total size of 1130.63 cM. Lateral stripes are inherited as a Mendelian trait and map to a single genomic interval that harbours a paralog of a gene with known function in stripe patterning. Dorsolateral and mid-lateral stripes were always coinherited and are thus under the same genetic control. Additionally, we directly quantify the genotyping error rates in RAD markers and offer guidelines for identifying and dealing with errors. Uncritical marker selection was found to severely impact linkage map construction. Fortunately, by applying appropriate quality control steps, a genotyping accuracy of >99.9% can be reached, thus allowing for efficient linkage mapping of evolutionarily relevant traits.
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Affiliation(s)
- Frederico Henning
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78457, Germany
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237
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Aymone ACB, Lothhammer N, Valente VLDS, de Araújo AM. Embryogenesis of Heliconius erato (Lepidoptera, Nymphalidae): a contribution to the anatomical development of an evo-devo model organism. Dev Growth Differ 2014; 56:448-59. [PMID: 25112499 DOI: 10.1111/dgd.12144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 04/23/2014] [Accepted: 05/11/2014] [Indexed: 11/28/2022]
Abstract
This study reports on the embryogenesis of Heliconius erato phyllis between blastoderm formation and the prehatching larval stage. Syncytial blastoderm formation occurred approximately 2 h after egg laying (AEL) and at about 4 h, the cellular blastoderm was formed. The germ band arose from the entire length of the blastoderm, and rapidly became compacted occupying approximately two-thirds of the egg length. At about 7 h AEL, protocephalon and protocorm differentiation occurred. Continued proliferation of the germ band was followed by penetration into the yolk mass, forming a C-shaped embryo at about 10 h. Approximately 12 h AEL, the gnathal, thoracic and abdominal segments became visible. The primordium of the mouthparts and thoracic legs formed as paired evaginations, while the prolegs formed as paired lobes. At about 30 h, the embryo reversed dorsoventrally. Approximately 32 h AEL, the protocephalon and gnathal segments fused, shifting the relative position of the rudimentary appendages in this region. At about 52 h, the embryo was U-shaped in lateral view and at approximately 56 h, the bristles began evagination from the larval cuticle. Larvae hatched at about 72 h. We found that H. erato phyllis followed an embryonic pattern consistent with long-germ embryogenesis. Thus, we believe that H. erato phyllis should be classified as a long-germ lepidopteran. The study of H. erato phyllis embryogenesis provided a structural glimpse into the morphogenetic events that occur in the Heliconius egg period. This study could help future molecular approaches to understanding the evolution of Heliconius development.
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Affiliation(s)
- Ana Carolina Bahi Aymone
- Post-Graduate Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, C.P. 15053, Porto Alegre, Rio Grande do Sul, 91501-970, Brazil
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238
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Different tradeoffs result from alternate genetic adaptations to a common environment. Proc Natl Acad Sci U S A 2014; 111:12121-6. [PMID: 25092325 DOI: 10.1073/pnas.1406886111] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Fitness tradeoffs are often assumed by evolutionary theory, yet little is known about the frequency of fitness tradeoffs during stress adaptation. Even less is known about the genetic factors that confer these tradeoffs and whether alternative adaptive mutations yield contrasting tradeoff dynamics. We addressed these issues using 114 clones of Escherichia coli that were evolved independently for 2,000 generations under thermal stress (42.2 °C). For each clone, we measured their fitness relative to the ancestral clone at 37 °C and 20 °C. Tradeoffs were common at 37 °C but more prevalent at 20 °C, where 56% of clones were outperformed by the ancestor. We also characterized the upper and lower thermal boundaries of each clone. All clones shifted their upper boundary to at least 45 °C; roughly half increased their lower niche boundary concomitantly, representing a shift of thermal niche. The remaining clones expanded their thermal niche by increasing their upper limit without a commensurate increase of lower limit. We associated these niche dynamics with genotypes and confirmed associations by engineering single mutations in the rpoB gene, which encodes the beta subunit of RNA polymerase, and the rho gene, which encodes a termination factor. Single mutations in the rpoB gene exhibit antagonistic pleiotropy, with fitness tradeoffs at 18 °C and fitness benefits at 42.2 °C. In contrast, a mutation within the rho transcriptional terminator, which defines an alternative adaptive pathway from that of rpoB, had no demonstrable effect on fitness at 18 °C. This study suggests that two different genetic pathways toward high-temperature adaptation have contrasting effects with respect to thermal tradeoffs.
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239
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Wilts BD, IJbema N, Stavenga DG. Pigmentary and photonic coloration mechanisms reveal taxonomic relationships of the Cattlehearts (Lepidoptera: Papilionidae: Parides). BMC Evol Biol 2014; 14:160. [PMID: 25064167 PMCID: PMC4236566 DOI: 10.1186/s12862-014-0160-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The colorful wing patterns of butterflies, a prime example of biodiversity, can change dramatically within closely related species. Wing pattern diversity is specifically present among papilionid butterflies. Whether a correlation between color and the evolution of these butterflies exists so far remained unsolved. RESULTS We here investigate the Cattlehearts, Parides, a small Neotropical genus of papilionid butterflies with 36 members, the wings of which are marked by distinctly colored patches. By applying various physical techniques, we investigate the coloration toolkit of the wing scales. The wing scales contain two different, wavelength-selective absorbing pigments, causing pigmentary colorations. Scale ridges with multilayered lamellae, lumen multilayers or gyroid photonic crystals in the scale lumen create structural colors that are variously combined with these pigmentary colors. CONCLUSIONS The pigmentary and structural traits strongly correlate with the taxonomical distribution of Parides species. The experimental findings add crucial insight into the evolution of butterfly wing scales and show the importance of morphological parameter mapping for butterfly phylogenetics.
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Affiliation(s)
- Bodo D Wilts
- Computational Physics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, NL-9747AG, The Netherlands
- Present address: Department of Physics, Cavendish Laboratories, University of Cambridge, 13 JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Natasja IJbema
- Computational Physics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, NL-9747AG, The Netherlands
- Present address: Accenture Nederland B.V, Gustav Mahlerplein 90, Amsterdam, NL-1082 MA, The Netherlands
| | - Doekele G Stavenga
- Computational Physics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, NL-9747AG, The Netherlands
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240
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Plachetzki DC, Sabrina Pankey M, Johnson BR, Ronne EJ, Kopp A, Grosberg RK. Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus. Integr Comp Biol 2014; 54:276-83. [PMID: 24935986 DOI: 10.1093/icb/icu080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Advances in sequencing technology have forced a quantitative revolution in Evolutionary Biology. One important feature of this renaissance is that comprehensive genomic resources can be obtained quickly for almost any taxon, thus speeding the development of new model organisms. Here, we analyze 20 RNA-seq libraries from morphologically, sexually, and genetically distinct polyp types from the gonochoristic colonial hydrozoan, Hydractinia symbiolongicarpus (Cnidaria). Analyses of these data using weighted gene co-expression networks highlight deeply conserved genetic elements of animal spermatogenesis and demonstrate the utility of these methods in identifying modules of genes that correlate with different zooid types across various statistical contrasts. RNA-seq data and analytical scripts described here are deposited in publicly available databases.
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Affiliation(s)
- David C Plachetzki
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - M Sabrina Pankey
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - Brian R Johnson
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - Eric J Ronne
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - Artyom Kopp
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
| | - Richard K Grosberg
- *Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH 03801, USA; Department of Ecology Evolution and Marine Biology, The University of California at Santa Barbara, Santa Barbara, CA 93106, USA; Department of Entomology, The University of California at Davis, Davis, CA 95616, USA; Department of Evolution and Ecology, Center for Population Biology, The University of California at Davis, Davis, CA 95616, USA
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241
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Dinwiddie A, Null R, Pizzano M, Chuong L, Leigh Krup A, Ee Tan H, Patel NH. Dynamics of F-actin prefigure the structure of butterfly wing scales. Dev Biol 2014; 392:404-18. [PMID: 24930704 DOI: 10.1016/j.ydbio.2014.06.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 06/02/2014] [Accepted: 06/04/2014] [Indexed: 11/24/2022]
Abstract
The wings of butterflies and moths consist of dorsal and ventral epidermal surfaces that give rise to overlapping layers of scales and hairs (Lepidoptera, "scale wing"). Wing scales (average length ~200 µm) are homologous to insect bristles (macrochaetes), and their colors create the patterns that characterize lepidopteran wings. The topology and surface sculpture of wing scales vary widely, and this architectural complexity arises from variations in the developmental program of the individual scale cells of the wing epithelium. One of the more striking features of lepidopteran wing scales are the longitudinal ridges that run the length of the mature (dead) cell, gathering the cuticularized scale cell surface into pleats on the sides of each scale. While also present around the periphery of other insect bristles and hairs, longitudinal ridges in lepidopteran wing scales gain new significance for their creation of iridescent color through microribs and lamellae. Here we show the dynamics of the highly organized F-actin filaments during scale cell development, and present experimental manipulations of actin polymerization that reveal the essential role of this cytoskeletal component in wing scale elongation and the positioning of longitudinal ribs.
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Affiliation(s)
- April Dinwiddie
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.
| | - Ryan Null
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720-3200, USA
| | - Maria Pizzano
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720-3200, USA
| | - Lisa Chuong
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720-3200, USA
| | - Alexis Leigh Krup
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720-3200, USA
| | - Hwei Ee Tan
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720-3200, USA
| | - Nipam H Patel
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720-3200, USA.
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242
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Ordway AJ, Hancuch KN, Johnson W, Wiliams TM, Rebeiz M. The expansion of body coloration involves coordinated evolution in cis and trans within the pigmentation regulatory network of Drosophila prostipennis. Dev Biol 2014; 392:431-40. [PMID: 24907418 DOI: 10.1016/j.ydbio.2014.05.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 05/09/2014] [Accepted: 05/25/2014] [Indexed: 11/16/2022]
Abstract
The generation of complex morphological features requires the precisely orchestrated expression of numerous genes during development. While several traits have been resolved to evolutionary changes within a single gene, the evolutionary path by which genes derive co-localized or mutually excluded expression patterns is currently a mystery. Here we investigate how the Drosophila pigmentation gene network was altered in Drosophila prostipennis, a species in the Drosophila melanogaster subgroup, that evolved expanded abdominal pigmentation. We show that this expansion involved broadened expression of the melanin-promoting enzyme genes tan and yellow, and a reciprocal withdrawn pattern of the melanin-suppressing enzyme gene ebony. To examine whether these coordinated changes to the network were generated through mutations in the cis-regulatory elements (CREs) of these genes, we cloned and tested CREs of D. prostipennis tan, ebony, and yellow in transgenic reporter assays. Regulatory regions of both tan and ebony failed to recapitulate the derived D. prostipennis expression phenotype, implicating the modification of a factor or factors upstream of both genes. However, the D. prostipennis yellow cis-regulatory region recapitulated the expanded expression pattern observed in this species, implicating causative mutations in cis to yellow. Our results provide an example in which a coordinated expression program evolved through independent changes at multiple loci, rather than through changes to a single "master regulator" directing a suite of downstream target genes. This implies a complex network structure in which each gene may be subject to a unique set of inputs, and resultantly may require individualized evolutionary paths to yield correlated gene expression patterns.
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Affiliation(s)
- Alison J Ordway
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Kerry N Hancuch
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Winslow Johnson
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Thomas M Wiliams
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
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243
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Ferreira WC, Marcon D. Revisiting the 1879 model for Evolutionary Mimicry by Fritz Müller: New mathematical approaches. ECOLOGICAL COMPLEXITY 2014. [DOI: 10.1016/j.ecocom.2013.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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244
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Friedman NR, McGraw KJ, Omland KE. History and mechanisms of carotenoid plumage evolution in the New World orioles ( Icterus ). Comp Biochem Physiol B Biochem Mol Biol 2014; 172-173:1-8. [DOI: 10.1016/j.cbpb.2014.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/18/2014] [Accepted: 03/27/2014] [Indexed: 10/25/2022]
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245
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Henning F, Meyer A. The evolutionary genomics of cichlid fishes: explosive speciation and adaptation in the postgenomic era. Annu Rev Genomics Hum Genet 2014; 15:417-41. [PMID: 24898042 DOI: 10.1146/annurev-genom-090413-025412] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With more than 1,500 species, cichlid fishes provide textbook examples of recent and diverse adaptive radiations, rapid rates of speciation, and the parallel evolution of adaptive phenotypes among both recently and distantly related lineages. This extraordinary diversity has attracted considerable interest from researchers across several biological disciplines. Their broad phenotypic variation coupled with recent divergence makes cichlids an ideal model system for understanding speciation, adaptation, and phenotypic diversification. Genetic mapping, genome-wide analyses, and genome projects have flourished in the past decade and have added new insights on the question of why there are so many cichlids. These recent findings also show that the sharing of older DNA polymorphisms is extensive and suggest that linage sorting is incomplete and that adaptive introgression played a role in the African radiation. Here, we review the results of genetic and genomic research on cichlids in the past decade and suggest some potential avenues to further exploit the potential of the cichlid model system to provide a better understanding of the genomics of adaptation and speciation.
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Affiliation(s)
- Frederico Henning
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany;
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246
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Khila A, Abouheif E, Rowe L. Comparative functional analyses of ultrabithorax reveal multiple steps and paths to diversification of legs in the adaptive radiation of semi-aquatic insects. Evolution 2014; 68:2159-70. [PMID: 24766229 DOI: 10.1111/evo.12444] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 04/14/2014] [Indexed: 01/16/2023]
Abstract
Invasion of new ecological habitats is often associated with lineage diversification, yet the genetic changes underlying invasions and radiations are poorly understood. Over 200 million years ago, the semi-aquatic insects invaded water surface from a common terrestrial ancestor and diversified to exploit a wide array of niches. Here, we uncover the changes in regulation and function of the gene Ultrabithorax associated with both the invasion of water surface and the subsequent diversification of the group. In the common ancestor of the semi-aquatic insects, a novel deployment of Ubx protein in the mid-legs increased their length, thereby enhancing their role in water surface walking. In derived lineages that specialize in rowing on the open water, additional changes in the timing of Ubx expression further elongated the mid-legs thereby facilitating their function as oars. In addition, Ubx protein function was selectively reversed to shorten specific rear-leg segments, thereby enabling their function as rudders. These changes in Ubx have generated distinct niche-specialized morphologies that account for the remarkable diversification of the semi-aquatic insects. Therefore, changes in the regulation and function of a key developmental gene may facilitate both the morphological change necessary to transition to novel habitats and fuel subsequent morphological diversification.
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Affiliation(s)
- Abderrahman Khila
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; Department of Biology, McGill University, Stewart Biological Sciences Building, Montreal, Quebec H3A 1B1, Canada; Institut de Genomique Fonctionnelle de Lyon, Ecole Normale Supérieure, CNRS UMR 5242, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
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247
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Nadeau NJ, Ruiz M, Salazar P, Counterman B, Medina JA, Ortiz-Zuazaga H, Morrison A, McMillan WO, Jiggins CD, Papa R. Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato. Genome Res 2014; 24:1316-33. [PMID: 24823669 PMCID: PMC4120085 DOI: 10.1101/gr.169292.113] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on color pattern. The comimetic species, H. erato and H. melpomene, have parallel hybrid zones in which both species undergo a change from one color pattern form to another. We use restriction-associated DNA sequencing to obtain several thousand genome-wide sequence markers and use these to analyze patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data—alignment to a reference genome and de novo assembly—and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato, ∼15% divergent) related to the reference sequence. Our results confirm that the color pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to color pattern differences. We also use association mapping to identify previously unmapped color pattern loci, in particular the Ro locus. Finally, we identify a new cryptic population of H. timareta in Ecuador, which occurs at relatively low altitude and is mimetic with H. melpomene malleti.
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Affiliation(s)
- Nicola J Nadeau
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Mayté Ruiz
- Department of Biology and Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, San Juan, Puerto Rico 00921
| | - Patricio Salazar
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom; Centro de Investigación en Biodiversidad y Cambio Climático (BioCamb), Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Brian Counterman
- Department of Biology, Mississippi State University, Mississippi 39762, USA
| | - Jose Alejandro Medina
- High Performance Computing Facility, University of Puerto Rico, San Juan, Puerto Rico, 00921
| | - Humberto Ortiz-Zuazaga
- High Performance Computing Facility, University of Puerto Rico, San Juan, Puerto Rico, 00921; Department of Computer Science, University of Puerto Rico, Rio Piedras, San Juan, Puerto Rico 00921
| | - Anna Morrison
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom; Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama
| | - Riccardo Papa
- Department of Biology and Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, San Juan, Puerto Rico 00921
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248
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Glazer AM, Cleves PA, Erickson PA, Lam AY, Miller CT. Parallel developmental genetic features underlie stickleback gill raker evolution. EvoDevo 2014; 5:19. [PMID: 24851181 PMCID: PMC4029907 DOI: 10.1186/2041-9139-5-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 04/23/2014] [Indexed: 01/08/2023] Open
Abstract
Background Convergent evolution, the repeated evolution of similar phenotypes in independent lineages, provides natural replicates to study mechanisms of evolution. Cases of convergent evolution might have the same underlying developmental and genetic bases, implying that some evolutionary trajectories might be predictable. In a classic example of convergent evolution, most freshwater populations of threespine stickleback fish have independently evolved a reduction of gill raker number to adapt to novel diets. Gill rakers are a segmentally reiterated set of dermal bones important for fish feeding. A previous large quantitative trait locus (QTL) mapping study using a marine × freshwater F2 cross identified QTL on chromosomes 4 and 20 with large effects on evolved gill raker reduction. Results By examining skeletal morphology in adult and developing sticklebacks, we find heritable marine/freshwater differences in gill raker number and spacing that are specified early in development. Using the expression of the Ectodysplasin receptor (Edar) gene as a marker of raker primordia, we find that the differences are present before the budding of gill rakers occurs, suggesting an early change to a lateral inhibition process controlling raker primordia spacing. Through linkage mapping in F2 fish from crosses with three independently derived freshwater populations, we find in all three crosses QTL overlapping both previously identified QTL on chromosomes 4 and 20 that control raker number. These two QTL affect the early spacing of gill raker buds. Conclusions Collectively, these data demonstrate that parallel developmental genetic features underlie the convergent evolution of gill raker reduction in freshwater sticklebacks, suggesting that even highly polygenic adaptive traits can have a predictable developmental genetic basis.
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Affiliation(s)
- Andrew M Glazer
- Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Phillip A Cleves
- Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Priscilla A Erickson
- Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Angela Y Lam
- Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Craig T Miller
- Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, CA 94720, USA
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249
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Comeault AA, Soria-Carrasco V, Gompert Z, Farkas TE, Buerkle CA, Parchman TL, Nosil P. Genome-Wide Association Mapping of Phenotypic Traits Subject to a Range of Intensities of Natural Selection in Timema cristinae. Am Nat 2014; 183:711-27. [DOI: 10.1086/675497] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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250
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Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre GP, Bank C, Brännström A, Brelsford A, Clarkson CS, Eroukhmanoff F, Feder JL, Fischer MC, Foote AD, Franchini P, Jiggins CD, Jones FC, Lindholm AK, Lucek K, Maan ME, Marques DA, Martin SH, Matthews B, Meier JI, Möst M, Nachman MW, Nonaka E, Rennison DJ, Schwarzer J, Watson ET, Westram AM, Widmer A. Genomics and the origin of species. Nat Rev Genet 2014; 15:176-92. [PMID: 24535286 DOI: 10.1038/nrg3644] [Citation(s) in RCA: 628] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.
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Affiliation(s)
- Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Roger K Butlin
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK; and the Sven Lovén Centre - Tjärnö, University of Gothenburg, S-452 96 Strömstad, Sweden
| | - Irene Keller
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and the Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Catherine E Wagner
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Janette W Boughman
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Department of Zoology; Ecology, Evolutionary Biology and Behavior Program; BEACON Center, Michigan State University, 203 Natural Sciences, East Lansing, Michigan 48824, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844-3051, USA
| | - Catherine L Peichel
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Glenn-Peter Saetre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Claudia Bank
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ake Brännström
- Integrated Science Laboratory and the Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Fabrice Eroukhmanoff
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556-0369 USA
| | - Martin C Fischer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Andrew D Foote
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. Present address: the Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Anna K Lindholm
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Kay Lucek
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Martine E Maan
- Behavioural Biology Group, Centre for Behaviour and Neurosciences, University of Groningen, PO BOX 11103, 9700 CC Groningen, The Netherlands
| | - David A Marques
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Blake Matthews
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Joana I Meier
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Markus Möst
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK; and the Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720-3160, USA
| | - Etsuko Nonaka
- Integrated Science Laboratory and Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden
| | - Diana J Rennison
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Julia Schwarzer
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Eric T Watson
- Department of Biology, The University of Texas at Arlington, 76010-0498 Texas, USA
| | - Anja M Westram
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
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