151
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Marques DA, Taylor JS, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments. PLoS Biol 2017; 15:e2001627. [PMID: 28399148 PMCID: PMC5388470 DOI: 10.1371/journal.pbio.2001627] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/06/2017] [Indexed: 11/18/2022] Open
Abstract
Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known. Here, we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago. We use whole genomes from 16 clearwater and 12 blackwater populations, and a selection experiment, in which stickleback were transplanted from a blackwater lake into an uninhabited clearwater pond and resampled after 19 y to test for selection on cone opsin genes. Patterns of haplotype homozygosity, genetic diversity, site frequency spectra, and allele-frequency change support a selective sweep centered on the adjacent blue- and red-light sensitive opsins SWS2 and LWS. The haplotype under selection carries seven amino acid changes in SWS2, including two changes known to cause a red-shift in light absorption, and is favored in blackwater lakes but disfavored in the clearwater habitat of the transplant population. Remarkably, the same red-shifting amino acid changes occurred after the duplication of SWS2 198 million years ago, in the ancestor of most spiny-rayed fish. Two distantly related fish species, bluefin killifish and black bream, express these old paralogs divergently in black- and clearwater habitats, while sticklebacks lost one paralog. Our study thus shows that convergent adaptation to the same environment can involve the same genetic changes on very different evolutionary time scales by reevolving lost mutations and reusing them repeatedly from standing genetic variation.
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Affiliation(s)
- David A. Marques
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
| | - John S. Taylor
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Felicity C. Jones
- Stanford University School of Medicine, Department of Developmental Biology, Stanford, California, United States of America
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Federica Di Palma
- Earlham Institute and University of East Anglia, Department of Biological Sciences, Norwich, United Kingdom
| | - David M. Kingsley
- Stanford University School of Medicine, Department of Developmental Biology, Stanford, California, United States of America
| | - Thomas E. Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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152
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Gandara ACP, Torres A, Bahia AC, Oliveira PL, Schama R. Evolutionary origin and function of NOX4-art, an arthropod specific NADPH oxidase. BMC Evol Biol 2017; 17:92. [PMID: 28356077 PMCID: PMC5372347 DOI: 10.1186/s12862-017-0940-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/16/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND NADPH oxidases (NOX) are ROS producing enzymes that perform essential roles in cell physiology, including cell signaling and antimicrobial defense. This gene family is present in most eukaryotes, suggesting a common ancestor. To date, only a limited number of phylogenetic studies of metazoan NOXes have been performed, with few arthropod genes. In arthropods, only NOX5 and DUOX genes have been found and a gene called NOXm was found in mosquitoes but its origin and function has not been examined. In this study, we analyzed the evolution of this gene family in arthropods. A thorough search of genomes and transcriptomes was performed enabling us to browse most branches of arthropod phylogeny. RESULTS We have found that the subfamilies NOX5 and DUOX are present in all arthropod groups. We also show that a NOX gene, closely related to NOX4 and previously found only in mosquitoes (NOXm), can also be found in other taxonomic groups, leading us to rename it as NOX4-art. Although the accessory protein p22-phox, essential for NOX1-4 activation, was not found in any of the arthropods studied, NOX4-art of Aedes aegypti encodes an active protein that produces H2O2. Although NOX4-art has been lost in a number of arthropod lineages, it has all the domains and many signature residues and motifs necessary for ROS production and, when silenced, H2O2 production is considerably diminished in A. aegypti cells. CONCLUSIONS Combining all bioinformatic analyses and laboratory work we have reached interesting conclusions regarding arthropod NOX gene family evolution. NOX5 and DUOX are present in all arthropod lineages but it seems that a NOX2-like gene was lost in the ancestral lineage leading to Ecdysozoa. The NOX4-art gene originated from a NOX4-like ancestor and is functional. Although no p22-phox was observed in arthropods, there was no evidence of neo-functionalization and this gene probably produces H2O2 as in other metazoan NOX4 genes. Although functional and present in the genomes of many species, NOX4-art was lost in a number of arthropod lineages.
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Affiliation(s)
- Ana Caroline Paiva Gandara
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - André Torres
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Ana Cristina Bahia
- Instituto de Biofísica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro L Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Rio de Janeiro, Brazil
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil. .,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Rio de Janeiro, Brazil.
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153
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Li Y, Geng X, Bao L, Elaswad A, Huggins KW, Dunham R, Liu Z. A deletion in the Hermansky–Pudlak syndrome 4 (Hps4) gene appears to be responsible for albinism in channel catfish. Mol Genet Genomics 2017; 292:663-670. [DOI: 10.1007/s00438-017-1302-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 02/11/2017] [Indexed: 10/20/2022]
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154
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Cartwright RA, Schwartz RS, Merry AL, Howell MM. The importance of selection in the evolution of blindness in cavefish. BMC Evol Biol 2017; 17:45. [PMID: 28173751 PMCID: PMC5297207 DOI: 10.1186/s12862-017-0876-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/09/2017] [Indexed: 12/04/2022] Open
Abstract
Background Blindness has evolved repeatedly in cave-dwelling organisms, and many hypotheses have been proposed to explain this observation, including both accumulation of neutral loss-of-function mutations and adaptation to darkness. Investigating the loss of sight in cave dwellers presents an opportunity to understand the operation of fundamental evolutionary processes, including drift, selection, mutation, and migration. Results Here we model the evolution of blindness in caves. This model captures the interaction of three forces: (1) selection favoring alleles causing blindness, (2) immigration of sightedness alleles from a surface population, and (3) mutations creating blindness alleles. We investigated the dynamics of this model and determined selection-strength thresholds that result in blindness evolving in caves despite immigration of sightedness alleles from the surface. We estimate that the selection coefficient for blindness would need to be at least 0.005 (and maybe as high as 0.5) for blindness to evolve in the model cave-organism, Astyanax mexicanus. Conclusions Our results indicate that strong selection is required for the evolution of blindness in cave-dwelling organisms, which is consistent with recent work suggesting a high metabolic cost of eye development. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0876-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, AZ, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | | | - Alexandra L Merry
- Barrett, The Honors College Arizona State University, Tempe, 85287, AZ, USA
| | - Megan M Howell
- Barrett, The Honors College Arizona State University, Tempe, 85287, AZ, USA
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155
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Roberts RB, Moore EC, Kocher TD. An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid fish. Mol Ecol 2017; 26:2625-2639. [PMID: 28027432 DOI: 10.1111/mec.13975] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/04/2016] [Accepted: 11/18/2016] [Indexed: 01/01/2023]
Abstract
Despite long-standing interest in the evolution and maintenance of discrete phenotypic polymorphisms, the molecular genetic basis of such polymorphism in the wild is largely unknown. Female sex-associated blotched colour polymorphisms found in cichlids of Lake Malawi, East Africa, represent a highly successful polymorphic phenotype, found and maintained in four genera across the geographic expanse of the lake. Previously, we identified an association with an allelic variant of the paired-box transcription factor gene pax7a and blotched colour morphs in Lake Malawi cichlid fishes. Although a diverse range of blotched phenotypes are present in Lake Malawi cichlid species, they all appeared to result from an allele of pax7a that produces increased levels of transcript. Here, we examine the developmental and genetic basis of variation among blotched morphs. First, we confirm that pax7a-associated blotch morphs result primarily from modulation of melanophore development and survival. From laboratory crosses and natural population studies, we identify at least three alleles of pax7a associated with discrete subtypes of blotched morphs, in addition to the ancestral pax7a allele. Genotypes at pax7a support initial evolution of a novel pax7a allele to produce the blotched class of morphs, followed by subsequent evolution of that pax7a blotched allele to produce additional alleles associated with discrete colour morphs. Variant alleles of pax7a produce different levels of pax7a transcript, correlating with pigmentation phenotype at the cellular level. This naturally selected allelic series should serve as a case study for understanding the molecular genetic control of pax7a expression and the evolution of sex-associated alleles.
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Affiliation(s)
- Reade B Roberts
- Department of Biological Sciences, North Carolina State University, 3510 Thomas Hall, Raleigh, NC, 27695, USA
| | - Emily C Moore
- Keck Center for Behavioral Biology, North Carolina State University, 3510 Thomas Hall, Raleigh, NC, 27695, USA
| | - Thomas D Kocher
- Department of Biology, University of Maryland, 1210 Biology-Psychology Building, College Park, MD, 20742, USA
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156
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Sugahara R, Tanaka S, Jouraku A, Shiotsuki T. Two types of albino mutants in desert and migratory locusts are caused by gene defects in the same signaling pathway. Gene 2017; 608:41-48. [PMID: 28119086 DOI: 10.1016/j.gene.2017.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/28/2016] [Accepted: 01/20/2017] [Indexed: 01/25/2023]
Abstract
Albinism is caused by mutations in the genes involved in melanin production. Albino nymphs of Locusta migratoria and Schistocerca gregaria reared under crowded conditions are uniformly creamy-white in color. However, nothing is known about the molecular mechanisms underlying this phenomenon in locusts. The albino strain of L. migratoria is known to lack the dark-color-inducing neuropeptide corazonin (Crz). In this study, we report that this albino strain has a 10-base-pair deletion in the gene LmCRZ, which encodes Crz. This mutation was found to cause a frame-shift, resulting in a null mutation in Crz. On the other hand, the albino strain of S. gregaria is known to have an intact Crz. This strain was found to possess a single-nucleotide substitution in the middle of the Crz receptor-encoding gene, SgCRZR, which caused a nonsense mutation, resulting in a truncated receptor. Silencing of SgCRZR in wild-type S. gregaria nymphs greatly reduced the area and intensity of their black patterning, suggesting that the functional defect of SgCRZR likely causes the albinism. The expression level of SgCRZR in the albino S. gregaria was comparable to that in the wild type. Unlike the wild type, the albino strain of this locust did not show a phase-dependent shift in a morphometric trait controlled by Crz. From these results, we conclude that the mutations in LmCRZ and SgCRZR are responsible for the albinism in L. migratoria and S. gregaria, respectively, indicating that the two types of albinism are caused by different genetic defects in the same Crz signaling pathway.
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Affiliation(s)
- Ryohei Sugahara
- National Agriculture and Food Research Organization, Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan.
| | - Seiji Tanaka
- National Agriculture and Food Research Organization, Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Akiya Jouraku
- National Agriculture and Food Research Organization, Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Takahiro Shiotsuki
- National Agriculture and Food Research Organization, Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan
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157
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Martin CH, Erickson PA, Miller CT. The genetic architecture of novel trophic specialists: larger effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation. Mol Ecol 2016; 26:624-638. [PMID: 27873369 DOI: 10.1111/mec.13935] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here, we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas, containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion. These specialized niches and trophic traits are unique among over 2000 related species. Measurements of the fitness landscape on San Salvador demonstrate multiple fitness peaks and a larger fitness valley isolating the scale-eater from the putative ancestral intermediate phenotype of the generalist, suggesting that more large-effect QTL should contribute to its unique phenotype. We evaluated this prediction using an F2 intercross between these specialists. We present the first linkage map for pupfishes and detect significant QTL for sex and eight skeletal traits. Large-effect QTL contributed more to enlarged scale-eater jaws than the molluscivore nasal protrusion, consistent with predictions from the adaptive landscape. The microevolutionary genetic architecture of large-effect QTL for oral jaws parallels the exceptional diversification rates of oral jaws within the San Salvador radiation observed over macroevolutionary timescales and may have facilitated exceptional trophic novelty in this system.
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Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina at Chapel Hill, Campus Box 3280, 120 South Rd, Chapel Hill, NC 27599-3280, USA
| | - Priscilla A Erickson
- Molecular and Cell Biology Department, University of California, Berkeley, CA 94720, USA.,Department of Biology, University of Virginia, 229 Gilmer Hall, 485 McCormick Road, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Craig T Miller
- Molecular and Cell Biology Department, University of California, Berkeley, CA 94720, USA
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158
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Cappai MG, Lunesu MGA, Accioni F, Liscia M, Pusceddu M, Burrai L, Nieddu M, Dimauro C, Boatto G, Pinna W. Blood serum retinol levels in Asinara white donkeys reflect albinism-induced metabolic adaptation to photoperiod at Mediterranean latitudes. Ecol Evol 2016; 7:390-398. [PMID: 28070301 PMCID: PMC5216663 DOI: 10.1002/ece3.2613] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/23/2016] [Accepted: 10/21/2016] [Indexed: 12/12/2022] Open
Abstract
Previous works on albinism form of Asinara white donkeys (Equus asinus) identified the mutation leading to the peculiar phenotype spread to all specimens of the breed. Inbreeding naturally occurred under geographic isolation, on Asinara Island, in the Mediterranean Sea. Albino individuals can be more susceptible to develop health problems when exposed to natural sun radiation. Alternative metabolic pathways involved in photoprotection were explored in this trial. Nutrition‐related metabolites are believed to contribute to the conservation of Asinara donkeys, in which melanin, guaranteeing photoprotection, is lacking. Biochemical profiles with particular focus on blood serum β‐carotene and retinol levels were monitored. Identical natural grazing conditions for both Asinara (albino) and Sardo (pigmented) donkey breeds were assured on same natural pastures throughout the experimental period. A comparative metabolic screening, with emphasis on circulating retinol and nutrient‐related metabolites between the two breeds, was carried out over one year. Potential intra‐ and interspecimen fluctuations of metabolites involved in photoprotection were monitored, both during negative and positive photoperiods. Differences (p = .064) between blood serum concentrations of retinol from Asinara versus Sardo breed donkeys (0.630 vs. 0.490 μg/ml, respectively) were found. Retinol levels of blood serum turned out to be similar in the two groups (0.523 vs. 0.493 μg/ml, respectively, p = .051) during the negative photoperiod, but markedly differed during the positive one (0.738 vs. 0.486, respectively, p = .016). Blood serum β‐carotene levels displayed to be constantly around the limit of sensitivity in all animals of both breeds. Variations in blood serum concentrations of retinol in Asinara white donkeys can reflect the need to cope with seasonal exposure to daylight at Mediterranean latitudes, as an alternative to the lack of melanin. These results may suggest that a pulsed mobilization of retinol from body stores occurs to increase circulating levels during positive photoperiod.
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Affiliation(s)
| | | | - Francesca Accioni
- Department of Chemistry and Pharmacy University of Sassari Sassari Italy
| | | | | | - Lucia Burrai
- Department of Chemistry and Pharmacy University of Sassari Sassari Italy
| | - Maria Nieddu
- Department of Chemistry and Pharmacy University of Sassari Sassari Italy
| | - Corrado Dimauro
- Department of Agricultural Sciences University of Sassari Sassari Italy
| | - Gianpiero Boatto
- Department of Chemistry and Pharmacy University of Sassari Sassari Italy
| | - Walter Pinna
- Department of Agricultural Sciences University of Sassari Sassari Italy
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159
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MacPherson A, Nuismer SL. The probability of parallel genetic evolution from standing genetic variation. J Evol Biol 2016; 30:326-337. [DOI: 10.1111/jeb.13006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 10/11/2016] [Accepted: 10/18/2016] [Indexed: 01/15/2023]
Affiliation(s)
- A. MacPherson
- Program of Bioinformatics and Computational Biology University of Idaho Moscow ID USA
- Department of Zoology University of British Columbia Vancouver BC Canada
| | - S. L. Nuismer
- Program of Bioinformatics and Computational Biology University of Idaho Moscow ID USA
- Department of Biological Sciences University of Idaho Moscow ID USA
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160
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Armbruster JW, Niemiller ML, Hart PB. Morphological Evolution of the Cave-, Spring-, and Swampfishes of the Amblyopsidae (Percopsiformes). COPEIA 2016. [DOI: 10.1643/ci-15-339] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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161
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Sumner-Rooney L, Sigwart JD, McAfee J, Smith L, Williams ST. Repeated eye reduction events reveal multiple pathways to degeneration in a family of marine snails. Evolution 2016; 70:2268-2295. [PMID: 27488448 DOI: 10.1111/evo.13022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 07/08/2016] [Accepted: 07/24/2016] [Indexed: 02/02/2023]
Abstract
Eye reduction occurs in many troglobitic, fossorial, and deep-sea animals but there is no clear consensus on its evolutionary mechanism. Given the highly conserved and pleiotropic nature of many genes instrumental to eye development, degeneration might be expected to follow consistent evolutionary trajectories in closely related animals. We tested this in a comparative study of ocular anatomy in solariellid snails from deep and shallow marine habitats using morphological, histological, and tomographic techniques, contextualized phylogenetically. Of 67 species studied, 15 lack retinal pigmentation and at least seven have eyes enveloped by surrounding epithelium. Independent instances of reduction follow numerous different morphological trajectories. We estimate eye loss has evolved at least seven times within Solariellidae, in at least three different ways: characters such as pigmentation loss, obstruction of eye aperture, and "lens" degeneration can occur in any order. In one instance, two morphologically distinct reduction pathways appear within a single genus, Bathymophila. Even amongst closely related animals living at similar depths and presumably with similar selective pressures, the processes leading to eye loss have more evolutionary plasticity than previously realized. Although there is selective pressure driving eye reduction, it is clearly not morphologically or developmentally constrained as has been suggested by previous studies.
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Affiliation(s)
- Lauren Sumner-Rooney
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland. .,Queen's University Marine Laboratory, Queen's University Belfast, Portaferry, Co. Down, BT22 1PF, Northern Ireland.
| | - Julia D Sigwart
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland.,Queen's University Marine Laboratory, Queen's University Belfast, Portaferry, Co. Down, BT22 1PF, Northern Ireland
| | - Jenny McAfee
- Queen's University Marine Laboratory, Queen's University Belfast, Portaferry, Co. Down, BT22 1PF, Northern Ireland
| | - Lisa Smith
- Core Research Facility, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Suzanne T Williams
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
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162
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Fraser CI, McGaughran A, Chuah A, Waters JM. The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages. Mol Ecol 2016; 25:3683-95. [PMID: 27238591 DOI: 10.1111/mec.13708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 04/27/2016] [Accepted: 05/18/2016] [Indexed: 01/03/2023]
Abstract
Genomewide SNP data generated by nontargeted methods such as RAD and GBS are increasingly being used in phylogenetic and phylogeographic analyses. When these methods are used in the absence of a reference genome, however, little is known about the locations and evolution of the SNPs. In using such data to address phylogenetic questions, researchers risk drawing false conclusions, particularly if a representative number of SNPs is not obtained. Here, we empirically test the robustness of phylogenetic inference based on SNP data for closely related lineages. We conducted a genomewide analysis of 75 712 SNPs, generated via GBS, of southern bull-kelp (Durvillaea). Durvillaea chathamensis co-occurs with D. antarctica on Chatham Island, but the two species have previously been found to be so genetically similar that the status of the former has been questioned. Our results show that D. chathamensis, which differs from D. antarctica ecologically as well as morphologically, is indeed a reproductively isolated species. Furthermore, our replicated analyses show that D. chathamensis cannot be reliably distinguished phylogenetically from closely related D. antarctica using subsets (ranging in size from 400 to 10 000 sites) of the 40 912 parsimony-informative SNPs in our data set and that bootstrap values alone can give misleading impressions of the strength of phylogenetic inferences. These results highlight the importance of independently replicating SNP analyses to verify that phylogenetic inferences based on nontargeted SNP data are robust. Our study also demonstrates that modern genomic approaches can be used to identify cases of recent or incipient speciation that traditional approaches (e.g. Sanger sequencing of a few loci) may be unable to detect or resolve.
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Affiliation(s)
- Ceridwen I Fraser
- Fenner School of Environment and Society, Australian National University, Canberra, Act, 2601, Australia
| | - Angela McGaughran
- CSIRO Land and Water, Black Mountain Laboratories, Clunies Ross Street, Canberra, Act, 2601, Australia
- School of BioSciences, University of Melbourne, 30 Flemington Road, Melbourne, Vic, 3010, Australia
| | - Aaron Chuah
- John Curtin School of Medical Research, Australian National University, Canberra, Act, 2601, Australia
| | - Jonathan M Waters
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
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163
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Martí-Solans J, Belyaeva OV, Torres-Aguila NP, Kedishvili NY, Albalat R, Cañestro C. Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate. Mol Biol Evol 2016; 33:2401-16. [PMID: 27406791 DOI: 10.1093/molbev/msw118] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The bloom of genomics is revealing gene loss as a pervasive evolutionary force generating genetic diversity that shapes the evolution of species. Outside bacteria and yeast, however, the understanding of the process of gene loss remains elusive, especially in the evolution of animal species. Here, using the dismantling of the retinoic acid metabolic gene network (RA-MGN) in the chordate Oikopleura dioica as a case study, we combine approaches of comparative genomics, phylogenetics, biochemistry, and developmental biology to investigate the mutational robustness associated to biased patterns of gene loss. We demonstrate the absence of alternative pathways for RA-synthesis in O. dioica, which suggests that gene losses of RA-MGN were not compensated by mutational robustness, but occurred in a scenario of regressive evolution. In addition, the lack of drastic phenotypic changes associated to the loss of RA-signaling provides an example of the inverse paradox of Evo-Devo. This work illustrates how the identification of patterns of gene coelimination-in our case five losses (Rdh10, Rdh16, Bco1, Aldh1a, and Cyp26)-is a useful strategy to recognize gene network modules associated to distinct functions. Our work also illustrates how the identification of survival genes helps to recognize neofunctionalization events and ancestral functions. Thus, the survival and extensive duplication of Cco and RdhE2 in O. dioica correlated with the acquisition of complex compartmentalization of expression domains in the digestive system and a process of enzymatic neofunctionalization of the Cco, while the surviving Aldh8 could be related to its ancestral housekeeping role against toxic aldehydes.
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Affiliation(s)
- Josep Martí-Solans
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama-Birmingham
| | - Nuria P Torres-Aguila
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama-Birmingham
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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164
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Fisher KJ, Lang GI. Experimental evolution in fungi: An untapped resource. Fungal Genet Biol 2016; 94:88-94. [PMID: 27375178 DOI: 10.1016/j.fgb.2016.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 10/21/2022]
Abstract
Historically, evolutionary biology has been considered an observational science. Examining populations and inferring evolutionary histories mold evolutionary theories. In contrast, laboratory evolution experiments make use of the amenability of traditional model organisms to study fundamental processes underlying evolution in real time in simple, but well-controlled, environments. With advances in high-throughput biology and next generation sequencing, it is now possible to propagate hundreds of parallel populations over thousands of generations and to quantify precisely the frequencies of various mutations over time. Experimental evolution combines the ability to simultaneously monitor replicate populations with the power to vary individual parameters to test specific evolutionary hypotheses, something that is impractical or infeasible in natural populations. Many labs are now conducting laboratory evolution experiments in nearly all model systems including viruses, bacteria, yeast, nematodes, and fruit flies. Among these systems, fungi occupy a unique niche: with a short generation time, small compact genomes, and sexual cycles, fungi are a particularly valuable and largely untapped resource for propelling future growth in the field of experimental evolution. Here, we describe the current state of fungal experimental evolution and why fungi are uniquely positioned to answer many of the outstanding questions in the field. We also review which fungal species are most well suited for experimental evolution.
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Affiliation(s)
- Kaitlin J Fisher
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.
| | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.
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165
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Gross JB, Powers AK, Davis EM, Kaplan SA. A pleiotropic interaction between vision loss and hypermelanism in Astyanax mexicanus cave x surface hybrids. BMC Evol Biol 2016; 16:145. [PMID: 27363593 PMCID: PMC4929771 DOI: 10.1186/s12862-016-0716-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/28/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Cave-dwelling animals evolve various traits as a consequence of life in darkness. Constructive traits (e.g., enhanced non-visual sensory systems) presumably arise under strong selective pressures. The mechanism(s) driving regression of features, however, are not well understood. Quantitative trait locus (QTL) analyses in Astyanax mexicanus Pachón cave x surface hybrids revealed phenotypic effects associated with vision and pigmentation loss. Vision QTL were uniformly associated with reductions in the homozygous cave condition, however pigmentation QTL demonstrated mixed phenotypic effects. This implied pigmentation might be lost through both selective and neutral forces. Alternatively, in this report, we examined if a pleiotropic interaction may exist between vision and pigmentation since vision loss has been shown to result in darker skin in other fish and amphibian model systems. RESULTS We discovered that certain members of Pachón x surface pedigrees are significantly darker than surface-dwelling fish. All of these "hypermelanic" individuals demonstrated severe visual system malformations suggesting they may be blind. A vision-mediated behavioral assay revealed that these fish, in stark contrast to surface fish, behaved the same as blind cavefish. Further, hypermelanic melanophores were larger and more dendritic in morphology compared to surface fish melanophores. However, hypermelanic melanophores responded normally to melanin-concentrating hormone suggesting darkening stemmed from vision loss, rather than a defect in pigment cell function. Finally, a number of genomic regions were coordinately associated with both reduced vision and increased pigmentation. CONCLUSIONS This work suggests hypermelanism in hybrid Astyanax results from blindness. This finding provides an alternative explanation for phenotypic effect studies of pigmentation QTL as stemming (at least in part) from environmental, rather than exclusively genetic, interactions between two regressive phenotypes. Further, this analysis reveals persistence of background adaptation in Astyanax. As the eye was lost in cave-dwelling forms, enhanced pigmentation resulted. Given the extreme cave environment, which is often devoid of nutrition, enhanced pigmentation may impose an energetic cost. Such an energetic cost would be selected against, as a means of energy conservation. Thus, the pleiotropic interaction between vision loss and pigmentation may reveal an additional selective pressure favoring the loss of pigmentation in cave-dwelling animals.
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Affiliation(s)
- Joshua B. Gross
- />Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45223 USA
- />Department of Biological Sciences, University of Cincinnati, Rieveschl Hall Room 711B, 312 Clifton Court, Cincinnati, Ohio 45221 USA
| | - Amanda K. Powers
- />Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45223 USA
| | - Erin M. Davis
- />Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45223 USA
| | - Shane A. Kaplan
- />Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45223 USA
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166
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Kowalko JE, Ma L, Jeffery WR. Genome Editing in Astyanax mexicanus Using Transcription Activator-like Effector Nucleases (TALENs). J Vis Exp 2016. [PMID: 27404092 DOI: 10.3791/54113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Identifying alleles of genes underlying evolutionary change is essential to understanding how and why evolution occurs. Towards this end, much recent work has focused on identifying candidate genes for the evolution of traits in a variety of species. However, until recently it has been challenging to functionally validate interesting candidate genes. Recently developed tools for genetic engineering make it possible to manipulate specific genes in a wide range of organisms. Application of this technology in evolutionarily relevant organisms will allow for unprecedented insight into the role of candidate genes in evolution. Astyanax mexicanus (A. mexicanus) is a species of fish with both surface-dwelling and cave-dwelling forms. Multiple independent lines of cave-dwelling forms have evolved from ancestral surface fish, which are interfertile with one another and with surface fish, allowing elucidation of the genetic basis of cave traits. A. mexicanus has been used for a number of evolutionary studies, including linkage analysis to identify candidate genes responsible for a number of traits. Thus, A. mexicanus is an ideal system for the application of genome editing to test the role of candidate genes. Here we report a method for using transcription activator-like effector nucleases (TALENs) to mutate genes in surface A. mexicanus. Genome editing using TALENs in A. mexicanus has been utilized to generate mutations in pigmentation genes. This technique can also be utilized to evaluate the role of candidate genes for a number of other traits that have evolved in cave forms of A. mexicanus.
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Affiliation(s)
| | - Li Ma
- Department of Biological Sciences, University of Cincinnati
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167
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Casane D, Rétaux S. Evolutionary Genetics of the Cavefish Astyanax mexicanus. ADVANCES IN GENETICS 2016; 95:117-59. [PMID: 27503356 DOI: 10.1016/bs.adgen.2016.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Blind and depigmented fish belonging to the species Astyanax mexicanus are outstanding models for evolutionary genetics. During their evolution in the darkness of caves, they have undergone a number of changes at the morphological, physiological, and behavioral levels, but they can still breed with their river-dwelling conspecifics. The fertile hybrids between these two morphotypes allow forward genetic approaches, from the search of quantitative trait loci to the identification of the mutations underlying the evolution of troglomorphism. We review here the past 30years of evolutionary genetics on Astyanax: from the first crosses and the discovery of convergent evolution of different Astyanax cavefish populations to the most recent evolutionary transcriptomics and genomics studies that have provided researchers with potential candidate genes to be tested using functional genetic approaches. Although significant progress has been made and some genes have been identified, cavefish have not yet fully revealed the secret of their adaptation to the absence of light. In particular, the genetic determinism of their loss of eyes seems complex and still puzzles researchers. We also discuss future research directions, including searches for the origin of cave alleles and searches for selection genome-wide, as well as the necessary but missing information on the timing of cave colonization by surface fish.
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Affiliation(s)
- D Casane
- Laboratory EGCE, CNRS and University of Paris-Sud, Gif-sur-Yvette, France; Paris Diderot University, Sorbonne Paris Cité, France
| | - S Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Sud, Gif-sur-Yvette, France
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168
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Abstract
The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
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169
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Husby A, Kawakami T, Rönnegård L, Smeds L, Ellegren H, Qvarnström A. Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait. Proc Biol Sci 2016; 282:20150156. [PMID: 25833857 PMCID: PMC4426624 DOI: 10.1098/rspb.2015.0156] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Understanding the genetic basis of traits involved in adaptation is a major
challenge in evolutionary biology but remains poorly understood. Here, we use
genome-wide association mapping using a custom 50 k single nucleotide
polymorphism (SNP) array in a natural population of collared flycatchers to
examine the genetic basis of clutch size, an important life-history trait in
many animal species. We found evidence for an association on chromosome 18 where
one SNP significant at the genome-wide level explained 3.9% of the
phenotypic variance. We also detected two suggestive quantitative trait loci
(QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were
generally weak and not significant, although there was some indication of a
sex-by-genotype interaction for lifetime reproductive success at the suggestive
QTL on chromosome 26. This implies that sexual antagonism may play a role in
maintaining genetic variation at this QTL. Our findings provide candidate
regions for a classic avian life-history trait that will be useful for future
studies examining the molecular and cellular function of, as well as
evolutionary mechanisms operating at, these loci.
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Affiliation(s)
- Arild Husby
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway Department of Biosciences, University of Helsinki, PO Box 65, Helsinki 00014, Finland
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Lars Rönnegård
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
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170
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Erickson PA, Glazer AM, Killingbeck EE, Agoglia RM, Baek J, Carsanaro SM, Lee AM, Cleves PA, Schluter D, Miller CT. Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks. Evolution 2016; 70:887-902. [PMID: 26947264 DOI: 10.1111/evo.12897] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 02/10/2016] [Accepted: 02/23/2016] [Indexed: 12/13/2022]
Abstract
The extent to which convergent adaptation to similar ecological niches occurs by a predictable genetic basis remains a fundamental question in biology. Threespine stickleback fish have undergone an adaptive radiation in which ancestral oceanic populations repeatedly colonized and adapted to freshwater habitats. In multiple lakes in British Columbia, two different freshwater ecotypes have evolved: a deep-bodied benthic form adapted to forage near the lake substrate, and a narrow-bodied limnetic form adapted to forage in open water. Here, we use genome-wide linkage mapping in marine × benthic F2 genetic crosses to test the extent of shared genomic regions underlying benthic adaptation in three benthic populations. We identify at least 100 Quantitative Trait Loci (QTL) harboring genes influencing skeletal morphology. The majority of QTL (57%) are unique to one cross. However, four genomic regions affecting eight craniofacial and armor phenotypes are found in all three benthic populations. We find that QTL are clustered in the genome and overlapping QTL regions are enriched for genomic signatures of natural selection. These findings suggest that benthic adaptation has occurred via both parallel and nonparallel genetic changes.
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Affiliation(s)
- Priscilla A Erickson
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Andrew M Glazer
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Emily E Killingbeck
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Rachel M Agoglia
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Jiyeon Baek
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Sara M Carsanaro
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Anthony M Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Phillip A Cleves
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Dolph Schluter
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720.
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171
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Wilkens H. Genetics and hybridization in surface and caveAstyanax(Teleostei): a comparison of regressive and constructive traits. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Horst Wilkens
- University of Hamburg; Centrum für Naturkunde - CeNak; Zoological Museum; Martin-Luther-King-Platz 3 20146 Hamburg Germany
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172
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Huang Y, Chain FJJ, Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E, Reusch TBH, Milinski M, Feulner PGD. Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. Mol Ecol 2016; 25:943-58. [PMID: 26749022 PMCID: PMC4790908 DOI: 10.1111/mec.13520] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 11/18/2015] [Accepted: 12/10/2015] [Indexed: 12/16/2022]
Abstract
The observation of habitat-specific phenotypes suggests the action of natural selection. The three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats across the northern hemisphere since the last glaciation, while giving rise to recurring phenotypes associated with specific habitats. Parapatric lake and river populations of sticklebacks harbour distinct parasite communities, a factor proposed to contribute to adaptive differentiation between these ecotypes. However, little is known about the transcriptional response to the distinct parasite pressure of those fish in a natural setting. Here, we sampled wild-caught sticklebacks across four geographical locations from lake and river habitats differing in their parasite load. We compared gene expression profiles between lake and river populations using 77 whole-transcriptome libraries from two immune-relevant tissues, the head kidney and the spleen. Differential expression analyses revealed 139 genes with habitat-specific expression patterns across the sampled population pairs. Among the 139 differentially expressed genes, eight are annotated with an immune function and 42 have been identified as differentially expressed in previous experimental studies in which fish have been immune challenged. Together, these findings reinforce the hypothesis that parasites contribute to adaptation of sticklebacks in lake and river habitats.
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Affiliation(s)
- Yun Huang
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Frédéric J J Chain
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Department of Biology, McGill University, Montreal, QC, Canada, H3A 1B1
| | - Mahesh Panchal
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Bioinformatics Infrastructures for Life Sciences (BILS), Uppsala Biomedicinska Centrum (BMC), Husargatan 3, 751 23, Uppsala, Sweden.,Institute of Medical Biochemistry and Microbiology, Uppsala Biomedicinska Centrum (BMC), Husargatan 3, 751 23, Uppsala, Sweden
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, London, UK
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Irene E Samonte
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Monika Stoll
- Institute of Human Genetics, Genetic Epidemiology, Westfälische Wilhelms University, 48149, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfälische Wilhelms University, 48149, Münster, Germany
| | - Thorsten B H Reusch
- Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105, Kiel, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Philine G D Feulner
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047, Kastanienbaum, Switzerland
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173
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Effect of spatial constraints on Hardy-Weinberg equilibrium. Sci Rep 2016; 6:19297. [PMID: 26771073 PMCID: PMC4725899 DOI: 10.1038/srep19297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 12/07/2015] [Indexed: 11/18/2022] Open
Abstract
Panmixia is a key issue in maintaining genetic diversity, which facilitates evolutionary potential during environmental changes. Additionally, conservation biologists suggest the importance of avoiding small or subdivided populations, which are prone to losing genetic diversity. In this paper, computer simulations were performed to the genetic drift of neutral alleles in random mating populations with or without spatial constraints by randomly choosing a mate among the closest neighbours. The results demonstrated that the number of generations required for the neutral allele to become homozygous (Th) varied proportionally to the population size and also strongly correlated with spatial constraints. The average Th for populations of the same size with spatial constraints was approximately one-and-a-half times longer than without constraints. With spatial constraints, homozygous population clusters formed, which reduced local diversity but preserved global diversity. Therefore, panmixia might be harmful in preserving the genetic diversity of an entire population. The results also suggested that the gene flow or gene exchange among the subdivided populations must be carefully processed to restrict diseases transmission or death during transportation and to monitor the genetic diversity. The application of this concept to similar systems, such as information transfer among peers, is also discussed.
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174
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Jeffery WR. The Comparative Organismal Approach in Evolutionary Developmental Biology: Insights from Ascidians and Cavefish. Curr Top Dev Biol 2016; 116:489-500. [PMID: 26970636 PMCID: PMC6143178 DOI: 10.1016/bs.ctdb.2015.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Important contributions to evolutionary developmental biology have been made using the comparative organismal approach. As examples, I describe insights obtained from studies of Molgula ascidians and Astyanax cavefish.
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Affiliation(s)
- William R Jeffery
- Department of Biology, University of Maryland, College Park, Maryland, USA.
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175
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Yang J, Chen X, Bai J, Fang D, Qiu Y, Jiang W, Yuan H, Bian C, Lu J, He S, Pan X, Zhang Y, Wang X, You X, Wang Y, Sun Y, Mao D, Liu Y, Fan G, Zhang H, Chen X, Zhang X, Zheng L, Wang J, Cheng L, Chen J, Ruan Z, Li J, Yu H, Peng C, Ma X, Xu J, He Y, Xu Z, Xu P, Wang J, Yang H, Wang J, Whitten T, Xu X, Shi Q. The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biol 2016; 14:1. [PMID: 26728391 PMCID: PMC4698820 DOI: 10.1186/s12915-015-0223-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/17/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.
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Affiliation(s)
- Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | | | - Jie Bai
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,Fauna & Flora International, Cambridge, CB1 2JD, UK.
| | - Dongming Fang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Ying Qiu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,China National Genebank, Shenzhen, 518083, China.
| | - Wansheng Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Hui Yuan
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Chao Bian
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Jiang Lu
- BGI-Shenzhen, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shiyang He
- BGI-Shenzhen, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Yaolei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xinxin You
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | | | - Ying Sun
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National Genebank, Shenzhen, 518083, China.
| | | | - Yong Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | | | - He Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiaoyong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xinhui Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Lanping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | | | - Le Cheng
- China National Genebank, Shenzhen, 518083, China. .,BGI-Yunnan, Kunming, 650106, China.
| | - Jieming Chen
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Zhiqiang Ruan
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Jia Li
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hui Yu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chao Peng
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Xingyu Ma
- Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
| | - Junmin Xu
- Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
| | - You He
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201204, China.
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210029, China.
| | - Pao Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China. .,James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| | - Tony Whitten
- Fauna & Flora International, Cambridge, CB1 2JD, UK.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Qiong Shi
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
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Gross JB, Stahl BA, Powers AK, Carlson BM. Natural bone fragmentation in the blind cave-dwelling fish, Astyanax mexicanus: candidate gene identification through integrative comparative genomics. Evol Dev 2016; 18:7-18. [PMID: 26153732 PMCID: PMC5226847 DOI: 10.1111/ede.12131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Animals that colonize dark and nutrient-poor subterranean environments evolve numerous extreme phenotypes. These include dramatic changes to the craniofacial complex, many of which are under genetic control. These phenotypes can demonstrate asymmetric genetic signals wherein a QTL is detected on one side of the face but not the other. The causative gene(s) underlying QTL are difficult to identify with limited genomic resources. We approached this task by searching for candidate genes mediating fragmentation of the third suborbital bone (SO3) directly inferior to the orbit of the eye. We integrated positional genomic information using emerging Astyanax resources, and linked these intervals to homologous (syntenic) regions of the Danio rerio genome. We identified a discrete, approximately 6 Mb, conserved region wherein the gene causing SO3 fragmentation likely resides. We interrogated this interval for genes demonstrating significant differential expression using mRNA-seq analysis of cave and surface morphs across life history. We then assessed genes with known roles in craniofacial evolution and development based on GO term annotation. Finally, we screened coding sequence alterations in this region, identifying two key genes: transforming growth factor β3 (tgfb3) and bone morphogenetic protein 4 (bmp4). Of these candidates, tgfb3 is most promising as it demonstrates significant differential expression across multiple stages of development, maps close (<1 Mb) to the fragmentation critical locus, and is implicated in a variety of other animal systems (including humans) in non-syndromic clefting and malformations of the cranial sutures. Both abnormalities are analogous to the failure-to-fuse phenotype that we observe in SO3 fragmentation. This integrative approach will enable discovery of the causative genetic lesions leading to complex craniofacial features analogous to human craniofacial disorders. This work underscores the value of cave-dwelling fish as a powerful evolutionary model of craniofacial disease, and demonstrates the power of integrative system-level studies for informing the genetic basis of craniofacial aberrations in nature.
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Affiliation(s)
- Joshua B. Gross
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
| | - Bethany A. Stahl
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
| | - Amanda K. Powers
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
| | - Brian M. Carlson
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
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Complex Evolutionary and Genetic Patterns Characterize the Loss of Scleral Ossification in the Blind Cavefish Astyanax mexicanus. PLoS One 2015; 10:e0142208. [PMID: 26649887 PMCID: PMC4674125 DOI: 10.1371/journal.pone.0142208] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/19/2015] [Indexed: 12/21/2022] Open
Abstract
The sclera is the tough outer covering of the eye that provides structural support and helps maintain intraocular pressure. In some fishes, reptiles, and birds, the sclera is reinforced with an additional ring of hyaline cartilage or bone that forms from scleral ossicles. Currently, the evolutionary and genetic basis of scleral ossification is poorly understood, especially in teleost fishes. We assessed scleral ossification among several groups of the Mexican tetra (Astyanax mexicanus), which exhibit both an eyed and eyeless morph. Although eyed Astyanax surface fish have bony sclera similar to other teleosts, the ossicles of blind Astyanax cavefish generally do not form. We first sampled cavefish from multiple independent populations and used ancestral character state reconstructions to determine how many times scleral ossification has been lost. We then confirmed these results by assessing complementation of scleral ossification among the F1 hybrid progeny of two cavefish populations. Finally, we quantified the number of scleral ossicles present among the F2 hybrid progeny of a cross between surface fish and cavefish, and used this information to identify quantitative trait loci (QTL) responsible for this trait. Our results indicate that the loss of scleral ossification is common-but not ubiquitous-among Astyanax cavefish, and that this trait has been convergently lost at least three times. The presence of wild-type, ossified sclera among the F1 hybrid progeny of a cross between different cavefish populations confirms the convergent evolution of this trait. However, a strongly skewed distribution of scleral ossicles found among surface fish x cavefish F2 hybrids suggests that scleral ossification is a threshold trait with a complex genetic basis. Quantitative genetic mapping identified a single QTL for scleral ossification on Astyanax linkage group 1. We estimate that the threshold for this trait is likely determined by at least three genetic factors which may control the severity and onset of lens degeneration in cavefishes. We conclude that complex evolutionary and genetic patterns underlie the loss of scleral ossification in Astyanax cavefish.
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Abstract
Should the tape of life be replayed, would it produce similar living beings? A classical answer has long been ‘no’, but accumulating data are now challenging this view. Repeatability in experimental evolution, in phenotypic evolution of diverse species and in the genes underlying phenotypic evolution indicates that despite unpredictability at the level of basic evolutionary processes (such as apparition of mutations), a certain kind of predictability can emerge at higher levels over long time periods. For instance, a survey of the alleles described in the literature that cause non-deleterious phenotypic differences among animals, plants and yeasts indicates that similar phenotypes have often evolved in distinct taxa through independent mutations in the same genes. Does this mean that the range of possibilities for evolution is limited? Does this mean that we can predict the outcomes of a replayed tape of life? Imagining other possible paths for evolution runs into four important issues: (i) resolving the influence of contingency, (ii) imagining living organisms that are different from the ones we know, (iii) finding the relevant concepts for predicting evolution, and (iv) estimating the probability of occurrence for complex evolutionary events that occurred only once during the evolution of life on earth.
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Affiliation(s)
- Virginie Orgogozo
- CNRS, UMR7592, Institut Jacques Monod , Univ Paris Diderot, Sorbonne Paris Cité , 15 rue Hélène Brion, 75013 Paris , France
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180
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Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene. Sci Rep 2015; 5:17118. [PMID: 26597053 PMCID: PMC4657000 DOI: 10.1038/srep17118] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/26/2015] [Indexed: 12/21/2022] Open
Abstract
The corn snake (Pantherophis guttatus) is a new model species particularly appropriate for investigating the processes generating colours in reptiles because numerous colour and pattern mutants have been isolated in the last five decades. Using our captive-bred colony of corn snakes, transcriptomic and genomic next-generation sequencing, exome assembly, and genotyping of SNPs in multiple families, we delimit the genomic interval bearing the causal mutation of amelanism, the oldest colour variant observed in that species. Proceeding with sequencing the candidate gene OCA2 in the uncovered genomic interval, we identify that the insertion of an LTR-retrotransposon in its 11th intron results in a considerable truncation of the p protein and likely constitutes the causal mutation of amelanism in corn snakes. As amelanistic snakes exhibit white, instead of black, borders around an otherwise normal pattern of dorsal orange saddles and lateral blotches, our results indicate that melanocytes lacking melanin are able to participate to the normal patterning of other colours in the skin. In combination with research in the zebrafish, this work opens the perspective of using corn snake colour and pattern variants to investigate the generative processes of skin colour patterning shared among major vertebrate lineages.
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181
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Utzeri VJ, Bertolini F, Ribani A, Schiavo G, Dall'Olio S, Fontanesi L. The albinism of the feral Asinara white donkeys (Equus asinus
) is determined by a missense mutation in a highly conserved position of the tyrosinase (TYR
) gene deduced protein. Anim Genet 2015; 47:120-4. [DOI: 10.1111/age.12386] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2015] [Indexed: 02/02/2023]
Affiliation(s)
- V. J. Utzeri
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - F. Bertolini
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - A. Ribani
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - G. Schiavo
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - S. Dall'Olio
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - L. Fontanesi
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
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182
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Alterations in Mc1r gene expression are associated with regressive pigmentation in Astyanax cavefish. Dev Genes Evol 2015; 225:367-75. [PMID: 26462499 DOI: 10.1007/s00427-015-0517-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/08/2015] [Indexed: 12/16/2022]
Abstract
Diverse changes in coloration across distant taxa are mediated through alterations in certain highly conserved pigmentation genes. Among these genes, Mc1r is a frequent target for mutation, and many documented alterations involve coding sequence changes. We investigated whether regulatory mutations in Mc1r may also contribute to pigmentation loss in the blind Mexican cavefish, Astyanax mexicanus. This species comprises multiple independent cave populations that have evolved reduced (or absent) melanic pigmentation as a consequence of living in darkness for millions of generations. Among the most salient cave-associated traits, complete absence (albinism) or reduced levels of pigmentation (brown) have long been the focus of degenerative pigmentation research in Astyanax. These two Mendelian traits have been linked to specific coding mutations in Oca2 (albinism) and Mc1r (brown). However, four of the seven caves harboring the brown phenotype exhibit unaffected coding sequences compared to surface fish. Thus, diverse genetic changes involving the same genes likely impact reduced pigmentation among cavefish populations. Using both sequence and expression analyses, we show that certain cave-dwelling populations harboring the brown mutation have substantial alterations to the putative Mc1r cis-regulatory region. Several of these sequence mutations in the Mc1r 5' region were present across multiple, independent cave populations. This study suggests that pigmentation reduction in Astyanax cavefish evolves through a combination of both coding and cis-regulatory mutations. Moreover, this study represents one of the first attempts to identify regulatory alterations linked to regressive changes in cave-dwelling populations of A. mexicanus.
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183
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Favé MJ, Johnson RA, Cover S, Handschuh S, Metscher BD, Müller GB, Gopalan S, Abouheif E. Past climate change on Sky Islands drives novelty in a core developmental gene network and its phenotype. BMC Evol Biol 2015; 15:183. [PMID: 26338531 PMCID: PMC4560157 DOI: 10.1186/s12862-015-0448-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/06/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND A fundamental and enduring problem in evolutionary biology is to understand how populations differentiate in the wild, yet little is known about what role organismal development plays in this process. Organismal development integrates environmental inputs with the action of gene regulatory networks to generate the phenotype. Core developmental gene networks have been highly conserved for millions of years across all animals, and therefore, organismal development may bias variation available for selection to work on. Biased variation may facilitate repeatable phenotypic responses when exposed to similar environmental inputs and ecological changes. To gain a more complete understanding of population differentiation in the wild, we integrated evolutionary developmental biology with population genetics, morphology, paleoecology and ecology. This integration was made possible by studying how populations of the ant species Monomorium emersoni respond to climatic and ecological changes across five 'Sky Islands' in Arizona, which are mountain ranges separated by vast 'seas' of desert. Sky Islands represent a replicated natural experiment allowing us to determine how repeatable is the response of M. emersoni populations to climate and ecological changes at the phenotypic, developmental, and gene network levels. RESULTS We show that a core developmental gene network and its phenotype has kept pace with ecological and climate change on each Sky Island over the last ~90,000 years before present (BP). This response has produced two types of evolutionary change within an ant species: one type is unpredictable and contingent on the pattern of isolation of Sky lsland populations by climate warming, resulting in slight changes in gene expression, organ growth, and morphology. The other type is predictable and deterministic, resulting in the repeated evolution of a novel wingless queen phenotype and its underlying gene network in response to habitat changes induced by climate warming. CONCLUSION Our findings reveal dynamics of developmental gene network evolution in wild populations. This holds important implications: (1) for understanding how phenotypic novelty is generated in the wild; (2) for providing a possible bridge between micro- and macroevolution; and (3) for understanding how development mediates the response of organisms to past, and potentially, future climate change.
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Affiliation(s)
- Marie-Julie Favé
- Department of Biology, McGill University, 1205 Dr. Penfield avenue, Montréal, Québec, Canada.
| | - Robert A Johnson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA.
| | - Stefan Cover
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Stephan Handschuh
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria.
| | - Brian D Metscher
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria.
| | - Gerd B Müller
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria.
| | - Shyamalika Gopalan
- Department of Biology, McGill University, 1205 Dr. Penfield avenue, Montréal, Québec, Canada.
| | - Ehab Abouheif
- Department of Biology, McGill University, 1205 Dr. Penfield avenue, Montréal, Québec, Canada.
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184
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Gross JB, Meyer B, Perkins M. The rise of Astyanax cavefish. Dev Dyn 2015; 244:1031-1038. [PMID: 25601346 PMCID: PMC4508244 DOI: 10.1002/dvdy.24253] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/08/2015] [Accepted: 01/10/2015] [Indexed: 01/01/2023] Open
Abstract
Numerous animals have invaded subterranean caverns and evolved remarkably similar features. These features include loss of vision and pigmentation, and gains in nonvisual sensation. This broad convergence echoes smaller-scale convergence, in which members of the same species repeatedly evolve the same cave-associated phenotypes. The blind Mexican tetra of the Sierra de El Abra region of northeastern Mexico has a complex origin, having recurrently colonized subterranean environments through numerous invasions of surface-dwelling fish. These colonizations likely occurred ∼1-5 MYa. Despite evidence of historical and contemporary gene flow between cave and surface forms, the cave-associated phenotype appears to remain quite stable in nature. This model system has provided insight to the mechanisms of phenotypic regression, the genetic basis for constructive trait evolution, and the origin of behavioral novelties. Here, we document the rise of this model system from its discovery by a Mexican surveyor in 1936, to a powerful system for cave biology and contemporary genetic research. The recently sequenced genome provides exciting opportunities for future research, and will help resolve several long-standing biological problems. Developmental Dynamics 244:1031-1038, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Joshua B Gross
- University of Cincinnati, Department of Biological Sciences, Cincinnati Ohio
| | - Bradley Meyer
- University of Cincinnati, Department of Biological Sciences, Cincinnati Ohio
| | - Molly Perkins
- University of Cincinnati, Department of Biological Sciences, Cincinnati Ohio
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185
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Cardoso JCR, Félix RC, Martins RST, Trindade M, Fonseca VG, Fuentes J, Power DM. PACAP system evolution and its role in melanophore function in teleost fish skin. Mol Cell Endocrinol 2015; 411:130-45. [PMID: 25933704 DOI: 10.1016/j.mce.2015.04.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 01/12/2023]
Abstract
Pituitary adenylate cyclase-activating polypeptide (PACAP) administered to tilapia melanophores ex-vivo causes significant pigment aggregation and this is a newly identified function for this peptide in fish. The G-protein coupled receptors (GPCRs), adcyap1r1a (encoding Pac1a) and vipr2a (encoding Vpac2a), are the only receptors in melanophores with appreciable levels of expression and are significantly (p < 0.05) down-regulated in the absence of light. Vpac2a is activated exclusively by peptide histidine isoleucine (PHI), which suggests that Pac1a mediates the melanin aggregating effect of PACAP on melanophores. Paradoxically activation of Pac1a with PACAP caused a rise in cAMP, which in fish melanophores is associated with melanin dispersion. We hypothesise that the duplicate adcyap1ra and vipr2a genes in teleosts have acquired a specific role in skin and that the melanin aggregating effect of PACAP results from the interaction of Pac1a with Ramp that attenuates cAMP-dependent PKA activity and favours the Ca(2+)/Calmodulin dependent pathway.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Rute C Félix
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Rute S T Martins
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Marlene Trindade
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Vera G Fonseca
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Juan Fuentes
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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186
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Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, Tomaso AWD, Gilbert SF, Hall B, Love AC, Lyons DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evol Dev 2015; 17:198-219. [PMID: 25963198 DOI: 10.1111/ede.12125] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.
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Affiliation(s)
- Armin P Moczek
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - Karen E Sears
- School of Integrative Biology and Institute for Genomic Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London, E1 4NS, UK
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Pamela Diggle
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Ian Dworkin
- Department of Biology, McMaster University, 1280 Main St. West Hamilton, Ontario, L8S 4K1, Canada
| | - Cristina Ledon-Rettig
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, 412 Life Sciences Building, Stony Brook, NY, 11794-5215, USA
| | - Siegfried Roth
- University of Cologne, Institute of Developmental Biology, Biocenter, Zülpicher Straße 47b, D-50674, Cologne, Germany
| | - Ehab Abouheif
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montréal Québec, H3A 1B1, Canada
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, no. 101, 05508-090, São Paulo, Brazil
| | - Chi-Hua Chiu
- Department of Biological Sciences, Kent State University, OH, USA
| | - C Sarah Cohen
- Biology Department, Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | | | - Scott F Gilbert
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA and Biotechnology Institute, University of Helsinki, 00014, Helsinki, Finland
| | - Brian Hall
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, CA, B3H 4R2, USA
| | - Alan C Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, USA
| | - Deirdre C Lyons
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Thomas J Sanger
- Department of Molecular Genetics and Microbiology, University of Florida, P.O. Box 103610, Gainesville, FL, 32610, USA
| | - Joel Smith
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Chelsea Specht
- Plant and Microbial Biology, Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, Scotland, UK
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, BioLabs 4103, Cambridge, MA, 02138, USA
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187
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Melanocortin 4 receptor mutations contribute to the adaptation of cavefish to nutrient-poor conditions. Proc Natl Acad Sci U S A 2015; 112:9668-73. [PMID: 26170297 DOI: 10.1073/pnas.1510802112] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite recent advances in the understanding of morphological evolution, the genetic underpinnings of behavioral and physiological evolution remain largely unknown. Here, we study the metabolic changes that evolved in independently derived populations of the Mexican cavefish, Astyanax mexicanus. A hallmark of cave environments is scarcity of food. Cavefish populations rely almost entirely on sporadic food input from outside of the caves. To survive under these conditions, cavefish have evolved a range of adaptations, including starvation resistance and binge eating when food becomes available. The use of these adaptive strategies differs among independently derived cave populations. Although all cavefish populations tested lose weight more slowly than their surface conspecifics during restricted rations, only a subset of cavefish populations consume more food than their surface counterparts. A candidate gene-based screen led to the identification of coding mutations in conserved residues of the melanocortin 4 receptor (MC4R) gene, contributing to the insatiable appetite found in some populations of cavefish. Intriguingly, one of the mutated residues has been shown to be linked to obesity in humans. We demonstrate that the allele results in both reduced maximal response and reduced basal activity of the receptor in vitro. We further validate in vivo that the mutated allele contributes to elevated appetite, growth, and starvation resistance. The allele appears to be fixed in cave populations in which the overeating phenotype is present. The presence of the same allele in multiple caves appears to be due to selection from standing genetic variation present in surface populations.
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188
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Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. PLoS One 2015; 10:e0130600. [PMID: 26075903 PMCID: PMC4468109 DOI: 10.1371/journal.pone.0130600] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/21/2015] [Indexed: 11/19/2022] Open
Abstract
Background Collembola (springtails) represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor. Method We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and performed comparative analysis with protein-coding gene sequences of three crustaceans and three insects to identify adaptive signatures associated with the evolution of hexapods within the pancrustacean clade. Results Assembly of the springtail transcriptomes resulted in 37,730 transcripts with predicted open reading frames for F. candida and 32,154 for O. cincta, of which 34.2% were functionally annotated for F. candida and 38.4% for O. cincta. Subsequently, we predicted orthologous clusters among eight species and applied the branch-site test to detect episodic positive selection in the Hexapoda and Collembola lineages. A subset of 250 genes showed significant positive selection along the Hexapoda branch and 57 in the Collembola lineage. Gene Ontology categories enriched in these genes include metabolism, stress response (i.e. DNA repair, immune response), ion transport, ATP metabolism, regulation and development-related processes (i.e. eye development, neurological development). Conclusions We suggest that the identified gene families represent processes that have played a key role in the divergence of hexapods within the pancrustacean clade that eventually evolved into the most species-rich group of all animals, the hexapods. Furthermore, some adaptive signatures in collembolans may provide valuable clues to understand evolution of hexapods on land.
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189
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Wakasa H, Cádiz A, Echenique-Díaz LM, Iwasaki WM, Kamiyama N, Nishimura Y, Yokoyama H, Tamura K, Kawata M. Developmental stages for the divergence of relative limb length between a twig and a trunk-ground Anolis lizard species. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:410-23. [PMID: 26055630 DOI: 10.1002/jez.b.22627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 03/20/2015] [Indexed: 11/09/2022]
Abstract
The divergent evolution of niche-related traits can facilitate adaptive radiation, yet identification of the genetic or molecular mechanisms underlying such trait changes remains a major challenge in evolutionary biology. Conducting a detailed morphological comparison along growth trajectories is a powerful method for observing the formation of differences in niche-related traits. Here, we focused on hindlimb length of Anolis lizards, differences in which are related to adaptation for use of different microhabitats. We measured the length of hindlimb skeletons in different ecomorphs of anole lizards (A. sagrei, a trunk-ground ecomorph with long hindlimbs, and A. angusticeps, a twig ecomorph with short hindlimbs) from early embryonic stages to adulthood, to determine which hindlimb elements mainly differentiate the species and the timing of the formation of these differences. With respect to the digit, differences between the species mainly occurred during the embryonic stages of interdigit reduction, when the cartilage of the distal phalanges was simultaneously forming. In addition, we compared the relative length of developing autopods in early embryonic stages using whole-mount in situ hybridization before the formation of the cartilaginous bones, and the results showed that the relative growth rate of the Hoxa11-negative distal region in A. sagrei was greater than that in A. angusticeps. Our results show that there are several important developmental stages for hindlimb length differentiation between A. angusticeps and A. sagrei, depending on which hindlimb element is considered. In particular, the species differences were largely due to variations in digit length, which arose at early embryonic stages.
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Affiliation(s)
- Hajime Wakasa
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Antonio Cádiz
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.,Faculty of Biology, Havana University, Havana, Cuba
| | | | - Watal M Iwasaki
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Namiko Kamiyama
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yuki Nishimura
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hitoshi Yokoyama
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Koji Tamura
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masakado Kawata
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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190
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Slavík O, Horký P, Maciak M. Ostracism of an albino individual by a group of pigmented catfish. PLoS One 2015; 10:e0128279. [PMID: 26018869 PMCID: PMC4446300 DOI: 10.1371/journal.pone.0128279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/23/2015] [Indexed: 11/18/2022] Open
Abstract
Physiological and behavioural constraints hinder albino individuals. Albino animals are rare in the wild; this trait is associated with easy detection by predators, non-native or damaged environments, and exclusively aphotic environments in total darkness. The social aspect of albinism is reported only for human beings, and the effect is distinguishable in time and space when social benefits, are used to a limited the extent. Thus far, the social consequences of albinism for animals remain unknown. We used socially established groups of the pigmented catfish, (Silurus glanis), to observe space and temporal distance detachment of albino specimens in laboratory conditions. The albino fish were separated at larger distances from the group than pigmented individuals with the same social status determined by familiarity, and this asymmetry also varied in time. Albinism-related ostracism results in a solitary existence, usually followed by enhanced predation risk. The motivation for an individual's exclusion from a group appears to be the avoidance of the predation risk that increases not only for an odd individual but also for conspecifics within a group. Our findings indicate a role for albinism in behavioural processes related to sociality in a group of conspecifics.
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Affiliation(s)
- Ondřej Slavík
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Prague, Czech Republic
- * E-mail:
| | - Pavel Horký
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Prague, Czech Republic
| | - Matúš Maciak
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, Canada
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191
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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: 84] [Impact Index Per Article: 9.3] [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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192
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Genome editing using TALENs in blind Mexican Cavefish, Astyanax mexicanus. PLoS One 2015; 10:e0119370. [PMID: 25774757 PMCID: PMC4361574 DOI: 10.1371/journal.pone.0119370] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 01/14/2015] [Indexed: 12/17/2022] Open
Abstract
Astyanax mexicanus, a teleost fish that exists in a river-dwelling surface form and multiple cave-dwelling forms, is an excellent system for studying the genetic basis of evolution. Cavefish populations, which independently evolved from surface fish ancestors multiple times, have evolved a number of morphological and behavioral traits. Quantitative trait loci (QTL) analyses have been performed to identify the genetic basis of many of these traits. These studies, combined with recent sequencing of the genome, provide a unique opportunity to identify candidate genes for these cave-specific traits. However, tools to test the requirement of these genes must be established to evaluate the role of candidate genes in generating cave-specific traits. To address this need, we designed transcription activator-like effector nucleases (TALENs) to target two genes that contain coding changes in cavefish relative to surface fish and map to the same location as QTL for pigmentation, oculocutaneous albinism 2 (oca2) and melanocortin 1 receptor (mc1r). We found that surface fish genes can be mutated using this method. TALEN-induced mutations in oca2 result in mosaic loss of melanin pigmentation visible as albino patches in F0 founder fish, suggesting biallelic gene mutations in F0s and allowing us to evaluate the role of this gene in pigmentation. The pigment cells in the albino patches can produce melanin upon treatment with L-DOPA, behaving similarly to pigment cells in albino cavefish and providing additional evidence that oca2 is the gene within the QTL responsible for albinism in cavefish. This technology has the potential to introduce a powerful tool for studying the role of candidate genes responsible for the evolution of cavefish traits.
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193
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Yoshizawa M. Behaviors of cavefish offer insight into developmental evolution. Mol Reprod Dev 2015; 82:268-80. [PMID: 25728684 PMCID: PMC5024055 DOI: 10.1002/mrd.22471] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 02/09/2015] [Indexed: 12/16/2022]
Abstract
Many developmental processes have evolved through natural selection, yet in only a few cases do we understand if and how a change of developmental process produces a benefit. For example, many studies in evolutionary biology have investigated the developmental mechanisms that lead to novel structures in an animal, but only a few have addressed if these structures actually benefit the animal at the behavioral level of prey hunting and mating. As such, this review discusses an animal's behavior as the integrated functional output of its evolved morphological and physiological traits. Specifically, we focus on recent findings about the blind Mexican cavefish, Astyanax mexicanus, for which clear relationships exist between its physical traits and ecosystem. This species includes two morphotypes: an eyed surface dweller versus many conspecific types of blind cave dwellers, some of which evolved independently; all of the blind subtypes derived from eyed surface dwellers. The blind cavefish evolved under clear selection pressures: food is sparse and darkness is perpetual. Simulating the major aspects of a cave ecosystem in the laboratory is relatively easy, so we can use this species to begin resolving the relationships between evolved traits and selection pressures—relationships which are more complex for other animals models. This review discusses the recent advances in cavefish research that have helped us establish some key relationships between morphological evolution and environmental shifts. Mol. Reprod. Dev. 82: 268–280, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Masato Yoshizawa
- Department of Biology, University of Nevada, Reno, Nevada; Department of Biology, University of Hawaii, Manoa, Hawaii
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194
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Yoshizawa M, Robinson BG, Duboué ER, Masek P, Jaggard JB, O'Quin KE, Borowsky RL, Jeffery WR, Keene AC. Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish. BMC Biol 2015; 13:15. [PMID: 25761998 PMCID: PMC4364459 DOI: 10.1186/s12915-015-0119-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sleep is characterized by extended periods of quiescence and reduced responsiveness to sensory stimuli. Animals ranging from insects to mammals adapt to environments with limited food by suppressing sleep and enhancing their response to food cues, yet little is known about the genetic and evolutionary relationship between these processes. The blind Mexican cavefish, Astyanax mexicanus is a powerful model for elucidating the genetic mechanisms underlying behavioral evolution. A. mexicanus comprises an extant ancestral-type surface dwelling morph and at least five independently evolved cave populations. Evolutionary convergence on sleep loss and vibration attraction behavior, which is involved in prey seeking, have been documented in cavefish raising the possibility that enhanced sensory responsiveness underlies changes in sleep. RESULTS We established a system to study sleep and vibration attraction behavior in adult A. mexicanus and used high coverage quantitative trait loci (QTL) mapping to investigate the functional and evolutionary relationship between these traits. Analysis of surface-cave F2 hybrid fish and an outbred cave population indicates that independent genetic factors underlie changes in sleep/locomotor activity and vibration attraction behavior. High-coverage QTL mapping with genotyping-by-sequencing technology identify two novel QTL intervals that associate with locomotor activity and include the narcolepsy-associated tp53 regulating kinase. These QTLs represent the first genomic localization of locomotor activity in cavefish and are distinct from two QTLs previously identified as associating with vibration attraction behavior. CONCLUSIONS Taken together, these results localize genomic regions underlying sleep/locomotor and sensory changes in cavefish populations and provide evidence that sleep loss evolved independently from enhanced sensory responsiveness.
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Affiliation(s)
- Masato Yoshizawa
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA. .,Department of Biology, University of Hawaii, Manoa, Honolulu, HI, 96822, USA.
| | - Beatriz G Robinson
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - Erik R Duboué
- Department of Biology, New York University, New York, NY, 10012, USA. .,Present address: Carnegie Institution for Science, Department of Embryology, Baltimore, MD, 21218, USA.
| | - Pavel Masek
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - James B Jaggard
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - Kelly E O'Quin
- Department of Biology, Centre College, Danville, KY, 40422, USA.
| | | | - William R Jeffery
- Department of Biology, University of Maryland, College Park, MD, 20742, USA.
| | - Alex C Keene
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
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195
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Gordon MS, Notar JC. Can systems biology help to separate evolutionary analogies (convergent homoplasies) from homologies? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:19-29. [PMID: 25620424 DOI: 10.1016/j.pbiomolbio.2015.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 12/22/2022]
Abstract
Convergent evolutionary analogies (homoplasies) of many kinds occur in diverse phylogenetic clades/lineages on both the animal and plant branches of the Tree of Life. Living organisms whose last common ancestors lived millions to hundreds of millions of years ago have later converged morphologically, behaviorally or at other levels of functionality (from molecular genetics through biochemistry, physiology and other organismic processes) as a result of long term strong natural selection that has constrained and channeled evolutionary processes. This happens most often when organisms belonging to different clades occupy ecological niches, habitats or environments sharing major characteristics that select for a relatively narrow range of organismic properties. Systems biology, broadly defined, provides theoretical and methodological approaches that are beginning to make it possible to answer a perennial evolutionary biological question relating to convergent homoplasies: Are at least some of the apparent analogies actually unrecognized homologies? This review provides an overview of the current state of knowledge of important aspects of this topic area. It also provides a resource describing many homoplasies that may be fruitful subjects for systems biological research.
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Affiliation(s)
- Malcolm S Gordon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
| | - Julia C Notar
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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196
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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: 8] [Impact Index Per Article: 0.9] [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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197
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Carlson BM, Onusko SW, Gross JB. A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology. G3 (BETHESDA, MD.) 2014; 5:241-51. [PMID: 25520037 PMCID: PMC4321032 DOI: 10.1534/g3.114.015438] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/11/2014] [Indexed: 12/17/2022]
Abstract
The Mexican tetra, Astyanax mexicanus, is a unique model system consisting of cave-adapted and surface-dwelling morphotypes that diverged >1 million years (My) ago. This remarkable natural experiment has enabled powerful genetic analyses of cave adaptation. Here, we describe the application of next-generation sequencing technology to the creation of a high-density linkage map. Our map comprises more than 2200 markers populating 25 linkage groups constructed from genotypic data generated from a single genotyping-by-sequencing project. We leveraged emergent genomic and transcriptomic resources to anchor hundreds of anonymous Astyanax markers to the genome of the zebrafish (Danio rerio), the most closely related model organism to our study species. This facilitated the identification of 784 distinct connections between our linkage map and the Danio rerio genome, highlighting several regions of conserved genomic architecture between the two species despite ~150 My of divergence. Using a Mendelian cave-associated trait as a proof-of-principle, we successfully recovered the genomic position of the albinism locus near the gene Oca2. Further, our map successfully informed the positions of unplaced Astyanax genomic scaffolds within particular linkage groups. This ability to identify the relative location, orientation, and linear order of unaligned genomic scaffolds will facilitate ongoing efforts to improve on the current early draft and assemble future versions of the Astyanax physical genome. Moreover, this improved linkage map will enable higher-resolution genetic analyses and catalyze the discovery of the genetic basis for cave-associated phenotypes.
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Affiliation(s)
- Brian M Carlson
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221
| | - Samuel W Onusko
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221
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198
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Bellono NW, Escobar IE, Lefkovith AJ, Marks MS, Oancea E. An intracellular anion channel critical for pigmentation. eLife 2014; 3:e04543. [PMID: 25513726 PMCID: PMC4270065 DOI: 10.7554/elife.04543] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/07/2014] [Indexed: 12/28/2022] Open
Abstract
Intracellular ion channels are essential regulators of organellar and cellular function, yet the molecular identity and physiological role of many of these channels remains elusive. In particular, no ion channel has been characterized in melanosomes, organelles that produce and store the major mammalian pigment melanin. Defects in melanosome function cause albinism, characterized by vision and pigmentation deficits, impaired retinal development, and increased susceptibility to skin and eye cancers. The most common form of albinism is caused by mutations in oculocutaneous albinism II (OCA2), a melanosome-specific transmembrane protein with unknown function. Here we used direct patch-clamp of skin and eye melanosomes to identify a novel chloride-selective anion conductance mediated by OCA2 and required for melanin production. Expression of OCA2 increases organelle pH, suggesting that the chloride channel might regulate melanin synthesis by modulating melanosome pH. Thus, a melanosomal anion channel that requires OCA2 is essential for skin and eye pigmentation.
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Affiliation(s)
- Nicholas W Bellono
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, United States
| | - Iliana E Escobar
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, United States
| | - Ariel J Lefkovith
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, United States
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, United States
| | - Elena Oancea
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, United States
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199
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Yoshizawa M, Jeffery WR. Evolutionary tuning of an adaptive behavior requires enhancement of the neuromast sensory system. Commun Integr Biol 2014. [DOI: 10.4161/cib.14118] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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200
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McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O’Quin KE, Rétaux S, Rohner N, Searle SMJ, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC. The cavefish genome reveals candidate genes for eye loss. Nat Commun 2014; 5:5307. [PMID: 25329095 PMCID: PMC4218959 DOI: 10.1038/ncomms6307] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/17/2014] [Indexed: 11/10/2022] Open
Abstract
Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.
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Affiliation(s)
- Suzanne E. McGaugh
- The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA
| | - Joshua B. Gross
- Department of Biological Sciences, University of Cincinnati, 711B Rieveschl Hall, 312 College Drive, Cincinnati, Ohio 45221, USA
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maryline Blin
- DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France
| | - Richard Borowsky
- Department of Biology, New York University, New York, New York 10003-6688, USA
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR 5242, UCBL, 46 allée d’Italie, Lyon F-69364, France
| | - Hélène Hinaux
- DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France
| | - William R. Jeffery
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Alex Keene
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Li Ma
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Patrick Minx
- The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA
| | - Daniel Murphy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kelly E. O’Quin
- Department of Biology, Centre College, 600 West Walnut St, Danville, Kentucky 40422, USA
| | - Sylvie Rétaux
- DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France
| | - Nicolas Rohner
- Harvard Medical School Department of Genetics, 77 Avenue Louis Pasteur; NRB 360, Boston, Massachusetts 02115, USA
| | - Steve M. J. Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Bethany A. Stahl
- Department of Biological Sciences, University of Cincinnati, 711B Rieveschl Hall, 312 College Drive, Cincinnati, Ohio 45221, USA
| | - Cliff Tabin
- Harvard Medical School Department of Genetics, 77 Avenue Louis Pasteur; NRB 360, Boston, Massachusetts 02115, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR 5242, UCBL, 46 allée d’Italie, Lyon F-69364, France
| | - Masato Yoshizawa
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Wesley C. Warren
- The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA
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