101
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Kusakabe M, Ishikawa A, Ravinet M, Yoshida K, Makino T, Toyoda A, Fujiyama A, Kitano J. Genetic basis for variation in salinity tolerance between stickleback ecotypes. Mol Ecol 2016; 26:304-319. [DOI: 10.1111/mec.13875] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Makoto Kusakabe
- Atmosphere and Ocean Research Institute; The University of Tokyo; Kashiwanoha 5-1-5 Kashiwa Chiba 277-8564 Japan
- Department of Biological Science; Faculty of Science; Shizuoka University; 836 Ohya, Suruga-ku Shizuoka 422-8529 Japan
| | - Asano Ishikawa
- Division of Ecological Genetics; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
| | - Mark Ravinet
- Division of Ecological Genetics; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
- Centre for Ecological and Evolutionary Synthesis; University of Oslo; P.O. Box 1066 Blindern Oslo NO-0316 Oslo Norway
| | - Kohta Yoshida
- Division of Ecological Genetics; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
| | - Takashi Makino
- Department of Ecology and Evolutionary Biology; Graduate School of Life Sciences; Tohoku University; Sendai Miyagi 980-8578 Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
| | - Jun Kitano
- Division of Ecological Genetics; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
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102
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Bernatchez S, Laporte M, Perrier C, Sirois P, Bernatchez L. Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses. Mol Ecol 2016; 25:4773-92. [DOI: 10.1111/mec.13795] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 07/18/2016] [Accepted: 08/04/2016] [Indexed: 12/19/2022]
Affiliation(s)
- S. Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Québec Canada G1V 0A6
| | - M. Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Québec Canada G1V 0A6
| | - C. Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Québec Canada G1V 0A6
- Centre d'Ecologie Fonctionnelle and Evolutive; CNRS; 34293 Montpellier 5 France
| | - P. Sirois
- Chaire de recherche sur les espèces aquatiques exploitées; Université du Québec à Chicoutimi; Chicoutimi Québec Canada G7H 2B1
| | - L. Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Québec Canada G1V 0A6
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103
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Kelly MW, Pankey MS, DeBiasse MB, Plachetzki DC. Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12725] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Morgan W. Kelly
- Department of Biological Sciences Louisiana State University Baton Rouge LA70803 USA
| | - M. Sabrina Pankey
- Molecular, Cellular, & Biomedical Sciences University of New Hampshire Rudman Hall 46 College Rd. Durham NH03824‐2618 USA
| | - Melissa B. DeBiasse
- Department of Biological Sciences Louisiana State University Baton Rouge LA70803 USA
| | - David C. Plachetzki
- Molecular, Cellular, & Biomedical Sciences University of New Hampshire Rudman Hall 46 College Rd. Durham NH03824‐2618 USA
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104
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Madeira D, Araújo JE, Vitorino R, Capelo JL, Vinagre C, Diniz MS. Ocean warming alters cellular metabolism and induces mortality in fish early life stages: A proteomic approach. ENVIRONMENTAL RESEARCH 2016; 148:164-176. [PMID: 27062348 DOI: 10.1016/j.envres.2016.03.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 06/05/2023]
Abstract
Climate change has pervasive effects on marine ecosystems, altering biodiversity patterns, abundance and distribution of species, biological interactions, phenology, and organisms' physiology, performance and fitness. Fish early life stages have narrow thermal windows and are thus more vulnerable to further changes in water temperature. The aim of this study was to address the sensitivity and underlying molecular changes of larvae of a key fisheries species, the sea bream Sparus aurata, towards ocean warming. Larvae were exposed to three temperatures: 18°C (control), 24°C (warm) and 30°C (heat wave) for seven days. At the end of the assay, i) survival curves were plotted for each temperature treatment and ii) entire larvae were collected for proteomic analysis via 2D gel electrophoresis, image analysis and mass spectrometry. Survival decreased with increasing temperature, with no larvae surviving at 30°C. Therefore, proteomic analysis was only carried out for 18°C and 24°C. Larvae up-regulated protein folding and degradation, cytoskeletal re-organization, transcriptional regulation and the growth hormone while mostly down-regulating cargo transporting and porphyrin metabolism upon exposure to heat stress. No changes were detected in proteins related to energetic metabolism suggesting that larval fish may not have the energetic plasticity needed to sustain cellular protection in the long-term. These results indicate that despite proteome modulation, S. aurata larvae do not seem able to fully acclimate to higher temperatures as shown by the low survival rates. Consequently, elevated temperatures seem to have bottleneck effects during fish early life stages, and future ocean warming can potentially compromise recruitment's success of key fisheries species.
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Affiliation(s)
- D Madeira
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - J E Araújo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - R Vitorino
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
| | - J L Capelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - C Vinagre
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - M S Diniz
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
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105
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Hébert FO, Grambauer S, Barber I, Landry CR, Aubin-Horth N. Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite. Gigascience 2016; 5:24. [PMID: 27259971 PMCID: PMC4891850 DOI: 10.1186/s13742-016-0128-3] [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: 12/16/2015] [Accepted: 05/11/2016] [Indexed: 01/06/2023] Open
Abstract
Background Schistocephalus solidus is a well-established model organism for studying the complex life cycle of cestodes and the mechanisms underlying host-parasite interactions. However, very few large-scale genetic resources for this species are available. We have sequenced and de novo-assembled the transcriptome of S. solidus using tissues from whole worms at three key developmental states - non-infective plerocercoid, infective plerocercoid and adult plerocercoid - to provide a resource for studying the evolution of complex life cycles and, more specifically, how parasites modulate their interactions with their hosts during development. Findings The de novo transcriptome assembly reconstructed the coding sequence of 10,285 high-confidence unigenes from which 24,765 non-redundant transcripts were derived. 7,920 (77 %) of these unigenes were annotated with a protein name and 7,323 (71 %) were assigned at least one Gene Ontology term. Our raw transcriptome assembly (unfiltered transcripts) covers 92 % of the predicted transcriptome derived from the S. solidus draft genome assembly currently available on WormBase. It also provides new ecological information and orthology relationships to further annotate the current WormBase transcriptome and genome. Conclusion This large-scale transcriptomic dataset provides a foundation for studies on how parasitic species with complex life cycles modulate their response to changes in biotic and abiotic conditions experienced inside their various hosts, which is a fundamental objective of parasitology. Furthermore, this resource will help in the validation of the S solidus gene features that have been predicted based on genomic sequence. Electronic supplementary material The online version of this article (doi:10.1186/s13742-016-0128-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- François Olivier Hébert
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugène-Marchand, Québec, G1V 0A6, Canada.
| | - Stephan Grambauer
- Department of Neuroscience, Psychology and Behaviour, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Iain Barber
- Department of Neuroscience, Psychology and Behaviour, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugène-Marchand, Québec, G1V 0A6, Canada
| | - Nadia Aubin-Horth
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugène-Marchand, Québec, G1V 0A6, Canada
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106
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Ehrenreich IM, Pfennig DW. Genetic assimilation: a review of its potential proximate causes and evolutionary consequences. ANNALS OF BOTANY 2016; 117:769-79. [PMID: 26359425 PMCID: PMC4845796 DOI: 10.1093/aob/mcv130] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 06/29/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Most, if not all, organisms possess the ability to alter their phenotype in direct response to changes in their environment, a phenomenon known as phenotypic plasticity. Selection can break this environmental sensitivity, however, and cause a formerly environmentally induced trait to evolve to become fixed through a process called genetic assimilation. Essentially, genetic assimilation can be viewed as the evolution of environmental robustness in what was formerly an environmentally sensitive trait. Because genetic assimilation has long been suggested to play a key role in the origins of phenotypic novelty and possibly even new species, identifying and characterizing the proximate mechanisms that underlie genetic assimilation may advance our basic understanding of how novel traits and species evolve. SCOPE This review begins by discussing how the evolution of phenotypic plasticity, followed by genetic assimilation, might promote the origins of new traits and possibly fuel speciation and adaptive radiation. The evidence implicating genetic assimilation in evolutionary innovation and diversification is then briefly considered. Next, the potential causes of phenotypic plasticity generally and genetic assimilation specifically are examined at the genetic, molecular and physiological levels and approaches that can improve our understanding of these mechanisms are described. The review concludes by outlining major challenges for future work. CONCLUSIONS Identifying and characterizing the proximate mechanisms involved in phenotypic plasticity and genetic assimilation promises to help advance our basic understanding of evolutionary innovation and diversification.
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Affiliation(s)
- Ian M Ehrenreich
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA and
| | - David W Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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107
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O'Connor CM, Marsh-Rollo SE, Aubin-Horth N, Balshine S. Species-specific patterns of nonapeptide brain gene expression relative to pair-bonding behavior in grouping and non-grouping cichlids. Horm Behav 2016; 80:30-38. [PMID: 26519858 DOI: 10.1016/j.yhbeh.2015.10.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/18/2015] [Accepted: 10/24/2015] [Indexed: 11/16/2022]
Abstract
Comparative studies have revealed that vasopressin-oxytocin pathways are associated with both pair bonding and grouping behavior. However, the relationship between pair bonding and grouping behavior remains unclear. In this study, our aim was to identify whether two species that differ in grouping behavior display a corresponding difference in their pair bonds, and in the underlying vasopressin-oxytocin hormonal pathways. Using two species of cichlid fishes, the highly social Neolamprologus pulcher and the non-social Telmatochromis temporalis, we measured proximity of pairs during pair bond formation, and then measured social behaviors (proximity, aggression, submission, affiliation) and brain gene expression of isotocin and arginine vasotocin (the teleost homologues of oxytocin and vasopressin, respectively), as well as their receptors, after a temporary separation and subsequent reunion of the bonded pairs. Pairs of the social species spent more time in close proximity relative to the non-social species. Rates of aggression increased in both species following the separation and reunion treatment, relative to controls that were not separated. Overall, whole brain expression of isotocin was higher in the social species relative to the non-social species, and correlated with proximity, submission, and affiliation, but only in the social species. Our results suggest that both a social and a non-social cichlid species have similar behavioral responses to a temporary separation from a mate, and we found no difference in the brain gene expression of measured hormones and receptors based on our separation-reunion treatment. However, our results highlight the importance of isotocin in mediating submissive and affiliative behaviors in cichlid fishes, and demonstrate that isotocin has species-specific correlations with socially relevant behaviors.
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Affiliation(s)
- Constance M O'Connor
- Aquatic Behavioural Ecology Lab, Department of Psychology, Neuroscience, and Behaviour, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.
| | - Susan E Marsh-Rollo
- Aquatic Behavioural Ecology Lab, Department of Psychology, Neuroscience, and Behaviour, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Nadia Aubin-Horth
- Département de Biologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Sigal Balshine
- Aquatic Behavioural Ecology Lab, Department of Psychology, Neuroscience, and Behaviour, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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108
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Kinnison MT, Hairston NG, Hendry AP. Cryptic eco-evolutionary dynamics. Ann N Y Acad Sci 2016; 1360:120-44. [PMID: 26619300 DOI: 10.1111/nyas.12974] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/22/2015] [Accepted: 10/23/2015] [Indexed: 12/17/2022]
Abstract
Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them.
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Affiliation(s)
| | - Nelson G Hairston
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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109
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Effects of parental care on the accumulation and release of cryptic genetic variation: review of mechanisms and a case study of dung beetles. Evol Ecol 2016. [DOI: 10.1007/s10682-015-9813-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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110
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Stanton-Geddes J, Nguyen A, Chick L, Vincent J, Vangala M, Dunn RR, Ellison AM, Sanders NJ, Gotelli NJ, Cahan SH. Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species. BMC Genomics 2016; 17:171. [PMID: 26934985 PMCID: PMC4776372 DOI: 10.1186/s12864-016-2466-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/12/2016] [Indexed: 12/03/2022] Open
Abstract
Background The distributions of species and their responses to climate change are in part determined by their thermal tolerances. However, little is known about how thermal tolerance evolves. To test whether evolutionary extension of thermal limits is accomplished through enhanced cellular stress response (enhanced response), constitutively elevated expression of protective genes (genetic assimilation) or a shift from damage resistance to passive mechanisms of thermal stability (tolerance), we conducted an analysis of the reactionome: the reaction norm for all genes in an organism’s transcriptome measured across an experimental gradient. We characterized thermal reactionomes of two common ant species in the eastern U.S, the northern cool-climate Aphaenogaster picea and the southern warm-climate Aphaenogaster carolinensis, across 12 temperatures that spanned their entire thermal breadth. Results We found that at least 2 % of all genes changed expression with temperature. The majority of upregulation was specific to exposure to low temperatures. The cool-adapted A. picea induced expression of more genes in response to extreme temperatures than did A. carolinensis, consistent with the enhanced response hypothesis. In contrast, under high temperatures the warm-adapted A. carolinensis downregulated many of the genes upregulated in A. picea, and required more extreme temperatures to induce down-regulation in gene expression, consistent with the tolerance hypothesis. We found no evidence for a trade-off between constitutive and inducible gene expression as predicted by the genetic assimilation hypothesis. Conclusions These results suggest that increases in upper thermal limits may require an evolutionary shift in response mechanism away from damage repair toward tolerance and prevention. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2466-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John Stanton-Geddes
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA. .,Data Scientist, Dealer.com, 1 Howard St, Burlington, VT, 05401, USA.
| | - Andrew Nguyen
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Lacy Chick
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - James Vincent
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA
| | - Mahesh Vangala
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA
| | - Robert R Dunn
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Aaron M Ellison
- Harvard Forest, Harvard University, Petersham, MA, 01336, USA
| | - Nathan J Sanders
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.,Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Nicholas J Gotelli
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Sara Helms Cahan
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
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111
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Laporte M, Claude J, Berrebi P, Perret P, Magnan P. Shape plasticity in response to water velocity in the freshwater blenny Salaria fluviatilis. JOURNAL OF FISH BIOLOGY 2016; 88:1191-1203. [PMID: 26935595 DOI: 10.1111/jfb.12902] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/17/2015] [Indexed: 06/05/2023]
Abstract
A non-random association between an environmental factor and a given trait could be explained by directional selection (genetic determinism) and by phenotypic plasticity (environmental determinism). A previous study showed a significant relationship between morphology and water velocity in Salaria fluviatilis that conformed to functional expectations. The objective of this study was to test whether this relationship could be explained by phenotypic plasticity. Salaria fluviatilis from a Corsican stream were placed in four experimental channels with different water velocities (0, 10, 20 and 30 cm s(-1)) to test whether there was a morphological response associated with this environmental factor. After 28 days, fish shape changed in response to water velocity without any significant growth. Fish in higher water velocities exhibited a more slender body shape and longer anal and caudal fins. These results indicate a high degree of morphological plasticity in riverine populations of S. fluviatilis and suggest that the previous relationship between morphology and water velocity observed in the field may largely be due to an environmental determinism.
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Affiliation(s)
- M Laporte
- Institut des Sciences de l'Évolution de Montpellier (ISEM), UMR 5554 UM2-CNRS-IRD, Université de Montpellier II, CC065, Place E. Bataillon, 34095, Montpellier, Cedex 5, France
- Centre de recherche sur les interactions bassins versants-écosystèmes aquatiques (RIVE), Université du Québec à Trois-Rivières, C. P. 500, Trois-Rivières, QC, G9A 5H7, Canada
| | - J Claude
- Institut des Sciences de l'Évolution de Montpellier (ISEM), UMR 5554 UM2-CNRS-IRD, Université de Montpellier II, CC065, Place E. Bataillon, 34095, Montpellier, Cedex 5, France
| | - P Berrebi
- Institut des Sciences de l'Évolution de Montpellier (ISEM), UMR 5554 UM2-CNRS-IRD, Université de Montpellier II, CC065, Place E. Bataillon, 34095, Montpellier, Cedex 5, France
| | - P Perret
- Centre d'Écologie Fonctionnelle et d'Évolution (CEFE), UMR 5175 CEFE-CNRS, Équipe Écologie Spatiale des Populations, 1919 route de Mende, F34293, Montpellier, Cedex 5, France
| | - P Magnan
- Centre de recherche sur les interactions bassins versants-écosystèmes aquatiques (RIVE), Université du Québec à Trois-Rivières, C. P. 500, Trois-Rivières, QC, G9A 5H7, Canada
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112
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Todd EV, Black MA, Gemmell NJ. The power and promise of RNA-seq in ecology and evolution. Mol Ecol 2016; 25:1224-41. [DOI: 10.1111/mec.13526] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/05/2015] [Accepted: 12/27/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Erica V. Todd
- Department of Anatomy; University of Otago; PO Box 913 Dunedin 9054 New Zealand
| | - Michael A. Black
- Department of Biochemistry; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Neil J. Gemmell
- Department of Anatomy; University of Otago; PO Box 913 Dunedin 9054 New Zealand
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113
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Shama LNS, Mark FC, Strobel A, Lokmer A, John U, Mathias Wegner K. Transgenerational effects persist down the maternal line in marine sticklebacks: gene expression matches physiology in a warming ocean. Evol Appl 2016; 9:1096-1111. [PMID: 27695518 PMCID: PMC5039323 DOI: 10.1111/eva.12370] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 01/28/2016] [Indexed: 12/25/2022] Open
Abstract
Transgenerational effects can buffer populations against environmental change, yet little is known about underlying mechanisms, their persistence or the influence of environmental cue timing. We investigated mitochondrial respiratory capacity (MRC) and gene expression of marine sticklebacks that experienced acute or developmental acclimation to simulated ocean warming (21°C) across three generations. Previous work showed that acute acclimation of grandmothers to 21°C led to lower (optimized) offspring MRCs. Here, developmental acclimation of mothers to 21°C led to higher, but more efficient offspring MRCs. Offspring with a 21°C × 17°C grandmother-mother environment mismatch showed metabolic compensation: their MRCs were as low as offspring with a 17°C thermal history across generations. Transcriptional analyses showed primarily maternal but also grandmaternal environment effects: genes involved in metabolism and mitochondrial protein biosynthesis were differentially expressed when mothers developed at 21°C, whereas 21°C grandmothers influenced genes involved in hemostasis and apoptosis. Genes involved in mitochondrial respiration all showed higher expression when mothers developed at 21° and lower expression in the 21°C × 17°C group, matching the phenotypic pattern for MRCs. Our study links transcriptomics to physiology under climate change, and demonstrates that mechanisms underlying transgenerational effects persist across multiple generations with specific outcomes depending on acclimation type and environmental mismatch between generations.
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Affiliation(s)
- Lisa N S Shama
- Coastal Ecology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Wadden Sea Station Sylt Germany
| | - Felix C Mark
- Integrative Ecophysiology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Bremerhaven Germany
| | - Anneli Strobel
- Integrative Ecophysiology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Bremerhaven Germany; Man Society Environment (MGU) Department of Environmental Sciences University of Basel Switzerland
| | - Ana Lokmer
- Coastal Ecology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Wadden Sea Station Sylt Germany
| | - Uwe John
- Ecological Chemistry Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Bremerhaven Germany
| | - K Mathias Wegner
- Coastal Ecology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Wadden Sea Station Sylt Germany
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114
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Teles MC, Cardoso SD, Oliveira RF. Social Plasticity Relies on Different Neuroplasticity Mechanisms across the Brain Social Decision-Making Network in Zebrafish. Front Behav Neurosci 2016; 10:16. [PMID: 26909029 PMCID: PMC4754415 DOI: 10.3389/fnbeh.2016.00016] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/29/2016] [Indexed: 11/20/2022] Open
Abstract
Social living animals need to adjust the expression of their behavior to their status within the group and to changes in social context and this ability (social plasticity) has an impact on their Darwinian fitness. At the proximate level social plasticity must rely on neuroplasticity in the brain social decision-making network (SDMN) that underlies the expression of social behavior, such that the same neural circuit may underlie the expression of different behaviors depending on social context. Here we tested this hypothesis in zebrafish by characterizing the gene expression response in the SDMN to changes in social status of a set of genes involved in different types of neural plasticity: bdnf, involved in changes in synaptic strength; npas4, involved in contextual learning and dependent establishment of GABAergic synapses; neuroligins (nlgn1 and nlgn2) as synaptogenesis markers; and genes involved in adult neurogenesis (wnt3 and neurod). Four social phenotypes were experimentally induced: Winners and Losers of a real-opponent interaction; Mirror-fighters, that fight their own image in a mirror and thus do not experience a change in social status despite the expression of aggressive behavior; and non-interacting fish, which were used as a reference group. Our results show that each social phenotype (i.e., Winners, Losers, and Mirror-fighters) present specific patterns of gene expression across the SDMN, and that different neuroplasticity genes are differentially expressed in different nodes of the network (e.g., BDNF in the dorsolateral telencephalon, which is a putative teleost homolog of the mammalian hippocampus). Winners expressed unique patterns of gene co-expression across the SDMN, whereas in Losers and Mirror-fighters the co-expression patterns were similar in the dorsal regions of the telencephalon and in the supracommissural nucleus of the ventral telencephalic area, but differents in the remaining regions of the ventral telencephalon. These results indicate that social plasticity relies on multiple neuroplasticity mechanisms across the SDMN, and that there is not a single neuromolecular module underlying this type of behavioral flexibility.
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Affiliation(s)
- Magda C Teles
- Instituto Superior de Psicologia Aplicada-Instituto UniversitárioLisboa, Portugal; Instituto Gulbenkian de CiênciaOeiras, Portugal; Champalimaud Neuroscience Programme, Champalimaud Centre for the UnknownLisboa, Portugal
| | - Sara D Cardoso
- Instituto Superior de Psicologia Aplicada-Instituto UniversitárioLisboa, Portugal; Instituto Gulbenkian de CiênciaOeiras, Portugal; Champalimaud Neuroscience Programme, Champalimaud Centre for the UnknownLisboa, Portugal
| | - Rui F Oliveira
- Instituto Superior de Psicologia Aplicada-Instituto UniversitárioLisboa, Portugal; Instituto Gulbenkian de CiênciaOeiras, Portugal; Champalimaud Neuroscience Programme, Champalimaud Centre for the UnknownLisboa, Portugal
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115
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Bell AM, Bukhari SA, Sanogo YO. Natural variation in brain gene expression profiles of aggressive and nonaggressive individual sticklebacks. BEHAVIOUR 2016; 153:1723-1743. [PMID: 29046592 DOI: 10.1163/1568539x-00003393] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within many species, some individuals are consistently more aggressive than others. We examine whether there are differences in brain gene expression between aggressive versus nonaggressive behavioural types of individuals within a natural population of male three-spined sticklebacks (Gasterosteus aculeatus). We compared gene expression profiles of aggressive male sticklebacks to nonaggressive males in four regions of the brain (brainstem, cerebellum, diencephalon and telencephalon). Relatively few genes were differentially expressed between behavioural types in telencephalon, cerebellum and diencephalon, but hundreds of genes were differentially expressed in brainstem, a brain area involved in detecting threats. Six genes that were differentially expressed in response to a territorial intrusion in a previous study were also differentially expressed between behavioural types in this study, implying primarily non-shared but some shared molecular mechanisms. Our findings offer new insights into the molecular causes and correlates of behavioural plasticity and individual variation in behaviour.
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Affiliation(s)
- Alison M Bell
- School of Integrative Biology, Program in Ecology, Evolution and Conservation, Program in Neuroscience, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, IL, USA
| | - Syed Abbas Bukhari
- Illinois Informatics Program, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, IL, USA
| | - Yibayiri Osee Sanogo
- Genomics Core, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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116
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Qiu T, Jiang L, Li S, Yang Y. Small-Scale Habitat-Specific Variation and Adaptive Divergence of Photosynthetic Pigments in Different Alkali Soils in Reed Identified by Common Garden and Genetic Tests. FRONTIERS IN PLANT SCIENCE 2016; 7:2016. [PMID: 28111586 PMCID: PMC5216671 DOI: 10.3389/fpls.2016.02016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/19/2016] [Indexed: 05/14/2023]
Abstract
Flexibility of photosynthetic pigment traits is an important adaptive mechanism through which plants can increase mean fitness in a variable environment. Unlike morphological traits in plants, photosythesis has been shown to exhibit phenotypic plasticity, responding rapidly to environmental conditions. Meanwhile, local adaptation at small scales is considered to be rare. Thus, detecting the small-scale adaptive divergence of photosynthetic pigments presents a challenge. Leaf concentrations of photosynthetic pigments under stressful conditions may be reduced or maintained. Concentrations of some pigments and/or ratio of Chlorophyll a (Chla) to Chlorophyll b (Chlb) do not change markedly in some species, such as the common reed, Phragmites australis, a cosmopolitan grass and common invader. Little is known about photosynthetic responses of this plant to varying levels of alkali salt. Few studies have attempted to account for the relationship between pigment accumulation and leaf position in wild plant populations in grasslands. In this study, photosynthetic pigment concentrations and the total Chl(a+b)/Car ratio decreased as the growing season progressed and were shown to be significantly lower in the habitat with a higher soil pH value and less moisture when compared between habitats. The Chla/Chlb ratio did not differ significantly between habitats, although it increased significantly over time. Leaves in the middle position may be functionally important in the response to soil conditions because only pigment concentrations and the Chl(a+b)/Car ratio of those leaves varied between habitats significantly. The outlier loci, used to evaluate molecular signatures of selection, were detected by Arlequin, Bayescan, and Bayenv analyses. In the simulated habitats of common garden, the local genotypes had higher values of Chla, Chlb, Chl(a+b), Car in their home habitat than did genotypes originating from the other habitat. QST-FST comparisons provided evidence of divergent selection. It appears likely that soil moisture, pH and electric conductivity drove local adaptation. Combined approaches that utilize information on phenotypes from field and common garden experiments, genome-wide markers, and environmental data will be the most informative for understanding the adaptive nature of the intraspecific divergence.
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Affiliation(s)
- Tian Qiu
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal UniversityChangchun, China
- School of Life Sciences, Changchun Normal UniversityChangchun, China
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Northeast Normal UniversityChangchun, China
| | - LiLi Jiang
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Northeast Normal UniversityChangchun, China
| | - ShanZhi Li
- School of Life Sciences, Changchun Normal UniversityChangchun, China
| | - YunFei Yang
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal UniversityChangchun, China
- *Correspondence: YunFei Yang
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117
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Aubin‐Horth N. Using an integrative approach to investigate the evolution of behaviour. Evol Appl 2016; 9:166-80. [PMID: 27087846 PMCID: PMC4780388 DOI: 10.1111/eva.12300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/24/2015] [Indexed: 12/26/2022] Open
Abstract
Behaviour is a central focus of interest in biology because it has an impact on several aspects of an organism's life. Evolutionary biologists have realised the advantage of an integrative approach that jointly studies the molecular, cellular and physiological levels of an individual to link them with the organismal behavioural phenotype. First, this mechanistic information helps in understanding physiological and evolutionary constraints acting on the behavioural response to the environment and its evolution. Second, it furthers our understanding of the process of molecular convergent evolution. Finally, we learn about natural variation in molecular, cellular and physiological traits present in wild populations and their underlying genetic basis, which can be a substrate for selection to act on. I illustrate these points using our work on behaviour variation in fishes. The information on the mechanistic bases of behaviour variation in various species and behaviours will contribute to an ecological annotation of genes and to uncover new mechanisms implicated in how this astonishing behavioural diversity arose, is maintained and will evolve.
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Affiliation(s)
- Nadia Aubin‐Horth
- Département de biologie & Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQCCanada
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118
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Alonzo SH. Integrating the how and why of within-individual and among-individual variation and plasticity in behavior. Curr Opin Behav Sci 2015. [DOI: 10.1016/j.cobeha.2015.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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119
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120
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Gao L, Geng Y, Yang H, Hu Y, Yang J. Gene Expression Reaction Norms Unravel the Molecular and Cellular Processes Underpinning the Plastic Phenotypes of Alternanthera Philoxeroides in Contrasting Hydrological Conditions. FRONTIERS IN PLANT SCIENCE 2015; 6:991. [PMID: 26617628 PMCID: PMC4641913 DOI: 10.3389/fpls.2015.00991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/29/2015] [Indexed: 05/25/2023]
Abstract
Alternanthera philoxeroides is an amphibious invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation. Little is known about the molecular basis underlying environment-induced phenotypic changes. Variation in transcript abundance in A. philoxeroides was characterized throughout the time-courses of pond and upland treatments using RNA-Sequencing. Seven thousand eight hundred and five genes demonstrated variable expression in response to different treatments, forming 11 transcriptionally coordinated gene groups. Functional enrichment analysis of plastically expressed genes revealed pathway changes in hormone-mediated signaling, osmotic adjustment, cell wall remodeling, and programmed cell death, providing a mechanistic understanding of the biological processes underlying the phenotypic changes in A. philoxeroides. Both transcriptional modulation of environmentally sensitive loci and environmentally dependent control of regulatory loci influenced the plastic responses to the environment. Phenotypic responses and gene expression patterns to contrasting hydrological conditions were compared between A. philoxeroides and its alien congener Alternanthera pungens. The terricolous A. pungens displayed limited phenotypic plasticity to different treatments. It was postulated based on gene expression comparison that the interspecific variation in plasticity between A. philoxeroides and A. pungens was not due to environmentally-mediated changes in hormone levels but to variations in the type and relative abundance of different signal transducers and receptors expressed in the target tissue.
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Affiliation(s)
- Lexuan Gao
- Center for Evolutionary Biology and Institute of Biodiversity Science, Fudan UniversityShanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical GardenShanghai, China
| | - Yupeng Geng
- School of Ecology and Environmental Sciences, Institute of Ecology and Geobotany, Yunnan UniversityKunming, China
| | - Hongxing Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical GardenShanghai, China
| | - Yonghong Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical GardenShanghai, China
| | - Ji Yang
- Center for Evolutionary Biology and Institute of Biodiversity Science, Fudan UniversityShanghai, China
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121
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Hoang K, Matzkin LM, Bono JM. Transcriptional variation associated with cactus host plant adaptation in
Drosophila mettleri
populations. Mol Ecol 2015; 24:5186-99. [DOI: 10.1111/mec.13388] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Kim Hoang
- Biology Department University of Colorado Colorado Springs 1420 Austin Bluffs Parkway Colorado Springs CO 80918 USA
| | - Luciano M. Matzkin
- Department of Biological Sciences University of Alabama in Huntsville 301 Sparkman Drive Huntsville AL 35899 USA
- HudsonAlpha Institute for Biotechnology 601 Genome Way Huntsville AL 35806 USA
| | - Jeremy M. Bono
- Biology Department University of Colorado Colorado Springs 1420 Austin Bluffs Parkway Colorado Springs CO 80918 USA
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122
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Murren CJ, Auld JR, Callahan H, Ghalambor CK, Handelsman CA, Heskel MA, Kingsolver JG, Maclean HJ, Masel J, Maughan H, Pfennig DW, Relyea RA, Seiter S, Snell-Rood E, Steiner UK, Schlichting CD. Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity. Heredity (Edinb) 2015; 115:293-301. [PMID: 25690179 PMCID: PMC4815460 DOI: 10.1038/hdy.2015.8] [Citation(s) in RCA: 313] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/21/2014] [Accepted: 12/15/2014] [Indexed: 12/13/2022] Open
Abstract
Phenotypic plasticity is ubiquitous and generally regarded as a key mechanism for enabling organisms to survive in the face of environmental change. Because no organism is infinitely or ideally plastic, theory suggests that there must be limits (for example, the lack of ability to produce an optimal trait) to the evolution of phenotypic plasticity, or that plasticity may have inherent significant costs. Yet numerous experimental studies have not detected widespread costs. Explicitly differentiating plasticity costs from phenotype costs, we re-evaluate fundamental questions of the limits to the evolution of plasticity and of generalists vs specialists. We advocate for the view that relaxed selection and variable selection intensities are likely more important constraints to the evolution of plasticity than the costs of plasticity. Some forms of plasticity, such as learning, may be inherently costly. In addition, we examine opportunities to offset costs of phenotypes through ontogeny, amelioration of phenotypic costs across environments, and the condition-dependent hypothesis. We propose avenues of further inquiry in the limits of plasticity using new and classic methods of ecological parameterization, phylogenetics and omics in the context of answering questions on the constraints of plasticity. Given plasticity's key role in coping with environmental change, approaches spanning the spectrum from applied to basic will greatly enrich our understanding of the evolution of plasticity and resolve our understanding of limits.
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Affiliation(s)
- C J Murren
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - J R Auld
- Department of Biology, West Chester University, West Chester, PA, USA
| | - H Callahan
- Barnard College, Columbia University, New York, NY, USA
| | - C K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - C A Handelsman
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - M A Heskel
- Research School of Biology, Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - J G Kingsolver
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - H J Maclean
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - J Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - D W Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - R A Relyea
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - S Seiter
- Department of Ecology and Evolution, University of Colorado Boulder, Boulder, CO, USA
| | - E Snell-Rood
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, USA
| | - U K Steiner
- Department of Biology, University of Southern Denmark, Max-Planck Odense Centre on the Biodemography of Aging, Odense, Denmark
| | - C D Schlichting
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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123
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Foster SA, Wund MA, Graham MA, Earley RL, Gardiner R, Kearns T, Baker JA. Iterative development and the scope for plasticity: contrasts among trait categories in an adaptive radiation. Heredity (Edinb) 2015; 115:335-48. [PMID: 26243135 PMCID: PMC4815453 DOI: 10.1038/hdy.2015.66] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 06/02/2015] [Accepted: 06/04/2015] [Indexed: 01/19/2023] Open
Abstract
Phenotypic plasticity can influence evolutionary change in a lineage, ranging from facilitation of population persistence in a novel environment to directing the patterns of evolutionary change. As the specific nature of plasticity can impact evolutionary consequences, it is essential to consider how plasticity is manifested if we are to understand the contribution of plasticity to phenotypic evolution. Most morphological traits are developmentally plastic, irreversible, and generally considered to be costly, at least when the resultant phenotype is mis-matched to the environment. At the other extreme, behavioral phenotypes are typically activational (modifiable on very short time scales), and not immediately costly as they are produced by constitutive neural networks. Although patterns of morphological and behavioral plasticity are often compared, patterns of plasticity of life history phenotypes are rarely considered. Here we review patterns of plasticity in these trait categories within and among populations, comprising the adaptive radiation of the threespine stickleback fish Gasterosteus aculeatus. We immediately found it necessary to consider the possibility of iterated development, the concept that behavioral and life history trajectories can be repeatedly reset on activational (usually behavior) or developmental (usually life history) time frames, offering fine tuning of the response to environmental context. Morphology in stickleback is primarily reset only in that developmental trajectories can be altered as environments change over the course of development. As anticipated, the boundaries between the trait categories are not clear and are likely to be linked by shared, underlying physiological and genetic systems.
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Affiliation(s)
- S A Foster
- Department of Biology, Clark University, Worcester, MA, USA
| | - M A Wund
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - M A Graham
- Department of Biology, Clark University, Worcester, MA, USA
| | - R L Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - R Gardiner
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - T Kearns
- Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - J A Baker
- Department of Biology, Clark University, Worcester, MA, USA
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124
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Komoroske LM, Connon RE, Jeffries KM, Fangue NA. Linking transcriptional responses to organismal tolerance reveals mechanisms of thermal sensitivity in a mesothermal endangered fish. Mol Ecol 2015; 24:4960-81. [DOI: 10.1111/mec.13373] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Lisa M. Komoroske
- National Research Council under contract to Southwest Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; 8901 La Jolla Shores Drive La Jolla CA 92037 USA
- Wildlife, Fish & Conservation Biology; University of California; One Shields Avenue Davis CA 95616 USA
- Anatomy, Physiology & Cell Biology; School of Veterinary Medicine; University of California; One Shields Avenue Davis CA 95616 USA
| | - Richard E. Connon
- Anatomy, Physiology & Cell Biology; School of Veterinary Medicine; University of California; One Shields Avenue Davis CA 95616 USA
| | - Ken M. Jeffries
- Wildlife, Fish & Conservation Biology; University of California; One Shields Avenue Davis CA 95616 USA
- Anatomy, Physiology & Cell Biology; School of Veterinary Medicine; University of California; One Shields Avenue Davis CA 95616 USA
| | - Nann A. Fangue
- Wildlife, Fish & Conservation Biology; University of California; One Shields Avenue Davis CA 95616 USA
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125
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Macias-Muñoz A, Smith G, Monteiro A, Briscoe AD. Transcriptome-Wide Differential Gene Expression in Bicyclus anynana Butterflies: Female Vision-Related Genes Are More Plastic. Mol Biol Evol 2015; 33:79-92. [PMID: 26371082 DOI: 10.1093/molbev/msv197] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Vision is energetically costly to maintain. Consequently, over time many cave-adapted species downregulate the expression of vision genes or even lose their eyes and associated eye genes entirely. Alternatively, organisms that live in fluctuating environments, with different requirements for vision at different times, may evolve phenotypic plasticity for expression of vision genes. Here, we use a global transcriptomic and candidate gene approach to compare gene expression in the heads of a polyphenic butterfly. Bicyclus anynana have two seasonal forms that display sexual dimorphism and plasticity in eye morphology, and female-specific plasticity in opsin gene expression. Nonchoosy dry season females downregulate opsin expression, consistent with the high physiological cost of vision. To identify other genes associated with sexually dimorphic and seasonally plastic differences in vision, we analyzed RNA-sequencing data from whole head tissues. We identified two eye development genes (klarsicht and warts homologs) and an eye pigment biosynthesis gene (henna) differentially expressed between seasonal forms. By comparing sex-specific expression across seasonal forms, we found that klarsicht, warts, henna, and another eye development gene (domeless) were plastic in a female-specific manner. In a male-only analysis, white (w) was differentially expressed between seasonal forms. Reverse transcription polymerase chain reaction confirmed that warts and white are expressed in eyes only, whereas klarsicht, henna and domeless are expressed in both eyes and brain. We find that differential expression of eye development and eye pigment genes is associated with divergent eye phenotypes in B. anynana seasonal forms, and that there is a larger effect of season on female vision-related genes.
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Affiliation(s)
- Aide Macias-Muñoz
- Ecology and Evolutionary Biology, University of California, Irvine BEACON Center for the Study of Evolution in Action
| | - Gilbert Smith
- Ecology and Evolutionary Biology, University of California, Irvine BEACON Center for the Study of Evolution in Action
| | - Antónia Monteiro
- Biological Sciences, National University of Singapore, Singapore Yale-NUS College, Singapore
| | - Adriana D Briscoe
- Ecology and Evolutionary Biology, University of California, Irvine BEACON Center for the Study of Evolution in Action
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126
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Cardoso SD, Teles MC, Oliveira RF. Neurogenomic mechanisms of social plasticity. ACTA ACUST UNITED AC 2015; 218:140-9. [PMID: 25568461 DOI: 10.1242/jeb.106997] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Group-living animals must adjust the expression of their social behaviour to changes in their social environment and to transitions between life-history stages, and this social plasticity can be seen as an adaptive trait that can be under positive selection when changes in the environment outpace the rate of genetic evolutionary change. Here, we propose a conceptual framework for understanding the neuromolecular mechanisms of social plasticity. According to this framework, social plasticity is achieved by rewiring or by biochemically switching nodes of a neural network underlying social behaviour in response to perceived social information. Therefore, at the molecular level, it depends on the social regulation of gene expression, so that different genomic and epigenetic states of this brain network correspond to different behavioural states, and the switches between states are orchestrated by signalling pathways that interface the social environment and the genotype. Different types of social plasticity can be recognized based on the observed patterns of inter- versus intra-individual occurrence, time scale and reversibility. It is proposed that these different types of social plasticity rely on different proximate mechanisms at the physiological, neural and genomic level.
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Affiliation(s)
- Sara D Cardoso
- ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal
| | - Magda C Teles
- ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal
| | - Rui F Oliveira
- ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal
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127
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Yashin AI, Arbeev KG, Arbeeva LS, Wu D, Akushevich I, Kovtun M, Yashkin A, Kulminski A, Culminskaya I, Stallard E, Li M, Ukraintseva SV. How the effects of aging and stresses of life are integrated in mortality rates: insights for genetic studies of human health and longevity. Biogerontology 2015; 17:89-107. [PMID: 26280653 DOI: 10.1007/s10522-015-9594-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/25/2015] [Indexed: 12/21/2022]
Abstract
Increasing proportions of elderly individuals in developed countries combined with substantial increases in related medical expenditures make the improvement of the health of the elderly a high priority today. If the process of aging by individuals is a major cause of age related health declines then postponing aging could be an efficient strategy for improving the health of the elderly. Implementing this strategy requires a better understanding of genetic and non-genetic connections among aging, health, and longevity. We review progress and problems in research areas whose development may contribute to analyses of such connections. These include genetic studies of human aging and longevity, the heterogeneity of populations with respect to their susceptibility to disease and death, forces that shape age patterns of human mortality, secular trends in mortality decline, and integrative mortality modeling using longitudinal data. The dynamic involvement of genetic factors in (i) morbidity/mortality risks, (ii) responses to stresses of life, (iii) multi-morbidities of many elderly individuals, (iv) trade-offs for diseases, (v) genetic heterogeneity, and (vi) other relevant aging-related health declines, underscores the need for a comprehensive, integrated approach to analyze the genetic connections for all of the above aspects of aging-related changes. The dynamic relationships among aging, health, and longevity traits would be better understood if one linked several research fields within one conceptual framework that allowed for efficient analyses of available longitudinal data using the wealth of available knowledge about aging, health, and longevity already accumulated in the research field.
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Affiliation(s)
- Anatoliy I Yashin
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA. .,The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, 2024 W. Main Street, Room A102E, Durham, NC, 27705, USA.
| | - Konstantin G Arbeev
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Liubov S Arbeeva
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Deqing Wu
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Igor Akushevich
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Mikhail Kovtun
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Arseniy Yashkin
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Alexander Kulminski
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Irina Culminskaya
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Eric Stallard
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Miaozhu Li
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Svetlana V Ukraintseva
- The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.,The Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, 2024 W. Main Street, Room A105, Durham, NC, 27705, USA
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128
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Rocker MM, Noonan S, Humphrey C, Moya A, Willis BL, Bay LK. Expression of calcification and metabolism-related genes in response to elevated pCO2 and temperature in the reef-building coral Acropora millepora. Mar Genomics 2015; 24 Pt 3:313-8. [PMID: 26275825 DOI: 10.1016/j.margen.2015.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/05/2015] [Accepted: 08/05/2015] [Indexed: 02/07/2023]
Abstract
Declining health of scleractinian corals in response to deteriorating environmental conditions is widely acknowledged, however links between physiological and functional genomic responses of corals are less well understood. Here we explore growth and the expression of 20 target genes with putative roles in metabolism and calcification in the branching coral, Acropora millepora, in two separate experiments: 1) elevated pCO2 (464, 822, 1187 and 1638 μatm) and ambient temperature (27°C), and 2) elevated pCO2 (490 and 822 μatm) and temperature (28 and 31 °C). After 14 days of exposure to elevated pCO2 and ambient temperatures, no evidence of differential expression of either calcification or metabolism genes was detected between control and elevated pCO2 treatments. After 37 days of exposure to control and elevated pCO2, Ubiquinol-Cytochrome-C Reductase Subunit 2 gene (QCR2; a gene involved in complex III of the electron chain transport within the mitochondria and critical for generation of ATP) was significantly down-regulated in the elevated pCO2 treatment in both ambient and elevated temperature treatments. Overall, the general absence of a strong response to elevated pCO2 and temperature by the other 19 targeted calcification and metabolism genes suggests that corals may not be affected by these stressors on longer time scales (37 days). These results also highlight the potential for QCR2 to act as a biomarker of coral genomic responses to changing environments.
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Affiliation(s)
- Melissa M Rocker
- Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia; AIMS@JCU, Australian Institute of Marine Science, James Cook University, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences, James Cook University, Townsville, QLD 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.
| | - Sam Noonan
- Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia
| | - Craig Humphrey
- Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Bette L Willis
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Line K Bay
- Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
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129
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Kijimoto T, Snell-Rood EC, Pespeni MH, Rocha G, Kafadar K, Moczek AP. The nutritionally responsive transcriptome of the polyphenic beetle Onthophagus taurus and the importance of sexual dimorphism and body region. Proc Biol Sci 2015; 281:rspb.2014.2084. [PMID: 25377458 DOI: 10.1098/rspb.2014.2084] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Developmental responses to nutritional variation represent one of the ecologically most important classes of adaptive plasticity. However, knowledge of genome-wide patterns of nutrition-responsive gene expression is limited. Here, we studied genome-wide transcriptional responses to nutritional variation and their dependency on trait and sex in the beetle Onthophagus taurus. We find that averaged across the transcriptome, nutrition contributes less to overall variation in gene expression than do sex or body region, but that for a modest subset of genes nutrition is by far the most important determinant of expression variation. Furthermore, our results reject the hypothesis that a common machinery may underlie nutrition-sensitive development across body regions. Instead, we find that magnitude (measured by number of differentially expressed contigs), composition (measured by functional enrichment) and evolutionary consequences (measured by patterns of sequence variation) are heavily dependent on exactly which body region is considered and the degree of sexual dimorphism observed on a morphological level. More generally, our findings illustrate that studies into the developmental mechanisms and evolutionary consequences of nutrition-biased gene expression must take into account the dynamics and complexities imposed by other sources of variation in gene expression such as sexual dimorphism and trait type.
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Affiliation(s)
- Teiya Kijimoto
- Department of Biology, Indiana University, 915 East Third St., Bloomington, IN 47405, USA
| | - Emilie C Snell-Rood
- Department of Biology, Indiana University, 915 East Third St., Bloomington, IN 47405, USA Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
| | - Melissa H Pespeni
- Department of Biology, Indiana University, 915 East Third St., Bloomington, IN 47405, USA
| | - Guilherme Rocha
- Department of Statistics, Indiana University, 309 North Park Avenue, Bloomington, IN 47408, USA
| | - Karen Kafadar
- Department of Statistics, Indiana University, 309 North Park Avenue, Bloomington, IN 47408, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, 915 East Third St., Bloomington, IN 47405, USA
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130
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Matsunami M, Kitano J, Kishida O, Michimae H, Miura T, Nishimura K. Transcriptome analysis of predator- and prey-induced phenotypic plasticity in the Hokkaido salamander (Hynobius retardatus). Mol Ecol 2015; 24:3064-76. [DOI: 10.1111/mec.13228] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 04/29/2015] [Accepted: 05/01/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Masatoshi Matsunami
- Graduate School of Fisheries Sciences; Hokkaido University; Hakodate 041-8611 Japan
- Laboratory of Ecological Genetics; Graduate School of Environmental Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Jun Kitano
- Ecological Genetics Laboratory; National Institute of Genetics; Mishima 411-8540 Japan
| | - Osamu Kishida
- Teshio Experimental Forest; Field Science Center for Northern Biosphere; Hokkaido University; Toikanbetsu Horonobe 098-2943 Japan
| | - Hirofumi Michimae
- School of Pharmacy; Department of Clinical Medicine (Biostatistics); Kitasato University; Tokyo 108-8641 Japan
| | - Toru Miura
- Laboratory of Ecological Genetics; Graduate School of Environmental Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Kinya Nishimura
- Graduate School of Fisheries Sciences; Hokkaido University; Hakodate 041-8611 Japan
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131
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RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs. G3-GENES GENOMES GENETICS 2015; 5:1481-91. [PMID: 26002924 PMCID: PMC4502382 DOI: 10.1534/g3.115.019067] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Parallel changes in body shape may evolve in response to similar environmental conditions, but whether such parallel phenotypic changes share a common genetic basis is still debated. The goal of this study was to assess whether parallel phenotypic changes could be explained by genetic parallelism, multiple genetic routes, or both. We first provide evidence for parallelism in fish shape by using geometric morphometrics among 300 fish representing five species pairs of Lake Whitefish. Using a genetic map comprising 3438 restriction site−associated DNA sequencing single-nucleotide polymorphisms, we then identified quantitative trait loci underlying body shape traits in a backcross family reared in the laboratory. A total of 138 body shape quantitative trait loci were identified in this cross, thus revealing a highly polygenic architecture of body shape in Lake Whitefish. Third, we tested for evidence of genetic parallelism among independent wild populations using both a single-locus method (outlier analysis) and a polygenic approach (analysis of covariation among markers). The single-locus approach provided limited evidence for genetic parallelism. However, the polygenic analysis revealed genetic parallelism for three of the five lakes, which differed from the two other lakes. These results provide evidence for both genetic parallelism and multiple genetic routes underlying parallel phenotypic evolution in fish shape among populations occupying similar ecological niches.
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132
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Podgorniak T, Milan M, Pujolar JM, Maes GE, Bargelloni L, De Oliveira E, Pierron F, Daverat F. Differences in brain gene transcription profiles advocate for an important role of cognitive function in upstream migration and water obstacles crossing in European eel. BMC Genomics 2015; 16:378. [PMID: 25962588 PMCID: PMC4427925 DOI: 10.1186/s12864-015-1589-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/27/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND European eel is a panmictic species, whose decline has been recorded since the last 20 years. Among human-induced environmental factors of decline, the impact of water dams during species migration is questioned. The main issue of this study was to pinpoint phenotypic traits that predisposed glass eels to successful passage by water barriers. The approach of the study was individual-centred and without any a priori hypothesis on traits involved in the putative obstacles selective pressure. We analyzed the transcription level of 14,913 genes. RESULTS Transcriptome analysis of three tissues (brain, liver and muscle) from individuals sampled on three successive forebays separated by water obstacles indicated different gene transcription profiles in brain between the two upstream forebays. No differences in gene transcription levels were observed in liver and muscle samples among segments. A total of 26 genes were differentially transcribed in brain. These genes encode for, among others, keratins, cytokeratins, calcium binding proteins (S100 family), cofilin, calmodulin, claudin and thy-1 membrane glycoprotein. The functional analysis of these genes highlighted a putative role of cytoskeletal dynamics and synaptic plasticity in fish upstream migration. CONCLUSION Synaptic connections in brain are solicited while eels are climbing the obstacles with poorly designed fishways. Successful passage by such barriers can be related to spatial learning and spatial orientation abilities when fish is out of the water.
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Affiliation(s)
- Tomasz Podgorniak
- Irstea Bordeaux, UR EABX, HYNES (Irstea - EDF R&D), 50 avenue de Verdun, Cestas, 33612, Cedex, France.
| | - Massimo Milan
- University of Padova, Viale dell'Università 16, Legnaro, 35020, PD, Italy.
| | - Jose Marti Pujolar
- University of Padova, Viale dell'Università 16, Legnaro, 35020, PD, Italy. .,Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C, DK-8000, Denmark.
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Marine and Environmental Sciences, James Cook University, Townsville, Qld 4811, Australia. .,Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), Leuven, B-3000, Belgium.
| | - Luca Bargelloni
- University of Padova, Viale dell'Università 16, Legnaro, 35020, PD, Italy.
| | - Eric De Oliveira
- EDF R&D LNHE, HYNES (Irstea-EDF R&D), 6, quai Watier, Bat Q, Chatou, 78400, France.
| | - Fabien Pierron
- Univ. Bordeaux, EPOC, UMR 5805, Talence, F-33400, France. .,CNRS, EPOC, UMR 5805, Talence, F-33400, France.
| | - Francoise Daverat
- Irstea Bordeaux, UR EABX, HYNES (Irstea - EDF R&D), 50 avenue de Verdun, Cestas, 33612, Cedex, France.
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133
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Defo MA, Bernatchez L, Campbell PGC, Couture P. Transcriptional and biochemical markers in transplanted Perca flavescens to characterize cadmium- and copper-induced oxidative stress in the field. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 162:39-53. [PMID: 25770975 DOI: 10.1016/j.aquatox.2015.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 06/04/2023]
Abstract
Despite recent progress achieved in elucidating the mechanisms underlying local adaptation to pollution, little is known about the evolutionary change that may be occurring at the molecular level. The goal of this study was to examine patterns of gene transcription and biochemical responses induced by metal accumulation in clean yellow perch (Perca flavescens) and metal depuration in contaminated fish in a mining and smelting region of Canada. Fish were collected from a reference lake (lake Opasatica) and a Cd, Cu and Zn contaminated lake (lake Dufault) located in the Rouyn-Noranda region (Qc, Canada) and caged for one or four weeks in their own lake or transplanted in the other lake. Free-ranging fish from the same lakes were also collected. Kidney Cd and Cu concentrations in clean fish caged in the contaminated lake increased with the time of exposure, but metal depuration did not occur in contaminated fish caged in the clean lake. After 4 weeks, the major retinoid metabolites analysed, the percentage of free dehydroretinol (dROH) and the retinol dehydrogenase-2 (rdh-2) transcription level in liver decreased in clean fish transplanted into the metal-contaminated lake, suggesting that metal exposure negatively impacted retinoid metabolism. However, we observed an increase in almost all of the retinoid parameters analysed in fish from the metal-impacted lake caged in the same lake, which we interpret as an adaptation response to higher ambient metal concentration. In support of this hypothesis, liver transcription levels of microsomal glutathione-S-transferase-3 (mgst-3) and glucose-6-phosphate dehydrogenase (g6pdh) were enhanced in clean fish transplanted into the metal-contaminated lake and this up-regulation was accompanied by an increase in the activities of corresponding enzymes, involved in antioxidant response. However, although in the same fish the transcription level of Cu/Zn superoxide dismutase (Cu/Zn sod) was also increased, this did not lead to a change in the activity of the SOD enzyme, suggesting that this upregulation was aimed at maintaining SOD-related antioxidant capacities. In contrast, the transcription level of the cat gene, which did not change in contaminated fish, did not compensate for the decrease of CAT activity. After 4 weeks of exposure, some plastic responses of the clean fish were observed when they were transplanted in the metal-contaminated lake. However, probably as a consequence of the prior 80 years of exposure to metals, the contaminated population showed a limited plastic response in the expression of the majority of the candidate genes tested, when they were transplanted in the reference lake. The overall findings of this field investigation highlight how yellow perch molecularly and biochemically responded to a sudden or relatively long-term exposure (4 weeks) to a cocktail of metals.
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Affiliation(s)
- Michel A Defo
- Institut National De La Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 De La Couronne, Québec, QC G1K 9A9, Canada
| | - Louis Bernatchez
- Institut De Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
| | - Peter G C Campbell
- Institut National De La Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 De La Couronne, Québec, QC G1K 9A9, Canada
| | - Patrice Couture
- Institut National De La Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 De La Couronne, Québec, QC G1K 9A9, Canada
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134
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Wilkinson GS, Breden F, Mank JE, Ritchie MG, Higginson AD, Radwan J, Jaquiery J, Salzburger W, Arriero E, Barribeau SM, Phillips PC, Renn SCP, Rowe L. The locus of sexual selection: moving sexual selection studies into the post-genomics era. J Evol Biol 2015; 28:739-55. [PMID: 25789690 DOI: 10.1111/jeb.12621] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 02/07/2023]
Abstract
Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology.
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Affiliation(s)
- G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
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135
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Leder EH, McCairns RJS, Leinonen T, Cano JM, Viitaniemi HM, Nikinmaa M, Primmer CR, Merilä J. The evolution and adaptive potential of transcriptional variation in sticklebacks--signatures of selection and widespread heritability. Mol Biol Evol 2015; 32:674-89. [PMID: 25429004 PMCID: PMC4327155 DOI: 10.1093/molbev/msu328] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Evidence implicating differential gene expression as a significant driver of evolutionary novelty continues to accumulate, but our understanding of the underlying sources of variation in expression, both environmental and genetic, is wanting. Heritability in particular may be underestimated when inferred from genetic mapping studies, the predominant "genetical genomics" approach to the study of expression variation. Such uncertainty represents a fundamental limitation to testing for adaptive evolution at the transcriptomic level. By studying the inheritance of expression levels in 10,495 genes (10,527 splice variants) in a threespine stickleback pedigree consisting of 563 individuals, half of which were subjected to a thermal treatment, we show that 74-98% of transcripts exhibit significant additive genetic variance. Dominance variance is also prevalent (41-99% of transcripts), and genetic sources of variation seem to play a more significant role in expression variance in the liver than a key environmental variable, temperature. Among-population comparisons suggest that the majority of differential expression in the liver is likely due to neutral divergence; however, we also show that signatures of directional selection may be more prevalent than those of stabilizing selection. This predominantly aligns with the neutral model of evolution for gene expression but also suggests that natural selection may still act on transcriptional variation in the wild. As genetic variation both within- and among-populations ultimately defines adaptive potential, these results indicate that broad adaptive potential may be found within the transcriptome.
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Affiliation(s)
- Erica H Leder
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - R J Scott McCairns
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Tuomas Leinonen
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - José M Cano
- Research Unit of Biodiversity (UO-CSIC-PA), University of Oviedo, Mieres, Spain
| | - Heidi M Viitaniemi
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - Mikko Nikinmaa
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - Craig R Primmer
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
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136
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Simões JM, Barata EN, Harris RM, O'Connell LA, Hofmann HA, Oliveira RF. Social odors conveying dominance and reproductive information induce rapid physiological and neuromolecular changes in a cichlid fish. BMC Genomics 2015; 16:114. [PMID: 25766511 PMCID: PMC4344806 DOI: 10.1186/s12864-015-1255-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 01/19/2015] [Indexed: 01/01/2023] Open
Abstract
Background Social plasticity is a pervasive feature of animal behavior. Animals adjust the expression of their social behavior to the daily changes in social life and to transitions between life-history stages, and this ability has an impact in their Darwinian fitness. This behavioral plasticity may be achieved either by rewiring or by biochemically switching nodes of the neural network underlying social behavior in response to perceived social information. Independent of the proximate mechanisms, at the neuromolecular level social plasticity relies on the regulation of gene expression, such that different neurogenomic states emerge in response to different social stimuli and the switches between states are orchestrated by signaling pathways that interface the social environment and the genotype. Here, we test this hypothesis by characterizing the changes in the brain profile of gene expression in response to social odors in the Mozambique Tilapia, Oreochromis mossambicus. This species has a rich repertoire of social behaviors during which both visual and chemical information are conveyed to conspecifics. Specifically, dominant males increase their urination frequency during agonist encounters and during courtship to convey chemical information reflecting their dominance status. Results We recorded electro-olfactograms to test the extent to which the olfactory epithelium can discriminate between olfactory information from dominant and subordinate males as well as from pre- and post-spawning females. We then performed a genome-scale gene expression analysis of the olfactory bulb and the olfactory cortex homolog in order to identify the neuromolecular systems involved in processing these social stimuli. Conclusions Our results show that different olfactory stimuli from conspecifics’ have a major impact in the brain transcriptome, with different chemical social cues eliciting specific patterns of gene expression in the brain. These results confirm the role of rapid changes in gene expression in the brain as a genomic mechanism underlying behavioral plasticity and reinforce the idea of an extensive transcriptional plasticity of cichlid genomes, especially in response to rapid changes in their social environment. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1255-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José M Simões
- Unidade de Investigação em Eco-Etologia, ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041, Lisbon, Portugal. .,Integrative Behavioural Biology Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal. .,Champalimaud Neuroscience Programme, Champalimaud Foundation, Lisbon, Portugal.
| | - Eduardo N Barata
- CCMAR-CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal. .,Departamento de Biologia, Universidade de Évora, Apartado 94, 7002-554, Évora, Portugal.
| | - Rayna M Harris
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA. .,Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Lauren A O'Connell
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA. .,Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA. .,Current address: FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA.
| | - Hans A Hofmann
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA. .,Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA. .,Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA.
| | - Rui F Oliveira
- Unidade de Investigação em Eco-Etologia, ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041, Lisbon, Portugal. .,Integrative Behavioural Biology Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal. .,Champalimaud Neuroscience Programme, Champalimaud Foundation, Lisbon, Portugal.
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137
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Cini A, Patalano S, Segonds-Pichon A, Busby GBJ, Cervo R, Sumner S. Social parasitism and the molecular basis of phenotypic evolution. Front Genet 2015; 6:32. [PMID: 25741361 PMCID: PMC4332356 DOI: 10.3389/fgene.2015.00032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/23/2015] [Indexed: 11/21/2022] Open
Abstract
Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer-Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization.
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Affiliation(s)
- Alessandro Cini
- Dipartimento di Biologia, Università di FirenzeFirenze, Italy
| | - Solenn Patalano
- Institute of Zoology, Zoological Society of LondonLondon, UK
- The Babraham Institute, Babraham Research Campus – CambridgeCambridge, UK
| | | | - George B. J. Busby
- Institute of Zoology, Zoological Society of LondonLondon, UK
- Wellcome Trust Centre for Human GeneticsOxford, UK
| | - Rita Cervo
- Dipartimento di Biologia, Università di FirenzeFirenze, Italy
| | - Seirian Sumner
- Institute of Zoology, Zoological Society of LondonLondon, UK
- School of Biological Sciences, University of BristolBristol, UK
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138
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Carvalho MJA, Mirth CK. Coordinating morphology with behavior during development: an integrative approach from a fly perspective. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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139
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Alvarez M, Schrey AW, Richards CL. Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution? Mol Ecol 2015; 24:710-25. [PMID: 25604587 DOI: 10.1111/mec.13055] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 12/13/2022]
Abstract
Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.
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Affiliation(s)
- Mariano Alvarez
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, USA
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Integrative Genomic Approaches to Studying Epigenetic Mechanisms of Phenotypic Plasticity in the Aphid. SHORT VIEWS ON INSECT GENOMICS AND PROTEOMICS 2015. [DOI: 10.1007/978-3-319-24235-4_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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141
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Evolutionary genetic bases of longevity and senescence. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 847:1-44. [PMID: 25916584 DOI: 10.1007/978-1-4939-2404-2_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Senescence, as a time-dependent developmental process, affects all organisms at every stage in their development and growth. During this process, genetic, epigenetic and environmental factors are known to introduce a wide range of variation for longevity among individuals. As an important life-history trait, longevity shows ontogenetic relationships with other complex traits, and hence may be viewed as a composite trait. Factors that influence the origin and maintenance of diversity of life are ultimately governed by Darwinian processes. Here we review evolutionary genetic mechanisms underlying longevity and senescence in humans from a life-history and genotype-epigenetic-phenotype (G-E-P) map prospective. We suggest that synergistic and cascading effects of cis-ruptive mechanisms in the genome, and epigenetic disruptive processes in relation to environmental factors may lead to sequential slippage in the G-E-P space. These mechanisms accompany age, stage and individual specific senescent processes, influenced by positive pleiotropy of certain genes, superior genome integrity, negative-frequency dependent selection and other factors that universally regulate rarity in nature. Finally we interpret life span as an inherent property of self-organizing systems that, accordingly, maintain species-specific limits for the entire complex of fitness traits. We conclude that Darwinian approaches provide unique opportunities to discover the biological bases of longevity as well as devise individual specific medical or other interventions toward improving health span.
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142
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Westbrook JW, Walker AR, Neves LG, Munoz P, Resende MFR, Neale DB, Wegrzyn JL, Huber DA, Kirst M, Davis JM, Peter GF. Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis across environments, ages, and populations. THE NEW PHYTOLOGIST 2015; 205:627-641. [PMID: 25266813 DOI: 10.1111/nph.13074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/14/2014] [Indexed: 06/03/2023]
Abstract
Genetically improving constitutive resin canal development in Pinus stems may enhance the capacity to synthesize terpenes for bark beetle resistance, chemical feedstocks, and biofuels. To discover genes that potentially regulate axial resin canal number (RCN), single nucleotide polymorphisms (SNPs) in 4027 genes were tested for association with RCN in two growth rings and three environments in a complex pedigree of 520 Pinus taeda individuals (CCLONES). The map locations of associated genes were compared with RCN quantitative trait loci (QTLs) in a (P. taeda × Pinus elliottii) × P. elliottii pseudo-backcross of 345 full-sibs (BC1). Resin canal number was heritable (h(2) ˜ 0.12-0.21) and positively genetically correlated with xylem growth (rg ˜ 0.32-0.72) and oleoresin flow (rg ˜ 0.15-0.51). Sixteen well-supported candidate regulators of RCN were discovered in CCLONES, including genes associated across sites and ages, unidirectionally associated with oleoresin flow and xylem growth, and mapped to RCN QTLs in BC1. Breeding is predicted to increase RCN 11% in one generation and could be accelerated with genomic selection at accuracies of 0.45-0.52 across environments. There is significant genetic variation for RCN in loblolly pine, which can be exploited in breeding for elevated terpene content.
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Affiliation(s)
- Jared W Westbrook
- Forest Genomics Laboratory, Genetics Institute, University of Florida, 1376 Mowry Rd, Rm 320, Gainesville, FL, 32611, USA; Plant Molecular and Cellular Biology graduate program, University of Florida, Gainesville, PO Box 110410, FL 32611, USA
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143
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Dixon GB, Bay LK, Matz MV. Bimodal signatures of germline methylation are linked with gene expression plasticity in the coral Acropora millepora. BMC Genomics 2014; 15:1109. [PMID: 25511458 PMCID: PMC4378018 DOI: 10.1186/1471-2164-15-1109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/10/2014] [Indexed: 11/24/2022] Open
Abstract
Background In invertebrates, genes belonging to dynamically regulated functional categories appear to be less methylated than “housekeeping” genes, suggesting that DNA methylation may modulate gene expression plasticity. To date, however, experimental evidence to support this hypothesis across different natural habitats has been lacking. Results Gene expression profiles were generated from 30 pairs of genetically identical fragments of coral Acropora millepora reciprocally transplanted between distinct natural habitats for 3 months. Gene expression was analyzed in the context of normalized CpG content, a well-established signature of historical germline DNA methylation. Genes with weak methylation signatures were more likely to demonstrate differential expression based on both transplant environment and population of origin than genes with strong methylation signatures. Moreover, the magnitude of expression differences due to environment and population were greater for genes with weak methylation signatures. Conclusions Our results support a connection between differential germline methylation and gene expression flexibility across environments and populations. Studies of phylogenetically basal invertebrates such as corals will further elucidate the fundamental functional aspects of gene body methylation in Metazoa. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1109) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Groves B Dixon
- Institute for Cell and Molecular Biology, University of Texas Austin, Austin, USA.
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144
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Rosvall KA, Peterson MP. Behavioral effects of social challenges and genomic mechanisms of social priming: What's testosterone got to do with it? Curr Zool 2014; 60:791-803. [PMID: 27721823 DOI: 10.1093/czoolo/60.6.791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Social challenges from rival conspecifics are common in the lives of animals, and changes in an animal's social environment can influence physiology and behavior in ways that appear to be adaptive in the face of continued social instability (i.e. social priming). Recently, it has become clear that testosterone, long thought to be the primary mediator of these effects, may not always change in response to social challenges, an observation that highlights gaps in our understanding of the proximate mechanisms by which animals respond to their social environment. Here, our goal is to address the degree to which testosterone mediates organismal responses to social cues. To this end, we review the behavioral and physiological consequences of social challenges, as well as their underlying hormonal and gene regulatory mechanisms. We also present a new case study from a wild songbird, the dark-eyed junco (Junco hyemalis), in which we find largely divergent genome-wide transcriptional changes induced by social challenges and testosterone, respectively, in muscle and liver tissue. Our review underscores the diversity of mechanisms that link the dynamic social environment with an organisms' genomic, hormonal, and behavioral state. This diversity among species, and even among tissues within an organism, reveals new insights into the pattern and process by which evolution may alter proximate mechanisms of social priming.
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Affiliation(s)
- Kimberly A Rosvall
- Indiana University, Department of Biology and Center for the Integrative Study of Animal Behavior
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145
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Mandic M, Ramon ML, Gracey AY, Richards JG. Divergent transcriptional patterns are related to differences in hypoxia tolerance between the intertidal and the subtidal sculpins. Mol Ecol 2014; 23:6091-103. [PMID: 25370158 DOI: 10.1111/mec.12991] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 11/28/2022]
Abstract
Transcriptionally mediated phenotypic plasticity as a mechanism of modifying traits in response to an environmental challenge remains an important area of study. We compared the transcriptional responses to low oxygen (hypoxia) of the hypoxia-tolerant intertidal fish, the tidepool sculpin (Oligocottus maculosus) with the closely related hypoxia-intolerant subtidal fish, the silverspotted sculpin (Blepsias cirrhosus) to determine whether these species use different mechanisms to cope with hypoxia. Individuals from each species were exposed to environmental O(2) tensions chosen to yield a similar level of tissue hypoxia, and gene transcription was assessed in the liver over time. There was an effect of time in hypoxia, where the greatest transcriptional change in the silverspotted sculpin occurred between 3 and 24 h in contrast to the tidepool sculpin where the largest transcriptional change occurred between 24 and 72 h of hypoxia. A number of genes showed similar hypoxia-induced transcription patterns in both species (e.g. genes associated with glycolysis and apoptosis) suggesting they are involved in a conserved hypoxia response. A large set of genes showed divergent transcriptional patterns in the two species, including fatty acid oxidation and oxidative phosphorylation, suggesting that these biological processes may contribute to explaining variation in hypoxia tolerance in these species. When both species were exposed to a single environmental O(2) tension, large transcriptional responses were seen in the hypoxia-intolerant silverspotted sculpin while almost no response was observed in the hypoxia-tolerant tidepool sculpin. Overall, divergent transcription patterns in response to both magnitude and duration of hypoxia provide insights into the processes that may determine an animal's capacity to tolerate frequent bouts of hypoxia in the wild.
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Affiliation(s)
- Milica Mandic
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada; Bamfield Marine Sciences Centre, 100 Pachena Rd., Bamfield, BC, V0R 1B0, Canada
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146
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Pertoldi C, Bundgaard J, Loeschcke V, Barker JSF. The phenotypic variance gradient - a novel concept. Ecol Evol 2014; 4:4230-6. [PMID: 25540685 PMCID: PMC4267862 DOI: 10.1002/ece3.1298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/22/2014] [Accepted: 10/01/2014] [Indexed: 11/13/2022] Open
Abstract
Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely "a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added". This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a "phenotypic variance gradient", are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization.
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Affiliation(s)
- Cino Pertoldi
- Department 18/Section of Environmental Engineering, Aalborg UniversityAalborg, Denmark
- Aalborg ZooAalborg, Denmark
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147
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Pfennig DW, Ehrenreich IM. Towards a gene regulatory network perspective on phenotypic plasticity, genetic accommodation and genetic assimilation. Mol Ecol 2014; 23:4438-40. [PMID: 25208504 DOI: 10.1111/mec.12887] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 08/14/2014] [Indexed: 12/15/2022]
Abstract
Many organisms can produce alternative phenotypes in direct response to different environmental conditions, a phenomenon known as phenotypic plasticity. The environmentally sensitive gene regulatory networks (GRNs) that mediate such developmental flexibility are largely unknown. Yet, characterizing these GRNs is important not only for elucidating plasticity's molecular basis, but also for shedding light onto whether and how plasticity might impact evolution. In this issue of Molecular Ecology, Schneider et al.) describe one of the first efforts to determine the GRN underlying a plastic trait. They focus on diet-induced plasticity in the cichlid fish, Astatoreochromis alluaudi. Depending on whether soft food (e.g. insects) or hard food (e.g. molluscs) is consumed, this species forms a lower pharyngeal jaw (LPJ) with many fine teeth or with fewer molar-like teeth, respectively (Fig. 1). The authors previously identified genes that are differentially expressed between LPJ morphs during early development. In the present study, they examine the expression of 19 of these genes across development and diet. By analysing these transcriptional data in combination with information on putative transcription factor binding sites, they construct a GRN that explains observed gene expression patterns and is likely to control LPJ morphology. This work advances our understanding of how plasticity can arise as a consequence of environmentally sensitive GRNs and promises to help illuminate how changes in such GRNs could facilitate evolution.
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Affiliation(s)
- David W Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
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148
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Plasticity-mediated persistence in new and changing environments. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2014; 2014:416497. [PMID: 25386380 PMCID: PMC4216699 DOI: 10.1155/2014/416497] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/18/2022]
Abstract
Baldwin's synthesis of the Organicist position, first published in 1896 and elaborated in 1902, sought to rescue environmentally induced phenotypes from disrepute by showing their Darwinian significance. Of particular interest to Baldwin was plasticity's mediating role during environmental change or colonization—plastic individuals were more likely to successfully survive and reproduce in new environments than were nonplastic individuals. Once a population of plastic individuals had become established, plasticity could further mediate the future course of evolution. The evidence for plasticity-mediated persistence (PMP) is reviewed here with a particular focus on evolutionary rescue experiments, studies on invasive success, and the role of learning in survival. Many PMP studies are methodologically limited, showing that preexistent plasticity has utility in new environments (soft PMP) rather than directly demonstrating that plasticity is responsible for persistence (hard PMP). An ideal PMP study would be able to demonstrate that (1) plasticity preexisted environmental change, (2) plasticity was fortuitously beneficial in the new environment, (3) plasticity was responsible for individual persistence in the new environment, and (4) plasticity was responsible for population persistence in succeeding generations. Although PMP is not ubiquitous, Baldwin's hypotheses have been largely vindicated in theoretical and empirical studies, but much work remains.
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Frías-Alvarez P, Macías Garcia C, Vázquez-Vega LF, Zúñiga-Vega JJ. Spatial and temporal variation in superfoetation and related life history traits of two viviparous fishes: Poeciliopsis gracilis and P. infans. Naturwissenschaften 2014; 101:1085-98. [DOI: 10.1007/s00114-014-1247-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/23/2014] [Accepted: 09/25/2014] [Indexed: 11/28/2022]
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Yampolsky LY, Zeng E, Lopez J, Williams PJ, Dick KB, Colbourne JK, Pfrender ME. Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia. BMC Genomics 2014; 15:859. [PMID: 25282344 PMCID: PMC4201682 DOI: 10.1186/1471-2164-15-859] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/23/2014] [Indexed: 12/01/2022] Open
Abstract
Background Gene expression regulation is one of the fundamental mechanisms of phenotypic plasticity and is expected to respond to selection in conditions favoring phenotypic response. The observation that many organisms increase their stress tolerance after acclimation to moderate levels of stress is an example of plasticity which has been long hypothesized to be based on adaptive changes in gene expression. We report genome-wide patterns of gene expression in two heat-tolerant and two heat-sensitive parthenogenetic clones of the zooplankton crustacean Daphnia pulex exposed for three generations to either optimal (18°C) or substressful (28°C) temperature. Results A large number of genes responded to temperature and many demonstrated a significant genotype-by-environment (GxE) interaction. Among genes with a significant GxE there were approximately equally frequent instances of canalization, i.e. stronger plasticity in heat-sensitive than in heat-tolerant clones, and of enhancement of plasticity along the evolutionary vector toward heat tolerance. The strongest response observed is the across-the-board down-regulation of a variety of genes occurring in heat-tolerant, but not in heat-sensitive clones. This response is particularly obvious among genes involved in core metabolic pathways and those responsible for transcription, translation and DNA repair. Conclusions The observed down-regulation of metabolism, consistent with previous findings in yeast and Drosophila, may reflect a general compensatory stress response. The associated down-regulation of DNA repair pathways potentially creates a trade-off between short-term benefits of survival at high temperature and long-term costs of accelerated mutation accumulation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-859) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lev Y Yampolsky
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN 37641, USA.
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