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Laplante K, Derome N. Parallel changes in the taxonomical structure of bacterial communities exposed to a similar environmental disturbance. Ecol Evol 2012; 1:489-501. [PMID: 22393517 PMCID: PMC3287327 DOI: 10.1002/ece3.37] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 11/25/2022] Open
Abstract
Bacterial communities play a central role in ecosystems, by regulating biogeochemical fluxes. Therefore, understanding how multiple functional interactions between species face environmental perturbations is a major concern in conservation biology. Because bacteria can use several strategies, including horizontal gene transfers (HGT), to cope with rapidly changing environmental conditions, potential decoupling between function and taxonomy makes the use of a given species as a general bioindicator problematic. The present work is a first step to characterize the impact of a recent polymetallic gradient over the taxonomical networks of five lacustrine bacterial communities. Given that evolutionary convergence represents one of the best illustration of natural selection, we focused on a system composed of two pairs of impacted and clean lakes in order to test whether similar perturbation exerts a comparable impact on the taxonomical networks of independent bacterial communities. First, we showed that similar environmental stress drove parallel structural changes at the taxonomic level on two independent bacterial communities. Second, we showed that a long-term exposure to contaminant gradients drove significant taxonomic structure changes within three interconnected bacterial communities. Thus, this model lake system is relevant to characterize the strategies, namely acclimation and/or adaptation, of bacterial communities facing environmental perturbations, such as metal contamination.
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Affiliation(s)
- Karine Laplante
- Institut de Biologie Intégrative et des Systèmes (IBIS) 1030 rue de la Médecine Université Laval, Québec, Canada
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52
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Evans ML, Bernatchez L. Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and nonparallel physiological divergence. J Evol Biol 2012; 25:1823-34. [PMID: 22830417 DOI: 10.1111/j.1420-9101.2012.02570.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 05/31/2012] [Indexed: 12/31/2022]
Abstract
Across multiple lakes in North America, lake whitefish (Coregonus clupeaformis) have independently evolved 'dwarf' and 'normal' sympatric species pairs that exhibit pronounced phenotypic and genetic divergence. In particular, traits associated with metabolism have been shown to be highly differentiated between whitefish species. Here, we examine the transcription of genes associated with the five mitochondrial and nuclear genome-encoded oxidative phosphorylation (OXPHOS) complexes, the primary physiological mechanism responsible for the production of ATP, in whitefish species pairs from Cliff Lake and Webster Lake in Maine, USA. We observed OXPHOS gene transcription divergence between dwarf and normal whitefish in each of the two lakes, with the former exhibiting transcription upregulation for genes associated with each of the OXPHOS complexes. We also observed a significant influence of lake on transcription levels for some of the genes, indicating that inter-lake ecological or genetic differences are contributing to variation in OXPHOS gene transcription levels. Together, our results support the hypothesis that metabolic divergence is a critical adaptation involved in whitefish speciation and implicate OXPHOS gene upregulation as a factor involved in meeting the enhanced energetic demands of dwarf whitefish. Further studies are now needed to evaluate the contribution of genetically vs. plasticity driven variation in transcription associated with this critical physiological pathway.
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Affiliation(s)
- M L Evans
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, QC, Canada.
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53
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EVANS MELISSAL, PRAEBEL KIM, PERUZZI STEFANO, BERNATCHEZ LOUIS. Parallelism in the oxygen transport system of the lake whitefish: the role of physiological divergence in ecological speciation. Mol Ecol 2012; 21:4038-50. [DOI: 10.1111/j.1365-294x.2012.05682.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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54
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Abstract
Populations that have independently evolved reproductive isolation from their ancestors while remaining reproductively cohesive have undergone parallel speciation. A specific type of parallel speciation, known as parallel ecological speciation, is one of several forms of evidence for ecology's role in speciation. In this paper we search the literature for candidate examples of parallel ecological speciation in plants. We use four explicit criteria (independence, isolation, compatibility, and selection) to judge the strength of evidence for each potential case. We find that evidence for parallel ecological speciation in plants is unexpectedly scarce, especially relative to the many well-characterized systems in animals. This does not imply that ecological speciation is uncommon in plants. It only implies that evidence from parallel ecological speciation is rare. Potential explanations for the lack of convincing examples include a lack of rigorous testing and the possibility that plants are less prone to parallel ecological speciation than animals.
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Pavey SA, Sutherland BJG, Leong J, Robb A, von Schalburg K, Hamon TR, Koop BF, Nielsen JL. Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka). BMC Ecol 2011; 11:31. [PMID: 22136247 PMCID: PMC3295673 DOI: 10.1186/1472-6785-11-31] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 12/02/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are a growing number of genomes sequenced with tentative functions assigned to a large proportion of the individual genes. Model organisms in laboratory settings form the basis for the assignment of gene function, and the ecological context of gene function is lacking. This work addresses this shortcoming by investigating expressed genes of sockeye salmon (Oncorhynchus nerka) muscle tissue. We compared morphology and gene expression in natural juvenile sockeye populations related to river and lake habitats. Based on previously documented divergent morphology, feeding strategy, and predation in association with these distinct environments, we expect that burst swimming is favored in riverine population and continuous swimming is favored in lake-type population. In turn we predict that morphology and expressed genes promote burst swimming in riverine sockeye and continuous swimming in lake-type sockeye. RESULTS We found the riverine sockeye population had deep, robust bodies and lake-type had shallow, streamlined bodies. Gene expression patterns were measured using a 16 k microarray, discovering 141 genes with significant differential expression. Overall, the identity and function of these genes was consistent with our hypothesis. In addition, Gene Ontology (GO) enrichment analyses with a larger set of differentially expressed genes found the "biosynthesis" category enriched for the riverine population and the "metabolism" category enriched for the lake-type population. CONCLUSIONS This study provides a framework for understanding sockeye life history from a transcriptomic perspective and a starting point for more extensive, targeted studies determining the ecological context of genes.
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Affiliation(s)
- Scott A Pavey
- National Park Service, Katmai National Park; PO Box 7, King Salmon, AK 99613, USA.
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56
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Whiteley AR, Bhat A, Martins EP, Mayden RL, Arunachalam M, Uusi-Heikkilä S, Ahmed ATA, Shrestha J, Clark M, Stemple D, Bernatchez L. Population genomics of wild and laboratory zebrafish (Danio rerio). Mol Ecol 2011; 20:4259-76. [PMID: 21923777 PMCID: PMC3627301 DOI: 10.1111/j.1365-294x.2011.05272.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST-based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among-clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall FST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low FST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.
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Affiliation(s)
- Andrew R Whiteley
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA.
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57
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Sanger TJ, Revell LJ, Gibson-Brown JJ, Losos JB. Repeated modification of early limb morphogenesis programmes underlies the convergence of relative limb length in Anolis lizards. Proc Biol Sci 2011; 279:739-48. [PMID: 21849319 DOI: 10.1098/rspb.2011.0840] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The independent evolution of similar morphologies has long been a subject of considerable interest to biologists. Does phenotypic convergence reflect the primacy of natural selection, or does development set the course of evolution by channelling variation in certain directions? Here, we examine the ontogenetic origins of relative limb length variation among Anolis lizard habitat specialists to address whether convergent phenotypes have arisen through convergent developmental trajectories. Despite the numerous developmental processes that could potentially contribute to variation in adult limb length, our analyses reveal that, in Anolis lizards, such variation is repeatedly the result of changes occurring very early in development, prior to formation of the cartilaginous long bone anlagen.
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Affiliation(s)
- Thomas J Sanger
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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58
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Elmer KR, Meyer A. Adaptation in the age of ecological genomics: insights from parallelism and convergence. Trends Ecol Evol 2011; 26:298-306. [PMID: 21459472 DOI: 10.1016/j.tree.2011.02.008] [Citation(s) in RCA: 269] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 02/18/2011] [Accepted: 02/22/2011] [Indexed: 12/19/2022]
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Abstract
Although parallel and convergent evolution are discussed extensively in technical articles and textbooks, their meaning can be overlapping, imprecise, and contradictory. The meaning of parallel evolution in much of the evolutionary literature grapples with two separate hypotheses in relation to phenotype and genotype, but often these two hypotheses have been inferred from only one hypothesis, and a number of subsidiary but problematic criteria, in relation to the phenotype. However, examples of parallel evolution of genetic traits that underpin or are at least associated with convergent phenotypes are now emerging. Four criteria for distinguishing parallelism from convergence are reviewed. All are found to be incompatible with any single proposition of homoplasy. Therefore, all homoplasy is equivalent to a broad view of convergence. Based on this concept, all phenotypic homoplasy can be described as convergence and all genotypic homoplasy as parallelism, which can be viewed as the equivalent concept of convergence for molecular data. Parallel changes of molecular traits may or may not be associated with convergent phenotypes but if so describe homoplasy at two biological levels-genotype and phenotype. Parallelism is not an alternative to convergence, but rather it entails homoplastic genetics that can be associated with and potentially explain, at the molecular level, how convergent phenotypes evolve.
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Affiliation(s)
- Robert W Scotland
- Department of Plant Sciences, South Parks Road, University of Oxford, Oxford, UK.
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60
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Xu P, McIntyre LM, Scardina J, Wheeler PA, Thorgaard GH, Nichols KM. Transcriptome profiling of embryonic development rate in rainbow trout advanced backcross introgression lines. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:215-231. [PMID: 20352270 DOI: 10.1007/s10126-010-9283-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 02/02/2010] [Indexed: 05/29/2023]
Abstract
In rainbow trout (Oncorhynchus mykiss) and other fishes, embryonic development rate is an ecologically and evolutionarily important trait that is closely associated with survival and physiological performance later in life. To identify genes differentially regulated in fast and slow-developing embryos of rainbow trout, we examined gene expression across developmental time points in rainbow trout embryos possessing alleles linked to a major quantitative trait loci (QTL) for fast versus slow embryonic development rate. Whole genome expression microarray analyses were conducted using embryos from a fourth generation backcross family, whereby each backcross generation involved the introgression of the fast-developing alleles for a major development rate QTL into a slow-developing clonal line of rainbow trout. Embryos were collected at 15, 19, and 28 days post-fertilization; sex and QTL genotype were determined using molecular markers, and cDNA from 48 embryos were used for microarray analysis. A total of 183 features were identified with significant differences between embryonic development rate genotypes. Genes associated with cell cycle growth, muscle contraction and protein synthesis were expressed significantly higher in embryos with the fast-developing allele (Clearwater) than those with the slow-developing allele (Oregon State University), which may associate with fast growth and early body mass construction in embryo development. Across time points, individuals with the fast-developing QTL allele appeared to have earlier onset of these developmental processes when compared to individuals with the slow development alleles, even as early as 15 days post-fertilization. Differentially expressed candidate genes chosen for linkage mapping were localized primarily to regions outside of the major embryonic development rate QTL, with the exception of a single gene (very low-density lipoprotein receptor precursor).
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Affiliation(s)
- Peng Xu
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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61
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JEUKENS J, BOYLE B, KUKAVICA‐IBRULJ I, ST‐CYR J, LÉVESQUE RC, BERNATCHEZ L. BAC library construction, screening and clone sequencing of lake whitefish (
Coregonus clupeaformis
, Salmonidae) towards the elucidation of adaptive species divergence. Mol Ecol Resour 2011; 11:541-9. [DOI: 10.1111/j.1755-0998.2011.02982.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. JEUKENS
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Quebec‐Ocean, Department of biology, Université Laval, Québec City, Québec, Canada
| | - B. BOYLE
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Arborea, Center for Forest Research, Université Laval, Québec City, Québec, Canada
| | - I. KUKAVICA‐IBRULJ
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Department of microbiology‐infectiology and immunology, Université Laval, Québec City, Québec, Canada
| | - J. ST‐CYR
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
| | - R. C. LÉVESQUE
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Department of microbiology‐infectiology and immunology, Université Laval, Québec City, Québec, Canada
| | - L. BERNATCHEZ
- Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada
- Quebec‐Ocean, Department of biology, Université Laval, Québec City, Québec, Canada
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62
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Fraser DJ, Weir LK, Bernatchez L, Hansen MM, Taylor EB. Extent and scale of local adaptation in salmonid fishes: review and meta-analysis. Heredity (Edinb) 2011; 106:404-20. [PMID: 21224881 DOI: 10.1038/hdy.2010.167] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
What is the extent and scale of local adaptation (LA)? How quickly does LA arise? And what is its underlying molecular basis? Our review and meta-analysis on salmonid fishes estimates the frequency of LA to be ∼55-70%, with local populations having a 1.2 times average fitness advantage relative to foreign populations or to their performance in new environments. Salmonid LA is evident at a variety of spatial scales (for example, few km to>1000 km) and can manifest itself quickly (6-30 generations). As the geographic scale between populations increases, LA is generally more frequent and stronger. Yet the extent of LA in salmonids does not appear to differ from that in other assessed taxa. Moreover, the frequency with which foreign salmonid populations outperform local populations (∼23-35%) suggests that drift, gene flow and plasticity often limit or mediate LA. The relatively few studies based on candidate gene and genomewide analyses have identified footprints of selection at both small and large geographical scales, likely reflecting the specific functional properties of loci and the associated selection regimes (for example, local niche partitioning, pathogens, parasites, photoperiodicity and seasonal timing). The molecular basis of LA in salmonids is still largely unknown, but differential expression at the same few genes is implicated in the convergent evolution of certain phenotypes. Collectively, future research will benefit from an integration of classical and molecular approaches to understand: (i) species differences and how they originate, (ii) variation in adaptation across scales, life stages, population sizes and environmental gradients, and (iii) evolutionary responses to human activities.
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Affiliation(s)
- D J Fraser
- Department of Biology, Concordia University, Montreal, Québec, Canada.
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63
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Brouillette LC, Donovan LA. Nitrogen stress response of a hybrid species: a gene expression study. ANNALS OF BOTANY 2011; 107:101-8. [PMID: 20947669 PMCID: PMC3002466 DOI: 10.1093/aob/mcq203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 08/13/2010] [Accepted: 09/17/2010] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Low soil fertility limits growth and productivity in many natural and agricultural systems, where the ability to sense and respond to nutrient limitation is important for success. Helianthus anomalus is an annual sunflower of hybrid origin that is adapted to desert sand-dune substrates with lower fertility than its parental species, H. annuus and H. petiolaris. Previous studies have shown that H. anomalus has traits generally associated with adaptation to low-fertility habitats, including a lower inherent relative growth rate and longer leaf lifetime. METHODS Here, a cDNA microarray is used to identify gene expression differences that potentially contribute to increased tolerance of low fertility of the hybrid species by comparing the nitrogen stress response of all three species with high- and low-nutrient treatments. KEY RESULTS Relative to the set of genes on the microarray, the genes showing differential expression in the hybrid species compared with its parents are enriched in stress-response genes, developmental genes, and genes involved in responses to biotic or abiotic stimuli. After a correction for multiple comparisons, five unique genes show a significantly different response to nitrogen limitation in H. anomalus compared with H. petiolaris and H. annuus. The Arabidopsis thaliana homologue of one of the five genes, catalase 1, has been shown to affect the timing of leaf senescence, and thus leaf lifespan. CONCLUSIONS The five genes identified in this analysis will be examined further as candidate genes for the adaptive stress response in H. anomalus. Genes that improve growth and productivity under nutrient stress could be used to improve crops for lower soil fertility which is common in marginal agricultural settings.
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64
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Larsen PF, Schulte PM, Nielsen EE. Gene expression analysis for the identification of selection and local adaptation in fishes. JOURNAL OF FISH BIOLOGY 2011; 78:1-22. [PMID: 21235543 DOI: 10.1111/j.1095-8649.2010.02834.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In recent years, variation in gene expression has been recognized as an important component of environmental adaptation in multiple model species, including a few fish species. There is, however, still little known about the genetic basis of adaptation in gene expression resulting from variation in the aquatic environment (e.g. temperature, salinity and oxygen) and the physiological effect and costs of such differences in gene expression. This review presents and discusses progress and pitfalls of applying gene expression analyses to fishes and suggests simple frameworks to get started with gene expression analysis. It is emphasized that well-planned gene expression studies can serve as an important tool for the identification of selection in local populations of fishes, even for non-traditional model species where limited genomic information is available. Recent studies focusing on gene expression variation among natural fish populations are reviewed, highlighting the latest applications that combine genetic evidence from neutral markers and gene expression data.
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Affiliation(s)
- P F Larsen
- Department of Biological Sciences, Aarhus Universit, Ny Munkegade, DK-8000 Aarhus C, Denmark.
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65
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Rapid evolution of osmoregulatory function by modification of gene transcription in steelhead trout. Genetica 2010; 139:233-42. [PMID: 21190065 DOI: 10.1007/s10709-010-9540-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 12/16/2010] [Indexed: 10/18/2022]
Abstract
Populations experiencing sudden environmental change must be capable of rapidly evolving to survive. Here we explore changes in gene transcription as a mechanism for rapid adaptation at four osmoregulatory genes (CFTR I, NaK ATPase1αa, NaK ATPase1αb and GHRII) in anadromous steelhead trout versus a derived land-locked population after 14 generations. Transcription was measured before and after a 24-h saltwater challenge in pure and reciprocal hybrid offspring of fish from both populations reared in a common environment for two generations. Significant differences between the landlocked and migratory populations were observed, particularly in fresh water at the NaK ATPase1αa and GHRII genes, indicating rapid evolutionary change, possibly associated with reduced energy expenditure in the landlocked lake system. Phenotypic divergence analysis (Q (ST)) shows that the observed transcriptional differences deviate from neutral expectations. Some reciprocal crosses exhibited anomalous transcription consistent with sex-linked epistatic or genetic imprinting effects. Our results highlight unpredictable phenotypic outcomes of hybridization among locally adapted populations and the need to exercise caution when interbreeding populations for conservation purposes.
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66
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Bell AM, Aubin-Horth N. What can whole genome expression data tell us about the ecology and evolution of personality? Philos Trans R Soc Lond B Biol Sci 2010; 365:4001-12. [PMID: 21078652 PMCID: PMC2992745 DOI: 10.1098/rstb.2010.0185] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Consistent individual differences in behaviour, aka personality, pose several evolutionary questions. For example, it is difficult to explain within-individual consistency in behaviour because behavioural plasticity is often advantageous. In addition, selection erodes heritable behavioural variation that is related to fitness, therefore we wish to know the mechanisms that can maintain between-individual variation in behaviour. In this paper, we argue that whole genome expression data can reveal new insights into the proximate mechanisms underlying personality, as well as its evolutionary consequences. After introducing the basics of whole genome expression analysis, we show how whole genome expression data can be used to understand whether behaviours in different contexts are affected by the same molecular mechanisms. We suggest strategies for using the power of genomics to understand what maintains behavioural variation, to study the evolution of behavioural correlations and to compare personality traits across diverse organisms.
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Affiliation(s)
- Alison M Bell
- Integrative Biology, University of Illinois, , Urbana-Champaign, Urbana, IL 61801, USA.
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67
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RENAUT SÉBASTIEN, NOLTE ARNEW, ROGERS SEANM, DEROME NICOLAS, BERNATCHEZ LOUIS. SNP signatures of selection on standing genetic variation and their association with adaptive phenotypes along gradients of ecological speciation in lake whitefish species pairs (Coregonus spp.). Mol Ecol 2010; 20:545-59. [DOI: 10.1111/j.1365-294x.2010.04952.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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68
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Renaut S, Bernatchez L. Transcriptome-wide signature of hybrid breakdown associated with intrinsic reproductive isolation in lake whitefish species pairs (Coregonus spp. Salmonidae). Heredity (Edinb) 2010; 106:1003-11. [PMID: 21119703 DOI: 10.1038/hdy.2010.149] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Genetic analyses of speciation have focused nearly exclusively on retrospective analyses of reproductive isolation between highly divergent species. Yet, a full understanding of the speciation process must encompass analysis of the consequences of genomic divergence in young lineages still capable of exchanging genes under natural conditions. The accumulation of conditionally neutral genetic variation may lead to the evolution of divergent gene networks. In a hybrid background, such mutations may no longer compensate one another, resulting in the appearance of selectively disadvantageous traits, including disruption of gene expression regulation. Here, we documented genome-wide patterns of gene expression divergence between young lineages of normal and dwarf lake whitefish and their backcross hybrids for which strong, yet incomplete post-zygotic isolation barriers exist. A significant proportion (33%) of backcross hybrids showed developmental abnormalities not seen in parental forms and eventually leading to death. Although the transcriptome of parental forms was nearly identical during embryonic development, suggesting a role for stabilizing selection, all hybrids displayed strongly divergent patterns of gene expression. By comparing healthy, surviving hybrids against moribund ones showing abnormal development, we observed that over 2000 genes were misregulated in these abnormal embryos. In particular, misregulation was significantly biased toward essential developmental genes, which were severely underexpressed. Furthermore, genes previously documented to be highly transgressive (exaggerated inter-individual variance) were almost invariably underexpressed in hybrids. Our results thus clearly showed a transcriptome-wide signature of hybrid breakdown in young, incipient species and demonstrated a persuasive link between misexpression of essential developmental genes and post-zygotic isolation.
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Affiliation(s)
- S Renaut
- Département de Biologie, IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, Canada.
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69
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Jeukens J, Renaut S, St-Cyr J, Nolte AW, Bernatchez L. The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. Mol Ecol 2010; 19:5389-403. [PMID: 21087448 DOI: 10.1111/j.1365-294x.2010.04934.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next-generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a 454 GS-FLX pyrosequencing experiment to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (i) investigate transcriptomic divergence as measured by liver RNA-Seq; (ii) test the correlation between divergence in expression and sequence polymorphism; and (iii) investigate the extent of allelic imbalance. We also compared the results of RNA-seq with those of a previous microarray study performed on the same fish. Following de novo assembly, results showed that normal whitefish overexpressed more contigs associated with protein synthesis while dwarf fish overexpressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA-Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele-specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next-generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.
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Affiliation(s)
- Julie Jeukens
- Institut de Biologie Intégrative et des Systèmes (IBIS), Québec-Océan, Université Laval, Québec, QC, Canada.
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Rice AM, Rudh A, Ellegren H, Qvarnström A. A guide to the genomics of ecological speciation in natural animal populations. Ecol Lett 2010; 14:9-18. [PMID: 21070555 DOI: 10.1111/j.1461-0248.2010.01546.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interest in ecological speciation is growing, as evidence accumulates showing that natural selection can lead to rapid divergence between subpopulations. However, whether and how ecological divergence can lead to the buildup of reproductive isolation remains under debate. What is the relative importance of natural selection vs. neutral processes? How does adaptation generate reproductive isolation? Can ecological speciation occur despite homogenizing gene flow? These questions can be addressed using genomic approaches, and with the rapid development of genomic technology, will become more answerable in studies of wild populations than ever before. In this article, we identify open questions in ecological speciation theory and suggest useful genomic methods for addressing these questions in natural animal populations. We aim to provide a practical guide for ecologists interested in incorporating genomic methods into their research programs. An increased integration between ecological research and genomics has the potential to shed novel light on the origin of species.
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Affiliation(s)
- Amber M Rice
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
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71
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Nadeau NJ, Jiggins CD. A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations. Trends Genet 2010; 26:484-92. [DOI: 10.1016/j.tig.2010.08.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/16/2010] [Accepted: 08/18/2010] [Indexed: 12/20/2022]
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72
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Schluter D, Marchinko KB, Barrett RDH, Rogers SM. Natural selection and the genetics of adaptation in threespine stickleback. Philos Trans R Soc Lond B Biol Sci 2010; 365:2479-86. [PMID: 20643737 DOI: 10.1098/rstb.2010.0036] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Growing knowledge of the molecular basis of adaptation in wild populations is expanding the study of natural selection. We summarize ongoing efforts to infer three aspects of natural selection--mechanism, form and history--from the genetics of adaptive evolution in threespine stickleback that colonized freshwater after the last ice age. We tested a mechanism of selection for reduced bony armour in freshwater by tracking genotype and allele frequency changes at an underlying major locus (Ectodysplasin) in transplanted stickleback populations. We inferred disruptive selection on genotypes at the same locus in a population polymorphic for bony armour. Finally, we compared the distribution of phenotypic effect sizes of genes underlying changes in body shape with that predicted by models of adaptive peak shifts following colonization of freshwater. Studies of the effects of selection on genes complement efforts to identify the molecular basis of adaptive differences, and improve our understanding of phenotypic evolution.
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Affiliation(s)
- Dolph Schluter
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, British Columbia, Canada.
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73
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Abstract
Ecological speciation is the process by which barriers to gene flow between populations evolve due to adaptive divergence via natural selection. A relatively unexplored area in ecological speciation is the role of gene expression. Gene expression may be associated with ecologically important phenotypes not evident from morphology and play a role during colonization of new environments. Here we review two potential roles of gene expression in ecological speciation: (1) its indirect role in facilitating population persistence and (2) its direct role in contributing to genetically based reproductive isolation. We find indirect evidence that gene expression facilitates population persistence, but direct tests are lacking. We also find clear examples of gene expression having effects on phenotypic traits and adaptive genetic divergence, but links to the evolution of reproductive isolation itself remain indirect. Gene expression during adaptive divergence seems to often involve complex genetic architectures controlled by gene networks, regulatory regions, and “eQTL hotspots.” Nonetheless, we review how approaches for isolating the functional mutations contributing to adaptive divergence are proving to be successful. The study of gene expression has promise for increasing our understanding ecological speciation, particularly when integrative approaches are applied.
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Affiliation(s)
- Scott A Pavey
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
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74
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LANDRY L, BERNATCHEZ L. Role of epibenthic resource opportunities in the parallel evolution of lake whitefish species pairs (Coregonus sp.). J Evol Biol 2010; 23:2602-13. [DOI: 10.1111/j.1420-9101.2010.02121.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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75
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Bernatchez L, Renaut S, Whiteley AR, Derome N, Jeukens J, Landry L, Lu G, Nolte AW, Ostbye K, Rogers SM, St-Cyr J. On the origin of species: insights from the ecological genomics of lake whitefish. Philos Trans R Soc Lond B Biol Sci 2010; 365:1783-800. [PMID: 20439281 DOI: 10.1098/rstb.2009.0274] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In contrast to the large amount of ecological information supporting the role of natural selection as a main cause of population divergence and speciation, an understanding of the genomic basis underlying those processes is in its infancy. In this paper, we review the main findings of a long-term research programme that we have been conducting on the ecological genomics of sympatric forms of whitefish (Coregonus spp.) engaged in the process of speciation. We present this system as an example of how applying a combination of approaches under the conceptual framework of the theory of adaptive radiation has yielded substantial insight into evolutionary processes in a non-model species. We also discuss how the joint use of recent biotechnological developments will provide a powerful means to address issues raised by observations made to date. Namely, we present data illustrating the potential offered by combining next generation sequencing technologies with other genomic approaches to reveal the genomic bases of adaptive divergence and reproductive isolation. Given increasing access to these new genomic tools, we argue that non-model species studied in their ecological context such as whitefish will play an increasingly important role in generalizing knowledge of speciation.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université, Laval, Québec, Canada.
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76
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Abstract
An important task within conservation genetics consists in defining intraspecific conservation units. Most conceptual frameworks involve two steps: (i) identifying demographically independent units, and (ii) evaluating their degree of adaptive divergence. Whereas a plethora of methods are available for delineating genetic population structure, assessment of functional genetic divergence remains a challenge. In this issue, Tymchuk et al. (2010) study Atlantic salmon (Salmo salar) populations using both microsatellite markers and analysis of global gene expression. They show that important gene expression differences exist that can be interpreted in the context of different ecological conditions experienced by the populations, along with the populations' histories. This demonstrates an important potential role of transcriptomics for designating conservation units.
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Affiliation(s)
- Michael M Hansen
- Department of Biological Sciences, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
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77
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Losos J. Adaptive Radiation, Ecological Opportunity, and Evolutionary Determinism. Am Nat 2010; 175:623-39. [DOI: 10.1086/652433] [Citation(s) in RCA: 457] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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78
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Fontanillas P, Landry CR, Wittkopp PJ, Russ C, Gruber JD, Nusbaum C, Hartl DL. Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Mol Ecol 2010; 19 Suppl 1:212-27. [PMID: 20331781 DOI: 10.1111/j.1365-294x.2010.04472.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Differences in gene expression are thought to be an important source of phenotypic diversity, so dissecting the genetic components of natural variation in gene expression is important for understanding the evolutionary mechanisms that lead to adaptation. Gene expression is a complex trait that, in diploid organisms, results from transcription of both maternal and paternal alleles. Directly measuring allelic expression rather than total gene expression offers greater insight into regulatory variation. The recent emergence of high-throughput sequencing offers an unprecedented opportunity to study allelic transcription at a genomic scale for virtually any species. By sequencing transcript pools derived from heterozygous individuals, estimates of allelic expression can be directly obtained. The statistical power of this approach is influenced by the number of transcripts sequenced and the ability to unambiguously assign individual sequence fragments to specific alleles on the basis of transcribed nucleotide polymorphisms. Here, using mathematical modelling and computer simulations, we determine the minimum sequencing depth required to accurately measure relative allelic expression and detect allelic imbalance via high-throughput sequencing under a variety of conditions. We conclude that, within a species, a minimum of 500-1000 sequencing reads per gene are needed to test for allelic imbalance, and consequently, at least five to 10 millions reads are required for studying a genome expressing 10 000 genes. Finally, using 454 sequencing, we illustrate an application of allelic expression by testing for cis-regulatory divergence between closely related Drosophila species.
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Affiliation(s)
- Pierre Fontanillas
- Department of Ecology and Evolution, University of Lausanne, Switzerland.
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79
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Goetz F, Rosauer D, Sitar S, Goetz G, Simchick C, Roberts S, Johnson R, Murphy C, Bronte CR, Mackenzie S. A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush). Mol Ecol 2010; 19 Suppl 1:176-96. [PMID: 20331779 DOI: 10.1111/j.1365-294x.2009.04481.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In Lake Superior there are three principal forms of lake trout (Salvelinus namaycush): lean, siscowet and humper. Wild lean and siscowet differ in the shape and relative size of the head, size of the fins, location and size of the eyes, caudal peduncle shape and lipid content of the musculature. To investigate the basis for these phenotypic differences, lean and siscowet lake trout, derived from gametes of wild populations in Lake Superior, were reared communally under identical environmental conditions for 2.5 years. Fish were analysed for growth, morphometry and lipid content, and differences in liver transcriptomics were investigated using Roche 454 GS-FLX pyrosequencing. The results demonstrate that key phenotypic differences between wild lean and siscowet lake trout such as condition factor, morphometry and lipid levels, persist in these two forms when reared in the laboratory under identical environmental conditions. This strongly suggests that these differences are genetic and not a result of environmental plasticity. Transcriptomic analysis involving the comparison of hepatic gene frequencies (RNA-seq) and expression (quantitative reverse transcription-polymerase chain reaction (qPCR)) between the two lake trout forms, indicated two primary gene groups that were differentially expressed; those involving lipid synthesis, metabolism and transport (acyl-CoA desaturase, acyl-CoA binding protein, peroxisome proliferator-activated receptor gamma, and apolipoproteins), and those involved with immunity (complement component C3, proteasome, FK506 binding protein 5 and C1q proteins). The results demonstrate that RNA-seq can be used to identify differentially expressed genes; however, some discrepancies between RNA-seq analysis and qPCR indicate that methods for deep sequencing may need to be refined and/or different RNA-seq platforms utilized.
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Affiliation(s)
- Frederick Goetz
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, 53204, USA.
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80
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Leong JS, Jantzen SG, von Schalburg KR, Cooper GA, Messmer AM, Liao NY, Munro S, Moore R, Holt RA, Jones SJM, Davidson WS, Koop BF. Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome. BMC Genomics 2010; 11:279. [PMID: 20433749 PMCID: PMC2886063 DOI: 10.1186/1471-2164-11-279] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 04/30/2010] [Indexed: 12/22/2022] Open
Abstract
Background Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (Salmo salar), but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution. Results From existing expressed sequence tag (EST) resources and three new full-length cDNA libraries, 9,057 reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-length clones were annotated from 29,221 northern pike (Esox lucius) ESTs. Pairwise dN/dS comparisons within each of 408 sets of duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection on salmon duplicates. Conclusions 9,057 full-length reference genes were characterized in S. salar and can be used to identify alleles and gene family members. Comparisons of duplicated genes show that while purifying selection is the predominant force acting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure on gene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs, allowing one of the pair to diverge at a faster rate.
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Affiliation(s)
- Jong S Leong
- Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada.
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81
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Angers B, Castonguay E, Massicotte R. Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Mol Ecol 2010; 19:1283-95. [PMID: 20298470 DOI: 10.1111/j.1365-294x.2010.04580.x] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Organisms often respond to environmental changes by producing alternative phenotypes. Epigenetic processes such as DNA methylation may contribute to environmentally induced phenotypic variation by modifying gene expression. Changes in DNA methylation, unlike DNA mutations, can be influenced by the environment; they are stable at the time scale of an individual and present different levels of heritability. These characteristics make DNA methylation a potentially important molecular process to respond to environmental change. The aim of this review is to present the implications of DNA methylation on phenotypic variations driven by environmental changes. More specifically, we explore epigenetic concepts concerning phenotypic change in response to the environment and heritability of DNA methylation, namely the Baldwin effect and genetic accommodation. Before addressing this point, we report major differences in DNA methylation across taxa and the role of this modification in producing and maintaining environmentally induced phenotypic variation. We also present the different methods allowing the detection of methylation polymorphism. We believe this review will be helpful to molecular ecologists, in that it highlights the importance of epigenetic processes in ecological and evolutionary studies.
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Affiliation(s)
- Bernard Angers
- Department of Biological Sciences, Université de Montréal. C.P. 6128, Succursale Centre-Ville, Montreal, QC, Canada.
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82
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RENAUT SÉBASTIEN, NOLTE ARNEW, BERNATCHEZ LOUIS. Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonusspp. Salmonidae). Mol Ecol 2010; 19 Suppl 1:115-31. [DOI: 10.1111/j.1365-294x.2009.04477.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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83
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Pavey SA, Nielsen JL, Hamon TR. Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka). Evolution 2009; 64:1773-83. [PMID: 20030707 PMCID: PMC2901516 DOI: 10.1111/j.1558-5646.2009.00927.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difficult in current populations and tools to differentiate genetic similarities due to migration versus recent common ancestry are only recently available. Using past volcanic eruption times as a framework, we combine morphological analyses of traits important to reproduction with a coalescent-based genetic analysis of two proximate sockeye salmon (Oncorhynchus nerka) populations. We find that this is the most recent (∼500 years, 100 generations) natural ecological divergence recorded in a fish species, and report that this divergence is occurring despite migration. Although studies of fish divergence following the retreat of glaciers (10,000–15,000 years ago) have contributed extensively to our understanding of speciation, the Aniakchak system of sockeye salmon provides a rare example of the initial stages of ecological divergence following natural colonization. Our results show that even in the face of continued migration, populations may diverge in the absence of a physical barrier.
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Affiliation(s)
- Scott A Pavey
- Biological Sciences Department, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
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84
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Martínez-Fernández M, Bernatchez L, Rolán-Alvarez E, Quesada H. Semi-quantitative differences in gene transcription profiles between sexes of a marine snail by a new variant of cDNA-AFLP analysis. Mol Ecol Resour 2009; 10:324-30. [PMID: 21565027 DOI: 10.1111/j.1755-0998.2009.02762.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A variant of the cDNA-AFLP method coupled to an automated sequencer was used to quantify transcripts differentially expressed between sexes of the marine snail Littorina saxatilis. First, we conducted a validation study of the technique using known concentrations of a commercial marker. Second, we analysed six replicates of males and females from a population showing no apparent sexual dimorphism. The results confirm that the method can be properly used within the range of DNA concentrations utilized. In addition, we detected a small percentage of spots (1.8%) differentially expressed between sexes, as expected from a low to moderately sexual dimorphic species.
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Affiliation(s)
- M Martínez-Fernández
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Campus As Lagoas-Marcosende Universidad de Vigo, 36310 Vigo, Spain Department of Biology, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Université Laval, Québec, QC, Canada G1V 0A6
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85
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Aubin-Horth N, Renn SCP. Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity. Mol Ecol 2009; 18:3763-80. [PMID: 19732339 DOI: 10.1111/j.1365-294x.2009.04313.x] [Citation(s) in RCA: 256] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenotypic plasticity is the development of different phenotypes from a single genotype, depending on the environment. Such plasticity is a pervasive feature of life, is observed for various traits and is often argued to be the result of natural selection. A thorough study of phenotypic plasticity should thus include an ecological and an evolutionary perspective. Recent advances in large-scale gene expression technology make it possible to also study plasticity from a molecular perspective, and the addition of these data will help answer long-standing questions about this widespread phenomenon. In this review, we present examples of integrative studies that illustrate the molecular and cellular mechanisms underlying plastic traits, and show how new techniques will grow in importance in the study of these plastic molecular processes. These techniques include: (i) heterologous hybridization to DNA microarrays; (ii) next generation sequencing technologies applied to transcriptomics; (iii) techniques for studying the function of noncoding small RNAs; and (iv) proteomic tools. We also present recent studies on genetic model systems that uncover how environmental cues triggering different plastic responses are sensed and integrated by the organism. Finally, we describe recent work on changes in gene expression in response to an environmental cue that persist after the cue is removed. Such long-term responses are made possible by epigenetic molecular mechanisms, including DNA methylation. The results of these current studies help us outline future avenues for the study of plasticity.
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Affiliation(s)
- Nadia Aubin-Horth
- Département de Sciences biologiques, Université de Montréal, Québec, Canada.
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86
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Bay LK, Nielsen HB, Jarmer H, Seneca F, van Oppen MJH. Transcriptomic variation in a coral reveals pathways of clonal organisation. Mar Genomics 2009; 2:119-25. [PMID: 21798180 DOI: 10.1016/j.margen.2009.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 07/21/2009] [Indexed: 11/18/2022]
Abstract
A microarray study was undertaken to examine the potential for clonal gene expression variation in a branching reef building coral, Acropora millepora. The role of small-scale gradients in light and water flow was examined by comparing gene expression levels between branch elevation (tip and base) and position (centre and edge) of replicate coral colonies (n=3). Analyses of variance revealed that almost 60% of variation in gene expression was present between colonies and 34 genes were considered differentially expressed between colonies (minimum P=6.5×10(-4)). These genes are associated with energy metabolism, protein biosynthesis and cell-cell recognition representing either genotypic variation in gene expression or the effects of specific environmental conditions that affect patterns of energy acquisition, growth and pathogen encounters. Less variation was present between central and peripheral branches (7%) and only a single gene was deemed differentially expressed (P=1.493×10(-3)). The function of this gene, a phosphatidylserine decarboxylase, suggests different growth patterns between branch positions within colonies and is consistent with the usual higher growth rates on the perimeter of corymbose-like branching coral colonies such as A. millepora. Four genes were differentially expressed between the tip and base of branches (P=3.239×10(-4)) and were associated with lysosome lipase activity and fluorescence, suggesting that branch tips may encounter higher pathogen loads or levels of mechanical stress and require greater levels of photo-protection associated with higher water flow and light levels. This study therefore confirms transcriptomic variation in response to small-scale environmental gradients consistent with differential resource allocation in clonal coral colonies.
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Affiliation(s)
- Line K Bay
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia; Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia
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87
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Whiteley AR, Persaud KN, Derome N, Montgomerie R, Bernatchez L. Reduced sperm performance in backcross hybrids between species pairs of whitefish (Coregonus clupeaformis). CAN J ZOOL 2009. [DOI: 10.1139/z09-042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Previous work has demonstrated that genomic incompatibilities work together with ecologically divergent selection to promote and maintain reproductive isolation between incipient species (dwarf and normal) of lake whitefish ( Coregonus clupeaformis (Mitchill, 1818)). Whitefish spawn in groups with external fertilization, which creates conditions for strong sperm competition. In this study, we asked whether reduced sperm performance in hybrids from whitefish species-pair matings might contribute to postzygotic isolating mechanisms between these taxa. We examined two sperm traits, sperm swimming speed and flagellum length, in pure dwarf and normal whitefish and in their F1 and backcross hybrids. We observed significantly reduced sperm swimming speed in backcross but not in F1 hybrids. Sperm flagellum length was not significantly correlated with sperm swimming speed. These results demonstrate that F1 hybrids formed in nature should be capable of the same fertilization success as the parental species during sperm competition, everything else being equal. However, reduced sperm performance in the backcross generation is consistent with other evidence suggesting that genomic incompatibilities create a range of negative fitness effects in post-F1 whitefish hybrids and provides evidence for an additional postzygotic isolation mechanism involved in the incipient speciation of sympatric dwarf and normal whitefish.
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Affiliation(s)
- A. R. Whiteley
- Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - K. N. Persaud
- Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - N. Derome
- Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - R. Montgomerie
- Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - L. Bernatchez
- Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
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88
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Mavarez J, Audet C, Bernatchez L. Major disruption of gene expression in hybrids between young sympatric anadromous and resident populations of brook charr (Salvelinus fontinalis Mitchill). J Evol Biol 2009; 22:1708-20. [PMID: 19549137 DOI: 10.1111/j.1420-9101.2009.01785.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome-wide analyses of the transcriptome have suggested that male-biased genes are the first targets of genomic incompatibilities (g.i.) in inter-specific hybrids. However, those studies have almost invariably focused on Drosophila species that diverged at least 0.9 Ma, and with sterile male hybrids. Here, we use microarrays to analyse patterns of gene expression in very closely related (divergence <12,000 years), sympatric, but ecologically divergent anadromous and resident populations of brook charr (Salvelinus fontinalis) and their F(1) hybrids. Our results show a dramatic breakdown of gene expression patterns in hybrids compared with their parental relatives. Several disrupted genes are related to energetic metabolism, immune response, osmoregulation and protection against oxidative stress, and none has sex-biased functions. Besides, pure individuals show no expression differences at most of the genes disrupted in hybrids, which may suggest the operation of some form of stabilizing selection. Taken together, these results both confirm the idea that perturbations of regulatory networks represent a significant source of g.i. and support the suggestion that developmental pathways can diverge through time without any manifest change in the phenotypic outcome. While the role of other evolutionary forces (e.g. genetic drift) cannot be ruled out, this study suggests that ecological selective processes may provide the initial driving force behind disruption of gene expression in inter-specific hybrids.
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Affiliation(s)
- Jesus Mavarez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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89
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Bay LK, Ulstrup KE, Nielsen HB, Jarmer H, Goffard N, Willis BL, Miller DJ, Van Oppen MJH. Microarray analysis reveals transcriptional plasticity in the reef building coral Acropora millepora. Mol Ecol 2009; 18:3062-75. [PMID: 19538339 DOI: 10.1111/j.1365-294x.2009.04257.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We investigated variation in transcript abundance in the scleractinian coral, Acropora millepora, within and between populations characteristically exposed to different turbidity regimes and hence different levels of light and suspended particulate matter. We examined phenotypic plasticity by comparing levels of gene expression between source populations and following 10 days of acclimatization to a laboratory environment. Analyses of variance revealed that 0.05% of genes were differentially expressed between source populations, 1.32% following translocation into a common laboratory and 0.07% in the interaction (source population-dependent responses to translocation). Functional analyses identified an over-representation of differentially expressed genes associated with metabolism and fluorescence categories (primarily downregulated), and environmental information processing (primarily upregulated) following translocation to a lower light and turbidity environment. Such metabolic downregulation may indicate nonoxidative stress, hibernation or caloric restriction associated with the changed environmental conditions. Green fluorescent protein-related genes were the most differentially expressed and were exclusively downregulated; however, green fluorescent protein levels remained unchanged following translocation. Photophysiological responses of corals from both locations were characterized by a decline when introduced to the common laboratory environment but remained healthy (F(v)/F(m) > 0.6). Declines in total lipid content following translocation were the greatest for inshore corals, suggesting that turbid water corals have a strong reliance on heterotrophic feeding.
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Affiliation(s)
- Line K Bay
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld 4811, Australia
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90
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MAGNANOU E, MALENKE JR, DEARING MD. Expression of biotransformation genes in woodrat (Neotoma) herbivores on novel and ancestral diets: identification of candidate genes responsible for dietary shifts. Mol Ecol 2009; 18:2401-14. [DOI: 10.1111/j.1365-294x.2009.04171.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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91
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Bychenko OS, Sukhanova LV, Ukolova SS, Skvortsov TA, Potapov VK, Azhikina TL, Sverdlov ED. [Genome similarity of Baikal omul and sig]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2009; 35:95-102. [PMID: 19377527 DOI: 10.1134/s1068162009010117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Two members of the Baikal sig family, a lake sig (Coregonus lavaretus baicalensis Dybovsky) and omul (C. autumnalis migratorius Georgi), are close relatives that diverged from the same ancestor 10-20 thousand years ago. In this work, we studied genomic polymorphism of these two fish species. The method of subtraction hybridization (SH) did not reveal the presence of extended sequences in the sig genome and their absence in the omul genome. All the fragments found by SH corresponded to polymorphous noncoding genome regions varying in mononucleotide substitutions and short deletions. Many of them are mapped close to genes of the immune system and have regions identical to the Tc-1-like transposons abundant among fish, whose transcription activity may affect the expression of adjacent genes. Thus, we showed for the first time that genetic differences between Baikal sig family members are extremely small and cannot be revealed by the SH method. This is another endorsement of the hypothesis on the close relationship between Baikal sig and omul and their evolutionarily recent divergence from a common ancestor.
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92
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Nolte AW, Renaut S, Bernatchez L. Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation. BMC Evol Biol 2009; 9:59. [PMID: 19291312 PMCID: PMC2662803 DOI: 10.1186/1471-2148-9-59] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Accepted: 03/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of barriers to reproduction is of key interest to understand speciation. However, there may be a current bias towards studying intrinsic postzygotic isolation in old species pairs as compared to the emergence of barriers to gene flow through adaptive divergence. This study evaluates the relative importance of both processes in the evolution of genomic isolation in incipient species of whitefish (Coregonus clupeaformis) for which preliminary data suggest that postzygotic isolation emerges with intrinsic factors acting at embryo stages but also due to extrinsic factors during adult life. RESULTS Gene expression data were screened using cDNA microarrays to identify regulatory changes at embryo and juvenile stages that provide evidence for genomic divergence at the underlying genetic factors. A comparison of different life history stages shows that 16-week old juvenile fish have 14 times more genes displaying significant regulatory divergence than embryos. Furthermore, regulatory changes in juvenile fish match patterns in adult fish suggesting that gene expression divergence is established early in juvenile fish and persists throughout the adult phase. Comparative analyses with results from previous studies on dwarf-normal species pairs show that at least 26 genetic factors identified in juvenile fish are candidate traits for adaptive divergence in adult fish. Eight of these show parallel directions of gene expression divergence independent of tissue type or age of the fish. The latter are associated with energy metabolism, a complex trait known to drive adaptive divergence in dwarf and normal whitefish. CONCLUSION Although experimental evidence suggests the existence of genetic factors that cause intrinsic postzygotic isolation acting in embryos, the analysis presented here provided few candidate genes in embryos, which also corroborate previous studies showing a lack of ecological divergence between sympatric dwarf and normal whitefish at the larval stage. In contrast, gene expression divergence in juveniles can be linked to adaptive traits and seems to be driven by positive selection. The results support the idea that adaptive differentiation may be more important in explaining the emergence of barriers to gene flow in an early phase of speciation by providing a broad genomic basis for extrinsic postzygotic isolation rather than intrinsic barriers.
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Affiliation(s)
- Arne W Nolte
- Département de Biologie, Pavillon Charles-Eugène-Marchand, Université Laval, Ste-Foy, Québec, G1V 0A6, Canada.
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93
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Affiliation(s)
- Patrik Nosil
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver BC, Canada.
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94
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Renaut S, Nolte AW, Bernatchez L. Gene expression divergence and hybrid misexpression between lake whitefish species pairs (Coregonus spp. Salmonidae). Mol Biol Evol 2009; 26:925-36. [PMID: 19174479 DOI: 10.1093/molbev/msp017] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Genomewide analyses of the transcriptome have confirmed that gene misexpression may underlie reproductive isolation mechanisms in interspecific hybrids. Here, using a 16,006 features cDNA microarray, we compared and contrasted gene expression divergence at two ontogenetic stages in incipient species of normal and dwarf whitefish (Coregonus clupeaformis) with that of first generation (normal x dwarf) and second-generation hybrid crosses (backcross: [normal x dwarf] x normal]. Our goal was to identify the main mode of action responsible for gene transcription and to discover key genes misexpressed in hybrids. Very few transcripts (five of 4,950 expressed) differed in mean expression level between parentals and hybrids at the embryonic stage, in contrast to 16-week-old juvenile fish for which 617 out of 5,359 transcripts differed significantly. We also found evidence for more misexpression in backcross hybrids whereby nonadditivity explained a larger fraction of hybrid inheritance patterns in backcross (54%) compared with F1-hybrids (9%). Gene expression in hybrids was more variable than in pure crosses and transgressive patterns of expression were ubiquitous in hybrids. In backcross embryos in particular, the expression of three key developmental genes involved in protein folding and mRNA translation was severely disrupted. Accordingly, gene misexpression in hybrids adds to other factors previously identified as contributing to the reproductive isolation of incipient species of lake whitefish.
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Affiliation(s)
- S Renaut
- Département de Biologie, IBIS (Institut de Biologie Intégrative et des Systémes), Université Laval, Québec, Canada.
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95
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Jeukens J, Bittner D, Knudsen R, Bernatchez L. Candidate Genes and Adaptive Radiation: Insights from Transcriptional Adaptation to the Limnetic Niche among Coregonine Fishes (Coregonus spp., Salmonidae). Mol Biol Evol 2008; 26:155-66. [DOI: 10.1093/molbev/msn235] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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96
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St-Cyr S, Aubin-Horth N. Integrative and genomics approaches to uncover the mechanistic bases of fish behavior and its diversity. Comp Biochem Physiol A Mol Integr Physiol 2008; 152:9-21. [PMID: 18824118 DOI: 10.1016/j.cbpa.2008.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 09/03/2008] [Accepted: 09/04/2008] [Indexed: 01/07/2023]
Abstract
Understanding the molecular mechanisms underlying fish behavior is of fundamental importance to further our understanding of the proximate and ultimate causes of variation in this trait and informs us on issues of animal husbandry, conservation, and welfare. One way to approach this question is to study variation in gene expression in individuals exhibiting different behaviors and relating it to variations at other phenotypic levels in an organismic, ecological and evolutionary context. Here we review studies that have shown that the use of such an integrative and genomics approach is greatly useful for shedding new light on the mechanisms of behaviors as diverse as social dominance, mate choice, reproduction and migration. We present studies that use functional genomics tools and integrate several biological levels of organization, including transcription variation, which are important in the context of integrative biology and genomics of fish behavior. We review studies of phenotype-level variation in transcription but also studies that focus on variation at the individual-level. Dissecting the molecular bases of among-individual variation in behavior, including the study of variation in temperament (behavioral syndrome/coping style) within and among populations, will gain importance in the field in the years to come.
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Affiliation(s)
- Sophie St-Cyr
- Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
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97
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The phenomics and expression quantitative trait locus mapping of brain transcriptomes regulating adaptive divergence in lake whitefish species pairs (Coregonus sp.). Genetics 2008; 180:147-64. [PMID: 18757926 DOI: 10.1534/genetics.108.089938] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our goals were to elucidate the genomic distribution and sex specificity of brain expression QTL (eQTL) and to determine the extent to which genes controlling transcriptional variation may underlie adaptive divergence in the recently evolved dwarf (limnetic) and normal (benthic) whitefish. We observed a sex bias in transcriptional genetic architecture, with more eQTL observed in males, as well as divergence in genome location of eQTL between the sexes. Hotspots of nonrandom aggregations of up to 32 eQTL in one location were observed. We identified candidate genes for species pair divergence involved with energetic metabolism, protein synthesis, and neural development on the basis of colocalization of eQTL for these genes with eight previously identified adaptive phenotypic QTL and four previously identified outlier loci from a genome scan in natural populations. Eighty-eight percent of eQTL-phenotypic QTL colocalization involved growth rate and condition factor QTL, two traits central to adaptive divergence between whitefish species pairs. Hotspots colocalized with phenotypic QTL in several cases, revealing possible locations where master regulatory genes, such as a zinc-finger protein in one case, control gene expression directly related to adaptive phenotypic divergence. We observed little evidence of colocalization of brain eQTL with behavioral QTL, which provides insight into the genes identified by behavioral QTL studies. These results extend to the transcriptome level previous work illustrating that selection has shaped recent parallel divergence between dwarf and normal lake whitefish species pairs and that metabolic, more than morphological, differences appear to play a key role in this divergence.
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98
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Natural variation in gene expression between wild and weedy populations of Helianthus annuus. Genetics 2008; 179:1881-90. [PMID: 18689879 DOI: 10.1534/genetics.108.091041] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The molecular genetic changes underlying the transformation of wild plants into agricultural weeds are poorly understood. Here we use a sunflower cDNA microarray to detect variation in gene expression between two wild (non-weedy) Helianthus annuus populations from Utah and Kansas and four weedy H. annuus populations collected from agricultural fields in Utah, Kansas, Indiana, and California. When grown in a common growth chamber environment, populations differed substantially in their gene expression patterns, indicating extensive genetic differentiation. Overall, 165 uni-genes, representing approximately 5% of total genes on the array, showed significant differential expression in one or more weedy populations when compared to both wild populations. This subset of genes is enriched for abiotic/biotic stimulus and stress response proteins, which may underlie niche transitions from the natural sites to agricultural fields for H. annuus. However, only a small proportion of the differentially expressed genes overlapped in multiple wild vs. weedy comparisons, indicating that most of the observed expression changes are due to local adaptation or neutral processes, as opposed to parallel genotypic adaptation to agricultural fields. These results are consistent with an earlier phylogeographic study suggesting that weedy sunflowers have evolved multiple times in different regions of the United States and further indicate that the evolution of weedy sunflowers has been accompanied by substantial gene expression divergence in different weedy populations.
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99
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Pervasive sex-linked effects on transcription regulation as revealed by expression quantitative trait loci mapping in lake whitefish species pairs (Coregonus sp., Salmonidae). Genetics 2008; 179:1903-17. [PMID: 18660540 DOI: 10.1534/genetics.107.086306] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied toward investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading to speciation events. Here, we conducted an eQTL mapping experiment to compare the genetic architecture of transcript regulation in adaptive traits, differentiating the recently evolved limnetic (dwarf) and benthic (normal) species pairs of lake whitefish. The eQTL were mapped in three data sets derived from an F(1) hybrid-dwarf backcrossed family: the entire set of 66 genotyped individuals and the two sexes treated separately. We identified strikingly more eQTL in the female data set (174), compared to both male (54) and combined (33) data sets. The majority of these genes were not differentially expressed between male and female progeny of the backcross family, thus providing evidence for a strong pleiotropic sex-linked effect in transcriptomic regulation. The subtelomeric region of a linkage group segregating in females encompassed >50% of all eQTL, which exhibited the most pronounced additive effects. We also conducted a direct comparison of transcriptomic profiles between pure dwarf and normal progeny reared in controlled conditions. We detected 34 differentially expressed transcripts associated with eQTL segregating only in sex-specific data sets and mostly belonging to functional groups that differentiate dwarf and normal whitefish in natural populations. Therefore, these eQTL are not related to interindividual variation, but instead to the adaptive and historical genetic divergence between dwarf and normal whitefish. This study exemplifies how the integration of genetic and transcriptomic data offers a strong means for dissecting the functional genomic response to selection by separating mapping family-specific effects from genetic factors under selection, potentially involved in the phenotypic divergence of natural populations.
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100
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Giger T, Excoffier L, Amstutz U, Day PJR, Champigneulle A, Hansen MM, Kelso J, Largiadèr CR. Population transcriptomics of life-history variation in the genus Salmo. Mol Ecol 2008; 17:3095-108. [PMID: 18522696 DOI: 10.1111/j.1365-294x.2008.03820.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we demonstrate the power of applying complementary DNA (cDNA) microarray technology to identifying candidate loci that exhibit subtle differences in expression levels associated with a complex trait in natural populations of a nonmodel organism. Using a highly replicated experimental design involving 180 cDNA microarray experiments, we measured gene-expression levels from 1098 transcript probes in 90 individuals originating from six brown trout (Salmo trutta) and one Atlantic salmon (Salmo salar) population, which follow either a migratory or a sedentary life history. We identified several candidate genes associated with preparatory adaptations to different life histories in salmonids, including genes encoding for transaldolase 1, constitutive heat-shock protein HSC70-1 and endozepine. Some of these genes clustered into functional groups, providing insight into the physiological pathways potentially involved in the expression of life-history related phenotypic differences. Such differences included the down-regulation of genes involved in the respiratory system of future migratory individuals. In addition, we used linear discriminant analysis to identify a set of 12 genes that correctly classified immature individuals as migratory or sedentary with high accuracy. Using the expression levels of these 12 genes, 17 out of 18 individuals used for cross-validation were correctly assigned to their respective life-history phenotype. Finally, we found various candidate genes associated with physiological changes that are likely to be involved in preadaptations to seawater in anadromous populations of the genus Salmo, one of which was identified to encode for nucleophosmin 1. Our findings thus provide new molecular insights into salmonid life-history variation, opening new perspectives in the study of this complex trait.
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Affiliation(s)
- Thomas Giger
- CMPG, Zoological Institute, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
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