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Sadeghi J, Zaib F, Heath DD. Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha). Heredity (Edinb) 2024; 133:54-66. [PMID: 38822131 PMCID: PMC11222526 DOI: 10.1038/s41437-024-00692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 06/02/2024] Open
Abstract
Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Department of Physical & Environmental Sciences, University of Toronto-Scarborough, Toronto, ON, Canada
| | - Farwa Zaib
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.
- Department of Integrative Biology, University of Windsor, Ontario, ON, Canada.
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2
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Li P, Xiao L, Du Q, Quan M, Song Y, He Y, Huang W, Xie J, Lv C, Wang D, Zhou J, Li L, Liu Q, El‐Kassaby YA, Zhang D. Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2002-2018. [PMID: 37392407 PMCID: PMC10502748 DOI: 10.1111/pbi.14108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/03/2023]
Abstract
Heterozygous alleles are widespread in outcrossing and clonally propagated woody plants. The variation in heterozygosity that underlies population adaptive evolution and phenotypic variation, however, remains largely unknown. Here, we describe a de novo chromosome-level genome assembly of Populus tomentosa, an economic and ecologically important native tree in northern China. By resequencing 302 natural accessions, we determined that the South subpopulation (Pop_S) encompasses the ancestral strains of P. tomentosa, while the Northwest subpopulation (Pop_NW) and Northeast subpopulation (Pop_NE) experienced different selection pressures during population evolution, resulting in significant population differentiation and a decrease in the extent of heterozygosity. Analysis of heterozygous selective sweep regions (HSSR) suggested that selection for lower heterozygosity contributed to the local adaptation of P. tomentosa by dwindling gene expression and genetic load in the Pop_NW and Pop_NE subpopulations. Genome-wide association studies (GWAS) revealed that 88 single nucleotide polymorphisms (SNPs) within 63 genes are associated with nine wood composition traits. Among them, the selection for the homozygous AA allele in PtoARF8 is associated with reductions in cellulose and hemicellulose contents by attenuating PtoARF8 expression, and the increase in lignin content is attributable to the selection for decreases in exon heterozygosity in PtoLOX3 during adaptive evolution of natural populations. This study provides novel insights into allelic variations in heterozygosity associated with adaptive evolution of P. tomentosa in response to the local environment and identifies a series of key genes for wood component traits, thereby facilitating genomic-based breeding of important traits in perennial woody plants.
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Affiliation(s)
- Peng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Liang Xiao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qingzhang Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Mingyang Quan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuepeng Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuling He
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Weixiong Huang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jianbo Xie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Chenfei Lv
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Dan Wang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jiaxuan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Lianzheng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qing Liu
- CSIRO Agriculture and Food, Black MountainCanberraAustralian Capital TerritoryAustralia
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Deqiang Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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Car C, Gilles A, Goujon E, Muller MLD, Camoin L, Frelon S, Burraco P, Granjeaud S, Baudelet E, Audebert S, Orizaola G, Armengaud J, Tenenhaus A, Garali I, Bonzom JM, Armant O. Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone. BMC Biol 2023; 21:164. [PMID: 37525144 PMCID: PMC10391870 DOI: 10.1186/s12915-023-01659-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/03/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Individual functional modifications shape the ability of wildlife populations to cope with anthropogenic environmental changes. But instead of adaptive response, human-altered environments can generate a succession of deleterious functional changes leading to the extinction of the population. To study how persistent anthropogenic changes impacted local species' population status, we characterised population structure, genetic diversity and individual response of gene expression in the tree frog Hyla orientalis along a gradient of radioactive contamination around the Chernobyl nuclear power plant. RESULTS We detected lower effective population size in populations most exposed to ionizing radiation in the Chernobyl Exclusion Zone that is not compensated by migrations from surrounding areas. We also highlighted a decreased body condition of frogs living in the most contaminated area, a distinctive transcriptomics signature and stop-gained mutations in genes involved in energy metabolism. While the association with dose will remain correlational until further experiments, a body of evidence suggests the direct or indirect involvement of radiation exposure in these changes. CONCLUSIONS Despite ongoing migration and lower total dose rates absorbed than at the time of the accident, our results demonstrate that Hyla orientalis specimens living in the Chernobyl Exclusion Zone are still undergoing deleterious changes, emphasizing the long-term impacts of the nuclear disaster.
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Affiliation(s)
- Clément Car
- Institut de Radioprotection Et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, France
- PSE-SANTE/SESANE/LRTox, Fontenay Aux Roses, France
| | - André Gilles
- UMR 1467 RECOVER, Aix-Marseille Université, INRAE, Centre Saint-Charles, Marseille, France.
| | - Elen Goujon
- Institut de Radioprotection Et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, France
- PSE-SANTE/SESANE/LRTox, Fontenay Aux Roses, France
- Laboratoire Des Signaux Et Systèmes, Université Paris-Saclay, CNRS, CentraleSupélec, 91190, Gif-Sur-Yvette, France
| | - Marie-Laure Delignette Muller
- Laboratoire de Biométrie Et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Villeurbanne, France
| | - Luc Camoin
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Sandrine Frelon
- Institut de Radioprotection Et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, France
- PSE-SANTE/SESANE/LRTox, Fontenay Aux Roses, France
| | - Pablo Burraco
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Centre, Uppsala University, 75236, Uppsala, Sweden
- Doñana Biological Station (CSIC), Seville, Spain
| | - Samuel Granjeaud
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Emilie Baudelet
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Stéphane Audebert
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Germán Orizaola
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Centre, Uppsala University, 75236, Uppsala, Sweden
- IMIB-Biodiversity Research Institute, University of Oviedo, 33600, Mieres-Asturias, Spain
- Zoology Unit, Department of Biology of Organisms and Systems, University of Oviedo, 33071, Oviedo-Asturias, Spain
| | - Jean Armengaud
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, Bagnols-Sur-Cèze, France
| | - Arthur Tenenhaus
- Laboratoire Des Signaux Et Systèmes, Université Paris-Saclay, CNRS, CentraleSupélec, 91190, Gif-Sur-Yvette, France
| | - Imène Garali
- Institut de Radioprotection Et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, France
- PSE-SANTE/SESANE/LRTox, Fontenay Aux Roses, France
| | - Jean-Marc Bonzom
- Institut de Radioprotection Et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, France
- PSE-SANTE/SESANE/LRTox, Fontenay Aux Roses, France
| | - Olivier Armant
- Institut de Radioprotection Et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, France.
- PSE-SANTE/SESANE/LRTox, Fontenay Aux Roses, France.
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4
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Leung C, Guscelli E, Chabot D, Bourret A, Calosi P, Parent GJ. The lack of genetic variation underlying thermal transcriptomic plasticity suggests limited adaptability of the Northern shrimp, Pandalus borealis. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1125134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
IntroductionGenetic variation underlies the populations’ potential to adapt to and persist in a changing environment, while phenotypic plasticity can play a key role in buffering the negative impacts of such change at the individual level.MethodsWe investigated the role of genetic variation in the thermal response of the northern shrimp Pandalus borealis, an ectotherm species distributed in the Arctic and North Atlantic Oceans. More specifically, we estimated the proportion transcriptomic responses explained by genetic variance of female shrimp from three origins after 30 days of exposure to three temperature treatments.ResultsWe characterized the P. borealis transcriptome (170,377 transcripts, of which 27.48% were functionally annotated) and then detected a total of 1,607 and 907 differentially expressed transcripts between temperatures and origins, respectively. Shrimp from different origins displayed high but similar level of transcriptomic plasticity in response to elevated temperatures. Differences in transcript expression among origins were not correlated to population genetic differentiation or diversity but to environmental conditions at origin during sampling.DiscussionThe lack of genetic variation explaining thermal plasticity suggests limited adaptability in this species’ response to future environmental changes. These results together with higher mortality observed at the highest temperature indicate that the thermal niche of P. borealis will likely be restricted to higher latitudes in the future. This prediction concurs with current decreases in abundance observed at the southern edge of this species geographical distribution, as it is for other cold-adapted crustaceans.
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5
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Predicting recombination frequency from map distance. Heredity (Edinb) 2023; 130:114-121. [PMID: 36566319 PMCID: PMC9981558 DOI: 10.1038/s41437-022-00585-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
Map distance is one of the key measures in genetics and indicates the expected number of crossovers between two loci. Map distance is estimated from the observed recombination frequency using mapping functions, the most widely used of those, Haldane and Kosambi, being developed at the time when the number of markers was low and unobserved crossovers had a substantial effect on the recombination fractions. In contemporary high-density marker data, the probability of multiple crossovers between adjacent loci is negligible and different mapping functions yield the same result, that is, the recombination frequency between adjacent loci is equal to the map distance in Morgans. However, high-density linkage maps contain an interpretation problem: the map distance over a long interval is additive and its association with recombination frequency is not defined. Here, we demonstrate with high-density linkage maps from humans and stickleback fishes that the inverses of Haldane's and Kosambi's mapping functions systematically underpredict recombination frequencies from map distance. To remedy this, we formulate a piecewise function that yields more accurate predictions of recombination frequency from map distance. Our results demonstrate that the association between map distance and recombination frequency is context-dependent and without a universal solution.
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6
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Carruthers M, Edgley DE, Saxon AD, Gabagambi NP, Shechonge A, Miska EA, Durbin R, Bridle JR, Turner GF, Genner MJ. Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes. Mol Biol Evol 2022; 39:msac251. [PMID: 36376993 PMCID: PMC10101686 DOI: 10.1093/molbev/msac251] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.
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Affiliation(s)
- Madeleine Carruthers
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Duncan E Edgley
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Andrew D Saxon
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Nestory P Gabagambi
- Tanzanian Fisheries Research Institute, Kyela Research
Centre, P.O. Box 98, Kyela, Mbeya, Tanzania
| | - Asilatu Shechonge
- Tanzanian Fisheries Research Institute, Dar es Salaam Research
Centre, P.O. Box 9750, Dar es Salaam, Tanzania
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge,
Cambridge CB2 1QN, United
Kingdom
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - George F Turner
- School of Natural Sciences, Bangor University,
Bangor, Wales LL57 2UW, United
Kingdom
| | - Martin J Genner
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
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7
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Detecting signatures of selection on gene expression. Nat Ecol Evol 2022; 6:1035-1045. [PMID: 35551249 DOI: 10.1038/s41559-022-01761-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
A substantial amount of phenotypic diversity results from changes in gene expression levels and patterns. Understanding how the transcriptome evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of gene expression evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene expression are subject to biases that can lead to false signatures of selection. Here we first outline the main approaches for describing expression evolution and their inherent biases. Next, we bridge the gap between the fields of phylogenetic comparative methods and transcriptomics to reinforce the main pitfalls of inferring selection on expression patterns and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of transcriptional variation and identifying major unanswered questions in disentangling how selection acts on the transcriptome.
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8
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Zhang Q, Yu Y, Luo Z, Xiang J, Li F. Comparison of Gene Expression Between Resistant and Susceptible Families Against VP AHPND and Identification of Biomarkers Used for Resistance Evaluation in Litopenaeus vannamei. Front Genet 2021; 12:772442. [PMID: 34899859 PMCID: PMC8662381 DOI: 10.3389/fgene.2021.772442] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND) has caused a heavy loss to shrimp aquaculture since its outbreak. Vibrio parahaemolyticus (VPAHPND) is regarded as one of the main pathogens that caused AHPND in the Pacific white shrimp Litopenaeus vannamei. In order to learn more about the mechanism of resistance to AHPND, the resistant and susceptible shrimp families were obtained through genetic breeding, and comparative transcriptome approach was used to analyze the gene expression patterns between resistant and susceptible families. A total of 95 families were subjected to VPAHPND challenge test, and significant variations in the resistance of these families were observed. Three pairs of resistant and susceptible families were selected for transcriptome sequencing. A total of 489 differentially expressed genes (DEGs) that presented in at least two pairwise comparisons were screened, including 196 DEGs highly expressed in the susceptible families and 293 DEGs in the resistant families. Among these DEGs, 16 genes demonstrated significant difference in all three pairwise comparisons. Gene set enrichment analysis (GSEA) of all 27,331 expressed genes indicated that some energy metabolism processes were enriched in the resistant families, while signal transduction and immune system were enriched in the susceptible families. A total of 32 DEGs were further confirmed in the offspring of the detected families, among which 19 genes were successfully verified. The identified genes in this study will be useful for clarifying the genetic mechanism of shrimp resistance against Vibrio and will further provide molecular markers for evaluating the disease resistance of shrimp in the breeding program.
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Affiliation(s)
- Qian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zheng Luo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, China
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9
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Chavarria-Pizarro T, Resl P, Janjic A, Werth S. Gene expression responses to thermal shifts in the endangered lichen Lobaria pulmonaria. Mol Ecol 2021; 31:839-858. [PMID: 34784096 DOI: 10.1111/mec.16281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022]
Abstract
Anthropogenic climate change has led to unprecedented shifts in temperature across many ecosystems. In a context of rapid environmental changes, acclimation is an important process as it may influence the capacity of organisms to survive under novel thermal conditions. Mechanisms of acclimation could involve upregulation of stress response genes involved in protein folding, DNA damage repair and the regulation of signal transduction genes, along with a simultaneous downregulation of genes involved in growth or the cell cycle, in order to maintain cellular functions and equilibria. We transplanted Lobaria pulmonaria lichens originating from different forests to determine the relative effects of long-term acclimation and genetic factors on the variability in expression of mycobiont and photobiont genes. We found a strong response of the mycobiont and photobiont to high temperatures, regardless of sample origin. The green-algal photobiont had an overall lower response than the mycobiont. Gene expression of both symbionts was also influenced by acclimation to transplantation sites and by genetic factors. L. pulmonaria seems to have evolved powerful molecular pathways to deal with environmental fluctuations and stress and can acclimate to new habitats by transcriptomic convergence. Although L. pulmonaria has the molecular machinery to counteract short-term thermal stress, survival of lichens such as L. pulmonaria depends mostly on their long-term positive carbon balance, which can be compromised by higher temperatures and reduced precipitation, and both these outcomes have been predicted for Central Europe in connection with global climate change.
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Affiliation(s)
| | - Philipp Resl
- Systematic Botany and Mycology, Faculty of Biology, LMU Munich, Munich, Germany.,Institute of Biology, University of Graz, Graz, Austria
| | - Aleksandar Janjic
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Silke Werth
- Systematic Botany and Mycology, Faculty of Biology, LMU Munich, Munich, Germany.,Institute of Biology, University of Graz, Graz, Austria
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10
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Blanc J, Kremling KAG, Buckler E, Josephs EB. Local adaptation contributes to gene expression divergence in maize. G3-GENES GENOMES GENETICS 2021; 11:6114460. [PMID: 33604670 PMCID: PMC8022924 DOI: 10.1093/g3journal/jkab004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/20/2020] [Indexed: 11/14/2022]
Abstract
Gene expression links genotypes to phenotypes, so identifying genes whose expression is shaped by selection will be important for understanding the traits and processes underlying local adaptation. However, detecting local adaptation for gene expression will require distinguishing between divergence due to selection and divergence due to genetic drift. Here, we adapt a QST−FST framework to detect local adaptation for transcriptome-wide gene expression levels in a population of diverse maize genotypes. We compare the number and types of selected genes across a wide range of maize populations and tissues, as well as selection on cold-response genes, drought-response genes, and coexpression clusters. We identify a number of genes whose expression levels are consistent with local adaptation and show that genes involved in stress response show enrichment for selection. Due to its history of intense selective breeding and domestication, maize evolution has long been of interest to researchers, and our study provides insight into the genes and processes important for in local adaptation of maize.
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Affiliation(s)
- Jennifer Blanc
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Karl A G Kremling
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Inari Agriculture, Cambridge, MA 02139, USA
| | - Edward Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.,United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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11
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Seppälä O, Çetin C, Cereghetti T, Feulner PGD, Adema CM. Examining adaptive evolution of immune activity: opportunities provided by gastropods in the age of 'omics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200158. [PMID: 33813886 PMCID: PMC8059600 DOI: 10.1098/rstb.2020.0158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
Parasites threaten all free-living organisms, including molluscs. Understanding the evolution of immune defence traits in natural host populations is crucial for predicting their long-term performance under continuous infection risk. Adaptive trait evolution requires that traits are subject to selection (i.e. contribute to organismal fitness) and that they are heritable. Despite broad interest in the evolutionary ecology of immune activity in animals, the understanding of selection on and evolutionary potential of immune defence traits is far from comprehensive. For instance, empirical observations are only rarely in line with theoretical predictions of immune activity being subject to stabilizing selection. This discrepancy may be because ecoimmunological studies can typically cover only a fraction of the complexity of an animal immune system. Similarly, molecular immunology/immunogenetics studies provide a mechanistic understanding of immunity, but neglect variation that arises from natural genetic differences among individuals and from environmental conditions. Here, we review the current literature on natural selection on and evolutionary potential of immune traits in animals, signal how merging ecological immunology and genomics will strengthen evolutionary ecological research on immunity, and indicate research opportunities for molluscan gastropods for which well-established ecological understanding and/or 'immune-omics' resources are already available. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Otto Seppälä
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Cansu Çetin
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Teo Cereghetti
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Philine G. D. Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Coen M. Adema
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, USA
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12
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Huang Y, Lack JB, Hoppel GT, Pool JE. Parallel and Population-specific Gene Regulatory Evolution in Cold-Adapted Fly Populations. Genetics 2021; 218:6275754. [PMID: 33989401 PMCID: PMC8864734 DOI: 10.1093/genetics/iyab077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/10/2021] [Indexed: 11/15/2022] Open
Abstract
Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find evidence for parallel expression evolution between them, with stronger parallelism at larval and adult stages than for pupae. We also implement a flexible method to estimate cis- vs trans-encoded contributions to expression or splicing differences at the adult stage. The apparent contributions of cis- vs trans-regulation to adaptive evolution vary substantially among population pairs. While two of three population pairs show a greater enrichment of cis-regulatory differences among adaptation candidates, trans-regulatory differences are more likely to be implicated in parallel expression changes between population pairs. Genes with significant cis-effects are enriched for signals of elevated genetic differentiation between cold- and warm-adapted populations, suggesting that they are potential targets of local adaptation. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.
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Affiliation(s)
- Yuheng Huang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Grant T Hoppel
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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13
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Kivikoski M, Rastas P, Löytynoja A, Merilä J. Automated improvement of stickleback reference genome assemblies with Lep-Anchor software. Mol Ecol Resour 2021; 21:2166-2176. [PMID: 33955177 DOI: 10.1111/1755-0998.13404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 01/06/2023]
Abstract
We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads, we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.6-Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.
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Affiliation(s)
- Mikko Kivikoski
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pasi Rastas
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Division of Ecology and Biodiversity, The University of Hong Kong, Hong Kong, Hong Kong, SAR
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14
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Transcriptome profiling of Lymnaea stagnalis (Gastropoda) for ecoimmunological research. BMC Genomics 2021; 22:144. [PMID: 33648459 PMCID: PMC7919325 DOI: 10.1186/s12864-021-07428-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/05/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Host immune function can contribute to numerous ecological/evolutionary processes. Ecoimmunological studies, however, typically use one/few phenotypic immune assays and thus do not consider the complexity of the immune system. Therefore, "omics" resources that allow quantifying immune activity across multiple pathways are needed for ecoimmunological models. We applied short-read based RNAseq (Illumina NextSeq 500, PE-81) to characterise transcriptome profiles of Lymnaea stagnalis (Gastropoda), a multipurpose model snail species. We used a genetically diverse snail stock and exposed individuals to immune elicitors (injury, bacterial/trematode pathogens) and changes in environmental conditions that can alter immune activity (temperature, food availability). RESULTS Immune defence factors identified in the de novo assembly covered elements broadly described in other gastropods. For instance, pathogen-recognition receptors (PRR) and lectins activate Toll-like receptor (TLR) pathway and cytokines that regulate cellular and humoral defences. Surprisingly, only modest diversity of antimicrobial peptides and fibrinogen related proteins were detected when compared with other taxa. Additionally, multiple defence factors that may contribute to the phenotypic immune assays used to quantify antibacterial activity and phenoloxidase (PO)/melanisation-type reaction in this species were found. Experimental treatments revealed factors from non-self recognition (lectins) and signalling (TLR pathway, cytokines) to effectors (e.g., antibacterial proteins, PO enzymes) whose transcription depended on immune stimuli and environmental conditions, as well as components of snail physiology/metabolism that may drive these effects. Interestingly, the transcription of many factors (e.g., PRR, lectins, cytokines, PO enzymes, antibacterial proteins) showed high among-individual variation. CONCLUSIONS Our results indicate several uniform aspects of gastropod immunity, but also apparent differences between L. stagnalis and some previously examined taxa. Interestingly, in addition to immune defence factors that responded to immune elicitors and changes in environmental conditions, many factors showed high among-individual variation across experimental snails. We propose that such factors are highly important to be included in future ecoimmunological studies because they may be the key determinants of differences in parasite resistance among individuals both within and between natural snail populations.
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15
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Bascuñán P, Gabrieli P, Mameli E, Catteruccia F. Mating-regulated atrial proteases control reinsemination rates in Anopheles gambiae females. Sci Rep 2020; 10:21974. [PMID: 33319823 PMCID: PMC7738481 DOI: 10.1038/s41598-020-78967-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/25/2020] [Indexed: 11/20/2022] Open
Abstract
Anopheles gambiae mosquitoes are the most important vectors of human malaria. The reproductive success of these mosquitoes relies on a single copulation event after which the majority of females become permanently refractory to further mating. This refractory behavior is at least partially mediated by the male-synthetized steroid hormone 20-hydroxyecdysone (20E), which is packaged together with other seminal secretions into a gelatinous mating plug and transferred to the female atrium during mating. In this study, we show that two 20E-regulated chymotrypsin-like serine proteases specifically expressed in the reproductive tract of An. gambiae females play an important role in modulating the female susceptibility to mating. Silencing these proteases by RNA interference impairs correct plug processing and slows down the release of the steroid hormone 20E from the mating plug. In turn, depleting one of these proteases, the Mating Regulated Atrial Protease 1 (MatRAP1), reduces female refractoriness to further copulation, so that a significant proportion of females mate again. Microscopy analysis reveals that MatRAP1 is localized on a previously undetected peritrophic matrix-like structure surrounding the mating plug. These data provide novel insight into the molecular mechanisms shaping the post-mating biology of these important malaria vectors.
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Affiliation(s)
- Priscila Bascuñán
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Dipartimento di Medicina Sperimentale, Università degli studi di Perugia, Perugia, Italy
- Centers for Disease Control and Prevention, Entomology Branch, Atlanta, GA, USA
| | - Paolo Gabrieli
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Dipartimento di Medicina Sperimentale, Università degli studi di Perugia, Perugia, Italy
- Dipartimento di Bioscienze, Università degli studi di Milano, Milan, Italy
| | - Enzo Mameli
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Dipartimento di Medicina Sperimentale, Università degli studi di Perugia, Perugia, Italy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Dipartimento di Medicina Sperimentale, Università degli studi di Perugia, Perugia, Italy.
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16
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Smith S, Brauer CJ, Sasaki M, Unmack PJ, Guillot G, Laporte M, Bernatchez L, Beheregaray LB. Latitudinal variation in climate-associated genes imperils range edge populations. Mol Ecol 2020; 29:4337-4349. [PMID: 32930432 DOI: 10.1111/mec.15637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 11/28/2022]
Abstract
The ecological impacts of increasing global temperatures are evident in most ecosystems on Earth, but our understanding of how climatic variation influences natural selection and adaptive resilience across latitudes remains largely unknown. Latitudinal gradients allow testing general ecosystem-level theories relevant to climatic adaptation. We assessed differences in adaptive diversity of populations along a latitudinal region spanning highly variable temperate to subtropical climates. We generated and integrated information from environmental mapping, phenotypic variation and genome-wide data from across the geographical range of the rainbowfish Melanotaenia duboulayi, an emerging aquatic system for studies of climate change. We detected, after controlling for spatial population structure, strong interactions between genotypes and environment associated with variation in stream flow and temperature. Some of these hydroclimate-associated genes were found to interact within functional protein networks that contain genes of adaptive significance for projected future climates in rainbowfish. Hydroclimatic selection was also associated with variation in phenotypic traits, including traits known to affect fitness of rainbowfish exposed to different flow environments. Consistent with predictions from the "climatic variability hypothesis," populations exposed to extremes of important environmental variables showed stronger adaptive divergence and less variation in climate-associated genes compared to populations at the centre of the environmental gradient. Our findings suggest that populations that evolved at environmental range margins and at geographical range edges may be more vulnerable to changing climates, a finding with implications for predicting adaptive resilience and managing biodiversity under climate change.
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Affiliation(s)
- Steve Smith
- Molecular Ecology Lab, Flinders University, Bedford Park, SA, Australia.,Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Chris J Brauer
- Molecular Ecology Lab, Flinders University, Bedford Park, SA, Australia
| | - Minami Sasaki
- Molecular Ecology Lab, Flinders University, Bedford Park, SA, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, University of Canberra, Bruce, ACT, Australia
| | - Gilles Guillot
- International Prevention Research Institute, Dardilly, France
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, Quebec City, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, Quebec City, QC, Canada
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17
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Logan ML, Cox CL. Genetic Constraints, Transcriptome Plasticity, and the Evolutionary Response to Climate Change. Front Genet 2020; 11:538226. [PMID: 33193610 PMCID: PMC7531272 DOI: 10.3389/fgene.2020.538226] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022] Open
Abstract
In situ adaptation to climate change will be critical for the persistence of many ectotherm species due to their relative lack of dispersal capacity. Climate change is causing increases in both the mean and the variance of environmental temperature, each of which may act as agents of selection on different traits. Importantly, these traits may not be heritable or have the capacity to evolve independently from one another. When genetic constraints prevent the "baseline" values of thermal performance traits from evolving rapidly, phenotypic plasticity driven by gene expression might become critical. We review the literature for evidence that thermal performance traits in ectotherms are heritable and have genetic architectures that permit their unconstrained evolution. Next, we examine the relationship between gene expression and both the magnitude and duration of thermal stress. Finally, we identify genes that are likely to be important for adaptation to a changing climate and determine whether they show patterns consistent with thermal adaptation. Although few studies have measured narrow-sense heritabilities of thermal performance traits, current evidence suggests that the end points of thermal reaction norms (tolerance limits) are moderately heritable and have the potential to evolve rapidly. By contrast, performance at intermediate temperatures has substantially lower evolutionary potential. Moreover, evolution in many species appears to be constrained by genetic correlations such that populations can adapt to either increases in mean temperature or temperature variability, but not both. Finally, many species have the capacity for plastic expression of the transcriptome in response to temperature shifts, with the number of differentially expressed genes increasing with the magnitude, but not the duration, of thermal stress. We use these observations to develop a conceptual model that describes the likely trajectory of genome evolution in response to changes in environmental temperature. Our results indicate that extreme weather events, rather than gradual increases in mean temperature, are more likely to drive genetic and phenotypic change in wild ectotherms.
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Affiliation(s)
- Michael L Logan
- Department of Biology, University of Nevada, Reno, Reno, NV, United States.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Christian L Cox
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, United States
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18
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Jallet AJ, Le Rouzic A, Genissel A. Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant Pathogen Zymoseptoria tritici. Front Microbiol 2020; 11:573829. [PMID: 33042084 PMCID: PMC7517895 DOI: 10.3389/fmicb.2020.573829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/17/2020] [Indexed: 11/28/2022] Open
Abstract
Most species live in a variable environment in nature. Yet understanding the evolutionary processes underlying molecular adaptation to fluctuations remains a challenge. In this study we investigate the transcriptome of the fungal wheat pathogen Zymoseptoria tritici after experimental evolution under stable or fluctuating temperature, by comparing ancestral and evolved populations simultaneously. We found that temperature regimes could have a large and pervasive effect on the transcriptome evolution, with as much as 38% of the genes being differentially expressed between selection regimes. Although evolved lineages showed different changes of gene expression based on ancestral genotypes, we identified a set of genes responding specifically to fluctuation. We found that transcriptome evolution in fluctuating conditions was repeatable between parallel lineages initiated from the same genotype for about 60% of the differentially expressed genes. Further, we detected several hotspots of significantly differentially expressed genes in the genome, in regions known to be enriched in repetitive elements, including accessory chromosomes. Our findings also evidenced gene expression evolution toward a gain of robustness (loss of phenotypic plasticity) associated with the fluctuating regime, suggesting robustness is adaptive in changing environment. This work provides valuable insight into the role of transcriptional rewiring for rapid adaptation to abiotic changes in filamentous plant pathogens.
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Affiliation(s)
- Arthur J. Jallet
- UMR BIOGER, Université Paris Saclay – INRAE – AgroParisTech, Thiverval-Grignon, France
| | - Arnaud Le Rouzic
- UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay – CNRS – IRD, Gif-sur-Yvette, France
| | - Anne Genissel
- UMR BIOGER, Université Paris Saclay – INRAE – AgroParisTech, Thiverval-Grignon, France
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19
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Huang X, Zhan A. Highly dynamic transcriptional reprogramming and shorter isoform shifts under acute stresses during biological invasions. RNA Biol 2020; 18:340-353. [PMID: 32804003 DOI: 10.1080/15476286.2020.1805904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Phenotypic plasticity has been increasingly recognized for its importance in adaptation to novel environments, and initial rapid plastic response to acute stresses usually serves as the stepping stone for future adaptation. Differential gene expression and alternative splicing have been proposed as two underlying mechanisms for rapid plastic response to environmental stresses. Here, we used an invasive model species, Ciona savignyi, to investigate the temporary plastic changes under temperature stresses on gene expression and alternative splicing. Our results revealed rapid and highly dynamic gene expression reprogramming and alternative splicing switch under acute stresses. Distinct transcriptional response profiles were triggered by two types of temperature stresses, showing resilience recovery and increasing divergence under heat and cold challenges, respectively. Interestingly, alternative exons were more inclined to be skipped under both heat and cold stresses, leading to shorter isoforms but with maintained Open Reading Frames (ORFs). Although similar response patterns were observed between differential gene expression and alternative splicing, low overlap between Differentially Expressed Genes (DEGs) and Differentially Alternative Spliced Genes (DASGs) suggests that distinct gene sets and associated functions should be involved in temperature challenges. Thus, alternative splicing should offer an additional layer of plastic response to environmental challenges. Finally, we identified key plastic genes involved in both gene expression regulation and alternative splicing. The results obtained here shed light on adaptation and accommodation mechanisms during biological invasions, particularly for acute environmental changes at early stages of biological invasions such as transport and introduction.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
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20
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Wang Y, Zhao Y, Wang Y, Li Z, Guo B, Merilä J. Population transcriptomics reveals weak parallel genetic basis in repeated marine and freshwater divergence in nine‐spined sticklebacks. Mol Ecol 2020; 29:1642-1656. [DOI: 10.1111/mec.15435] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yingnan Wang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Yongxin Zhao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Yu Wang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Zitong Li
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
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21
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Koch EL, Guillaume F. Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum. PLoS Genet 2020; 16:e1008768. [PMID: 32379753 PMCID: PMC7238888 DOI: 10.1371/journal.pgen.1008768] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 05/19/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Gene expression is known to be highly responsive to the environment and important for adjustment of metabolism but there is also growing evidence that differences in gene regulation contribute to species divergence and differences among locally adapted populations. However, most studies so far investigated populations when divergence had already occurred. Selection acting on expression levels at the onset of adaptation to an environmental change has not been characterized. Understanding the mechanisms is further complicated by the fact that environmental change is often multivariate, meaning that organisms are exposed to multiple stressors simultaneously with potentially interactive effects. Here we use a novel approach by combining fitness and whole-transcriptome data in a large-scale experiment to investigate responses to drought, heat and their combination in Tribolium castaneum. We found that fitness was reduced by both stressors and their combined effect was almost additive. Expression data showed that stressor responses were acting independently and did not interfere physiologically. Since we measured expression and fitness within the same individuals, we were able to estimate selection on gene expression levels. We found that variation in fitness can be attributed to gene expression variation and that selection pressures were environment dependent and opposite between control and stress conditions. We could further show that plastic responses of expression were largely adaptive, i.e. in the direction that should increase fitness.
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Affiliation(s)
- Eva L. Koch
- Department of Evolutionary Biology and Environmental Studies, University
of Zürich, Zürich, Switzerland
- Department of Animal and Plant Science, University of Sheffield, Western
Bank, Sheffield, United Kingdom
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University
of Zürich, Zürich, Switzerland
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22
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Huang Y, Feulner PGD, Eizaguirre C, Lenz TL, Bornberg-Bauer E, Milinski M, Reusch TBH, Chain FJJ. Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes. Genome Biol Evol 2020; 11:2344-2359. [PMID: 31298693 PMCID: PMC6735750 DOI: 10.1093/gbe/evz148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments.
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Affiliation(s)
- Yun Huang
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, Westfälische Wilhelms University, Münster, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, USA
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23
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Toews SD, Wellband KW, Dixon B, Heath DD. Variation in juvenile Chinook salmon (Oncorhynchus tshawytscha) transcription profiles among and within eight population crosses from British Columbia, Canada. Mol Ecol 2019; 28:1890-1903. [DOI: 10.1111/mec.15025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 01/02/2019] [Accepted: 01/07/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Shelby D. Toews
- Great Lakes Institute for Environmental Research University of Windsor Windsor Ontario Canada
| | - Kyle W. Wellband
- Great Lakes Institute for Environmental Research University of Windsor Windsor Ontario Canada
- Institute de Biologie Intégrative et des SystèmesUniversité LavalQuébec Québec Canada
| | - Brian Dixon
- Department of Biology University of Waterloo Waterloo Ontario Canada
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research University of Windsor Windsor Ontario Canada
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24
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Härer A, Meyer A, Torres‐Dowdall J. Convergent phenotypic evolution of the visual system via different molecular routes: How Neotropical cichlid fishes adapt to novel light environments. Evol Lett 2018; 2:341-354. [PMID: 30283686 PMCID: PMC6121847 DOI: 10.1002/evl3.71] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 12/17/2022] Open
Abstract
How predictable is evolution? This remains a fundamental but contested issue in evolutionary biology. When independent lineages colonize the same environment, we are presented with a natural experiment that allows us to ask if genetic and ecological differences promote species-specific evolutionary outcomes or whether species phenotypically evolve in a convergent manner in response to shared selection pressures. If so, are the molecular mechanisms underlying phenotypic convergence the same? In Nicaragua, seven species of cichlid fishes concurrently colonized two novel photic environments. Hence, their visual system represents a compelling model to address these questions, particularly since the adaptive value of phenotypic changes is well-understood. By analyzing retinal transcriptomes, we found that differential expression of genes responsible for color vision (cone opsins and cyp27c1) produced rapid and mostly convergent changes of predicted visual sensitivities. Notably, these changes occurred in the same direction in all species although there were differences in underlying gene expression patterns illustrating nonconvergence at the molecular level. Adaptive phenotypes evolved deterministically, even when species differ substantially in ecology and genetic variation. This provides strong evidence that phenotypic evolution of the visual system occurred in response to similar selective forces of the photic environment.
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Affiliation(s)
- Andreas Härer
- Zoology and Evolutionary Biology, Department of BiologyUniversity of KonstanzGermany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of BiologyUniversity of KonstanzGermany
- Radcliffe Institute for Advanced StudyHarvard UniversityCambridgeMassachusetts02138
| | - Julián Torres‐Dowdall
- Zoology and Evolutionary Biology, Department of BiologyUniversity of KonstanzGermany
- Zukunftskolleg, University of KonstanzKonstanzGermany
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25
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Analysis of natural female post-mating responses of Anopheles gambiae and Anopheles coluzzii unravels similarities and differences in their reproductive ecology. Sci Rep 2018; 8:6594. [PMID: 29700344 PMCID: PMC5920108 DOI: 10.1038/s41598-018-24923-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 03/20/2018] [Indexed: 11/18/2022] Open
Abstract
Anopheles gambiae and An. coluzzii, the two most important malaria vectors in sub-Saharan Africa, are recently radiated sibling species that are reproductively isolated even in areas of sympatry. In females from these species, sexual transfer of male accessory gland products, including the steroid hormone 20-hydroxyecdysone (20E), induces vast behavioral, physiological, and transcriptional changes that profoundly shape their post-mating ecology, and that may have contributed to the insurgence of post-mating, prezygotic reproductive barriers. As these barriers can be detected by studying transcriptional changes induced by mating, we set out to analyze the post-mating response of An. gambiae and An. coluzzii females captured in natural mating swarms in Burkina Faso. While the molecular pathways shaping short- and long-term mating-induced changes are largely conserved in females from the two species, we unravel significant inter-specific differences that suggest divergent regulation of key reproductive processes such as egg development, processing of seminal secretion, and mating behavior, that may have played a role in reproductive isolation. Interestingly, a number of these changes occur in genes previously shown to be regulated by the sexual transfer of 20E and may be due to divergent utilization of this steroid hormone in the two species.
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26
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Oostra V, Saastamoinen M, Zwaan BJ, Wheat CW. Strong phenotypic plasticity limits potential for evolutionary responses to climate change. Nat Commun 2018. [PMID: 29520061 PMCID: PMC5843647 DOI: 10.1038/s41467-018-03384-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Phenotypic plasticity, the expression of multiple phenotypes from one genome, is a widespread adaptation to short-term environmental fluctuations, but whether it facilitates evolutionary adaptation to climate change remains contentious. Here, we investigate seasonal plasticity and adaptive potential in an Afrotropical butterfly expressing distinct phenotypes in dry and wet seasons. We assess the transcriptional architecture of plasticity in a full-factorial analysis of heritable and environmental effects across 72 individuals, and reveal pervasive gene expression differences between the seasonal phenotypes. Strikingly, intra-population genetic variation for plasticity is largely absent, consistent with specialisation to a particular environmental cue reliably predicting seasonal transitions. Under climate change, deteriorating accuracy of predictive cues will likely aggravate maladaptive phenotype-environment mismatches and increase selective pressures on reaction norms. However, the observed paucity of genetic variation for plasticity limits evolutionary responses, potentially weakening prospects for population persistence. Thus, seasonally plastic species may be especially vulnerable to climate change.
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Affiliation(s)
- Vicencio Oostra
- Department of Genetics, Evolution and Environment, University College London, The Darwin Building, Gower Street, London, WC1E 6BT, UK. .,Department of Plant Sciences, Laboratory of Genetics, Wageningen University, PO Box 16, 6700AA, Wageningen, The Netherlands.
| | - Marjo Saastamoinen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, PO Box 65, Helsinki, FI-00014, Finland
| | - Bas J Zwaan
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, PO Box 16, 6700AA, Wageningen, The Netherlands
| | - Christopher W Wheat
- Department of Zoology, Population Genetics, Stockholm University, S-10691, Stockholm, Sweden
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27
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Mäkinen H, Sävilammi T, Papakostas S, Leder E, Vøllestad LA, Primmer CR. Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence. Genome Biol Evol 2018; 10:77-93. [PMID: 29293993 PMCID: PMC5758911 DOI: 10.1093/gbe/evx278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying coexpressed modules now enable systems genetics approaches also in nonmodel species for better understanding of gene expression responses during early divergence. Here, we combined gene coexpression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16,622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that coexpression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.
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Affiliation(s)
| | | | | | - Erica Leder
- Department of Biology, University of Turku, Finland
- Natural History Museum, University of Oslo, Norway
| | - Leif A Vøllestad
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Craig R Primmer
- Department of Biosciences, University of Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Finland
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28
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Brauer CJ, Unmack PJ, Beheregaray LB. Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish. Mol Ecol 2017; 26:6841-6856. [DOI: 10.1111/mec.14432] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/23/2017] [Accepted: 10/25/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
| | - Peter J. Unmack
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
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29
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Environmental and genetic determinants of transcriptional plasticity in Chinook salmon. Heredity (Edinb) 2017; 120:38-50. [PMID: 29234168 DOI: 10.1038/s41437-017-0009-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/30/2017] [Accepted: 09/13/2017] [Indexed: 11/08/2022] Open
Abstract
Variation in gene transcription is widely believed to be the mechanistic basis of phenotypically plastic traits; however, comparatively little is known about the inheritance patterns of transcriptional variation that would allow us to predict its response to selection. In addition, acclimation to different environmental conditions influences acute transcriptional responses to stress and it is unclear if these effects are heritable. To address these gaps in knowledge, we assayed levels of messenger RNA for 14 candidate genes at rest and in response to a 24-h confinement stress for 72 half-sib families of Chinook salmon reared in two different environments (hatchery and semi-natural stream channel). We observed extensive plasticity for mRNA levels of metabolic and stress response genes and demonstrated that mRNA level plasticity due to rearing environment affects mRNA level plasticity in response to stress. These effects have important implications for natural populations experiencing multiple stressors. We identified genotype-by-environment interactions for mRNA levels that were dominated by maternal effects; however, mRNA level response to challenge also exhibited a non-additive genetic basis. Our results indicate that while plasticity for mRNA levels can evolve, predicting the outcome of selection will be difficult. The inconsistency in genetic architecture among treatment groups suggests there is considerable cryptic genetic variation for gene expression.
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30
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Small CM, Milligan-Myhre K, Bassham S, Guillemin K, Cresko WA. Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut. Genome Biol Evol 2017; 9:504-520. [PMID: 28391321 PMCID: PMC5381569 DOI: 10.1093/gbe/evx014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2017] [Indexed: 02/07/2023] Open
Abstract
Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes.
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Affiliation(s)
- Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | | | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
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31
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Perrier C, Ferchaud AL, Sirois P, Thibault I, Bernatchez L. Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish. Mol Ecol 2017; 26:6317-6335. [PMID: 29024140 DOI: 10.1111/mec.14361] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 01/01/2023]
Abstract
Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.
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Affiliation(s)
- Charles Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Pascal Sirois
- Chaire de Recherche sur les Espèces Aquatiques Exploitées, Laboratoire des Sciences Aquatiques, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Isabel Thibault
- Direction de l'expertise sur la Faune Aquatique, Ministère des Forêts de la Faune et des Parcs du Québec, Québec, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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32
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Passow CN, Henpita C, Shaw JH, Quackenbush CR, Warren WC, Schartl M, Arias-Rodriguez L, Kelley JL, Tobler M. The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish. Mol Ecol 2017; 26:6384-6399. [PMID: 28926156 DOI: 10.1111/mec.14360] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/22/2022]
Abstract
The notorious plasticity of gene expression responses and the complexity of environmental gradients complicate the identification of adaptive differences in gene regulation among populations. We combined transcriptome analyses in nature with common-garden and exposure experiments to establish cause-effect relationships between the presence of a physiochemical stressor and expression differences, as well as to test how evolutionary change and plasticity interact to shape gene expression variation in natural systems. We studied two evolutionarily independent population pairs of an extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulphide (H2 S)-rich springs and adjacent nontoxic habitats and assessed genomewide expression patterns of wild-caught and common-garden-raised individuals exposed to different concentrations of H2 S. We found that 7.7% of genes that were differentially expressed between sulphidic and nonsulphidic ecotypes remained differentially expressed in the laboratory, indicating that sources of selection other than H2 S-or plastic responses to other environmental factors-contribute substantially to gene expression patterns observed in the wild. Concordantly differentially expressed genes in the wild and the laboratory were primarily associated with H2 S detoxification, sulphur processing and metabolic physiology. While shared, ancestral plasticity played a minor role in shaping gene expression variation observed in nature, we documented evidence for evolved population differences in the constitutive expression as well as the H2 S inducibility of candidate genes. Mechanisms underlying gene expression variation also varied substantially across the two ecotype pairs. These results provide a springboard for studying evolutionary modifications of gene regulatory mechanisms that underlie expression variation in locally adapted populations.
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Affiliation(s)
| | - Chathurika Henpita
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Jennifer H Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Manfred Schartl
- Physiological Chemistry, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.,Hagler Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, TX, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, México
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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33
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Gates K, Sandoval-Castillo J, Bernatchez L, Beheregaray LB. De novo transcriptome assembly and annotation for the desert rainbowfish ( Melanotaenia splendida tatei ) with comparison with candidate genes for future climates. Mar Genomics 2017; 35:63-68. [DOI: 10.1016/j.margen.2017.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/15/2017] [Indexed: 01/25/2023]
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34
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Yan J, Song Z, Xu Q, Kang L, Zhu C, Xing S, Liu W, Greimler J, Züst T, Li J, Sang T. Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops. Mol Ecol 2017; 26:5911-5922. [PMID: 28833782 DOI: 10.1111/mec.14338] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 12/11/2022]
Abstract
The use of transcriptome data in the study of the population genetics of a species can capture faint signals of both genetic variation and expression variation and can provide a broad picture of a species' genomic response to environmental conditions. In this study, we characterized the genetic and expression diversity of Miscanthus lutarioriparius by comparing more than 16,225 transcripts obtained from 78 individuals, belonging to 10 populations distributed across the species' entire geographic range. We only observed a low level of nucleotide diversity (π = 0.000434) among the transcriptome data of these populations, which is consistent with highly conserved sequences of functional elements and protein-coding genes captured with this method. Tests of population divergence using the transcriptome data were consistent with previous microsatellite data but proved to be more sensitive, particularly if gene expression variation was considered as well. For example, the analysis of expression data showed that genes involved in photosynthetic processes and responses to temperature or reactive oxygen species stimuli were significantly enriched in certain populations. This differential gene expression was primarily observed among populations and not within populations. Interestingly, nucleotide diversity was significantly negatively correlated with expression diversity within populations, while this correlation was positive among populations. This suggests that genetic and expression variation play separate roles in adaptation and population persistence. Combining analyses of genetic and gene expression variation represents a promising approach for studying the population genetics of wild species and may uncover both adaptive and nonadaptive processes.
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Affiliation(s)
- Juan Yan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Zhihong Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qin Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lifang Kang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Caiyun Zhu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shilai Xing
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Josef Greimler
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Tobias Züst
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Jianqiang Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Tao Sang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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35
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Challenges and advances for transcriptome assembly in non-model species. PLoS One 2017; 12:e0185020. [PMID: 28931057 PMCID: PMC5607178 DOI: 10.1371/journal.pone.0185020] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 09/04/2017] [Indexed: 12/28/2022] Open
Abstract
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence). Here we focus on gene identification and not on resolving the whole set of transcripts (i.e. the complete transcriptome). For simulated datasets, the transcriptome-guided assembly based on blastn recovers 94.8% of genes irrespective of read length at 0% divergence; however, assignment rate of reads is negatively correlated with both increasing divergence level and reducing read lengths. Nevertheless, we still observe 92.6% of recovered genes at 30% divergence irrespective of read length. This analysis also produces a categorization of genes relative to their assignment, and suggests guidelines for data processing prior to analyses of comparative transcriptomics and gene expression to minimize potential inferential bias associated with incorrect transcript assignment. We also compare the performances of de novo assembly alone vs in combination with a transcriptome-guided assembly based on blastn both via simulation and empirically, using data from a cyprinid fish species and from an oak species. For any simulated scenario, the transcriptome-guided assembly using blastn outperforms the de novo approach alone, including when the divergence level is beyond the reach of traditional mapping methods. Combining de novo assembly and a related reference transcriptome for read assignment also addresses the bias/error in contigs caused by the dependence on a related reference alone. Empirical data corroborate these findings when assembling transcriptomes from the two non-model organisms: Parachondrostoma toxostoma (fish) and Quercus pubescens (plant). For the fish species, out of the 31,944 genes known from D. rerio, the guided and de novo assemblies recover respectively 20,605 and 20,032 genes but the performance of the guided assembly approach is much higher for both the contiguity and completeness metrics. For the oak, out of the 29,971 genes known from Vitis vinifera, the transcriptome-guided and de novo assemblies display similar performance, but the new guided approach detects 16,326 genes where the de novo assembly only detects 9,385 genes.
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36
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Hanson D, Hu J, Hendry AP, Barrett RDH. Heritable gene expression differences between lake and stream stickleback include both parallel and antiparallel components. Heredity (Edinb) 2017; 119:339-348. [PMID: 28832577 PMCID: PMC5637370 DOI: 10.1038/hdy.2017.50] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/05/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022] Open
Abstract
The repeated phenotypic patterns that characterize populations undergoing parallel evolution provide support for a deterministic role of adaptation by natural selection. Determining the level of parallelism also at the genetic level is thus central to our understanding of how natural selection works. Many studies have looked for repeated genomic patterns in natural populations, but work on gene expression is less common. The studies that have examined gene expression have found some support for parallelism, but those studies almost always used samples collected from the wild that potentially confounds the effects of plasticity with heritable differences. Here we use two independent pairs of lake and stream threespine stickleback (Gasterosteus aculeatus) raised in common garden conditions to assess both parallel and antiparallel (that is, similar versus different directions of lake–stream expression divergence in the two watersheds) heritable gene expression differences as measured by total RNA sequencing. We find that more genes than expected by chance show either parallel (22 genes, 0.18% of expressed genes) or antiparallel (24 genes, 0.20% of expressed genes) lake–stream expression differences. These results correspond well with previous genomic studies in stickleback ecotype pairs that found similar levels of parallelism. We suggest that parallelism might be similarly constrained at the genomic and transcriptomic levels.
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Affiliation(s)
- D Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - J Hu
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - A P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - R D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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37
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Lohman BK, Stutz WE, Bolnick DI. Gene expression stasis and plasticity following migration into a foreign environment. Mol Ecol 2017; 26:4657-4670. [DOI: 10.1111/mec.14234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/09/2017] [Accepted: 06/21/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Brian K. Lohman
- Department of Integrative Biology; University of Texas at Austin; Austin TX USA
| | - William E. Stutz
- Office of Institutional Research; Western Michigan University; Kalamazoo MI USA
| | - Daniel I. Bolnick
- Department of Integrative Biology; University of Texas at Austin; Austin TX USA
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38
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Siren J, Ovaskainen O, Merilä J. Structure and stability of genetic variance-covariance matrices: A Bayesian sparse factor analysis of transcriptional variation in the three-spined stickleback. Mol Ecol 2017; 26:5099-5113. [PMID: 28746754 DOI: 10.1111/mec.14265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/06/2017] [Indexed: 11/30/2022]
Abstract
The genetic variance-covariance matrix (G) is a quantity of central importance in evolutionary biology due to its influence on the rate and direction of multivariate evolution. However, the predictive power of empirically estimated G-matrices is limited for two reasons. First, phenotypes are high-dimensional, whereas traditional statistical methods are tuned to estimate and analyse low-dimensional matrices. Second, the stability of G to environmental effects and over time remains poorly understood. Using Bayesian sparse factor analysis (BSFG) designed to estimate high-dimensional G-matrices, we analysed levels variation and covariation in 10,527 expressed genes in a large (n = 563) half-sib breeding design of three-spined sticklebacks subject to two temperature treatments. We found significant differences in the structure of G between the treatments: heritabilities and evolvabilities were higher in the warm than in the low-temperature treatment, suggesting more and faster opportunity to evolve in warm (stressful) conditions. Furthermore, comparison of G and its phenotypic equivalent P revealed the latter is a poor substitute of the former. Most strikingly, the results suggest that the expected impact of G on evolvability-as well as the similarity among G-matrices-may depend strongly on the number of traits included into analyses. In our results, the inclusion of only few traits in the analyses leads to underestimation in the differences between the G-matrices and their predicted impacts on evolution. While the results highlight the challenges involved in estimating G, they also illustrate that by enabling the estimation of large G-matrices, the BSFG method can improve predicted evolutionary responses to selection.
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Affiliation(s)
- J Siren
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - O Ovaskainen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - J Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
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39
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Kim SY, Costa MM, Esteve-Codina A, Velando A. Transcriptional mechanisms underlying life-history responses to climate change in the three-spined stickleback. Evol Appl 2017; 10:718-730. [PMID: 28717391 PMCID: PMC5511362 DOI: 10.1111/eva.12487] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 04/13/2017] [Indexed: 01/10/2023] Open
Abstract
Phenotypic plasticity, the ability of an organism to express different phenotypes depending on the environment, provides an important mechanism by which an animal population can persist under rapid climate change. We experimentally tested both life‐history and transcriptional responses of an ecological model species, the three‐spined stickleback, to warm acclimation at the southern edge of its European range. We explored cross‐environment genetic correlations of key life‐history traits in male sticklebacks exposed to long‐term temperature changes to examine whether the plasticity pattern was variable among genotypes by using a character‐state approach. We also studied gene expression plasticity by analysing both whole‐transcriptome and candidate gene expression in brain and liver. Male sticklebacks that developed under warmer conditions during winter were smaller in size and invested less in nuptial coloration at the beginning of the breeding season, showing similar responses across different genotypes. The lack of genetic variation in life‐history responses may limit any future evolution of the thermal reaction norm in the study population. After long‐term exposure to increased winter temperatures, genes responsible for several metabolic and oxidation–reduction processes were upregulated, and some hormone genes involved in growth and reproduction were downregulated in the brain. In the liver, there was no significantly represented gene ontology by the differentially expressed genes. Since a higher temperature leads to a higher resting metabolic rate, living in warmer environments may incur higher energetic costs for ectotherms to maintain cellular homoeostasis, resulting in negative consequences for life‐history traits. The expression of genes related to metabolism, cellular homoeostasis and regulatory signalling may underlie temperature‐induced changes in life history.
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Affiliation(s)
- Sin-Yeon Kim
- Departamento de Ecoloxía e Bioloxía Animal Universidade de Vigo Vigo Spain
| | - Maria M Costa
- Departamento de Ecoloxía e Bioloxía Animal Universidade de Vigo Vigo Spain
| | - Anna Esteve-Codina
- CNAG-CRG Barcelona Institute of Science and Technology Barcelona Spain.,Universitat Pompeu Fabra Barcelona Spain
| | - Alberto Velando
- Departamento de Ecoloxía e Bioloxía Animal Universidade de Vigo Vigo Spain
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40
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Moshtaghi A, Rahi ML, Mather PB, Hurwood DA. Understanding the Genomic Basis of Adaptive Response to Variable Osmotic Niches in Freshwater Prawns: A Comparative Intraspecific RNA-Seq Analysis of Macrobrachium australiense. J Hered 2017; 108:544-552. [DOI: 10.1093/jhered/esx045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/03/2017] [Indexed: 12/30/2022] Open
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41
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Liao Z, Wan Q, Shang X, Su J. Large-scale SNP screenings identify markers linked with GCRV resistant traits through transcriptomes of individuals and cell lines in Ctenopharyngodon idella. Sci Rep 2017; 7:1184. [PMID: 28446772 PMCID: PMC5430748 DOI: 10.1038/s41598-017-01338-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/28/2017] [Indexed: 02/02/2023] Open
Abstract
Grass carp (Ctenopharyngodon idella) is an important economic species in freshwater aquaculture and its industry has been confined due to variety degeneration and frequent diseases. Marker-assisted selection is a feasible method for selective breeding of new varieties. Transcriptome data have greatly facilitated high-throughput single nucleotide polymorphism (SNP) marker discovery and phenotype association study. In this study, we gained a total of 25,981 and 5,775 high quality SNPs in two transcriptomes from individuals and cell lines, respectively. Comparative transcriptome analysis identified 413 and 832 grass carp reovirus (GCRV)-resistant-association SNPs as well as 1,381 and 1,606 GCRV-susceptible-association SNPs in individuals and cell lines, respectively. Integrated analysis indicated 22 genes with single SNP share common resistant/susceptible traits in two transcriptomes. Furthermore, we infected grass carp with GCRV, genotyping and association analyses were performed, and 9 in 22 SNPs were confirmed by PCR-RFLP. Meanwhile, mRNA expression profiles of 6 genes containing confirmed SNPs were examined by qRT-PCR. The results demonstrated that mRNA expressions were significant differences in resistant/susceptible individuals and cell lines. The present study develops an important strategy for high throughput screening of phenotype association genetic markers and the results will serve in grass carp breeding for GCRV resistance.
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Affiliation(s)
- Zhiwei Liao
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Quanyuan Wan
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueying Shang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Su
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
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42
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Bentley BP, Haas BJ, Tedeschi JN, Berry O. Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress. Mol Ecol 2017; 26:2978-2992. [PMID: 28267875 DOI: 10.1111/mec.14087] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 02/15/2017] [Accepted: 02/21/2017] [Indexed: 12/30/2022]
Abstract
Oviparous reptile embryos are expected to breach their critical thermal maxima if temperatures reach those predicted under current climate change models due to the lack of the maternal buffering processes and parental care. Heat-shock proteins (HSPs) are integral in the molecular response to thermal stress, and their expression is heritable, but the roles of other candidate families such as the heat-shock factors (HSFs) have not been determined in reptiles. Here, we subject embryonic sea turtles (Caretta caretta) to a biologically realistic thermal stress and employ de novo transcriptomic profiling of brain tissue to investigate the underlying molecular response. From a reference transcriptome of 302 293 transcripts, 179 were identified as differentially expressed between treatments. As anticipated, genes enriched in the heat-shock treatment were primarily associated with the Hsp families, or were genes whose products play similar protein editing and chaperone functions (e.g. bag3, MYOC and serpinh1). Unexpectedly, genes encoding the HSFs were not significantly upregulated under thermal stress, indicating their presence in unstressed cells in an inactive state. Genes that were downregulated under thermal stress were less well functionally defined but were associated with stress response, development and cellular organization, suggesting that developmental processes may be compromised at realistically high temperatures. These results confirm that genes from the Hsp families play vital roles in the thermal tolerance of developing reptile embryos and, in addition with a number of other genes, should be targets for evaluating the capacity of oviparous reptiles to respond adaptively to the effects of climate change.
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Affiliation(s)
- Blair P Bentley
- Centre for Evolutionary Biology, School of Animal Biology (M092), University of Western Australia, Perth, 6009, Australia.,Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organization (CSIRO), Floreat, 6014, Australia
| | - Brian J Haas
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jamie N Tedeschi
- Centre for Evolutionary Biology, School of Animal Biology (M092), University of Western Australia, Perth, 6009, Australia
| | - Oliver Berry
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organization (CSIRO), Floreat, 6014, Australia
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43
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Mähler N, Wang J, Terebieniec BK, Ingvarsson PK, Street NR, Hvidsten TR. Gene co-expression network connectivity is an important determinant of selective constraint. PLoS Genet 2017; 13:e1006402. [PMID: 28406900 PMCID: PMC5407845 DOI: 10.1371/journal.pgen.1006402] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 04/27/2017] [Accepted: 03/31/2017] [Indexed: 12/12/2022] Open
Abstract
While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure. Here we utilised RNA-Sequencing to assay gene expression in winter buds undergoing bud flush in a natural population of Populus tremula, an outbreeding forest tree species. We performed expression Quantitative Trait Locus (eQTL) mapping and identified 164,290 significant eQTLs associating 6,241 unique genes (eGenes) with 147,419 unique SNPs (eSNPs). We found approximately four times as many local as distant eQTLs, with local eQTLs having significantly higher effect sizes. eQTLs were primarily located in regulatory regions of genes (UTRs or flanking regions), regardless of whether they were local or distant. We used the gene expression data to infer a co-expression network and investigated the relationship between network topology, the genetic architecture of gene expression and signatures of selection. Within the co-expression network, eGenes were underrepresented in network module cores (hubs) and overrepresented in the periphery of the network, with a negative correlation between eQTL effect size and network connectivity. We additionally found that module core genes have experienced stronger selective constraint on coding and non-coding sequence, with connectivity associated with signatures of selection. Our integrated genetics and genomics results suggest that purifying selection is the primary mechanism underlying the genetic architecture of natural variation in gene expression assayed in flushing leaf buds of P. tremula and that connectivity within the co-expression network is linked to the strength of purifying selection.
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Affiliation(s)
- Niklas Mähler
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Jing Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Centre for Integrative Genetics, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Barbara K. Terebieniec
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Pär K. Ingvarsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nathaniel R. Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Torgeir R. Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
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44
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Ishikawa A, Kusakabe M, Yoshida K, Ravinet M, Makino T, Toyoda A, Fujiyama A, Kitano J. Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes. Evolution 2017; 71:565-581. [PMID: 28075479 DOI: 10.1111/evo.13175] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/21/2016] [Indexed: 12/12/2022]
Abstract
Differential gene expression can play an important role in phenotypic evolution and divergent adaptation. Although differential gene expression can be caused by both local- and distant-regulatory changes, we know little about their relative contribution to transcriptome evolution in natural populations. Here, we conducted expression quantitative trait loci (eQTL) analysis to investigate the genetic architecture underlying transcriptome divergence between marine and stream ecotypes of threespine sticklebacks (Gasterosteus aculeatus). We identified both local and distant eQTLs, some of which constitute hotspots, regions with a disproportionate number of significant eQTLs relative to the genomic background. The majority of local eQTLs including those in the hotspots caused expression changes consistent with the direction of transcriptomic divergence between ecotypes. Genome scan analysis showed that many local eQTLs overlapped with genomic regions of high differentiation. In contrast, nearly half of the distant eQTLs including those in the hotspots caused opposite expression changes, and few overlapped with regions of high differentiation, indicating that distant eQTLs may act as a constraint of transcriptome evolution. Finally, a comparison between two salinity conditions revealed that nearly half of eQTL hotspots were environment specific, suggesting that analysis of genetic architecture in multiple conditions is essential for predicting response to selection.
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Affiliation(s)
- Asano Ishikawa
- Division of Ecological Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Makoto Kusakabe
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.,Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Kohta Yoshida
- Division of Ecological Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Mark Ravinet
- Division of Ecological Genetics, National Institute of Genetics, Shizuoka, Japan.,Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Takashi Makino
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Jun Kitano
- Division of Ecological Genetics, National Institute of Genetics, Shizuoka, Japan
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45
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Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus. G3-GENES GENOMES GENETICS 2017; 7:165-178. [PMID: 27836907 PMCID: PMC5217106 DOI: 10.1534/g3.116.033241] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution. We collected transcriptomic and genomic data from 60 half-sib families using an expression microarray and genotyping-by-sequencing, and located expression quantitative trait loci (eQTL) underlying the variation in gene expression in liver tissue using an interval mapping approach. We identified eQTL for several thousand expression traits. Expression was influenced by polymorphism in both cis- and trans-regulatory regions. Trans-eQTL clustered into hotspots. We did not identify master transcriptional regulators in hotspot locations: rather, the presence of hotspots may be driven by complex interactions between multiple transcription factors. One observed hotspot colocated with a QTL recently found to underlie salinity tolerance in the threespine stickleback. However, most other observed hotspots did not colocate with regions of the genome known to be involved in adaptive divergence between marine and freshwater habitats.
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46
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Gómez-Robles A, Hopkins WD, Schapiro SJ, Sherwood CC. The heritability of chimpanzee and human brain asymmetry. Proc Biol Sci 2016; 283:20161319. [PMID: 28003442 PMCID: PMC5204159 DOI: 10.1098/rspb.2016.1319] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
Human brains are markedly asymmetric in structure and lateralized in function, which suggests a relationship between these two properties. The brains of other closely related primates, such as chimpanzees, show similar patterns of asymmetry, but to a lesser degree, indicating an increase in anatomical and functional asymmetry during hominin evolution. We analysed the heritability of cerebral asymmetry in chimpanzees and humans using classic morphometrics, geometric morphometrics, and quantitative genetic techniques. In our analyses, we separated directional asymmetry and fluctuating asymmetry (FA), which is indicative of environmental influences during development. We show that directional patterns of asymmetry, those that are consistently present in most individuals in a population, do not have significant heritability when measured through simple linear metrics, but they have marginally significant heritability in humans when assessed through three-dimensional configurations of landmarks that reflect variation in the size, position, and orientation of different cortical regions with respect to each other. Furthermore, genetic correlations between left and right hemispheres are substantially lower in humans than in chimpanzees, which points to a relatively stronger environmental influence on left-right differences in humans. We also show that the level of FA has significant heritability in both species in some regions of the cerebral cortex. This suggests that brain responsiveness to environmental influences, which may reflect neural plasticity, has genetic bases in both species. These results have implications for the evolvability of brain asymmetry and plasticity among humans and our close relatives.
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Affiliation(s)
- Aida Gómez-Robles
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - William D Hopkins
- Neuroscience Institute, Georgia State University, Atlanta, GA 30302, USA
- Division of Developmental and Cognitive Neuroscience, Yerkes National Primate Research Center, Atlanta, GA 30322, USA
| | - Steven J Schapiro
- National Center for Chimpanzee Care, Department of Veterinary Sciences, The University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
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47
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Polster R, Petropoulos CJ, Bonhoeffer S, Guillaume F. Epistasis and Pleiotropy Affect the Modularity of the Genotype-Phenotype Map of Cross-Resistance in HIV-1. Mol Biol Evol 2016; 33:3213-3225. [PMID: 27678053 PMCID: PMC5100054 DOI: 10.1093/molbev/msw206] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The genotype–phenotype (GP) map is a central concept in evolutionary biology as it describes the mapping of molecular genetic variation onto phenotypic trait variation. Our understanding of that mapping remains partial, especially when trying to link functional clustering of pleiotropic gene effects with patterns of phenotypic trait co-variation. Only on rare occasions have studies been able to fully explore that link and tend to show poor correspondence between modular structures within the GP map and among phenotypes. By dissecting the structure of the GP map of the replicative capacity of HIV-1 in 15 drug environments, we provide a detailed view of that mapping from mutational pleiotropic variation to phenotypic co-variation, including epistatic effects of a set of amino-acid substitutions in the reverse transcriptase and protease genes. We show that epistasis increases the pleiotropic degree of single mutations and provides modularity to the GP map of drug resistance in HIV-1. Moreover, modules of epistatic pleiotropic effects within the GP map match the phenotypic modules of correlated replicative capacity among drug classes. Epistasis thus increases the evolvability of cross-resistance in HIV by providing more drug- and class-specific pleiotropic profiles to the main effects of the mutations. We discuss the implications for the evolution of cross-resistance in HIV.
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Affiliation(s)
- Robert Polster
- ETH Zürich, Institute of Integrative Biology, Universitätsstr. 16, Zürich, Switzerland
| | | | - Sebastian Bonhoeffer
- ETH Zürich, Institute of Integrative Biology, Universitätsstr. 16, Zürich, Switzerland
| | - Frédéric Guillaume
- ETH Zürich, Institute of Integrative Biology, Universitätsstr. 16, Zürich, Switzerland .,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
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48
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Kelly MW, Pankey MS, DeBiasse MB, Plachetzki DC. Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12725] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Morgan W. Kelly
- Department of Biological Sciences Louisiana State University Baton Rouge LA70803 USA
| | - M. Sabrina Pankey
- Molecular, Cellular, & Biomedical Sciences University of New Hampshire Rudman Hall 46 College Rd. Durham NH03824‐2618 USA
| | - Melissa B. DeBiasse
- Department of Biological Sciences Louisiana State University Baton Rouge LA70803 USA
| | - David C. Plachetzki
- Molecular, Cellular, & Biomedical Sciences University of New Hampshire Rudman Hall 46 College Rd. Durham NH03824‐2618 USA
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49
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Akman M, Carlson JE, Holsinger KE, Latimer AM. Transcriptome sequencing reveals population differentiation in gene expression linked to functional traits and environmental gradients in the South African shrub Protea repens. THE NEW PHYTOLOGIST 2016; 210:295-309. [PMID: 26618926 DOI: 10.1111/nph.13761] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/15/2015] [Indexed: 05/11/2023]
Abstract
Understanding the environmental and genetic mechanisms underlying locally adaptive trait variation across the ranges of species is a major focus of evolutionary biology. Combining transcriptome sequencing with common garden experiments on populations spanning geographical and environmental gradients holds promise for identifying such mechanisms. The South African shrub Protea repens displays diverse phenotypes in the wild along drought and temperature gradients. We grew plants from seeds collected at 19 populations spanning this species' range, and sequenced the transcriptomes of these plants to reveal gene pathways associated with adaptive trait variation. We related expression in co-expressed gene networks to trait phenotypes measured in the common garden and to source population climate. We found that expression in gene networks correlated with source-population environment and with plant traits. In particular, the activity of gene networks enriched for growth related pathways correlated strongly with source site minimum winter temperature and with leaf size, stem diameter and height in the garden. Other gene networks with enrichments for photosynthesis related genes showed associations with precipitation. Our results strongly suggest that this species displays population-level differences in gene expression that have been shaped by source population site climate, and that are reflected in trait variation along environmental gradients.
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Affiliation(s)
- Melis Akman
- Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Jane E Carlson
- Department of Biological Sciences, Nicholls State University, PO Box 2021, Thibodaux, LA, 70310, USA
| | - Kent E Holsinger
- Department of Ecology & Evolutionary Biology, University of Connecticut, U-3043, Storrs, CT, 06269-3043, USA
| | - Andrew M Latimer
- Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
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50
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McCairns RJS, Smith S, Sasaki M, Bernatchez L, Beheregaray LB. The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes. Evol Appl 2016; 9:531-45. [PMID: 27099620 PMCID: PMC4831457 DOI: 10.1111/eva.12363] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/14/2016] [Indexed: 12/14/2022] Open
Abstract
Whilst adaptation and phenotypic plasticity might buffer species against habitat degradation associated with global climate change, few studies making such claims also possess the necessary and sufficient data to support them. Doing so requires demonstration of heritable variation in traits affecting fitness under new environmental conditions. We address this issue using an emerging aquatic system to study adaptation to climate change, the crimson-spotted rainbowfish (Melanotaenia duboulayi), a freshwater species from a region of eastern Australia projected to be affected by marked temperature increases. Captive born M. duboulayi of known pedigree were used to assess the long-term effects of contemporary and 2070-projected summer temperatures on the expression of genes previously identified in a climate change transcriptomics (RNA-Seq) experiment. Nearly all genes responded to increasing temperature. Significant additive genetic variance explained a moderate proportion of transcriptional variation for all genes. Most genes also showed broad-sense genetic variation in transcriptional plasticity. Additionally, molecular pathways of candidate genes co-occur with genes inferred to be under climate-mediated selection in wild M. duboulayi populations. Together, these results indicate the presence of existing variation in important physiological traits, and the potential for adaptive responses to a changing thermal environment.
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Affiliation(s)
- R. J. Scott McCairns
- Molecular Ecology LaboratoryFlinders UniversityAdelaideSAAustralia
- Centre National de la Recherche ScientifiqueUMR 7263 (IMBE) Institut Méditerranéen de la Biodiversité et d'Ecologie Marine et ContinentaleMarseilleFrance
| | - Steve Smith
- Molecular Ecology LaboratoryFlinders UniversityAdelaideSAAustralia
- Department of Integrative Biology and EvolutionUniversity of Veterinary MedicineViennaAustria
| | - Minami Sasaki
- Molecular Ecology LaboratoryFlinders UniversityAdelaideSAAustralia
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQCCanada
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