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Zhang C, Qin Q, Wang Y, Wang Z, Liu Z. Identification of Key Proteins Related to Cashmere Fiber Diameter by Integrated Proteomics and Bioinformatic Analyses in the Alpas and Alxa Goat Breeds. Genes (Basel) 2024; 15:1154. [PMID: 39336745 PMCID: PMC11431775 DOI: 10.3390/genes15091154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/18/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Goats (Capra hircus) have always been a source of fiber for human use and hold an important place in international high-end textiles. Fiber diameter is the most concerning economic indicator for producers. Understanding the formation mechanism of fiber diameter and its related key proteins can help optimize and control the production of cashmere. METHODS Cashmere goats (n = 36) of the Alpas (n = 18) and Alxa (n = 18) breeds, with a similar age (2 years old) and live weight (25-26 kg), were selected from the Yiwei White Cashmere Goat Breeding Farm, Erdos, Inner Mongolia. Using phenotypic indicators, we evaluated the diameter of the cashmere fibers in Alxa and Alpas goats. We also used electron microscopy to examine the cashmere fiber's structure and label-free liquid chromatography-tandem mass spectrometry to determine the protein content of the two cashmere fibers. The proteins affecting fiber diameter were identified and analyzed by Western blot, Co-Immunoprecipitation, and bioinformatics analysis. RESULTS The average diameter of the Alxa breed was smaller (p < 0.05) than that of the Alpas breed (Alxa's cashmere vs. Alpas' cashmere). Proteomics technology enabled the highly confident detection of 171 proteins. A total of 68 differentially expressed proteins were identified in the two types of cashmere; 131 proteins were specifically expressed in Alpas goats, and 40 proteins were specifically expressed in Alxa goats. A key protein group that could cause variations in fiber diameter was found using the protein-protein interaction network. To ascertain the reason for the variation in fiber diameter, a structural study of the major protein groups was carried out. CONCLUSIONS KRT10, KRT14, KRT17, and KRT82 are the main proteins impacting the diameter difference, and they have a substantial effect on the average fiber diameter.
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Affiliation(s)
- Chongyan Zhang
- Animal Science Department, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.Z.)
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China
| | - Qing Qin
- Animal Science Department, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.Z.)
- Key Laboratory of Mutton Sheep & Goat Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China
| | - Yichuan Wang
- Animal Science Department, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.Z.)
- Key Laboratory of Mutton Sheep & Goat Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China
| | - Zhixin Wang
- Animal Science Department, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.Z.)
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China
| | - Zhihong Liu
- Animal Science Department, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.Z.)
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot 010018, China
- Key Laboratory of Mutton Sheep & Goat Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China
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Hamann E, Groen SC, Dunivant TS, Ćalić I, Cochran C, Konshok R, Purugganan MD, Franks SJ. Selection on genome-wide gene expression plasticity of rice in wet and dry field environments. Mol Ecol 2024:e17522. [PMID: 39215462 DOI: 10.1111/mec.17522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/29/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Gene expression can be highly plastic in response to environmental variation. However, we know little about how expression plasticity is shaped by natural selection and evolves in wild and domesticated species. We used genotypic selection analysis to characterize selection on drought-induced plasticity of over 7,500 leaf transcripts of 118 rice accessions (genotypes) from different environmental conditions grown in a field experiment. Gene expression plasticity was neutral for most gradually plastic transcripts, but transcripts with discrete patterns of expression showed stronger selection on expression plasticity. Whether plasticity was adaptive and co-gradient or maladaptive and counter-gradient varied among varietal groups. No transcripts that experienced selection for plasticity across environments showed selection against plasticity within environments, indicating a lack of evidence for costs of adaptive plasticity that may constrain its evolution. Selection on expression plasticity was influenced by degree of plasticity, transcript length and gene body methylation. We observed positive selection on plasticity of co-expression modules containing transcripts involved in photosynthesis, translation and responsiveness to abiotic stress. Taken together, these results indicate that patterns of selection on expression plasticity were context-dependent and likely associated with environmental conditions of varietal groups, but that the evolution of adaptive plasticity would likely not be constrained by opposing patterns of selection on plasticity within compared to across environments. These results offer a genome-wide view of patterns of selection and ecological constraints on gene expression plasticity and provide insights into the interplay between plastic and evolutionary responses to drought at the molecular level.
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Affiliation(s)
- Elena Hamann
- Department of Biological Sciences, Fordham University, Bronx, New York, USA
- Department of Biology, Institute of Plant Ecology and Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Simon C Groen
- Department of Nematology, University of California Riverside, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - Taryn S Dunivant
- Department of Nematology, University of California Riverside, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, USA
| | - Irina Ćalić
- Department of Biological Sciences, Fordham University, Bronx, New York, USA
| | - Colleen Cochran
- Department of Biological Sciences, Fordham University, Bronx, New York, USA
| | - Rachel Konshok
- Department of Biological Sciences, Fordham University, Bronx, New York, USA
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
- Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Steven J Franks
- Department of Biological Sciences, Fordham University, Bronx, New York, USA
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Ahrens CW, Murray K, Mazanec RA, Ferguson S, Jones A, Tissue DT, Byrne M, Borevitz JO, Rymer PD. Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla. BMC Genomics 2024; 25:640. [PMID: 38937661 PMCID: PMC11209971 DOI: 10.1186/s12864-024-10531-8] [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: 09/15/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla. RESULTS We found 273 genomic variants determining traits with moderate heritability (h2SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. CONCLUSIONS Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
- Cesar Australia, Brunswick, VIC, 3058, Australia.
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Richard A Mazanec
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Scott Ferguson
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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Martino C, Di Luca A, Bennato F, Ianni A, Passamonti F, Rampacci E, Henry M, Meleady P, Martino G. Label-Free Quantitative Analysis of Pig Liver Proteome after Hepatitis E Virus Infection. Viruses 2024; 16:408. [PMID: 38543773 PMCID: PMC10976091 DOI: 10.3390/v16030408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 05/23/2024] Open
Abstract
Hepatitis E represents an emerging zoonotic disease caused by the Hepatitis E virus (HEV), for which the main route of transmission is foodborne. In particular, infection in humans has been associated with the consumption of contaminated undercooked meat of pig origin. The aim of this study was to apply comparative proteomics to determine if porcine liver protein profiles could be used to distinguish between pigs seropositive and seronegative for HEV. Preliminarily, an ELISA was used to evaluate the presence of anti-HEV antibodies in the blood serum of 136 animals sent to slaughter. Among the analyzed samples, a seroprevalence of 72.8% was estimated, and it was also possible to identify 10 animals, 5 positive and 5 negative, coming from the same farm. This condition created the basis for the quantitative proteomics comparison between homogeneous animals, in which only the contact with HEV should represent the discriminating factor. The analysis of the proteome in all samples of liver exudate led to the identification of 554 proteins differentially expressed between the two experimental groups, with 293 proteins having greater abundance in positive samples and 261 more represented in negative exudates. The pathway enrichment analysis allowed us to highlight the effect of the interaction between HEV and the host biological system in inducing the potential enrichment of 69 pathways. Among these, carbon metabolism stands out with the involvement of 41 proteins, which were subjected to interactomic analysis. This approach allowed us to focus our attention on three enzymes involved in glycolysis: glucose-6-phosphate isomerase (GPI), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and fructose-bisphosphate aldolase A (ALDOA). It therefore appears that infection with HEV induced a strengthening of the process, which involves the breakdown of glucose to obtain energy and carbon residues useful for the virus's survival. In conclusion, the label-free LC-MS/MS approach showed effectiveness in highlighting the main differences induced on the porcine liver proteome by the interaction with HEV, providing crucial information in identifying a viral signature on the host metabolism.
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Affiliation(s)
- Camillo Martino
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (C.M.); (F.P.); (E.R.)
| | - Alessio Di Luca
- Department of BioScience and Technology for Food, Agriculture, and Environment, University of Teramo, 64100 Teramo, Italy; (A.D.L.); (F.B.); (G.M.)
| | - Francesca Bennato
- Department of BioScience and Technology for Food, Agriculture, and Environment, University of Teramo, 64100 Teramo, Italy; (A.D.L.); (F.B.); (G.M.)
| | - Andrea Ianni
- Department of BioScience and Technology for Food, Agriculture, and Environment, University of Teramo, 64100 Teramo, Italy; (A.D.L.); (F.B.); (G.M.)
| | - Fabrizio Passamonti
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (C.M.); (F.P.); (E.R.)
| | - Elisa Rampacci
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (C.M.); (F.P.); (E.R.)
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, D09 DX63 Dublin, Ireland; (M.H.); (P.M.)
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, D09 DX63 Dublin, Ireland; (M.H.); (P.M.)
| | - Giuseppe Martino
- Department of BioScience and Technology for Food, Agriculture, and Environment, University of Teramo, 64100 Teramo, Italy; (A.D.L.); (F.B.); (G.M.)
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Cutter AD. Sexual conflict, heterochrony and tissue specificity as evolutionary problems of adaptive plasticity in development. Proc Biol Sci 2023; 290:20231854. [PMID: 37817601 PMCID: PMC10565415 DOI: 10.1098/rspb.2023.1854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Abstract
Differential gene expression represents a fundamental cause and manifestation of phenotypic plasticity. Adaptive phenotypic plasticity in gene expression as a trait evolves when alleles that mediate gene regulation serve to increase organismal fitness by improving the alignment of variation in gene expression with variation in circumstances. Among the diverse circumstances that a gene encounters are distinct cell types, developmental stages and sexes, as well as an organism's extrinsic ecological environments. Consequently, adaptive phenotypic plasticity provides a common framework to consider diverse evolutionary problems by considering the shared implications of alleles that produce context-dependent gene expression. From this perspective, adaptive plasticity represents an evolutionary resolution to conflicts of interest that arise from any negatively pleiotropic effects of expression of a gene across ontogeny, among tissues, between the sexes, or across extrinsic environments. This view highlights shared properties within the general relation of fitness, trait expression and context that may nonetheless differ substantively in the grain of selection within and among generations to influence the likelihood of adaptive plasticity as an evolutionary response. Research programmes that historically have focused on these separate issues may use the insights from one another by recognizing their shared dependence on context-dependent gene regulatory evolution.
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Affiliation(s)
- Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
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Zhang X, Wolinska J, Blair D, Hu W, Yin M. Responses to predation pressure involve similar sets of genes in two divergent species of Daphnia. J Anim Ecol 2023; 92:1743-1758. [PMID: 37337454 DOI: 10.1111/1365-2656.13969] [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: 07/12/2022] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Species that are not closely related can express similar inducible traits, but molecular mechanisms underlying the observed responses are often unknown, nor is it known if these mechanisms are shared between such species. Here, we compared transcriptional profiles of two Daphnia species (D. mitsukuri and D. sinensis) from different subgenera, at both juvenile and adult developmental stages. Both species were exposed to the same predation threat (fish kairomones), and both showed similar induced morphological changes (reduced body length). At the early developmental stage, response to predation risk resulted in similar changes in expression levels of 23 orthologues in both species. These orthologues, involved in 107 GO categories, changed in the same direction in both species (over- or underexpressed), in comparison to non-exposed controls. Several of these orthologues were associated with DNA replication, structural constituents of cuticle or innate immune response. In both species, the differentially expressed (DE) genes on average had higher ω (dN /dS ) values than non-DE genes, suggesting that these genes had experienced greater positive selection or lower purifying selection than non-DE genes. Overall, our results suggest that similar suites of genes, responding in similar ways to predation pressure, have been retained in Daphnia for many millions of years.
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Affiliation(s)
- Xiuping Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
- Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
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Hackerott S, Virdis F, Flood PJ, Souto DG, Paez W, Eirin-Lopez JM. Relationships between phenotypic plasticity and epigenetic variation in two Caribbean Acropora corals. Mol Ecol 2023; 32:4814-4828. [PMID: 37454286 DOI: 10.1111/mec.17072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
The plastic ability for a range of phenotypes to be exhibited by the same genotype allows organisms to respond to environmental variation and may modulate fitness in novel environments. Differing capacities for phenotypic plasticity within a population, apparent as genotype by environment interactions (GxE), can therefore have both ecological and evolutionary implications. Epigenetic gene regulation alters gene function in response to environmental cues without changes to the underlying genetic sequence and likely mediates phenotypic variation. DNA methylation is currently the most well described epigenetic mechanism and is related to transcriptional homeostasis in invertebrates. However, evidence quantitatively linking variation in DNA methylation with that of phenotype is lacking in some taxa, including reef-building corals. In this study, spatial and seasonal environmental variation in Bonaire, Caribbean Netherlands was utilized to assess relationships between physiology and DNA methylation profiles within genetic clones across different genotypes of Acropora cervicornis and A. palmata corals. The physiology of both species was highly influenced by environmental variation compared to the effect of genotype. GxE effects on phenotype were only apparent in A. cervicornis. DNA methylation in both species differed between genotypes and seasons and epigenetic variation was significantly related to coral physiological metrics. Furthermore, plastic shifts in physiology across seasons were significantly positively correlated with shifts in DNA methylation profiles in both species. These results highlight the dynamic influence of environmental conditions and genetic constraints on the physiology of two important Caribbean coral species. Additionally, this study provides quantitative support for the role of epigenetic DNA methylation in mediating phenotypic plasticity in invertebrates.
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Affiliation(s)
- Serena Hackerott
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, Florida, USA
- Florida International University, Miami, Florida, USA
| | - Francesca Virdis
- Reef Renewal Foundation Bonaire, Kralendijk, Caribbean Netherlands
| | - Peter J Flood
- Florida International University, Miami, Florida, USA
| | - Daniel Garcia Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Wendy Paez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, Florida, USA
- Florida International University, Miami, Florida, USA
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, Florida, USA
- Florida International University, Miami, Florida, USA
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van Oers K, van den Heuvel K, Sepers B. The Epigenetics of Animal Personality. Neurosci Biobehav Rev 2023; 150:105194. [PMID: 37094740 DOI: 10.1016/j.neubiorev.2023.105194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
Animal personality, consistent individual differences in behaviour, is an important concept for understanding how individuals vary in how they cope with environmental challenges. In order to understand the evolutionary significance of animal personality, it is crucial to understand the underlying regulatory mechanisms. Epigenetic marks such as DNA methylation are hypothesised to play a major role in explaining variation in phenotypic changes in response to environmental alterations. Several characteristics of DNA methylation also align well with the concept of animal personality. In this review paper, we summarise the current literature on the role that molecular epigenetic mechanisms may have in explaining personality variation. We elaborate on the potential for epigenetic mechanisms to explain behavioural variation, behavioural development and temporal consistency in behaviour. We then suggest future routes for this emerging field and point to potential pitfalls that may be encountered. We conclude that a more inclusive approach is needed for studying the epigenetics of animal personality and that epigenetic mechanisms cannot be studied without considering the genetic background.
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Affiliation(s)
- Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands.
| | - Krista van den Heuvel
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Bernice Sepers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
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9
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Wund MA, Stevens DR. An introduction to the Special Issue honouring Susan A. Foster. Anim Behav 2023. [DOI: 10.1016/j.anbehav.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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10
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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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Huang P, Hameed R, Abbas M, Balooch S, Alharthi B, Du Y, Abbas A, Younas A, Du D. Integrated omic techniques and their genomic features for invasive weeds. Funct Integr Genomics 2023; 23:44. [PMID: 36680630 DOI: 10.1007/s10142-023-00971-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/01/2023] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.
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Affiliation(s)
- Ping Huang
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Rashida Hameed
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Manzer Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, Sichuan Province, People's Republic of China
| | - Sidra Balooch
- Institute of Botany, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, PO. Box 11099, Taif, 21944, Saudi Arabia
| | - Yizhou Du
- Faculty of Engineering, School of Computer Science, University of Sydney, Sydney, New South Wales, Australia
| | - Adeel Abbas
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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A Label-Free Quantitative Analysis for the Search of Proteomic Differences between Goat Breeds. Animals (Basel) 2022; 12:ani12233336. [PMID: 36496858 PMCID: PMC9740416 DOI: 10.3390/ani12233336] [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: 09/28/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
The intensification and standardization of livestock farming are causing a decline in the number of animal breeds in many species, such as the goat. The availability of more studies on the potentiality of goat breeds could raise awareness of their importance, conservation and productive possibilities. Label-free quantitative analysis was applied in this study to investigate the proteomic differences between the autochthon Teramana and Saanen goats that could be useful for defining peculiar features of these breeds. A total of 2093 proteins were characterized in the muscle exudate proteome of the Teramana and Saanen breeds. A total of 41 proteins clearly separated the two breeds. Eukaryotic initiation factor proteins and aldehyde-dehydrogenase 7 family-member A1 were up-regulated in the autochthon breed and associated with its resilience, whereas catalase was down-regulated and associated with lower muscular mass. This study is the most detailed report of goat muscle proteome. Several differentially regulated proteins between the two breeds were identified, providing insights into functional pathways that define this organism and its biology.
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13
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Levis NA, McKay DJ, Pfennig DW. Disentangling the developmental origins of a novel phenotype: enhancement versus reversal of environmentally induced gene expression. Proc Biol Sci 2022; 289:20221764. [PMID: 36285495 PMCID: PMC9597403 DOI: 10.1098/rspb.2022.1764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/03/2022] [Indexed: 11/12/2022] Open
Abstract
Increasing evidence suggests that many novel traits might have originated via plasticity-led evolution (PLE). Yet, little is known of the developmental processes that underpin PLE, especially in its early stages. One such process is 'phenotypic accommodation', which occurs when, in response to a change in the environment, an organism experiences adjustments across variable parts of its phenotype that improve its fitness. Here, we asked if environmentally induced changes in gene expression are enhanced or reversed during phenotypic accommodation of a novel, complex phenotype in spadefoot toad tadpoles (Spea multiplicata). More genes than expected were affected by both the environment and phenotypic accommodation in the liver and brain. However, although phenotypic accommodation primarily reversed environmentally induced changes in gene expression in liver tissue, it enhanced these changes in brain tissue. Thus, depending on the tissue, phenotypic accommodation may either minimize functional disruption via reversal of gene expression patterns or promote novelty via enhancement of existing expression patterns. Our study thereby provides insights into the developmental origins of a novel phenotype and the incipient stages of PLE.
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Affiliation(s)
- Nicholas A. Levis
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel J. McKay
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David W. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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14
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Li G, Zhao Y, Liu F, Shi M, Guan Y, Zhang T, Zhao F, Qiao Q, Geng Y. Transcriptional memory of gene expression across generations participates in transgenerational plasticity of field pennycress in response to cadmium stress. FRONTIERS IN PLANT SCIENCE 2022; 13:953794. [PMID: 36247570 PMCID: PMC9561902 DOI: 10.3389/fpls.2022.953794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Transgenerational plasticity (TGP) occurs when maternal environments influence the expression of traits in offspring, and in some cases may increase fitness of offspring and have evolutionary significance. However, little is known about the extent of maternal environment influence on gene expression of offspring, and its relationship with trait variations across generations. In this study, we examined TGP in the traits and gene expression of field pennycress (Thlaspi arvense) in response to cadmium (Cd) stress. In the first generation, along with the increase of soil Cd concentration, the total biomass, individual height, and number of seeds significantly decreased, whereas time to flowering, superoxide dismutase (SOD) activity, and content of reduced glutathione significantly increased. Among these traits, only SOD activity showed a significant effect of TGP; the offspring of Cd-treated individuals maintained high SOD activity in the absence of Cd stress. According to the results of RNA sequencing and bioinformatic analysis, 10,028 transcripts were identified as Cd-responsive genes. Among them, only 401 were identified as transcriptional memory genes (TMGs) that maintained the same expression pattern under normal conditions in the second generation as in Cd-treated parents in the first generation. These genes mainly participated in Cd tolerance-related processes such as response to oxidative stress, cell wall biogenesis, and the abscisic acid signaling pathways. The results of weighted correlation network analysis showed that modules correlated with SOD activity recruited more TMGs than modules correlated with other traits. The SOD-coding gene CSD2 was found in one of the modules correlated with SOD activity. Furthermore, several TMGs co-expressed with CSD2 were hub genes that were highly connected to other nodes and critical to the network's topology; therefore, recruitment of TMGs in offspring was potentially related to TGP. These findings indicated that, across generations, transcriptional memory of gene expression played an important role in TGP. Moreover, these results provided new insights into the trait evolution processes mediated by phenotypic plasticity.
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Affiliation(s)
- Gengyun Li
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yuewan Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Fei Liu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Minnuo Shi
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yabin Guan
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Fangqing Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Yupeng Geng
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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15
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Aubry LM, Williams CT. Vertebrate Phenological Plasticity: from Molecular Mechanisms to Ecological and Evolutionary Implications. Integr Comp Biol 2022; 62:958-971. [PMID: 35867980 DOI: 10.1093/icb/icac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/12/2022] Open
Abstract
Seasonal variation in the availability of essential resources is one of the most important drivers of natural selection on the phasing and duration of annually recurring life-cycle events. Shifts in seasonal timing are among the most commonly reported responses to climate change and the capacity of organisms to adjust their timing, either through phenotypic plasticity or evolution, is a critical component of resilience. Despite growing interest in documenting and forecasting the impacts of climate change on phenology, our ability to predict how individuals, populations, and species might alter their seasonal timing in response to their changing environments is constrained by limited knowledge regarding the cues animals use to adjust timing, the endogenous genetic and molecular mechanisms that transduce cues into neural and endocrine signals, and the inherent capacity of animals to alter their timing and phasing within annual cycles. Further, the fitness consequences of phenological responses are often due to biotic interactions within and across trophic levels, rather than being simple outcomes of responses to changes in the abiotic environment. Here, we review the current state of knowledge regarding the mechanisms that control seasonal timing in vertebrates, as well as the ecological and evolutionary consequences of individual, population, and species-level variation in phenological responsiveness. Understanding the causes and consequences of climate-driven phenological shifts requires combining ecological, evolutionary, and mechanistic approaches at individual, populational, and community scales. Thus, to make progress in forecasting phenological responses and demographic consequences, we need to further develop interdisciplinary networks focused on climate change science.
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Affiliation(s)
- Lise M Aubry
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Cory T Williams
- Department of Biology, Colorado State University, 1878 Campus Delivery Fort Collins, CO 80523, USA
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16
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Oliver A, Cavalheri HB, Lima TG, Jones NT, Podell S, Zarate D, Allen E, Burton RS, Shurin JB. Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation. PLoS One 2022; 17:e0265103. [PMID: 35834446 PMCID: PMC9282536 DOI: 10.1371/journal.pone.0265103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
Daphnia, an ecologically important zooplankton species in lakes, shows both genetic adaptation and phenotypic plasticity in response to temperature and fish predation, but little is known about the molecular basis of these responses and their potential interactions. We performed a factorial experiment exposing laboratory-propagated Daphnia pulicaria clones from two lakes in the Sierra Nevada mountains of California to normal or high temperature (15°C or 25°C) in the presence or absence of fish kairomones, then measured changes in life history and gene expression. Exposure to kairomones increased upper thermal tolerance limits for physiological activity in both clones. Cloned individuals matured at a younger age in response to higher temperature and kairomones, while size at maturity, fecundity and population intrinsic growth were only affected by temperature. At the molecular level, both clones expressed more genes differently in response to temperature than predation, but specific genes involved in metabolic, cellular, and genetic processes responded differently between the two clones. Although gene expression differed more between clones from different lakes than experimental treatments, similar phenotypic responses to predation risk and warming arose from these clone-specific patterns. Our results suggest that phenotypic plasticity responses to temperature and kairomones interact synergistically, with exposure to fish predators increasing the tolerance of Daphnia pulicaria to stressful temperatures, and that similar phenotypic responses to temperature and predator cues can be produced by divergent patterns of gene regulation.
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Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Hamanda B. Cavalheri
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Thiago G. Lima
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Natalie T. Jones
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Daniela Zarate
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Eric Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Ronald S. Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan B. Shurin
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
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17
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He XJ, Barron AB, Yang L, Chen H, He YZ, Zhang LZ, Huang Q, Wang ZL, Wu XB, Yan WY, Zeng ZJ. Extent and complexity of RNA processing in honey bee queen and worker caste development. iScience 2022; 25:104301. [PMID: 35573188 PMCID: PMC9097701 DOI: 10.1016/j.isci.2022.104301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/12/2022] [Accepted: 04/21/2022] [Indexed: 11/03/2022] Open
Abstract
The distinct honeybee (Apis mellifera) worker and queen castes have become a model for the study of genomic mechanisms of phenotypic plasticity. Here we performed a nanopore-based direct RNA sequencing with exceptionally long reads to compare the mRNA transcripts between queen and workers at three points during their larval development. We found thousands of significantly differentially expressed transcript isoforms (DEIs) between queen and worker larvae. These DEIs were formatted by a flexible splicing system. We showed that poly(A) tails participated in this caste differentiation by negatively regulating the expression of DEIs. Hundreds of isoforms uniquely expressed in either queens or workers during their larval development, and isoforms were expressed at different points in queen and worker larval development demonstrating a dynamic relationship between isoform expression and developmental mechanisms. These findings show the full complexity of RNA processing and transcript expression in honey bee phenotypic plasticity. Honeybee caste differentiation has a complexity of RNA processing Isoforms differentially express between queens and workers during larval development Isoforms are formatted by a flexible alternative splicing system Poly(A) tails are negatively correlated with isoform expression
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Affiliation(s)
- Xu Jiang He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China.,Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi 330045, P. R. of China
| | - Andrew B Barron
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Liu Yang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, P. R. of China
| | - Hu Chen
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, P. R. of China
| | - Yu Zhu He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Li Zhen Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Zi Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Xiao Bo Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Wei Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Zhi Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China.,Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi 330045, P. R. of China
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18
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Oomen RA, Hutchings JA. Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. J Anim Ecol 2022; 91:1073-1087. [PMID: 35445402 PMCID: PMC9325537 DOI: 10.1111/1365-2656.13707] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common‐garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity. Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change. Here, we describe the utility of integrating genomics with common‐garden‐gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential. An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco‐evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high‐dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts. We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco‐evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common‐garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible.
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Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway
| | - Jeffrey A Hutchings
- Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway.,Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
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19
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Leitwein M, Wellband K, Cayuela H, Le Luyer J, Mohns K, Withler R, Bernatchez L. Strong parallel differential gene expression induced by hatchery rearing weakly associated with methylation signals in adult Coho Salmon (O. kisutch). Genome Biol Evol 2022; 14:6547269. [PMID: 35276004 PMCID: PMC8995047 DOI: 10.1093/gbe/evac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 11/14/2022] Open
Abstract
Human activities and resource exploitation led to a massive decline of wild salmonid populations, consequently, numerous conservation programs have been developed to supplement wild populations. However, many studies documented reduced fitness of hatchery-born relative to wild fish. Here, by using both RNA sequencing and Whole Genome Bisulfite Sequencing of hatchery and wild-born adult Coho salmon (Oncorhynchus kisutch) originating from two previously studied river systems, we show that early-life hatchery-rearing environment-induced significant and parallel gene expression differentiation is maintained until Coho come back to their natal river for reproduction. A total of 3,643 genes differentially expressed and 859 coexpressed genes were downregulated in parallel in hatchery-born fish from both rivers relative to their wild congeners. Among those genes, 26 displayed a significant relationship between gene expression and the median gene body methylation and 669 single CpGs displayed a significant correlation between methylation level and the associated gene expression. The link between methylation and gene expression was weak suggesting that DNA methylation is not the only player in mediating hatchery-related expression differences. Yet, significant gene expression differentiation was observed despite 18 months spent in a common environment (i.e., the sea). Finally, the differentiation is observed in parallel in two different river systems, highlighting the fact that early-life environment may account for at least some of the reduced fitness of the hatchery salmon in the wild. These results illustrate the relevance and importance of considering both epigenome and transcriptome to evaluate the costs and benefits of large-scale supplementation programs.
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Affiliation(s)
- Maeva Leitwein
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada, G1V 0A6.,Centre pour la Biodiversité Marine, l'exploitation et la Conservation, Université de Montpellier, Centre National de la Recherche Scientifique, Ifremer, Institut de Recherche pour le Développement, Palavas-les-Flots, France
| | - Kyle Wellband
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada, G1V 0A6.,Fisheries and Oceans Canada, Pacific Science Enterprise Centre, West Vancouver, British Columbia, Canada, V7V 1N6
| | - Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada, G1V 0A6.,Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-769622, Villeurbanne, France
| | - Jérémy Le Luyer
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens, Centre Ifremer du Pacifique, BP 49, 98719 Tahiti, Polynésie française
| | - Kayla Mohns
- Department of Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada, V9T 6N7
| | - Ruth Withler
- Department of Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada, V9T 6N7
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada, G1V 0A6
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20
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Goldenberg J, Bisschop K, D'Alba L, Shawkey MD. The link between body size, colouration and thermoregulation and their integration into ecogeographical rules: a critical appraisal in light of climate change. OIKOS 2022. [DOI: 10.1111/oik.09152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jonathan Goldenberg
- Evolution and Optics of Nanostructures group, Dept of Biology, Ghent Univ. Ghent Belgium
| | - Karen Bisschop
- Inst. for Biodiversity and Ecosystem Dynamics, Univ. of Amsterdam Amsterdam the Netherlands
- Laboratory of Aquatic Biology, Dept of Biology, KU Leuven KULAK Kortrijk Belgium
| | - Liliana D'Alba
- Evolution and Optics of Nanostructures group, Dept of Biology, Ghent Univ. Ghent Belgium
| | - Matthew D. Shawkey
- Evolution and Optics of Nanostructures group, Dept of Biology, Ghent Univ. Ghent Belgium
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21
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Yagound B, West AJ, Richardson MF, Selechnik D, Shine R, Rollins LA. Brain transcriptome analysis reveals gene expression differences associated with dispersal behaviour between range-front and range-core populations of invasive cane toads in Australia. Mol Ecol 2022; 31:1700-1715. [PMID: 35028988 PMCID: PMC9303232 DOI: 10.1111/mec.16347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/19/2021] [Accepted: 01/07/2022] [Indexed: 11/27/2022]
Abstract
Understanding the mechanisms allowing invasive species to adapt to novel environments is a challenge in invasion biology. Many invaders demonstrate rapid evolution of behavioural traits involved in range expansion such as locomotor activity, exploration and risk‐taking. However, the molecular mechanisms that underpin these changes are poorly understood. In 86 years, invasive cane toads (Rhinella marina) in Australia have drastically expanded their geographic range westward from coastal Queensland to Western Australia. During their range expansion, toads have undergone extensive phenotypic changes, particularly in behaviours that enhance the toads’ dispersal ability. Common‐garden experiments have shown that some changes in behavioural traits related to dispersal are heritable. At the molecular level, it is currently unknown whether these changes in dispersal‐related behaviour are underlain by small or large differences in gene expression, nor is known the biological function of genes showing differential expression. Here, we used RNA‐seq to gain a better understanding of the molecular mechanisms underlying dispersal‐related behavioural changes. We compared the brain transcriptomes of toads from the Hawai'ian source population, as well as three distinct populations from across the Australian invasive range. We found markedly different gene expression profiles between the source population and Australian toads. By contrast, toads from across the Australian invasive range had very similar transcriptomic profiles. Yet, key genes with functions putatively related to dispersal behaviour showed differential expression between populations located at each end of the invasive range. These genes could play an important role in the behavioural changes characteristic of range expansion in Australian cane toads.
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Affiliation(s)
- Boris Yagound
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Andrea J West
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Mark F Richardson
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Daniel Selechnik
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Lee A Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
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22
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Kordyum E, Dubyna D. The role of epigenetic regulation in adaptive phenotypic plasticity of plants. UKRAINIAN BOTANICAL JOURNAL 2021. [DOI: 10.15407/ukrbotj78.05.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In recent decades, knowledge about the role of epigenetic regulation of gene expression in plant responses to external stimuli and in adaptation of plants to adverse environmental fluctuations have extended significantly. DNA methylation is considered as the main molecular mechanism that provides genomic information and contributes to the understanding of the molecular basis of phenotypic variations based on epigenetic modifications. Unfortunately, the vast majority of research in this area has been performed on the model species Arabidopsis thaliana. The development of the methylation-sensitive amplified polymorphism (MSAP) method has made it possible to implement the large-scale detection of DNA methylation alterations in wild non-model and agricultural plants with large and highly repetitive genomes in natural and manipulated habitats. The article presents current information on DNA methylation in species of natural communities and crops and its importance in plant development and adaptive phenotypic plasticity, along with brief reviews of current ideas about adaptive phenotypic plasticity and epigenetic regulation of gene expression. The great potential of further studies of the epigenetic role in phenotypic plasticity of a wide range of non-model species in natural populations and agrocenoses for understanding the molecular mechanisms of plant existence in the changing environment in onto- and phylogeny, directly related to the key tasks of forecasting the effects of global warming and crop selection, is emphasized. Specific taxa of the Ukrainian flora, which, in authors’ opinion, are promising and interesting for this type of research, are recommended.
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23
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Bailey NW, Desjonquères C, Drago A, Rayner JG, Sturiale SL, Zhang X. A neglected conceptual problem regarding phenotypic plasticity's role in adaptive evolution: The importance of genetic covariance and social drive. Evol Lett 2021; 5:444-457. [PMID: 34621532 PMCID: PMC8484725 DOI: 10.1002/evl3.251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/12/2021] [Accepted: 07/19/2021] [Indexed: 01/16/2023] Open
Abstract
There is tantalizing evidence that phenotypic plasticity can buffer novel, adaptive genetic variants long enough to permit their evolutionary spread, and this process is often invoked in explanations for rapid adaptive evolution. However, the strength and generality of evidence for it is controversial. We identify a conceptual problem affecting this debate: recombination, segregation, and independent assortment are expected to quickly sever associations between genes controlling novel adaptations and genes contributing to trait plasticity that facilitates the novel adaptations by reducing their indirect fitness costs. To make clearer predictions about this role of plasticity in facilitating genetic adaptation, we describe a testable genetic mechanism that resolves the problem: genetic covariance between new adaptive variants and trait plasticity that facilitates their persistence within populations. We identify genetic architectures that might lead to such a covariance, including genetic coupling via physical linkage and pleiotropy, and illustrate the consequences for adaptation rates using numerical simulations. Such genetic covariances may also arise from the social environment, and we suggest the indirect genetic effects that result could further accentuate the process of adaptation. We call the latter mechanism of adaptation social drive, and identify methods to test it. We suggest that genetic coupling of plasticity and adaptations could promote unusually rapid ‘runaway’ evolution of novel adaptations. The resultant dynamics could facilitate evolutionary rescue, adaptive radiations, the origin of novelties, and other commonly studied processes.
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Affiliation(s)
- Nathan W Bailey
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom
| | - Camille Desjonquères
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom.,Department of Biological Sciences University of Wisconsin-Milwaukee Milwaukee Wisconsin 53201
| | - Ana Drago
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom
| | - Jack G Rayner
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom
| | - Samantha L Sturiale
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom.,Current Address: Department of Biology Georgetown University Washington DC 20057
| | - Xiao Zhang
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom
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24
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Leitwein M, Laporte M, Le Luyer J, Mohns K, Normandeau E, Withler R, Bernatchez L. Epigenomic modifications induced by hatchery rearing persist in germ line cells of adult salmon after their oceanic migration. Evol Appl 2021; 14:2402-2413. [PMID: 34745334 PMCID: PMC8549618 DOI: 10.1111/eva.13235] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/18/2021] [Accepted: 03/25/2021] [Indexed: 12/28/2022] Open
Abstract
Human activities induce direct or indirect selection pressure on natural population and may ultimately affect population's integrity. While numerous conservation programs aimed to minimize human-induced genomic variation, human-induced environmental variation may generate epigenomic variation potentially affecting fitness through phenotypic modifications. Major questions remain pertaining to how much epigenomic variation arises from environmental heterogeneity, whether this variation can persist throughout life, and whether it can be transmitted across generations. We performed whole genome bisulfite sequencing (WGBS) on the sperm of genetically indistinguishable hatchery and wild-born migrating adults of Coho salmon (Oncorhynchus kisutch) from two geographically distant rivers at different epigenome scales. Our results showed that coupling WGBS with fine-scale analyses (local and chromosomal) allows the detection of parallel early-life hatchery-induced epimarks that differentiate wild from hatchery-reared salmon. Four chromosomes and 183 differentially methylated regions (DMRs) displayed a significant signal of methylation differentiation between hatchery and wild-born Coho salmon. Moreover, those early-life epimarks persisted in germ line cells despite about 1.5 year spent in the ocean following release from hatchery, opening the possibility for transgenerational inheritance. Our results strengthen the hypothesis that epigenomic modifications environmentally induced during early-life development persist in germ cells of adults until reproduction, which could potentially impact their fitness.
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Affiliation(s)
- Maeva Leitwein
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Jeremy Le Luyer
- IfremerIRDInstitut Louis‐MalardéUniv Polynésie Française, EIOTahitiFrance
| | - Kayla Mohns
- Department of Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Ruth Withler
- Department of Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
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Luangharn T, Karunarathna SC, Dutta AK, Paloi S, Promputtha I, Hyde KD, Xu J, Mortimer PE. Ganoderma (Ganodermataceae, Basidiomycota) Species from the Greater Mekong Subregion. J Fungi (Basel) 2021; 7:819. [PMID: 34682240 PMCID: PMC8541142 DOI: 10.3390/jof7100819] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 01/28/2023] Open
Abstract
The cosmopolitan fungal genus Ganoderma is an important pathogen on arboreal plant hosts, particularly in tropical and temperate regions. It has long been used as a traditional medicine because of its medicinal properties and chemical constituents. In this study, Ganoderma collections were made in the Greater Mekong Subregion (GMS), encompassing tropical parts of Laos, Myanmar, Thailand, Vietnam, and temperate areas in Yunnan Province, China. The specimens used in this study are described based on micro-macro-characteristics and phylogenetic analysis of combined ITS, LSU, TEF1α, and RPB2 sequence data. In this comprehensive study, we report 22 Ganoderma species from the GMS, namely, G. adspersum, G. applanatum, G. australe, G. calidophilum, G. ellipsoideum, G. flexipes, G. gibbosum, G. heohnelianum, G. hochiminhense, G. leucocontextum, G. lucidum, G. multiplicatum, G. multipileum, G. myanmarense, G. orbiforme, G. philippii, G. resinaceum, G. sichuanense, G. sinense, G. subresinosum, G. williamsianum, and G. tsugae. Some of these species were reported in more than one country within the GMS. Of these 22 species, 12 were collected from Yunnan Province, China; three were collected from Laos; three species, two new records, and one new species were collected from Myanmar; 15 species and four new records were collected from Thailand, and one new species was collected from Vietnam. Comprehensive descriptions, color photographs of macro- and micro-characteristics, the distribution of Ganoderma within the GMS, as well as a phylogenetic tree showing the placement of all reported Ganoderma from the GMS are provided.
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Affiliation(s)
- Thatsanee Luangharn
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China; (T.L.); (S.C.K.); (K.D.H.); (J.X.)
- CIFOR-ICRAF, World Agroforestry Centre (ICRAF), Kunming 650201, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Samantha C. Karunarathna
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China; (T.L.); (S.C.K.); (K.D.H.); (J.X.)
- CIFOR-ICRAF, World Agroforestry Centre (ICRAF), Kunming 650201, China
| | - Arun Kumar Dutta
- Department of Botany, West Bengal State University, Barasat 700126, India;
| | - Soumitra Paloi
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonuyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand;
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kevin D. Hyde
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China; (T.L.); (S.C.K.); (K.D.H.); (J.X.)
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou 510225, China
| | - Jianchu Xu
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China; (T.L.); (S.C.K.); (K.D.H.); (J.X.)
- CIFOR-ICRAF, World Agroforestry Centre (ICRAF), Kunming 650201, China
| | - Peter E. Mortimer
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China; (T.L.); (S.C.K.); (K.D.H.); (J.X.)
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Renn SC, Hurd PL. Epigenetic Regulation and Environmental Sex Determination in Cichlid Fishes. Sex Dev 2021; 15:93-107. [PMID: 34433170 PMCID: PMC8440468 DOI: 10.1159/000517197] [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] [Received: 01/01/2021] [Accepted: 05/12/2021] [Indexed: 12/14/2022] Open
Abstract
Studying environmental sex determination (ESD) in cichlids provides a phylogenetic and comparative approach to understand the evolution of the underlying mechanisms, their impact on the evolution of the overlying systems, and the neuroethology of life history strategies. Natural selection normally favors parents who invest equally in the development of male and female offspring, but evolution may favor deviations from this 50:50 ratio when environmental conditions produce an advantage for doing so. Many species of cichlids demonstrate ESD in response to water chemistry (temperature, pH, and oxygen concentration). The relative strengths of and the exact interactions between these factors vary between congeners, demonstrating genetic variation in sensitivity. The presence of sizable proportions of the less common sex towards the environmental extremes in most species strongly suggests the presence of some genetic sex-determining loci acting in parallel with the ESD factors. Sex determination and differentiation in these species does not seem to result in the organization of a final and irreversible sexual fate, so much as a life-long ongoing battle between competing male- and female-determining genetic and hormonal networks governed by epigenetic factors. We discuss what is and is not known about the epigenetic mechanism behind the differentiation of both gonads and sex differences in the brain. Beyond the well-studied tilapia species, the 2 best-studied dwarf cichlid systems showing ESD are the South American genus Apistogramma and the West African genus Pelvicachromis. Both species demonstrate male morphs with alternative reproductive tactics. We discuss the further neuroethology opportunities such systems provide to the study of epigenetics of alternative life history strategies and other behavioral variation.
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Affiliation(s)
| | - Peter L Hurd
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, CA
- Department of Psychology, University of Alberta, Edmonton, AB, CA
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Casasa S, Biddle JF, Koutsovoulos GD, Ragsdale EJ. Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks. Mol Biol Evol 2021; 38:331-343. [PMID: 32931588 PMCID: PMC7826178 DOI: 10.1093/molbev/msaa235] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Developmental polyphenism, the ability to switch between phenotypes in response to environmental variation, involves the alternating activation of environmentally sensitive genes. Consequently, to understand how a polyphenic response evolves requires a comparative analysis of the components that make up environmentally sensitive networks. Here, we inferred coexpression networks for a morphological polyphenism, the feeding-structure dimorphism of the nematode Pristionchus pacificus. In this species, individuals produce alternative forms of a novel trait—moveable teeth, which in one morph enable predatory feeding—in response to environmental cues. To identify the origins of polyphenism network components, we independently inferred coexpression modules for more conserved transcriptional responses, including in an ancestrally nonpolyphenic nematode species. Further, through genome-wide analyses of these components across the nematode family (Diplogastridae) in which the polyphenism arose, we reconstructed how network components have changed. To achieve this, we assembled and resolved the phylogenetic context for five genomes of species representing the breadth of Diplogastridae and a hypothesized outgroup. We found that gene networks instructing alternative forms arose from ancestral plastic responses to environment, specifically starvation-induced metabolism and the formation of a conserved diapause (dauer) stage. Moreover, loci from rapidly evolving gene families were integrated into these networks with higher connectivity than throughout the rest of the P. pacificus transcriptome. In summary, we show that the modular regulatory outputs of a polyphenic response evolved through the integration of conserved plastic responses into networks with genes of high evolutionary turnover.
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Affiliation(s)
- Sofia Casasa
- Department of Biology, Indiana University, Bloomington, Bloomington, IN
| | - Joseph F Biddle
- Department of Biology, Indiana University, Bloomington, Bloomington, IN
| | | | - Erik J Ragsdale
- Department of Biology, Indiana University, Bloomington, Bloomington, IN
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Thyroid hormones regulate the formation and environmental plasticity of white bars in clownfishes. Proc Natl Acad Sci U S A 2021; 118:2101634118. [PMID: 34031155 DOI: 10.1073/pnas.2101634118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Determining how plasticity of developmental traits responds to environmental conditions is a challenge that must combine evolutionary sciences, ecology, and developmental biology. During metamorphosis, fish alter their morphology and color pattern according to environmental cues. We observed that juvenile clownfish (Amphiprion percula) modulate the developmental timing of their adult white bar formation during metamorphosis depending on the sea anemone species in which they are recruited. We observed an earlier formation of white bars when clownfish developed with Stichodactyla gigantea (Sg) than with Heteractis magnifica (Hm). As these bars, composed of iridophores, form during metamorphosis, we hypothesized that timing of their development may be thyroid hormone (TH) dependent. We treated clownfish larvae with TH and found that white bars developed earlier than in control fish. We further observed higher TH levels, associated with rapid white bar formation, in juveniles recruited in Sg than in Hm, explaining the faster white bar formation. Transcriptomic analysis of Sg recruits revealed higher expression of duox, a dual oxidase implicated in TH production as compared to Hm recruits. Finally, we showed that duox is an essential regulator of iridophore pattern timing in zebrafish. Taken together, our results suggest that TH controls the timing of adult color pattern formation and that shifts in duox expression and TH levels are associated with ecological differences resulting in divergent ontogenetic trajectories in color pattern development.
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Liedtke HC, Harney E, Gomez-Mestre I. Cross-species transcriptomics uncovers genes underlying genetic accommodation of developmental plasticity in spadefoot toads. Mol Ecol 2021; 30:2220-2234. [PMID: 33730392 DOI: 10.1111/mec.15883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/29/2021] [Accepted: 02/26/2021] [Indexed: 10/21/2022]
Abstract
That hardcoded genomes can manifest as plastic phenotypes responding to environmental perturbations is a fascinating feature of living organisms. How such developmental plasticity is regulated at the molecular level is beginning to be uncovered aided by the development of -omic techniques. Here, we compare the transcriptome-wide responses of two species of spadefoot toads with differing capacity for developmental acceleration of their larvae in the face of a shared environmental risk: pond drying. By comparing gene expression profiles over time and performing cross-species network analyses, we identified orthologues and functional gene pathways whose environmental sensitivity in expression have diverged between species. Genes related to lipid, cholesterol and steroid biosynthesis and metabolism make up most of a module of genes environmentally responsive in one species, but canalized in the other. The evolutionary changes in the regulation of the genes identified through these analyses may have been key in the genetic accommodation of developmental plasticity in this system.
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Affiliation(s)
- Hans Christoph Liedtke
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana, CSIC, Seville, Spain
| | - Ewan Harney
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Ivan Gomez-Mestre
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana, CSIC, Seville, Spain
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Akiyama R, Sun J, Hatakeyama M, Lischer HEL, Briskine RV, Hay A, Gan X, Tsiantis M, Kudoh H, Kanaoka MM, Sese J, Shimizu KK, Shimizu‐Inatsugi R. Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species. THE NEW PHYTOLOGIST 2021; 229:3587-3601. [PMID: 33222195 PMCID: PMC7986779 DOI: 10.1111/nph.17101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 11/09/2020] [Indexed: 05/09/2023]
Abstract
Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors. We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing. We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally. These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.
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Affiliation(s)
- Reiko Akiyama
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
| | - Jianqiang Sun
- Research Center for Agricultural Information TechnologyNational Agriculture and Food Research Organization3‐1‐1 KannondaiTsukubaIbaraki305‐8517Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Functional Genomics Center ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Swiss Institute of BioinformaticsQuartier Sorge – Batiment GenopodeLausanneCH‐1015Switzerland
| | - Heidi E. L. Lischer
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Swiss Institute of BioinformaticsQuartier Sorge – Batiment GenopodeLausanneCH‐1015Switzerland
- Interfaculty Bioinformatics UnitUniversity of BernBaltzerstrasse 6BernCH‐3012Switzerland
| | - Roman V. Briskine
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Functional Genomics Center ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
| | - Angela Hay
- Department of Comparative Development and GeneticsMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10Köln50829Germany
| | - Xiangchao Gan
- Department of Comparative Development and GeneticsMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10Köln50829Germany
| | - Miltos Tsiantis
- Department of Comparative Development and GeneticsMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10Köln50829Germany
| | - Hiroshi Kudoh
- Center for Ecological ResearchKyoto UniversityHirano 2‐509‐3Otsu520‐2113Japan
| | - Masahiro M. Kanaoka
- Division of Biological Science, Graduate School of ScienceNagoya UniversityFuro‐cho, Chikusa‐kuNagoya464‐8602Japan
| | - Jun Sese
- Humanome Lab, Inc.L‐HUB 3F1‐4, Shumomiyabi‐choShinjukuTokyo162‐0822Japan
- Artificial Intelligence Research CenterAIST2‐3‐26 AomiKoto‐kuTokyo135‐0064Japan
- AIST‐Tokyo Tech RWBC‐OIL2‐12‐1 OkayamaMeguro‐kuTokyo152‐8550Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Kihara Institute for Biological Research (KIBR)Yokohama City University641‐12 MaiokaTotsuka‐wardYokohama244‐0813Japan
| | - Rie Shimizu‐Inatsugi
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
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Genotype by environment interaction for fat and protein yields via reaction norms in Holstein cattle of southern Brazil. J DAIRY RES 2021; 88:16-22. [PMID: 33593451 DOI: 10.1017/s0022029921000029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Our objective was to evaluate the genetic merit of Holstein cattle population in southern Brazil in response to variations in the regional temperature by analyzing the genotype by environment interaction using reaction norms. Fat yield (FY) and protein yield (PY) data of 67 360 primiparous cows were obtained from the database of the Paraná Holstein Breeders Association, Brazil (APCBRH). The regional average annual temperature was used as the environmental variable. A random regression model was adopted applying mixed models with Restricted Maximum Likelihood (REML) algorithm using WOMBAT software. The genetic merit of the 15 most representative bulls, depending on the temperature gradient, was evaluated. Heritability ranged from 0.21 to 0.27 for FY and from 0.14 to 0.20 for PY. The genetic correlation observed among the environmental gradients proved to be higher than 0.80 for both traits. Slight reranking of bulls for both traits was detected, demonstrating that non-relevant genotype by environment interaction for FY and PY were observed. Consequently, no inclusion of the temperature effect in the model of genetic evaluation in southern Brazilian Holstein breed is required.
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Plasticity of Leaf Traits of Juglans regia L. f. luodianense Liu et Xu Seedlings Under Different Light Conditions in Karst Habitats. FORESTS 2021. [DOI: 10.3390/f12010081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This study examined the effects of light intensity on the plasticity of the leaves of Juglans regia f. luodianense seedlings in karst habitat and how they respond to changes in light intensity. The light intensity of 1-year-old seedlings of J. regia f. luodianense in different niches in a karst area was set as 100% (bare land), 75% (forest margin), 50% (forest gap), and 25% (under forest) of natural light. The material harvested after four months was compared to analyze the differences in various morphological characteristics, biomass allocation, and physiological characteristics of the leaves of seedlings of J. regia f. luodianense, and a comprehensive evaluation of the plasticity indexes was conducted. The results showed that under moderate (50%) full light intensity, the leaf area, specific leaf area, leaf biomass, and chlorophyll content increased, and improved photosynthesis and promoted the accumulation of free proline content and peroxidase (POD) activity. The accumulation of malondialdehyde was also the lowest in this treatment, indicating that the plants had the strongest adaptability under this light intensity. Moreover, under high (75%) full light intensity, the above functional characteristics of plants showed good performance. Under low (25%) full light intensity, plants also had higher specific leaf area, leaf biomass, and photosynthetic parameters. However, under full light, the cell membrane permeability decreased, the chlorophyll accumulation was the lowest, and the photosynthetic index was seriously inhibited. Our results showed that the plasticity of morphological characters was greater than that of biomass allocation and physiological characters; POD activity and stomatal conductance were the highest, followed by leaf area and chlorophyll b, whereas the plasticity of palisade tissue/sponge tissue thickness and lower-epidermis thickness were the lowest. In summary, there are evident differences in the sensitivity and regulation mechanisms of morphological characteristics, biomass allocation, and physiological indices of the seedling leaves of J. regia f. luodianense in response to light intensity. During the stage of seedling establishment, only the plants in the bare ground under full light can be induced to show obvious inhibition of phenotypic traits. In contrast, the plants in the forest margins and gaps and under the forest habitats under light intensity can regulate their own characteristics to maintain their growth and development. The wide light range and strong plasticity of the species might be two of the important reasons for its existence in a highly heterogeneous karst habitat.
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Komoroske LM, Jeffries KM, Whitehead A, Roach JL, Britton M, Connon RE, Verhille C, Brander SM, Fangue NA. Transcriptional flexibility during thermal challenge corresponds with expanded thermal tolerance in an invasive compared to native fish. Evol Appl 2020. [DOI: 10.1111/eva.13172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Lisa M. Komoroske
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
| | - Ken M. Jeffries
- Department of Biological Sciences University of Manitoba Winnipeg MB Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Jennifer L. Roach
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Monica Britton
- Bioinformatics Core Facility, Genome Center University of California, Davis Davis CA USA
| | - Richard E. Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine University of California, Davis Davis CA USA
| | | | - Susanne M. Brander
- Department of Fisheries and Wildlife, Coastal Oregon Marine Experiment Station Oregon State University Corvallis OR USA
| | - Nann A. Fangue
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
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34
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Rajkov J, El Taher A, Böhne A, Salzburger W, Egger B. Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish. Mol Ecol 2020; 30:274-296. [PMID: 33107988 DOI: 10.1111/mec.15709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/08/2020] [Accepted: 10/19/2020] [Indexed: 11/29/2022]
Abstract
Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune responses can be of relevance in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes have often relied on only one pair of populations, targeted the expression of only a subset of genes or used wild-caught individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological abilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish Astatotilapia burtoni. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond set-up. In all investigated population pairs, lake fish were more heavily parasitized than river fish, in terms of both parasite taxon composition and infection abundance. The innate immune response in the wild was higher in lake than in river populations and was elevated in a river population exposed to lake parasites in the pond set-up. Environmental differences between lake and river habitat and their distinct parasite communities have shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond set-up were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimatized to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.
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Affiliation(s)
- Jelena Rajkov
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Athimed El Taher
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Astrid Böhne
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Bernd Egger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
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Grecias L, Hebert FO, Alves VA, Barber I, Aubin-Horth N. Host behaviour alteration by its parasite: from brain gene expression to functional test. Proc Biol Sci 2020; 287:20202252. [PMID: 33171082 PMCID: PMC7735270 DOI: 10.1098/rspb.2020.2252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Many parasites with complex life cycles modify their intermediate hosts' behaviour, presumably to increase transmission to their final host. The threespine stickleback (Gasterosteus aculeatus) is an intermediate host in the cestode Schistocephalus solidus life cycle, which ends in an avian host, and shows increased risky behaviours when infected. We studied brain gene expression profiles of sticklebacks infected with S. solidus to determine the proximal causes of these behavioural alterations. We show that infected fish have altered expression levels in genes involved in the inositol pathway. We thus tested the functional implication of this pathway and successfully rescued normal behaviours in infected sticklebacks using lithium exposure. We also show that exposed but uninfected fish have a distinct gene expression profile from both infected fish and control individuals, allowing us to separate gene activity related to parasite exposure from consequences of a successful infection. Finally, we find that selective serotonin reuptake inhibitor-treated sticklebacks and infected fish do not have similarly altered gene expression, despite their comparable behaviours, suggesting that the serotonin pathway is probably not the main driver of phenotypic changes in infected sticklebacks. Taken together, our results allow us to predict that if S. solidus directly manipulates its host, it could target the inositol pathway.
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Affiliation(s)
- Lucie Grecias
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Francois Olivier Hebert
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Verônica Angelica Alves
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Iain Barber
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, UK
| | - Nadia Aubin-Horth
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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Jiang L, Griffin CH, Wu R. SEGN: Inferring real-time gene networks mediating phenotypic plasticity. Comput Struct Biotechnol J 2020; 18:2510-2521. [PMID: 33005313 PMCID: PMC7516210 DOI: 10.1016/j.csbj.2020.08.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 12/13/2022] Open
Abstract
The capacity of an organism to alter its phenotype in response to environmental perturbations changes over developmental time and is a process determined by multiple genes that are co-expressed in intricate but organized networks. Characterizing the spatiotemporal change of such gene networks can offer insight into the genomic signatures underlying organismic adaptation, but it represents a major methodological challenge. Here, we integrate the holistic view of systems biology and the interactive notion of evolutionary game theory to reconstruct so-called systems evolutionary game networks (SEGN) that can autonomously detect, track, and visualize environment-induced gene networks along the time axis. The SEGN overcomes the limitations of traditional approaches by inferring context-specific networks, encapsulating bidirectional, signed, and weighted gene-gene interactions into fully informative networks, and monitoring the process of how networks topologically alter across environmental and developmental cues. Based on the design principle of SEGN, we perform a transcriptional plasticity study by culturing Euphrates poplar, a tree that can grow in the saline desert, in saline-free and saline-stress conditions. SEGN characterize previously unknown gene co-regulation that modulates the time trajectories of the trees' response to salt stress. As a marriage of multiple disciplines, SEGN shows its potential to interpret gene interdependence, predict how transcriptional co-regulation responds to various regimes, and provides a hint for exploring the mass, energetic, or signal basis that drives various types of gene interactions.
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Affiliation(s)
- Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Christopher H. Griffin
- Applied Research Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA 17033, USA
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Dorant Y, Cayuela H, Wellband K, Laporte M, Rougemont Q, Mérot C, Normandeau E, Rochette R, Bernatchez L. Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species. Mol Ecol 2020; 29:4765-4782. [DOI: 10.1111/mec.15565] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Kyle Wellband
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Rémy Rochette
- Department of Biology University of New Brunswick Saint John NB Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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38
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Mulim HA, Pinto LFB, Valloto AA, Pedrosa VB. Genotype by environment interaction for somatic cell score in Holstein cattle of southern Brazil via reaction norms. Anim Biosci 2020; 34:499-505. [PMID: 32777892 PMCID: PMC7961275 DOI: 10.5713/ajas.20.0031] [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: 01/15/2020] [Accepted: 04/20/2020] [Indexed: 11/27/2022] Open
Abstract
Objective The objective of this study was to evaluate the genetic behavior of a population of Holstein cattle in response to the variation of environmental temperature by analyzing the effects of genotype by environment interaction (GEI) through reaction norms for the somatic cell score (SCS). Methods Data was collected for 67,206 primiparous cows from the database of the Paraná Holstein Breeders Association in Brazil, with the aim of evaluating the temperature effect, considered as an environmental variable, distinguished under six gradients, with the variation range found being 17°C to 19.5°C, over the region. A reaction norm model was adopted utilizing the fourth order under the Legendre polynomials, using the mixed models of analysis by the restricted maximum likelihood method by the WOMBAT software. Additionally, the genetic behavior of the 15 most representative bulls was assessed, in response to the changes in the temperature gradient. Results A mean score of 2.66 and a heritability variation from 0.17 to 0.23 was found in the regional temperature increase. The correlation between the environmental gradients proved to be higher than 0.80. Distinctive genetic behaviors were observed according to the increase in regional temperature, with an observed increase of up to 0.258 in the breeding values of some animals, as well as a reduction in the breeding of up to 0.793, with occasional reclassifications being observed as the temperature increased. Conclusion Non-relevant GEI for SCS were observed in Holstein cattle herds of southern Brazil. Thus, the inclusion of the temperature effect in the model of genetic evaluation of SCS for the southern Brazilian Holstein breed is not required.
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Affiliation(s)
- Henrique Alberto Mulim
- Department of Animal Science, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | | | | | - Victor Breno Pedrosa
- Department of Animal Science, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
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Gene Expression and Photophysiological Changes in Pocillopora acuta Coral Holobiont Following Heat Stress and Recovery. Microorganisms 2020; 8:microorganisms8081227. [PMID: 32806647 PMCID: PMC7463449 DOI: 10.3390/microorganisms8081227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 12/25/2022] Open
Abstract
The ability of corals to withstand changes in their surroundings is a critical survival mechanism for coping with environmental stress. While many studies have examined responses of the coral holobiont to stressful conditions, its capacity to reverse responses and recover when the stressor is removed is not well-understood. In this study, we investigated among-colony responses of Pocillopora acuta from two sites with differing distance to the mainland (Kusu (closer to the mainland) and Raffles Lighthouse (further from the mainland)) to heat stress through differential expression analysis of target genes and quantification of photophysiological metrics. We then examined how these attributes were regulated after the stressor was removed to assess the recovery potential of P. acuta. The fragments that were subjected to heat stress (2 °C above ambient levels) generally exhibited significant reduction in their endosymbiont densities, but the extent of recovery following stress removal varied depending on natal site and colony. There were minimal changes in chl a concentration and maximum quantum yield (Fv/Fm, the proportion of variable fluorescence (Fv) to maximum fluorescence (Fm)) in heat-stressed corals, suggesting that the algal endosymbionts’ Photosystem II was not severely compromised. Significant changes in gene expression levels of selected genes of interest (GOI) were observed following heat exposure and stress removal among sites and colonies, including Actin, calcium/calmodulin-dependent protein kinase type IV (Camk4), kinesin-like protein (KIF9), and small heat shock protein 16.1 (Hsp16.1). The most responsive GOIs were Actin, a major component of the cytoskeleton, and the adaptive immune-related Camk4 which both showed significant reduction following heat exposure and subsequent upregulation during the recovery phase. Our findings clearly demonstrate specific responses of P. acuta in both photophysiological attributes and gene expression levels, suggesting differential capacity of P. acuta corals to tolerate heat stress depending on the colony, so that certain colonies may be more resilient than others.
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Stanford BC, Clake DJ, Morris MR, Rogers SM. The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors. Evol Appl 2020; 13:1166-1182. [PMID: 32684953 PMCID: PMC7359838 DOI: 10.1111/eva.12935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Rapid environmental changes impact the global distribution and abundance of species, highlighting the urgency to understand and predict how populations will respond. The analysis of differentially expressed genes has elucidated areas of the genome involved in adaptive divergence to past and present environmental change. Such studies however have been hampered by large numbers of differentially expressed genes and limited knowledge of how these genes work in conjunction with each other. Recent methods (broadly termed "pathway analyses") have emerged that aim to group genes that behave in a coordinated fashion to a factor of interest. These methods aid in functional annotation and uncovering biological pathways, thereby collapsing complex datasets into more manageable units, providing more nuanced understandings of both the organism-level effects of modified gene expression, and the targets of adaptive divergence. Here, we reanalyze a dataset that investigated temperature-induced changes in gene expression in marine-adapted and freshwater-adapted threespine stickleback (Gasterosteus aculeatus), using Weighted Gene Co-expression Network Analysis (WGCNA) with PANTHER Gene Ontology (GO)-Slim overrepresentation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Six modules exhibited a conserved response and six a divergent response between marine and freshwater stickleback when acclimated to 7°C or 22°C. One divergent module showed freshwater-specific response to temperature, and the remaining divergent modules showed differences in height of reaction norms. PPARAa, a transcription factor that regulates fatty acid metabolism and has been implicated in adaptive divergence, was located in a module that had higher expression at 7°C and in freshwater stickleback. This updated methodology revealed patterns that were not found in the original publication. Although such methods hold promise toward predicting population response to environmental stressors, many limitations remain, particularly with regard to module expression representation, database resources, and cross-database integration.
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Affiliation(s)
| | - Danielle J. Clake
- Department of Biological SciencesUniversity of CalgaryCalgaryABCanada
| | | | - Sean M. Rogers
- Department of Biological SciencesUniversity of CalgaryCalgaryABCanada
- Bamfield Marine Sciences CentreBamfieldBCCanada
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Brain transcriptomics of agonistic behaviour in the weakly electric fish Gymnotus omarorum, a wild teleost model of non-breeding aggression. Sci Rep 2020; 10:9496. [PMID: 32528029 PMCID: PMC7289790 DOI: 10.1038/s41598-020-66494-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 05/22/2020] [Indexed: 11/28/2022] Open
Abstract
Differences in social status are often mediated by agonistic encounters between competitors. Robust literature has examined social status-dependent brain gene expression profiles across vertebrates, yet social status and reproductive state are often confounded. It has therefore been challenging to identify the neuromolecular mechanisms underlying social status independent of reproductive state. Weakly electric fish, Gymnotus omarorum, display territorial aggression and social dominance independent of reproductive state. We use wild-derived G. omarorum males to conduct a transcriptomic analysis of non-breeding social dominance relationships. After allowing paired rivals to establish a dominance hierarchy, we profiled the transcriptomes of brain sections containing the preoptic area (region involved in regulating aggressive behaviour) in dominant and subordinate individuals. We identified 16 differentially expressed genes (FDR < 0.05) and numerous genes that co-varied with behavioural traits. We also compared our results with previous reports of differential gene expression in other teleost species. Overall, our study establishes G. omarorum as a powerful model system for understanding the neuromolecular bases of social status independent of reproductive state.
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Forebrain Transcriptional Response to Transient Changes in Circulating Androgens in a Cichlid Fish. G3-GENES GENOMES GENETICS 2020; 10:1971-1982. [PMID: 32276961 PMCID: PMC7263668 DOI: 10.1534/g3.119.400947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
It has been hypothesized that androgens respond to the social interactions as a way to adjust the behavior of individuals to the challenges of the social environment in an adaptive manner. Therefore, it is expected that transient changes in circulating androgen levels within physiological scope should impact the state of the brain network that regulates social behavior, which should translate into adaptive behavioral changes. Here, we examined the effect that a transient peak in androgen circulating levels, which mimics socially driven changes in androgen levels, has on the forebrain state, which harbors most nuclei of the social decision-making network. For this purpose, we successfully induced transient changes in circulating androgen levels in an African cichlid fish (Mozambique tilapia, Oreochromis mossambicus) commonly used as a model in behavioral neuroendocrinology by injecting 11-ketotestosterone or testosterone, and compared the forebrain transcriptome of these individuals to control fish injected with vehicle. Forebrain samples were collected 30 min and 60 min after injection and analyzed using RNAseq. Our results showed that a transient peak in 11-ketotestosterone drives more accentuated changes in forebrain transcriptome than testosterone, and that transcriptomic impact was greater at the 30 min than at the 60 min post-androgen administration. Several genes involved in the regulation of translation, steroid metabolism, ion channel membrane receptors, and genes involved in epigenetic mechanisms were differentially expressed after 11-ketotestosterone or testosterone injection. In summary, this study identified specific candidate genes that may regulate socially driven changes in behavioral flexibility mediated by androgens.
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43
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Developmental plasticity shapes social traits and selection in a facultatively eusocial bee. Proc Natl Acad Sci U S A 2020; 117:13615-13625. [PMID: 32471944 PMCID: PMC7306772 DOI: 10.1073/pnas.2000344117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Developmental processes are an important source of phenotypic variation, but the extent to which this variation contributes to evolutionary change is unknown. We used integrative genomic analyses to explore the relationship between developmental and social plasticity in a bee species that can adopt either a social or solitary lifestyle. We find genes regulating this social flexibility also regulate development, and positive selection on these genes is influenced by their function during development. This suggests that developmental plasticity may influence the evolution of sociality. Our additional finding of genetic variants linked to differences in social behavior sheds light on how phenotypic variation derived from development may become encoded into the genome, and thus contribute to evolutionary change. Developmental plasticity generates phenotypic variation, but how it contributes to evolutionary change is unclear. Phenotypes of individuals in caste-based (eusocial) societies are particularly sensitive to developmental processes, and the evolutionary origins of eusociality may be rooted in developmental plasticity of ancestral forms. We used an integrative genomics approach to evaluate the relationships among developmental plasticity, molecular evolution, and social behavior in a bee species (Megalopta genalis) that expresses flexible sociality, and thus provides a window into the factors that may have been important at the evolutionary origins of eusociality. We find that differences in social behavior are derived from genes that also regulate sex differentiation and metamorphosis. Positive selection on social traits is influenced by the function of these genes in development. We further identify evidence that social polyphenisms may become encoded in the genome via genetic changes in regulatory regions, specifically in transcription factor binding sites. Taken together, our results provide evidence that developmental plasticity provides the substrate for evolutionary novelty and shapes the selective landscape for molecular evolution in a major evolutionary innovation: Eusociality.
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44
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Bilandžija H, Hollifield B, Steck M, Meng G, Ng M, Koch AD, Gračan R, Ćetković H, Porter ML, Renner KJ, Jeffery W. Phenotypic plasticity as a mechanism of cave colonization and adaptation. eLife 2020; 9:51830. [PMID: 32314737 PMCID: PMC7173965 DOI: 10.7554/elife.51830] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
A widely accepted model for the evolution of cave animals posits colonization by surface ancestors followed by the acquisition of adaptations over many generations. However, the speed of cave adaptation in some species suggests mechanisms operating over shorter timescales. To address these mechanisms, we used Astyanax mexicanus, a teleost with ancestral surface morphs (surface fish, SF) and derived cave morphs (cavefish, CF). We exposed SF to completely dark conditions and identified numerous altered traits at both the gene expression and phenotypic levels. Remarkably, most of these alterations mimicked CF phenotypes. Our results indicate that many cave-related traits can appear within a single generation by phenotypic plasticity. In the next generation, plasticity can be further refined. The initial plastic responses are random in adaptive outcome but may determine the subsequent course of evolution. Our study suggests that phenotypic plasticity contributes to the rapid evolution of cave-related traits in A. mexicanus. The Mexican tetra is a fish that has two forms: a surface-dwelling form, which has eyes and silvery grey appearance, and a cave-dwelling form, which is blind and has lost its pigmentation. Recent studies have shown that the cave-dwelling form evolved rapidly within the last 200,000 years from an ancestor that lived at the surface. The recent evolution of the cave-dwelling form of the tetra poses an interesting evolutionary question: how did the surface-dwelling ancestor of the tetra quickly adapt to the new and challenging environment found in the caves? ‘Phenotypic plasticity’ is a phenomenon through which a single set of genes can produce different observable traits depending on the environment. An example of phenotypic plasticity occurs in response to diet: in animals, poor diets can lead to an increase in the size of the digestive organs and to the animals eating more. To see if surface-dwelling tetras can quickly adapt to cave environments through phenotypic plasticity, Bilandžija et al. have exposed these fish to complete darkness (the major feature of the cave environment) for two years. After spending up to two years in the dark, these fish were compared to normal surface-dwelling and cave-dwelling tetras. Results revealed that surface-dwelling tetras raised in the dark exhibited traits associated with cave-dwelling tetras. These traits included changes in the activity of many genes involved in diverse processes, resistance to starvation, metabolism, and levels of hormones and molecules involved in neural signaling, which could lead to changes in behavior. However, the fish also exhibited traits, including an increase in the cells responsible for pigmentation, that would have no obvious benefit in the darkness. Even though the changes observed require no genetic mutations, they can help or hinder the fish’s survival once they occur, possibly determining subsequent evolution. Thus, a trait beneficial for surviving in the dark that appears simply through phenotypic plasticity may eventually be selected for and genetic mutations that encode it more reliably may appear too. These results shed light on how species may quickly adapt to new environments without accumulating genetic mutations, which can take hundreds of thousands of years. They also may help to explain how colonizer species succeed in challenging environments. The principles described by Bilandžija et al. can be applied to different organisms adapting to new environments, and may help understand the role of phenotypic plasticity in evolution.
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Affiliation(s)
- Helena Bilandžija
- Department of Biology, University of Maryland, College Park, United States.,Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Breanna Hollifield
- Department of Biology, University of Maryland, College Park, United States
| | - Mireille Steck
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, United States
| | - Guanliang Meng
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Mandy Ng
- Department of Biology, University of Maryland, College Park, United States
| | - Andrew D Koch
- Department of Biology, University of South Dakota, Vermillion, United States
| | - Romana Gračan
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Helena Ćetković
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, United States
| | - Kenneth J Renner
- Department of Biology, University of South Dakota, Vermillion, United States
| | - William Jeffery
- Department of Biology, University of Maryland, College Park, United States
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Waldvogel A, Feldmeyer B, Rolshausen G, Exposito‐Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M. Evolutionary genomics can improve prediction of species' responses to climate change. Evol Lett 2020; 4:4-18. [PMID: 32055407 PMCID: PMC7006467 DOI: 10.1002/evl3.154] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/31/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023] Open
Abstract
Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco-evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large-scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco-evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available resources more effectively, to implement mitigation measures before species go extinct and ecosystems lose important functions.
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Affiliation(s)
- Ann‐Marie Waldvogel
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | | | | | - Robert Kofler
- Institute of Population GeneticsVetmeduni ViennaAustria
| | - Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwichUnited Kingdom
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute of Ecology, Evolution and DiversityGoethe‐UniversityFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
| | | | | | - Alan Bergland
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia
| | - Thomas Flatt
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Frederic Guillaume
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
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46
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Nyman C, Hebert FO, Bessert‐Nettelbeck M, Aubin‐Horth N, Taborsky B. Transcriptomic signatures of social experience during early development in a highly social cichlid fish. Mol Ecol 2019; 29:610-623. [DOI: 10.1111/mec.15335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/23/2019] [Accepted: 12/10/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Cecilia Nyman
- Division of Behavioural Ecology Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Francois Olivier Hebert
- Département de Biologie and Institut de Biologie Intégrative et des Systèmes Université Laval Laval QC Canada
| | | | - Nadia Aubin‐Horth
- Département de Biologie and Institut de Biologie Intégrative et des Systèmes Université Laval Laval QC Canada
| | - Barbara Taborsky
- Division of Behavioural Ecology Institute of Ecology and Evolution University of Bern Bern Switzerland
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47
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Fruciano C, Meyer A, Franchini P. Divergent Allometric Trajectories in Gene Expression and Coexpression Produce Species Differences in Sympatrically Speciating Midas Cichlid Fish. Genome Biol Evol 2019; 11:1644-1657. [PMID: 31124568 PMCID: PMC6563553 DOI: 10.1093/gbe/evz108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2019] [Indexed: 12/19/2022] Open
Abstract
The mechanisms of speciation without geographic isolation (i.e., sympatric speciation) remain debated. This is due in part to the fact that the genomic landscape that could promote or hinder species divergence in the presence of gene flow is still largely unknown. However, intensive research is now centered on understanding the genetic architecture of adaptive traits associated with this process as well as how gene expression might affect these traits. Here, using RNA-Seq data, we investigated gene expression of sympatrically speciating benthic and limnetic Neotropical cichlid fishes at two developmental stages. First, we identified groups of coexpressed genes (modules) at each stage. Although there are a few large and well-preserved modules, most of the other modules are not preserved across life stages. Second, we show that later in development more and larger coexpression modules are associated with divergence between benthic and limnetic fish compared with the earlier life stage. This divergence between benthic and limnetic fish in coexpression mirrors divergence in overall expression between benthic and limnetic fish, which is more pronounced later in life. Our results reveal that already at 1-day posthatch benthic and limnetic fish diverge in (co)expression, and that this divergence becomes more substantial when fish are free-swimming but still unlikely to have divergent swimming and feeding habits. More importantly, our study describes how the coexpression of several genes through development, as opposed to individual genes, is associated with benthic–limnetic species differences, and how two morphogenetic trajectories diverge as fish grow older.
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Affiliation(s)
- Carmelo Fruciano
- Department of Biology, University of Konstanz, Germany.,Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS UMR 8197, Paris, France
| | - Axel Meyer
- Department of Biology, University of Konstanz, Germany
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48
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Bentz AB, Thomas GWC, Rusch DB, Rosvall KA. Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly. Sci Rep 2019; 9:15849. [PMID: 31676844 PMCID: PMC6825141 DOI: 10.1038/s41598-019-52312-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
Tree swallows (Tachycineta bicolor) are one of the most commonly studied wild birds in North America. They have advanced numerous research areas, including life history, physiology, and organismal responses to global change; however, transcriptomic resources are scarce. To further advance the utility of this system for biologists across disciplines, we generated a transcriptome for the tree swallow using six tissues (brain, blood, ovary, spleen, liver, and muscle) collected from breeding females. We de novo assembled 207,739 transcripts, which we aligned to 14,717 high confidence protein-coding genes. We then characterized each tissue with regard to its unique genes and processes and applied this transcriptome to two fundamental questions in evolutionary biology and endocrinology. First, we analyzed 3,015 single-copy orthologs and identified 46 genes under positive selection in the tree swallow lineage, including those with putative links to adaptations in this species. Second, we analyzed tissue-specific expression patterns of genes involved in sex steroidogenesis and processing. Enzymes capable of synthesizing these behaviorally relevant hormones were largely limited to the ovary, whereas steroid binding genes were found in nearly all other tissues, highlighting the potential for local regulation of sex steroid-mediated traits. These analyses provide new insights into potential sources of phenotypic variation in a free-living female bird and advance our understanding of fundamental questions in evolutionary and organismal biology.
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Affiliation(s)
- Alexandra B Bentz
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA. .,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA.
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Kimberly A Rosvall
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
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Harrison JW, Palmer JH, Rittschof CC. Altering social cue perception impacts honey bee aggression with minimal impacts on aggression-related brain gene expression. Sci Rep 2019; 9:14642. [PMID: 31601943 PMCID: PMC6787081 DOI: 10.1038/s41598-019-51223-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/24/2019] [Indexed: 02/01/2023] Open
Abstract
Gene expression changes resulting from social interactions may give rise to long term behavioral change, or simply reflect the activity of neural circuitry associated with behavioral expression. In honey bees, social cues broadly modulate aggressive behavior and brain gene expression. Previous studies suggest that expression changes are limited to contexts in which social cues give rise to stable, relatively long-term changes in behavior. Here we use a traditional beekeeping approach that inhibits aggression, smoke exposure, to deprive individuals of aggression-inducing olfactory cues and evaluate whether behavioral changes occur in absence of expression variation in a set of four biomarker genes (drat, cyp6g1/2, GB53860, inos) associated with aggression in previous studies. We also evaluate two markers of a brain hypoxic response (hif1α, hsf) to determine whether smoke induces molecular changes at all. We find that bees with blocked sensory perception as a result of smoke exposure show a strong, temporary inhibition of aggression relative to bees allowed to perceive normal social cues. However, blocking sensory perception had minimal impacts on aggression-relevant gene expression, althought it did induce a hypoxic molecular response in the brain. Results suggest that certain genes differentiate social cue-induced changes in aggression from long-term modulation of this phenotype.
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Affiliation(s)
- James W Harrison
- Department of Entomology, University of Kentucky, S-225 Agricultural Science Center North, Lexington, KY, 40546, USA
| | - Joseph H Palmer
- Department of Entomology, University of Kentucky, S-225 Agricultural Science Center North, Lexington, KY, 40546, USA
- College of Agriculture, Communities, and the Environment, Kentucky State University, 400 E. Main St., Frankfort, KY, 40601, USA
| | - Clare C Rittschof
- Department of Entomology, University of Kentucky, S-225 Agricultural Science Center North, Lexington, KY, 40546, USA.
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Jeffrey JD, Jeffries KM, Suski CD. Physiological status of silver carp (Hypophthalmichthys molitrix) in the Illinois River: An assessment of fish at the leading edge of the invasion front. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 32:100614. [PMID: 31419603 DOI: 10.1016/j.cbd.2019.100614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/08/2019] [Accepted: 07/24/2019] [Indexed: 01/29/2023]
Abstract
Silver carp (Hypophthalmichthys molitrix) are invasive to North America, and their range has expanded within the Mississippi River Basin, seemingly unchecked, since their introduction in the late 1970s, with the exception of the upper reaches of the Illinois River. With the imminent threat of their movement into the Great Lakes, the goal of the present study was to assess whether differences in the physiological status between silver carp at the leading edge of their invasion front and core population sites could explain their lack of expansion upstream toward Lake Michigan over the past decade. A transcriptomic approach using RNA sequencing and analysis of plasma variables were used to quantify differences among fish at the leading edge and two downstream core population sites. Leading-edge fish exhibited upregulation of genes associated with xenobiotic defense (e.g., ATP-binding cassette C1 [abcc1], abcc2, abcc6), decreased cell integrity (i.e., macroautophagy and apoptosis; autophagy-related protein 9A [atg9a], caspase 3b [casp3b]), and cholesterol metabolism (e.g., abca1, apolipoprotein A1 [apoa1], sterol O-acyltransferase [soat1]) and downregulation of genes associated with DNA repair (e.g., tumor suppressor p53-binding protein 1 [tp53bp1]) compared to core population sites. Transcriptomic profiles of leading-edge fish were consistent with fish inhabiting a polluted environment and suggest that poorer water quality conditions upstream of the leading edge may represent a non-permanent barrier to silver carp range expansion. The present study provides potential molecular targets for monitoring the physiological status of silver carp over time and in response to future improvements in water quality upstream of their leading edge.
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Affiliation(s)
- Jennifer D Jeffrey
- Department of Natural Resources and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Ken M Jeffries
- Department of Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Cory D Suski
- Department of Natural Resources and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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