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Berardi S, Rhodes JA, Berner MC, Greenblum SI, Bitter MC, Behrman EL, Betancourt NJ, Bergland AO, Petrov DA, Rajpurohit S, Schmidt P. Drosophila melanogaster pigmentation demonstrates adaptive phenotypic parallelism but genomic unpredictability over multiple timescales. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607378. [PMID: 39211235 PMCID: PMC11361081 DOI: 10.1101/2024.08.09.607378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Populations are capable of responding to environmental change over ecological timescales via adaptive tracking. However, the translation from patterns of allele frequency change to rapid adaptation of complex traits remains unresolved. We used abdominal pigmentation in Drosophila melanogaster as a model phenotype to address the nature, genetic architecture, and repeatability of rapid adaptation in the field. We show that D. melanogaster pigmentation evolves as a highly parallel and deterministic response to shared environmental gradients across latitude and season in natural North American populations. We then experimentally evolved replicate, genetically diverse fly populations in field mesocosms to remove any confounding effects of demography and/or cryptic structure that may drive patterns in wild populations; we show that pigmentation rapidly responds, in parallel, in fewer than ten generations. Thus, pigmentation evolves concordantly in response to spatial and temporal climatic gradients. We next examined whether phenotypic differentiation was associated with allele frequency change at loci with established links to genetic variance in pigmentation in natural populations. We found that across all spatial and temporal scales, phenotypic patterns were associated with variation at pigmentation-related loci, and the sets of genes we identified in each context were largely nonoverlapping. Therefore, our findings suggest that parallel phenotypic evolution is associated with an unpredictable genomic response, with distinct components of the polygenic architecture shifting across each environmental gradient to produce redundant adaptive patterns. Significance Statement Shifts in global climate conditions have heightened our need to understand the dynamics and pace of adaptation in natural populations. In order to anticipate the population-level response to rapidly changing environmental conditions, we need to understand whether trait evolution is predictable over short timescales, and whether the genetic basis of adaptation is shared or distinct across multiple timescales. Here, we explored parallelism in the adaptive response of a complex phenotype, D. melanogaster pigmentation, to shared conditions that varied over multiple spatiotemporal scales. Our results demonstrate that while phenotypic adaptation proceeds as a predictable response to environmental gradients, even over short timescales, the genetic basis of the adaptive response is variable and nuanced across spatial and temporal contexts.
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Orteu A, Hornett EA, Reynolds LA, Warren IA, Hurst GDD, Martin SH, Jiggins CD. Optix and cortex/ivory/mir-193 again: the repeated use of two mimicry hotspot loci. Proc Biol Sci 2024; 291:20240627. [PMID: 39045691 PMCID: PMC11267468 DOI: 10.1098/rspb.2024.0627] [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: 03/15/2024] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024] Open
Abstract
The extent to which evolution is repeatable has been a debated topic among evolutionary biologists. Although rewinding the tape of life perhaps would not lead to the same outcome every time, repeated evolution of analogous genes for similar functions has been extensively reported. Wing phenotypes of butterflies and moths have provided a wealth of examples of gene re-use, with certain 'hotspot loci' controlling wing patterns across diverse taxa. Here, we present an example of convergent evolution in the molecular genetic basis of Batesian wing mimicry in two Hypolimnas butterfly species. We show that mimicry is controlled by variation near cortex/ivory/mir-193, a known butterfly hotspot locus. By dissecting the genetic architecture of mimicry in Hypolimnas misippus and Hypolimnas bolina, we present evidence that distinct non-coding regions control the development of white pattern elements in the forewing and hindwing of the two species, suggesting independent evolution, and that no structural variation is found at the locus. Finally, we also show that orange coloration in H. bolina is associated with optix, a well-known patterning gene. Overall, our study once again implicates variation near the hotspot loci cortex/ivory/mir-193 and optix in butterfly wing mimicry and thereby highlights the repeatability of adaptive evolution.
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Affiliation(s)
- Anna Orteu
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Emily A. Hornett
- Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Liverpool, UK
- Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Biology, University of Oxford, Oxford, UK
| | - Louise A. Reynolds
- Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Liverpool, UK
| | - Ian A. Warren
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Gregory D. D. Hurst
- Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Liverpool, UK
| | - Simon H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Kitano J, Ansai S, Takehana Y, Yamamoto Y. Diversity and Convergence of Sex-Determination Mechanisms in Teleost Fish. Annu Rev Anim Biosci 2024; 12:233-259. [PMID: 37863090 DOI: 10.1146/annurev-animal-021122-113935] [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] [Indexed: 10/22/2023]
Abstract
Sexual reproduction is prevalent across diverse taxa. However, sex-determination mechanisms are so diverse that even closely related species often differ in sex-determination systems. Teleost fish is a taxonomic group with frequent turnovers of sex-determining mechanisms and thus provides us with great opportunities to investigate the molecular and evolutionary mechanisms underlying the turnover of sex-determining systems. Here, we compile recent studies on the diversity of sex-determination mechanisms in fish. We demonstrate that genes in the TGF-β signaling pathway are frequently used for master sex-determining (MSD) genes. MSD genes arise via two main mechanisms, duplication-and-transposition and allelic mutations, with a few exceptions. We also demonstrate that temperature influences sex determination in many fish species, even those with sex chromosomes, with higher temperatures inducing differentiation into males in most cases. Finally, we review theoretical models for the turnover of sex-determining mechanisms and discuss what questions remain elusive.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan;
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan;
| | - Yusuke Takehana
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan;
| | - Yoji Yamamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan;
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Uebbing S, Kocher AA, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan JP. Evolutionary innovation in conserved regulatory elements across the mammalian tree of life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578197. [PMID: 38352419 PMCID: PMC10862883 DOI: 10.1101/2024.01.31.578197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Transcriptional enhancers orchestrate cell type- and time point-specific gene expression programs. Evolution of enhancer sequences can alter target gene expression without causing detrimental misexpression in other contexts. It has long been thought that this modularity allows evolutionary changes in enhancers to escape pleiotropic constraints, which is especially important for evolutionary constrained developmental patterning genes. However, there is still little data supporting this hypothesis. Here we identified signatures of accelerated evolution in conserved enhancer elements across the mammalian phylogeny. We found that pleiotropic genes involved in gene regulatory and developmental processes were enriched for accelerated sequence evolution within their enhancer elements. These genes were associated with an excess number of enhancers compared to other genes, and due to this they exhibit a substantial degree of sequence acceleration over all their enhancers combined. We provide evidence that sequence acceleration is associated with turnover of regulatory function. We studied one acceleration event in depth and found that its sequence evolution led to the emergence of a new enhancer activity domain that may be involved in the evolution of digit reduction in hoofed mammals. Our results provide tangible evidence that enhancer evolution has been a frequent contributor to modifications involving constrained developmental signaling genes in mammals.
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Affiliation(s)
- Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven CT, USA
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven CT, USA
- Present address: Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Yu Ji
- Department of Genetics, Yale School of Medicine, New Haven CT, USA
| | - Suxia Bai
- Yale Genome Editing Center, Yale School of Medicine, New Haven CT, USA
| | - Xiaojun Xing
- Yale Genome Editing Center, Yale School of Medicine, New Haven CT, USA
| | - Timothy Nottoli
- Yale Genome Editing Center, Yale School of Medicine, New Haven CT, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven CT, USA
- Wu Tsai Institute, Yale University, New Haven CT, USA
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Kiontke K, Kolysh S, Ng R, Fitch DHA. Homologies and evolution of male tail characters in rhabditid and diplogastrid nematodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568293. [PMID: 38045386 PMCID: PMC10690243 DOI: 10.1101/2023.11.22.568293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
A major question in evolutionary biology is how often the same developmental events, mechanisms and genes are reused in the recurrent evolution of similar phenotypes. If this happens frequently, it would suggest that evolution is often constrained by developmental genetic mechanisms. To help address this question, we used adherens junction staining and laser ablation to analyze the development underlying several features of nematode male tails have evolved recurrently. We find that recurrent evolution has sometimes employed similar developmental events (parallel evolution) and sometimes different events (convergent evolution). Specifically, phasmid position changed four times via cell migration and never by switches in cell lineage polarity; different genital papillae are missing in species with less than nine; and tail tip morphogenesis was gained at least twice (once with tail tip cell fusions and once without) and lost at least twice. As in previous analyses, we also find that genital papilla positions have shifted differently in different lineages relative to their conserved positions of origin in the lateral hypodermis. In particular, the v1 papilla homolog in diplogastrids has moved dorsally relative to the other v-papillae and lies posterior to the v2 papilla. The prevalence of recurrently evolved characters (homoplasy) suggests that caution should be exercised when using these characters for phylogenetic inference. On the other hand, because of their recurrent evolution, these characters provide good models for investigating how developmental and genetic systems may bias, constrain or allow phenotypic evolution.
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Aristide L, Fernández R. Genomic Insights into Mollusk Terrestrialization: Parallel and Convergent Gene Family Expansions as Key Facilitators in Out-of-the-Sea Transitions. Genome Biol Evol 2023; 15:evad176. [PMID: 37793176 PMCID: PMC10581543 DOI: 10.1093/gbe/evad176] [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: 08/11/2023] [Revised: 09/08/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023] Open
Abstract
Animals abandoned their marine niche and successfully adapted to life on land multiple times throughout evolution, providing a rare opportunity to study the mechanisms driving large scale macroevolutionary convergence. However, the genomic factors underlying this process remain largely unknown. Here, we investigate the macroevolutionary dynamics of gene repertoire evolution during repeated transitions out of the sea in mollusks, a lineage that has transitioned to freshwater and terrestrial environments multiple independent times. Through phylogenomics and phylogenetic comparative methods, we examine ∼100 genomic data sets encompassing all major molluskan lineages. We introduce a conceptual framework for identifying and analyzing parallel and convergent evolution at the orthogroup level (groups of genes derived from a single ancestral gene in the species in question) and explore the extent of these mechanisms. Despite deep temporal divergences, we found that parallel expansions of ancient gene families played a major role in facilitating adaptation to nonmarine habitats, highlighting the relevance of the preexisting genomic toolkit in facilitating adaptation to new environments. The expanded functions primarily involve metabolic, osmoregulatory, and defense-related systems. We further found functionally convergent lineage-exclusive gene gains, while family contractions appear to be driven by neutral processes. Also, genomic innovations likely contributed to fuel independent habitat transitions. Overall, our study reveals that various mechanisms of gene repertoire evolution-parallelism, convergence, and innovation-can simultaneously contribute to major evolutionary transitions. Our results provide a genome-wide gene repertoire atlas of molluskan terrestrialization that paves the way toward further understanding the functional and evolutionary bases of this process.
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Affiliation(s)
- Leandro Aristide
- Metazoa Phylogenomics Laboratory Biodiversity Program, Institute of Evolutionary Biology (Spanish Research Council-University Pompeu Fabra), BarcelonaSpain
| | - Rosa Fernández
- Metazoa Phylogenomics Laboratory Biodiversity Program, Institute of Evolutionary Biology (Spanish Research Council-University Pompeu Fabra), BarcelonaSpain
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7
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Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages. Mol Biol Evol 2023; 40:msad188. [PMID: 37739926 PMCID: PMC10516590 DOI: 10.1093/molbev/msad188] [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] [Indexed: 09/24/2023] Open
Abstract
Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.
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Affiliation(s)
- Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego, CA, USA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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8
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Wang X, Li J, Han L, Liang C, Li J, Shang X, Miao X, Luo Z, Zhu W, Li Z, Li T, Qi Y, Li H, Lu X, Li L. QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize. Nat Commun 2023; 14:5232. [PMID: 37633966 PMCID: PMC10460418 DOI: 10.1038/s41467-023-41022-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023] Open
Abstract
Genetic dissection of agronomic traits is important for crop improvement and global food security. Phenotypic variation of tassel branch number (TBN), a major breeding target, is controlled by many quantitative trait loci (QTLs). The lack of large-scale QTL cloning methodology constrains the systematic dissection of TBN, which hinders modern maize breeding. Here, we devise QTG-Miner, a multi-omics data-based technique for large-scale and rapid cloning of quantitative trait genes (QTGs) in maize. Using QTG-Miner, we clone and verify seven genes underlying seven TBN QTLs. Compared to conventional methods, QTG-Miner performs well for both major- and minor-effect TBN QTLs. Selection analysis indicates that a substantial number of genes and network modules have been subjected to selection during maize improvement. Selection signatures are significantly enriched in multiple biological pathways between female heterotic groups and male heterotic groups. In summary, QTG-Miner provides a large-scale approach for rapid cloning of QTGs in crops and dissects the genetic base of TBN for further maize breeding.
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Affiliation(s)
- Xi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Juan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chengyong Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jiaxin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiaoyang Shang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xinxin Miao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Wanchao Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Tianhuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yongwen Qi
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510325, Guangdong, China
| | - Huihui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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9
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Flury JM, Meusemann K, Martin S, Hilgers L, Spanke T, Böhne A, Herder F, Mokodongan DF, Altmüller J, Wowor D, Misof B, Nolte AW, Schwarzer J. Potential Contribution of Ancient Introgression to the Evolution of a Derived Reproductive Strategy in Ricefishes. Genome Biol Evol 2023; 15:evad138. [PMID: 37493080 PMCID: PMC10465105 DOI: 10.1093/gbe/evad138] [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: 07/05/2022] [Revised: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023] Open
Abstract
Transitions from no parental care to extensive care are costly and involve major changes in life history, behavior, and morphology. Nevertheless, in Sulawesi ricefishes, pelvic brooding evolved from transfer brooding in two distantly related lineages within the genera Adrianichthys and Oryzias, respectively. Females of pelvic brooding species carry their eggs attached to their belly until the fry hatches. Despite their phylogenetic distance, both pelvic brooding lineages share a set of external morphological traits. A recent study found no direct gene flow between pelvic brooding lineages, suggesting independent evolution of the derived reproductive strategy. Convergent evolution can, however, also rely on repeated sorting of preexisting variation of an admixed ancestral population, especially when subjected to similar external selection pressures. We thus used a multispecies coalescent model and D-statistics to identify gene-tree-species-tree incongruencies, to evaluate the evolution of pelvic brooding with respect to interspecific gene flow not only between pelvic brooding lineages but also between pelvic brooding lineages and other Sulawesi ricefish lineages. We found a general network-like evolution in Sulawesi ricefishes, and as previously reported, we detected no gene flow between the pelvic brooding lineages. Instead, we found hybridization between the ancestor of pelvic brooding Oryzias and the common ancestor of the Oryzias species from the Lake Poso area. We further detected signs of introgression within the confidence interval of a quantitative trait locus associated with pelvic brooding in O. eversi. Our results hint toward a contribution of ancient standing genetic variation to the evolution of pelvic brooding in Oryzias.
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Affiliation(s)
- Jana M Flury
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Karen Meusemann
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Sebastian Martin
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Leon Hilgers
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Tobias Spanke
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Astrid Böhne
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Fabian Herder
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Daniel F Mokodongan
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, West Java, Indonesia
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Cologne University, Cologne, Germany
| | - Daisy Wowor
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, West Java, Indonesia
| | - Bernhard Misof
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Arne W Nolte
- Department of Ecological Genomics, Carl von Ossietzky Universität, Oldenburg, Germany
| | - Julia Schwarzer
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
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Pereira AG, Kohlsdorf T. Repeated evolution of similar phenotypes: Integrating comparative methods with developmental pathways. Genet Mol Biol 2023; 46:e20220384. [PMID: 37486083 PMCID: PMC10364090 DOI: 10.1590/1678-4685-gmb-2022-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/24/2023] [Indexed: 07/25/2023] Open
Abstract
Repeated phenotypes, often referred to as 'homoplasies' in cladistic analyses, may evolve through changes in developmental processes. Genetic bases of recurrent evolution gained attention and have been studied in the past years using approaches that combine modern analytical phylogenetic tools with the stunning assemblage of new information on developmental mechanisms. In this review, we evaluated the topic under an integrated perspective, revisiting the classical definitions of convergence and parallelism and detailing comparative methods used to evaluate evolution of repeated phenotypes, which include phylogenetic inference, estimates of evolutionary rates and reconstruction of ancestral states. We provide examples to illustrate how a given methodological approach can be used to identify evolutionary patterns and evaluate developmental mechanisms associated with the intermittent expression of a given trait along the phylogeny. Finally, we address why repeated trait loss challenges strict definitions of convergence and parallelism, discussing how changes in developmental pathways might explain the high frequency of repeated trait loss in specific lineages.
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Affiliation(s)
- Anieli Guirro Pereira
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
| | - Tiana Kohlsdorf
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
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11
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Pelletier K, Pitchers WR, Mammel A, Northrop-Albrecht E, Márquez EJ, Moscarella RA, Houle D, Dworkin I. Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild-caught populations of Drosophila melanogaster. Genetics 2023; 224:iyad050. [PMID: 36961731 PMCID: PMC10324948 DOI: 10.1093/genetics/iyad050] [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: 12/15/2022] [Revised: 03/14/2023] [Accepted: 03/18/2023] [Indexed: 03/25/2023] Open
Abstract
Identifying the genetic architecture of complex traits is important to many geneticists, including those interested in human disease, plant and animal breeding, and evolutionary genetics. Advances in sequencing technology and statistical methods for genome-wide association studies have allowed for the identification of more variants with smaller effect sizes, however, many of these identified polymorphisms fail to be replicated in subsequent studies. In addition to sampling variation, this failure to replicate reflects the complexities introduced by factors including environmental variation, genetic background, and differences in allele frequencies among populations. Using Drosophila melanogaster wing shape, we ask if we can replicate allelic effects of polymorphisms first identified in a genome-wide association studies in three genes: dachsous, extra-macrochaete, and neuralized, using artificial selection in the lab, and bulk segregant mapping in natural populations. We demonstrate that multivariate wing shape changes associated with these genes are aligned with major axes of phenotypic and genetic variation in natural populations. Following seven generations of artificial selection along the dachsous shape change vector, we observe genetic differentiation of variants in dachsous and genomic regions containing other genes in the hippo signaling pathway. This suggests a shared direction of effects within a developmental network. We also performed artificial selection with the extra-macrochaete shape change vector, which is not a part of the hippo signaling network, but showed a largely shared direction of effects. The response to selection along the emc vector was similar to that of dachsous, suggesting that the available genetic diversity of a population, summarized by the genetic (co)variance matrix (G), influenced alleles captured by selection. Despite the success with artificial selection, bulk segregant analysis using natural populations did not detect these same variants, likely due to the contribution of environmental variation and low minor allele frequencies, coupled with small effect sizes of the contributing variants.
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Affiliation(s)
- Katie Pelletier
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - William R Pitchers
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- BiomeBank, 2 Ann Nelson Dr, Thebarton, Adelaide, SA 5031, Australia
| | - Anna Mammel
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- Neurocode USA, 3548 Meridian St, Bellingham, WA 98225, USA
| | - Emmalee Northrop-Albrecht
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905USA
| | - Eladio J Márquez
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
- Branch Biosciences, 1 Marina Park Dr., Boston, MA 02210, USA
| | - Rosa A Moscarella
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
- Department of Biology, University of Massachusetts, 221 Morrill Science Center III, 611 North Pleasant Street, Amherst, MA 01003-9297, USA
| | - David Houle
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Ian Dworkin
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
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12
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Cutter AD. Speciation and development. Evol Dev 2023; 25:289-327. [PMID: 37545126 DOI: 10.1111/ede.12454] [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: 03/07/2023] [Revised: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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13
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Moran RL, Richards EJ, Ornelas-García CP, Gross JB, Donny A, Wiese J, Keene AC, Kowalko JE, Rohner N, McGaugh SE. Selection-driven trait loss in independently evolved cavefish populations. Nat Commun 2023; 14:2557. [PMID: 37137902 PMCID: PMC10156726 DOI: 10.1038/s41467-023-37909-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found that phenotypic convergence is due to parallel genetic changes. This suggests a substantial role for constraint and determinism in evolution and indicates that certain mutations are more likely to contribute to phenotypic evolution. Here we use whole genome resequencing in the Mexican tetra, Astyanax mexicanus, to investigate how selection has shaped the repeated evolution of both trait loss and enhancement across independent cavefish lineages. We show that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Our findings provide empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the cave environment may impact the rate at which mutations occur.
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Affiliation(s)
- Rachel L Moran
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA.
- Department of Biology, Texas A&M University, College Station, TX, USA.
| | - Emilie J Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Claudia Patricia Ornelas-García
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior S/N. CP 04510, D. F. México, México City, México
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Alexandra Donny
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Jonathan Wiese
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Johanna E Kowalko
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular & Integrative Physiology, KU Medical Center, Kansas City, KS, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
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14
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Graham AM, Jamison JM, Bustos M, Cournoyer C, Michaels A, Presnell JS, Richter R, Crocker DE, Fustukjian A, Hunter ME, Rea LD, Marsillach J, Furlong CE, Meyer WK, Clark NL. Reduction of Paraoxonase Expression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization. Mol Biol Evol 2023; 40:msad104. [PMID: 37146172 PMCID: PMC10202596 DOI: 10.1093/molbev/msad104] [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: 11/14/2022] [Revised: 03/27/2023] [Accepted: 04/17/2023] [Indexed: 05/07/2023] Open
Abstract
Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages-Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.
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Affiliation(s)
- Allie M Graham
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Jerrica M Jamison
- Department of Biological Sciences, University of Toronto—Scarborough, Scarborough, Ontario, Canada
| | - Marisol Bustos
- Department of Biomedical Engineering, University of Texas—San Antonio, San Antonio, TX
| | | | - Alexa Michaels
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA
- The Jackson Laboratory, Bar Harbor, ME
| | - Jason S Presnell
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Rebecca Richter
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Daniel E Crocker
- Department of Biology, Sonoma State University, Rohnert Park, CA
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL
| | - Lorrie D Rea
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska—Fairbanks, Fairbanks, AK
| | - Judit Marsillach
- Department of Environmental & Occupational Health Sciences, University of Washington School of Public Health, Seattle, WA
| | - Clement E Furlong
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA
| | - Nathan L Clark
- Department of Human Genetics, University of Utah, Salt Lake City, UT
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15
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Deng S. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Heliyon 2023; 9:e14466. [PMID: 36967965 PMCID: PMC10036676 DOI: 10.1016/j.heliyon.2023.e14466] [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: 02/22/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.
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Affiliation(s)
- Shaojie Deng
- Chongqing (Fengjie) Municipal Bureau of Planning and Natural Resources, China
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16
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Ling L, Mühling B, Jaenichen R, Gompel N. Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila. SCIENCE ADVANCES 2023; 9:eade6529. [PMID: 36800429 PMCID: PMC9937571 DOI: 10.1126/sciadv.ade6529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
The loss of discrete morphological traits, the most common evolutionary transition, is typically driven by changes in developmental gene expression. Mutations accumulating in regulatory elements of these genes can disrupt DNA binding sites for transcription factors patterning their spatial expression, or delete entire enhancers. Regulatory elements, however, may be silenced through changes in chromatin accessibility or the emergence of repressive elements. Here, we show that increased chromatin accessibility at the gene yellow, combined with the gain of a repressor site, underlies the loss of a wing spot pigmentation pattern in a Drosophila species. The gain of accessibility of this repressive element is regulated by E93, a transcription factor governing the progress of metamorphosis. This convoluted evolutionary scenario contrasts with the parsimonious mutational paths generally envisioned and often documented for morphological losses. It illustrates how evolutionary changes in chromatin accessibility may directly contribute to morphological diversification.
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17
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Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526059. [PMID: 36778215 PMCID: PMC9915506 DOI: 10.1101/2023.01.30.526059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 wild fish species that either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences (CONDELs) in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA , a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, s yngnathid, and synbranchid species with caudal fin reduction, and which alters caudal fin development when targeted by genome editing. Our study illustrates a general strategy for mapping phenotypes to genotypes across a tree of vertebrate species, and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes during 100 million years of fish evolution.
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Affiliation(s)
- Heidi I. Chen
- Department of Developmental Biology, Stanford University School of Medicine, CA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, CA
- Department of Biomedical Data Science, Stanford University School of Medicine, CA
- Department of Computer Science, Stanford University School of Engineering, CA
- Department of Pediatrics, Stanford University School of Medicine, CA
| | - David M. Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, CA
- Howard Hughes Medical Institute, Stanford University, CA
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18
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Laurentino TG, Dittmer DE, Grundler MR, Pina‐Martins F, Haddock J, Hibbitts TJ, Rosenblum EB. Repeated evolution of blanched coloration in a lizard across independent white-sand habitats. Ecol Evol 2022; 12:e9555. [PMID: 36506826 PMCID: PMC9729009 DOI: 10.1002/ece3.9555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
The White Sands lizards of New Mexico are a rare and classic example of convergent evolution where three species have evolved blanched coloration on the white gypsum dunes. Until now, no geological replicate of the pattern had been described. However, one of the White Sands species, the lesser earless lizard (Holbrookia maculata), has been discovered to also inhabit the Salt Basin Dunes of Texas, where it has also evolved a blanched morph. We here present a first phenotypic and genetic description of the Salt Basin Dunes population of H. maculata. Phylogenetic inference based on a housekeeping gene (ND4) and a classic candidate gene in the melanin-synthesis pathway (Melanocortin 1 Receptor; Mc1r) shows the newly discovered population as an independent lineage, with no evidence of genetic parallelism in the coding region of Mc1r. Initial morphological data suggest that while this population displays convergent evolution in blanched coloration, there are divergent patterns in limb length and habitat use behavior between the gypsum environments. Our findings present the White Sands/Salt Basin Dunes as an exceptionally promising comparative model for studies of adaptation and convergent evolution.
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Affiliation(s)
- Telma G. Laurentino
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | | | - Maggie R. Grundler
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Francisco Pina‐Martins
- cE3c‐Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de Lisboa (ULisboa)LisbonPortugal
| | - Janey Haddock
- Division of MammalogyBiodiversity Institute, University of KansasLawrenceKansasUSA
| | - Toby J. Hibbitts
- Biodiversity Research and Teaching Collection, Department of Ecology and Conservation BiologyTexas A&M UniversityCollege StationTexasUSA
- Natural Resources InstituteTexas A&M UniversityCollege StationTexasUSA
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
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19
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Birkeland S, Slotte T, Brysting AK, Gustafsson ALS, Hvidsten TR, Brochmann C, Nowak MD. What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance? Mol Ecol 2022; 31:4271-4285. [PMID: 35753053 PMCID: PMC9546214 DOI: 10.1111/mec.16581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Little is known about the evolution of cold tolerance in polar plant species and how they differ from temperate relatives. To gain insight into their biology and the evolution of cold tolerance, we compared the molecular basis of cold response in three Arctic Brassicaceae species. We conducted a comparative time series experiment to examine transcriptional responses to low temperature. RNA was sampled at 22°C, and after 3, 6, and 24 at 2°C. We then identified sets of genes that were differentially expressed in response to cold and compared them between species, as well as to published data from the temperate Arabidopsis thaliana. Most differentially expressed genes were species‐specific, but a significant portion of the cold response was also shared among species. Among thousands of differentially expressed genes, ~200 were shared among the three Arctic species and A. thaliana, while ~100 were exclusively shared among the three Arctic species. Our results show that cold response differs markedly between Arctic Brassicaceae species, but probably builds on a conserved basis found across the family. They also confirm that highly polygenic traits such as cold tolerance may show little repeatability in their patterns of adaptation.
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Affiliation(s)
- Siri Birkeland
- Natural History Museum, University of Oslo, Oslo, Norway.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Tanja Slotte
- Natural History Museum, University of Oslo, Oslo, Norway.,Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Anne K Brysting
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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20
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Genetic load: genomic estimates and applications in non-model animals. Nat Rev Genet 2022; 23:492-503. [PMID: 35136196 DOI: 10.1038/s41576-022-00448-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 12/11/2022]
Abstract
Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.
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21
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Population genetics and independently replicated evolution of predator-associated burst speed ecophenotypy in mosquitofish. Heredity (Edinb) 2022; 128:45-55. [PMID: 34876658 PMCID: PMC8733020 DOI: 10.1038/s41437-021-00487-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023] Open
Abstract
Many species show replicated ecophenotypy due to recurring patterns of natural selection. Based on the presence or absence of pursuit predators, at least 17 species of fish repeatedly differentiated in body shape in a manner that increases burst swimming speed and the likelihood of predator escape. The predator-associated burst speed (PABS) ecophenotype is characterized by a small head and trunk and enlarged caudal region. Mechanisms promoting replicated phenotype-environment association include selection (without evolution), a single instance of adaptive evolution followed by biased habitat occupation, repeated instances of local adaptation, or adaptive phenotypic plasticity. Common garden rearing of mosquitofish, Gambusia affinis, demonstrated a likely heritable basis for PABS phenotypy, but it is unknown whether populations are otherwise genetically distinct or whether replicated ecophenotypy represents a single or replicated instances of adaptation. To genetically characterize the populations and test hypotheses of single or multiple adaptations, we characterized variation in 12 polymorphic DNA microsatellites in the previously studied G. affinis populations. Populations were genetically distinct by multilocus analysis, exhibited high allelic diversity, and were heterozygote deficient, which effects were attributed to G. affinis's shoaling nature and habitat patchiness. Genetic and phenotypic distances among populations were correlated for non-PABS but not PABS morphology. Multilocus analysis demonstrated ecophenotype polyphyly and scattered multivariate genetic structure which support only the replicated-adaptation model. As all of the diverse tests performed demonstrated lack of congruence between patterns of molecular genetic and PABS differentiation, it is likely that divergent natural selection drove multiple instances of adaptive evolution.
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22
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Reeve J, Li Q, Lindtke D, Yeaman S. Comparing genome scans among species of the stickleback order reveals three different patterns of genetic diversity. Ecol Evol 2022; 12:e8502. [PMID: 35127027 PMCID: PMC8796908 DOI: 10.1002/ece3.8502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/03/2022] Open
Abstract
Comparing genome scans among species is a powerful approach for investigating the patterns left by evolutionary processes. In particular, this offers a way to detect candidate genes that drive convergent evolution. We compared genome scan results to investigate if patterns of genetic diversity and divergence are shared among divergent species within the stickleback order (Gasterosteiformes): the threespine stickleback (Gasterosteus aculeatus), ninespine stickleback (Pungitius pungitus), and tubesnout (Aulorhynchus flavidus). Populations were sampled from the southern and northern edges of each species' range, to identify patterns associated with latitudinal changes in genetic diversity. Weak correlations in genetic diversity (F ST and expected heterozygosity) and three different patterns in the genomic landscape were found among these species. Additionally, no candidate genes for convergent evolution were detected. This is a counterexample to the growing number of studies that have shown overlapping genetic patterns, demonstrating that genome scan comparisons can be noisy due to the effects of several interacting evolutionary forces.
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Affiliation(s)
- James Reeve
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Present address:
Tjärnö Marina LaboratoriumGöteborgs UniversitetStrömstadSweden
| | - Qiushi Li
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Present address:
Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Dorothea Lindtke
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Present address:
Institute of Plant SciencesUniversity of BernBernSwitzerland
| | - Samuel Yeaman
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
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23
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Takeishi T, Fujiwara K, Osada N, Mita A, Takada T, Shiroishi T, Suzuki H. Phylogeographic study using nuclear genome sequences of <i>Asip</i> to infer the origins of ventral fur color variation in the house mouse <i>Mus musculus</i>. Genes Genet Syst 2021; 96:271-284. [DOI: 10.1266/ggs.21-00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Toki Takeishi
- Laboratory of Ecology and Genetics Graduate School of Environmental Science, Hokkaido University
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University
| | | | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center
| | | | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics Graduate School of Environmental Science, Hokkaido University
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24
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Montoya QV, Martiarena MJS, Bizarria R, Gerardo NM, Rodrigues A. Fungi inhabiting attine ant colonies: reassessment of the genus Escovopsis and description of Luteomyces and Sympodiorosea gens. nov. IMA Fungus 2021; 12:23. [PMID: 34429165 PMCID: PMC8383443 DOI: 10.1186/s43008-021-00078-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 08/10/2021] [Indexed: 11/15/2022] Open
Abstract
Escovopsis is a diverse group of fungi, which are considered specialized parasites of the fungal cultivars of fungus-growing ants. The lack of a suitable taxonomic framework and phylogenetic inconsistencies have long hampered Escovopsis research. The aim of this study is to reassess the genus Escovopsis using a taxonomic approach and a comprehensive multilocus phylogenetic analysis, in order to set the basis of the genus systematics and the stage for future Escovopsis research. Our results support the separation of Escovopsis into three distinct genera. In light of this, we redefine Escovopsis as a monophyletic clade whose main feature is to form terminal vesicles on conidiophores. Consequently, E. kreiselii and E. trichodermoides were recombined into two new genera, Sympodiorosea and Luteomyces, as S. kreiselii and L. trichodermoides, respectively. This study expands our understanding of the systematics of Escovopsis and related genera, thereby facilitating future research on the evolutionary history, taxonomic diversity, and ecological roles of these inhabitants of the attine ant colonies.
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Affiliation(s)
- Quimi Vidaurre Montoya
- Department of General and Applied Biology, São Paulo State University (UNESP), Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13.506-900, Brazil. .,Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP, Brazil.
| | - Maria Jesus Sutta Martiarena
- Department of General and Applied Biology, São Paulo State University (UNESP), Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13.506-900, Brazil.,Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Rodolfo Bizarria
- Department of General and Applied Biology, São Paulo State University (UNESP), Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13.506-900, Brazil.,Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Nicole Marie Gerardo
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, USA
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13.506-900, Brazil. .,Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP, Brazil.
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25
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Lightfoot JW, Dardiry M, Kalirad A, Giaimo S, Eberhardt G, Witte H, Wilecki M, Rödelsperger C, Traulsen A, Sommer RJ. Sex or cannibalism: Polyphenism and kin recognition control social action strategies in nematodes. SCIENCE ADVANCES 2021; 7:7/35/eabg8042. [PMID: 34433565 PMCID: PMC8386922 DOI: 10.1126/sciadv.abg8042] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/01/2021] [Indexed: 05/10/2023]
Abstract
Resource polyphenisms, where single genotypes produce alternative feeding strategies in response to changing environments, are thought to be facilitators of evolutionary novelty. However, understanding the interplay between environment, morphology, and behavior and its significance is complex. We explore a radiation of Pristionchus nematodes with discrete polyphenic mouth forms and associated microbivorous versus cannibalistic traits. Notably, comparing 29 Pristionchus species reveals that reproductive mode strongly correlates with mouth-form plasticity. Male-female species exhibit the microbivorous morph and avoid parent-offspring conflict as indicated by genetic hybrids. In contrast, hermaphroditic species display cannibalistic morphs encouraging competition. Testing predation between 36 co-occurring strains of the hermaphrodite P. pacificus showed that killing inversely correlates with genomic relatedness. These empirical data together with theory reveal that polyphenism (plasticity), kin recognition, and relatedness are three major factors that shape cannibalistic behaviors. Thus, developmental plasticity influences cooperative versus competitive social action strategies in diverse animals.
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Affiliation(s)
- James W Lightfoot
- Max Planck Institute for Developmental Biology, Max-Planck Ring 9, 72076 Tübingen, Germany
- Max Planck Research Group Self-Recognition and Cannibalism, Center of Advanced European Studies and Research (CAESAR), Ludwig-Erhard-Allee 2, Bonn 53175, Germany
| | - Mohannad Dardiry
- Max Planck Institute for Developmental Biology, Max-Planck Ring 9, 72076 Tübingen, Germany
- Department of Genetics, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ata Kalirad
- Max Planck Institute for Developmental Biology, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - Stefano Giaimo
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Gabi Eberhardt
- Max Planck Institute for Developmental Biology, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - Hanh Witte
- Max Planck Institute for Developmental Biology, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - Martin Wilecki
- Max Planck Institute for Developmental Biology, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - Arne Traulsen
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Ralf J Sommer
- Max Planck Institute for Developmental Biology, Max-Planck Ring 9, 72076 Tübingen, Germany.
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26
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Magota K, Sakaguchi S, Lee JS, Yamamoto M, Takahashi D, Nagano AJ, Setoguchi H. Phylogeographic analysis of Saxifraga fortunei complex (Saxifragaceae) reveals multiple origins of morphological and ecological variations in the Japanese Archipelago. Mol Phylogenet Evol 2021; 163:107230. [PMID: 34133947 DOI: 10.1016/j.ympev.2021.107230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
Phenotypic polymorphism within a species is a notable phenomenon in evolutionary biology to understand the process of adaptive speciation and other historical events. The Saxifraga fortunei complex is a widespread herb found in East Asia. It includes several ecotypic taxa corresponding to their habitat environments. The distribution of the various ecotypes in a limited area of the Japanese Archipelago makes the species a suitable model to investigate the impact of population demographic history and natural selection on lineage diversification. Here, Sanger-based sequencing was used to estimate the divergence timeframe between populations of the Eurasian continent and Japan. Genome-wide SNPs obtained by ddRAD sequencing were used to investigate the phylogeographic origins of ecotypic taxa. The phylogenetic analyses revealed the divergence of the Japanese population from the continental population in the late Miocene. Two distinct regional clades of North and South Japan were identified; phenotypic diversification was evident only in the southern clade. The South Japan clades displayed a historical distribution expansion from north to south. The phenotypic variations appeared to have generated during the expansion. The ecotypic boundaries were incongruent with the genetic grouping. We propose that morphological and ecological specialization in Japanese populations was repeatedly generated by local natural selection.
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Affiliation(s)
- Kana Magota
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan.
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Jung-Sim Lee
- Korean National Arboretum, 415 Gwangneung Sumokwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-Province 11186, Republic of Korea
| | - Masaya Yamamoto
- Hyogo University of Teacher Education, 942-1 Shimokume, Kato, Hyogo 673-1494, Japan
| | - Daiki Takahashi
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
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27
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Xie VC, Pu J, Metzger BP, Thornton JW, Dickinson BC. Contingency and chance erase necessity in the experimental evolution of ancestral proteins. eLife 2021; 10:67336. [PMID: 34061027 PMCID: PMC8282340 DOI: 10.7554/elife.67336] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/30/2021] [Indexed: 12/13/2022] Open
Abstract
The roles of chance, contingency, and necessity in evolution are unresolved because they have never been assessed in a single system or on timescales relevant to historical evolution. We combined ancestral protein reconstruction and a new continuous evolution technology to mutate and select proteins in the B-cell lymphoma-2 (BCL-2) family to acquire protein–protein interaction specificities that occurred during animal evolution. By replicating evolutionary trajectories from multiple ancestral proteins, we found that contingency generated over long historical timescales steadily erased necessity and overwhelmed chance as the primary cause of acquired sequence variation; trajectories launched from phylogenetically distant proteins yielded virtually no common mutations, even under strong and identical selection pressures. Chance arose because many sets of mutations could alter specificity at any timepoint; contingency arose because historical substitutions changed these sets. Our results suggest that patterns of variation in BCL-2 sequences – and likely other proteins, too – are idiosyncratic products of a particular and unpredictable course of historical events. One of the most fundamental and unresolved questions in evolutionary biology is whether the outcomes of evolution are predictable. Is the diversity of life we see today the expected result of organisms adapting to their environment throughout history (also known as natural selection) or the product of random chance? Or did chance events early in history shape the paths that evolution could take next, determining the biological forms that emerged under natural selection much later? These questions are hard to study because evolution happened only once, long ago. To overcome this barrier, Xie, Pu, Metzger et al. developed an experimental approach that can evolve reconstructed ancestral proteins that existed deep in the past. Using this method, it is possible to replay evolution multiple times, from various historical starting points, under conditions similar to those that existed long ago. The end products of the evolutionary trajectories can then be compared to determine how predictable evolution actually is. Xie, Pu, Metzger et al. studied proteins belonging to the BCL-2 family, which originated some 800 million years ago. These proteins have diversified greatly over time in both their genetic sequences and their ability to bind to specific partner proteins called co-regulators. Xie, Pu, Metzger et al. synthesized BCL-2 proteins that existed at various times in the past. Each ancestral protein was then allowed to evolve repeatedly under natural selection to acquire the same co-regulator binding functions that evolved during history. At the end of each evolutionary trajectory, the genetic sequence of the resulting BCL-2 proteins was recorded. This revealed that the outcomes of evolution were almost completely unpredictable: trajectories initiated from the same ancestral protein produced proteins with very different sequences, and proteins launched from different ancestral starting points were even more dissimilar. Further experiments identified the mutations in each trajectory that caused changes in coregulator binding. When these mutations were introduced into other ancestral proteins, they did not yield the same change in function. This suggests that early chance events influenced each protein’s evolution in an unpredictable way by opening and closing the paths available to it in the future. This research expands our understanding of evolution on a molecular level whilst providing a new experimental approach for studying evolutionary drivers in more detail. The results suggest that BCL-2 proteins, in all their various forms, are unique products of a particular, unpredictable course of history set in motion by ancient chance events.
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Affiliation(s)
| | - Jinyue Pu
- Department of Chemistry, University of Chicago, Chicago, United States
| | - Brian Ph Metzger
- Department of Ecology and Evolution, University of Chicago, Chicago, United States
| | - Joseph W Thornton
- Department of Ecology and Evolution, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
| | - Bryan C Dickinson
- Department of Chemistry, University of Chicago, Chicago, United States
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28
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Bohutínská M, Vlček J, Yair S, Laenen B, Konečná V, Fracassetti M, Slotte T, Kolář F. Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives. Proc Natl Acad Sci U S A 2021; 118:e2022713118. [PMID: 34001609 PMCID: PMC8166048 DOI: 10.1073/pnas.2022713118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ∼0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.
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Affiliation(s)
- Magdalena Bohutínská
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic;
- Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Jakub Vlček
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
- Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Sivan Yair
- Center for Population Biology, University of California, Davis, CA 95616
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Veronika Konečná
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Marco Fracassetti
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic;
- Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
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29
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Baduel P, Leduque B, Ignace A, Gy I, Gil J, Loudet O, Colot V, Quadrana L. Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana. Genome Biol 2021; 22:138. [PMID: 33957946 PMCID: PMC8101250 DOI: 10.1186/s13059-021-02348-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/09/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND How species can adapt to abrupt environmental changes, particularly in the absence of standing genetic variation, is poorly understood and a pressing question in the face of ongoing climate change. Here we leverage publicly available multi-omic and bio-climatic data for more than 1000 wild Arabidopsis thaliana accessions to determine the rate of transposable element (TE) mobilization and its potential to create adaptive variation in natural settings. RESULTS We demonstrate that TE insertions arise at almost the same rate as base substitutions. Mobilization activity of individual TE families varies greatly between accessions, in association with genetic and environmental factors as well as through complex gene-environment interactions. Although the distribution of TE insertions across the genome is ultimately shaped by purifying selection, reflecting their typically strong deleterious effects when located near or within genes, numerous recent TE-containing alleles show signatures of positive selection. Moreover, high rates of transposition appear positively selected at the edge of the species' ecological niche. Based on these findings, we predict through mathematical modeling higher transposition activity in Mediterranean regions within the next decades in response to global warming, which in turn should accelerate the creation of large-effect alleles. CONCLUSIONS Our study reveals that TE mobilization is a major generator of genetic variation in A. thaliana that is finely modulated by genetic and environmental factors. These findings and modeling indicate that TEs may be essential genomic players in the demise or rescue of native populations in times of climate crises.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Basile Leduque
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Amandine Ignace
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Isabelle Gy
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - José Gil
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
- Present Address: Institut Curie, 26 rue d'Ulm, 75005, Paris, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Vincent Colot
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
| | - Leandro Quadrana
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
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30
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Munds RA, Titus CL, Moreira LAA, Eggert LS, Blomquist GE. Examining the molecular basis of coat color in a nocturnal primate family (Lorisidae). Ecol Evol 2021; 11:4442-4459. [PMID: 33976821 PMCID: PMC8093732 DOI: 10.1002/ece3.7338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023] Open
Abstract
Organisms use color for camouflage, sexual signaling, or as a warning sign of danger. Primates are one of the most vibrantly colored Orders of mammals. However, the genetics underlying their coat color are poorly known, limiting our ability to study molecular aspects of its evolution. The role of the melanocortin 1 receptor (MC1R) in color evolution has been implicated in studies on rocket pocket mice (Chaetodipus intermediusi), toucans (Ramphastidae), and many domesticated animals. From these studies, we know that changes in MC1R result in a yellow/red or a brown/black morphology. Here, we investigate the evolution of MC1R in Lorisidae, a monophyletic nocturnal primate family, with some genera displaying high contrast variation in color patterns and other genera being monochromatic. Even more unique, the Lorisidae family has the only venomous primate: the slow loris (Nycticebus). Research has suggested that the contrasting coat patterns of slow lorises are aposematic signals for their venom. If so, we predict the MC1R in slow lorises will be under positive selection. In our study, we found that Lorisidae MC1R is under purifying selection (ω = 0.0912). In Lorisidae MC1R, there were a total of 75 variable nucleotides, 18 of which were nonsynonymous. Six of these nonsynonymous substitutions were found on the Perodicticus branch, which our reconstructions found to be the only member of Lorisidae that has predominantly lighter coat color; no substitutions were associated with Nycticebus. Our findings generate new insight into the genetics of pelage color and evolution among a unique group of nocturnal mammals and suggest putative underpinnings of monochromatic color evolution in the Perodicticus lineage.
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Affiliation(s)
- Rachel A. Munds
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
- Nocturnal Primate Research GroupOxford Brookes UniversityOxfordUK
| | - Chelsea L. Titus
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Lais A. A. Moreira
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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31
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Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJ, Yang JH, Collins JJ. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science 2021; 371:371/6531/eaba0862. [PMID: 33602825 DOI: 10.1126/science.aba0862] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 09/16/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022]
Abstract
Although metabolism plays an active role in antibiotic lethality, antibiotic resistance is generally associated with drug target modification, enzymatic inactivation, and/or transport rather than metabolic processes. Evolution experiments of Escherichia coli rely on growth-dependent selection, which may provide a limited view of the antibiotic resistance landscape. We sequenced and analyzed E. coli adapted to representative antibiotics at increasingly heightened metabolic states. This revealed various underappreciated noncanonical genes, such as those related to central carbon and energy metabolism, which are implicated in antibiotic resistance. These metabolic alterations lead to lower basal respiration, which prevents antibiotic-mediated induction of tricarboxylic acid cycle activity, thus avoiding metabolic toxicity and minimizing drug lethality. Several of the identified metabolism-specific mutations are overrepresented in the genomes of >3500 clinical E. coli pathogens, indicating clinical relevance.
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Affiliation(s)
- Allison J Lopatkin
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering; Harvard University, Boston, MA, USA.,Department of Biology, Barnard College, New York, NY, USA.,Data Science Institute, Columbia University, New York, NY, USA.,Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - Sarah C Bening
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan M Stokes
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering; Harvard University, Boston, MA, USA
| | - Michael A Kohanski
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ahmed H Badran
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicole J Cheney
- Ruy V. Lourenço Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA.,Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Jason H Yang
- Ruy V. Lourenço Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA.,Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - James J Collins
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering; Harvard University, Boston, MA, USA.,Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
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32
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Lau ES, Oakley TH. Multi-level convergence of complex traits and the evolution of bioluminescence. Biol Rev Camb Philos Soc 2020; 96:673-691. [PMID: 33306257 DOI: 10.1111/brv.12672] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022]
Abstract
Evolutionary convergence provides natural opportunities to investigate how, when, and why novel traits evolve. Many convergent traits are complex, highlighting the importance of explicitly considering convergence at different levels of biological organization, or 'multi-level convergent evolution'. To investigate multi-level convergent evolution, we propose a holistic and hierarchical framework that emphasizes breaking down traits into several functional modules. We begin by identifying long-standing questions on the origins of complexity and the diverse evolutionary processes underlying phenotypic convergence to discuss how they can be addressed by examining convergent systems. We argue that bioluminescence, a complex trait that evolved dozens of times through either novel mechanisms or conserved toolkits, is particularly well suited for these studies. We present an updated estimate of at least 94 independent origins of bioluminescence across the tree of life, which we calculated by reviewing and summarizing all estimates of independent origins. Then, we use our framework to review the biology, chemistry, and evolution of bioluminescence, and for each biological level identify questions that arise from our systematic review. We focus on luminous organisms that use the shared luciferin substrates coelenterazine or vargulin to produce light because these organisms convergently evolved bioluminescent proteins that use the same luciferins to produce bioluminescence. Evolutionary convergence does not necessarily extend across biological levels, as exemplified by cases of conservation and disparity in biological functions, organs, cells, and molecules associated with bioluminescence systems. Investigating differences across bioluminescent organisms will address fundamental questions on predictability and contingency in convergent evolution. Lastly, we highlight unexplored areas of bioluminescence research and advances in sequencing and chemical techniques useful for developing bioluminescence as a model system for studying multi-level convergent evolution.
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Affiliation(s)
- Emily S Lau
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, U.S.A
| | - Todd H Oakley
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, U.S.A
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33
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Saeed M. Fractal genomics of SOD1 evolution. Immunogenetics 2020; 72:439-445. [PMID: 33237378 DOI: 10.1007/s00251-020-01184-4] [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: 09/11/2020] [Accepted: 10/28/2020] [Indexed: 10/22/2022]
Abstract
To understand the fundamental processes of gene evolution such as the impact of point mutations and segmental duplications on statistical topography, superoxide dismutase-1 (SOD1) orthologous sequences (n = 50) are studied. These demonstrate scale invariant self-similarity patterns and long-range correlations (LRCs) indicating fractal organization. Phylogenetic hierarchies change when SOD1 orthologs are grouped according to fractal measures, indicating that statistical topographies can be used to study gene evolution. Sliding window k-mer analysis show that majority of k-mers across all SOD1 orthologs are unique, with very few duplications. Orthologs from simpler species contribute minimally (< 1% of k-mers) to more complex species. Both simple and complex random processes fail to produce significant matching k-mer sequences for SOD1 orthologs. Point mutations causing amyotrophic lateral sclerosis do not impact the fractal organization of human SOD1. Hence, SOD1 did not evolve by a patchwork of repetitive sequences modified by point mutations. Moreover, fractal and other methods described here can be used to study the origin and evolution of genomes.
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34
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Mas A, Lagadeuc Y, Vandenkoornhuyse P. Reflections on the Predictability of Evolution: Toward a Conceptual Framework. iScience 2020; 23:101736. [PMID: 33225244 PMCID: PMC7666346 DOI: 10.1016/j.isci.2020.101736] [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] [Indexed: 02/06/2023] Open
Abstract
Evolution is generally considered to be unpredictable because genetic variations are known to occur randomly. However, remarkable patterns of repeated convergent evolution are observed, for instance, loss of pigments by organisms living in caves. Analogous phenotypes appear in similar environments, sometimes in response to similar constraints. Alongside randomness, a certain evolutionary determinism also exists, for instance, the selection of particular phenotypes subjected to particular environmental constraints in the “evolutionary funnel.” We pursue the idea that eco-evolutionary specialization is in some way determinist. The conceptual framework of phenotypic changes entailing specialization presented in this essay explains how evolution can be predicted. We also discuss how the predictability of evolution could be tested using the case of metabolic specialization through gene losses. We also put forward that microorganisms could be key models to test and possibly make headway evolutionary predictions and knowledge about evolution.
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Affiliation(s)
- Alix Mas
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Yvan Lagadeuc
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
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35
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Bainbridge HE, Brien MN, Morochz C, Salazar PA, Rastas P, Nadeau NJ. Limited genetic parallels underlie convergent evolution of quantitative pattern variation in mimetic butterflies. J Evol Biol 2020; 33:1516-1529. [DOI: 10.1111/jeb.13704] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/05/2020] [Accepted: 09/04/2020] [Indexed: 01/28/2023]
Affiliation(s)
- Hannah E. Bainbridge
- Department of Animal and Plant Sciences The University of Sheffield Sheffield UK
| | - Melanie N. Brien
- Department of Animal and Plant Sciences The University of Sheffield Sheffield UK
| | - Carlos Morochz
- Biology & Research Department Mashpi Lodge Mashpi Ecuador
| | - Patricio A. Salazar
- Department of Animal and Plant Sciences The University of Sheffield Sheffield UK
| | - Pasi Rastas
- Institute of Biotechnology University of Helsinki Helsinki Finland
| | - Nicola J. Nadeau
- Department of Animal and Plant Sciences The University of Sheffield Sheffield UK
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36
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Abstract
Form diversity is fueled by changes in the expression of genes that build organisms. New expression often results from the emergence of new DNA switches, known as transcriptional enhancers. Many enhancers are thought to appear through the recycling of older enhancers, a process called evolutionary co-option. Enhancer co-option is difficult to assess, and the molecular mechanisms explaining its prevalence are elusive. Using state-of-the-art quantification and analyses, we reveal that the sequences of an ancestral and a derived enhancer overlap extensively. They contain specific binding sites for regulators imparting spatial activities. We found that the two enhancers also share a site facilitating access to chromatin in a region where they overlap. The diversity of forms in multicellular organisms originates largely from the spatial redeployment of developmental genes [S. B. Carroll, Cell 134, 25–36 (2008)]. Several scenarios can explain the emergence of cis-regulatory elements that govern novel aspects of a gene expression pattern [M. Rebeiz, M. Tsiantis, Curr. Opin. Genet. Dev. 45, 115–123 (2017)]. One scenario, enhancer co-option, holds that a DNA sequence producing an ancestral regulatory activity also becomes the template for a new regulatory activity, sharing regulatory information. While enhancer co-option might fuel morphological diversification, it has rarely been documented [W. J. Glassford et al., Dev. Cell 34, 520–531 (2015)]. Moreover, if two regulatory activities are borne from the same sequence, their modularity, considered a defining feature of enhancers [J. Banerji, L. Olson, W. Schaffner, Cell 33, 729–740 (1983)], might be affected by pleiotropy. Sequence overlap may thereby play a determinant role in enhancer function and evolution. Here, we investigated this problem with two regulatory activities of the Drosophila gene yellow, the novel spot enhancer and the ancestral wing blade enhancer. We used precise and comprehensive quantification of each activity in Drosophila wings to systematically map their sequences along the locus. We show that the spot enhancer has co-opted the sequences of the wing blade enhancer. We also identified a pleiotropic site necessary for DNA accessibility of a shared regulatory region. While the evolutionary steps leading to the derived activity are still unknown, such pleiotropy suggests that enhancer accessibility could be one of the molecular mechanisms seeding evolutionary co-option.
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QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants. G3-GENES GENOMES GENETICS 2020; 10:2411-2421. [PMID: 32430305 PMCID: PMC7341141 DOI: 10.1534/g3.120.401122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Linkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. While it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs of known causal genes as the training set. The model trained with orthologs could recall about 64% of Arabidopsis and 83% of rice causal genes when the top 20% ranked genes were considered, which is similar to the performance of models trained with known causal genes. The average precision was 0.027 for Arabidopsis and 0.029 for rice. We further extended the algorithm to include polymorphisms in conserved non-coding sequences and gene presence/absence variation as additional features. Using this algorithm, QTG-Finder2, we trained and cross-validated Sorghum bicolor and Setaria viridis models. The S. bicolor model was validated by causal genes curated from the literature and could recall 70% of causal genes when the top 20% ranked genes were considered. In addition, we applied the S. viridis model and public transcriptome data to prioritize a plant height QTL and identified 13 candidate genes. QTL-Finder2 can accelerate the discovery of causal genes in any plant species and facilitate agricultural trait improvement.
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Machnicki AL, Reno PL. Great apes and humans evolved from a long-backed ancestor. J Hum Evol 2020; 144:102791. [DOI: 10.1016/j.jhevol.2020.102791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
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Monteil CL, Grouzdev DS, Perrière G, Alonso B, Rouy Z, Cruveiller S, Ginet N, Pignol D, Lefevre CT. Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria. THE ISME JOURNAL 2020; 14:1783-1794. [PMID: 32296121 PMCID: PMC7305187 DOI: 10.1038/s41396-020-0647-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/27/2022]
Abstract
Under the same selection pressures, two genetically divergent populations may evolve in parallel toward the same adaptive solutions. Here, we hypothesized that magnetotaxis (i.e., magnetically guided chemotaxis) represents a key adaptation to micro-oxic habitats in aquatic sediments and that its parallel evolution homogenized the phenotypes of two evolutionary divergent clusters of freshwater spirilla. All magnetotactic bacteria affiliated to the Magnetospirillum genus (Alphaproteobacteria class) biomineralize the same magnetic particle chains and share highly similar physiological and ultrastructural features. We looked for the processes that could have contributed at shaping such an evolutionary pattern by reconciling species and gene trees using newly sequenced genomes of Magnetospirillum related bacteria. We showed that repeated horizontal gene transfers and homologous recombination of entire operons contributed to the parallel evolution of magnetotaxis. We propose that such processes could represent a more parsimonious and rapid solution for adaptation compared with independent and repeated de novo mutations, especially in the case of traits as complex as magnetotaxis involving tens of interacting proteins. Besides strengthening the idea about the importance of such a function in micro-oxic habitats, these results reinforce previous observations in experimental evolution suggesting that gene flow could alleviate clonal interference and speed up adaptation under some circumstances.
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Affiliation(s)
- Caroline L Monteil
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France.
| | - Denis S Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Université Claude Bernard - Lyon 1, 69622, Villeurbanne, France
| | - Béatrice Alonso
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France
| | - Zoé Rouy
- LABGeM, Genomique Metabolique, CEA, Genoscope, Institut Francois Jacob, CNRS, Universite d'Evry, Universite Paris-Saclay, Evry, France
| | - Stéphane Cruveiller
- LABGeM, Genomique Metabolique, CEA, Genoscope, Institut Francois Jacob, CNRS, Universite d'Evry, Universite Paris-Saclay, Evry, France
| | - Nicolas Ginet
- Aix Marseille University, CNRS, LCB, Marseille, France
| | - David Pignol
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France
| | - Christopher T Lefevre
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France.
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Hou Y, Qi F, Bai X, Ren T, Shen X, Chu Q, Zhang X, Lu X. Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals. BMC Genomics 2020; 21:204. [PMID: 32131728 PMCID: PMC7057487 DOI: 10.1186/s12864-020-6613-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 02/24/2020] [Indexed: 12/19/2022] Open
Abstract
Background In response to ecological niche of domestication, domesticated mammals and birds developed adaptively phenotypic homoplasy in behavior modifications like fearlessness, altered sociability, exploration and cognition, which partly or indirectly result in consequences for economic productivity. Such independent adaptations provide an excellent model to investigate molecular mechanisms and patterns of evolutionary convergence driven by artificial selection. Results First performing population genomic and brain transcriptional comparisons in 68 wild and domesticated chickens, we revealed evolutionary trajectories, genetic architectures and physiologic bases of adaptively behavioral alterations. To extensively decipher molecular convergence on behavioral changes thanks to domestication, we investigated selection signatures in hundreds of genomes and brain transcriptomes across chicken and 6 other domesticated mammals. Although no shared substitution was detected, a common enrichment of the adaptive mutations in regulatory sequences was observed, presenting significance to drive adaptations. Strong convergent pattern emerged at levels of gene, gene family, pathway and network. Genes implicated in neurotransmission, semaphorin, tectonic protein and modules regulating neuroplasticity were central focus of selection, supporting molecular repeatability of homoplastic behavior reshapes. Genes at nodal positions in trans-regulatory networks were preferably targeted. Consistent down-regulation of majority brain genes may be correlated with reduced brain size during domestication. Up-regulation of splicesome genes in chicken rather mammals highlights splicing as an efficient way to evolve since avian-specific genomic contraction of introns and intergenics. Genetic burden of domestication elicits a general hallmark. The commonly selected genes were relatively evolutionary conserved and associated with analogous neuropsychiatric disorders in human, revealing trade-off between adaption to life with human at the cost of neural changes affecting fitness in wild. Conclusions After a comprehensive investigation on genomic diversity and evolutionary trajectories in chickens, we revealed basis, pattern and evolutionary significance of molecular convergence in domesticated bird and mammals, highlighted the genetic basis of a compromise on utmost adaptation to the lives with human at the cost of high risk of neurophysiological changes affecting animals’ fitness in wild.
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Affiliation(s)
- Yali Hou
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China. .,China National Center for Bioinformation, Beijing, People's Republic of China.
| | - Furong Qi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.,China National Center for Bioinformation, Beijing, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xue Bai
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.,China National Center for Bioinformation, Beijing, People's Republic of China
| | - Tong Ren
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xu Shen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Xiquan Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China.
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, People's Republic of China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China.
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Larter M, Dunbar-Wallis A, Berardi AE, Smith SD. Convergent Evolution at the Pathway Level: Predictable Regulatory Changes during Flower Color Transitions. Mol Biol Evol 2020; 35:2159-2169. [PMID: 29878153 DOI: 10.1093/molbev/msy117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The predictability of evolution, or whether lineages repeatedly follow the same evolutionary trajectories during phenotypic convergence remains an open question of evolutionary biology. In this study, we investigate evolutionary convergence at the biochemical pathway level and test the predictability of evolution using floral anthocyanin pigmentation, a trait with a well-understood genetic and regulatory basis. We reconstructed the evolution of floral anthocyanin content across 28 species of the Andean clade Iochrominae (Solanaceae) and investigated how shifts in pigmentation are related to changes in expression of seven key anthocyanin pathway genes. We used phylogenetic multivariate analysis of gene expression to test for phenotypic and developmental convergence at a macroevolutionary scale. Our results show that the four independent losses of the ancestral pigment delphinidin involved convergent losses of expression of the three late pathway genes (F3'5'h, Dfr, and Ans). Transitions between pigment types affecting floral hue (e.g., blue to red) involve changes to the expression of branching genes F3'h and F3'5'h, while the expression levels of early steps of the pathway are strongly conserved in all species. These patterns support the idea that the macroevolution of floral pigmentation follows predictable evolutionary trajectories to reach convergent phenotype space, repeatedly involving regulatory changes. This is likely driven by constraints at the pathway level, such as pleiotropy and regulatory structure.
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Affiliation(s)
- Maximilian Larter
- Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Boulder, CO
| | - Amy Dunbar-Wallis
- Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Boulder, CO
| | - Andrea E Berardi
- Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Boulder, CO.,Department of Biology, Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Boulder, CO
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VanKuren NW, Massardo D, Nallu S, Kronforst MR. Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations. Mol Biol Evol 2020; 36:2842-2853. [PMID: 31504750 DOI: 10.1093/molbev/msz194] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptation. However, the causes of gene reuse remain unclear. A small number of large-effect Mendelian loci control a huge diversity of mimetic butterfly wing color patterns, but reasons for their reuse are difficult to identify because the genetic basis of mimicry has primarily been studied in two systems with correlated factors: female-limited Batesian mimicry in Papilio swallowtails (Papilionidae) and non-sex-limited Müllerian mimicry in Heliconius longwings (Nymphalidae). Here, we break the correlation between phylogenetic relationship and sex-limited mimicry by identifying loci controlling female-limited mimicry polymorphism Hypolimnas misippus (Nymphalidae) and non-sex-limited mimicry polymorphism in Papilio clytia (Papilionidae). The Papilio clytia polymorphism is controlled by the genome region containing the gene cortex, the classic P supergene in Heliconius numata, and loci controlling color pattern variation across Lepidoptera. In contrast, female-limited mimicry polymorphism in Hypolimnas misippus is associated with a locus not previously implicated in color patterning. Thus, although many species repeatedly converged on cortex and its neighboring genes over 120 My of evolution of diverse color patterns, female-limited mimicry polymorphisms each evolved using a different gene. Our results support conclusions that gene reuse occurs mainly within ∼10 My and highlight the puzzling diversity of genes controlling seemingly complex female-limited mimicry polymorphisms.
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Affiliation(s)
| | - Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
| | - Sumitha Nallu
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
| | - Marcus R Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
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The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes. Genes (Basel) 2019; 10:genes10121027. [PMID: 31835491 PMCID: PMC6947334 DOI: 10.3390/genes10121027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/01/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022] Open
Abstract
Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two Takifugu are likely the same, but the genes used for the similar phenotype in Takifugu and distantly related fishes are not the same. Meanwhile, Fgfrl1, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since Fgfr1a1, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to Takifugu, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development.
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Baeckens S, Goeyers C, Van Damme R. Convergent Evolution of Claw Shape in a Transcontinental Lizard Radiation. Integr Comp Biol 2019; 60:10-23. [DOI: 10.1093/icb/icz151] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
AbstractSpecies occupying similar selective environments often share similar phenotypes as the result of natural selection. Recent discoveries, however, have led to the understanding that phenotypes may also converge for other reasons than recurring selection. We argue that the vertebrate claw system constitutes a promising but understudied model system for testing the adaptive nature of phenotypic, functional, and genetic convergence. In this study, we combine basic morphometrics and advanced techniques in form analysis to examine claw shape divergence in a transcontinental lizard radiation (Lacertidae). We find substantial interspecific variation in claw morphology and phylogenetic comparative statistics reveal a strong correlation with structural habitat use: ground-dwelling species living in open areas are equipped with long, thick, weakly curved, slender-bodied claws, whereas climbing species carry high, short, strongly curved, full-bodied claws. Species occupying densely vegetated habitats tend to carry intermediately shaped claws. Evolutionary models suggest that claw shape evolves toward multiple adaptive peaks, with structural habitat use pulling species toward a specific selective optimum. Contrary to findings in several other vertebrate taxa, our analyses indicate that environmental pressures, not phylogenetic relatedness, drive convergent evolution of similarly shaped claws in lacertids. Overall, our study suggests that lacertids independently evolved similarly shaped claws as an adaptation to similar structural environments in order to cope with the specific locomotory challenges posed by the habitat. Future biomechanical studies that link form and function in combination with genomic and development research will prove valuable in better understanding the adaptive significance of claw shape divergence.
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Affiliation(s)
- Simon Baeckens
- Functional Morphology Lab, Department of Biology, University of Antwerp, Wilrijk, Belgium
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Charlotte Goeyers
- Functional Morphology Lab, Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Raoul Van Damme
- Functional Morphology Lab, Department of Biology, University of Antwerp, Wilrijk, Belgium
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Selection and gene flow shape niche-associated variation in pheromone response. Nat Ecol Evol 2019; 3:1455-1463. [PMID: 31548647 PMCID: PMC6764921 DOI: 10.1038/s41559-019-0982-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/14/2019] [Indexed: 11/18/2022]
Abstract
From quorum sensing in bacteria to pheromone signaling in social insects, chemical communication mediates interactions among individuals in a local population. In Caenorhabditis elegans, ascaroside pheromones can dictate local population density, in which high levels of pheromones inhibit the reproductive maturation of individuals. Little is known about how natural genetic diversity affects the pheromone responses of individuals from diverse habitats. Here, we show that a niche-associated variation in pheromone receptor genes contributes to natural differences in pheromone responses. We identified putative loss-of-function deletions that impair duplicated pheromone receptor genes (srg-36 and srg-37), which were shown previously to be lost in population-dense laboratory cultures. A common natural deletion in srg-37 arose recently from a single ancestral population that spread throughout the world and underlies reduced pheromone sensitivity across the global C. elegans population. We found that many local populations harbor individuals with wild-type or a deletion allele of srg-37, suggesting that balancing selection has maintained the recent variation in this pheromone receptor gene. The two srg-37 genotypes are associated with niche diversity underlying boom-and-bust population dynamics. We hypothesize that human activities likely contributed to the gene flow and balancing selection of srg-37 variation through facilitating migration of species and providing favorable niche for recently arose srg-37 deletion.
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46
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Yudin N, Larkin DM. Shared Signatures of Selection Related to Adaptation and Acclimation in Local Cattle and Sheep Breeds from Russia. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Morris J, Navarro N, Rastas P, Rawlins LD, Sammy J, Mallet J, Dasmahapatra KK. The genetic architecture of adaptation: convergence and pleiotropy in Heliconius wing pattern evolution. Heredity (Edinb) 2019; 123:138-152. [PMID: 30670842 PMCID: PMC6781118 DOI: 10.1038/s41437-018-0180-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 12/14/2022] Open
Abstract
Unravelling the genetic basis of adaptive traits is a major challenge in evolutionary biology. Doing so informs our understanding of evolution towards an adaptive optimum, the distribution of locus effect sizes, and the influence of genetic architecture on the evolvability of a trait. In the Müllerian co-mimics Heliconius melpomene and Heliconius erato some Mendelian loci affecting mimicry shifts are well known. However, several phenotypes in H. melpomene remain to be mapped, and the quantitative genetics of colour pattern variation has rarely been analysed. Here we use quantitative trait loci (QTL) analyses of crosses between H. melpomene races from Peru and Suriname to map, for the first time, the control of the broken band phenotype to WntA and identify a ~100 kb region controlling this variation. Additionally, we map variation in basal forewing red-orange pigmentation to a locus centred around the gene ventral veins lacking (vvl). The locus also appears to affect medial band shape variation as it was previously known to do in H. erato. This adds to the list of homologous regions controlling convergent phenotypes between these two species. Finally we show that Heliconius wing-patterning genes are strikingly pleiotropic among wing pattern traits. Our results demonstrate how genetic architecture can shape, aid and constrain adaptive evolution.
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Affiliation(s)
- Jake Morris
- Department of Biology, University of York, Heslington, YO10 5DD, UK.
| | - Nicolas Navarro
- EPHE, PSL University, 21000, Dijon, France
- Biogéosciences, UMR CNRS 6282, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Pasi Rastas
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Lauren D Rawlins
- Department of Environment and Geography, University of York, Heslington, YO10 5DD, UK
| | - Joshua Sammy
- Department of Biology, University of York, Heslington, YO10 5DD, UK
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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Larter M, Dunbar‐Wallis A, Berardi AE, Smith SD. Developmental control of convergent floral pigmentation across evolutionary timescales. Dev Dyn 2019; 248:1091-1100. [DOI: 10.1002/dvdy.82] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 11/07/2022] Open
Affiliation(s)
- Maximilian Larter
- Department of Ecology and Evolutionary BiologyUniversity of Colorado‐Boulder Boulder Colorado
| | - Amy Dunbar‐Wallis
- Department of Ecology and Evolutionary BiologyUniversity of Colorado‐Boulder Boulder Colorado
| | - Andrea E. Berardi
- Department of Ecology and Evolutionary BiologyUniversity of Colorado‐Boulder Boulder Colorado
- Institute of Plant SciencesUniversity of Bern Bern Switzerland
| | - Stacey D. Smith
- Department of Ecology and Evolutionary BiologyUniversity of Colorado‐Boulder Boulder Colorado
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Sackton TB, Clark N. Convergent evolution in the genomics era: new insights and directions. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190102. [PMID: 31154976 DOI: 10.1098/rstb.2019.0102] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
| | - Nathan Clark
- 2 Computational and Systems Biology, University of Pittsburgh , PA , USA
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50
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Lammers M, Kraaijeveld K, Mariën J, Ellers J. Gene expression changes associated with the evolutionary loss of a metabolic trait: lack of lipogenesis in parasitoids. BMC Genomics 2019; 20:309. [PMID: 31014246 PMCID: PMC6480896 DOI: 10.1186/s12864-019-5673-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/08/2019] [Indexed: 12/24/2022] Open
Abstract
Background Trait loss is a pervasive phenomenon in evolution, yet the underlying molecular causes have been identified in only a handful of cases. Most of these cases involve loss-of-function mutations in one or more trait-specific genes. However, in parasitoid insects the evolutionary loss of a metabolic trait is not associated with gene decay. Parasitoids have lost the ability to convert dietary sugars into fatty acids. Earlier research suggests that lack of lipogenesis in the parasitoid wasp Nasonia vitripennis is caused by changes in gene regulation. Results We compared transcriptomic responses to sugar-feeding in the non-lipogenic parasitoid species Nasonia vitripennis and the lipogenic Drosophila melanogaster. Both species adjusted their metabolism within 4 hours after sugar-feeding, but there were sharp differences between the expression profiles of the two species, especially in the carbohydrate and lipid metabolic pathways. Several genes coding for key enzymes in acetyl-CoA metabolism, such as malonyl-CoA decarboxylase (mcd) and HMG-CoA synthase (hmgs) differed in expression between the two species. Their combined action likely blocks lipogenesis in the parasitoid species. Network-based analysis showed connectivity of genes to be negatively correlated to the fold change of gene expression. Furthermore, genes involved in the fatty acid metabolic pathway were more connected than the set of genes of all metabolic pathways combined. Conclusion High connectivity of lipogenesis genes is indicative of pleiotropic effects and could explain the absence of gene degradation. We conclude that modification of expression levels of only a few little-connected genes, such as mcd, is sufficient to enable complete loss of lipogenesis in N. vitripennis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5673-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark Lammers
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Ken Kraaijeveld
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Janine Mariën
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Jacintha Ellers
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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