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Bohutínská M, Peichel CL. Divergence time shapes gene reuse during repeated adaptation. Trends Ecol Evol 2024; 39:396-407. [PMID: 38155043 DOI: 10.1016/j.tree.2023.11.007] [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: 08/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.
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Affiliation(s)
- Magdalena Bohutínská
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland; Department of Botany, Faculty of Science, Charles University, Prague, 12800, Czech Republic.
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
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2
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Ahatović Hajro A, Hasanović M, Murtić S, Kalajdžić A, Pojskić N, Durmić-Pašić A. Serpentine environment prevails over geographic distribution in shaping the genetic diversity of Medicago lupulina L. Mol Genet Genomics 2024; 299:28. [PMID: 38472470 DOI: 10.1007/s00438-024-02124-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/03/2024] [Indexed: 03/14/2024]
Abstract
Edaphic conditions of serpentine soils, naturally rich in heavy metals, act as a strong selection pressure that shapes specific metal-tolerant ecotypes. Medicago lupulina L. (black medick) is not only a widespread plant species that prefers calcareous and dry soil types but also grows at the borders of serpentine formations. It can also be found in waste and disturbed habitats. This is a species with reported phytoremediation potential, however, there is no published data regarding the impact of the environment on the genetic distribution of this species. The aim of our research was to explore how selection pressure of serpentine soils affects genetic diversity of M. lupulina and to test heavy-metal accumulation capacity of this species. Specimens of 11 M. lupulina populations were collected from serpentine outcrops located in Central and Eastern Bosnia as well as from non-serpentine sites. Soil and plant samples were analyzed for the total contents of heavy metals using air-acetylene flame atomic absorption spectroscopy. Genetic diversity was analyzed using AFLP (Amplified Fragment Length Polymorphism) markers. Serpentine soils showed high nickel, cobalt, chromium and iron concentrations. Nickel and manganese concentrations in soil samples and plant material showed statistically significant correlation. Although plants in two populations show the ability to extract Ni, M. lupulina does not show hyperaccumulating properties. Despite severe selective pressure, genetic diversity in serpentine populations is not reduced. Analyses of intrapopulation and interpopulation genetic diversity showed significant genetic differentiation among populations which is not related to their geographic distance. Population from non-metalliferous soil showed clear separation from all other populations. Diversity data suggest that serpentine populations maintain genetic diversity by undetected mechanisms and that edaphic factors rather than geography influence genetic structure analyzed M. lupulina populations.
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Affiliation(s)
- Anesa Ahatović Hajro
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina.
| | - Mujo Hasanović
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Senad Murtić
- Faculty of Agriculture and Food Sciences, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Abdurahim Kalajdžić
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Naris Pojskić
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Adaleta Durmić-Pašić
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Zmaja Od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
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3
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Lipánová V, Kabátová KN, Zeisek V, Kolář F, Chrtek J. Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates. Mol Phylogenet Evol 2023; 189:107940. [PMID: 37820762 DOI: 10.1016/j.ympev.2023.107940] [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: 01/16/2023] [Revised: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
One of the major goals of contemporary evolutionary biology is to elucidate the relative roles of allopatric and ecological differentiation and polyploidy in speciation. In this study, we address the taxonomically intricate Sabulina verna group, which has a disjunct Arctic-alpine postglacial range in Europe and occupies a broad range of ecological niches, including substrates toxic to plants. Using genome-wide ddRAD sequencing combined with morphometric analyses based on extensive sampling of 111 natural populations, we aimed to disentangle internal evolutionary relationships and examine their correspondence with the pronounced edaphic and ploidy diversity within the group. We identified two spatially distinct groups of diploids: a widespread Arctic-alpine group and a spatially restricted yet diverse Balkan group. Most tetraploids exhibited a considerably admixed ancestry derived from both these groups, suggesting their allopolyploid origin. Four genetic clusters in congruence with geography and mostly supported by morphological traits were recognized in the diploid Arctic-alpine group. Tetraploids are split into two distinct and geographically vicariant groups, indicating their repeated polytopic origin. Furthermore, our results also revealed at least five-fold parallel colonization of toxic substrates (serpentine and metalliferous), altogether demonstrating a complex interaction between geography, challenging substrates and polyploidy in the evolution of the group. Finally, we propose a new taxonomic treatment of this complex.
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Affiliation(s)
- Veronika Lipánová
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | | | - Vojtěch Zeisek
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Jindřich Chrtek
- Department of Botany, Faculty of Science, Charles University, 128 00 Prague, Czech Republic; Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic.
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4
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Koner S, Chen JS, Rathod J, Hussain B, Hsu BM. Unravelling the ultramafic rock-driven serpentine soil formation leading to the geo-accumulation of heavy metals: An impact on the resident microbiome, biogeochemical cycling and acclimatized eco-physiological profiles. ENVIRONMENTAL RESEARCH 2023; 216:114664. [PMID: 36336091 DOI: 10.1016/j.envres.2022.114664] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
In the present study, we have underpinned the serpentine rock, serpentinized ultramafic soil and rhizosphere's microbial communities, signifying their heavy metals-exposed taxa signatures and functional repertoires in comparison to non-serpentine soils. The results revealed that the serpentine rock embedded soil highlighted the geo-accumulation of higher amount of Cr and Ni impacting soil microbial diversity negatively by metal stress-driven selection. Biolog Ecoplate CLPP defined a restricted spectrum of C-utilization in the higher heavy metal-containing serpentine samples compared to non-serpentine. The linear discriminant analysis (LDA) score identified a higher abundance of Desulfobacterota, Opitutales, and Bacteroidales in low Cr and Ni-stressed non-serpentine-exposed samples. Whereas the abundance of Propionibacteriales and Actinobacteriota were significantly enriched in the serpentine niche. Further, the C, N, S, Fe, and methane biogeochemical cycles linked functional members were identified, and showing higher functional diversity in low Cr and Ni concentration-containing rhizosphere JS-soils. The Pearson correlation coefficient (r) value confirmed the abundance of functional members linked to specific biogeochemical cycle, positively correlated with relevant pathway enrichment. Ultimately, this study highlighted the heavy metal stress within a serpentine setting that could limit the resident microbial community's metabolic diversity and further select the bacteria that could thrive in the serpentine-associated heavy metal-stressed soils. These acclimatized microbes could pave the way for the future applications in the soil conservation and management.
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Affiliation(s)
- Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Jagat Rathod
- Department of Environmental Biotechnology, Gujarat Biotechnology University, Near Gujarat International Finance and Tec (GIFT)-City, Gandhinagar, 382355, Gujarat, India
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Center for Innovative on Aging Society, National Chung Cheng University, Chiayi County, Taiwan.
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5
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Cohen JI, Ruane LG. Conservation genetics of Phlox hirsuta, a serpentine endemic. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01478-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Konečná V, Šustr M, Požárová D, Čertner M, Krejčová A, Tylová E, Kolář F. Genomic basis and phenotypic manifestation of (non-)parallel serpentine adaptation in Arabidopsis arenosa. Evolution 2022; 76:2315-2331. [PMID: 35950324 DOI: 10.1111/evo.14593] [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: 05/04/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 01/22/2023]
Abstract
Parallel evolution is common in nature and provides one of the most compelling examples of rapid environmental adaptation. In contrast to the recent burst of studies addressing genomic basis of parallel evolution, integrative studies linking genomic and phenotypic parallelism are scarce. Edaphic islands of toxic serpentine soils provide ideal systems for studying rapid parallel adaptation in plants, imposing strong, spatially replicated selection on recently diverged populations. We leveraged threefold independent serpentine adaptation of Arabidopsis arenosa and combined reciprocal transplants, ion uptake phenotyping, and available genome-wide polymorphisms to test if parallelism is manifested to a similar extent at both genomic and phenotypic levels. We found pervasive phenotypic parallelism in functional traits yet with varying magnitude of fitness differences that was congruent with neutral genetic differentiation between populations. Limited costs of serpentine adaptation suggest absence of soil-driven trade-offs. On the other hand, the genomic parallelism at the gene level was significant, although relatively minor. Therefore, the similarly modified phenotypes, for example, of ion uptake arose possibly by selection on different loci in similar functional pathways. In summary, we bring evidence for the important role of genetic redundancy in rapid adaptation involving traits with polygenic architecture.
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Affiliation(s)
- Veronika Konečná
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic.,Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Marek Šustr
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, 128 00, Czech Republic
| | - Doubravka Požárová
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic.,Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Anna Krejčová
- Faculty of Chemical Technology, University of Pardubice, Pardubice, 532 10, Czech Republic
| | - Edita Tylová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, 128 00, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic.,Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
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7
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Venkateswaran MR, Vadivel TE, Jayabal S, Murugesan S, Rajasekaran S, Periyasamy S. A review on network pharmacology based phytotherapy in treating diabetes- An environmental perspective. ENVIRONMENTAL RESEARCH 2021; 202:111656. [PMID: 34265348 DOI: 10.1016/j.envres.2021.111656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/19/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Diabetes has become common lifestyle disorder associated with obesity and cardiovascular diseases. Environmental factors like physical inactivity, polluted surroundings and unhealthy dieting also plays a vital role in diabetes pathogenesis. As the current anti-diabetic drugs possess unprecedented side effects, traditional herbal medicine can be used an alternative therapy. The paramount challenge with the herbal formulation usage is the lack of standardized procedure, entangled with little knowledge on drug safety and mechanism of drug action. Heavy metal contamination is a major environmental hazard where plants tend to accumulate toxic metals like nickel, chromium and lead through industrial and agricultural activities. It becomes inappropriate to use these plants for phytotherapy as it may affect the human health on long term consumption. This review discuss about the environmental risk factors related to diabetes and better implication of medicinal plants in anti-diabetic therapy using network pharmacology. It is an in silico analytical tool that helps to unravel the multi-targeted action of herbal formulations rich in secondary metabolites. Also, a special focus is attempted to pool the databases regarding the medicinal plants for diabetes and associated diseases, their bioactive compounds, possible diabetic targets, drug-target interaction and toxicology reports that may open an aisle in safer, effective and toxicity-free drug discovery.
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Affiliation(s)
- Meenakshi R Venkateswaran
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Tamil Elakkiya Vadivel
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Sasidharan Jayabal
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Selvakumar Murugesan
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Subbiah Rajasekaran
- Department of Biochemistry, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | - Sureshkumar Periyasamy
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India.
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Ke F, Vasseur L, Yi H, Yang L, Wei X, Wang B, Kang M. Gene flow, linked selection, and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists. Mol Ecol 2021; 31:104-118. [PMID: 34664755 DOI: 10.1111/mec.16226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022]
Abstract
Interpreting the formation of genomic variation landscape, especially genomic regions with elevated differentiation (i.e. islands), is fundamental to a better understanding of the genomic consequences of adaptation and speciation. Edaphic islands provide excellent systems for understanding the interplay of gene flow and selection in driving population divergence and speciation. However, discerning the relative contribution of these factors that modify patterns of genomic variation remains difficult. We analysed 132 genomes from five recently divergent species in Primulina genus, with four species distributed in Karst limestone habitats and the fifth one growing in Danxia habitats. We demonstrated that both gene flow and linked selection have contributed to genome-wide variation landscape, where genomic regions with elevated differentiation (i.e., islands) were largely derived by divergent sorting of ancient polymorphism. Specifically, we identified several lineage-specific genomic islands that might have facilitated adaptation of P. suichuanensis to Danxia habitats. Our study is amongst the first cases disentangling evolutionary processes that shape genomic variation of plant specialists, and demonstrates the important role of ancient polymorphism in the formation of genomic islands that potentially mediate adaptation and speciation of endemic plants in special soil habitats.
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Affiliation(s)
- Fushi Ke
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Liette Vasseur
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao Wei
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin, China
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles. Nat Commun 2021; 12:4979. [PMID: 34404804 PMCID: PMC8370997 DOI: 10.1038/s41467-021-25256-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/21/2021] [Indexed: 01/26/2023] Open
Abstract
Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms. Relative contributions of pre-existing versus de novo genomic variation to adaptation remain unclear. Here, the authors address this problem by examining the adaptation of autotetraploid Arabidopsis arenosa to serpentine soils and find that both types of variations contribute to rapid adaptation.
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