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Xu S, Shao S, Feng X, Li S, Zhang L, Wu W, Liu M, Tracy ME, Zhong C, Guo Z, Wu CI, Shi S, He Z. Adaptation in Unstable Environments and Global Gene Losses: Small but Stable Gene Networks by the May-Wigner Theory. Mol Biol Evol 2024; 41:msae059. [PMID: 38507653 PMCID: PMC10991078 DOI: 10.1093/molbev/msae059] [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: 01/12/2024] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
Although gene loss is common in evolution, it remains unclear whether it is an adaptive process. In a survey of seven major mangrove clades that are woody plants in the intertidal zones of daily environmental perturbations, we noticed that they generally evolved reduced gene numbers. We then focused on the largest clade of Rhizophoreae and observed the continual gene set reduction in each of the eight species. A great majority of gene losses are concentrated on environmental interaction processes, presumably to cope with the constant fluctuations in the tidal environments. Genes of the general processes for woody plants are largely retained. In particular, fewer gene losses are found in physiological traits such as viviparous seeds, high salinity, and high tannin content. Given the broad and continual genome reductions, we propose the May-Wigner theory (MWT) of system stability as a possible mechanism. In MWT, the most effective solution for buffering continual perturbations is to reduce the size of the system (or to weaken the total genic interactions). Mangroves are unique as immovable inhabitants of the compound environments in the land-sea interface, where environmental gradients (such as salinity) fluctuate constantly, often drastically. Extending MWT to gene regulatory network (GRN), computer simulations and transcriptome analyses support the stabilizing effects of smaller gene sets in mangroves vis-à-vis inland plants. In summary, we show the adaptive significance of gene losses in mangrove plants, including the specific role of promoting phenotype innovation and a general role in stabilizing GRN in unstable environments as predicted by MWT.
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Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Sen Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Lingjie Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Miles E Tracy
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cairong Zhong
- Institute of Wetland Research, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
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Madeira AG, Tsuda Y, Nagano Y, Iwasaki T, Zucchi MI, Kajita T, Mori GM. The role of oceanic currents in the dispersal and connectivity of the mangrove Rhizophora mangle on the Southwest Atlantic region. Mol Ecol Resour 2023. [PMID: 37173824 DOI: 10.1111/1755-0998.13807] [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: 11/26/2022] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
Dispersal is a crucial mechanism to living beings, allowing them to reach new resources such that populations and species can occupy new environments. However, directly observing the dispersal mechanisms of widespread species can be costly or even impractical, which is the case for mangrove trees. The influence of ocean currents on mangrove dispersal is increasingly evident; however, few studies mechanistically relate the patterns of population distribution with the dispersal by oceanic currents under an integrated framework. Here, we evaluate the role of oceanic currents on connectivity of Rhizophora mangle along the Southwest Atlantic. We inferred population genetic structure and migration rates, simulated the displacement of propagules and tested our hypotheses with Mantel tests and redundancy analysis. We observed populations structured in two major groups, north and south, which is corroborated by other studies with Rhizophora and other coastal plants. Inferred recent migration rates do not indicate ongoing gene flow between sites. Conversely, long-term migration rates were low across groups and contrasting dispersal patterns within each one, which is consistent with long-distance dispersal events. Our hypothesis tests suggest that both isolation by distance and isolation by oceanography (derived from the oceanic currents) can explain the neutral genetic variation of R. mangle in the region. Our findings expand current knowledge of mangrove connectivity and highlight how the association of molecular methods with oceanographic simulations improve the interpretation of the dispersal process. This integrative approach is a cost- and time-efficient strategy to include dispersal and connectivity data into marine protected areas planning and management.
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Affiliation(s)
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | | | | | - Tadashi Kajita
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
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Hodel RGJ, Soltis DE, Soltis PS. Hindcast‐validated species distribution models reveal future vulnerabilities of mangroves and salt marsh species. Ecol Evol 2022; 12:e9252. [PMID: 36188510 PMCID: PMC9484403 DOI: 10.1002/ece3.9252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
Rapid climate change is threatening biodiversity via habitat loss, range shifts, increases in invasive species, novel species interactions, and other unforeseen changes. Coastal and estuarine species are especially vulnerable to the impacts of climate change due to sea level rise and may be severely impacted in the next several decades. Species distribution modeling can project the potential future distributions of species under scenarios of climate change using bioclimatic data and georeferenced occurrence data. However, models projecting suitable habitat into the future are impossible to ground truth. One solution is to develop species distribution models for the present and project them to periods in the recent past where distributions are known to test model performance before making projections into the future. Here, we develop models using abiotic environmental variables to quantify the current suitable habitat available to eight Neotropical coastal species: four mangrove species and four salt marsh species. Using a novel model validation approach that leverages newly available monthly climatic data from 1960 to 2018, we project these niche models into two time periods in the recent past (i.e., within the past half century) when either mangrove or salt marsh dominance was documented via other data sources. Models were hindcast‐validated and then used to project the suitable habitat of all species at four time periods in the future under a model of climate change. For all future time periods, the projected suitable habitat of mangrove species decreased, and suitable habitat declined more severely in salt marsh species.
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Affiliation(s)
- Richard G. J. Hodel
- Department of Botany National Museum of Natural History Washington DC USA
- Department of Biology University of Florida Gainesville Florida USA
- Florida Museum of Natural History University of Florida Gainesville Florida USA
| | - Douglas E. Soltis
- Department of Biology University of Florida Gainesville Florida USA
- Florida Museum of Natural History University of Florida Gainesville Florida USA
- The Genetics Institute, University of Florida Gainesville Florida USA
| | - Pamela S. Soltis
- Florida Museum of Natural History University of Florida Gainesville Florida USA
- The Genetics Institute, University of Florida Gainesville Florida USA
- The Biodiversity Institute University of Florida Gainesville Florida USA
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de Deus Vidal Junior J, Mori GM, Cruz MV, da Silva MF, de Moura YA, de Souza AP. Differential Adaptive Potential and Vulnerability to Climate-Driven Habitat Loss in Brazilian Mangroves. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.763325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Geographic and environmental differences have been identified as factors influencing Brazilian mangrove trees' genetic diversity. Geographically, distinct species have convergent spatial genetic structures, indicating a limited gene flow between northern and southern populations. Environmentally, genomic studies and common garden experiments have found evidence of local adaptations along the latitudinal gradient of the Brazilian coast. However, little is known about how such adaptive heterogeneity could be affected by a rapidly changing climate in the coming decades, and the combination of deforestation and climate-induced habitat loss may affect these forests and their genetic diversity. Here, we applied two genomic-environmental association methods to model the turnover of potentially adaptive alleles for two dominant mangrove trees: Avicennia germinans and A. schaueriana. We analyzed a total of 134 individuals from six populations of A. germinans and 10 populations of A. schaueriana spanning the Brazilian coast from 1 °S to 28 °S. Gradient forest models identified temperature-related variables as the most important predictors for A. germinans outlier loci, whereas both temperature and precipitation were important for A. schaueriana. We modeled allele frequencies and projected them for future climatic scenarios to estimate adaptively driven vulnerability. We assessed climate-driven habitat loss through climate-only distribution models and calculated annual deforestation rates for each sampled region. Finally, to assess the vulnerability of individual populations, we combined the environmental suitability, deforestation data, and adaptive vulnerability projections. For both species, subtropical populations presented a higher vulnerability than equatorial populations to climate-driven habitat loss. We also identified deforestation rates at the sampled sites that were alarmingly higher than the global average mangrove deforestation rate. Our results provide improved estimates of the impacts of ongoing climate change and human-caused habitat loss on the distribution of mangroves and highlight the importance of site-based conservation strategies that consider individual subtropical and equatorial mangrove forests.
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Da Silva MF, Cruz MV, Vidal Júnior JDD, Zucchi MI, Mori GM, De Souza AP. Geographical and environmental contributions to genomic divergence in mangrove forests. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Assessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves occur along the continent–ocean interface of tropical and subtropical latitudes, regions considered inhospitable to many other types of plants. Here, we used landscape genomics approaches to investigate the relative contributions of geographical and environmental variables to the genetic variation of two black mangrove species, Avicennia schaueriana and Avicennia germinans, along the South American coast. Using single nucleotide polymorphisms, our results revealed an important role of ocean currents and geographical distance in the gene flow of A. schaueriana and an isolation-by-environment pattern in the organization of the genetic diversity of A. germinans. Additionally, for A. germinans, we observed significant correlations between genetic variation with evidence of selection and the influence of precipitation regimens, solar radiation and temperature patterns. These discoveries expand our knowledge about the evolution of mangrove trees and provide important information to predict future responses of coastal species to the expected global changes during this century.
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Affiliation(s)
- Michele Fernandes Da Silva
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - João De Deus Vidal Júnior
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Gustavo Maruyama Mori
- Institute of Biosciences, São Paulo State University (UNESP), São Vicente, SP, Brazil
| | - Anete Pereira De Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
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Winkler DE, Chapin KJ, Garmon JD, Gaut BS, Huxman TE. Sahara mustard as a major threat to desert biodiversity in the southwest United States and the need to integrate contemporary methods to understand its biology. Ecol Evol 2020; 10:14453-14455. [PMID: 33391728 PMCID: PMC7771142 DOI: 10.1002/ece3.6936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 11/18/2022] Open
Affiliation(s)
- Daniel E. Winkler
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
- Present address:
U.S. Geological SurveySouthwest Biological Science CenterMoabUTUSA
| | - Kenneth J. Chapin
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaLos AngelesUSA
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonUSA
| | | | - Brandon S. Gaut
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
| | - Travis E. Huxman
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
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Kennedy JP, Dangremond EM, Hayes MA, Preziosi RF, Rowntree JK, Feller IC. Hurricanes overcome migration lag and shape intraspecific genetic variation beyond a poleward mangrove range limit. Mol Ecol 2020; 29:2583-2597. [PMID: 32573031 DOI: 10.1111/mec.15513] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022]
Abstract
Expansion of many tree species lags behind climate change projections. Extreme storms can rapidly overcome this lag, especially for coastal species, but how will storm-driven expansion shape intraspecific genetic variation? Do storms provide recruits only from the nearest sources, or from more distant sources? Answers to these questions have ecological and evolutionary implications, but empirical evidence is absent from the literature. In 2017, Hurricane Irma provided an opportunity to address this knowledge gap at the northern range limit of the neotropical black mangrove (Avicennia germinans) on the Atlantic coast of Florida, USA. We observed massive post-hurricane increases in beach-stranded A. germinans propagules at, and past, this species' present day range margin when compared to a previously surveyed nonhurricane year. Yet, propagule dispersal does not guarantee subsequent establishment and reproductive success (i.e., effective dispersal). We also evaluated prior effective dispersal along this coastline with isolated A. germinans trees identified beyond the most northern established population. We used 12 nuclear microsatellite loci to genotype 896 hurricane-driven drift propagules from nine sites and 10 isolated trees from four sites, determined their sources of origin, and estimated dispersal distances. Almost all drift propagules and all isolated trees came from the nearest sources. This research suggests that hurricanes are a prerequisite for poleward range expansion of a coastal tree species and that storms can shape the expanding gene pool by providing almost exclusively range-margin genotypes. These insights and empirical estimates of hurricane-driven dispersal distances should improve our ability to forecast distributional shifts of coastal species.
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Affiliation(s)
- John Paul Kennedy
- Ecology and Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Emily M Dangremond
- Department of Biological, Physical, and Health Sciences, Roosevelt University, Chicago, IL, USA
| | - Matthew A Hayes
- Australian Rivers Institute - Coast & Estuaries, School of Environment & Science, Griffith University, Gold Coast, Queensland, Australia
| | - Richard F Preziosi
- Ecology and Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Jennifer K Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Ilka C Feller
- Smithsonian Environmental Research Center, Smithsonian Institution, Edgewater, MD, USA
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