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Dong X, Stokes MF, Hendry AP, Larsen LG, Dolby GA. Geo-evolutionary feedbacks: integrating rapid evolution and landscape change. Trends Ecol Evol 2024:S0169-5347(24)00119-8. [PMID: 38862356 DOI: 10.1016/j.tree.2024.05.008] [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: 02/19/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/13/2024]
Abstract
We develop a conceptual framework for geo-evolutionary feedbacks which describes the mutual interplay between landscape change and the evolution of traits of organisms residing on the landscape, with an emphasis on contemporary timeframes. Geo-evolutionary feedbacks can be realized via the direct evolution of geomorphic engineering traits or can be mediated by the evolution of trait variation that affects the population size and distribution of the specific geomorphic engineering organisms involved. Organisms that modify their local environments provide the basis for patch-scale geo-evolutionary feedbacks, whereas spatial self-organization provides a mechanism for geo-evolutionary feedbacks at the landscape scale. Understanding these likely prevalent geo-evolutionary feedbacks, that occur at timescales similar to anthropogenic climate change, will be essential to better predict landscape adaptive capacity and change.
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Affiliation(s)
- Xiaoli Dong
- Department of Environmental Science and Policy, University of California, Davis, CA, USA.
| | - Maya F Stokes
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Andrew P Hendry
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Laurel G Larsen
- Department of Geography and Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Greer A Dolby
- Department of Biology, University of Alabama, Birmingham, AL, USA
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2
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Chen J, Jiang K, Qi T, Li Y, Liu H, Xue H, Ye Z, Wang S, Bu W. Integrative taxonomy, phylogenetics and historical biogeography of subgenus Aeschyntelus Stål, 1872 (Hemiptera: Heteroptera: Rhopalidae). Mol Phylogenet Evol 2024:108121. [PMID: 38851309 DOI: 10.1016/j.ympev.2024.108121] [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: 03/29/2024] [Revised: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
The subgenus Aeschyntelus includes six species that show variations in body color and shape, thus making it difficult to identify them based on morphological identification alone. To date, no genetic study has evaluated species within this genus. Herein, we collected 171 individuals from 90 localities of Rhopalus and employed an integrative taxonomic approach that incorporated morphological data, mitochondrial genomic data (COI, whole mitochondrial data) and nuclear genomic data (18S + 28S rRNAs, nuclear genome-wide SNPs) to delineate species boundaries. Our analyses confirmed the status of nine described species of Rhopalus and proposed the recognition of one new species known as Rhopalus qinlinganus sp. nov., which is classified within the subgenus Aeschyntelus. Discrepancies arising from nuclear and mitochondrial data suggest the presence of mito-nuclear discordance. Specifically, mitochondrial data indicated admixture within Clade A, comprising R. kerzhneri and R. latus, whereas genome-wide SNPs unambiguously identified two separate species, aligning with morphological classification. Conversely, mitochondrial data clearly distinguished Clade B- consisting of R. sapporensis into two lineages, whereas genome-wide SNPs unequivocally identified a single species. Our study also provides insights into the evolutionary history of Aeschyntelus, thus indicating that it likely originated in East Asia during the middle Miocene. The development of Aeschyntelus biodiversity in the southwestern mountains of China occurred via an uplift-driven diversification process. Our findings highlight the necessity of integrating both morphological and multiple molecular datasets for precise species identification, particularly when delineating closely related species. Additionally, it reveals the important role of mountain orogenesis on speciation within the southwestern mountains of China.
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Affiliation(s)
- Juhong Chen
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Kun Jiang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; School of Ecology and Environment, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Tianyi Qi
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Yanfei Li
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Huaxi Liu
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Shujing Wang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.
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3
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Yang FS, Liu M, Guo X, Xu C, Jiang J, Mu W, Fang D, Xu YC, Zhang FM, Wang YH, Yang T, Chen H, Sahu SK, Li R, Wang G, Wang Q, Xu X, Ge S, Liu H, Guo YL. Signatures of Adaptation and Purifying Selection in Highland Populations of Dasiphora fruticosa. Mol Biol Evol 2024; 41:msae099. [PMID: 38768215 PMCID: PMC11156201 DOI: 10.1093/molbev/msae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
High mountains harbor a considerable proportion of biodiversity, but we know little about how diverse plants adapt to the harsh environment. Here we finished a high-quality genome assembly for Dasiphora fruticosa, an ecologically important plant distributed in the Qinghai-Tibetan Plateau and lowland of the Northern Hemisphere, and resequenced 592 natural individuals to address how this horticulture plant adapts to highland. Demographic analysis revealed D. fruticosa underwent a bottleneck after Naynayxungla Glaciation. Selective sweep analysis of two pairs of lowland and highland populations identified 63 shared genes related to cell wall organization or biogenesis, cellular component organization, and dwarfism, suggesting parallel adaptation to highland habitats. Most importantly, we found that stronger purging of estimated genetic load due to inbreeding in highland populations apparently contributed to their adaptation to the highest mountain. Our results revealed how plants could tolerate the extreme plateau, which could provide potential insights for species conservation and crop breeding.
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Affiliation(s)
- Fu-Sheng Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Juan Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weixue Mu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Hui Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Hongyun Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Ruirui Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Guanlong Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Qiang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Shipley BR, McGuire JL. The environmental conditions of endemism hotspots shape the functional traits of mammalian assemblages. Proc Biol Sci 2024; 291:20232773. [PMID: 38471553 DOI: 10.1098/rspb.2023.2773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Endemic (small-ranged) species are distributed non-randomly across the globe. Regions of high topography and stable climates have higher endemism than flat, climatically unstable regions. However, it is unclear how these environmental conditions interact with and filter mammalian traits. Here, we characterize the functional traits of highly endemic mammalian assemblages in multiple ways, testing the hypothesis that these assemblages are trait-filtered (less functionally diverse) and dominated by species with traits associated with small range sizes. Compiling trait data for more than 5000 mammal species, we calculated assemblage means and multidimensional functional metrics to evaluate the distribution of traits across each assemblage. We then related these metrics to the endemism of global World Wildlife Fund ecoregions using linear models and phylogenetic fourth-corner regression. Highly endemic mammalian assemblages had small average body masses, low fecundity, short lifespans and specialized habitats. These traits relate to the stable climate and rough topography of endemism hotspots and to mammals' ability to expand their ranges, suggesting that the environmental conditions of endemism hotspots allowed their survival. Furthermore, species living in endemism hotspots clustered near the edges of their communities' functional spaces, indicating that abiotic trait filtering and biotic interactions act in tandem to shape these communities.
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Affiliation(s)
- Benjamin R Shipley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jenny L McGuire
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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5
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Karimi N, Krieg CP, Spalink D, Lemmon AR, Lemmon EM, Eifler E, Hernández AI, Chan PW, Rodríguez A, Landis JB, Strickler SR, Specht CD, Givnish TJ. Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae). Proc Natl Acad Sci U S A 2024; 121:e2305228121. [PMID: 38394215 DOI: 10.1073/pnas.2305228121] [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: 03/31/2023] [Accepted: 12/20/2023] [Indexed: 02/25/2024] Open
Abstract
We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades-inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)-began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.
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Affiliation(s)
- Nisa Karimi
- Science and Conservation Division, Missouri Botanical Garden, St. Louis, MO 63110
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Daniel Spalink
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77845
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306
| | | | - Evan Eifler
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| | - Adriana I Hernández
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853
| | - Patricia W Chan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| | - Aarón Rodríguez
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco 45200, Mexico
| | - Jacob B Landis
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco 45200, Mexico
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853
| | | | - Chelsea D Specht
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
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6
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Wacker KS, Winger BM. An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates. Am Nat 2024; 203:362-381. [PMID: 38358813 DOI: 10.1086/728598] [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: 02/17/2024]
Abstract
AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.
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7
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Shipley BR, McGuire JL. Disentangling the drivers of continental mammalian endemism. GLOBAL CHANGE BIOLOGY 2023; 29:2421-2435. [PMID: 36749035 DOI: 10.1111/gcb.16628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 05/28/2023]
Abstract
Endemic species and species with small ranges are ecologically and evolutionarily distinct and are vulnerable to extinction. Determining which abiotic and biotic factors structure patterns of endemism on continents can advance our understanding of global biogeographic processes, but spatial patterns of mammalian endemism have not yet been effectively predicted and reconstructed. Using novel null model techniques, we reconstruct trends in mammalian endemism and describe the isolated and combined effects of physiographic, ecological, and evolutionary factors on endemism. We calculated weighted endemism for global continental ecoregions and compared the spatial distribution of endemism to niche-based, geographic null models of endemism. These null models distribute species randomly across continents, simulating their range sizes from their degree of climatic specialization. They isolate the effects of physiography (topography and climate) and species richness on endemism. We then ran linear and structural models to determine how topography and historical climate stability influence endemism. The highest rates of mammalian endemism were found in topographically rough, climatically stable ecoregions with many species. The null model that isolated physiography did not closely approximate the observed distribution of endemism (r2 = .09), whereas the null model that incorporated both physiography and species richness did (r2 = .59). The linear models demonstrate that topography and climatic stability both influenced endemism values, but that average climatic niche breadth was not highly correlated with endemism. Climate stability and topography both influence weighted endemism in mammals, but the spatial distribution of mammalian endemism is driven by a combination of physiography and species richness. Despite its relationship to individual range size, average climate niche breadth has only a weak influence on endemism. The results highlight the importance of historical biogeographic processes (e.g. centers of speciation) and geography in driving endemism patterns, and disentangle the mechanisms structuring species ranges worldwide.
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Affiliation(s)
- Benjamin R Shipley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jenny L McGuire
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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8
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Chen C, Ruhfel BR, Li J, Wang Z, Zhang L, Zhang L, Mao X, Wang J, He D, Luo Y, Hu Q, Duan Y, Xu X, Xi Z, Liu J. Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36749624 DOI: 10.1111/jipb.13464] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.
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Affiliation(s)
- Chunlin Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Brad R Ruhfel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zefu Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lushui Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xingxing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ji Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Dashan He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yue Luo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Quanjun Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yuanwen Duan
- Institute Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaoting Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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9
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Ma Y, Mao X, Wang J, Zhang L, Jiang Y, Geng Y, Ma T, Cai L, Huang S, Hollingsworth P, Mao K, Kang M, Li Y, Yang W, Wu H, Chen Y, Davis CC, Shrestha N, Ree RH, Xi Z, Hu Q, Milne RI, Liu J. Pervasive hybridization during evolutionary radiation of Rhododendron subgenus Hymenanthes in mountains of southwest China. Natl Sci Rev 2022; 9:nwac276. [PMID: 36687562 PMCID: PMC9844246 DOI: 10.1093/nsr/nwac276] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022] Open
Abstract
Radiations are especially important for generating species biodiversity in mountainous ecosystems. The contribution of hybridization to such radiations has rarely been examined. Here, we use extensive genomic data to test whether hybridization was involved in evolutionary radiation within Rhododendron subgenus Hymenanthes, whose members show strong geographic isolation in the mountains of southwest China. We sequenced genomes for 143 species of this subgenus and 93 species of four other subgenera, and found that Hymenanthes was monophyletic and radiated during the late Oligocene to middle Miocene. Widespread hybridization events were inferred within and between the identified clades and subclades. This suggests that hybridization occurred both early and late during diversification of subgenus Hymenanthes, although the extent to which hybridization, speciation through mixing-isolation-mixing or hybrid speciation, accelerated the diversification needs further exploration. Cycles of isolation and contact in such and other montane ecosystems may have together promoted species radiation through hybridization between diverging populations and species. Similar radiation processes may apply to other montane floras in this region and elsewhere.
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Affiliation(s)
| | | | | | - Lei Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuying Geng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Liming Cai
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA 02138, USA
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | | | - Kangshan Mao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Minghui Kang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yiling Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wenlu Yang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haolin Wu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yang Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA 02138, USA
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Richard H Ree
- Negaunee Integrative Research Center, Field Museum, Chicago, IL 60605, USA
| | - Zhenxiang Xi
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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Integrating Earth–life systems: a geogenomic approach. Trends Ecol Evol 2022; 37:371-384. [DOI: 10.1016/j.tree.2021.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/04/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
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11
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Val P, Lyons NJ, Gasparini N, Willenbring JK, Albert JS. Landscape Evolution as a Diversification Driver in Freshwater Fishes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.788328] [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
The exceptional concentration of vertebrate diversity in continental freshwaters has been termed the “freshwater fish paradox,” with > 15,000 fish species representing more than 20% of all vertebrate species compressed into tiny fractions of the Earth’s land surface area (<0.5%) or total aquatic habitat volume (<0.001%). This study asks if the fish species richness of the world’s river basins is explainable in terms of river captures using topographic metrics as proxies. The River Capture Hypothesis posits that drainage-network rearrangements have accelerated biotic diversification through their combined effects on dispersal, speciation, and extinction. Yet rates of river capture are poorly constrained at the basin scale worldwide. Here we assess correlations between fish species density (data for 14,953 obligate freshwater fish species) and basin-wide metrics of landscape evolution (data for 3,119 river basins), including: topography (elevation, average relief, slope, drainage area) and climate (average rainfall and air temperature). We assess the results in the context of both static landscapes (e.g., species-area and habitat heterogeneity relationships) and transient landscapes (e.g., river capture, tectonic activity, landscape disequilibrium). We also relax assumptions of functional neutrality of basins (tropical vs. extratropical, tectonically stable vs. active terrains). We found a disproportionate number of freshwater species in large, lowland river basins of tropical South America, Africa, and Southeast Asia, under predictable conditions of large geographic area, tropical climate, low topographic relief, and high habitat volume (i.e., high rainfall rates). However, our results show that these conditions are only necessary, but not fully sufficient, to explain the basins with the highest diversity. Basins with highest diversity are all located on tectonically stable regions, places where river capture is predicted to be most conducive to the formation of high fish species richness over evolutionary timescales. Our results are consistent with predictions of several landscape evolution models, including the River Capture Hypothesis, Mega Capture Hypothesis, and Intermediate Capture Rate Hypothesis, and support conclusions of numerical modeling studies indicating landscape transience as a mechanistic driver of net diversification in riverine and riparian organisms with widespread continental distributions.
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