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Ma XG, Ren YB, Sun H. Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China. Cladistics 2024; 40:357-373. [PMID: 38197450 DOI: 10.1111/cla.12570] [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: 04/17/2023] [Revised: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 01/11/2024] Open
Abstract
Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.
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Affiliation(s)
- Xiang-Guang Ma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yue-Bo Ren
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Yang Q, Li J, Wang Y, Wang Z, Pei Z, Street NR, Bhalerao RP, Yu Z, Gao Y, Ni J, Jiao Y, Sun M, Yang X, Chen Y, Liu P, Wang J, Liu Y, Li G. Genomic basis of the distinct biosynthesis of β-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species. THE NEW PHYTOLOGIST 2024; 242:2702-2718. [PMID: 38515244 DOI: 10.1111/nph.19711] [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: 10/18/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024]
Abstract
Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.
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Affiliation(s)
- Qinsong Yang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Jinjin Li
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Yan Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zefu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Ziqi Pei
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, 90754, Sweden
- SciLifeLab, Umeå University, Umeå, 90754, Sweden
| | - Rishikesh P Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187, Umeå, Sweden
| | - Zhaowei Yu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Yuhao Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Junbei Ni
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yang Jiao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Minghui Sun
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Xiong Yang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Yixin Chen
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Puyuan Liu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Jiaxi Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Yong Liu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
| | - Guolei Li
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing, 100083, China
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Morales-Saldaña S, Hipp AL, Valencia-Ávalos S, Hahn M, González-Elizondo MS, Gernandt DS, Pham KK, Oyama K, González-Rodríguez A. Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae). ANNALS OF BOTANY 2024; 133:1007-1024. [PMID: 38428030 PMCID: PMC11089265 DOI: 10.1093/aob/mcae030] [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: 11/07/2023] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND AND AIMS Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. METHODS Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. KEY RESULTS The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. CONCLUSIONS The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.
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Affiliation(s)
- Saddan Morales-Saldaña
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Andrew L Hipp
- The Morton Arboretum, Lisle, IL 60532-1293, USA
- The Field Museum, Chicago, IL 60605, USA
| | - Susana Valencia-Ávalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | | | | | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex‐Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
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Liu X, Zhang W, Zhang Y, Yang J, Zeng P, Tian Z, Sun W, Cai J. Chromosome-scale genomes of Quercus sichourensis and Quercus rex provide insights into the evolution and adaptation of Fagaceae. J Genet Genomics 2024; 51:554-565. [PMID: 38575109 DOI: 10.1016/j.jgg.2024.03.012] [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: 12/26/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Abstract
The Fagaceae, a plant family with a wide distribution and diverse adaptability, has garnered significant interest as a subject of study in plant speciation and adaptation. Meanwhile, certain Fagaceae species are regarded as highly valuable wood resources due to the exceptional quality of their wood. In this study, we present two high-quality, chromosome-scale genome sequences for Quercus sichourensis (848.75 Mb) and Quercus rex (883.46 Mb). Comparative genomics analysis reveals that the difference in the number of plant disease resistance genes and the nonsynonymous and synonymous substitution ratio (Ka/Ks) of protein-coding genes among Fagaceae species are related to different environmental adaptations. Interestingly, most genes related to starch synthesis in the investigated Quercoideae species are located on a single chromosome, as compared to the outgroup species, Fagus sylvatica. Furthermore, resequencing and population analysis of Q. sichourensis and Q. rex reveal that Q. sichourensis has lower genetic diversity and higher deleterious mutations compared to Q. rex. The high-quality, chromosome-level genomes and the population genomic analysis of the critically endangered Q. sichourensis and Q. rex will provide an invaluable resource as well as insights for future study in these two species, even the genus Quercus, to facilitate their conservation.
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Affiliation(s)
- Xue Liu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Weixiong Zhang
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Yongting Zhang
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Jing Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Peng Zeng
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Zunzhe Tian
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Jing Cai
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China.
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Song Y, Xu GB, Long KX, Wang CC, Chen R, Li H, Jiang XL, Deng M. Ensemble species distribution modeling and multilocus phylogeography provide insight into the spatial genetic patterns and distribution dynamics of a keystone forest species, Quercus glauca. BMC PLANT BIOLOGY 2024; 24:168. [PMID: 38438905 PMCID: PMC10910841 DOI: 10.1186/s12870-024-04830-1] [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: 12/13/2023] [Accepted: 02/16/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Forests are essential for maintaining species diversity, stabilizing local and global climate, and providing ecosystem services. Exploring the impact of paleogeographic events and climate change on the genetic structure and distribution dynamics of forest keystone species could help predict responses to future climate change. In this study, we combined an ensemble species distribution model (eSDM) and multilocus phylogeography to investigate the spatial genetic patterns and distribution change of Quercus glauca Thunb, a keystone of East Asian subtropical evergreen broad-leaved forest. RESULTS A total of 781 samples were collected from 77 populations, largely covering the natural distribution of Q. glauca. The eSDM showed that the suitable habitat experienced a significant expansion after the last glacial maximum (LGM) but will recede in the future under a general climate warming scenario. The distribution centroid will migrate toward the northeast as the climate warms. Using nuclear SSR data, two distinct lineages split between east and west were detected. Within-group genetic differentiation was higher in the West than in the East. Based on the identified 58 haplotypes, no clear phylogeographic structure was found. Populations in the Nanling Mountains, Wuyi Mountains, and the southwest region were found to have high genetic diversity. CONCLUSIONS A significant negative correlation between habitat stability and heterozygosity might be explained by the mixing of different lineages in the expansion region after LGM and/or hybridization between Q. glauca and closely related species. The Nanling Mountains may be important for organisms as a dispersal corridor in the west-east direction and as a refugium during the glacial period. This study provided new insights into spatial genetic patterns and distribution dynamics of Q. glauca.
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Affiliation(s)
- Ying Song
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Gang-Biao Xu
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Ke-Xin Long
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Chun-Cheng Wang
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Ran Chen
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - He Li
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Xiao-Long Jiang
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.
| | - Min Deng
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650500, China.
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Jin ZT, Hodel RGJ, Ma DK, Wang H, Liu GN, Ren C, Ge BJ, Fan Q, Jin SH, Xu C, Wu J, Liu BB. Nightmare or delight: Taxonomic circumscription meets reticulate evolution in the phylogenomic era. Mol Phylogenet Evol 2023; 189:107914. [PMID: 37666378 DOI: 10.1016/j.ympev.2023.107914] [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: 03/28/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of Stranvaesia and introduce a new genus, Weniomeles. This new genus is distinguished by its purple-black fruits, thorns trunk and/or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly-applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.
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Affiliation(s)
- Ze-Tao Jin
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; State Key Laboratory of Plant Diversity and Specialty Crops / 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
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Dai-Kun Ma
- State Key Laboratory of Plant Diversity and Specialty Crops / 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; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Wang
- State Key Laboratory of Plant Diversity and Specialty Crops / 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 Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | | | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Bin-Jie Ge
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Shui-Hu Jin
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Chao Xu
- State Key Laboratory of Plant Diversity and Specialty Crops / 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
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Bin-Bin Liu
- State Key Laboratory of Plant Diversity and Specialty Crops / 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.
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McLay TGB, Fowler RM, Fahey PS, Murphy DJ, Udovicic F, Cantrill DJ, Bayly MJ. Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia. Mol Phylogenet Evol 2023; 187:107869. [PMID: 37423562 DOI: 10.1016/j.ympev.2023.107869] [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: 03/31/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/11/2023]
Abstract
Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.
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Affiliation(s)
- Todd G B McLay
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia.
| | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Patrick S Fahey
- Research Centre for Ecosystem Resilience, The Royal Botanic Garden Sydney, Sydney 2000, NSW, Australia; Qld Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia 4072, Qld, Australia
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Frank Udovicic
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia
| | - David J Cantrill
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Michael J Bayly
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
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8
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Kinneberg VB, Lü DS, Peris D, Ravinet M, Skrede I. Introgression between highly divergent fungal sister species. J Evol Biol 2023; 36:1133-1149. [PMID: 37363874 DOI: 10.1111/jeb.14190] [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: 11/24/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA-BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations.
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Affiliation(s)
- Vilde Bruhn Kinneberg
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Evolution and Paleobiology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Dabao Sun Lü
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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Denk T, Grimm GW, Hipp AL, Bouchal JM, Schulze ED, Simeone MC. Niche evolution in a northern temperate tree lineage: biogeographical legacies in cork oaks (Quercus section Cerris). ANNALS OF BOTANY 2023; 131:769-787. [PMID: 36805162 PMCID: PMC10184457 DOI: 10.1093/aob/mcad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/15/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Despite being a small clade, they display a range of leaf morphologies comparable to the largest sections (>100 spp.) in Quercus. Their fossil record extends back to the Eocene. Here, we explore how cork oaks achieved their modern ranges and how legacy effects might explain niche evolution in modern species of section Cerris and its sister section Ilex, the holly oaks. METHODS We inferred a dated phylogeny for cork and holly oaks using a reduced-representation next-generation sequencing method, restriction site-associated DNA sequencing (RAD-seq), and used D-statistics to investigate gene flow hypotheses. We estimated divergence times using a fossilized birth-death model calibrated with 47 fossils. We used Köppen profiles, selected bioclimatic parameters and forest biomes occupied by modern species to infer ancestral climatic and biotic niches. KEY RESULTS East Asian and Western Eurasian cork oaks diverged initially in the Eocene. Subsequently, four Western Eurasian lineages (subsections) differentiated during the Oligocene and Miocene. Evolution of leaf size, form and texture was correlated, in part, with multiple transitions from ancestral humid temperate climates to mediterranean, arid and continental climates. Distantly related but ecologically similar species converged on similar leaf traits in the process. CONCLUSIONS Originating in temperate (frost-free) biomes, Eocene to Oligocene ranges of the primarily deciduous cork oaks were restricted to higher latitudes (Siberia to north of Paratethys). Members of the evergreen holly oaks (section Ilex) also originated in temperate biomes but migrated southwards and south-westwards into then-(sub)tropical southern China and south-eastern Tibet during the Eocene, then westwards along existing pre-Himalayan mountain ranges. Divergent biogeographical histories and deep-time phylogenetic legacies (in cold and drought tolerance, nutrient storage and fire resistance) thus account for the modern species mosaic of Western Eurasian oak communities, which are composed of oaks belonging to four sections.
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Affiliation(s)
- Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | | | | | - Johannes M Bouchal
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | | | - Marco C Simeone
- Department of Agricultural and Forestry Sciences, University of Tuscia, 01100 Viterbo, Italy
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10
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Stull GW, Pham KK, Soltis PS, Soltis DE. Deep reticulation: the long legacy of hybridization in vascular plant evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:743-766. [PMID: 36775995 DOI: 10.1111/tpj.16142] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 05/27/2023]
Abstract
Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.
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Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
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11
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Benítez-Villaseñor A, Granados Mendoza C, Wanke S, Peñafiel Cevallos M, Freire ME, Lemmon EM, Lemmon AR, Magallón S. The use of Anchored Hybrid Enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to Asterales (Eudicotyledoneae; Angiosperms). Mol Phylogenet Evol 2023; 181:107714. [PMID: 36708940 DOI: 10.1016/j.ympev.2023.107714] [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: 05/02/2022] [Revised: 10/28/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
Anchored Hybrid Enrichment (AHE) is a tool for capturing orthologous regions of the nuclear genome shared in low or single copy across lineages. Despite the increasing number of studies using this method, its usefulness to estimate relationships at deeper taxonomic levels in plants has not been fully explored. Here we present a proof of concept about the performance of nuclear loci obtained with AHE to infer phylogenetic relationships and explore the use of gene sampling schemes to estimate divergence times in Asterales. We recovered low-copy nuclear loci using the AHE method from herbarium material and silica-preserved samples. Maximum likelihood, Bayesian inference, and coalescence approaches were used to reconstruct phylogenomic relationships. Dating analyses were conducted under a multispecies coalescent approach by jointly inferring species tree and divergence times with random gene sampling schemes and multiple calibrations. We recovered 403 low-copy nuclear loci for 63 species representing nine out of eleven families of Asterales. Phylogenetic hypotheses were congruent among the applied methods and previously published results. Analyses with concatenated datasets were strongly supported, but coalescence-based analyses showed low support for the phylogenetic position of families Argophyllaceae and Alseuosmiaceae. Estimated family ages were congruent among gene sampling schemes, with the mean age for Asterales around 130 Myr. Our study documents the usefulness of AHE for resolving phylogenetic relationships at deep phylogenetic levels in Asterales. Observed phylogenetic inconsistencies were possibly due to the non-inclusion of families Phellinceae and Pentaphragmataceae. Random gene sampling schemes produced consistent age estimates with coalescence and species tree relaxed clock approaches.
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Affiliation(s)
- Adriana Benítez-Villaseñor
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 70-153, C.P.04510 Ciudad de México, Mexico.
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Marcia Peñafiel Cevallos
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - M Efraín Freire
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL 32306-4295, United States.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306-4120, United States.
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico.
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12
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Martin SL, Lujan Toro B, James T, Sauder CA, Laforest M. Insights from the genomes of 4 diploid Camelina spp. G3 (BETHESDA, MD.) 2022; 12:jkac182. [PMID: 35976116 PMCID: PMC9713399 DOI: 10.1093/g3journal/jkac182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 06/12/2022] [Indexed: 11/12/2022]
Abstract
Plant evolution has been a complex process involving hybridization and polyploidization making understanding the origin and evolution of a plant's genome challenging even once a published genome is available. The oilseed crop, Camelina sativa (Brassicaceae), has a fully sequenced allohexaploid genome with 3 unknown ancestors. To better understand which extant species best represent the ancestral genomes that contributed to C. sativa's formation, we sequenced and assembled chromosome level draft genomes for 4 diploid members of Camelina: C. neglecta C. hispida var. hispida, C. hispida var. grandiflora, and C. laxa using long and short read data scaffolded with proximity data. We then conducted phylogenetic analyses on regions of synteny and on genes described for Arabidopsis thaliana, from across each nuclear genome and the chloroplasts to examine evolutionary relationships within Camelina and Camelineae. We conclude that C. neglecta is closely related to C. sativa's sub-genome 1 and that C. hispida var. hispida and C. hispida var. grandiflora are most closely related to C. sativa's sub-genome 3. Further, the abundance and density of transposable elements, specifically Helitrons, suggest that the progenitor genome that contributed C. sativa's sub-genome 3 maybe more similar to the genome of C. hispida var. hispida than that of C. hispida var. grandiflora. These diploid genomes show few structural differences when compared to C. sativa's genome indicating little change to chromosome structure following allopolyploidization. This work also indicates that C. neglecta and C. hispida are important resources for understanding the genetics of C. sativa and potential resources for crop improvement.
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Affiliation(s)
- Sara L Martin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0CA, Canada
| | - Beatriz Lujan Toro
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0CA, Canada
| | - Tracey James
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0CA, Canada
| | - Connie A Sauder
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0CA, Canada
| | - Martin Laforest
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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13
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Lu WX, Hu XY, Wang ZZ, Rao GY. Hyb-Seq provides new insights into the phylogeny and evolution of the Chrysanthemum zawadskii species complex in China. Cladistics 2022; 38:663-683. [PMID: 35766338 DOI: 10.1111/cla.12514] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 02/06/2023] Open
Abstract
A species complex is an assemblage of closely related species with blurred boundaries, and from which species could arise from different speciation processes and/or a speciation continuum. Such a complex can provide an opportunity to investigate evolutionary mechanisms acting on speciation. The Chrysanthemum zawadskii species complex in China, a monophyletic group of Chrysanthemum, consists of seven species with considerable morphological variation, diverse habitats and different distribution patterns. Here, we used Hyb-Seq data to construct a well-resolved phylogeny of the C. zawadskii complex. Then, we performed comparative analyses of variation patterns in morphology, ecology and distribution to investigate the roles of geography and ecology in this complex's diversification. Lastly, we implemented divergence time estimation, species distribution modelling and ancestral area reconstruction to trace the evolutionary history of this complex. We concluded that the C. zawadskii complex originated in the Qinling-Daba mountains during the early Pliocene and then spread west and northward along the mountain ranges to northern China. During this process, geographical and ecological factors imposing different influences resulted in the current diversification and distribution patterns of this species complex, which is composed of both well-diverged species and diverging lineages on the path of speciation.
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Affiliation(s)
- Wen-Xun Lu
- School of Life Sciences, Peking University, Beijing, China
| | - Xue-Ying Hu
- School of Life Sciences, Peking University, Beijing, China
| | - Zi-Zhao Wang
- School of Life Sciences, Peking University, Beijing, China
| | - Guang-Yuan Rao
- School of Life Sciences, Peking University, Beijing, China
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14
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Cueva D, Bravo GA, Silveira LF. Systematics of Thraupis (Aves, Passeriformes) reveals an extensive hybrid zone between T. episcopus (Blue-gray Tanager) and T. sayaca (Sayaca Tanager). PLoS One 2022; 17:e0270892. [PMID: 36197923 PMCID: PMC9534438 DOI: 10.1371/journal.pone.0270892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
The Neotropical avian genus Thraupis (Passeriformes, Thraupidae) currently comprises seven species that are widespread and abundant throughout their ranges. However, no phylogenetic hypothesis with comprehensive intraspecific sampling is available for the group and, therefore, currently accepted species limits remain untested. We obtained sequence data for two mitochondrial (ND2, cyt-b) and three non-coding nuclear (TGFB2, MUSK, and βF5) markers from 118 vouchered museum specimens. We conducted population structure and coalescent-based species-tree analyses using a molecular clock calibration. We integrated these results with morphometric and coloration analyses of 1,003 museum specimens to assess species limits within Thraupis. Our results confirm that Thraupis is a monophyletic group and support its origin in the late Miocene and subsequent diversification during the Pleistocene. However, we found conflicts with previous phylogenies. We recovered Thraupis glaucocolpa to be sister to all other species in the genus, and T. cyanoptera to the remaining five species. Our phylogenetic trees and population structure analyses uncovered phylogeographic structure within Thraupis episcopus that is congruent with geographic patterns of phenotypic variation and distributions of some named taxa. The first genetic and phenotypic cluster in T. episcopus occurs east of the Andes and is diagnosed by the white patch on the lesser and median wing coverts, whereas the second group has a blue patch on the wing and distributes to the west of Colombia's eastern Andes. Finally, we present evidence of hybridization and ongoing gene flow between several taxa at different taxonomic levels and discuss its taxonomic implications.
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Affiliation(s)
- Diego Cueva
- Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá, Colombia
- * E-mail:
| | - Gustavo A. Bravo
- Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá, Colombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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15
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Crowl AA, Fritsch PW, Tiley GP, Lynch NP, Ranney TG, Ashrafi H, Manos PS. A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus). AMERICAN JOURNAL OF BOTANY 2022; 109:1596-1606. [PMID: 36109839 DOI: 10.1002/ajb2.16065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The true blueberries (Vaccinium sect. Cyanococcus; Ericaceae), endemic to North America, have been intensively studied for over a century. However, with species estimates ranging from nine to 24 and much confusion regarding species boundaries, this ecologically and economically valuable group remains inadequately understood at a basic evolutionary and taxonomic level. As a first step toward understanding the evolutionary history and taxonomy of this species complex, we present the first phylogenomic hypothesis of the known diploid blueberries. METHODS We used flow cytometry to verify the ploidy of putative diploid taxa and a target-enrichment approach to obtain a genomic data set for phylogenetic analyses. RESULTS Despite evidence of gene flow, we found that a primary phylogenetic signal is present. Monophyly for all morphospecies was recovered, with two notable exceptions: one sample of V. boreale was consistently nested in the V. myrtilloides clade and V. caesariense was nested in the V. fuscatum clade. One diploid taxon, Vaccinium pallidum, is implicated as having a homoploid hybrid origin. CONCLUSIONS This foundational study represents the first attempt to elucidate evolutionary relationships of the true blueberries of North America with a phylogenomic approach and sets the stage for multiple avenues of future study such as a taxonomic revision of the group, the verification of a homoploid hybrid taxon, and the study of polyploid lineages within the context of a diploid phylogeny.
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Affiliation(s)
- Andrew A Crowl
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27607, USA
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, Fort Worth, Texas, 76107, USA
| | - George P Tiley
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | - Nathan P Lynch
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27607, USA
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, North Carolina, 28759, USA
| | - Thomas G Ranney
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27607, USA
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, North Carolina, 28759, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27607, USA
| | - Paul S Manos
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
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16
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Zhou W, Jenny Xiang QY. Phylogenomics and Biogeography of Castanea (Chestnut) and Hamamelis (Witch-hazel) - Choosing between RAD-seq and Hyb-Seq Approaches. Mol Phylogenet Evol 2022; 176:107592. [DOI: 10.1016/j.ympev.2022.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/18/2022] [Accepted: 07/20/2022] [Indexed: 10/31/2022]
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17
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Otero A, Vargas P, Fernández-Mazuecos M, Jiménez-Mejías P, Valcárcel V, Villa-Machío I, Hipp AL. A snapshot of progenitor-derivative speciation in Iberodes (Boraginaceae). Mol Ecol 2022; 31:3192-3209. [PMID: 35390211 DOI: 10.1111/mec.16459] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 03/27/2022] [Accepted: 04/01/2022] [Indexed: 11/28/2022]
Abstract
Traditional classification of speciation modes has focused on physical barriers to gene flow. Allopatric speciation with complete reproductive isolation is viewed as the most common mechanism of speciation. Parapatry and sympatry, by contrast, entail speciation in the face of ongoing gene flow, making them more difficult to detect. The genus Iberodes (Boraginaceae, NW Europe) comprises five species with contrasting morphological traits, habitats, and species distributions. Based on the predominance of narrow and geographically distant endemic species, we hypothesized that geographic barriers were responsible for most speciation events in Iberodes. We undertook an integrative study including: (i) phylogenomics through restriction-site associated DNA sequencing, (ii) genetic structure analyses, (iii) demographic modeling, (iv) morphometrics, and (v) climatic niche modeling and niche overlap analysis. Results revealed a history of recurrent progenitor-derivative speciation manifested by a paraphyletic pattern of nested species differentiation. Budding speciation mediated by ecological differentiation is suggested for the coastal lineage, deriving from the inland widespread I. linifolia during Late Pliocene. Meanwhile, geographic isolation followed by niche shifts are suggested for the more recent differentiation of the coastland taxa. Our work provides a model for distinguishing speciation via ecological differentiation of peripheral, narrowly endemic I. kuzinskyanae and I. littoralis from a widespread extant ancestor, I. linifolia. Ultimately, our results illustrate a case of Pliocene speciation in the probable absence of geographic barriers and get away from the traditional cladistic perspective of speciation as producing two species from an extinct ancestor, thus reminding us that phylogenetic trees tell only part of the story.
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Affiliation(s)
- Ana Otero
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, 1400 S. DuSable Lake Shore Dr, 60605, Chicago, Illinois, USA.,Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC). Pza. de Murillo, 28014, Madrid, Spain
| | - Pablo Vargas
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC). Pza. de Murillo, 28014, Madrid, Spain
| | - Mario Fernández-Mazuecos
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC). Pza. de Murillo, 28014, Madrid, Spain.,Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Departamento de Biología (Botánica), Universidad Autónoma de Madrid, C/ Darwin, 2, 28049, Madrid, Spain
| | - Pedro Jiménez-Mejías
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Departamento de Biología (Botánica), Universidad Autónoma de Madrid, C/ Darwin, 2, 28049, Madrid, Spain
| | - Virginia Valcárcel
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Departamento de Biología (Botánica), Universidad Autónoma de Madrid, C/ Darwin, 2, 28049, Madrid, Spain
| | - Irene Villa-Machío
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC). Pza. de Murillo, 28014, Madrid, Spain
| | - Andrew L Hipp
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, 1400 S. DuSable Lake Shore Dr, 60605, Chicago, Illinois, USA.,The Morton Arboretum, 4100 Illinois Route 53, 60532, Lisle, Illinois, USA
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18
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Ai W, Liu Y, Mei M, Zhang X, Tan E, Liu H, Han X, Zhan H, Lu X. A chromosome-scale genome assembly of the Mongolian oak (Quercus mongolica). Mol Ecol Resour 2022; 22:2396-2410. [PMID: 35377556 DOI: 10.1111/1755-0998.13616] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/13/2022] [Accepted: 03/29/2022] [Indexed: 11/26/2022]
Abstract
Mongolian oak (Quercus mongolica Fisch.) is an ecologically and economically important white oak species native to and widespread in the temperate zone of East Asia. Here, we present a chromosome-scale reference genome assembly of Q. mongolica, a representative white oak species, by combining Illumina and PacBio data with Hi-C mapping technologies that is the first reference genome created for an Asian oak. Our results showed that the PacBio draft genome size was 809.84 Mb, with a BUSCO complete gene percentage of 92.71%. Hi-C scaffolding anchored 774.59 Mb contigs (95.65% of draft assembly) onto 12 pseudochromosomes. The contig N50 and scaffold N50 were 2.64 Mb and 66.74 Mb, respectively. Of the 36,553 protein-coding genes predicted in the study, approximately 95% had functional annotations in public databases. A total of 435.34 Mb (53.75% of the genome) of repetitive sequences were predicted in the assembled genome. Genome evolution analysis showed that Q. mongolica is closely related to Q. robur from Europe, and they shared a common ancestor ~11.8 million years ago. Gene family evolution analysis of Q. mongolica revealed that the nucleotide-binding site (NBS)-encoding gene family related to disease resistance was significantly contracted, whereas the ECERIFERUM 1 (CER1) homologous genes related to cuticular wax biosynthesis was significantly expanded. This pioneering Asian oak genome resource represents an important supplement to the oak genomics community and will improve our understanding of Asian white oak biology and evolution.
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Affiliation(s)
- Wanfeng Ai
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yanqun Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Mei Mei
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.,Biotechnology and Analysis Test Center, Liaoning Academy of Forest Science, Shenyang, 110032, Liaoning, China
| | - Xiaolin Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Enguang Tan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Hanzhang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Xiaoyi Han
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Hao Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Xiujun Lu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.,College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
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19
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Zhou BF, Yuan S, Crowl AA, Liang YY, Shi Y, Chen XY, An QQ, Kang M, Manos PS, Wang B. Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere. Nat Commun 2022; 13:1320. [PMID: 35288565 PMCID: PMC8921187 DOI: 10.1038/s41467-022-28917-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses of nuclear and plastid genomes to investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. Innovation related to seed dispersal is implicated in triggering waves of continental radiations beginning with the rapid diversification of major lineages and resulting in unparalleled transformation of forest dynamics within 15 million years following the K-Pg extinction. We detect introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, which may have further amplified the diversification of white oaks across Eurasia. Fagaceae are diverse family including trees of ecological and economic importance. This phylogenomic analysis of nuclear and plastid genomes reconstructs evolutionary history and finds evidence of multiple adaptive introgression events in this important plant family.
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Li Y, Zhang X, Wang L, Sork VL, Mao L, Fang Y. Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China. ANNALS OF BOTANY 2022; 129:231-245. [PMID: 34893791 PMCID: PMC8796672 DOI: 10.1093/aob/mcab140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/31/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. METHODS We analyse genetic variation at seven nuclear microsatellites (1111 individuals) and three chloroplast intergenic spacers (576 individuals) to determine the present admixture pattern and ancient hybridization history. We apply an information-theoretic model selection approach to explore the associations of genetic admixture degree with past climatic niche suitability at multiple spatial scales. KEY RESULTS More than 70 % of the hybrids determined by Bayesian clustering analysis and more than 90 % of the individuals with locally shared chloroplast haplotypes are concentrated within a mid-Pliocene contact zone between ~30°N and 35°N. Climatic niche suitabilities for Q. chenii during the mid-Pliocene Warm Period [mPWP, ~3.264-3.025 million years ago (mya)] and during the Last Glacial Maximum (LGM, ~0.022 mya) best explain the admixture patterns across all Q. acutissima populations and across those within the ancient contact zone, respectively. CONCLUSIONS Our results highlight that palaeoclimate change shapes present admixture patterns by influencing the extent of historical range overlap. Specifically, the mid-Pliocene warm climate promoted ancient contact, allowing widespread hybridization throughout central China. In contrast, the Pleistocene cool climate caused the local extinction of Q. chenii, reducing the probability of interspecific gene flow in most areas except those sites having a high level of ecological stability.
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Affiliation(s)
- Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xingwang Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
| | - Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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21
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Morales-Briones DF, Gehrke B, Huang CH, Liston A, Ma H, Marx HE, Tank DC, Yang Y. Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae). Syst Biol 2021; 71:190-207. [PMID: 33978764 PMCID: PMC8677558 DOI: 10.1093/sysbio/syab032] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 12/16/2022] Open
Abstract
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone to errors in orthology inference or removing large numbers of genes. By removing entire genes, valuable information that could be used to detect and place WGD events is discarded. Here, we used an automated approach for orthology inference in a target enrichment data set of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested ancient WGDs in the group. However, both the phylogenetic location and putative parental lineages of these WGD events remain unknown. By taking paralogs into consideration and inferring orthologs from target enrichment data, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach, we established the autopolyploid origin of the entire Alchemilla s.l. and the nested allopolyploid origin of four major clades within the group. Here, we showed the utility of automated tree-based orthology inference methods, previously designed for genomic or transcriptomic data sets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment data sets.[Alchemilla; allopolyploidy; autopolyploidy; gene tree discordance; orthology inference; paralogs; Rosaceae; target enrichment; whole genome duplication.].
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Affiliation(s)
- Diego F Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844, USA
| | - Berit Gehrke
- University Gardens, University Museum, University of Bergen, Mildeveien 240, 5259 Hjellestad, Norway
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, USA
| | - Hong Ma
- Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, 510D Mueller Laboratory, University Park, PA 16802 USA
| | - Hannah E Marx
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - David C Tank
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
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Abstract
Quercus species (oaks) have been an integral part of the landscape in the northern hemisphere for millions of years. Their ability to adapt and spread across different environments and their contributions to many ecosystem services is well documented. Human activity has placed many oak species in peril by eliminating or adversely modifying habitats through exploitative land usage and by practices that have exacerbated climate change. The goal of this review is to compile a list of oak species of conservation concern, evaluate the genetic data that is available for these species, and to highlight the gaps that exist. We compiled a list of 124 Oaks of Concern based on the Red List of Oaks 2020 and the Conservation Gap Analysis for Native U.S. Oaks and their evaluations of each species. Of these, 57% have been the subject of some genetic analysis, but for most threatened species (72%), the only genetic analysis was done as part of a phylogenetic study. While nearly half (49%) of published genetic studies involved population genetic analysis, only 16 species of concern (13%) have been the subject of these studies. This is a critical gap considering that analysis of intraspecific genetic variability and genetic structure are essential for designing conservation management strategies. We review the published population genetic studies to highlight their application to conservation. Finally, we discuss future directions in Quercus conservation genetics and genomics.
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An Updated Infrageneric Classification of the North American Oaks (Quercus Subgenus Quercus): Review of the Contribution of Phylogenomic Data to Biogeography and Species Diversity. FORESTS 2021. [DOI: 10.3390/f12060786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The oak flora of North America north of Mexico is both phylogenetically diverse and species-rich, including 92 species placed in five sections of subgenus Quercus, the oak clade centered on the Americas. Despite phylogenetic and taxonomic progress on the genus over the past 45 years, classification of species at the subsectional level remains unchanged since the early treatments by WL Trelease, AA Camus, and CH Muller. In recent work, we used a RAD-seq based phylogeny including 250 species sampled from throughout the Americas and Eurasia to reconstruct the timing and biogeography of the North American oak radiation. This work demonstrates that the North American oak flora comprises mostly regional species radiations with limited phylogenetic affinities to Mexican clades, and two sister group connections to Eurasia. Using this framework, we describe the regional patterns of oak diversity within North America and formally classify 62 species into nine major North American subsections within sections Lobatae (the red oaks) and Quercus (the white oaks), the two largest sections of subgenus Quercus. We also distill emerging evolutionary and biogeographic patterns based on the impact of phylogenomic data on the systematics of multiple species complexes and instances of hybridization.
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Li
X, Wei G, El-Kassaby YA, Fang Y. Hybridization and introgression in sympatric and allopatric populations of four oak species. BMC PLANT BIOLOGY 2021; 21:266. [PMID: 34107871 PMCID: PMC8188795 DOI: 10.1186/s12870-021-03007-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/05/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Hybridization and introgression are vital sources of novel genetic variation driving diversification during reticulated evolution. Quercus is an important model clade, having extraordinary diverse and abundant members in the Northern hemisphere, that are used to studying the introgression of species boundaries and adaptive processes. China is the second-largest distribution center of Quercus, but there are limited studies on introgressive hybridization. RESULTS Here, we screened 17 co-dominant nuclear microsatellite markers to investigate the hybridization and introgression of four oaks (Quercus acutissima, Quercus variabilis, Quercus fabri, and Quercus serrata) in 10 populations. We identified 361 alleles in the four-oak species across 17 loci, and all loci were characterized by high genetic variability (HE = 0.844-0.944) and moderate differentiation (FST = 0.037-0.156) levels. A population differentiation analysis revealed the following: allopatric homologous (FST = 0.064) < sympatric heterogeneous (FST = 0.071) < allopatric heterogeneous (FST = 0.084). A Bayesian admixture analysis determined four types of hybrids (Q. acutissima × Q. variabilis, Q. fabri × Q. serrata, Q. acutissima × Q. fabri, and Q. acutissima × Q. variabilis × Q. fabri) and their asymmetric introgression. Our results revealed that interspecific hybridization is commonly observed within the section Quercus, with members having tendency to hybridize. CONCLUSIONS Our study determined the basic hybridization and introgression states among the studied four oak species and extended our understanding of the evolutionary role of hybridization. The results provide useful theoretical data for formulating conservation strategies.
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Affiliation(s)
- Xuan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 PR China
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Gaoming Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 PR China
- School of Physics and Electronics Henan University, Jinming Avenue, Jinming District, Kaifeng, 475001 PR China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 PR China
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Yang Y, Zhou T, Qian Z, Zhao G. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing. Genomics 2021; 113:1438-1447. [PMID: 33744343 DOI: 10.1016/j.ygeno.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 01/29/2023]
Abstract
China is a second center of oak diversity but with less intensively systematic studies. Here, with 49 species representing all four sections in China, we firstly gave insight into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes. Our results recovered a robust phylogenetic framework and provided strong support for most nodes. The phylogenetic tree supported Quercus section Ilex as not monophyletic, in which Quercus section Cyclobalanopsis and Quercus section Cerris were nested. Most likely, incomplete lineage sorting and/or introgression among ancestral lineages in these three sections resulted in this complex pattern. The current distribution, diversification and molecular differentiation of Q. sect. Ilex in China are likely consequences of local adaptation to the geographic and paleoclimatic changes, which were driven by the uplift of Tibetan Plateau, the Hengduan Mountains and the Himalayas.
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Affiliation(s)
- Yanci Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China; School of Biological Science and Technology, Baotou Teachers' College, Baotou, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Zengqiang Qian
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China.
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Cortés AJ, Restrepo-Montoya M, Bedoya-Canas LE. Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate. FRONTIERS IN PLANT SCIENCE 2020; 11:583323. [PMID: 33193532 PMCID: PMC7609427 DOI: 10.3389/fpls.2020.583323] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/29/2020] [Indexed: 05/02/2023]
Abstract
Studying the genetics of adaptation to new environments in ecologically and industrially important tree species is currently a major research line in the fields of plant science and genetic improvement for tolerance to abiotic stress. Specifically, exploring the genomic basis of local adaptation is imperative for assessing the conditions under which trees will successfully adapt in situ to global climate change. However, this knowledge has scarcely been used in conservation and forest tree improvement because woody perennials face major research limitations such as their outcrossing reproductive systems, long juvenile phase, and huge genome sizes. Therefore, in this review we discuss predictive genomic approaches that promise increasing adaptive selection accuracy and shortening generation intervals. They may also assist the detection of novel allelic variants from tree germplasm, and disclose the genomic potential of adaptation to different environments. For instance, natural populations of tree species invite using tools from the population genomics field to study the signatures of local adaptation. Conventional genetic markers and whole genome sequencing both help identifying genes and markers that diverge between local populations more than expected under neutrality, and that exhibit unique signatures of diversity indicative of "selective sweeps." Ultimately, these efforts inform the conservation and breeding status capable of pivoting forest health, ecosystem services, and sustainable production. Key long-term perspectives include understanding how trees' phylogeographic history may affect the adaptive relevant genetic variation available for adaptation to environmental change. Encouraging "big data" approaches (machine learning-ML) capable of comprehensively merging heterogeneous genomic and ecological datasets is becoming imperative, too.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, Rionegro, Colombia
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
| | - Manuela Restrepo-Montoya
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
| | - Larry E. Bedoya-Canas
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
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27
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Xiao TW, Xu Y, Jin L, Liu TJ, Yan HF, Ge XJ. Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae). PeerJ 2020; 8:e10155. [PMID: 33088627 PMCID: PMC7568859 DOI: 10.7717/peerj.10155] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/21/2020] [Indexed: 11/20/2022] Open
Abstract
Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict. Results We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node. Conclusions Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.
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Affiliation(s)
- Tian-Wen Xiao
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lu Jin
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tong-Jian Liu
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Hai-Fei Yan
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Xue-Jun Ge
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
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Piredda R, Grimm GW, Schulze ED, Denk T, Simeone MC. High-throughput sequencing of 5S-IGS in oaks: Exploring intragenomic variation and algorithms to recognize target species in pure and mixed samples. Mol Ecol Resour 2020; 21:495-510. [PMID: 32997899 DOI: 10.1111/1755-0998.13264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 11/30/2022]
Abstract
Measuring biological diversity is a crucial but difficult undertaking, as exemplified in oaks where complex patterns of morphological, ecological, biogeographical and genetic differentiation collide with traditional taxonomy, which measures biodiversity in number of species (or higher taxa). In this pilot study, we generated high-throughput sequencing amplicon data of the intergenic spacer of the 5S nuclear ribosomal DNA cistron (5S-IGS) in oaks, using six mock samples that differ in geographical origin, species composition and pool complexity. The potential of the marker for automated genotaxonomy applications was assessed using a reference data set of 1,770 5S-IGS cloned sequences, covering the entire taxonomic breadth and distribution range of western Eurasian Quercus, and applying similarity (blast) and evolutionary approaches (maximum-likelihood trees and Evolutionary Placement Algorithm). Both methods performed equally well, allowing correct identification of species in sections Ilex and Cerris in the pure and mixed samples, and main lineages shared by species of sect. Quercus. Application of different cut-off thresholds revealed that medium- to high-abundance (>10 or 25) sequences suffice for a net species identification of samples containing one or a few individuals. Lower thresholds identify phylogenetic correspondence with all target species in highly mixed samples (analogous to environmental bulk samples) and include rare variants pointing towards reticulation, incomplete lineage sorting, pseudogenic 5S units and in situ (natural) contamination. Our pipeline is highly promising for future assessments of intraspecific and interpopulation diversity, and of the genetic resources of natural ecosystems, which are fundamental to empower fast and solid biodiversity conservation programmes worldwide.
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Affiliation(s)
| | - Guido W Grimm
- Orléans, France.,Department of Palaeontology, University of Vienna, Vienna, Austria
| | | | - Thomas Denk
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Marco Cosimo Simeone
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli studi della Tuscia, Viterbo, Italy
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Feng Y, Comes HP, Qiu YX. Phylogenomic insights into the temporal-spatial divergence history, evolution of leaf habit and hybridization in Stachyurus (Stachyuraceae). Mol Phylogenet Evol 2020; 150:106878. [DOI: 10.1016/j.ympev.2020.106878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/07/2020] [Accepted: 06/01/2020] [Indexed: 12/14/2022]
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30
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Yang J, Guo YF, Chen XD, Zhang X, Ju MM, Bai GQ, Liu ZL, Zhao GF. Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1024. [PMID: 32823635 PMCID: PMC7464331 DOI: 10.3390/plants9081024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022]
Abstract
Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak's lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene-Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak's lineage.
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Affiliation(s)
- Jia Yang
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Yu-Fan Guo
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Xiao-Dan Chen
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Xiao Zhang
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Miao-Miao Ju
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Guo-Qing Bai
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
- Institute of Botany of Shaanxi Province, Xi’an 710061, China
| | - Zhan-Lin Liu
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Gui-Fang Zhao
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
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31
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Ramírez-Valiente JA, López R, Hipp AL, Aranda I. Correlated evolution of morphology, gas exchange, growth rates and hydraulics as a response to precipitation and temperature regimes in oaks (Quercus). THE NEW PHYTOLOGIST 2020; 227:794-809. [PMID: 31733106 DOI: 10.1111/nph.16320] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
It is hypothesised that tree distributions in Europe are largely limited by their ability to cope with the summer drought imposed by the Mediterranean climate in the southern areas and by their competitive potential in central regions with more mesic conditions. We investigated the extent to which leaf and plant morphology, gas exchange, leaf and stem hydraulics and growth rates have evolved in a coordinated way in oaks (Quercus) as a result of adaptation to contrasting environmental conditions in this region. We implemented an experiment in which seedlings of 12 European/North African oaks were grown under two watering treatments, a well-watered treatment and a drought treatment in which plants were subjected to three cycles of drought. Consistent with our hypothesis, species from drier summers had traits conferring more tolerance to drought such as small sclerophyllous leaves and lower percent loss of hydraulic conductivity. However, these species did not have lower growth rates as expected by a trade-off with drought tolerance. Overall, our results revealed that climate is an important driver of functional strategies in oaks and that traits have evolved along two coordinated functional axes to adapt to different precipitation and temperature regimes.
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Affiliation(s)
- José Alberto Ramírez-Valiente
- Centro de Investigación Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Carretera de La Coruña Km 7.5, Madrid, 28040, Spain
| | - Rosana López
- Departamento de Sistemas y Recursos Naturales, Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Andrew L Hipp
- The Morton Arboretum, Lisle, IL, 60532-1293, USA
- The Field Museum, Chicago, IL, 60605, USA
| | - Ismael Aranda
- Centro de Investigación Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Carretera de La Coruña Km 7.5, Madrid, 28040, Spain
- Instituto de Investigaciones Agroambientales y de Economía del Agua (INAGEA), Carretera de Valldemossa, Palma de Mallorca, 07122, Spain
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Morales-Briones DF, Kadereit G, Tefarikis DT, Moore MJ, Smith SA, Brockington SF, Timoneda A, Yim WC, Cushman JC, Yang Y. Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l. Syst Biol 2020; 70:219-235. [PMID: 32785686 PMCID: PMC7875436 DOI: 10.1093/sysbio/syaa066] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/01/2020] [Accepted: 09/03/2020] [Indexed: 12/26/2022] Open
Abstract
Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]
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Affiliation(s)
- Diego F Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
| | - Gudrun Kadereit
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Delphine T Tefarikis
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH 44074-1097, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge CB2 3EA, UK
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge CB2 3EA, UK
| | - Won C Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89577, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89577, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
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Kremer A, Hipp AL. Oaks: an evolutionary success story. THE NEW PHYTOLOGIST 2020; 226:987-1011. [PMID: 31630400 PMCID: PMC7166131 DOI: 10.1111/nph.16274] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 09/13/2019] [Indexed: 05/10/2023]
Abstract
The genus Quercus is among the most widespread and species-rich tree genera in the northern hemisphere. The extraordinary species diversity in America and Asia together with the continuous continental distribution of a limited number of European species raise questions about how macro- and microevolutionary processes made the genus Quercus an evolutionary success. Synthesizing conclusions reached during the past three decades by complementary approaches in phylogenetics, phylogeography, genomics, ecology, paleobotany, population biology and quantitative genetics, this review aims to illuminate evolutionary processes leading to the radiation and expansion of oaks. From opposing scales of time and geography, we converge on four overarching explanations of evolutionary success in oaks: accumulation of large reservoirs of diversity within populations and species; ability for rapid migration contributing to ecological priority effects on lineage diversification; high rates of evolutionary divergence within clades combined with convergent solutions to ecological problems across clades; and propensity for hybridization, contributing to adaptive introgression and facilitating migration. Finally, we explore potential future research avenues, emphasizing the integration of microevolutionary and macroevolutionary perspectives.
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Affiliation(s)
- Antoine Kremer
- BIOGECO, INRA, Université de Bordeaux, 69 Route
d'Arcachon, 33612 Cestas, France
| | - Andrew L. Hipp
- The Morton Arboretum, Lisle IL 60532-1293, USA
- The Field Museum, Chicago IL 60605, USA
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Plomion C, Martin F. Oak genomics is proving its worth. THE NEW PHYTOLOGIST 2020; 226:943-946. [PMID: 32301515 DOI: 10.1111/nph.16560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 05/10/2023]
Affiliation(s)
| | - Francis Martin
- INRAE, UMR IAM, Centre INRAE-Grand Est, Université de Lorraine, F-54280, Champenoux, France
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Hipp AL, Manos PS, Hahn M, Avishai M, Bodénès C, Cavender-Bares J, Crowl AA, Deng M, Denk T, Fitz-Gibbon S, Gailing O, González-Elizondo MS, González-Rodríguez A, Grimm GW, Jiang XL, Kremer A, Lesur I, McVay JD, Plomion C, Rodríguez-Correa H, Schulze ED, Simeone MC, Sork VL, Valencia-Avalos S. Genomic landscape of the global oak phylogeny. THE NEW PHYTOLOGIST 2020; 226:1198-1212. [PMID: 31609470 DOI: 10.1111/nph.16162] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/05/2019] [Indexed: 05/10/2023]
Abstract
The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity. The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
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Affiliation(s)
- Andrew L Hipp
- The Morton Arboretum, Lisle, IL, 60532-1293, USA
- The Field Museum, Chicago, IL, 60605, USA
| | | | - Marlene Hahn
- The Morton Arboretum, Lisle, IL, 60532-1293, USA
| | - Michael Avishai
- Previously of, The Hebrew University of Jerusalem, Botanical Garden, Zalman Shne'ur St. 1, Jerusalem, Israel
| | | | | | | | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Thomas Denk
- Swedish Museum of Natural History, Stockholm, 10405, Sweden
| | | | - Oliver Gailing
- Büsgen-Institute, Georg-August-University Göttingen, Göttingen, D-37077, Germany
| | | | - Antonio González-Rodríguez
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, 58190, México
| | | | - Xiao-Long Jiang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | | | | | | | | | - Hernando Rodríguez-Correa
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, 58190, México
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Hans-Knoell-Str. 10, Jena, 07745, Germany
| | | | - Victoria L Sork
- University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Susana Valencia-Avalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Circuito Exterior, s.n., Ciudad Universitaria, Coyoacán, México City, CP 04510, México
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36
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Wang M, Zhang L, Zhang Z, Li M, Wang D, Zhang X, Xi Z, Keefover-Ring K, Smart LB, DiFazio SP, Olson MS, Yin T, Liu J, Ma T. Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection. THE NEW PHYTOLOGIST 2020; 225:1370-1382. [PMID: 31550399 DOI: 10.1111/nph.16215] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 09/16/2019] [Indexed: 05/10/2023]
Abstract
Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere. We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re-sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple-species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence. We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection-mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.
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Affiliation(s)
- Mingcheng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhiyang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Mengmeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI, 53706, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 25606, USA
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Granados Mendoza C, Jost M, Hágsater E, Magallón S, van den Berg C, Lemmon EM, Lemmon AR, Salazar GA, Wanke S. Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum. FRONTIERS IN PLANT SCIENCE 2020; 10:1761. [PMID: 32063915 PMCID: PMC7000662 DOI: 10.3389/fpls.2019.01761] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/16/2019] [Indexed: 05/12/2023]
Abstract
Universal angiosperm enrichment probe sets designed to enrich hundreds of putatively orthologous nuclear single-copy loci are increasingly being applied to infer phylogenetic relationships of different lineages of angiosperms at a range of evolutionary depths. Studies applying such probe sets have focused on testing the universality and performance of the target nuclear loci, but they have not taken advantage of off-target data from other genome compartments generated alongside the nuclear loci. Here we do so to infer phylogenetic relationships in the orchid genus Epidendrum and closely related genera of subtribe Laeliinae. Our aims are to: 1) test the technical viability of applying the plant anchored hybrid enrichment (AHE) method (Angiosperm v.1 probe kit) to our focal group, 2) mine plastid protein coding genes from off-target reads; and 3) evaluate the performance of the target nuclear and off-target plastid loci in resolving and supporting phylogenetic relationships along a range of taxonomical depths. Phylogenetic relationships were inferred from the nuclear data set through coalescent summary and site-based methods, whereas plastid loci were analyzed in a concatenated partitioned matrix under maximum likelihood. The usefulness of target and flanking non-target nuclear regions and plastid loci was assessed through the estimation of their phylogenetic informativeness. Our study successfully applied the plant AHE probe kit to Epidendrum, supporting the universality of this kit in angiosperms. Moreover, it demonstrated the feasibility of mining plastome loci from off-target reads generated with the Angiosperm v.1 probe kit to obtain additional, uniparentally inherited sequence data at no extra sequencing cost. Our analyses detected some strongly supported incongruences between nuclear and plastid data sets at shallow divergences, an indication of potential lineage sorting, hybridization, or introgression events in the group. Lastly, we found that the per site phylogenetic informativeness of the ycf1 plastid gene surpasses that of all other plastid genes and several nuclear loci, making it an excellent candidate for assessing phylogenetic relationships at medium to low taxonomic levels in orchids.
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Affiliation(s)
- Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Eric Hágsater
- Herbario AMO, Instituto Chinoin, A.C., Mexico City, Mexico
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States
| | - Gerardo A. Salazar
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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López de Heredia U, Mora-Márquez F, Goicoechea PG, Guillardín-Calvo L, Simeone MC, Soto Á. ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids. FRONTIERS IN PLANT SCIENCE 2020; 11:564414. [PMID: 33013984 PMCID: PMC7498617 DOI: 10.3389/fpls.2020.564414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/13/2020] [Indexed: 05/03/2023]
Abstract
Hybridization and its relevance is a hot topic in ecology and evolutionary biology. Interspecific gene flow may play a key role in species adaptation to environmental change, as well as in the survival of endangered populations. Despite the fact that hybridization is quite common in plants, many hybridizing species, such as Quercus spp., maintain their integrity, while precise determination of genomic boundaries between species remains elusive. Novel high throughput sequencing techniques have opened up new perspectives in the comparative analysis of genomes and in the study of historical and current interspecific gene flow. In this work, we applied ddRADseq technique and developed an ad hoc bioinformatics pipeline for the study of ongoing hybridization between two relevant Mediterranean oaks, Q. ilex and Q. suber. We adopted a local scale approach, analyzing adult hybrids (sensu lato) identified in a mixed stand and their open-pollinated progenies. We have identified up to 9,435 markers across the genome and have estimated individual introgression levels in adults and seedlings. Estimated contribution of Q. suber to the genome is higher, on average, in hybrid progenies than in hybrid adults, suggesting preferential backcrossing with this parental species, maybe followed by selection during juvenile stages against individuals with higher Q. suber genomic contribution. Most discriminating markers seem to be scattered throughout the genome, suggesting that a large number of small genomic regions underlie boundaries between these species. A noticeable proportion of the markers (26%) showed allelic frequencies in adult hybrids very similar to one of the parental species, and very different from the other; a finding that seems relevant for understanding the hybridization process and the occurrence of adaptive introgression. Candidate marker databases developed in this study constitute a valuable resource to design large scale re-sequencing experiments in Mediterranean sclerophyllous oak species and could provide insight in species boundaries and on adaptive introgression between Q. suber and Q. ilex.
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Affiliation(s)
- Unai López de Heredia
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando Mora-Márquez
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Laura Guillardín-Calvo
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Marco C. Simeone
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Álvaro Soto
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
- *Correspondence: Álvaro Soto,
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39
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Vázquez ML. Molecular evolution of the internal transcribed spacers in red oaks (Quercus sect. Lobatae). Comput Biol Chem 2019; 83:107117. [PMID: 31581032 DOI: 10.1016/j.compbiolchem.2019.107117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/09/2019] [Accepted: 08/26/2019] [Indexed: 10/26/2022]
Abstract
Previous studies of the Internal Transcribed Spacers of the nuclear ribosomal DNA (ITS) in sections Quercus (white oaks), Protobalanus (intermediate or golden cup oaks), Cerris (Cerris oaks), and Ilex (Ilex oaks) suggest that ITS regions undergo full concerted evolution in oaks; however, ITS evolution patterns in red oaks (section Lobatae) are unknown due to scant representation in published work. To determine whether full concerted evolution occurs in red oaks, the purpose of this study was to examine ITS sequences from 40 red oak species. The results show incomplete concerted evolution and the presence of three ITS ribotypes of lengths 505, 609, 601 bp, hereafter referred to as ITS-S (small), I ITS-M (medium), and ITS-L (large), respectively. Thirty species had only one ribotype (ITS-M), nine species had two ribotypes (different combinations of ITS-L, ITS-M, and ITS-S), and only one species had all three ribotypes. Furthermore, examination of these three ribotypes showed that only ITS-M is putatively functional and ITS-L and ITS-S are pseudogenes. Bayesian analysis strongly supported (100%) two pseudogenes clades but provided weak support for the monophyly of a putative functional clade (ITS-M); moreover, within the "functional" clade, species relationships were uncertain and, in most cases, sequences from the same species failed to group together. The results of the current study suggest that ITS may not be appropriate for phylogeny reconstruction of red oaks due to low levels of interspecific variation and incomplete concerted evolution.
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Affiliation(s)
- M Lucía Vázquez
- Biology Department, University of Illinois Springfield, One University Plaza, Springfield, IL, 62794-9243, USA.
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