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Wang M, Zhu M, Qian J, Yang Z, Shang F, Egan AN, Li P, Liu L. Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes. Mol Phylogenet Evol 2024; 197:108093. [PMID: 38740145 DOI: 10.1016/j.ympev.2024.108093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Mulberries (genus Morus), belonging to the order Rosales, family Moraceae, are important woody plants due to their economic values in sericulture, as well as for nutritional benefits and medicinal values. However, the taxonomy and phylogeny of Morus, especially for the Asian species, remains challenging due to its wide geographical distribution, morphological plasticity, and interspecific hybridization. To better understand the evolutionary history of Morus, we combined plastomes and a large-scale nuclear gene analyses to investigate their phylogenetic relationships. We assembled the plastomes and screened 211 single-copy nuclear genes from 13 Morus species and related taxa. The plastomes of Morus species were relatively conserved in terms of genome size, gene content, synteny, IR boundary and codon usage. Using nuclear data, our results elucidated identical topologies based on coalescent and concatenation methods. The genus Morus was supported as monophyletic, with M. notabilis as the first diverging lineage and the two North American Morus species, M. microphylla and M. rubra, as sister to the other Asian species. In the Asian Morus species, interspecific relationships were completely resolved. However, cyto-nuclear discordances and gene tree-species tree conflicts were detected in the phylogenies of Morus, with multiple evidences supporting hybridization/introgression as the main cause of discordances between nuclear and plastid phylogenies, while gene tree-species tree conflicts were mainly caused by ILS.
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Affiliation(s)
- Meizhen Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453000, China; Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mengmeng Zhu
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Jiayi Qian
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhaoping Yang
- College of Life Sciences and Technologies, Tarim University, Alar 843300, China
| | - Fude Shang
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng 475001, China; College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Ashley N Egan
- Department of Biology, Utah Valley University, Orem, UT 84058, United States.
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Luxian Liu
- College of Life Sciences, Henan Normal University, Xinxiang 453000, China; Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng 475001, China.
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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae. PLoS One 2024; 19:e0302365. [PMID: 38768140 PMCID: PMC11104678 DOI: 10.1371/journal.pone.0302365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
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Naranjo AA, Edwards CE, Gitzendanner MA, Soltis DE, Soltis PS. Abundant incongruence in a clade endemic to a biodiversity hotspot: Phylogenetics of the scrub mint clade (Lamiaceae). Mol Phylogenet Evol 2024; 192:108014. [PMID: 38199595 DOI: 10.1016/j.ympev.2024.108014] [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: 10/07/2023] [Revised: 12/26/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
The Scrub Mint clade(Lamiaceae) provides a unique system for investigating the evolutionary processes driving diversification in the North American Coastal Plain from both a systematic and biogeographic context. The clade comprisesDicerandra, Conradina, Piloblephis, Stachydeoma, and four species of the broadly defined genus Clinopodium(Mentheae; Lamiaceae), almost all of which are endemic to the North American Eastern Coastal Plain. Most species of this clade are threatened or endangered and restricted to sandhill or a mosaic of scrub habitats. We analyzed relationships in this clade to understand the evolution of the group and identify evolutionary mechanisms acting on the clade, with important implications for conservation. We used a target-capture method to sequence and analyze 238 nuclear loci across all species of scrub mints, reconstructed the phylogeny, and calculated gene tree concordance, gene tree estimation error, and reticulation indices for every node in the tree using ML methods. Phylogenetic networks were used to determine reticulation events. Our nuclear phylogenetic estimates were consistent with previous results, while greatly increasing the robustness of taxon sampling. The phylogeny resolved the full relationship between Dicerandra and Conradina and the less-studied members of the clade (Piloblephis, Stachydeoma, Clinopodium spp.). We found hotspots of gene tree discordance and reticulation throughout the tree, especially in perennial Dicerandra. Several instances of reticulation events were uncovered between annual and perennial Dicerandra, and within the Conradina + allies clade. Incomplete lineage sorting also likely contributed to phylogenetic discordance. These results clarify phylogenetic relationships in the clade and provide insight on important evolutionary drivers in the clade, such as hybridization. General relationships in the group were confirmed, while the large amount of gene tree discordance is likely due to reticulation across the phylogeny.
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Affiliation(s)
- Andre A Naranjo
- Institute of Environment, Department of Biological Sciences, Florida International University, 11200 SW 8th ST, Miami, FL 33199, USA; Florida Museum of Natural History, University of Florida, 1659 Museum Road, PO Box 117800, Gainesville, FL 32611-7800, USA.
| | | | - Matthew A Gitzendanner
- Department of Biology, University of Florida, PO Box 118526, Gainesville, FL 32611-8526, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, PO Box 117800, Gainesville, FL 32611-7800, USA; Department of Biology, University of Florida, PO Box 118526, Gainesville, FL 32611-8526, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, PO Box 117800, Gainesville, FL 32611-7800, USA
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Han B, Tong B, Zhang J, Bu Z, Zhao L, Xian Y, Li D, Xie X. Genomic divergence and demographic history of Quercus aliena populations. BMC PLANT BIOLOGY 2024; 24:39. [PMID: 38195447 PMCID: PMC10775429 DOI: 10.1186/s12870-023-04623-y] [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: 06/19/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024]
Abstract
BACKGROUND Quercus aliena is a major montane tree species of subtropical and temperate forests in China, with important ecological and economic value. In order to reveal the species' population dynamics, genetic diversity, genetic structure, and association with mountain habitats during the evolutionary process, we re-sequenced the genomes of 72 Q. aliena individuals. RESULTS The whole chloroplast and nuclear genomes were used for this study. Phylogenetic analysis using the chloroplast genome dataset supported four clades of Q. aliena, while the nuclear dataset supported three major clades. Sex-biased dispersal had a critical role in causing discordance between the chloroplast and nuclear genomes. Population structure analysis showed two groups in Q. aliena. The effective population size sharply declined 1 Mya, coinciding with the Poyang Glaciation in Eastern China. Using genotype-climate association analyses, we found a positive correlation between allele frequency variation in SNPs and temperature, suggesting the species has the capacity to adapt to changing temperatures. CONCLUSION Overall, this study illustrates the genetic divergence, genomic variation, and evolutionary processes behind the demographic history of Q. aliena.
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Affiliation(s)
- Biao Han
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Boqiang Tong
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Jiliang Zhang
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Ziheng Bu
- School of Life Sciences, Shandong University, Qingdao, 266237, Shandong, China
| | - Lijun Zhao
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Yang Xian
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Dezhu Li
- 3Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Xiaoman Xie
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China.
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Zhang SY, Yan HF, Wei L, Liu TJ, Chen L, Hao G, Wu X, Zhang QL. Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae). BMC PLANT BIOLOGY 2024; 24:23. [PMID: 38166728 PMCID: PMC10763413 DOI: 10.1186/s12870-023-04697-8] [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: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Spiraea L. is a genus comprising approximately 90 species that are distributed throughout the northern temperate regions. China is recognized as the center of species diversity for this genus, hosting more than 70 species, including 47 endemic species. While Spiraea is well-known for its ornamental value, its taxonomic and phylogenetic studies have been insufficient. RESULTS In this study, we conducted sequencing and assembly of the plastid genomes (plastomes) of 34 Asiatic Spiraea accessions (representing 27 Asiatic Spiraea species) from China and neighboring regions. The Spiraea plastid genome exhibits typical quadripartite structures and encodes 113-114 genes, including 78-79 protein-coding genes (PCGs), 30 tRNA genes, and 4 rRNA genes. Linear regression analysis revealed a significant correlation between genome size and the length of the SC region. By the sliding windows method, we identified several hypervariable hotspots within the Spiraea plastome, all of which were localized in the SC regions. Our phylogenomic analysis successfully established a robust phylogenetic framework for Spiraea, but it did not support the current defined section boundaries. Additionally, we discovered that the genus underwent diversification after the Early Oligocene (~ 30 Ma), followed by a rapid speciation process during the Pliocene and Pleistocene periods. CONCLUSIONS The plastomes of Spiraea provided us invaluable insights into its phylogenetic relationships and evolutionary history. In conjunction with plastome data, further investigations utilizing other genomes, such as the nuclear genome, are urgently needed to enhance our understanding of the evolutionary history of this genus.
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Affiliation(s)
- Shu-Yan Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lei Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lin Chen
- Hangzhou Xixi National Wetland Park Service Center (Hangzhou Xixi National Wetland Park Ecology & Culture Research Center), Hangzhou, 310013, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xing Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Qiao-Ling Zhang
- Hangzhou Xixi National Wetland Park Service Center (Hangzhou Xixi National Wetland Park Ecology & Culture Research Center), Hangzhou, 310013, 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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Caycho E, La Torre R, Orjeda G. Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae). BMC PLANT BIOLOGY 2023; 23:570. [PMID: 37974117 PMCID: PMC10652460 DOI: 10.1186/s12870-023-04581-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Neltuma pallida is a tree that grows in arid soils in northwestern Peru. As a predominant species of the Equatorial Dry Forest ecoregion, it holds significant economic and ecological value for both people and environment. Despite this, the species is severely threatened and there is a lack of genetic and genomic research, hindering the proposal of evidence-based conservation strategies. RESULTS In this work, we conducted the assembly, annotation, analysis and comparison of the chloroplast genome of a N. pallida specimen with those of related species. The assembled chloroplast genome has a length of 162,381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC content was 35.97%. However, this is variable between regions, with a higher GC content observed in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 22 contained at least one intron in their sequence. A substantial number of repetitive sequences of different types were identified in the assembled genome, predominantly tandem repeats (> 300). In particular, 142 microsatellites (SSR) markers were identified. The phylogenetic reconstruction showed that N. pallida grouped with the other Neltuma species and with Prosopis cineraria. The analysis of sequence divergence between the chloroplast genome sequences of N. pallida, N. juliflora, P. farcta and Strombocarpa tamarugo revealed a high degree of similarity. CONCLUSIONS The N. pallida chloroplast genome was found to be similar to those of closely related species. With a size of 162,831 bp, it had the classical chloroplast quadripartite structure and GC content of 35.97%. Most of the 132 identified genes were protein-coding genes. Additionally, over 800 repetitive sequences were identified, including 142 SSR markers. In the phylogenetic analysis, N. pallida grouped with other Neltuma spp. and P. cineraria. Furthermore, N. pallida chloroplast was highly conserved when compared with genomes of closely related species. These findings can be of great potential for further diversity studies and genetic improvement of N. pallida.
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Affiliation(s)
- Esteban Caycho
- Laboratory of Genomics and Bioinformatics for Biodiversity, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, 15081, Lima, Peru
| | - Renato La Torre
- Laboratory of Genomics and Bioinformatics for Biodiversity, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, 15081, Lima, Peru
| | - Gisella Orjeda
- Laboratory of Genomics and Bioinformatics for Biodiversity, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, 15081, Lima, Peru.
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Zhang C, Meng R, Meng Y, Guo BL, Liu QR, Nie ZL. Parallel evolution, atavism, and extensive introgression explain the radiation of Epimedium sect. Diphyllon (Berberidaceae) in southern East Asia. FRONTIERS IN PLANT SCIENCE 2023; 14:1234148. [PMID: 37915504 PMCID: PMC10616310 DOI: 10.3389/fpls.2023.1234148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
East Asia is the richest region of plant biodiversity in the northern temperate zone, and its radiation provides key insights for understanding rapid speciation, including evolutionary patterns and processes. However, it is challenging to investigate the recent evolutionary radiation among plants because of the lack of genetic divergence, phenotypic convergence, and interspecific gene flow. Epimedium sect. Diphyllon is a rarely studied plant lineage endemic to East Asia, especially highly diversified in its southern part. In this study, we report a robust phylogenomic analysis based on genotyping-by-sequencing data of this lineage. The results revealed a clear biogeographic pattern for Epimedium sect. Diphyllon with recognition into two major clades corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms of East Asian Flora and rapid diversification of the extant species dated to the Pleistocene. Evolutionary radiation of Epimedium sect. Diphyllon is characterized by recent and predominant parallel evolution and atavism between the two subkingdom regions, with extensive reticulating hybridization within each region during the course of diversification in southern East Asia. A parallel-atavism-introgression hypothesis is referred to in explaining the radiation of plant diversity in southern East Asia, which represents a potential model for the rapid diversification of plants under global climate cooling in the late Tertiary. Our study advances our understanding of the evolutionary processes of plant radiation in East Asia as well as in other biodiversity hotspot regions.
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Affiliation(s)
- Cheng Zhang
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ran Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ying Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Bao-Lin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Quan-Ru Liu
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ze-Long Nie
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, 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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Yang Z, Ma X, Wang Q, Tian X, Sun J, Zhang Z, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae. Nat Commun 2023; 14:5542. [PMID: 37696791 PMCID: PMC10495350 DOI: 10.1038/s41467-023-41137-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.
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Affiliation(s)
- Zhiping Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolin Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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11
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Baldwin E, McNair M, Leebens-Mack J. Rampant chloroplast capture in Sarracenia revealed by plastome phylogeny. FRONTIERS IN PLANT SCIENCE 2023; 14:1237749. [PMID: 37711293 PMCID: PMC10497973 DOI: 10.3389/fpls.2023.1237749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/20/2023] [Indexed: 09/16/2023]
Abstract
Introgression can produce novel genetic variation in organisms that hybridize. Sympatric species pairs in the carnivorous plant genus Sarracenia L. frequently hybridize, and all known hybrids are fertile. Despite being a desirable system for studying the evolutionary consequences of hybridization, the extent to which introgression occurs in the genus is limited to a few species in only two field sites. Previous phylogenomic analysis of Sarracenia estimated a highly resolved species tree from 199 nuclear genes, but revealed a plastid genome that is highly discordant with the species tree. Such cytonuclear discordance could be caused by chloroplast introgression (i.e. chloroplast capture) or incomplete lineage sorting (ILS). To better understand the extent to which introgression is occurring in Sarracenia, the chloroplast capture and ILS hypotheses were formally evaluated. Plastomes were assembled de-novo from sequencing reads generated from 17 individuals in addition to reads obtained from the previous study. Assemblies of 14 whole plastomes were generated and annotated, and the remaining fragmented assemblies were scaffolded to these whole-plastome assemblies. Coding sequence from 79 homologous genes were aligned and concatenated for maximum-likelihood phylogeny estimation. The plastome tree is extremely discordant with the published species tree. Plastome trees were simulated under the coalescent and tree distance from the species tree was calculated to generate a null distribution of discordance that is expected under ILS alone. A t-test rejected the null hypothesis that ILS could cause the level of discordance seen in the plastome tree, suggesting that chloroplast capture must be invoked to explain the discordance. Due to the extreme level of discordance in the plastome tree, it is likely that chloroplast capture has been common in the evolutionary history of Sarracenia.
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Affiliation(s)
- Ethan Baldwin
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Mason McNair
- Department of Plant & Environmental Science, Clemson University, Florence, SC, United States
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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12
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Liu TJ, Zhang SY, Wei L, Lin W, Yan HF, Hao G, Ge XJ. Plastome evolution and phylogenomic insights into the evolution of Lysimachia (Primulaceae: Myrsinoideae). BMC PLANT BIOLOGY 2023; 23:359. [PMID: 37452336 PMCID: PMC10347800 DOI: 10.1186/s12870-023-04363-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Lysimachia L., the second largest genus within the subfamily Myrsinoideae of Primulaceae, comprises approximately 250 species worldwide. China is the species diversity center of Lysimachia, containing approximately 150 species. Despite advances in the backbone phylogeny of Lysimachia, species-level relationships remain poorly understood due to limited genomic information. This study analyzed 50 complete plastomes for 46 Lysimachia species. We aimed to identify the plastome structure features and hypervariable loci of Lysimachia. Additionally, the phylogenetic relationships and phylogenetic conflict signals in Lysimachia were examined. RESULTS These fifty plastomes within Lysimachia had the typical quadripartite structure, with lengths varying from 152,691 to 155,784 bp. Plastome size was positively correlated with IR and intron length. Thirteen highly variable regions in Lysimachia plastomes were identified. Additionally, ndhB, petB and ycf2 were found to be under positive selection. Plastid ML trees and species tree strongly supported that L. maritima as sister to subg. Palladia + subg. Lysimachia (Christinae clade), while the nrDNA ML tree clearly placed L. maritima and subg. Palladia as a sister group. CONCLUSIONS The structures of these plastomes of Lysimachia were generally conserved, but potential plastid markers and signatures of positive selection were detected. These genomic data provided new insights into the interspecific relationships of Lysimachia, including the cytonuclear discordance of the position of L. maritima, which may be the result of ghost introgression in the past. Our findings have established a basis for further exploration of the taxonomy, phylogeny and evolutionary history within Lysimachia.
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Affiliation(s)
- Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Shu-Yan Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Lei Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Lin
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, 510650, China
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13
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Slovák M, Melichárková A, Štubňová EG, Kučera J, Mandáková T, Smyčka J, Lavergne S, Passalacqua NG, Vďačný P, Paun O. Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae). Syst Biol 2023; 72:491-504. [PMID: 36331548 PMCID: PMC10276626 DOI: 10.1093/sysbio/syac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2024] Open
Abstract
Hybridization is a key mechanism involved in lineage diversification and speciation, especially in ecosystems that experienced repeated environmental oscillations. Recently radiated plant groups, which have evolved in mountain ecosystems impacted by historical climate change provide an excellent model system for studying the impact of gene flow on speciation. We combined organellar (whole-plastome) and nuclear genomic data (RAD-seq) with a cytogenetic approach (rDNA FISH) to investigate the effects of hybridization and introgression on evolution and speciation in the genus Soldanella (snowbells, Primulaceae). Pervasive introgression has already occurred among ancestral lineages of snowbells and has persisted throughout the entire evolutionary history of the genus, regardless of the ecology, cytotype, or distribution range size of the affected species. The highest extent of introgression has been detected in the Carpathian species, which is also reflected in their extensive karyotype variation. Introgression occurred even between species with dysploid and euploid cytotypes, which were considered to be reproductively isolated. The magnitude of introgression detected in snowbells is unprecedented in other mountain genera of the European Alpine System investigated hitherto. Our study stresses the prominent evolutionary role of hybridization in facilitating speciation and diversification on the one hand, but also enriching previously isolated genetic pools. [chloroplast capture; diversification; dysploidy; European Alpine system; introgression; nuclear-cytoplasmic discordance; ribosomal DNA.].
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Affiliation(s)
- Marek Slovák
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Department of Botany, Charles University, Prague, Czech Republic
| | - Andrea Melichárková
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Eliška Gbúrová Štubňová
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Slovak National Museum, Natural History Museum, Bratislava, Slovakia
| | - Jaromír Kučera
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Terezie Mandáková
- Central European Institute of Technology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Jan Smyčka
- Department of Botany, Charles University, Prague, Czech Republic
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, Jilská 1, 110 00 Praha, Czech Republic
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | - Sébastien Lavergne
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | | | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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14
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Dong W, Gao L, Xu C, Song Y, Poczai P. Editorial: Rise to the challenges in plastome phylogenomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1200302. [PMID: 37324700 PMCID: PMC10267445 DOI: 10.3389/fpls.2023.1200302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Affiliation(s)
- Wenpan Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lianming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Normal University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, China
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Museomics Research Group, Helsinki Institute of Life Science (HiLIFE), Helsinki, Finland
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15
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Nie ZL, Hodel R, Ma ZY, Johnson G, Ren C, Meng Y, Ickert-Bond SM, Liu XQ, Zimmer E, Wen J. Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1183-1203. [PMID: 36772845 DOI: 10.1111/jipb.13466] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/08/2023] [Indexed: 05/13/2023]
Abstract
The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.
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Affiliation(s)
- Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Richard Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Stefanie M Ickert-Bond
- Herbarium (ALA), University of Alaska Museum of the North, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Elizabeth Zimmer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
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16
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Kantor A, Kučera J, Šlenker M, Breidy J, Dönmez AA, Marhold K, Slovák M, Svitok M, Zozomová-Lihová J. Evolution of hygrophytic plant species in the Anatolia-Caucasus region: insights from phylogenomic analyses of Cardamine perennials. ANNALS OF BOTANY 2023; 131:585-600. [PMID: 36656962 PMCID: PMC10147327 DOI: 10.1093/aob/mcad008] [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: 10/10/2022] [Accepted: 01/10/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Southwestern Asia is a significant centre of biodiversity and a cradle of diversification for many plant groups, especially xerophytic elements. In contrast, little is known about the evolution and diversification of its hygrophytic flora. To fill this gap, we focus on Cardamine (Brassicaceae) species that grow in wetlands over a wide altitudinal range. We aimed to elucidate their evolution, assess the extent of presumed historical gene flow between species, and draw inferences about intraspecific structure. METHODS We applied the phylogenomic Hyb-Seq approach, ecological niche analyses and multivariate morphometrics to a total of 85 Cardamine populations from the target region of Anatolia-Caucasus, usually treated as four to six species, and supplemented them with close relatives from Europe. KEY RESULTS Five diploids are recognized in the focus area, three of which occur in regions adjacent to the Black and/or Caspian Sea (C. penzesii, C. tenera, C. lazica), one species widely distributed from the Caucasus to Lebanon and Iran (C. uliginosa), and one western Anatolian entity (provisionally C. cf. uliginosa). Phylogenomic data suggest recent speciation during the Pleistocene, likely driven by both geographic separation (allopatry) and ecological divergence. With the exception of a single hybrid (allotetraploid) speciation event proven for C. wiedemanniana, an endemic of southern Turkey, no significant traces of past or present interspecific gene flow were observed. Genetic variation within the studied species is spatially structured, suggesting reduced gene flow due to geographic and ecological barriers, but also glacial survival in different refugia. CONCLUSIONS This study highlights the importance of the refugial regions of the Black and Caspian Seas for both harbouring and generating hygrophytic species diversity in Southwestern Asia. It also supports the significance of evolutionary links between Anatolia and the Balkan Peninsula. Reticulation and polyploidization played a minor evolutionary role here in contrast to the European relatives.
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Affiliation(s)
- Adam Kantor
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, 128 01Prague, Czechia
| | - Jaromír Kučera
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
| | - Marek Šlenker
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
| | - Joêlle Breidy
- National Genebank, Lebanese Agricultural Research Institute, Zahle 1801, Lebanon
| | - Ali A Dönmez
- Botany Section, Department of Biology, Faculty of Science, Hacettepe University, 06800 Beytepe-Ankara, Turkey
| | - Karol Marhold
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, 128 01Prague, Czechia
| | - Marek Slovák
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, 128 01Prague, Czechia
| | - Marek Svitok
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, 960 01Zvolen, Slovakia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Judita Zozomová-Lihová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
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17
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Yu J, Niu Y, You Y, Cox CJ, Barrett RL, Trias-Blasi A, Guo J, Wen J, Lu L, Chen Z. Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains. THE NEW PHYTOLOGIST 2023; 238:888-903. [PMID: 36305244 DOI: 10.1111/nph.18580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation. Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal. We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.
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Affiliation(s)
- Jinren Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanting Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yichen You
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, 2567, NSW, Australia
| | | | - Jing Guo
- 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
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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18
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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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Phylogenomics of Aralia sect. Aralia (Araliaceae): Signals of hybridization and insights into its species delimitations and intercontinental biogeography. Mol Phylogenet Evol 2023; 181:107727. [PMID: 36754338 DOI: 10.1016/j.ympev.2023.107727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
Genome-scale data have significantly increased the number of informative characters for phylogenetic analyses and recent studies have also revealed widespread phylogenomic discordance in many plant lineages. Aralia sect. Aralia is a small plant lineage (14 spp.) of the ginseng family Araliaceae with a disjunct distribution between eastern Asia (11 spp.) and North America (3 spp.). We herein employ sequences of hundreds of nuclear loci and the complete plastomes using targeted sequence capture and genome skimming to reconstruct the phylogenetic and biogeographic history of this section. We detected substantial conflicts among nuclear genes, yet different analytical strategies generated largely congruent topologies from the nuclear data. Significant cytonuclear discordance was detected, especially concerning the positions of the three North American species. The phylogenomic results support two intercontinental disjunctions: (1) Aralia californica of western North America is sister to the eastern Asian clade consisting of A. cordata and A. continentalis in the nuclear tree, and (2) the eastern North American A. racemosa forms a clade with A. bicrenata from southwestern North America, and the North American A. racemosa - A. bicrenata clade is then sister to the eastern Asian clade consisting of A. glabra (Japan), A. fargesii (C China), and A. apioides and A. atropurpurea (the Hengduan Mountains). Aralia cordata is supported to be disjunctly distributed in Japan, Taiwan, the Ulleung island of Korea, and in Central, Southwest and South China, and Aralia continentalis is redefined with a narrower distribution in Northeast China, eastern Russia and peninsular Korea.
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20
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Luo D, Song MS, Xu B, Zhang Y, Zhang JW, Ma XG, Hao XJ, Sun H. A clue to the evolutionary history of modern East Asian flora: insights from phylogeography and diterpenoid alkaloid distribution pattern of the Spiraea japonica complex. Mol Phylogenet Evol 2023; 184:107772. [PMID: 36977458 DOI: 10.1016/j.ympev.2023.107772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/07/2023] [Accepted: 03/21/2023] [Indexed: 03/28/2023]
Abstract
Each subkingdom of East Asian flora (EAF) has a unique evolutionary history, but which has rarely been described based on phylogeographic studies of EAF species. The Spiraea japonica L. complex, which is widespread in East Asia (EA), has received considerable attention because of the presence of diterpenoid alkaloids (DAs). It provides a proxy for understanding the genetic diversity and DA distribution patterns of species under various environmental conditions associated with the geological background in EA. In the present study, the plastome and chloroplast/nuclear DNA of 71 populations belonging to the S. japonica complex and its congeners were sequenced, combined with DA identification, environmental analyses, and ecological niche modelling, to investigate their phylogenetic relationships, genetic and DAs distribution patterns, biogeography, and demographic dynamics. An "ampliative" S. japonica complex was put forward, comprising all species of Sect. Calospira Ser. Japonicae, of which three evolutionary units carrying their respective unique types of DAs were identified and associated with the regionalization of EAF (referring to the Hengduan Mountains, central China, and east China). Moreover, a transition belt in central China with its biogeographic significance was revealed by genetic and DA distribution patterns from the perspective of ecological adaptation. The origin and onset differentiation of the "ampliative" S. japonica complex was estimated in the early Miocene (22.01/19.44 Ma). The formation of Japanese populations (6.75 Ma) was facilitated by the land bridge, which subsequently had a fairly stable demographic history. The populations in east China have undergone a founder effect after the Last Glacial Maximum, which may have been promoted by the expansion potential of polyploidization. Overall, the in-situ origin and diversification of the "ampliative" S. japonica complex since the early Miocene is a vertical section of the formation and development of modern EAF and was shaped by the geological history of each subkingdom.
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Affiliation(s)
- Dong Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Min-Shu Song
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Bo Xu
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Yu Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Jian-Wen Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Xiang-Guang Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Xiao-Jiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
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21
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Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars. Int J Mol Sci 2023; 24:ijms24043606. [PMID: 36835020 PMCID: PMC9964644 DOI: 10.3390/ijms24043606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/30/2022] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Lagerstroemia indica L. is a well-known ornamental plant with large pyramidal racemes, long flower duration, and diverse colors and cultivars. It has been cultivated for nearly 1600 years and is essential for investigating the germplasm and assessing genetic variation to support international cultivar identification and breeding programs. In this study, 20 common Lagerstroemia indica cultivars from different varietal groups and flower morphologies, as well as multiple wild relative species, were analyzed to investigate the maternal donor of Lagerstroemia indica cultivars and to discover the genetic variation and relationships among cultivars based on plastome and nuclear ribosomal DNA (nrDNA) sequences. A total of 47 single nucleotide polymorphisms (SNPs) and 24 insertion/deletions (indels) were identified in the 20 L. indica cultivars' plastome and 25 SNPs were identified in the nrDNA. Phylogenetic analysis based on the plastome sequences showed that all the cultivars formed a clade with the species of L. indica, indicating that L. indica was the maternal donor of the cultivars. Population structure and PCA analyses supported two clades of cultivars, which exhibited significant genetic differences according to the plastome dataset. The results of the nrDNA supported that all 20 cultivars were divided into three clades and most of the cultivars had at least two genetic backgrounds and higher gene flow. Our results suggest that the plastome and nrDNA sequences can be used as molecular markers for assessing the genetic variation and relationships of L. indica cultivars.
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22
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Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
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23
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Secci-Petretto G, Englmaier GK, Weiss SJ, Antonov A, Persat H, Denys GPJ, Schenekar T, Romanov VI, Taylor EB, Froufe E. Evaluating a species phylogeny using ddRAD SNPs: Cyto-nuclear discordance and introgression in the salmonid genus Thymallus (Salmonidae). Mol Phylogenet Evol 2023; 178:107654. [PMID: 36336233 DOI: 10.1016/j.ympev.2022.107654] [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: 06/10/2022] [Revised: 10/05/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Hybridization and introgression are very common among freshwater fishes due to the dynamic nature of hydrological landscapes. Cyclic patterns of allopatry and secondary contact provide numerous opportunities for interspecific gene flow, which can lead to discordant paths of evolution for mitochondrial and nuclear genomes. Here, we used double digest restriction-site associated DNA sequencing (ddRADseq) to obtain a genome-wide single nucleotide polymorphism (SNP) dataset comprehensive for allThymallus (Salmonidae)species to infer phylogenetic relationships and evaluate potential recent and historical gene flow among species. The newly obtained nuclear phylogeny was largely concordant with a previously published mitogenome-based topology but revealed a few cyto-nuclear discordances. These incongruencies primarily involved the placement of internal nodes rather than the resolution of species, except for one European species where anthropogenic stock transfers are thought to be responsible for the observed pattern. The analysis of four contact zones where multiple species are found revealed a few cases of mitochondrial capture and limited signals of nuclear introgression. Interestingly, the mechanisms restricting interspecific gene flow might be distinct; while in zones of secondary contact, small-scale physical habitat separation appeared as a limiting factor, biologically based reinforcement mechanisms are presumed to be operative in areas where species presumably evolved in sympatry. Signals of historical introgression were largely congruent with the routes of species dispersal previously inferred from mitogenome data. Overall, the ddRADseq dataset provided a robust phylogenetic reconstruction of the genus Thymallus including new insights into historical hybridization and introgression, opening up new questions concerning their evolutionary history.
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Affiliation(s)
- Giulia Secci-Petretto
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Portugal
| | - Gernot K Englmaier
- University of Graz, Institute of Biology, Universitätsplatz 2, 8010 Graz, Austria
| | - Steven J Weiss
- University of Graz, Institute of Biology, Universitätsplatz 2, 8010 Graz, Austria.
| | - Alexander Antonov
- Institute of Water and Ecological Problems, Far East Branch, Russian Academy of Sciences, ul. Kim Yu Chena 65, Khabarovsk, 680063 Russia
| | - Henri Persat
- Société Française d'Ichthyologie, Muséum National d'Histoire Naturelle Paris, France, 57 rue Cuvier CP26, 75005 Paris, France
| | - Gael P J Denys
- Unité Patrimoine Naturel - Centre d'expertise et de données (2006 OFB - CNRS - MNHN), Muséum national d'Histoire naturelle, 36 rue Geoffroy Saint-Hilaire CP 41, 75005 Paris, France; Biologie des organismes et écosystèmes aquatiques (BOREA 8067), MNHN, CNRS, IRD, SU, UCN, UA, 57 rue Cuvier CP26, 75005 Paris, France
| | - Tamara Schenekar
- University of Graz, Institute of Biology, Universitätsplatz 2, 8010 Graz, Austria
| | | | - Eric B Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z, Canada
| | - Elsa Froufe
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.
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24
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Stubbs RL, Theodoridis S, Mora‐Carrera E, Keller B, Yousefi N, Potente G, Léveillé‐Bourret É, Celep F, Kochjarová J, Tedoradze G, Eaton DAR, Conti E. Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot. THE NEW PHYTOLOGIST 2023; 237:656-671. [PMID: 36210520 PMCID: PMC10099377 DOI: 10.1111/nph.18525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in Primula. Biogeographic analyses support the 'out-of-the-Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots.
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Affiliation(s)
- Rebecca L. Stubbs
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Spyros Theodoridis
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am Main60325Germany
| | - Emiliano Mora‐Carrera
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Étienne Léveillé‐Bourret
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV)Université de MontréalQuébecH1X 2B2Canada
| | - Ferhat Celep
- Department of Biology, Faculty of Arts and SciencesKırıkkale UniversityKırıkkale71450Turkey
| | - Judita Kochjarová
- Department of Phytology, Faculty of ForestryTechnical University in ZvolenZvolen96001Slovak Republic
| | - Giorgi Tedoradze
- Department of Plant Systematics and Geography, Institute of BotanyIlia State UniversityTbilisi0105Georgia
| | - Deren A. R. Eaton
- Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNY10027USA
| | - Elena Conti
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
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25
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Rose JP, Sytsma KJ. Phylogeography and genetic variation in Western Jacob's ladder (Polemonium occidentale) provide insights into the origin and conservation of rare species in the Great Lakes region. Mol Ecol 2023; 32:79-94. [PMID: 36217576 DOI: 10.1111/mec.16730] [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: 01/18/2022] [Revised: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022]
Abstract
The perennial herb Western Jacob's Ladder (Polemonium occidentale, Polemoniaceae) is widespread in the mountains of western North America but reappears as a disjunct in the Great Lakes Region in Minnesota and Wisconsin, USA as the narrow endemic P. occidentale subsp. lacustre. This distribution is shown by a diverse assemblage of angiosperms. It has been hypothesized that these species became isolated just after the Last Glacial Maximum, but this has not been tested. Additionally, the genetic diversity and population connectivity of the endemic Great Lakes flora has been understudied, with important conservation implications. Using genotyping-by-sequencing, we examined the relationship of P. occidentale subsp. lacustre to its closest relatives, relationships among all known populations, and genetic diversity within these populations. Polemonium occidentale subsp. lacustre represents an isolated, unique lineage that diverged from its closest relatives 1.3 Ma and arrived in the Great Lakes Region by at least 38 ka. Nearly all extant populations diverged prior to the Last Glacial Maximum, are genetically distinct, and show little within-population genetic diversity. Clonality may mitigate reduction in diversity due to drift. Mixed population signal between Wisconsin and some Minnesota populations may be due to gene flow during the Late Pleistocene. While populations of P. occidentale subsp. lacustre may be relictual from a now extinct western relative, it is best treated as a distinct species. Conservation efforts should focus more on ensuring that current populations remain rather than maintaining large populations sizes across a few populations. However, encouraging habitat heterogeneity may accomplish both simultaneously.
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Affiliation(s)
- Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
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26
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Xiao J, Lyu R, He J, Li M, Ji J, Cheng J, Xie L. Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:1059379. [PMID: 36452086 PMCID: PMC9703796 DOI: 10.3389/fpls.2022.1059379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Clematis is one of the largest genera of Ranunculaceae with many phylogenetic problems left to be resolved. Clematis species have considerable genome size of more than 7 Gbp, and there was no whole-genome reference sequence published in this genus. This raises difficulties in acquiring nuclear genome data for its phylogenetic analysis. Previous studies based on Sanger sequencing data, plastid genome data, and nrDNA sequences did not well resolve the phylogeny of Clematis. In this study, we used genome skimming and transcriptome data to assemble the plastid genome sequences, nuclear single nucleotide polymorphisms (SNPs) datasets, and single-copy nuclear orthologous genes (SCOGs) to reconstruct the phylogenetic backbone of Clematis, and test effectiveness of these genome partitioning methods. We also further analyzed the discordance among nuclear gene trees and between plastid and nuclear phylogenies. The results showed that the SCOGs datasets, assembled from transcriptome method, well resolved the phylogenetic backbone of Clematis. The nuclear SNPs datasets from genome skimming method can also produce similar results with the SCOGs data. In contrast to the plastid phylogeny, the phylogeny resolved by nuclear genome data is more robust and better corresponds to morphological characters. Our results suggested that rapid species radiation may have generated high level of incomplete lineage sorting, which was the major cause of nuclear gene discordance. Our simulation also showed that there may have been frequent interspecific hybridization events, which led to some of the cyto-nuclear discordances in Clematis. This study not only provides the first robust phylogenetic backbone of Clematis based on nuclear genome data, but also provides suggestions of genome partitioning strategies for the phylogenomic study of other plant taxa.
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Affiliation(s)
- Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Mingyang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jiaxin Ji
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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27
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Xiao TW, Ge XJ. Plastome structure, phylogenomics, and divergence times of tribe Cinnamomeae (Lauraceae). BMC Genomics 2022; 23:642. [PMID: 36076185 PMCID: PMC9461114 DOI: 10.1186/s12864-022-08855-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tribe Cinnamomeae is a species-rich and ecologically important group in tropical and subtropical forests. Previous studies explored its phylogenetic relationships and historical biogeography using limited loci, which might result in biased molecular dating due to insufficient parsimony-informative sites. Thus, 15 plastomes were newly sequenced and combined with published plastomes to study plastome structural variations, gene evolution, phylogenetic relationships, and divergence times of this tribe. RESULTS Among the 15 newly generated plastomes, 14 ranged from 152,551 bp to 152,847 bp, and the remaining one (Cinnamomum chartophyllum XTBGLQM0164) was 158,657 bp. The inverted repeat (IR) regions of XTBGLQM0164 contained complete ycf2, trnICAU, rpl32, and rpl2. Four hypervariable plastid loci (ycf1, ycf2, ndhF-rpl32-trnLUAG, and petA-psbJ) were identified as candidate DNA barcodes. Divergence times based on a few loci were primarily determined by prior age constraints rather than by DNA data. In contrast, molecular dating using complete plastid protein-coding genes (PCGs) was determined by DNA data rather than by prior age constraints. Dating analyses using PCGs showed that Cinnamomum sect. Camphora diverged from C. sect. Cinnamomum in the late Oligocene (27.47 Ma). CONCLUSIONS This study reports the first case of drastic IR expansion in tribe Cinnamomeae, and indicates that plastomes have sufficient parsimony-informative sites for molecular dating. Besides, the dating analyses provide preliminary insights into the divergence time within tribe Cinnamomeae and can facilitate future studies on its historical biogeography.
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Affiliation(s)
- Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
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28
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Barrett CF, Santee MV, Fama NM, Freudenstein JV, Simon SJ, Sinn BT. Lineage and role in integrative taxonomy of a heterotrophic orchid complex. Mol Ecol 2022; 31:4762-4781. [PMID: 35837745 PMCID: PMC9452484 DOI: 10.1111/mec.16617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Mathilda V. Santee
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Nicole M. Fama
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - John V. Freudenstein
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 1315 Kinnear Rd., Columbus, Ohio, USA 43212
| | - Sandra J. Simon
- Department of Biology, West Virginia University Institute of Technology, Beckley, WV, USA
| | - Brandon T. Sinn
- Department of Biology and Earth Science, Otterbein University, Westerville, OH, USA
- Department of Botany and Ecology, University of Latvia, Jelgavas iela 1, Riga, LV-1004, Latvia
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29
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Kao T, Wang T, Ku C. Rampant nuclear-mitochondrial-plastid phylogenomic discordance in globally distributed calcifying microalgae. THE NEW PHYTOLOGIST 2022; 235:1394-1408. [PMID: 35556250 PMCID: PMC9539906 DOI: 10.1111/nph.18219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Incongruent phylogenies have been widely observed between nuclear and plastid or mitochondrial genomes in terrestrial plants and animals. However, few studies have examined these patterns in microalgae or the discordance between the two organelles. Here we investigated the nuclear-mitochondrial-plastid phylogenomic incongruence in Emiliania-Gephyrocapsa, a group of cosmopolitan calcifying phytoplankton with enormous populations and recent speciations. We assembled mitochondrial and plastid genomes of 27 strains from across global oceans and temperature regimes, and analyzed the phylogenomic histories of the three compartments using concatenation and coalescence methods. Six major clades with varying morphology and distribution are well recognized in the nuclear phylogeny, but such relationships are absent in the mitochondrial and plastid phylogenies, which also differ substantially from each other. The rampant phylogenomic discordance is due to a combination of organellar capture (introgression), organellar genome recombination, and incomplete lineage sorting of ancient polymorphic organellar genomes. Hybridization can lead to replacements of whole organellar genomes without introgression of nuclear genes and the two organelles are not inherited as a single cytoplasmic unit. This study illustrates the convoluted evolution and inheritance of organellar genomes in isogamous haplodiplontic microalgae and provides a window into the phylogenomic complexity of marine unicellular eukaryotes.
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Affiliation(s)
- Tzu‐Tong Kao
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Tzu‐Haw Wang
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Chuan Ku
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
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Stojilkovič V, Záveská E, Frajman B. From Western Asia to the Mediterranean Basin: Diversification of the Widespread Euphorbia nicaeensis Alliance (Euphorbiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:815379. [PMID: 35812903 PMCID: PMC9262032 DOI: 10.3389/fpls.2022.815379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/05/2022] [Indexed: 05/19/2023]
Abstract
The Mediterranean Basin is an important biodiversity hotspot and one of the richest areas in the world in terms of plant diversity. Its flora parallels in several aspects that of the Eurasian steppes and the adjacent Irano-Turanian floristic region. The Euphorbia nicaeensis alliance spans this immense area from the western Mediterranean to Central Asia. Using an array of complementary methods, ranging from phylogenomic and phylogenetic data through relative genome size (RGS) estimation to morphometry, we explored relationships and biogeographic connections among taxa of this group. We identified the main evolutionary lineages, which mostly correspond to described taxa. However, despite the use of highly resolving Restriction Site Associated DNA (RAD) sequencing data, relationships among the main lineages remain ambiguous. This is likely due to hybridisation, lineage sorting triggered by rapid range expansion, and polyploidisation. The phylogenomic data identified cryptic diversity in the Mediterranean, which is also correlated with RGS and, partly, also, morphological divergence, rendering the description of a new species necessary. Biogeographic analyses suggest that Western Asia is the source area for the colonisation of the Mediterranean by this plant group and highlight the important contribution of the Irano-Turanian region to the high diversity in the Mediterranean Basin. The diversification of the E. nicaeensis alliance in the Mediterranean was triggered by vicariance in isolated Pleistocene refugia, morphological adaptation to divergent ecological conditions, and, to a lesser extent, by polyploidisation.
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Affiliation(s)
- Valentina Stojilkovič
- Department of Botany, University of Innsbruck, Innsbruck, Austria
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Eliška Záveská
- Department of Botany, University of Innsbruck, Innsbruck, Austria
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Innsbruck, Austria
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He J, Lyu R, Luo Y, Xiao J, Xie L, Wen J, Li W, Pei L, Cheng J. A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae. Mol Phylogenet Evol 2022; 174:107545. [PMID: 35690374 DOI: 10.1016/j.ympev.2022.107545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022]
Abstract
The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and downloaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using these data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. Evolution of the three Ranunculaceae chromosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms.
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Affiliation(s)
- Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | - Wenhe Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Linying Pei
- Beijing Engineering Technology Research Center for Garden Plants, Beijing Forestry University Forest Science Co. Ltd., Beijing 100083, PR China
| | - Jin Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
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Interpreting phylogenetic conflict: Hybridization in the most speciose genus of lichen-forming fungi. Mol Phylogenet Evol 2022; 174:107543. [PMID: 35690378 DOI: 10.1016/j.ympev.2022.107543] [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: 06/11/2021] [Revised: 02/06/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022]
Abstract
While advances in sequencing technologies have been invaluable for understanding evolutionary relationships, increasingly large genomic data sets may result in conflicting evolutionary signals that are often caused by biological processes, including hybridization. Hybridization has been detected in a variety of organisms, influencing evolutionary processes such as generating reproductive barriers and mixing standing genetic variation. Here, we investigate the potential role of hybridization in the diversification of the most speciose genus of lichen-forming fungi, Xanthoparmelia. As Xanthoparmelia is projected to have gone through recent, rapid diversification, this genus is particularly suitable for investigating and interpreting the origins of phylogenomic conflict. Focusing on a clade of Xanthoparmelia largely restricted to the Holarctic region, we used a genome skimming approach to generate 962 single-copy gene regions representing over 2 Mbp of the mycobiont genome. From this genome-scale dataset, we inferred evolutionary relationships using both concatenation and coalescent-based species tree approaches. We also used three independent tests for hybridization. Although different species tree reconstruction methods recovered largely consistent and well-supported trees, there was widespread incongruence among individual gene trees. Despite challenges in differentiating hybridization from ILS in situations of recent rapid radiations, our genome-wide analyses detected multiple potential hybridization events in the Holarctic clade, suggesting one possible source of trait variability in this hyperdiverse genus. This study highlights the value in using a pluralistic approach for characterizing genome-scale conflict, even in groups with well-resolved phylogenies, while highlighting current challenges in detecting the specific impacts of hybridization.
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Garrett P, Becher H, Gussarova G, dePamphilis CW, Ness RW, Gopalakrishnan S, Twyford AD. Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights ( Euphrasia, Orobanchaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:869583. [PMID: 35720561 PMCID: PMC9197813 DOI: 10.3389/fpls.2022.869583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Disentangling the phylogenetic relationships of taxonomically complex plant groups is often mired by challenges associated with recent speciation, hybridization, complex mating systems, and polyploidy. Here, we perform a phylogenomic analysis of eyebrights (Euphrasia), a group renowned for taxonomic complexity, with the aim of documenting the extent of phylogenetic discordance at both deep and at shallow phylogenetic scales. We generate whole-genome sequencing data and integrate this with prior genomic data to perform a comprehensive analysis of nuclear genomic, nuclear ribosomal (nrDNA), and complete plastid genomes from 57 individuals representing 36 Euphrasia species. The species tree analysis of 3,454 conserved nuclear scaffolds (46 Mb) reveals that at shallow phylogenetic scales postglacial colonization of North Western Europe occurred in multiple waves from discrete source populations, with most species not being monophyletic, and instead combining genomic variants from across clades. At a deeper phylogenetic scale, the Euphrasia phylogeny is structured by geography and ploidy, and partially by taxonomy. Comparative analyses show Southern Hemisphere tetraploids include a distinct subgenome indicative of independent polyploidy events from Northern Hemisphere taxa. In contrast to the nuclear genome analyses, the plastid genome phylogeny reveals limited geographic structure, while the nrDNA phylogeny is informative of some geographic and taxonomic affinities but more thorough phylogenetic inference is impeded by the retention of ancestral polymorphisms in the polyploids. Overall our results reveal extensive phylogenetic discordance at both deeper and shallower nodes, with broad-scale geographic structure of genomic variation but a lack of definitive taxonomic signal. This suggests that Euphrasia species either have polytopic origins or are maintained by narrow genomic regions in the face of extensive homogenizing gene flow. Moreover, these results suggest genome skimming will not be an effective extended barcode to identify species in groups such as Euphrasia, or many other postglacial species groups.
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Affiliation(s)
- Phen Garrett
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Becher
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Galina Gussarova
- Natural History Museum, University of Oslo, Oslo, Norway
- Botany Department, Faculty of Biology and Soil Science, St Petersburg State University, St Petersburg, Russia
- Tromsø University Museum, University of Tromsø, Tromsø, Norway
| | - Claude W. dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Rob W. Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | | | - Alex D. Twyford
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
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Liu BB, Ren C, Kwak M, Hodel RGJ, Xu C, He J, Zhou WB, Huang CH, Ma H, Qian GZ, Hong DY, Wen J. Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1020-1043. [PMID: 35274452 DOI: 10.1111/jipb.13246] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.
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Affiliation(s)
- Bin-Bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Myounghai Kwak
- National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Wen-Bin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, 27965, NC, USA
| | - 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
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, 510D Mueller Laboratory, University Park, Pennsylvania, 16802, USA
| | - Guan-Ze Qian
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - De-Yuan Hong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, 20013-7012, DC, USA
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Dong W, Li E, Liu Y, Xu C, Wang Y, Liu K, Cui X, Sun J, Suo Z, Zhang Z, Wen J, Zhou S. Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family. BMC Biol 2022; 20:92. [PMID: 35468824 PMCID: PMC9040247 DOI: 10.1186/s12915-022-01297-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/13/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Deep-branching phylogenetic relationships are often difficult to resolve because phylogenetic signals are obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, and incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- and shallow-scale relationships across all branches of the tree of life. The olive family (Oleaceae) is composed of 25 genera classified into five tribes with tribe Oleeae consisting of four subtribes. Previous phylogenetic analyses showed that ILS and/or hybridization led to phylogenetic incongruence in the family. It was essential to distinguish phylogenetic signal conflicts, and explore mechanisms for the uncertainties concerning relationships of the olive family, especially at the deep-branching nodes. RESULTS We used the whole plastid genome and nuclear single nucleotide polymorphism (SNP) data to infer the phylogenetic relationships and to assess the variation and rates among the main clades of the olive family. We also used 2608 and 1865 orthologous nuclear genes to infer the deep-branching relationships among tribes of Oleaceae and subtribes of tribe Oleeae, respectively. Concatenated and coalescence trees based on the plastid genome, nuclear SNPs and multiple nuclear genes suggest events of ILS and/or ancient introgression during the diversification of Oleaceae. Additionally, there was extreme heterogeneity in the substitution rates across the tribes. Furthermore, our results supported that introgression/hybridization, rather than ILS, is the main factor for phylogenetic discordance among the five tribes of Oleaceae. The tribe Oleeae is supported to have originated via ancient hybridization and polyploidy, and its most likely parentages are the ancestral lineage of Jasmineae or its sister group, which is a "ghost lineage," and Forsythieae. However, ILS and ancient introgression are mainly responsible for the phylogenetic discordance among the four subtribes of tribe Oleeae. CONCLUSIONS This study showcases that using multiple sequence datasets (plastid genomes, nuclear SNPs and thousands of nuclear genes) and diverse phylogenomic methods such as data partition, heterogeneous models, quantifying introgression via branch lengths (QuIBL) analysis, and species network analysis can facilitate untangling long and complex evolutionary processes of ancient introgression, paleopolyploidization, and ILS.
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Affiliation(s)
- Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yushuang Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Xingyong Cui
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA.
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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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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Xu Y, Liao B, Ostevik KL, Zhou H, Wang F, Wang B, Xia H. The Maternal Donor of Chrysanthemum Cultivars Revealed by Comparative Analysis of the Chloroplast Genome. FRONTIERS IN PLANT SCIENCE 2022; 13:923442. [PMID: 35720568 PMCID: PMC9202620 DOI: 10.3389/fpls.2022.923442] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/13/2022] [Indexed: 05/05/2023]
Abstract
Chrysanthemum (Chrysanthemum morifolium Ramat) is an important floricultural crop and medicinal herb. Modern chrysanthemum cultivars have complex genetic backgrounds because of multiple cycles of hybridization, polyploidization, and prolonged cultivation. Understanding the genetic background and hybrid origin of modern chrysanthemum cultivars can provide pivotal information for chrysanthemum genetic improvement and breeding. By now, the origin of cultivated chrysanthemums remains unclear. In this study, 36 common chrysanthemum cultivars from across the world and multiple wild relatives were studied to identify the maternal donor of modern chrysanthemum. Chloroplast (cp) genomes of chrysanthemum cultivars were assembled and compared with those of the wild relatives. The structure of cp genomes was highly conserved among cultivars and wild relatives. Phylogenetic analyses based on the assembled cp genomes showed that all chrysanthemum cultivars grouped together and shared 64 substitutions that were distinct from those of their wild relatives. These results indicated that a diverged lineage of the genus Chrysanthemum, which was most likely an extinct or un-sampled species/population, provided a maternal source for modern cultivars. These findings provide important insights into the origin of chrysanthemum cultivars, and a source of valuable genetic markers for chrysanthemum breeding programs.
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Affiliation(s)
- Yufen Xu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Borong Liao
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Kate L. Ostevik
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, United States
| | - Hougao Zhou
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Fenglan Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hanhan Xia
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- *Correspondence: Hanhan Xia,
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Terra V, Ringelberg JJ, Maslin B, Koenen EJM, Ebinger J, Seigler D, Hughes CE. Dilemmas in generic delimitation of Senegalia and allies (Caesalpinioideae, mimosoid clade): how to reconcile phylogenomic evidence with morphology and taxonomy? PHYTOKEYS 2022; 205:261-278. [PMID: 36762013 PMCID: PMC9849036 DOI: 10.3897/phytokeys.205.79378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/06/2022] [Indexed: 05/10/2023]
Abstract
Senegalia comprises 219 species distributed in tropical and subtropical regions of North and South America, Africa, Asia and Australia. Two sections are currently recognised within Senegalia and these are most readily distinguished by the differences in disposition of their cauline prickles, i.e. sect. Senegalia with prickles at or near leaf nodes and sect. Monacanthea with mostly internodal prickles. Previous phylogenetic studies, based primarily on small numbers of plastid DNA loci, found Senegalia to be monophyletic with two large subclades corresponding to the sections. Here, we present new phylogenomic evidence from 997 single-copy nuclear gene sequences for a small, but representative set of species. These new analyses show that Senegalia is non-monophyletic, but instead, forms a grade that is paraphyletic with respect to the remainder of the ingoid clade (i.e. Ingeae + Acacia s.s. + Acaciella), comprising two well-supported subclades most likely representing the same clades as found in previous phylogenetic studies of the genus and, interspersed between these, a third, moderately supported clade, comprising the genera Mariosousa, Pseudosenegalia and Parasenegalia. In marked contrast to the nuclear phylogeny, the two Senegalia clades are sister groups in the plastid phylogeny, based on analyses of 72 chloroplast genes, rendering the genus monophyletic, based on plastid data alone. We discuss this new evidence that Senegalia is non-monophyletic in relation to the marked cytonuclear discordance, high gene tree conflict and lack of resolution across this senegalioid grade and review the consistency of the key morphological characters distinguishing the two sections of Senegalia. We conclude that it is likely that Senegalia will need to be split into two (or possibly more) genera: a re-circumscribed Senegalia s.s. that corresponds to the existing Senegaliasect.Senegalia plus the S.ataxacantha group (Senegaliasect.Monacanthea s.s.; future studies may show that this group warrants generic status) and a new genus corresponding to the remainder of sect. Monacanthea (here designated as Senegaliasect.Monacanthea p.p.). However, re-delimiting Senegalia now would be premature given that the key morphological characters are not fully congruent with the two sections and pending denser phylogenetic sampling of taxa. A judiciously selected list of critical taxa is presented to facilitate future phylogenomic studies. Finally, we discuss the identity of Albizialeonardii, which is also placed in this senegalioid grade in these new phylogenomic analyses and place it in synonymy with Parasenegaliavogeliana.
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Affiliation(s)
- Vanessa Terra
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Rodovia LMG 746, Km01, s/n, Bloco 1A, sala 413, 38500-000, Monte Carmelo, Minas Gerais, BrazilUniversidade Federal de UberlândiaMonte CarmeloBrazil
| | - Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
| | - Bruce Maslin
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, PO Box 104, WA, 6983, AustraliaWestern Australian HerbariumBentley Delivery CentreAustralia
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
- Emeritus Professor of Botany, Eastern Illinois University, Charleston, IL 61920, USAUniversité Libre de BruxellesBruxellesBelgium
| | - John Ebinger
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801, USAEastern Illinois UniversityCharlestonUnited States of America
| | - David Seigler
- Present address: Evolutionary Biology & Ecology, Université Libre de Bruxelles, Faculté des Sciences, Campus du Solbosch - CP 160/12, Avenue F.D. Roosevelt, 50, 1050 Bruxelles, BelgiumUniversity of IllinoisUrbanaUnited States of America
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
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Ringelberg JJ, Koenen EJM, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Hughes CE. Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae). PHYTOKEYS 2022; 205:3-58. [PMID: 36762007 PMCID: PMC9848904 DOI: 10.3897/phytokeys.205.85866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/27/2022] [Indexed: 05/05/2023]
Abstract
Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.
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Affiliation(s)
- Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
- Present address: Evolutionary Biology & Ecology, Université Libre de Bruxelles, Faculté des Sciences, Campus du Solbosch - CP 160/12, Avenue F.D. Roosevelt, 50, 1050 Bruxelles, BelgiumUniversité Libre de BruxellesBruxellesBelgium
| | - João R. Iganci
- Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, Capão do Leão 96010-900, Rio Grande do Sul, BrazilUniversidade Federal de PelotasRio Grande do SulBrazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, 91501-970, BrazilUniversidade Federal do Rio Grande do SulRio Grande do SulBrazil
| | - Luciano P. de Queiroz
- Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n – Novo Horizonte, 44036-900, Feira de Santana, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, AustraliaRoyal Botanic Gardens VictoriaMelbourneAustralia
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, FranceInstitut de Systématique, Evolution, Biodiversité (ISYEB)ParisFrance
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, CanadaUniversité de MontréalMontrealCanada
| | - Melissa Luckow
- School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USACornell UniversityIthacaUnited States of America
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UKAccelerated Taxonomy Department, Royal Botanic GardensRichmondUnited Kingdom
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
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Rose JP, Kriebel R, Kahan L, DiNicola A, González-Gallegos JG, Celep F, Lemmon EM, Lemmon AR, Sytsma KJ, Drew BT. Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:767478. [PMID: 34899789 PMCID: PMC8652245 DOI: 10.3389/fpls.2021.767478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 05/13/2023]
Abstract
Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.
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Affiliation(s)
- Jeffrey P. Rose
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, United States
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Larissa Kahan
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Alexa DiNicola
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | | | - Ferhat Celep
- Department of Biology, Faculty of Arts and Sciences, Kırıkkale University, Yahşihan, Turkey
| | - Emily M. 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
| | - Kenneth J. Sytsma
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Bryan T. Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, United States
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Dong W, Liu Y, Li E, Xu C, Sun J, Li W, Zhou S, Zhang Z, Suo Z. Phylogenomics and biogeography of Catalpa (Bignoniaceae) reveal incomplete lineage sorting and three dispersal events. Mol Phylogenet Evol 2021; 166:107330. [PMID: 34687844 DOI: 10.1016/j.ympev.2021.107330] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 01/21/2023]
Abstract
Catalpa Scop. (Bignoniaceae) is a small genus (8 spp.) of trees that is disjunctly distributed among eastern Asia, eastern United States, and the West Indies. Catalpa bears beautiful inflorescences and have been cultivated as important ornamental trees for landscaping, gardening, and timber. However, the phylogenetic relationships and biogeographic history of the genus have remained unresolved. In this study, we used a large genomic dataset that includes data from the chloroplast (plastomes), and nuclear genomes (ITS and 5,759 single-copy nuclear genes) to reconstruct phylogenetic relationship within Catalpa, test interspecific gene flow events within the genus, and infer its biogeographic history. Our phylogenetic results indicate that Catalpa is monophyletic containing two main clades, section Catalpa and section Macrocatalpa. Section Catalpa is further divided into three subclades. While most relationships are congruent between the chloroplast and nuclear datasets, the position of C. ovata differs, likely due to incomplete lineage sorting. Interspecific gene flow events include C. bungei s.s. with vectors of inheritance from C. duclouxii and C. fargesii, supporting a combination of these three species and recognizing a broadly circumscribed C. bungei s.l. Our biogeographic study suggests three main dispersal events, two of which occurred during the Oligocene. The first dispersal event occurred from southwestern North America and Mexico into the Greater Antilles giving rise to the ancestor of the section of Macrocatalpa. The second dispersal event also occurred from southwestern North America and Mexico, but led to central and northern North America, subsequently reaching China through the Bering land bridge, and also reaching Europe through the North Atlantic land bridge. The third dispersal event took place in the Miocene from China to North America and gave rise to a clade composed of C. bignonioides and C. speciosa. This study uses a phylogenomic approach and biogeographical methods to infer the evolutionary history of Catalpa, highlighting issues associated with gene tree discordance, and suggesting that incomplete lineage sorting likely played an important role in the evolutionary history of Catalpa.
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Affiliation(s)
- Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wenying Li
- Institute of Forestry New Technologies, Chinese Academy of Forestry, Beijing 100091, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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42
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Xu L, Yu R, Lin X, Zhang B, Li N, Lin K, Zhang D, Bai W. Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts. THE NEW PHYTOLOGIST 2021; 232:388-403. [PMID: 34143496 PMCID: PMC8519134 DOI: 10.1111/nph.17564] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/13/2021] [Indexed: 05/03/2023]
Abstract
Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance. We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance. Our findings indicate that the chloroplast genome had substantially deeper divergence (branch-length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation-by-distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome. Altogether, this study highlights a critical role of sex-biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.
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Affiliation(s)
- Lin‐Lin Xu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Rui‐Min Yu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Xin‐Rui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Bo‐Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
- Centre for Individualised Infection Medicine (CiiM) & TWINCOREJoint ventures between the Helmholtz‐Centre for Infection Research (HZI) and the Hannover Medical School (MHH)Hannover30625Germany
| | - Nan Li
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Da‐Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Wei‐Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
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Lindsey CR, Rosenzweig F, Herron MD. Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae. BMC Biol 2021; 19:182. [PMID: 34465312 PMCID: PMC8408923 DOI: 10.1186/s12915-021-01087-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The volvocine algae, which include the single-celled species Chlamydomonas reinhardtii and the colonial species Volvox carteri, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the history of this group have by and large relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. As a result, volvocine phylogenies lack concordance depending on the number and/or type of genes (i.e., chloroplast vs nuclear) chosen for phylogenetic inference. While multiple studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group, other studies call into question one or more of these conclusions. An accurate assessment of the evolutionary history of the volvocine algae requires inference of a more robust phylogeny. RESULTS We performed RNA sequencing (RNA-seq) on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We then compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes and subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation arose independently at least four, and possibly as many as six times, within the volvocine algae. CONCLUSIONS Altogether, our results demonstrate that multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming the importance of this group as a model system for the study of major transitions in the history of life.
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Affiliation(s)
- Charles Ross Lindsey
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Atlanta, USA
| | - Matthew D Herron
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Xue C, Geng FD, Li JJ, Zhang DQ, Gao F, Huang L, Zhang XH, Kang JQ, Zhang JQ, Ren Y. Divergence in the Aquilegia ecalcarata complex is correlated with geography and climate oscillations: Evidence from plastid genome data. Mol Ecol 2021; 30:5796-5813. [PMID: 34448283 DOI: 10.1111/mec.16151] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/03/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022]
Abstract
Quaternary climate oscillations and geographical heterogeneity play important roles in determining species and genetic diversity distribution patterns, but how these factors affect the migration and differentiation of East Asian plants species at the population level remains poorly understood. The Aquilegia ecalcarata complex, a group that originated in the Late Tertiary and is widely distributed throughout East Asia, displays high genetic variation that is suitable for studying elaborate phylogeographic patterns and demographic history related to the impact of Quaternary climate and geography. We used plastid genome data from 322 individuals in 60 populations of the A. ecalcarata complex to thoroughly explore the impact of Quaternary climate oscillations and geography on the phylogeographic patterns and demographic history of the A. ecalcarata complex through a series of phylogenetic, divergence time estimation, and demographic history analyses. The dry, cold climate and frequent climate oscillations that occurred during the early Pleistocene and the Mid-Pleistocene transition led to the differentiation of the A. ecalcarata complex, which was isolated in various areas. Geographically, the A. ecalcarata complex can be divided into Eastern and Western Clades and five subclades, which conform to the divergence of the East Asian flora. Our results clearly show the impact of Quaternary climate and geography on evolutionary history at the population level. These findings promote the understanding of the relationship between plant genetic differentiation and climate and geographical factors of East Asia at the population level.
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Affiliation(s)
- Cheng Xue
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Fang-Dong Geng
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Jiao-Jie Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Dan-Qing Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Fei Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Xiao-Hui Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Ju-Qing Kang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Jian-Qiang Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Yi Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
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Duan L, Li SJ, Su C, Sirichamorn Y, Han LN, Ye W, Lôc PK, Wen J, Compton JA, Schrire B, Nie ZL, Chen HF. Phylogenomic framework of the IRLC legumes (Leguminosae subfamily Papilionoideae) and intercontinental biogeography of tribe Wisterieae. Mol Phylogenet Evol 2021; 163:107235. [PMID: 34146677 DOI: 10.1016/j.ympev.2021.107235] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
The inverted repeat-lacking clade (IRLC) is one of the most derived clades within the subfamily Papilionoideae of the legume family, and includes various economically important plants, e.g., chickpeas, peas, liquorice, and the largest genus of angiosperms, Astragalus. Tribe Wisterieae is one of the earliest diverged groups of the IRLC, and its generic delimitation and spatiotemporal diversification needs further clarifications. Based on genome skimming data, we herein reconstruct the phylogenomic framework of the IRLC, and infer the inter-generic relationships and historical biogeography of Wisterieae. We redefine tribe Caraganeae to contain Caragana only, and tribe Astragaleae is reduced to the Erophaca-Astragalean clade. The chloroplast capture scenario was hypothesized as the most plausible explanation of the topological incongruences between the chloroplast CDSs and nuclear ribosomal DNA trees in both the Glycyrrhizinae-Adinobotrys-Wisterieae clade and the Chesneyeae-Caraganeae-Hedysareae clade. A new name, Caragana lidou L. Duan & Z.Y. Chang, is proposed within Caraganeae. Thirteen genera are herein supported within Wisterieae, including a new genus, Villosocallerya L. Duan, J. Compton & Schrire, segregated from Callerya. Our biogeographic analyses suggest that Wisterieae originated in the late Eocene and its most recent common ancestor (MRCA) was distributed in continental southeastern Asia. Lineages of Wisterieae remained in the ancestral area from the early Oligocene to the early Miocene. By the middle Miocene, Whitfordiodendron and the MRCA of Callerya-Kanburia-Villosocallerya Clade became disjunct between the Sunda area and continental southeastern Asia, respectively; the MRCA of Wisteria migrated to North America via the Bering land bridge. The ancestor of Austrocallerya and Padbruggea migrated to the Wallacea-Oceania area, which split in the early Pliocene. In the Pleistocene, Wisteria brachybotrys, W. floribunda and Wisteriopsis japonica reached Japan, and Callerya cinerea dispersed to South Asia. This study provides a solid phylogenomic for further evolutionary/biogeographic/systematic investigations on the ecologically diverse and economically important IRLC legumes.
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Affiliation(s)
- Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shi-Jin Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chun Su
- College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Yotsawate Sirichamorn
- Silpakorn University, Department of Biology, Faculty of Science, Sanam Chandra Palace Campus, Nakhon Pathom 73000, Thailand
| | - Li-Na Han
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Wen Ye
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Phan Ke Lôc
- Department of Botany and HNU, Faculty of Biology, VNU Hanoi University of Science (HUS), Hanoi, Viet Nam
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, D.C. 20013-7012, USA.
| | | | - Brian Schrire
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Hong-Feng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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