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Sherlock MB, Streicher JW, Gower DJ, Maddock ST, Nussbaum RA, Oommen OV, Serra Silva A, Day JJ, Wilkinson M. Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles. Mol Phylogenet Evol 2024; 198:108130. [PMID: 38889862 DOI: 10.1016/j.ympev.2024.108130] [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: 10/31/2023] [Revised: 06/05/2024] [Accepted: 06/15/2024] [Indexed: 06/20/2024]
Abstract
Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands.These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.
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Affiliation(s)
- Miranda B Sherlock
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | | | - David J Gower
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles
| | - Simon T Maddock
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles; School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Ronald A Nussbaum
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1079, USA
| | - Oommen V Oommen
- Department of Zoology, University of Kerala, Kariavattom 695 581, Thiruvananthapuram, Kerala, India
| | - Ana Serra Silva
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; School of Earth Sciences, University of Bristol, Queens Road, Bristol BS8 1RL, UK
| | - Julia J Day
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Mark Wilkinson
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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Garner AG, Goulet-Scott BE, Hopkins R. Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers. THE NEW PHYTOLOGIST 2024; 243:451-465. [PMID: 38764373 DOI: 10.1111/nph.19802] [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: 10/06/2023] [Accepted: 03/22/2024] [Indexed: 05/21/2024]
Abstract
The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation. Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification. Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species. Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non-model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity.
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Affiliation(s)
- Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
| | - Benjamin E Goulet-Scott
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
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Franco FF, Amaral DT, Bonatelli IAS, Meek JB, Moraes EM, Zappi DC, Taylor NP, Eaton DAR. A historical stepping-stone path for an island-colonizing cactus across a submerged "bridge" archipelago. Heredity (Edinb) 2024; 132:296-308. [PMID: 38637723 PMCID: PMC11166651 DOI: 10.1038/s41437-024-00683-4] [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: 07/29/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Here we use population genomic data (ddRAD-Seq) and ecological niche modeling to test biogeographic hypotheses for the divergence of the island-endemic cactus species Cereus insularis Hemsl. (Cereeae; Cactaceae) from its sister species C. fernambucensis Lem. The Cereus insularis grows in the Fernando de Noronha Islands (FNI), a Neotropical archipelago located 350 km off the Brazilian Atlantic Forest (BAF) coast. Phylogeographic reconstructions support a northward expansion by the common ancestor of C. insularis and C. fernambucensis along the mainland BAF coast, with C. insularis diverging from the widespread mainland taxon C. fernambucensis after colonizing FNI in the late Pleistocene. The morphologically distinct C. insularis is monophyletic and nested within C. fernambucensis, as expected from a progenitor-derivative speciation model. We tested alternative biogeographic and demographic hypotheses for the colonization of the FNI using Approximate Bayesian Computation. We found the greatest support for a stepping-stone path that emerged during periods of decreased sea level (the "bridge" hypothesis), in congruence with historical ecological niche modeling that shows highly suitable habitats on stepping-stone islands during glacial periods. The outlier analyses reveal signatures of selection in C. insularis, suggesting a putative role of adaptation driving rapid anagenic differentiation of this species in FNI.
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Affiliation(s)
- Fernando Faria Franco
- Departamento de Biologia. Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, Brazil.
| | - Danilo Trabuco Amaral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
- Programa de Pós Graduação em Biologia Comparada. Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Isabel A S Bonatelli
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas. Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Jared B Meek
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA
| | - Evandro Marsola Moraes
- Departamento de Biologia. Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, Brazil
| | - Daniela Cristina Zappi
- Programa de Pós Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, PO Box 04457, Brasília, DF, 70910970, Brazil
| | - Nigel Paul Taylor
- Departamento de Biologia. Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, Brazil
| | - Deren A R Eaton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA
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Amaral DT, Bonatelli IAS, Romeiro-Brito M, Telhe MC, Moraes EM, Zappi DC, Taylor NP, Franco FF. Comparative transcriptome analysis reveals lineage- and environment-specific adaptations in cacti from the Brazilian Atlantic Forest. PLANTA 2024; 260:4. [PMID: 38775846 DOI: 10.1007/s00425-024-04442-x] [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: 01/24/2024] [Accepted: 05/14/2024] [Indexed: 07/03/2024]
Abstract
MAIN CONCLUSION Natural selection influenced adaptive divergence between Cereus fernambucensis and Cereus insularis, revealing key genes governing abiotic stress responses and supporting neoteny in C. insularis. Uncovering the molecular mechanisms driving adaptive divergence in traits related to habitat adaptation remains a central challenge. In this study, we focused on the cactus clade, which includes Cereus sericifer F.Ritter, Cereus fernambucensis Lem., and Cereus insularis Hemsley. These allopatric species inhabit distinct relatively drier regions within the Brazilian Atlantic Forest, each facing unique abiotic conditions. We leveraged whole transcriptome data and abiotic variables datasets to explore lineage-specific and environment-specific adaptations in these species. Employing comparative phylogenetic methods, we identified genes under positive selection (PSG) and examined their association with non-synonymous genetic variants and abiotic attributes through a PhyloGWAS approach. Our analysis unveiled signatures of selection in all studied lineages, with C. fernambucensis northern populations and C. insularis showing the most PSGs. These PSGs predominantly govern abiotic stress regulation, encompassing heat tolerance, UV stress response, and soil salinity adaptation. Our exclusive observation of gene expression tied to early developmental stages in C. insularis supports the hypothesis of neoteny in this species. We also identified genes associated with abiotic variables in independent lineages, suggesting their role as environmental filters on genetic diversity. Overall, our findings suggest that natural selection played a pivotal role in the geographic range of these species in response to environmental and biogeographic transitions.
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Affiliation(s)
- Danilo T Amaral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Isabel A S Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Monique Romeiro-Brito
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Milena C Telhe
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil
| | - Daniela Cristina Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), Brasília, Brazil
| | - Nigel Paul Taylor
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil
| | - Fernando F Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil.
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Romeiro-Brito M, Taylor NP, Zappi DC, Telhe MC, Franco FF, Moraes EM. Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing. ANNALS OF BOTANY 2023; 132:989-1006. [PMID: 37815357 PMCID: PMC10808018 DOI: 10.1093/aob/mcad153] [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: 05/20/2023] [Accepted: 10/09/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND AND AIMS Cactaceae are succulent plants, quasi-endemic to the American continent, and one of the most endangered plant groups in the world. Molecular phylogenies have been key to unravelling phylogenetic relationships among major cactus groups, previously hampered by high levels of morphological convergence. Phylogenetic studies using plastid markers have not provided adequate resolution for determining generic relationships within cactus groups. This is the case for the tribe Cereeae s.l., a highly diverse group from tropical America. Here we aimed to reconstruct a well-resolved phylogenetic tree of tribe Cereeae and update the circumscription of suprageneric and generic groups in this tribe. METHODS We integrated sequence data from public gene and genomic databases with new target sequences (generated using the customized Cactaceae591 probe set) across representatives of this tribe, with a denser taxon sampling of the subtribe Cereinae. We inferred concatenated and coalescent phylogenetic trees and compared the performance of both approaches. KEY RESULTS Six well-supported suprageneric clades were identified using different datasets. However, only genomic datasets, especially the Cactaceae591, were able to resolve the contentious relationships within the subtribe Cereinae. CONCLUSIONS We propose a new taxonomic classification within Cereeae based on well-resolved clades, including new subtribes (Aylosterinae subtr. nov., Uebelmanniinae subtr. nov. and Gymnocalyciinae subtr. nov.) and revised subtribes (Trichocereinae, Rebutiinae and Cereinae). We emphasize the importance of using genomic datasets allied with coalescent inference to investigate evolutionary patterns within the tribe Cereeae.
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Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, Gibraltar
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas Universidade de Brasília (UNB), Brasília, Distrito Federal, Brazil
| | - Milena C Telhe
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Fernando F Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
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Seo J, Lee JS, Shim SL, In JG, Park CS, Lee YJ, Ahn HJ. Development and authentication of Panax ginseng cv. Sunhong with high yield and multiple tolerance to heat damage, rusty roots and lodging. HORTICULTURE, ENVIRONMENT AND BIOTECHNOLOGY 2023:1-12. [PMID: 37361129 PMCID: PMC10202357 DOI: 10.1007/s13580-023-00526-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 06/28/2023]
Abstract
Ginseng (Panax ginseng) has been used as a valuable medicinal plant in Asia, and the demand for ginseng production for health functional food is increasing worldwide after the COVID-19 crisis. Although a number of cultivars have been developed to increase ginseng production, none of them were widely cultivated in Korea because they could not resist various environmental stresses while being grown in one place for at least 4 years. To address this, Sunhong was developed as a ginseng cultivar with high yield and multiple stress tolerance by pure line selection. Sunhong showed high yield and heat tolerance comparable to Yunpoong, a representative high-yielding cultivar, and exhibited 1.4 times lower prevalence of rusty roots than Yunpoong, suggesting that Sunhong can keep its high yield and quality during long-term cultivation. In addition, distinct color and lodging resistance were expected to increase the convenience of cultivation. To supply pure seeds to farmers, we also established a reliable high-throughput authentication system for Sunhong and seven ginseng cultivars through genotyping-by-sequencing (GBS) analysis. The GBS approach enabled to identify a sufficient number of informative SNPs in ginseng, a heterozygous and polyploid species. These results contribute to the improvement of yield, quality, and homogeneity, and therefore promote the ginseng industry. Supplementary Information The online version contains supplementary material available at 10.1007/s13580-023-00526-x.
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Affiliation(s)
- Jiho Seo
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Joon-Soo Lee
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Sung-Lye Shim
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Jun-Gyo In
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Chol-Soo Park
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Yong-Jae Lee
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Hee-Jun Ahn
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
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Romeiro-Brito M, Khan G, Perez MF, Zappi DC, Taylor NP, Olsthoorn G, Franco FF, Moraes EM. Revisiting phylogeny, systematics, and biogeography of a Pleistocene radiation. AMERICAN JOURNAL OF BOTANY 2023; 110:1-17. [PMID: 36708517 DOI: 10.1002/ajb2.16134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Pilosocereus (Cactaceae) is an important dry forest element in all subregions and transitional zones of the neotropics, with the highest diversity in eastern Brazil. The genus is subdivided into informal taxonomic groups; however, most of these are not supported by recent molecular phylogenetic inferences. This lack of confidence is probably due to the use of an insufficient number of loci and the complexity of cactus diversification. Here, we explored the species relationships in Pilosocereus in more detail, integrating multilocus phylogenetic approaches with the assessment of the ancestral range and the effect of geography on diversification shifts. METHODS We used 28 nuclear, plastid, and mitochondrial loci from 54 plant samples of 31 Pilosocereus species for phylogenetic analyses. We used concatenated and coalescent phylogenetic trees and Bayesian models to estimate the most likely ancestral range and diversification shifts. RESULTS All Pilosocereus species were clustered in the same branch, except P. bohlei. The phylogenetic relationships were more associated with the geographic distribution than taxonomic affinities among taxa. The genus began diversifying during the Plio-Pleistocene transition in the Caatinga domain and experienced an increased diversification rate during the Calabrian age. CONCLUSIONS We recovered a well-supported multispecies coalescent phylogeny. Our results refine the pattern of rapid diversification of Pilosocereus species across neotropical drylands during the Pleistocene and highlight the need for taxonomic rearrangements in the genus. We recovered a pulse of diversification during the Pleistocene that was likely driven by multiple dispersal and vicariance events within and among the Caatinga, Cerrado, and Atlantic Forest domains.
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Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky-University Oldenburg, Carl von Ossietzky-Str. 9-11, 26111, Oldenburg, Germany
| | - Manolo F Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), PO Box 04457, Brasília, DF, 70910-970, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, The Alameda, PO Box 843, GX11 1AA, Gibraltar
| | | | - Fernando F Franco
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
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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: 24] [Impact Index Per Article: 24.0] [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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Wright JJ, Bruce SA, Sinopoli DA, Palumbo JR, Stewart DJ. Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage. Sci Rep 2022; 12:16514. [PMID: 36192509 PMCID: PMC9529906 DOI: 10.1038/s41598-022-20875-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
The Bowfin (Amia calva), as currently recognized, represents the sole living member of the family Amiidae, which dates back to approximately 150 Ma. Prior to 1896, 13 species of extant Bowfins had been described, but these were all placed into a single species with no rationale or analysis given. This situation has persisted until the present day, with little attention given to re-evaluation of those previously described nominal forms. Here, we present a phylogenomic analysis based on over 21,000 single nucleotide polymorphisms (SNPs) from 94 individuals that unambiguously demonstrates the presence of at least two independent evolutionary lineages within extant Amia populations that merit species-level standing, as well as the possibility of two more. These findings not only expand the recognizable species diversity in an iconic, ancient lineage, but also demonstrate the utility of such methods in addressing previously intractable questions of molecular systematics and phylogeography in slowly evolving groups of ancient fishes.
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Affiliation(s)
- Jeremy J Wright
- Research & Collections, New York State Museum, 3140 Cultural Education Center, Albany, NY, USA.
| | - Spencer A Bruce
- Department of Information Technology Services, University at Albany-State University of New York, Albany, NY, USA
| | - Daniel A Sinopoli
- Department of Biological Sciences, Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Jay R Palumbo
- Department of Environmental Science & Ecology, State University of New York at Brockport, Brockport, NY, USA
| | - Donald J Stewart
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA.
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Ocampo D, Winker K, Miller MJ, Sandoval L, Albert C. Uy J. Rapid diversification of the Variable Seedeater superspecies complex despite widespread gene flow. Mol Phylogenet Evol 2022; 173:107510. [DOI: 10.1016/j.ympev.2022.107510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022]
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A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae. Genes (Basel) 2022; 13:genes13040707. [PMID: 35456513 PMCID: PMC9032687 DOI: 10.3390/genes13040707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2022] [Accepted: 04/15/2022] [Indexed: 02/05/2023] Open
Abstract
The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve its contentious relationships. Here, we explored the genome and transcriptome assemblies available for Cactaceae and identified putative orthologous regions shared among lineages of the subfamily Cactoideae. Then we developed a probe set, named Cactaceae591, targeting both coding and noncoding nuclear regions for representatives from the subfamilies Pereskioideae, Opuntioideae, and Cactoideae. We also sampled inter- and intraspecific variation to evaluate the potential of this panel to be used in phylogeographic studies. We retrieved on average of 547 orthologous regions per sample. Targeting noncoding nuclear regions showed to be crucial to resolving inter- and intraspecific relationships. Cactaceae591 covers 13 orthologous genes shared with the Angiosperms353 kit and two plastid regions largely used in Cactaceae studies, enabling the phylogenies generated by our panel to be integrated with angiosperm and Cactaceae phylogenies, using these sequences. We highlighted the importance of using coalescent-based species tree approaches on the Cactaceae591 dataset to infer accurate phylogenetic trees in the presence of extensive incomplete lineage sorting in this family.
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Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects. Genes (Basel) 2022; 13:genes13030452. [PMID: 35328006 PMCID: PMC8952820 DOI: 10.3390/genes13030452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.
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Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese Curcuma (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera. FORESTS 2022. [DOI: 10.3390/f13020280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Curcuma is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of Curcuma (Chinese Curcuma, a recent Qinghai–Tibetan Plateau diversification genera) scattered in China. However, little is known about the incongruent phylogenetic signals within this genera from different inheritance patterns that will militate against the further development of this genera. In this research, we applied complete chloroplast genome data together with double-digest restriction site-associated DNA sequencing data (ddRAD-seq) strategy to investigate phylogenetic signals of Chinese Curcuma species, clustering using two RAD analysis pipelines (STACKS and pyRAD). Phylogenetic trees were obtained from each locus based on the maximum likelihood (ML) and multispecies coalescent (BEAST) methods. For visual comparison, multi-method and different datasets were used to infer the phylogeny. We discovered inconsistent relationships for the Chinese Curcuma with varying degrees of support using different methods and datasets.
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