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Shipunov A, Fernández-Alonso JL, Hassemer G, Alp S, Lee HJ, Pay K. Molecular and Morphological Data Improve the Classification of Plantagineae (Lamiales). PLANTS (BASEL, SWITZERLAND) 2021; 10:2299. [PMID: 34834664 PMCID: PMC8625185 DOI: 10.3390/plants10112299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The tribe Plantagineae (Lamiales) is a group of plants with worldwide distribution, notorious for its complicated taxonomy and still unresolved natural history. We describe the result of a broadly sampled phylogenetic study of tribe. The expanded sampling dataset is based on the trnL-F spacer, rbcL, and ITS2 markers across all three included genera (Aragoa, Littorella and Plantago) and makes this the most comprehensive study to date. The other dataset uses five markers and provides remarkably good resolution throughout the tree, including support for all of the major clades. In addition to the molecular phylogeny, a morphology database of 114 binary characters was assembled to provide comparison with the molecular phylogeny and to develop a means to assign species not sampled in the molecular analysis to their most closely related species that were sampled. Based on the molecular phylogeny and the assignment algorithm to place unsampled species, a key to sections is presented, and a revised classification of the tribe is provided. We also include the description of new species from North America.
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Affiliation(s)
- Alexey Shipunov
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| | | | - Gustavo Hassemer
- Três Lagoas Campus, Federal University of Mato Grosso do Sul, Três Lagoas CEP 79610-100, Brazil;
| | - Sean Alp
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| | - Hye Ji Lee
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| | - Kyle Pay
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
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2
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Mower JP, Guo W, Partha R, Fan W, Levsen N, Wolff K, Nugent JM, Pabón-Mora N, González F. Plastomes from tribe Plantagineae (Plantaginaceae) reveal infrageneric structural synapormorphies and localized hypermutation for Plantago and functional loss of ndh genes from Littorella. Mol Phylogenet Evol 2021; 162:107217. [PMID: 34082129 DOI: 10.1016/j.ympev.2021.107217] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/14/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Tribe Plantagineae (Plantaginaceae) comprises ~ 270 species in three currently recognized genera (Aragoa, Littorella, Plantago), of which Plantago is most speciose. Plantago plastomes exhibit several atypical features including large inversions, expansions of the inverted repeat, increased repetitiveness, intron losses, and gene-specific increases in substitution rate, but the prevalence of these plastid features among species and subgenera is unknown. To assess phylogenetic relationships and plastomic evolutionary dynamics among Plantagineae genera and Plantago subgenera, we generated 25 complete plastome sequences and compared them with existing plastome sequences from Plantaginaceae. Using whole plastome and partitioned alignments, our phylogenomic analyses provided strong support for relationships among major Plantagineae lineages. General plastid features-including size, GC content, intron content, and indels-provided additional support that reinforced major Plantagineae subdivisions. Plastomes from Plantago subgenera Plantago and Coronopus have synapomorphic expansions and inversions affecting the size and gene order of the inverted repeats, and particular genes near the inversion breakpoints exhibit accelerated nucleotide substitution rates, suggesting localized hypermutation associated with rearrangements. The Littorella plastome lacks functional copies of ndh genes, which may be related to an amphibious lifestyle and partial reliance on CAM photosynthesis.
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Affiliation(s)
- Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA.
| | - Wenhu Guo
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Raghavendran Partha
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Weishu Fan
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Nick Levsen
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Kirsten Wolff
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Jacqueline M Nugent
- Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Apartado 1226, Medellín, Colombia
| | - Favio González
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Instituto de Ciencias Naturales, Apartado 7495, Colombia
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Penczykowski RM, Sieg RD. Plantago spp. as Models for Studying the Ecology and Evolution of Species Interactions across Environmental Gradients. Am Nat 2021; 198:158-176. [PMID: 34143715 DOI: 10.1086/714589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractA central challenge in ecology and evolutionary biology is to understand how variation in abiotic and biotic factors combine to shape the distribution, abundance, and diversity of focal species. Environmental gradients, whether natural (e.g., latitude, elevation, ocean proximity) or anthropogenic (e.g., land-use intensity, urbanization), provide compelling settings for addressing this challenge. However, not all organisms are amenable to the observational and experimental approaches required for untangling the factors that structure species along gradients. Here we highlight herbaceous plants in the genus Plantago as models for studying the ecology and evolution of species interactions along abiotic gradients. Plantago lanceolata and P. major are native to Europe and Asia but distributed globally, and they are established models for studying population ecology and interactions with herbivores, pathogens, and soil microbes. Studying restricted range congeners in comparison with those cosmopolitan species can provide insight into abiotic and biotic determinants of range size and population structure. We highlight one such species, P. rugelii, which is endemic to eastern North America. We give an overview of the literature on these focal Plantago species and explain why they are logical candidates for studies of species interactions across environmental gradients. Finally, we emphasize collaborative and community science approaches that can facilitate such research and note the amenability of Plantago for authentic research projects in science education.
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4
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Behling AH, Shepherd LD, Cox MP. The importance and prevalence of allopolyploidy in Aotearoa New Zealand. J R Soc N Z 2019. [DOI: 10.1080/03036758.2019.1676797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Anna H. Behling
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Murray P. Cox
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
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5
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Hassemer G, Bruun-Lund S, Shipunov AB, Briggs BG, Meudt HM, Rønsted N. The application of high-throughput sequencing for taxonomy: The case of Plantago subg. Plantago (Plantaginaceae). Mol Phylogenet Evol 2019; 138:156-173. [DOI: 10.1016/j.ympev.2019.05.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 12/11/2022]
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Kwon W, Kim Y, Park CH, Park J. The complete chloroplast genome sequence of traditional medical herb, Plantago depressa Willd. (Plantaginaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2019. [DOI: 10.1080/23802359.2018.1553530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Woochan Kwon
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Chan-Ho Park
- National Institute of Biological Resources, Incheon, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Hassemer G, Meudt HM, Rønsted N. Nomenclatural and taxonomic notes on Mediterranean narrow-leaved plantains (Plantago section Maritima, Plantaginaceae). ACTA ACUST UNITED AC 2017. [DOI: 10.1080/00837792.2017.1349066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Gustavo Hassemer
- Natural History Museum of Denmark, University of Copenhagen , Copenhagen, Denmark
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa Tongarewa , Wellington, New Zealand
| | - Nina Rønsted
- Natural History Museum of Denmark, University of Copenhagen , Copenhagen, Denmark
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Rothfels CJ, Pryer KM, Li FW. Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. THE NEW PHYTOLOGIST 2017; 213:413-429. [PMID: 27463214 DOI: 10.1111/nph.14111] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/14/2016] [Indexed: 05/27/2023]
Abstract
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (Purc)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi-labeled species tree for a subset of our accessions. We amplified four c. 1-kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. Purc infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, Purc was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
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Affiliation(s)
- Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | | | - Fay-Wei Li
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- Department of Biology, Duke University, Durham, NC, 27705, USA
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Hassemer G, Rønsted N. Yet another new species from one of the best-studied neotropical areas: Plantago humboldtiana (Plantaginaceae), an extremely narrow endemic new species from a waterfall in southern Brazil. PeerJ 2016; 4:e2050. [PMID: 27231665 PMCID: PMC4878378 DOI: 10.7717/peerj.2050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 04/28/2016] [Indexed: 11/25/2022] Open
Abstract
This article presents and describes Plantago humboldtiana, an extremely narrow endemic rheophytic new species from a waterfall in Corupá, Santa Catarina state, southern Brazil. The new species is unique in presenting a combination of type-G antrorse trichomes on scapes, pendulous inflorescences and 1-seeded pyxidia. Only one population is known to exist, despite intensive search efforts in nearby, similar environments. Its conservation status is assessed as critically endangered (CR) as the only known population is restricted to a dramatically small area, and is subject to extreme fluctuation due to occasional floods, and also to intense visitation by tourists, which can disturb its fragile habitat. We also present an updated identification key to the species of Plantago that occur in Santa Catarina. The recent description of three narrow endemic, threatened new species of Plantago in Santa Catarina, which is the Brazilian state with its flora best studied, highlights the need for more taxonomic research, especially in the neotropics.
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Affiliation(s)
- Gustavo Hassemer
- />Statens Naturhistoriske Museum, Københavns Universitet, Copenhagen, Denmark
| | - Nina Rønsted
- />Statens Naturhistoriske Museum, Københavns Universitet, Copenhagen, Denmark
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Walsh BM, Adhikary D, Maughan PJ, Emshwiller E, Jellen EN. Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data. AMERICAN JOURNAL OF BOTANY 2015; 102:533-43. [PMID: 25878087 DOI: 10.3732/ajb.1400344] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 03/04/2015] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Single-copy nuclear loci can provide powerful insights into polyploid evolution. Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50-75 species. The genus includes several polyploid species, some of which are considered noxious agricultural weeds, and a few are domesticated crops. Very little research has addressed their evolutionary origin to date. We construct a phylogeny for Chenopodium based on two introns of the single-copy nuclear locus Salt Overly Sensitive 1 (SOS1) to clarify the relationships among the genomes of the allotetraploid and allohexaploid species, and to help identify their genome donors. METHODS Diploid species were sequenced directly, whereas homeologous sequences of polyploid genomes were first separated by plasmid-mediated cloning. Data were evaluated in maximum likelihood and Bayesian phylogenetic analyses. KEY RESULTS Homeologous sequences of polyploid species were found in four clades, which we designate as A-D. Two distinct polyploid lineages were identified: one composed of American tetraploid species with A and B class homeologs and a second composed of Eastern Hemisphere hexaploid species with B, C, and D class homeologs. CONCLUSIONS We infer that the two polyploid lineages arose independently and that each lineage may have originated only once. The American diploid, C. standleyanum, was identified as the closest living diploid relative of the A genome donor for American tetraploids, including domesticated C. quinoa, and is of potential importance for quinoa breeding. The east Asian diploid species, C. bryoniifolium, groups with American diploid species, which suggests a transoceanic dispersal.
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Affiliation(s)
- Brian M Walsh
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Dinesh Adhikary
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Eve Emshwiller
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric N Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
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11
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Ishikawa N, Ikeda H, Yi TS, Takabe-Ito E, Okada H, Tsukaya H. Lineage diversification and hybridization in the Cayratia japonica–Cayratia tenuifolia species complex. Mol Phylogenet Evol 2014; 75:227-38. [DOI: 10.1016/j.ympev.2014.01.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/15/2014] [Accepted: 01/28/2014] [Indexed: 11/27/2022]
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Wong C, Murray BG. Variable changes in genome size associated with different polyploid events in Plantago (Plantaginaceae). J Hered 2012; 103:711-9. [PMID: 22945947 DOI: 10.1093/jhered/ess049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The genus Plantago (Plantaginaceae) in New Zealand comprises species that can be difficult to delimit and contains a wide range of ploidy levels from diploid to 16-ploid. To investigate whether there have been changes in genome size associated with polyploid events and whether pollen and guard cell size can be used as an initial guide to identify polyploids, we have used flow cytometry with propidium iodide as the stain to measure the genome size (DNA C-value) in a range of Plantago species with different ploidy levels. Light microscopy was used to measure pollen diameter and guard cell length in these plants to see whether these could be used for ploidy level identification. Large differences in C-value were observed between species but the extent of changes associated with different polyploid events was highly variable. Pollen diameter was correlated with C-value but not necessarily with ploidy level. Guard cell lengths were different between diploids and polyploids but not between the different polyploid species. The significance of the changes in genome size and its relationship to pollen and stomatal guard cell size is discussed.
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Affiliation(s)
- Charles Wong
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
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Tsukaya H, Ishikawa N, Okada H. A hypothesis on the origin of genetic heterozygosity in diploids and triploids in Japanese Cayratia japonica species complex (Vitaceae). JOURNAL OF PLANT RESEARCH 2012; 125:475-481. [PMID: 22200910 DOI: 10.1007/s10265-011-0467-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 11/26/2011] [Indexed: 05/31/2023]
Abstract
We previously reported the occurrence of triploid strains in Japanese populations of Cayratia japonica (Thunb.) Gagnep. Interestingly, the triploid and most diploid strains had variably reduced pollen fertility. Two questions emerged from this earlier work: (1) How do triploids arise, and are they allotriploids or autotriploids? and (2) Why is there low pollen fertility in some diploid plants? We used a molecular genetic approach to determine the phylogenetic origins of triploids in C. japonica and the closely related species Cayratia tenuifolia (Wight & Arn.) Gagnep. In our analysis, we compared the sequences of the nuclear single-copy genes LEAFY and ASYMMETRIC LEAVES1. As a result, most triploids and diploids were heterozygous for the loci examined; the triploid genome shared an allele with the diploid genome, but other alleles differed between the ploidies. Therefore, Japanese populations of C. japonica and C. tenuifolia almost certainly arose from repeated hybridization events among genetically differentiated strains. Using our sequence data, we discuss possible scenarios accounting for the occurrence of triploids in the two species of Cayratia.
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Affiliation(s)
- Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan.
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Zhang YX, Zeng CX, Li DZ. Complex evolution in Arundinarieae (Poaceae: Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies. Mol Phylogenet Evol 2012; 63:777-97. [PMID: 22415014 DOI: 10.1016/j.ympev.2012.02.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
Abstract
The monophyly of tribe Arundinarieae (the temperate woody bamboos) has been unequivocally recovered in previous molecular phylogenetic studies. In a recent phylogenetic study, 10 major lineages in Arundinarieae were resolved based on eight non-coding plastid regions, which conflicted significantly with morphological classifications both at the subtribal and generic levels. Nevertheless, relationships among and within the 10 lineages remain unclear. In order to further unravel the evolutionary history of Arundinarieae, we used the nuclear GBSSI gene sequences along with those of eight plastid regions for phylogenetic reconstruction, with an emphasis on Chinese species. The results of the plastid analyses agreed with previous studies, whereas 13 primary clades revealed in the GBSSI phylogeny were better resolved at the generic level than the plastid phylogeny. Our analyses also revealed many inconsistencies between the plastid DNA and the nuclear GBSSI trees. These results implied that the nuclear genome and the plastid genome had different evolutionary trajectories. The patterns of incongruence suggested that lack of informative characters, incomplete lineage sorting, and/or hybridization (introgression) could be the causes. Seven putative hybrid species were hypothesized, four of which are discussed in detail on the basis of topological incongruence, chromosome numbers, morphology, and distribution patterns, and those taxa probably resulted from homoploid hybrid speciation. Overall, our study indicates that the tribe Arundinarieae has undergone a complex evolution.
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Affiliation(s)
- Yu-Xiao Zhang
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming, Yunnan 650201, PR China
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