Academic literature on the topic 'Plant taxonomy; DNA barcoding; phylogenetic diversity'
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Journal articles on the topic "Plant taxonomy; DNA barcoding; phylogenetic diversity"
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Aneva, Ina, Petar Zhelev, Georgi Bonchev, Irina Boycheva, Stiliana Simeonova, and Denitsa Kancheva. "DNA Barcoding Study of Representative Thymus Species in Bulgaria." Plants 11, no. 3 (January 20, 2022): 270. http://dx.doi.org/10.3390/plants11030270.
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We present a study on the taxonomy of eleven Thymus species, belonging to two sections and occurring naturally in Bulgaria. Four DNA barcoding markers—matK, rbcL, trnH-psbA and ITS—were applied to discriminate the species and to reveal their phylogenetic relationships. The results showed that rbcL has the lowest discriminating power regarding the studied species, while the other markers yielded results fitting better to the existing taxonomic schemes based on morphological traits. However, even in the case of better performing markers, the results were not straightforward—morphologically distinct species belonging to different sections were grouped together, and closely related species appeared genetically distinct. The results are typical for taxonomically complex groups, such as the genus Thymus, characterized in Bulgaria with great diversity, high percentage of endemism and still requiring a full and comprehensive taxonomic study. The results are discussed in the light of unresolved taxonomic problems and application of DNA barcoding methods.
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Nikitina, E. V., N. Yu. Beshko, and S. A. Omarov. "Assessment of plant species diversity (Lamiaceae Lindle.) in Uzbekistan based on DNA barcoding." IOP Conference Series: Earth and Environmental Science 1068, no. 1 (July 1, 2022): 012042. http://dx.doi.org/10.1088/1755-1315/1068/1/012042.
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Abstract Biological diversity preservation is important concept in modern science and environmental policy of Uzbekistan, improving the status of global biodiversity. Flora of Uzbekistan accounts over 4380 species of vascular plants. 378 taxa representing approximately 9% of currently recognized species diversity of Uzbekistan are considered as a national endemics. The present study aimed at species identification and inventory of wild, rare and endangered plant species based on molecular genetic techniques. For effective species identification and high results reliability, the genotyping of three-four loci of the combinations nuclear and chloroplast DNA-barcodes was performed for all studied species. The genotyping of marker sequences ITS, rbcL, trnL-trnF, matK for Dracocephalum adylovii I.I. Malzev is conducted the first time in Uzbekistan. The reliable similarity in the BLAST database is determined at the genus taxonomic level. 78 consensus nucleotide sequences were obtained for Lamiaceae species. The results of molecular phylogenetic analysis based on marker sequence encoding the matK fragment are presented for representative of three subfamilies: Lamioideae, Nepetoideae, Scutellarioideae recorded in the flora of Uzbekistan. Currently, the solution of biological diversity preservation is global. The possibility of successful application of DNA-barcoding for ecological monitoring is demonstrated.
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Ariyanti, Yanti, Ika Rini, Indah Oktaviani, and Sovia Leksikowati. "DNA Barcoding for Selected Mangrove-Based Estuary Fishes from Way Kambas National Park, Lampung Province, Indonesia." Journal of Tropical Life Science 11, no. 2 (May 31, 2021): 151–60. http://dx.doi.org/10.11594/jtls.11.02.04.
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Over the past decade, DNA barcoding has provided new insight into fish ecology and biosystematics and led to new species' discovery. DNA barcoding is a method for the recognition and identification of species using short, standardised DNA fragments. The correct taxonomic identification of species is critical for the assessment and monitoring of biodiversity. This study applied DNA barcoding techniques to identify selected fish species from a mangrove-based estuary in Way Kambas National Park, Lampung Province, Indonesia. The gene encoding cytochrome c oxidase subunit I (COI) was amplified and bi-directionally sequenced from 22 specimens. The resulting 680 base pairs (bp) sequence was used to identify species, obtain phylogenetic information, and analyse genetic distances. A neighbour-joining tree was constructed based on the mitochondrial COI gene using the Kimura two-parameter model. This study also exhibits conservation status for those identified species. Our findings will facilitate future studies of fish species diversity in mangrove estuary-based ecosystems and provide preliminary data in policymaking in conservation areas such as National Park.
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Sonexay, Rasphone, Thanh Dang Long, Thi Hoang Ho Nhi, Quang Nguyen Co, and Thi Hong Truong Hai. "Phylogenetic analysis of black piper (Piper spp.) population collected in different locations of Viet Nam based on the ITSU1-4 gene region." Research Journal of Biotechnology 17, no. 7 (June 25, 2022): 1–9. http://dx.doi.org/10.25303/1707rjbt001009.
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The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses and it has been recommended as a core plant DNA barcode. To compare and find out the genetic diversity difference, some individuals Peper were collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes was tested for suitability as DNA barcoding regions of thirty-nine Peper individuals. Universal primers were used and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program. We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals ranging from 0.000 to 0.155. The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region which ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; p < 0.05, D* = -1.205; not significant, p > 0.10 and F* = -1.699; not significant, 0.10 > p > 0.05) indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value of Strobeck’s S is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst are shown in the pairs of groups II and III (Fst = 0.151) and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756. This database is an important resource for researchers working on Species of Peper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.
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Palomares-Rius, Juan Emilio, Antonio Archidona-Yuste, Ilenia Clavero-Camacho, José A. Carreira de la Fuente, Ana Rey, Benjamín Viñegla, Gracia Liébanas, Carolina Cantalapiedra-Navarrete, and Pablo Castillo. "DNA Barcoding and Morphometry Reveal Further Cryptic Bio-Diversity within the Pin Nematode Genus Paratylenchus (Nematoda: Tylenchulidae)." Plants 11, no. 23 (December 5, 2022): 3385. http://dx.doi.org/10.3390/plants11233385.
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Paratylenchus species are obligate ectoparasitic nematodes on cultivated and wild herbaceous and woody plants occupying numerous soil categories. Several species may cause damage to several crops (viz. P. dianthus, P. enigmaticus, P. microdorus, P. hamatus and P. epacris on carnation, lettuce, rose and walnut, respectively). This investigation proves and emphasizes the relevance of applying integrative taxonomy for the accurate detection of Paratylenchus species in mountainous wild environments in the Malaga province, Southern Spain. This research analyzed 45 soil samples of maritimus pine and one of green heather in southern Spain and identified fourteen Paratylenchus species, two of them are described herein as new species (P. paraaonli sp. nov., P. plesiostraeleni sp. nov.), six of them were first reports for Spain (P. canchicus, P. nainianus, P. neonanus, P. salubris, Paratylenchus sp. 2 SAS, and P. wuae), and six species (P. caravaquenus, P. microdorus, P. nanus, P. neoamblycephalus, P. sheri, and P. variabilis) have been already reported in Spain. Accordingly, these data increase the biodiversity of pin nematodes in Spain comprising a total of 47 species (33.1% out of 142 total species of this genus). Phylogenetic analyses based on ribosomal and mitochondrial markers (D2-D3, ITS, and partial COI) resulted in a consistent position for the newly described Paratylenchus species in this study (P. plesiostraeleni sp. nov., P. paraaonli sp. nov.). Paratylenchus plesiostraeleni sp. nov. grouped in a separated subclade as unequivocal species from the P. straeleni-complex species (including P. straeleni and P. parastraeleni), and P. paraaonli sp. nov. clustered with P. vitecus, but clearly separate from this species. This study indicates that Paratylenchus species diversity in natural environments may be higher than expected, and this study may help in accurate identifications.
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El-Esawi, Mohamed A., Mohamed M. A. Elashtokhy, Sahar A. M. Shamseldin, Enas M. El-Ballat, Ehab M. Zayed, and Yasmin M. Heikal. "Analysis of Genetic Diversity and Phylogenetic Relationships of Wheat (Triticum aestivum L.) Genotypes Using Phenological, Molecular and DNA Barcoding Markers." Genes 14, no. 1 (December 22, 2022): 34. http://dx.doi.org/10.3390/genes14010034.
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Wheat (Triticum aestivum L.) is a key food crop, accounting for approximately 765 million tons produced worldwide. The present study evaluated 16 wheat genotypes using 19 morphological and phenological traits, 16 molecular markers (Inter Simple Sequence Repeats and Start Codon Targeted; ISSR and SCoT) and rbcL and matK plastid gene barcoding. The 16 wheat genotypes showed significant genetic variation using the markers assayed. Cell plot of phenological parameters revealed significant differences among the 16-day-old seedlings of wheat genotypes at Z1.1 growth stage. Collectively, W2 genotype had the lowest shoot length (SL), length of first internodes (LFI) and leaf area (LA) values, while W8 genotype had the highest diameter of first internode (DFI) and LA values. Furthermore, W7 genotype had the maximum plant biomass (PB) and leaf width (LW) values. Geometric models grouped wheat kernels into “rounded” and “nearly elongated”. Estimates of heritability (H2) for these morphological characters ranged from 4.93 to 100%. The highest H2 values were recorded for root number (RN) (100%) followed by SL (88.72%), LFI (88.30%), LA (87.76%) and Feret diameter (86.68%), while the lowest H2 value was recorded for DFI (4.93%). Furthermore, highly significant genotypic and phenotypic correlations were also observed among those traits. Reproducible fingerprinting profiles and high levels of polymorphism (PPB%) of SCoT (95.46%) and ISSR (82.41%) were recorded, indicating that they are effective tools for detecting genetic variation levels among wheat genotypes. The informativeness of markers were measured through estimation of polymorphic information content (PIC), resolving power (RP) and marker index (MI). The RP and PPB% of SCoT were significantly higher compared to those of ISSR. Comparatively, the two molecular markers were effective for studying genetic diversity among wheat genotypes, but SCoT markers were more informative. Moreover, based on the two chloroplast DNA regions (rbcL and matK), MatK was found to be more reliable for differentiating among T. aestivum genotypes. Taken together, using all the studied attributes, a clear taxonomic relationship can be used to identify T. aestivum species and improve their pragmatic production and development.
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Hasan, Ariba, Pirzada Jamal Ahmed Siddiqui, Shabir Ali Amir, and Jean-Dominique Durand. "DNA Barcoding of Mullets (Family Mugilidae) from Pakistan Reveals Surprisingly High Number of Unknown Candidate Species." Diversity 13, no. 6 (May 26, 2021): 232. http://dx.doi.org/10.3390/d13060232.
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The mullets are a widespread group of ecologically and economically important fishes of disputed taxonomy due to their uniform external morphology. Barcoding and phylogenetic studies from various locations around the world largely highlighted the species diversity underestimation using morphological criteria used to establish the taxonomy of the family. Here, we investigated the mullet species diversity from Pakistan, a biogeographic area where nearly no mullet species were genetically characterized. Morphological examination of 40 mullets reveals 6 known species (Planiliza macrolepis, P. klunzingeri, P. subviridis, Crenimugil seheli, Ellochelon vaigiensis, and Mugil cephalus). Using a references DNA barcode library, the DNA barcode-based species identification flagged eight molecular operational taxonomic units (MOTUs) belonging to five genera (Crenimugil, Ellochelon, Mugil, Osteomugil, and Planiliza). Among these MOTUs, only one was already present in Barcode of Life Data system, all other representing new Barcode Index Numbers (BIN). These results emphasize the importance of the recognition of cryptic species and the necessity to re-evaluate the overall diversity by the genetic characterization of different species of this family. DNA barcoding is an effective tool to reveal cryptic species that need to be considered in conservation and management measures of fisheries in Pakistan.
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Carneiro de Melo Moura, Carina, Fabian Brambach, Kevin Jair Hernandez Bado, Konstantin V. Krutovsky, Holger Kreft, Sri Sudarmiyati Tjitrosoedirdjo, Iskandar Z. Siregar, and Oliver Gailing. "Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra." Plants 8, no. 11 (October 30, 2019): 461. http://dx.doi.org/10.3390/plants8110461.
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DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.
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Veldkornet, D. A., J. B. Adams, J. S. Boatwright, and A. Rajkaran. "Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline." Genome 62, no. 9 (September 2019): 585–95. http://dx.doi.org/10.1139/gen-2018-0067.
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Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.
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Farrington, Lachlan, Phyllis MacGillivray, Renate Faast, and Andrew Austin. "Investigating DNA barcoding options for the identification of Caladenia (Orchidaceae) species." Australian Journal of Botany 57, no. 4 (2009): 276. http://dx.doi.org/10.1071/bt08138.
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The application of molecular techniques for defining evolutionary units in Caladenia has largely focussed on addressing relationships at the subgeneric and deeper levels. However, in light of the morphological complexity present in this diverse genus, molecular markers offer additional characters for the refinement of taxonomy at the species level. In the present study, we explored the utility of marker systems with demonstrated application for defining fine-scale units, both in terms of phylogenetic information and in the context of DNA barcoding. We also provide a working example of the use of molecular techniques for identifying the source plants of pollinia collected from passively sampled pollinators and for identifying sterile plants.
Dissertations / Theses on the topic "Plant taxonomy; DNA barcoding; phylogenetic diversity"
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Costion, Craig Mitchell. "Plant biodiversity science, discovery, and conservation : case studies from Australasia and the Pacific." Thesis, 2012. http://hdl.handle.net/2440/96161.
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This thesis advances plant biodiversity knowledge in three separate bioregions, Micronesia, the Queensland Wet Tropics, and South Australia. A systematic treatment of the endemic flora of Micronesia is presented for the first time thus advancing alpha taxonomy for the Micronesia-Polynesia biodiversity hotspot region. The recognized species boundaries are used in combination with all known botanical collections as a basis for assessing the degree of threat for the endemic plants of the Palau archipelago located at the western most edge of Micronesia’s Caroline Islands. A preliminary assessment is conducted utilizing the IUCN red list Criteria followed by a new proposed alternative methodology that enables a degree of threat to be established utilizing existing data. Historical records and archaeological evidence are reviewed to establish the minimum extent of deforestation on the islands of Palau since the arrival of humans. This enabled a quantification of population declines of the majority of plants endemic to the archipelago. In the state of South Australia, the importance of establishing concepts of endemism is emphasized even further. A thorough scientific assessment is presented on the state’s proposed biological corridor reserve network. The report highlights the exclusion from the reserve system of one of the state’s most important hotspots of plant endemism that is highly threatened from habitat fragmentation and promotes the use of biodiversity indices to guide conservation priorities in setting up reserve networks. In the Queensland Wet Tropics the thesis achieves two additional outcomes. A localized pilot study test the accuracy of plant DNA barcodes to estimate species richness. Species richness estimations were performed with high accuracy suggesting the suitability of the approach in poorly known floras where the identity of samples is known or from samples in a cryptic life stage that are difficult to identify. The methodology is promising for areas of the world, such as the tropics, that contain a high percentage of undescribed or poorly known taxa. In addition, a large dataset from northeast Queensland was utilized to assess broad scale patterns of phylogenetic diversity. A linear relationship between phylogenetic diversity and genus richness is found to have high statistical support suggesting that taxon richness is an accurate predictor of hot spots of evolutionary history. When the affects of taxon richness are removed through linear regression however, a strong biogeographic pattern is unveiled. Sites with higher phylogenetic diversity than expected based on genus richness are best explained by having a lower percent of Gondwanan or endemic Australian elements of the flora. These sites have a higher percentage of Indomalayan or other foreign lineages that dispersed to Australia and are more frequent in the lowland rainforest areas below 200 meters. Phylogenetic diversity is shown to be effective at unraveling broad scale patterns of evolutionary history at the biome scale, which may prove useful for justifying the preservation of not just species but assemblages of species that represent different epochs of the earth’s evolutionary history.Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2012
Book chapters on the topic "Plant taxonomy; DNA barcoding; phylogenetic diversity"
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le Roux, Johannes J. "Molecular ecology of plant-microbial interactions during invasions: progress and challenges." In Plant invasions: the role of biotic interactions, 340–62. Wallingford: CABI, 2020. http://dx.doi.org/10.1079/9781789242171.0340.
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Abstract Microbes are omnipresent, yet their interactions with invasive plants remain understudied. This is surprising, given the importance of microbes in plant community ecology and their influence on plant performance in new environments. Recent advances in molecular genetic approaches have opened the door to studying this unseen majority in great detail and to understand how they fit into ecological interaction networks. Molecular approaches allow rapid assessments of microbial diversity at reasonable cost while providing both taxonomic and evolutionary information. Here I discuss how these approaches have contributed to a better understanding of plant-microbial interactions in the context of biological invasions. By drawing insights from various case studies, I illustrate how next-generation sequencing (DNA barcoding) has revolutionized the way we understand such interactions. Tight-knit and coevolved mutualist (e.g. mycorrhizal) and antagonist (e.g. pathogen) interactions appear particularly promising to understand the structure and function of invasive plant-microbial interaction networks, the impacts of invasive plants on native networks and the vulnerability of native networks to infiltration by non-native species. I also discuss novel ways in which molecular data can aid the study of invasive plant-microbial interactions, such as incorporating phylogenetic data into network analyses to better understand the role of evolutionary history in network dynamics and how such dynamics respond to plant invasions. DNA barcoding of microbes also presents unique challenges to the study of network ecology, such as uncertainty in the legitimacy and efficiency of interactions. Future research should incorporate overall plant-associated microbial communities (microbiomes) into interaction networks to better understand the role microbes play during plant invasions.
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Le Roux, Johannes J. "Molecular ecology of plant-microbial interactions during invasions: progress and challenges." In Plant invasions: the role of biotic interactions, 340–62. CABI, 2020. http://dx.doi.org/10.1079/9781789242171.0019.
Full textAbstract:
Microbes are omnipresent, yet their interactions with invasive plants remain understudied. This is surprising, given the importance of microbes in plant community ecology and their influence on plant performance in new environments. Recent advances in molecular genetic approaches have opened the door to studying this unseen majority in great detail and to understand how they fit into ecological interaction networks. Molecular approaches allow rapid assessments of microbial diversity at reasonable cost while providing both taxonomic and evolutionary information. Here I discuss how these approaches have contributed to a better understanding of plant-microbial interactions in the context of biological invasions. By drawing insights from various case studies, I illustrate how next-generation sequencing (DNA barcoding) has revolutionized the way we understand such interactions. Tight-knit and coevolved mutualist (e.g. mycorrhizal) and antagonist (e.g. pathogen) interactions appear particularly promising to understand the structure and function of invasive plant-microbial interaction networks, the impacts of invasive plants on native networks and the vulnerability of native networks to infiltration by non-native species. I also discuss novel ways in which molecular data can aid the study of invasive plant-microbial interactions, such as incorporating phylogenetic data into network analyses to better understand the role of evolutionary history in network dynamics and how such dynamics respond to plant invasions. DNA barcoding of microbes also presents unique challenges to the study of network ecology, such as uncertainty in the legitimacy and efficiency of interactions. Future research should incorporate overall plant-associated microbial communities (microbiomes) into interaction networks to better understand the role microbes play during plant invasions.