1
|
Croy JR, Meyerson LA, Allen WJ, Bhattarai GP, Cronin JT. Lineage and latitudinal variation inPhragmites australistolerance to herbivory: implications for invasion success. OIKOS 2020. [DOI: 10.1111/oik.07260] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jordan R. Croy
- Dept of Biological Sciences, Louisiana State Univ. Baton Rouge LA 70803 USA
- Dept of Ecology and Evolutionary Biology, Univ. of California Irvine CA 92697 USA
| | - Laura A. Meyerson
- Dept of Natural Resource Sciences, Univ. of Rhode Island Kingston RI USA
| | - Warwick J. Allen
- Dept of Biological Sciences, Louisiana State Univ. Baton Rouge LA 70803 USA
- The Bio‐Protection Research Centre, School of Biological Sciences, Univ. of Canterbury Christchurch New Zealand
| | - Ganesh P. Bhattarai
- Dept of Biological Sciences, Louisiana State Univ. Baton Rouge LA 70803 USA
- Dept of Entomology, Kansas State Univ. Manhattan KS USA
| | - James T. Cronin
- Dept of Biological Sciences, Louisiana State Univ. Baton Rouge LA 70803 USA
| |
Collapse
|
2
|
Song Y, Chen Y, Lv J, Xu J, Zhu S, Li M. Comparative Chloroplast Genomes of Sorghum Species: Sequence Divergence and Phylogenetic Relationships. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5046958. [PMID: 31016191 PMCID: PMC6444266 DOI: 10.1155/2019/5046958] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/22/2019] [Accepted: 02/26/2019] [Indexed: 11/18/2022]
Abstract
Sorghum comprises 31 species that exhibit considerable morphological and ecological diversity. The phylogenetic relationships among Sorghum species still remain unresolved due to lower information on the traditional DNA markers, which provides a limited resolution for identifying Sorghum species. In this study, we sequenced the complete chloroplast genomes of Sorghum sudanense and S. propinquum and analyzed the published chloroplast genomes of S. bicolor and S. timorense to retrieve valuable chloroplast molecular resources for Sorghum. The chloroplast genomes ranged in length from 140,629 to 140,755 bp, and their gene contents, gene orders, and GC contents were similar to those for other Poaceae species but were slightly different in the number of SSRs. Comparative analyses among the four chloroplast genomes revealed 651 variable sites, 137 indels, and nine small inversions. Four highly divergent DNA regions (rps16-trnQ, trnG-trnM, rbcL-psaI, and rps15-ndhF), which were suitable for phylogenetic and species identification, were detected in the Sorghum chloroplast genomes. A phylogenetic analysis strongly supported that Sorghum is a monophyletic group in the tribe Andropogoneae. Overall, the genomic resources in this study could provide potential molecular markers for phylogeny and species identification in Sorghum.
Collapse
Affiliation(s)
- Yun Song
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Yan Chen
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Jizhou Lv
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Jin Xu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - MingFu Li
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| |
Collapse
|
3
|
Freeland JR. The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA. Genome 2016; 60:358-374. [PMID: 28177833 DOI: 10.1139/gen-2016-0100] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Environmental DNA (eDNA) comprises DNA fragments that have been shed into the environment by organisms, and which can be extracted from environmental samples such as water or soil. Characterization of eDNA can allow researchers to infer the presence or absence of species from a particular site without the need to locate and identify individuals, and therefore may provide an extremely valuable tool for quantifying biodiversity. However, as is often the case with relatively new protocols, methodological challenges remain. A number of earlier reviews have discussed these challenges, but none have provided extensive treatment of the critical decisions surrounding molecular markers and primer development for use in eDNA assays. This review discusses a number of options and approaches that can be used when determining which primers and gene regions are most appropriate for either targeted species detection or metabarcoding macro-organisms from eDNA. The latter represents a new field that is growing rapidly, and which has the potential to revolutionize future assessments of community and ecosystem diversity.
Collapse
Affiliation(s)
- Joanna R Freeland
- Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada.,Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada
| |
Collapse
|
4
|
|
5
|
Lambertini C. Heteroplasmy due to chloroplast paternal leakage: another insight into Phragmites haplotypic diversity in North America. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1193-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
6
|
Colin R, Eguiarte LE. Phylogeographic analyses and genetic structure illustrate the complex evolutionary history of Phragmites australis in Mexico. AMERICAN JOURNAL OF BOTANY 2016; 103:876-887. [PMID: 27208356 DOI: 10.3732/ajb.1500399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/06/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Genetic data suggest that three lineages of Phragmites australis are found in North America: the Native North American lineage, the Gulf Coast lineage, and the Invasive lineage. In Mexico, P. australis is a common species, but nothing is known about the distribution or ecology of these lineages. We examined the phylogeography of P. australis to analyze the current geographic distribution of genetic variation, demographic history, and dispersal patterns to better understand its evolutionary history in Mexico. METHODS We sampled 427 individuals from 28 populations. We used two noncoding regions of chloroplast DNA to estimate the levels of genetic variation and identified the genetic groups across the species' geographical range in Mexico. We compared the genealogical relationships among haplotypes with those previously reported. A hypothesis of demographic expansion was also tested for the Mexican P. australis lineages. KEY RESULTS We found 13 new haplotypes native to Mexico that might be undergoing an active process of expansion and diversification. Genealogical analyses provided evidence that two independent lineages of P. australis are present in Mexico. The invasive lineage was not detected with our sampling. Our estimates of population expansions in Mexico ranged from 0.202 to 0.726 mya. CONCLUSIONS Phragmites australis is a native species that has been in Mexico for thousands of years. Genetic data suggest that climatic changes during the Pleistocene played an important role in the demographic expansion of the populations that constitute the different genetic groups of P. australis in Mexico.
Collapse
Affiliation(s)
- Ricardo Colin
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito exterior s/n anexo al Jardín Botánico, Ciudad Universitaria 04510 México D.F., México
| | - Luis E Eguiarte
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito exterior s/n anexo al Jardín Botánico, Ciudad Universitaria 04510 México D.F., México
| |
Collapse
|
7
|
Multitrophic enemy escape of invasive Phragmites australis and its introduced herbivores in North America. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0968-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
8
|
Conservation genetics of Magnolia acuminata, an endangered species in Canada: Can genetic diversity be maintained in fragmented, peripheral populations? CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0746-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
9
|
Wheeler GL, Dorman HE, Buchanan A, Challagundla L, Wallace LE. A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps.1400059. [PMID: 25506520 PMCID: PMC4259455 DOI: 10.3732/apps.1400059] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/06/2014] [Indexed: 05/02/2023]
Abstract
Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995-2013. These markers are an important and economical tool for plant biologists and continue to be used alongside modern genomics approaches to study genetic diversity and structure, evolutionary history, and hybridization in native and agricultural species. Studies using species-specific primers reported a greater number of polymorphic loci than those employing universal primers. A major disadvantage to cpSSRs is fragment size homoplasy; therefore, we documented its occurrence at several cpSSR loci within and between species of Acmispon (Fabaceae). Based on our empirical data set, we recommend targeted sequencing of a subset of samples combined with fragment genotyping as a cost-efficient, data-rich approach to the use of cpSSRs and as a test of homoplasy. The availability of genomic resources for plants aids in the development of primers for new study systems, thereby enhancing the utility of cpSSRs across plant biology.
Collapse
Affiliation(s)
- Gregory L. Wheeler
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Hanna E. Dorman
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Alenda Buchanan
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Lavanya Challagundla
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Lisa E. Wallace
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| |
Collapse
|
10
|
Heinze B, Koziel-Monte A, Jahn D. Analysis of variation in chloroplast DNA sequences. Methods Mol Biol 2014; 1115:85-120. [PMID: 24415471 DOI: 10.1007/978-1-62703-767-9_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This chapter introduces and reviews methods for analyzing variation in chloroplast DNA, mainly by polymerase chain reaction (PCR) and subsequent revelation of polymorphisms. Sources for chloroplast primers are discussed, as well as methods such as Sanger sequencing, PCR followed by restriction fragment length polymorphism (RFLP), gel electrophoresis, fragment analysis on automated DNA sequencers, denaturing high-performance liquid chromatography (dHPLC), and next-generation sequencing (NGS). A special section deals with peculiarities of chloroplast DNA variation, such as tandem repeats and mini- and microsatellites.
Collapse
MESH Headings
- Base Sequence
- Chromatography, High Pressure Liquid
- DNA Primers/genetics
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Chloroplast/isolation & purification
- Databases, Genetic
- Electrophoresis, Agar Gel
- Electrophoresis, Polyacrylamide Gel
- Genetic Techniques
- Genetic Variation
- High-Throughput Nucleotide Sequencing
- Nucleic Acid Denaturation
- Polymerase Chain Reaction
- Polymorphism, Genetic
- Polymorphism, Restriction Fragment Length
- Sequence Analysis, DNA
- Tandem Repeat Sequences/genetics
Collapse
Affiliation(s)
- Berthold Heinze
- Department of Genetics, Federal Research Centre for Forests, Vienna, Austria
| | | | | |
Collapse
|
11
|
Nybom H, Weising K, Rotter B. DNA fingerprinting in botany: past, present, future. INVESTIGATIVE GENETICS 2014; 5:1. [PMID: 24386986 PMCID: PMC3880010 DOI: 10.1186/2041-2223-5-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/02/2013] [Indexed: 12/20/2022]
Abstract
Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".
Collapse
Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University for Agricultural Sciences, Fjälkestadsvägen 459, Kristianstad 29194, Sweden
| | - Kurt Weising
- Plant Molecular Systematics, Institute of Biology, University of Kassel, Kassel 34109, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, Frankfurt 60438, Germany
| |
Collapse
|
12
|
Nelson EB, Karp MA. Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands. Ecol Evol 2013; 3:5254-67. [PMID: 24455153 PMCID: PMC3892333 DOI: 10.1002/ece3.900] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 01/08/2023] Open
Abstract
Soil pathogens are believed to be major contributors to negative plant-soil feedbacks that regulate plant community dynamics and plant invasions. While the theoretical basis for pathogen regulation of plant communities is well established within the plant-soil feedback framework, direct experimental evidence for pathogen community responses to plants has been limited, often relying largely on indirect evidence based on above-ground plant responses. As a result, specific soil pathogen responses accompanying above-ground plant community dynamics are largely unknown. Here, we examine the oomycete pathogens in soils conditioned by established populations of native noninvasive and non-native invasive haplotypes of Phragmites australis (European common reed). Our aim was to assess whether populations of invasive plants harbor unique communities of pathogens that differ from those associated with noninvasive populations and whether the distribution of taxa within these communities may help to explain invasive success. We compared the composition and abundance of pathogenic and saprobic oomycete species over a 2-year period. Despite a diversity of oomycete taxa detected in soils from both native and non-native populations, pathogen communities from both invaded and noninvaded soils were dominated by species of Pythium. Pathogen species that contributed the most to the differences observed between invaded and noninvaded soils were distributed between invaded and noninvaded soils. However, the specific taxa in invaded soils responsible for community differences were distinct from those in noninvaded soils that contributed to community differences. Our results indicate that, despite the phylogenetic relatedness of native and non-native P. australis haplotypes, pathogen communities associated with the dominant non-native haplotype are distinct from those of the rare native haplotype. Pathogen taxa that dominate either noninvaded or invaded soils suggest different potential mechanisms of invasion facilitation. These findings are consistent with the hypothesis that non-native plant species that dominate landscapes may "cultivate" a different soil pathogen community to their rhizosphere than those of rarer native species.
Collapse
Affiliation(s)
- Eric B Nelson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University 334 Plant Science Building, Ithaca, New York, 14853-4203
| | - Mary Ann Karp
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University 334 Plant Science Building, Ithaca, New York, 14853-4203
| |
Collapse
|
13
|
Guo WY, Lambertini C, Li XZ, Meyerson LA, Brix H. Invasion of Old World Phragmites australis in the New World: precipitation and temperature patterns combined with human influences redesign the invasive niche. GLOBAL CHANGE BIOLOGY 2013; 19:3406-3422. [PMID: 23765641 DOI: 10.1111/gcb.12295] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/13/2013] [Accepted: 05/25/2013] [Indexed: 06/02/2023]
Abstract
After its introduction into North America, Euro-Asian Phragmites australis became an aggressive invasive wetland grass along the Atlantic coast of North America. Its distribution range has since expanded to the middle, south and southwest of North America, where invasive P. australis has replaced millions of hectares of native plants in inland and tidal wetlands. Another P. australis invasion from the Mediterranean region is simultaneously occurring in the Gulf region of the United States and some countries in South America. Here, we analysed the occurrence records of the two Old World invasive lineages of P. australis (Haplotype M and Med) in both their native and introduced ranges using environmental niche models (ENMs) to assess (i) whether a niche shift accompanied the invasions in the New World; (ii) the role of biologically relevant climatic variables and human influence in the process of invasion; and (iii) the current potential distribution of these two lineages. We detected local niche shifts along the East Coast of North America and the Gulf Coast of the United States for Haplotype M and around the Mississippi Delta and Florida of the United States for Med. The new niche of the introduced Haplotype M accounts for temperature fluctuations and increased precipitation. The introduced Med lineage has enlarged its original subtropical niche to the tropics-subtropics, invading regions with a high annual mean temperature (> ca. 10 °C) and high precipitation in the driest period. Human influence is an important factor for both niches. We suggest that an increase in precipitation in the 20th century, global warming and human-made habitats have shaped the invasive niches of the two lineages in the New World. However, as the invasions are ongoing and human and natural disturbances occur concomitantly, the future distribution ranges of the two lineages may diverge from the potential distribution ranges detected in this study.
Collapse
Affiliation(s)
- Wen-Yong Guo
- Department of Bioscience, Plant Biology, Aarhus University, Ole Worms Allé 1, Aarhus C, 8000, Denmark; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | | | | | | | | |
Collapse
|
14
|
Evidence for multiple introductions of Phragmites australis to North America: detection of a new non-native haplotype. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0491-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
15
|
Worth JRP, Sakaguchi S, Tanaka N, Yamasaki M, Isagi Y. Northern richness and southern poverty: contrasting genetic footprints of glacial refugia in the relictual treeSciadopitys verticillata(Coniferales: Sciadopityaceae). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.02017.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James R. P. Worth
- Laboratory of Forest Biology; Division of Forest and Biomaterials Science; Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho; Sakyo-ku Kyoto; 606-8502; Japan
| | - Shota Sakaguchi
- Laboratory of Forest Biology; Division of Forest and Biomaterials Science; Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho; Sakyo-ku Kyoto; 606-8502; Japan
| | - Nobuyuki Tanaka
- Department of Plant Ecology; Forestry and Forest Products Research Institute; 1, Matsunosato, Tsukuba; Ibaraki; 305-8687; Japan
| | - Michimasa Yamasaki
- Laboratory of Forest Biology; Division of Forest and Biomaterials Science; Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho; Sakyo-ku Kyoto; 606-8502; Japan
| | - Yuji Isagi
- Laboratory of Forest Biology; Division of Forest and Biomaterials Science; Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho; Sakyo-ku Kyoto; 606-8502; Japan
| |
Collapse
|
16
|
Ciotir C, Kirk H, Row JR, Freeland JR. Intercontinental dispersal of Typha angustifolia and T. latifolia between Europe and North America has implications for Typha invasions. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0377-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
17
|
References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
18
|
Lambertini C, Sorrell BK, Riis T, Olesen B, Brix H. Exploring the borders of European Phragmites within a cosmopolitan genus. AOB PLANTS 2012; 2012:pls020. [PMID: 22962631 PMCID: PMC3435523 DOI: 10.1093/aobpla/pls020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 07/10/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Two Phragmites australis taxa are recognized in Europe: P. australis ssp. altissimus, also known as Phragmites isiaca, in the Mediterranean region and P. australis in the temperate region. Another taxonomic group in the Mediterranean is Phragmites frutescens. European genotypes are diverse genetically, cytologically and morphologically, and are related to African, Asiatic and American genotypes. We investigated chloroplast DNA (cpDNA) diversity in Europe and defined the current borders of the European gene pool. METHODOLOGY We analysed chloroplast variation with parsimony and genetic distance methods, and compared it with that of nuclear amplified fragment length polymorphism and microsatellites. We also investigated the phenological pattern of 188 genotypes collected worldwide in a common garden in Denmark. We assumed that non-flowering genotypes could indicate climatic, geographic and/or reproductive barriers to dispersal and would have been recorded in the genetic pattern as groups genetically isolated from, or within, the European pool. PRINCIPAL RESULTS The European P. australis gene pool extends from North America to the Far East and South Africa. However, African and North American genotypes are differentiating from the European genotypes. Mediterranean P. australis is genetically different from temperate P. australis and shares several similarities with Phragmites mauritianus in Africa and Phragmites karka in Asia. Phragmites frutescens shares the cpDNA sequences with both these tropical species. Two DNA bands can distinguish Mediterranean P. australis from P. frutescens and P. mauritianus and from temperate P. australis, and reveal possible hybrids among these species in the Mediterranean region. Phenological data confirmed possible gene flow within the temperate region of Europe, whereas the Mediterranean genotypes did not set inflorescences in Denmark, suggesting reproductive barriers between temperate and Mediterranean P. australis. CONCLUSIONS European P. australis appears as one of four main Phragmites groups known in the world. Further research is needed to understand the implications of long-distance dispersal at the population level.
Collapse
Affiliation(s)
- Carla Lambertini
- Department of Bioscience, Plant Biology, Aarhus University, Ole Worms Allé 1, bld. 1135, 8000 Aarhus C, Denmark
| | | | | | | | | |
Collapse
|
19
|
Saltonstall K, Lambertini C. The value of repetitive sequences in chloroplast DNA for phylogeographic inference: a comment on Vachon & Freeland 2011. Mol Ecol Resour 2012; 12:581-5; discussion 586-9. [PMID: 22533707 DOI: 10.1111/j.1755-0998.2012.03146.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In a recent Technical Advance article, Vachon and Freeland (2011, Molecular Ecology Resources, 11, 279-285.) evaluate the utility of repetitive and non-repetitive variation in the chloroplast genome for phylogeographic inference, using variation in Phragmites australis as an example. While we agree that repetitive and nonrepetitive regions evolve at different rates and homoplasy can impact results, we disagree with the conclusion that repetitive regions are inappropriate for large-scale phylogeographic studies. Here we describe limitations to the study dataset and analysis, and provide an alternative viewpoint on the utility of repetitive regions for phylogeographic studies.
Collapse
Affiliation(s)
- Kristin Saltonstall
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, Republic of Panamá.
| | | |
Collapse
|
20
|
FREELAND JOANNA, VACHON NICOLE. Repetitive sequences in phylogeographic inference: a reply to Saltonstall and Lambertini (2012). Mol Ecol Resour 2012. [DOI: 10.1111/j.1755-0998.2012.03145.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- JOANNA FREELAND
- Department of Biology, Trent University, Peterborough, Ontario, Canada K9J 7B8
| | - NICOLE VACHON
- Department of Biology, Trent University, Peterborough, Ontario, Canada K9J 7B8
| |
Collapse
|
21
|
Lambertini C, Mendelssohn IA, Gustafsson MHG, Olesen B, Riis T, Sorrell BK, Brix H. Tracing the origin of Gulf Coast Phragmites (Poaceae): a story of long-distance dispersal and hybridization. AMERICAN JOURNAL OF BOTANY 2012; 99:538-51. [PMID: 22334449 DOI: 10.3732/ajb.1100396] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Long-distance dispersal can affect speciation processes in two opposing ways. Dispersal can promote geographic isolation or it can bring together geographically distant and distantly related genotypes, thus counteracting local differentiation. We used the Gulf Coast of North America (GC), a "hot spot" of reed diversity and evolutionary dynamics, as a model system to study the diversification processes within the invasive, cosmopolitan, polyploid grass Phragmites. METHODS Genetic diversity was studied using collections representing all species of the genus and from all continents (except Antarctica). A range of molecular markers, including chloroplast and nuclear sequences, microsatellites, and AFLPs, was analyzed to detect DNA variation from the population to the species level and to infer phylogenetic relationships across continents. KEY RESULTS An interspecific hybrid, Phragmites mauritianus × P. australis, and four P. australis cp-DNA haplotypes from Africa, Europe, and North America have been dispersed to the GC and interbreed with each other. CONCLUSIONS Long-distance dispersal and weak breeding barriers appear to be recurring phenomena, not only in the GC, but worldwide. We present data strongly suggesting that interspecific hybridization and introgression among different Phragmites species take place and appear to have contributed significantly to the diversification processes within the genus. Hence, the application of traditional species concepts within Phragmites might be inappropriate.
Collapse
Affiliation(s)
- Carla Lambertini
- Department of Bioscience, Plant Biology, Aarhus University, Ole Worms Allé 1, 8000 Aarhus C, Denmark.
| | | | | | | | | | | | | |
Collapse
|
22
|
Escobar García P, Winkler M, Flatscher R, Sonnleitner M, Krejčíková J, Suda J, Hülber K, Schneeweiss GM, Schönswetter P. Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae). Mol Ecol 2012; 21:1255-70. [PMID: 22276934 PMCID: PMC3306793 DOI: 10.1111/j.1365-294x.2012.05456.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent evidence suggests that survival of arctic-alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organism’s Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences and analysed them, among others, within a graph theoretic framework and using novel Bayesian methods of phylogeographic inference. On the basis of patterns of genetic diversity, occurrence of rare markers, distribution of distinct genetic lineages and patterns of range connectivity both interior refugia in the formerly strongly glaciated central Alps and peripheral refugia along the southern margin of the Alps were identified. The presence of refugia congruently inferred by markers resolving at different time levels suggests that these refugia acted as such throughout several glacial cycles. The high degree of range persistence together with gradual range expansion, which contrasts with the extent of range shifts implied for other Alpine species, is likely responsible for incipient lineage differentiation evident from the genetic data. Replacing a simplistic peripheral vs. interior refugia dualism by more complex models involving both types of refugia and considering different time levels will help identifying common phylogeographic patterns with respect to, for instance, location of refugia and colonization routes and elucidating their underlying genetic and/or ecological causes.
Collapse
Affiliation(s)
- Pedro Escobar García
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, Vienna, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Meyerson LA, Lambertini C, McCormick MK, Whigham DF. Hybridization of common reed in North America? The answer is blowing in the wind. AOB PLANTS 2012; 2012:pls022. [PMID: 22993684 PMCID: PMC3444738 DOI: 10.1093/aobpla/pls022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 07/26/2012] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS We review evidence for hybridization of Phragmites australis in North America and the implications for the persistence of native P. australis ssp. americanus populations in North America. We also highlight the need for an updated classification system, which takes P. australis intraspecific variation and hybridization into account. METHODOLOGY We reviewed available published, in press and in preparation literature to assess the likelihood of hybridization and interbreeding in genotypes of P. australis present in North America. PRINCIPAL RESULTS Experimental results demonstrate that hybridization among introduced and native haplotypes is possible within the genus Phragmites, yet evidence that hybridization has occurred naturally is only starting to emerge. The lag in identifying hybridization in Phragmites in North America may be related to under-sampling in some parts of North America and to a lack of molecular tools that provide the capability to recognize hybrids. CONCLUSIONS Our understanding of the gene flow within and between species in the genus Phragmites is moving at a fast pace, especially on the east and Gulf coasts of North America. More attention should also be focused on the Great Lakes region, the southwestern and the west coast of the USA, where sympatry has created opportunities for hybridization. Where hybridizations have been detected, there are currently no published data on how hybridization affects plant vigour, morphology, invasiveness or conservation of the genetic integrity of the North American native subspecies. We conclude that the detection of more hybridization is highly likely and that there is a need to develop new markers for the different Phragmites species and lineages to fill current knowledge gaps. Finally, we suggest that the classification system for P. australis should be updated and published to help clarify the nomenclature.
Collapse
Affiliation(s)
- L. A. Meyerson
- Department of Invasion Ecology, Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice CZ 252 43, Czech Republic
- Department of Natural Resources Science, University of Rhode Island, Kingston, RI 02881, USA
- Corresponding author's e-mail address:
| | - C. Lambertini
- Department of Biosciences, Aarhus University, Aarhus, Denmark
| | - M. K. McCormick
- Smithsonian Environmental Research Center, PO Box 28, Edgewater, MD 20137, USA
| | - D. F. Whigham
- Smithsonian Environmental Research Center, PO Box 28, Edgewater, MD 20137, USA
| |
Collapse
|
24
|
Aguirre-Planter É, Jaramillo-Correa JP, Gómez-Acevedo S, Khasa DP, Bousquet J, Eguiarte LE. Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context. Mol Phylogenet Evol 2012; 62:263-74. [DOI: 10.1016/j.ympev.2011.09.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 11/27/2022]
|
25
|
Freeland JR, Biss P, Silvertown J. Contrasting patterns of pollen and seed flow influence the spatial genetic structure of sweet vernal grass (Anthoxanthum odoratum) populations. ACTA ACUST UNITED AC 2011; 103:28-35. [PMID: 22003195 DOI: 10.1093/jhered/esr111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The spatial genetic structure of plant populations is determined by a combination of gene flow, genetic drift, and natural selection. Gene flow in most plants can result from either seed or pollen dispersal, but detailed investigations of pollen and seed flow among populations that have diverged following local adaptation are lacking. In this study, we compared pollen and seed flow among 10 populations of sweet vernal grass (Anthoxanthum odoratum) on the Park Grass Experiment. Overall, estimates of genetic differentiation that were based on chloroplast DNA (cpDNA) and, which therefore resulted primarily from seed flow, were lower (average F(ST) = 0.058) than previously published estimates that were based on nuclear DNA (average F(ST) = 0.095). Unlike nuclear DNA, cpDNA showed no pattern of isolation by adaptation; cpDNA differentiation was, however, inversely correlated with the number of additions (nutrients and lime) that each plot had received. We suggest that natural selection is restricting pollen flow among plots, whereas nutrient additions are increasing seed flow and genetic diversity by facilitating the successful germination and growth of immigrant seeds. This study highlights the importance of considering all potential gene flow mechanisms when investigating determinants of spatial genetic structure, and cautions against the widespread assumption that pollen flow is more important than seed flow for population connectivity in wind-pollinated species.
Collapse
Affiliation(s)
- Joanna R Freeland
- Department of Biology, Trent University, Peterborough, Ontario, Canada.
| | | | | |
Collapse
|
26
|
Besnard G, Hernández P, Khadari B, Dorado G, Savolainen V. Genomic profiling of plastid DNA variation in the Mediterranean olive tree. BMC PLANT BIOLOGY 2011; 11:80. [PMID: 21569271 PMCID: PMC3115843 DOI: 10.1186/1471-2229-11-80] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 05/10/2011] [Indexed: 05/08/2023]
Abstract
BACKGROUND Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs) of cpDNA haplotypes in the Mediterranean olive tree. RESULTS Eight complete cpDNA genomes of Olea were sequenced de novo. The nucleotide divergence between olive cpDNA lineages was low and not exceeding 0.07%. Based on these sequences, markers were developed for studying two single nucleotide substitutions and length polymorphism of 62 regions (with variable microsatellite motifs or other indels). They were then used to genotype the cpDNA variation in cultivated and wild Mediterranean olive trees (315 individuals). Forty polymorphic loci were detected on this sample, allowing the distinction of 22 haplotypes belonging to the three Mediterranean cpDNA lineages known as E1, E2 and E3. The discriminating power of cpDNA variation was particularly low for the cultivated olive tree with one predominating haplotype, but more diversity was detected in wild populations. CONCLUSIONS We propose a method for a rapid characterisation of the Mediterranean olive germplasm. The low variation in the cultivated olive tree indicated that the utility of cpDNA variation for forensic analyses is limited to rare haplotypes. In contrast, the high cpDNA variation in wild populations demonstrated that our markers may be useful for phylogeographic and populations genetic studies in O. europaea.
Collapse
Affiliation(s)
- Guillaume Besnard
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
- CNRS, UPS, ENFA, Laboratoire Evolution & Diversité Biologique, UMR 5174, 31062 Toulouse 4, France
| | - Pilar Hernández
- Instituto de Agricultura Sostenible (IAS-CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain
| | - Bouchaib Khadari
- INRA, CBNMED, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), 34398 Montpellier, France
| | - Gabriel Dorado
- Dep. Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Vincent Savolainen
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| |
Collapse
|