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Massatti R, Belus MT, Dowlatshahi S, Allan GJ. Genetic analyses of Astragalus sect. Humillimi (Fabaceae) resolve taxonomy and enable effective conservation. AMERICAN JOURNAL OF BOTANY 2018; 105:1703-1711. [PMID: 30222180 DOI: 10.1002/ajb2.1157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Astragalus sect. Humillimi is distributed across the southwestern United States and contains two endangered taxa, A. cremnophylax var. cremnophylax and A. humillimus. The former was originally described from the South Rim of the Grand Canyon. Analysis of individuals discovered on the North Rim of the Grand Canyon yielded some evidence that the population represented a distinct species. To enable effective conservation, we clarify the group's taxonomy and characterize the genetic diversity of A. cremnophylax and A. humillimus. METHODS We used AFLPs to genotype most species in sect. Humillimi, focusing on the two endangered forms. We examined patterns of genetic diversity using complementary analytical approaches. KEY RESULTS Our results demonstrate that North Rim populations group with A. c. var. cremnophylax. We found low levels of genetic diversity at certain localities and strong differentiation among populations. Astragalus humillimus, which has suffered recent and severe population declines, exhibits weak differentiation among and low diversity within populations. CONCLUSIONS Our results clarify the taxonomy of sect. Humillimi and define the boundaries of A. c. var. cremnophylax, which is shown to inhabit both rims of the Grand Canyon. This clarification, and detailed analysis of genetic variation within both endangered taxa, may advance ongoing efforts to conserve these taxa. Our results suggest that range-wide genetic analysis of A. humillimus may inform recovery strategies for this taxon.
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Affiliation(s)
- Rob Massatti
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, Arizona, 86001, USA
| | - Matthew T Belus
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, Arizona, 86001, USA
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Shahed Dowlatshahi
- National Park Service, Science and Resource Management Division, 17 South Entrance Rd, Grand Canyon, Arizona, 86023, USA
| | - Gerard J Allan
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
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Pozzi AC, Bautista-Guerrero HH, Abby SS, Herrera-Belaroussi A, Abrouk D, Normand P, Menu F, Fernandez MP. Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size. Syst Appl Microbiol 2018; 41:311-323. [DOI: 10.1016/j.syapm.2018.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 10/17/2022]
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Diversification of Bromelioideae (Bromeliaceae) in the Brazilian Atlantic rainforest: A case study in Aechmea subgenus Ortgiesia. Mol Phylogenet Evol 2016; 98:346-57. [PMID: 26957015 DOI: 10.1016/j.ympev.2016.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 12/26/2015] [Accepted: 03/01/2016] [Indexed: 11/21/2022]
Abstract
Aechmea subgenus Ortgiesia comprises ca. 20 species distributed in Brazil, Argentina, Paraguay, and Uruguay, with a center of diversity in the Brazilian Atlantic rainforest. We examined interspecific relationships of Ortgiesia based on Amplified Fragment Length Polymorphisms (AFLP). Ninety-six accessions belonging to 14 species of Ortgiesia were sampled, and genotyped with 11 AFLP primer combinations. The neighbor joining (NJ) tree depicted two main genetic groups within Aechmea subgenus Ortgiesia, and four subgroups. The NJ tree showed short internal branches, indicating an overall shallow genetic divergence among Ortgiesia species as expected for the recently radiated subfamily Bromelioideae. Our results suggest that hybridization and/or incomplete lineage sorting may have hampered the reconstruction of interspecific relationships in Aechmea subgenus Ortgiesia. The mapping of petal color (yellow, blue, pink, or white), inflorescence type (simple or compound), and inflorescence shape (ellipsoid, subcylindric, cylindric, or pyramidal) against the NJ tree indicated that these characters are of limited taxonomic use in Aechmea subgenus Ortgiesia due to homoplasy. An analysis of the current distribution of Ortgiesia identified the southern region of the Brazilian Atlantic rainforest, between latitudes of 26° and 27°S, as the center of diversity for the subgenus.
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Vitales D, García-Fernández A, Pellicer J, Vallès J, Santos-Guerra A, Cowan RS, Fay MF, Hidalgo O, Garnatje T. Key processes for Cheirolophus (Asteraceae) diversification on oceanic islands inferred from AFLP data. PLoS One 2014; 9:e113207. [PMID: 25412495 PMCID: PMC4239036 DOI: 10.1371/journal.pone.0113207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/21/2014] [Indexed: 11/18/2022] Open
Abstract
The radiation of the genus Cheirolophus (Asteraceae) in Macaronesia constitutes a spectacular case of rapid diversification on oceanic islands. Twenty species - nine of them included in the IUCN Red List of Threatened Species - have been described to date inhabiting the Madeiran and Canarian archipelagos. A previous phylogenetic study revealed that the diversification of Cheirolophus in Macaronesia started less than 2 Ma. As a result of such an explosive speciation process, limited phylogenetic resolution was reported, mainly due to the low variability of the employed molecular markers. In the present study, we used highly polymorphic AFLP markers to i) evaluate species' boundaries, ii) infer their evolutionary relationships and iii) investigate the patterns of genetic diversity in relation to the potential processes likely involved in the radiation of Cheirolophus. One hundred and seventy-two individuals representing all Macaronesian Cheirolophus species were analysed using 249 AFLP loci. Our results suggest that geographic isolation played an important role in this radiation process. This was likely driven by the combination of poor gene flow capacity and a good ability for sporadic long-distance colonisations. In addition, we also found some traces of introgression and incipient ecological adaptation, which could have further enhanced the extraordinary diversification of Cheirolophus in Macaronesia. Last, we hypothesize that current threat categories assigned to Macaronesian Cheirolophus species do not reflect their respective evolutionary relevance, so future evaluations of their conservation status should take into account the results presented here.
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Affiliation(s)
- Daniel Vitales
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Alfredo García-Fernández
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Barcelona, Catalonia, Spain
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Joan Vallès
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | | | - Robyn S. Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Oriane Hidalgo
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Barcelona, Catalonia, Spain
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Smith TA, Ciccotto PJ, Mendelson TC, Page LM. Dense Taxon Sampling Using AFLPs Leads to Greater Accuracy in Phylogeny Estimation and Classification of Darters (Percidae: Etheostomatinae). COPEIA 2014. [DOI: 10.1643/ot-13-039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Hipp AL, Eaton DAR, Cavender-Bares J, Fitzek E, Nipper R, Manos PS. A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS One 2014; 9:e93975. [PMID: 24705617 PMCID: PMC3976371 DOI: 10.1371/journal.pone.0093975] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 03/05/2014] [Indexed: 11/19/2022] Open
Abstract
Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23-33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters. RAD-Seq data were readily combined across runs, with no difference in phylogenetic placement between technical replicates, which overlapped by only 43-64% in locus coverage. 17% (4,715) of the loci we analyzed could be mapped with high confidence to one or more expressed sequence tags in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as equal-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. We introduce a partitioned RAD visualization method (implemented in the R package RADami; http://cran.r-project.org/web/packages/RADami) to investigate the possibility that suboptimal topologies supported by large numbers of loci--due, for example, to reticulate evolution or lineage sorting--are masked by the globally optimal tree. We find no evidence for strongly-supported alternative topologies in our study, suggesting that the phylogeny we recover is a robust estimate of large-scale phylogenetic patterns in the American oak clade. Our study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23-33 million year-old clade.
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Affiliation(s)
- Andrew L. Hipp
- The Morton Arboretum, Lisle, Illinois, United States of America
- The Field Museum, Department of Botany, Chicago, Illinois, United States of America
- * E-mail:
| | - Deren A. R. Eaton
- The Field Museum, Department of Botany, Chicago, Illinois, United States of America
- University of Chicago, Committee on Evolutionary Biology, Chicago, Illinois, United States of America
| | - Jeannine Cavender-Bares
- University of Minnesota, College of Biological Sciences, Saint Paul, Minnesota, United States of America
| | | | - Rick Nipper
- Floragenex, Inc., Eugene, Oregon, United States of America
| | - Paul S. Manos
- Duke University, Department of Biology, Durham, North Carolina, United States of America
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García-Pereira MJ, Carvajal-Rodríguez A, Whelan S, Caballero A, Quesada H. Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers. Mol Phylogenet Evol 2014; 76:102-9. [PMID: 24631855 DOI: 10.1016/j.ympev.2014.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
Deep coalescence and the nongenealogical pattern of descent caused by recombination have emerged as a common problem for phylogenetic inference at the species level. Here we use computer simulations to assess whether AFLP-based phylogenies are robust to the uncertainties introduced by these factors. Our results indicate that phylogenetic signal can prevail even in the face of extensive deep coalescence allowing recovering the correct species tree topology. The impact of recombination on tree accuracy was related to total tree depth and species effective population size. The correct tree topology could be recovered upon many simulation settings due to a trade-off between the conflicting signals resulting from intra-locus recombination and the benefits of the joint consideration of unlinked loci that better matched overall the true species tree. Errors in tree topology were not only determined by deep coalescence, but also by the timing of divergence and the tree-building errors arising from an insufficient number of characters. DNA sequences generally outperformed AFLPs upon any simulated scenario, but this difference in performance was nearly negligible when a sufficient number of AFLP characters were sampled. Our simulations suggest that the impact of deep coalescence and intra-locus recombination on the reliability of AFLP trees could be minimal for effective population sizes equal to or lower than 10,000 (typical of many vertebrates and tree plants) given tree depths above 0.02 substitutions per site.
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Affiliation(s)
- María Jesús García-Pereira
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain.
| | - Antonio Carvajal-Rodríguez
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain.
| | - Simon Whelan
- Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala 75236-SE, Sweden.
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain.
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain.
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Kirchberger PC, Sefc KM, Sturmbauer C, Koblmüller S. Outgroup effects on root position and tree topology in the AFLP phylogeny of a rapidly radiating lineage of cichlid fish. Mol Phylogenet Evol 2014; 70:57-62. [PMID: 24055738 PMCID: PMC3842234 DOI: 10.1016/j.ympev.2013.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/26/2022]
Abstract
Phylogenetic analyses of rapid radiations are particularly challenging as short basal branches and incomplete lineage sorting complicate phylogenetic inference. Multilocus data of presence-absence polymorphisms such as obtained by AFLP genotyping overcome some of the difficulties, but also present their own intricacies. Here we analyze >1000 AFLP markers to address the evolutionary history of the Limnochromini, a cichlid fish lineage endemic to Lake Tanganyika, and to test for potential effects of outgroup composition on tree topology. The data support previous mitochondrial evidence on the tribe's taxonomy by confirming the polyphyly of the genus Limnochromis and - in contradiction to a recent taxonomic revision - nesting the genus Greenwoodochromis within the Limnochromini. Species relationships suggest that ecological segregation occurred during the rapid basal radiation of the Limnochromini. The large phylogenetic distance between candidate outgroup taxa and the Limnochromini radiation caused random outgroup effects. Bootstrap support for ingroup nodes was lower in outgroup-rooted than in midpoint-rooted trees, and root positions and ingroup tree topologies varied in response to the composition of the outgroup. These observations suggest that the predisposition for homoplastic evolution makes AFLP-based phylogenetic analyses particularly susceptible to random biases introduced by too-distant outgroup taxa.
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Affiliation(s)
| | | | | | - Stephan Koblmüller
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, A-8010 Graz, Austria
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Caballero A, García-Pereira MJ, Quesada H. Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species. BMC Genomics 2013; 14:528. [PMID: 24060007 PMCID: PMC3750350 DOI: 10.1186/1471-2164-14-528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Amplified fragment length polymorphism (AFLP) markers are frequently used for a wide range of studies, such as genome-wide mapping, population genetic diversity estimation, hybridization and introgression studies, phylogenetic analyses, and detection of signatures of selection. An important issue to be addressed for some of these fields is the distribution of the markers across the genome, particularly in relation to gene sequences. RESULTS Using in-silico restriction fragment analysis of the genomes of nine eukaryotic species we characterise the distribution of AFLP fragments across the genome and, particularly, in relation to gene locations. First, we identify the physical position of markers across the chromosomes of all species. An observed accumulation of fragments around (peri) centromeric regions in some species is produced by repeated sequences, and this accumulation disappears when AFLP bands rather than fragments are considered. Second, we calculate the percentage of AFLP markers positioned within gene sequences. For the typical EcoRI/MseI enzyme pair, this ranges between 28 and 87% and is usually larger than that expected by chance because of the higher GC content of gene sequences relative to intergenic ones. In agreement with this, the use of enzyme pairs with GC-rich restriction sites substantially increases the above percentages. For example, using the enzyme system SacI/HpaII, 86% of AFLP markers are located within gene sequences in A. thaliana, and 100% of markers in Plasmodium falciparun. We further find that for a typical trait controlled by 50 genes of average size, if 1000 AFLPs are used in a study, the number of those within 1 kb distance from any of the genes would be only about 1-2, and only about 50% of the genes would have markers within that distance. CONCLUSIONS The high coverage of AFLP markers across the genomes and the high proportion of markers within or close to gene sequences make them suitable for genome scans and detecting large islands of differentiation in the genome. However, for specific traits, the percentage of AFLP markers close to genes can be rather small. Therefore, genome scans directed towards the search of markers closely linked to selected loci can be a difficult task in many instances.
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Affiliation(s)
- Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, 36310 Vigo, Spain.
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Wan Y, Schwaninger HR, Baldo AM, Labate JA, Zhong GY, Simon CJ. A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change. BMC Evol Biol 2013; 13:141. [PMID: 23826735 PMCID: PMC3750556 DOI: 10.1186/1471-2148-13-141] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 05/28/2013] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations. RESULTS Vitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 - 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 - 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species. CONCLUSIONS Phylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.
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Affiliation(s)
- Yizhen Wan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Heidi R Schwaninger
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
| | - Angela M Baldo
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
- US Department of Agriculture, Agriculture Research Service, Grape Genetic Research Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
| | - Joanne A Labate
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
| | - Gan-Yuan Zhong
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
- US Department of Agriculture, Agriculture Research Service, Grape Genetic Research Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
| | - Charles J Simon
- US Department of Agriculture, Agriculture Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
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Givnish TJ, Bean GJ, Ames M, Lyon SP, Sytsma KJ. Phylogeny, floral evolution, and inter-island dispersal in Hawaiian Clermontia (Campanulaceae) based on ISSR variation and plastid spacer sequences. PLoS One 2013; 8:e62566. [PMID: 23658747 PMCID: PMC3642221 DOI: 10.1371/journal.pone.0062566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 03/22/2013] [Indexed: 11/22/2022] Open
Abstract
Previous studies based on DNA restriction-site and sequence variation have shown that the Hawaiian lobeliads are monophyletic and that the two largest genera, Cyanea and Clermontia, diverged from each other ca. 9.7 Mya. Sequence divergence among species of Clermontia is quite limited, however, and extensive hybridization is suspected, which has interfered with production of a well-resolved molecular phylogeny for the genus. Clermontia is of considerable interest because several species posses petal-like sepals, raising the question of whether such a homeotic mutation has arisen once or several times. In addition, morphological and molecular studies have implied different patterns of inter-island dispersal within the genus. Here we use nuclear ISSRs (inter-simple sequence repeat polymorphisms) and five plastid non-coding sequences to derive biparental and maternal phylogenies for Clermontia. Our findings imply that (1) Clermontia is not monophyletic, with Cl. pyrularia nested within Cyanea and apparently an intergeneric hybrid; (2) the earliest divergent clades within Clermontia are native to Kauài, then Òahu, then Maui, supporting the progression rule of dispersal down the chain toward progressively younger islands, although that rule is violated in later-evolving taxa in the ISSR tree; (3) almost no sequence divergence among several Clermontia species in 4.5 kb of rapidly evolving plastid DNA; (4) several apparent cases of hybridization/introgression or incomplete lineage sorting (i.e., Cl. oblongifolia, peleana, persicifolia, pyrularia, samuelii, tuberculata), based on extensive conflict between the ISSR and plastid phylogenies; and (5) two origins and two losses of petaloid sepals, or--perhaps more plausibly--a single origin and two losses of this homeotic mutation, with its introgression into Cl. persicifolia. Our phylogenies are better resolved and geographically more informative than others based on ITS and 5S-NTS sequences and nuclear SNPs, but agree with them in supporting Clermontia's origin on Kauài or some older island and dispersal down the chain subsequently.
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Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
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Kück P, Greve C, Misof B, Gimnich F. Automated masking of AFLP markers improves reliability of phylogenetic analyses. PLoS One 2012; 7:e49119. [PMID: 23152859 PMCID: PMC3494671 DOI: 10.1371/journal.pone.0049119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/04/2012] [Indexed: 12/24/2022] Open
Abstract
The amplified fragment length polymorphisms (AFLP) method has become an attractive tool in phylogenetics due to the ease with which large numbers of characters can be generated. In contrast to sequence-based phylogenetic approaches, AFLP data consist of anonymous multilocus markers. However, potential artificial amplifications or amplification failures of fragments contained in the AFLP data set will reduce AFLP reliability especially in phylogenetic inferences. In the present study, we introduce a new automated scoring approach, called “AMARE” (AFLP MAtrix REduction). The approach is based on replicates and makes marker selection dependent on marker reproducibility to control for scoring errors. To demonstrate the effectiveness of our approach we record error rate estimations, resolution scores, PCoA and stemminess calculations. As in general the true tree (i.e. the species phylogeny) is not known, we tested AMARE with empirical, already published AFLP data sets, and compared tree topologies of different AMARE generated character matrices to existing phylogenetic trees and/or other independent sources such as morphological and geographical data. It turns out that the selection of masked character matrices with highest resolution scores gave similar or even better phylogenetic results than the original AFLP data sets.
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Affiliation(s)
- Patrick Kück
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Carola Greve
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
- * E-mail:
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - France Gimnich
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
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LEGA MARGHERITA, FIOR SIMONE, PROSSER FILIPPO, BERTOLLI ALESSIO, LI MINGAI, VAROTTO CLAUDIO. Application of the unified species concept reveals distinct lineages for disjunct endemics of the Brassica repanda (Brassicaceae) complex. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01887.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Grubisha LC, Levsen N, Olson MS, Lee Taylor D. Intercontinental divergence in the Populus-associated ectomycorrhizal fungus, Tricholoma populinum. THE NEW PHYTOLOGIST 2012; 194:548-560. [PMID: 22332931 DOI: 10.1111/j.1469-8137.2012.04066.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The ectomycorrhizal fungus Tricholoma populinum is host-specific with Populus species. T. populinum has wind-dispersed progagules and may be capable of long-distance dispersal. In this study, we tested the hypothesis of a panmictic population between Scandinavia and North America. DNA sequences from five nuclear loci were used to assess phylogeographic structure and nucleotide divergence between continents. Tricholoma populinum was composed of Scandinavian and North American lineages with complete absence of shared haplotypes and only one shared nucleotide mutation. Divergence of these lineages was estimated at approx. 1.7-1.0 million yr ago (Ma), which occurred after the estimated divergence of host species Populus tremula and Populus balsamifera/Populus trichocarpa at 5 Ma. Phylogeographic structure was not observed within Scandinavian or North American lineages of T. populinum. Intercontinental divergence appears to have resulted from either allopatric isolation; a recent, rare long-distance dispersal founding event followed by genetic drift; or the response in an obligate mycorrhizal fungus with a narrow host range to contractions and expansion of host distribution during glacial and interglacial episodes within continents. Understanding present genetic variation in populations is important for predicting how obligate symbiotic fungi will adapt to present and future changing climatic conditions.
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Affiliation(s)
- Lisa C Grubisha
- Institute of Arctic Biology, 902 N. Koyukuk Drive, 311 Irving 1 Building, University of Alaska Fairbanks, Fairbanks, AK 99775-7000, USA
- Present address: Biology Program, Centre College, Danville, KY 40422, USA
| | - Nicholas Levsen
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Matthew S Olson
- Institute of Arctic Biology, 902 N. Koyukuk Drive, 311 Irving 1 Building, University of Alaska Fairbanks, Fairbanks, AK 99775-7000, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - D Lee Taylor
- Institute of Arctic Biology, 902 N. Koyukuk Drive, 311 Irving 1 Building, University of Alaska Fairbanks, Fairbanks, AK 99775-7000, USA
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García-Pereira MJ, Quesada H, Caballero A, Carvajal-Rodríguez A. AFLPMax: a user-friendly application for computing the optimal number of amplified fragment length polymorphism markers needed in phylogenetic reconstruction. Mol Ecol Resour 2012; 12:566-9. [PMID: 22268698 DOI: 10.1111/j.1755-0998.2011.03113.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amplified fragment length polymorphisms (AFLPs) are widely used for phylogenetic inference especially in non-model species. Frequently, trees obtained with other nuclear or mitochondrial markers or with morphological information need additional resolution, increased branch support, or independent data sources (i.e. unlinked loci). In such cases, the use of AFLPs is a quick and cheap option. Computer simulation has shown that dominant AFLP markers lead to less accurate tree topologies than bi-allelic codominant markers such as SNPs, but this difference becomes negligible for shallow trees when using AFLP data sets that include a sufficiently large number of characters. Thus, determining how many AFLP characters are required to recover a given phylogeny is a key issue regarding the appropriateness of AFLPs for phylogenetic reconstruction. Here, we present a user-friendly, java-based graphical interface, AFLPMax, which executes an automatic pipeline of different programs providing the user with the optimal number of AFLP characters needed to recover a given phylogeny with high accuracy and support. Executables for Windows, linux and MacOS X operating systems, source code and user manual are available from: http://webs.uvigo.es/acraaj/AFLPMax.htm.
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Affiliation(s)
- M J García-Pereira
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310 Vigo, Spain.
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Gaudeul M, Rouhan G, Gardner MF, Hollingsworth PM. AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:68-81. [PMID: 22184275 DOI: 10.3732/ajb.1100321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Despite its small size, New Caledonia is characterized by a very diverse flora and striking environmental gradients, which make it an ideal setting to study species diversification. Thirteen of the 19 Araucaria species are endemic to the territory and form a monophyletic group, but patterns and processes that lead to such a high species richness are largely unexplored. METHODS We used 142 polymorphic AFLP markers and performed analyses based on Bayesian clustering algorithms, genetic distances, and cladistics on 71 samples representing all New Caledonian Araucaria species. We examined correlations between the inferred evolutionary relationships and shared morphological, ecological, or geographic parameters among species, to investigate evolutionary processes that may have driven speciation. KEY RESULTS We showed that genetic divergence among the present New Caledonian Araucaria species is low, suggesting recent diversification rather than pre-existence on Gondwana. We identified three genetic groups that included small-leaved, large-leaved, and coastal species, but detected no association with soil preference, ecological habitat, or rainfall. The observed patterns suggested that speciation events resulted from both differential adaptation and vicariance. Last, we hypothesize that speciation is ongoing and/or there are cryptic species in some genetically (sometimes also morphologically) divergent populations. CONCLUSIONS Further data are required to provide better resolution and understanding of the diversification of New Caledonian Araucaria species. Nevertheless, our study allowed insights into their evolutionary relationships and provides a framework for future investigations on the evolution of this emblematic group of plants in one of the world's biodiversity hotspots.
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Affiliation(s)
- Myriam Gaudeul
- Muséum National d'Histoire Naturelle, UMR CNRS 'Origine, Structure et Evolution de la Biodiversité', Paris, France.
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García-Pereira MJ, Caballero A, Quesada H. The relative contribution of band number to phylogenetic accuracy in AFLP data sets. J Evol Biol 2011; 24:2346-56. [PMID: 21848979 DOI: 10.1111/j.1420-9101.2011.02361.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examined the effect of increasing the number of sampled amplified fragment length polymorphism (AFLP) bands to reconstruct an accurate and well-supported AFLP-based phylogeny. In silico AFLP was performed using simulated DNA sequences evolving along balanced and unbalanced model trees with recent, uniform and ancient radiations and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.05 substitutions per site. Trees were estimated by minimum evolution (ME) and maximum parsimony (MP) methods from both DNA sequences and virtual AFLP fingerprints. The comparison of the true tree with the estimated AFLP trees suggests that moderate numbers of AFLP bands are necessary to recover the correct topology with high bootstrap support values (i.e. >70%). Fewer numbers of bands are necessary for shorter tree lengths and for balanced than for unbalanced tree topologies. However, branch length estimation was rather unreliable and did not improve substantially after a certain number of bands were sampled. These results hold for different levels of genome coverage and number of taxa analysed. In silico AFLP using bacterial genomic DNA sequences recovered a well-supported tree topology that mirrored an empirical phylogeny based on a set of 31 orthologous gene sequences when as few as 263 AFLP bands were scored. These results suggest that AFLPs may be an efficient alternative to traditional DNA sequencing for accurate topology reconstruction of shallow trees when not very short ancestral branches exist.
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Affiliation(s)
- M J García-Pereira
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, Vigo, Spain
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Fávaro LCDL, de Melo FL, Aguilar-Vildoso CI, Araújo WL. Polyphasic analysis of intraspecific diversity in Epicoccum nigrum warrants reclassification into separate species. PLoS One 2011; 6:e14828. [PMID: 21853017 PMCID: PMC3154903 DOI: 10.1371/journal.pone.0014828] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 12/15/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Epicoccum nigrum Link (syn. E. purpurascens Ehrenb. ex Schlecht) is a saprophytic ascomycete distributed worldwide which colonizes a myriad of substrates. This fungus has been known as a biological control agent for plant pathogens and produces a variety of secondary metabolites with important biological activities as well as biotechnological application. E. nigrum produces darkly pigmented muriform conidia on short conidiophores on sporodochia and is a genotypically and phenotypically highly variable species. Since different isolates identified as E. nigrum have been evaluated as biological control agents and used for biocompound production, it is highly desirable that this species name refers to only one lineage. However, according to morphological and genetic variation, E. nigrum present two genotypes that may comprise more than one species. METHODOLOGY/PRINCIPAL FINDINGS We report the application of combined molecular (ITS and β-tubulin gene sequence analysis, PCR-RFLP and AFLP techniques), morphometric, physiological, genetic compatibility and recombination analysis to study the taxonomic relationships within an endophytic population that has been identified as E. nigrum. This combined analysis established two genotypes showing morphological, physiological and genetic divergence as well as genetic incompatibility characterized by colony inhibition, strongly indicating that these genotypes correspond to different species. Genotype 1 corresponds to E. nigrum while genotype 2 represents a new species, referred to in this study as Epicoccum sp. CONCLUSIONS/SIGNIFICANCE This research contributes to the knowledge of the Epicoccum genus and asserts that the classification of E. nigrum as a single variable species should be reassessed. In fact, based on the polyphasic approach we suggest the occurrence of cryptic species within E. nigrum and also that many of the sequences deposited as E. nigrum in GenBank and culture collection of microbial strains should be reclassified, including the reference strain CBS 161.73 sequenced in this work. In addition, this study provides valuable tools for differentiation of Epicoccum species.
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Affiliation(s)
| | | | | | - Welington Luiz Araújo
- Laboratory of Molecular Biology and Microbial Ecology, NIB, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, Brazil
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AFLPs support deep relationships among darters (Percidae: Etheostomatinae) consistent with morphological hypotheses. Heredity (Edinb) 2011; 107:579-88. [PMID: 21712845 DOI: 10.1038/hdy.2011.50] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent attention has focused on the efficacy of amplified fragment length polymorphisms (AFLPs) for resolving deep evolutionary relationships. Here we show that AFLPs provide resolution of deep relationships within the family Percidae that are more consistent with previous morphological hypotheses than are relationships proposed by previous molecular analyses. Despite in silico predictions, we were able to resolve relatively ancient divergences, estimated at >25 MA. We show that the most distantly related species share the fewest fragments, but suggest that large data sets and extensive taxon sampling are sufficient to overcome this obstacle of the AFLP technique for deep divergences. We compare genetic distances estimated from mitochondrial DNA with those from AFLPs and contrast traditional PAUP(*) Nei-Li AFLP genetic distances with a recently proposed method utilizing the Dice equation with constraining nucleotides.
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Guan L, Shiraishi S. Improved AFLP protocol using dual-suppression PCR and its application to species with large genomes. Mol Ecol Resour 2011; 11:854-61. [PMID: 21676205 DOI: 10.1111/j.1755-0998.2011.03029.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To improve the amplified fragment length polymorphism assay, dual-suppression PCR was introduced into the preamplification step of the assay. The dual-suppression PCR blocked completely the amplification of fragments with the same sequence (Bsp1407I-Bsp1407I or NlaIII-NlaIII) at both ends and amplified selectively fragments with different adaptor sequences (Bsp1407I-NlaIII) at each end. Two protocols, referred to as A and B, were established for species with medium- and large-sized genomes, respectively. Both protocols incorporated the dual-suppression PCR. Protocol A resulted in high-quality electrophoretic profiles for black cottonwood and rice, which have medium-sized genomes. In protocol B, an intensely selective PCR step was added to protocol A. Protocol B yielded profiles for Japanese black pine and Japanese cedar that were improved significantly relative to protocol A: the number of strong peaks increased and that of low peaks decreased. Japanese black pine and Japanese cedar have large genomes. The optimal profiles were generated with a total of eight or nine selective nucleotides.
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Affiliation(s)
- Lanhua Guan
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan
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Genomospecies identification and phylogenomic relevance of AFLP analysis of isolated and non-isolated strains of Frankia spp. Syst Appl Microbiol 2011; 34:200-6. [DOI: 10.1016/j.syapm.2010.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 10/21/2010] [Accepted: 10/28/2010] [Indexed: 11/23/2022]
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