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Bober S, Glaubrecht M, Hausdorf B, Neiber MT. One, two or three? Integrative species delimitation of short-range endemic Hemicycla species (Gastropoda: Helicidae) from the Canary Islands based on morphology, barcoding, AFLP and ddRADseq data. Mol Phylogenet Evol 2021; 161:107153. [PMID: 33741537 DOI: 10.1016/j.ympev.2021.107153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 11/26/2022]
Abstract
Hemicycla mascaensis and H. diegoi are short-range endemics that occur allopatrically in small areas in the Teno Mountains in the western part of Tenerife (Canary Islands). Both taxa have been recognised as distinct species based on differences in shell morphology and genital anatomy. Preliminary molecular analyses using mitochondrial markers suggested a potential paraphyly of H. diegoi with regard to H. mascaensis. We here use multilocus AFLP data and ddRADseq data as well as distribution data, data on shell morphology and genital anatomy to assess the status of these taxa using phylogenetic analyses, species tree reconstruction and molecular species delimitation based on the multispecies coalescent as implemented in BFD* and BPP in an integrative approach. Our analyses show that, based on the analysis of multilocus data, the two taxa are reciprocally monophyletic. Species delimitation methods, however, tend to recognise all investigated populations as distinct species, albeit neither lending unambiguous support to any of the species hypotheses. The comparison of the anatomy of distal genital organs further suggests differentiation within H. mascaensis. This highlights the need for a balanced weighting of arguments from different lines of evidence to determine species status and calls for cautious interpretations of the results of molecular species delimitation analyses, especially in organisms with low active dispersal capacities and expected distinct population structuring such as land snails. Taking all available evidence into account, we favour to recognise H. mascaensis and H. diegoi as distinct species, acknowledging, though, that the recognition of both taxa as subspecies (with possibly a third yet undescribed) would also be an option as morphological differentiation is within the limits of other land snail species that are traditionally subdivided into subspecies.
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Affiliation(s)
- Simon Bober
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Matthias Glaubrecht
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Bernhard Hausdorf
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Marco T Neiber
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany.
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2
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Phylogeography of western Mediterranean Cymbalaria (Plantaginaceae) reveals two independent long-distance dispersals and entails new taxonomic circumscriptions. Sci Rep 2018; 8:18079. [PMID: 30591708 PMCID: PMC6308241 DOI: 10.1038/s41598-018-36412-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 11/19/2018] [Indexed: 11/24/2022] Open
Abstract
The Balearic Islands, Corsica and Sardinia (BCS) constitute biodiversity hotspots in the western Mediterranean Basin. Oligocene connections and long distance dispersal events have been suggested to cause presence of BCS shared endemic species. One of them is Cymbalaria aequitriloba, which, together with three additional species, constitute a polyploid clade endemic to BCS. Combining amplified fragment length polymorphism (AFLP) fingerprinting, plastid DNA sequences and morphometrics, we inferred the phylogeography of the group and evaluated the species’ current taxonomic circumscriptions. Based on morphometric and AFLP data we propose a new circumscription for C. fragilis to additionally comprise a group of populations with intermediate morphological characters previously included in C. aequitriloba. Consequently, we suggest to change the IUCN category of C. fragilis from critically endangered (CR) to near threatened (NT). Both morphology and AFLP data support the current taxonomy of the single island endemics C. hepaticifolia and C. muelleri. The four species had a common origin in Corsica-Sardinia, and two long-distance dispersal events to the Balearic Islands were inferred. Finally, plastid DNA data suggest that interspecific gene flow took place where two species co-occur.
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3
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Genomic comparisons of Rhizobium species using in silico AFLP-PCR, endonuclease restriction, and AMPylating enzymes. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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4
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Wagner MD, Blanton RE. Do River Drainage Boundaries Coincide with Phylogeographic Breaks in the Redband Darter? COPEIA 2017. [DOI: 10.1643/ci-16-414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Restrepo CM, Llanes A, Lleonart R. Use of AFLP for the study of eukaryotic pathogens affecting humans. INFECTION GENETICS AND EVOLUTION 2017; 63:360-369. [PMID: 28935612 DOI: 10.1016/j.meegid.2017.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 12/29/2022]
Abstract
Amplified fragment length polymorphism (AFLP) is a genotyping technique based on PCR amplification of specific restriction fragments from a particular genome. The methodology has been extensively used in plant biology to solve a variety of scientific questions, including taxonomy, molecular epidemiology, systematics, population genetics, among many others. The AFLP share advantages and disadvantages with other types of molecular markers, being particularly useful in organisms with no previous DNA sequence knowledge. In eukaryotic pathogens, the technique has not been extensively used, although it has the potential to solve many important issues as it allows the simultaneous examination of hundreds or even thousands of polymorphic sites in the genome of the organism. Here we describe the main applications published on the use of AFLP in eukaryotic pathogens, with emphasis in species of the groups fungi, protozoa and helminths, and discuss the role of this methodology in the context of new techniques derived from the advances of the next generation sequencing.
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Affiliation(s)
- Carlos M Restrepo
- Center for Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Edificio 219, Ciudad del Saber, Apartado 0843-01103, Ciudad de Panamá, Panama.; Department of Biotechnology, Acharya Nagarjuna University, Guntur, India..
| | - Alejandro Llanes
- Center for Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Edificio 219, Ciudad del Saber, Apartado 0843-01103, Ciudad de Panamá, Panama.; Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Ricardo Lleonart
- Center for Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Edificio 219, Ciudad del Saber, Apartado 0843-01103, Ciudad de Panamá, Panama..
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Glynou K, Ali T, Kia SH, Thines M, Maciá-Vicente JG. Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation. Mol Ecol 2017; 26:4618-4630. [PMID: 28667772 DOI: 10.1111/mec.14231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 04/09/2017] [Accepted: 06/08/2017] [Indexed: 12/25/2022]
Abstract
Studying community structure and dynamics of plant-associated fungi is the basis for unravelling their interactions with hosts and ecosystem functions. A recent sampling revealed that only a few fungal groups, as defined by internal transcribed spacer region (ITS) sequence similarity, dominate culturable root endophytic communities of nonmycorrhizal Microthlaspi spp. plants across Europe. Strains of these fungi display a broad phenotypic and functional diversity, which suggests a genetic variability masked by ITS clustering into operational taxonomic units (OTUs). The aims of this study were to identify how genetic similarity patterns of these fungi change across environments and to evaluate their ability to disperse and adapt to ecological conditions. A first ITS-based haplotype analysis of ten widespread OTUs mostly showed a low to moderate genotypic differentiation, with the exception of a group identified as Cadophora sp. that was highly diverse. A multilocus phylogeny based on additional genetic loci (partial translation elongation factor 1α, beta-tubulin and actin) and amplified fragment length polymorphism profiling of 185 strains representative of the five dominant OTUs revealed a weak association of genetic differences with geography and environmental conditions, including bioclimatic and soil factors. Our findings suggest that dominant culturable root endophytic fungi have efficient dispersal capabilities, and that their distribution is little affected by environmental filtering. Other processes, such as inter- and intraspecific biotic interactions, may be more important for the local assembly of their communities.
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Affiliation(s)
- Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
| | - Tahir Ali
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Sevda Haghi Kia
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany.,Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Jose G Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
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Greve C, Haase M, Hutterer R, Rödder D, Ihlow F, Misof B. Snails in the desert: Species diversification of Theba (Gastropoda: Helicidae) along the Atlantic coast of NW Africa. Ecol Evol 2017; 7:5524-5538. [PMID: 28770088 PMCID: PMC5528248 DOI: 10.1002/ece3.3138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 05/11/2017] [Accepted: 05/13/2017] [Indexed: 11/10/2022] Open
Abstract
The spatial subdivision of species often plays a pivotal role in speciation. Across their entire range, species are rarely panmictic and crucial consequences of spatial subdivision are (1) random genetic drift including historical factors, (2) uniform selection, and (3) divergent selection. Each of these consequences may result in geographic variation and eventually reproductive isolation, but their relative importance in speciation is still unclear. In this study, we used a combination of genetic, morphological, and climatic data to obtain a comprehensive picture of differentiation among three closely related, parapatrically distributed taxa of the land snail genus Theba occurring along the Atlantic coasts of South Morocco and Western Sahara. We conducted Mantel and partial Mantel tests to relate phenotypic and genotypic variation of these species to geography and/or climate. As null hypothesis for an evolutionary scenario, we assumed nonadaptive speciation and expected a pattern of isolation by distance among taxa. Rejection of the null hypothesis would indicate isolation by environment due to adaptation. Generally, genetic drift plays an important role but is rarely considered as sole driver of speciation. It is the combination of drift and selection that predominantly drives speciation. This study, however, provides a potential example, in which nonadaptive speciation, that is, genetic drift, is apparently the main driver of shaping the diversity of Theba in NW Africa. Restriction of gene flow between populations caused by geographic isolation probably has played an important role. Climate oscillations during the Plio- and Pleistocene may have led to repeated ecological changes in NW Africa and disruptions of habitats promoting differentiation by geographic isolation. The inferred evolutionary scenario, however, did not fully explain the incongruence between the AFLP- and mtDNA-tree topologies. This incongruence might indicate past hybridization among the studied Theba forms.
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Affiliation(s)
- Carola Greve
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
| | - Martin Haase
- Vogelwarte, Zoologisches Institut und MuseumErnst‐Moritz‐Arndt‐Universität GreifswaldGreifswaldGermany
| | - Rainer Hutterer
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
| | - Dennis Rödder
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
| | - Flora Ihlow
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
| | - Bernhard Misof
- Stiftung Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
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8
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Diazgranados M, Barber JC. Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands. PeerJ 2017; 5:e2968. [PMID: 28168124 PMCID: PMC5292030 DOI: 10.7717/peerj.2968] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/09/2017] [Indexed: 12/02/2022] Open
Abstract
Background The páramo ecosystem, located above the timberline in the tropical Andes, has been the setting for some of the most dramatic plant radiations, and it is one of the world’s fastest evolving and most diverse high-altitude ecosystems. Today 144+ species of frailejones (subtribe Espeletiinae Cuatrec., Asteraceae) dominate the páramo. Frailejones have intrigued naturalists and botanists, not just for their appealing beauty and impressive morphological diversity, but also for their remarkable adaptations to the extremely harsh environmental conditions of the páramo. Previous attempts to reconstruct the evolutionary history of this group failed to resolve relationships among genera and species, and there is no agreement regarding the classification of the group. Thus, our goal was to reconstruct the phylogeny of the frailejones and to test the influence of the geography on it as a first step to understanding the patterns of radiation of these plants. Methods Field expeditions in 70 páramos of Colombia and Venezuela resulted in 555 collected samples from 110 species. Additional material was obtained from herbarium specimens. Sequence data included nrDNA (ITS and ETS) and cpDNA (rpl16), for an aligned total of 2,954 bp. Fragment analysis was performed with AFLP data using 28 primer combinations and yielding 1,665 fragments. Phylogenies based on sequence data were reconstructed under maximum parsimony, maximum likelihood and Bayesian inference. The AFLP dataset employed minimum evolution analyses. A Monte Carlo permutation test was used to infer the influence of the geography on the phylogeny. Results Phylogenies reconstructed suggest that most genera are paraphyletic, but the phylogenetic signal may be misled by hybridization and incomplete lineage sorting. A tree with all the available molecular data shows two large clades: one of primarily Venezuelan species that includes a few neighboring Colombian species; and a second clade of only Colombian species. Results from the Monte Carlo permutation test suggests a very strong influence of the geography on the phylogenetic relationships. Venezuelan páramos tend to hold taxa that are more distantly-related to each other than Colombian páramos, where taxa are more closely-related to each other. Conclusions Our data suggest the presence of two independent radiations: one in Venezuela and the other in Colombia. In addition, the current generic classification will need to be deeply revised. Analyses show a strong geographic structure in the phylogeny, with large clades grouped in hotspots of diversity at a regional scale, and in páramo localities at a local scale. Differences in the degrees of relatedness between sympatric species of Venezuelan and Colombian páramos may be explained because of the younger age of the latter páramos, and the lesser time for speciation of Espeletiinae in them.
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Affiliation(s)
- Mauricio Diazgranados
- Natural Capital and Plant Health Department, Wakehurst Place, Royal Botanic Gardens, Kew , Ardingly , West Sussex , United Kingdom
| | - Janet C Barber
- Department of Biology, Saint Louis University, Saint Louis, MO, United States; Missouri Botanical Garden, Saint Louis, MO, United States
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9
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Winkler M, Escobar García P, Gattringer A, Sonnleitner M, Hülber K, Schönswetter P, Schneeweiss GM. A novel method to infer the origin of polyploids from Amplified Fragment Length Polymorphism data reveals that the alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy. Mol Ecol Resour 2017; 17:877-892. [PMID: 27978605 DOI: 10.1111/1755-0998.12641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 11/30/2022]
Abstract
Despite its evolutionary and ecological relevance, the mode of polyploid origin has been notoriously difficult to be reconstructed from molecular data. Here, we present a method to identify the putative parents of polyploids and thus to infer the mode of their origin (auto- vs. allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen's d of distances between in silico polyploids, generated within a priori defined scenarios of origin from a priori delimited putative parental entities (e.g. taxa, genetic lineages), and natural polyploids. Simulations show that the discriminatory power of the proposed method increases mainly with increasing divergence between the lower-ploid putative ancestors and less so with increasing delay of polyploidization relative to the time of divergence. We apply the new method to the Senecio carniolicus aggregate, distributed in the European Alps and comprising two diploid, one tetraploid and one hexaploid species. In the eastern part of its distribution, the S. carniolicus aggregate was inferred to comprise an autopolyploid series, whereas for western populations of the tetraploid species, an allopolyploid origin involving the two diploid species was the most likely scenario. Although this suggests that the tetraploid species has two independent origins, other evidence (ribotype distribution, morphology) is consistent with the hypothesis of an autopolyploid origin with subsequent introgression by the second diploid species. Altogether, identifying the best among alternative scenarios using Cohen's d can be straightforward, but particular scenarios, such as allopolyploid origin vs. autopolyploid origin with subsequent introgression, remain difficult to be distinguished.
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Affiliation(s)
- Manuela Winkler
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.,GLORIA Co-ordination, Center for Global Change and Sustainability, University of Natural Resources and Life Sciences Vienna (BOKU) & Institute for Interdisciplinary Mountain Research, Austrian Academy of Sciences, Silbergasse 30/3, Vienna, A-1190, Austria
| | - Pedro Escobar García
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Andreas Gattringer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Michaela Sonnleitner
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Karl Hülber
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.,Vienna Institute for Nature Conservation & Analyses, Giessergasse 6/7, Vienna, A-1090, Austria
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, Innsbruck, A-6020, Austria
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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Semerikova SA, Semerikov VL. Phylogeny of firs (genus Abies, Pinaceae) based on multilocus nuclear markers (AFLP). RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416110132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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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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Georgescu L, Stefanakis MK, Kokkini S, Katerinopoulos HE, Pirintsos SA. Chemical and genetic characterization of Phlomis species and wild hybrids in Crete. PHYTOCHEMISTRY 2016; 122:91-102. [PMID: 26612318 DOI: 10.1016/j.phytochem.2015.11.007] [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: 09/01/2015] [Revised: 11/10/2015] [Accepted: 11/14/2015] [Indexed: 06/05/2023]
Abstract
The genus Phlomis is represented in the island of Crete (Greece, Eastern Mediterranean) by three species Phlomis cretica C. Presl., Phlomis fruticosa L., the island endemic Phlomis lanata Willd. and three hybrids Phlomis x cytherea Rech.f. (P. cretica x P. fruticosa), Phlomis x commixta Rech.f. (P. cretica x P. lanata) and Phlomis x sieberi Vierh. (P. fruticosa x P. lanata). This work describes (a) the profile of hybrids and parental species concerning their volatile compounds, (b) the suitability of ribosomal nuclear (ITS region), chloroplast (trnH-psbA), and AFLP markers to identify hybrids and (c) their competence to characterize the different chemotypes of both hybrids and their parental species. The cluster analysis and PCA constructed from chemical data (volatile oils) suggest that there are three groups of taxa. Group IA includes P. cretica and P. fruticosa, group IB includes P. x cytherea, whereas group II consists of P. x commixta, P. x sieberi and P. lanata. Volatile compounds detected only in the hybrids P. x sieberi and P. x commixta correspond to the 3% of the total compounds, value that is much higher in P. x cytherea (21%). Neighbor-joining, statistical parsimony analysis and the observations drawn from ribotypes spectrum of ITS markers divided Phlomis species in two groups, P. lanata and the complex P. cretica/P. fruticosa. In contrast to the ITS region, the plastid DNA marker follows a geographically related pattern. Neighbor-Net, PCA and Bayesian assignment analysis performed for AFLP markers separated the genotypes into three groups corresponding to populations of P. cretica, P. fruticosa, and P. lanata, respectively, while populations of P. x commixta, P. x cytherea, and P. x sieberi presented admixed ancestry. Most of the P. x cytherea samples were identified as F1 hybrids by Bayesian assignment test, while those of P. x commixta and P. x sieberi were identified as F2 hybrids. Overall, high chemical differentiation is revealed in one of the three hybrids, which is likely related with niche variation. Moreover, molecular markers show potential to identify Phlomis taxa.
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Affiliation(s)
- Luciana Georgescu
- Department of Biology, University of Crete, Heraklion 714 09, Crete, Greece
| | | | - Stella Kokkini
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki 541 24, Greece
| | - Haralambos E Katerinopoulos
- Department of Chemistry, University of Crete, Heraklion 710 03, Crete, Greece; Botanical Garden, University of Crete, Gallos Campus, 741 00 Rethymnon, Greece
| | - Stergios A Pirintsos
- Department of Biology, University of Crete, Heraklion 714 09, Crete, Greece; Botanical Garden, University of Crete, Gallos Campus, 741 00 Rethymnon, Greece.
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Shafique A, Ali Z, Talha AM, Aftab MH, Gul A, Hakeem KR. Plant Interactomics Under Salt and Drought Stress. PLANT OMICS: TRENDS AND APPLICATIONS 2016:493-514. [DOI: 10.1007/978-3-319-31703-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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14
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Mrinalini, Thorpe RS, Creer S, Lallias D, Dawnay L, Stuart BL, Malhotra A. Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers. Mol Phylogenet Evol 2015; 92:266-79. [DOI: 10.1016/j.ympev.2015.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 04/24/2015] [Accepted: 06/03/2015] [Indexed: 10/23/2022]
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15
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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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Slovák M, Kučera J, Záveská E, Vd'ačný P. Dealing with discordant genetic signal caused by hybridisation, incomplete lineage sorting and paucity of primary nucleotide homologies: a case study of closely related members of the genus Picris subsection Hieracioides (Compositae). PLoS One 2014; 9:e104929. [PMID: 25192431 PMCID: PMC4156297 DOI: 10.1371/journal.pone.0104929] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/15/2014] [Indexed: 12/24/2022] Open
Abstract
We investigated genetic variation and evolutionary history of closely related taxa of Picris subsect. Hieracioides with major focus on the widely distributed P. hieracioides and its closely related congeners, P. hispidissima, P. japonica, P. olympica, and P. nuristanica. Accessions from 140 sample sites of the investigated Picris taxa were analyzed on the infra- and the inter-specific level using nuclear (ITS1-5.8S-ITS2 region) and chloroplast (rpl32-trnL(UAG) region) DNA sequences. Genetic patterns of P. hieracioides, P. hispidissima, and P. olympica were shown to be incongruent and, in several cases, both plastid and nuclear alleles transcended borders of the taxa and genetic lineages. The widespread P. hieracioides was genetically highly variable and non-monophyletic across both markers, with allele groups having particular geographic distributions. Generally, all gene trees and networks displayed only a limited and statistically rather unsupported resolution among ingroup taxa causing their phylogenetic relationships to remain rather unresolved. More light on these intricate evolutionary relationships was cast by the Bayesian coalescent-based analysis, although some relationships were still left unresolved. A combination of suite of phylogenetic analyses revealed the ingroup taxa to represent a complex of genetically closely related and morphologically similar entities that have undergone a highly dynamic and recent evolution. This has been especially affected by the extensive and recurrent gene flow among and within the studied taxa and/or by the maintenance of ancestral variation. Paucity of phylogenetically informative signal further hampers the reconstruction of relationships on the infra- as well as on the inter-specific level. In the present study, we have demonstrated that a combination of various phylogenetic analyses of datasets with extremely complex and incongruent phylogenetic signal may shed more light on the interrelationships and evolutionary history of analysed species groups.
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Affiliation(s)
- Marek Slovák
- Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- * E-mail:
| | - Jaromír Kučera
- Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eliška Záveská
- Department of Botany, Charles University, Praha, Czech Republic
| | - Peter Vd'ačný
- Department of Zoology, Comenius University, Bratislava, Slovakia
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Robarts DWH, Wolfe AD. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology(1.). APPLICATIONS IN PLANT SCIENCES 2014; 2:apps.1400017. [PMID: 25202637 PMCID: PMC4103474 DOI: 10.3732/apps.1400017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/15/2014] [Indexed: 05/10/2023]
Abstract
In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance.
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Affiliation(s)
- Daniel W. H. Robarts
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 West 12th Avenue, Columbus, Ohio 43210 USA
| | - Andrea D. Wolfe
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 West 12th Avenue, Columbus, Ohio 43210 USA
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18
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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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21
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Turner B, Paun O, Munzinger J, Duangjai S, Chase MW, Samuel R. Analyses of amplified fragment length polymorphisms (AFLP) indicate rapid radiation of Diospyros species (Ebenaceae) endemic to New Caledonia. BMC Evol Biol 2013; 13:269. [PMID: 24330478 PMCID: PMC3881503 DOI: 10.1186/1471-2148-13-269] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 12/09/2013] [Indexed: 11/24/2022] Open
Abstract
Background Radiation in some plant groups has occurred on islands and due to the characteristic rapid pace of phenotypic evolution, standard molecular markers often provide insufficient variation for phylogenetic reconstruction. To resolve relationships within a clade of 21 closely related New Caledonian Diospyros species and evaluate species boundaries we analysed genome-wide DNA variation via amplified fragment length polymorphisms (AFLP). Results A neighbour-joining (NJ) dendrogram based on Dice distances shows all species except D. minimifolia, D. parviflora and D. vieillardii to form unique clusters of genetically similar accessions. However, there was little variation between these species clusters, resulting in unresolved species relationships and a star-like general NJ topology. Correspondingly, analyses of molecular variance showed more variation within species than between them. A Bayesian analysis with BEAST produced a similar result. Another Bayesian method, this time a clustering method, Structure, demonstrated the presence of two groups, highly congruent with those observed in a principal coordinate analysis (PCO). Molecular divergence between the two groups is low and does not correspond to any hypothesised taxonomic, ecological or geographical patterns. Conclusions We hypothesise that such a pattern could have been produced by rapid and complex evolution involving a widespread progenitor for which an initial split into two groups was followed by subsequent fragmentation into many diverging populations, which was followed by range expansion of then divergent entities. Overall, this process resulted in an opportunistic pattern of phenotypic diversification. The time since divergence was probably insufficient for some species to become genetically well-differentiated, resulting in progenitor/derivative relationships being exhibited in a few cases. In other cases, our analyses may have revealed evidence for the existence of cryptic species, for which more study of morphology and ecology are now required.
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Affiliation(s)
- Barbara Turner
- Department of Systematic and Evolutionary Botany, Faculty of Life Sciences, University Vienna, Rennweg 14, 1030 Wien, Austria.
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22
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Andres JA, Thampy PR, Mathieson MT, Loye J, Zalucki MP, Dingle H, Carroll SP. Hybridization and adaptation to introduced balloon vines in an Australian soapberry bug. Mol Ecol 2013; 22:6116-30. [PMID: 24237450 DOI: 10.1111/mec.12553] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 09/23/2013] [Accepted: 09/25/2013] [Indexed: 11/29/2022]
Abstract
Contemporary adaptation of plant feeding insects to introduced hosts provides clear cases of ecologically based population divergence. In most cases the mechanisms permitting rapid differentiation are not well known. Here we study morphological and genetic variation associated with recent shifts by the Australian soapberry bug Leptocoris tagalicus onto two naturalized Neotropical balloon vines, Cardiospermum halicacabum and C. grandiflorum that differ in time since introduction. Our results show that these vines have much larger fruits than the native hosts (Whitewood tree -Atalaya hemiglauca- and Woolly Rambutan -Alectryon tomentosus-) and that bugs living on them have evolved significantly longer beaks and new allometries. Genetic analyses of mitochondrial haplotypes and amplified fragment length polymorphic (AFLP) markers indicate that the lineage of bugs on the annual vine C. halicacabum, the older introduction, is intermediate between the two subspecies of L. tagalicus found on native hosts. Moreover, where the annual vine and Whitewood tree co-occur, the morphology and genomic composition of the bugs are similar to those occurring in allopatry. These results show that hybridization provided the genetic elements underlying the strongly differentiated 'Halicacabum bugs'. In contrast, the bugs feeding on the recently introduced perennial balloon vine (C. grandiflorum) showed no evidence of admixture, and are genetically indistinguishable from the nearby populations on a native host.
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Affiliation(s)
- J A Andres
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK, Canada, SK S7N-5E2
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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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Arthofer W, Rauch H, Thaler-Knoflach B, Moder K, Muster C, Schlick-Steiner BC, Steiner FM. How diverse isMitopus morio? Integrative taxonomy detects cryptic species in a small-scale sample of a widespread harvestman. Mol Ecol 2013; 22:3850-63. [DOI: 10.1111/mec.12340] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 04/04/2013] [Accepted: 04/08/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Wolfgang Arthofer
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Hannes Rauch
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Barbara Thaler-Knoflach
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Karl Moder
- Institute of Mathematics and Applied Statistics; Department of Spatial, Landscape, and Infrastructure Sciences; University of Natural Resources and Life Sciences; Peter Jordan-Strasse 82, 1180 Vienna Austria
| | - Christoph Muster
- General Zoology and Zoological Systematics; Zoological Institute and Museum; University of Greifswald; Johann Sebastian Bach-Str 11/12, 17487 Greifswald Germany
| | - Birgit C. Schlick-Steiner
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Florian M. Steiner
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
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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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Genetic differentiation in populations of the yellow-necked mouse, Apodemus flavicollis, harbouring B chromosomes in different frequencies. POPUL ECOL 2012. [DOI: 10.1007/s10144-012-0333-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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28
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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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Greve C, Gimnich F, Hutterer R, Misof B, Haase M. Radiating on oceanic islands: patterns and processes of speciation in the land snail genus Theba (Risso 1826). PLoS One 2012; 7:e34339. [PMID: 22493687 PMCID: PMC3321021 DOI: 10.1371/journal.pone.0034339] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 03/01/2012] [Indexed: 11/19/2022] Open
Abstract
Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors.
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Affiliation(s)
- Carola Greve
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.
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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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Genetic Risk Assessment of a Threatened Remnant Population of Hairy Prairie-Clover (Dalea villosa var. villosa) in the Canadian Prairie. DIVERSITY 2011. [DOI: 10.3390/d3030375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Rivers MC, Brummitt NA, Lughadha EN, Meagher TR. Genetic variation in Delonix s.l. (Leguminosae) in Madagascar revealed by AFLPs: fragmentation, conservation status and taxonomy. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0234-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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SAFER STEFAN, TREMETSBERGER KARIN, GUO YANPING, KOHL GUDRUN, SAMUEL MARYR, STUESSY TODF, STUPPNER HERMANN. Phylogenetic relationships in the genus Leontopodium (Asteraceae: Gnaphalieae) based on AFLP data. BOTANICAL JOURNAL OF THE LINNEAN SOCIETY. LINNEAN SOCIETY OF LONDON 2011; 165:364-377. [PMID: 23258943 PMCID: PMC3524420 DOI: 10.1111/j.1095-8339.2011.01117.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The genus Leontopodium comprises 30-41 species. The centre of diversity is the Sino-Himalayan region in south-western China, where about 15 species occur. The two species native to Europe, L. alpinum (known as the common 'Edelweiss') and L. nivale, are part of the cultural heritage of the people living there. Despite its importance, very little is known about the systematics of the genus. Because recent molecular studies have shown that species within this genus are closely related and difficult to distinguish with rDNA and cpDNA data, we used AFLPs to obtain a more detailed understanding of the phylogeny of the genus. Our main aims were as follows: (1) to clarify species relationships within the genus; and (2) to reveal information about the biogeography of the genus. We used AFLPs with six primer combinations to investigate 216 individuals in 38 populations of 16 different species. With AFLPs, we were able to recognize 10 different groups, all of which had strong bootstrap support. These results were also congruent with the morphology-based taxonomy of the genus. Most private and rare fragments were found in the Yunnan region (south-western China) relative to Europe and Mongolia/central China, suggesting a long-lasting in situ history of populations in the centre of diversity of the genus. Our results illustrate the utility of AFLPs to resolve phylogenetic relationships between these closely related species.
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Affiliation(s)
- STEFAN SAFER
- Institute of Pharmacy/Pharmacognosy, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - KARIN TREMETSBERGER
- Institute of Botany, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | - YAN-PING GUO
- College of Life Sciences, Beijing Normal University, no. 19 Xinjiekouwai Street, Beijing 100875, China
| | - GUDRUN KOHL
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - MARY R. SAMUEL
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - TOD F. STUESSY
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - HERMANN STUPPNER
- Institute of Pharmacy/Pharmacognosy, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
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Poczai P, Hyvönen J. On the origin of Solanum nigrum: can networks help? Mol Biol Rep 2011; 38:1171-85. [PMID: 20574711 DOI: 10.1007/s11033-010-0215-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 06/11/2010] [Indexed: 10/25/2022]
Abstract
Black nightshades are a group of species best known for their 'poisonous' or noxious weedy reputation. It is not so well known that species of this group serve as emerging food source in many countries worldwide especially in the African continent. Despite the fact that the section has recently been studied extensively, taxonomy is still unsettled and debated because of inter- and intraspecific hybridization, phenotypic plasticity and polyploidization. In this study we analyze the genetic relationships among diploid, tetraploid and hexaploid species of sect. Solanum, which have possibly taken part in the formation of Solanum nigrum, utilizing multi-locus (SCoT, ISSR) markers combined with chloroplast trnL-F sequence data and morphological characters. We scored 51 morphological characters united with SCoT (171), ISSR (224) and trnL-F (1042), for simultaneous analysis of 49 terminals and 1488 characters. The topology of the tree is concordant with the results of the network analysis. In the phylogenetic networks, all the accessions of the diploid species shared a split with all of the polyploid species. This reflected a high portion of shared ISSR and SCoT bands between diploids and polyploids. In addition, a strong split divided the diploid species. The history of S. nigrum might be reticulate with hybrid speciation playing an important rule. Genetically differentiated diploids in few combinations have created a series of genetically distinct polyploid populations. The insufficient isolation that permitted further recombination between ancient polyploids and diploids have resulted in high level of genotypic and phenotypic polymorphism. This high level of novel genomic variability obviously enabled species to succeed in their new environment.
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Affiliation(s)
- Péter Poczai
- Plant Biology, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland.
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Reeves PA, Richards CM. Species delimitation under the general lineage concept: an empirical example using wild North American hops (Cannabaceae: Humulus lupulus). Syst Biol 2010; 60:45-59. [PMID: 21088008 DOI: 10.1093/sysbio/syq056] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There is an emerging consensus that the intent of most species concepts is to identify evolutionarily distinct lineages. However, the criteria used to identify lineages differ among concepts depending on the perceived importance of various attributes of evolving populations. We have examined five different species criteria to ask whether the three taxonomic varieties of Humulus lupulus (hops) native to North America are distinct lineages. Three criteria (monophyly, absence of genetic intermediates, and diagnosability) focus on evolutionary patterns and two (intrinsic reproductive isolation and niche specialization) consider evolutionary processes. Phylogenetic analysis of amplified fragment length polymorphism (AFLP) data under a relaxed molecular clock, a stochastic Dollo substitution model, and parsimony identified all varieties as monophyletic, thus they satisfy the monophyly criterion for species delimitation. Principal coordinate analysis and a Bayesian assignment procedure revealed deep genetic subdivisions and little admixture between varieties, indicating an absence of genetic intermediates and compliance with the genotypic cluster species criterion. Diagnostic morphological and AFLP characters were found for all varieties, thus they meet the diagnosability criterion. Natural history information suggests that reproductive isolating barriers may have evolved in var. pubescens, potentially qualifying it as a species under a criterion of intrinsic reproductive isolation. Environmental niche modeling showed that the preferred habitat of var. neomexicanus is climatically unique, suggesting niche specialization and thus compliance with an ecological species criterion. Isolation by distance coupled with imperfect sampling can lead to erroneous lineage identification using some species criteria. Compliance with complementary pattern- and process-oriented criteria provides powerful corroboration for a species hypothesis and mitigates the necessity for comprehensive sampling of the entire species range, a practical impossibility in many systems. We hypothesize that var. pubescens maintains its genetic identity, despite substantial niche overlap with var. lupuloides, via the evolution of partial reproductive isolating mechanisms. Variety neomexicanus, conversely, will likely persist as a distinct lineage, regardless of limited gene flow with vars. lupuloides and pubescens because of ecological isolation--adaptation to the unique conditions of the Rocky Mountain cordillera. Thus, we support recognition of vars. neomexicanus and pubescens as species, but delay making a recommendation for var. lupuloides until sampling of genetic variation is complete or a stable biological process can be identified to explain its observed genetic divergence.
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Affiliation(s)
- Patrick A Reeves
- United States Department of Agriculture, Agricultural Research Service, National Center for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, CO 80521, USA
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Fink S, Fischer MC, Excoffier L, Heckel G. Genomic scans support repetitive continental colonization events during the rapid radiation of voles (Rodentia: Microtus): the utility of AFLPs versus mitochondrial and nuclear sequence markers. Syst Biol 2010; 59:548-72. [PMID: 20834011 DOI: 10.1093/sysbio/syq042] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single locus studies might not resolve phylogenetic relationships and the evolutionary history of taxa. The analysis of multiple markers promises higher resolution, and congruence among loci may indicate that the phylogenies represent the underlying species history. Here, we examine the utility of a genome-wide approach based on amplified fragment length polymorphisms (AFLP) and several DNA sequence markers in resolving phylogenetic signals in the rapidly radiating rodent genus Microtus which produced about 70 vole species within the last 1.2-2 myr. The current Holarctic distribution of Microtus is assumed to have resulted from three independent colonization events out of Asia to North America, Europe, and northern Asia without subsequent colonization, which would have led to deep splits between species from different continents. We investigated this hypothesis of three single colonization events by reconstructing the phylogenetic relationships among species from all three continents based on data from the first exon of the nuclear arginine vasopressin receptor 1a gene (EXON1), an adjacent noncoding region and the mitochondrial cytochrome b gene. The phylogenetic patterns obtained from these sequence markers are contrasted to genome-wide data on more than 1800 amplified fragment length polymorphisms (AFLP) analyzed for the same samples. Our results show that the single sequence markers partially resolve the phylogenetic relationships within Microtus, but with some incongruence mostly between EXON1 and the other loci. However, deeper nodes of the radiation are only weakly supported and neither the combination of the markers nor additional nuclear sequences improved the resolution significantly. AFLPs provided much stronger support for major continent-specific clades, and show also that reciprocal monophyly of American and European voles is incomplete. Our results demonstrate that Microtus voles colonized the American and European continents each repeatedly in several independent events on similar colonization routes during their radiation. More generally, this study supports the suitability of AFLPs as an alternative to sequence markers to resolve the evolutionary history of rapidly radiating taxa.
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Affiliation(s)
- Sabine Fink
- Department of Biology, Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
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Freedman AH, Thomassen HA, Buermann W, Smith TB. Genomic signals of diversification along ecological gradients in a tropical lizard. Mol Ecol 2010; 19:3773-88. [PMID: 20618893 DOI: 10.1111/j.1365-294x.2010.04684.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adam H Freedman
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA.
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McCusker MR, Bentzen P. Phylogeography of 3 North Atlantic Wolffish species (Anarhichas spp.) with phylogenetic relationships within the family Anarhichadidae. ACTA ACUST UNITED AC 2010; 101:591-601. [PMID: 20511379 DOI: 10.1093/jhered/esq062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Phylogenetic analyses of all 4 wolffish species (Atlantic, Spotted, Northern, and Bering wolffishes) and the Wolfeel were assessed with both mitochondrial (D-loop and ND1) and nuclear (amplified fragment length polymorphism) DNA to resolve relationships within the family Anarhichadidae. Species-specific mitochondrial DNA (mtDNA) mutation rates were estimated based on 2 possible dates of divergence between the Pacific and Atlantic lineages. Phylogeographic patterns within each of the 3 North Atlantic wolffishes were investigated with Markov chain Monte Carlo simulations based on mtDNA to determine whether population size changes occurred following the last glaciation and where wolffishes likely survived glaciation. All 3 species of North Atlantic wolffishes showed evidence of postglacial expansion but did not show evidence of persistence in multiple refugia in both the eastern and western Atlantic Ocean. Rather, the data supported persistence in a single refuge, with postglacial expansion into the rest of the range. Nucleotide diversity, in particular, was low in wolffishes compared with other marine fishes, possibly related to reductions in population sizes during the last glaciation.
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Affiliation(s)
- Megan R McCusker
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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Makowsky R, Cox CL, Roelke C, Chippindale PT. Analyzing the relationship between sequence divergence and nodal support using Bayesian phylogenetic analyses. Mol Phylogenet Evol 2010; 57:485-94. [PMID: 20472081 DOI: 10.1016/j.ympev.2010.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 05/06/2010] [Accepted: 05/11/2010] [Indexed: 11/26/2022]
Abstract
Determining the appropriate gene for phylogeny reconstruction can be a difficult process. Rapidly evolving genes tend to resolve recent relationships, but suffer from alignment issues and increased homoplasy among distantly related species. Conversely, slowly evolving genes generally perform best for deeper relationships, but lack sufficient variation to resolve recent relationships. We determine the relationship between sequence divergence and Bayesian phylogenetic reconstruction ability using both natural and simulated datasets. The natural data are based on 28 well-supported relationships within the subphylum Vertebrata. Sequences of 12 genes were acquired and Bayesian analyses were used to determine phylogenetic support for correct relationships. Simulated datasets were designed to determine whether an optimal range of sequence divergence exists across extreme phylogenetic conditions. Across all genes we found that an optimal range of divergence for resolving the correct relationships does exist, although this level of divergence expectedly depends on the distance metric. Simulated datasets show that an optimal range of sequence divergence exists across diverse topologies and models of evolution. We determine that a simple to measure property of genetic sequences (genetic distance) is related to phylogenic reconstruction ability in Bayesian analyses. This information should be useful for selecting the most informative gene to resolve any relationships, especially those that are difficult to resolve, as well as minimizing both cost and confounding information during project design.
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Affiliation(s)
- Robert Makowsky
- University of Texas at Arlington, Department of Biology, Box 19498, Arlington, TX 76019, USA.
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Dissecting comimetic radiations in Heliconius reveals divergent histories of convergent butterflies. Proc Natl Acad Sci U S A 2010; 107:7365-70. [PMID: 20368448 DOI: 10.1073/pnas.0911572107] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mimicry among Heliconius butterflies provides a classic example of coevolution but unresolved relationships among mimetic subspecies have prevented examination of codiversification between species. We present amplified fragment length polymorphism and mtDNA datasets for the major comimetic races of Heliconius erato and H. melpomene. The AFLP data reveal unprecedented resolution, clustering samples by geography and race in both species. Our results show that, although H. erato and H. melpomene co-occur, mimic each other, and exhibit parallel shifts in color pattern, they experienced very different modes of diversification and geographic histories. Our results suggest that H. erato originated on the western side of South America whereas H. melpomene originated in the east. H. erato underwent rapid diversification and expansion with continued gene-flow following diversification, resulting in widely dispersed sister taxa. In contrast, H. melpomene underwent a slower pace of diversification with lower levels of gene flow, producing a stepwise directional expansion from west to east. Our results also suggest that each of the three main wing pattern phenotypes originated and/or was lost multiple times in each species. The rayed pattern is likely to be the ancestral phenotype in H. erato whereas postman or red patch is likely to be ancestral in H. melpomene. Finally, H. cydno and H. himera are monophyletic entities clearly nested within H. melpomene and H. erato, rather than being their respective sister species. Estimates of mtDNA divergence suggest a minimum age of 2.8 and 2.1 My for H. erato and H. melpomene, respectively, placing their origins in the late Pliocene.
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Triplett JK, Oltrogge KA, Clark LG. Phylogenetic relationships and natural hybridization among the North American woody bamboos (Poaceae: Bambusoideae: Arundinaria). AMERICAN JOURNAL OF BOTANY 2010; 97:471-92. [PMID: 21622410 DOI: 10.3732/ajb.0900244] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In spite of the ecological and economic importance of temperate bamboos, relatively little is known about their population biology or evolutionary history. Recently, hybridization has emerged as a potential source of diversity in this group, as well as an underlying cause of taxonomic problems. As part of a broader phylogenetic study of the temperate bamboos, we report the results of an analysis of the North American Arundinaria gigantea species complex, including estimates of genetic variation and molecular evidence of natural hybridization among A. gigantea, A. tecta, and A. appalachiana. The study involved a comparative analysis of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA sequences representing diversity within and among all three species plus individuals with intermediate or unusual morphological characteristics (putative hybrids). Molecular results support the recognition of three species previously defined on the basis of morphology, anatomy, and ecology, with most of the molecular variance accounted for by among-species variation. Molecular evidence also demonstrates that A. tecta and A. appalachiana are sister species, forming a clade that is significantly divergent from A. gigantea. The role of hybridization in the phylogenetic history of Arundinaria is discussed along with implications for the evolution and taxonomy of the temperate woody bamboos.
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Affiliation(s)
- Jimmy K Triplett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011-1020 USA
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Caballero A, Quesada H. Homoplasy and Distribution of AFLP Fragments: An Analysis In Silico of the Genome of Different Species. Mol Biol Evol 2010; 27:1139-51. [DOI: 10.1093/molbev/msq001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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García-Pereira MJ, Caballero A, Quesada H. Evaluating the relationship between evolutionary divergence and phylogenetic accuracy in AFLP data sets. Mol Biol Evol 2009; 27:988-1000. [PMID: 20026482 DOI: 10.1093/molbev/msp315] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Using in silico amplified fragment length polymorphism (AFLP) fingerprints, we explore the relationship between sequence similarity and phylogeny accuracy to test when, in terms of genetic divergence, the quality of AFLP data becomes too low to be informative for a reliable phylogenetic reconstruction. We generated DNA sequences with known phylogenies using balanced and unbalanced trees with recent, uniform and ancient radiations, and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.4 substitutions per site. The resulting sequences were used to emulate the AFLP procedure. Trees were estimated by maximum parsimony (MP), neighbor-joining (NJ), and minimum evolution (ME) methods from both DNA sequences and virtual AFLP fingerprints. The estimated trees were compared with the reference trees using a score that measures overall differences in both topology and relative branch length. As expected, the accuracy of AFLP-based phylogenies decreased dramatically in the more divergent data sets. Above a divergence of approximately 0.05, AFLP-based phylogenies were largely inaccurate irrespective of the distinct topology, radiation model, or phylogenetic method used. This value represents an upper bound of expected tree accuracy for data sets with a simple divergence history; AFLP data sets with a similar divergence but with unbalanced topologies and short ancestral branches produced much less accurate trees. The lack of homology of AFLP bands quickly increases with divergence and reaches its maximum value (100%) at a divergence of only 0.4. Low guanine-cytosine (GC) contents increase the number of nonhomologous bands in AFLP data sets and lead to less reliable trees. However, the effect of the lack of band homology on tree accuracy is surprisingly small relative to the negative impact due to the low information content of AFLP characters. Tree-building methods based on genetic distance displayed similar trends and outperformed parsimony at low but not at high divergences. However, the impact of using alternative phylogenetic methods on tree accuracy was generally small relative to the uncertainty arising from factors such as divergence, nonhomology of bands, or the low information content of AFLP characters. Nevertheless, our data suggest that under certain circumstances, AFLPs may be suitable to reconstruct deeper phylogenies than usually accepted.
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Affiliation(s)
- María Jesús García-Pereira
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, Vigo, Spain
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Larson SR, Culumber CM, Schweigert RN, Chatterton NJ. Species delimitation tests of endemic Lepidium papilliferum and identification of other possible evolutionarily significant units in the Lepidium montanum complex (Brassicaceae) of western North America. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-0002-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kingston SE, Adams LD, Rosel PE. Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae). BMC Evol Biol 2009; 9:245. [PMID: 19811651 PMCID: PMC2770059 DOI: 10.1186/1471-2148-9-245] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 10/07/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear. RESULTS Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA) control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP) analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not. CONCLUSION For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference.
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Affiliation(s)
- Sarah E Kingston
- NOAA Fisheries, Southeast Fisheries Science Center, 646 Cajundome Blvd. Suite 234, Lafayette, LA 70506, USA
- University of Maryland, College of Chemical and Life Sciences, Program in Behavior, Ecology, Evolution, and Systematics, Biology-Psychology Building 1204C, College Park, MD 20742, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Rd, Suitland, MD 20746, USA
| | - Lara D Adams
- NOAA Fisheries, Southeast Fisheries Science Center, 646 Cajundome Blvd. Suite 234, Lafayette, LA 70506, USA
- National Ocean Service, 219 Fort Johnson Road, Charleston, SC 29412, USA
| | - Patricia E Rosel
- NOAA Fisheries, Southeast Fisheries Science Center, 646 Cajundome Blvd. Suite 234, Lafayette, LA 70506, USA
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Rossi M, Bitocchi E, Bellucci E, Nanni L, Rau D, Attene G, Papa R. Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl 2009; 2:504-22. [PMID: 25567895 PMCID: PMC3352449 DOI: 10.1111/j.1752-4571.2009.00082.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 05/24/2009] [Indexed: 01/07/2023] Open
Abstract
Together with the knowledge of the population structure, a critical aspect for the planning of association and/or population genomics studies is the level of linkage disequilibrium (LD) that characterizes the species and the population used for such an analysis. We have analyzed the population structure and LD in wild and domesticated populations of Phaseolus vulgaris L. using amplified fragment length polymorphism markers, most of which were genetically mapped in two recombinant inbred populations. Our results reflect the previous knowledge of the occurrence of two major wild gene pools of P. vulgaris, from which two independent domestication events originated, one in the Andes and one in Mesoamerica. The high level of LD in the whole sample was mostly due to the gene pool structure, with a much higher LD in domesticated compared to wild populations. In relation to association studies, our results also suggest that whole-genome-scan approaches are feasible in the common bean. Interestingly, an excess of inter-chromosomal LD was found in the domesticated populations, which suggests an important role for epistatic selection during domestication. Moreover, our results indicate the occurrence of a strong bottleneck in the Andean wild population before domestication, suggesting a Mesoamerican origin of P. vulgaris. Finally, our data support the occurrence of a single domestication event in Mesoamerica, and the same scenario in the Andes.
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Affiliation(s)
- Monica Rossi
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
| | - Elena Bitocchi
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
| | - Elisa Bellucci
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
| | - Laura Nanni
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
| | - Domenico Rau
- Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari Sassari, Italy
| | - Giovanna Attene
- Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari Sassari, Italy
| | - Roberto Papa
- Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy
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Perrie LR, Shepherd LD. Reconstructing the species phylogeny of Pseudopanax (Araliaceae), a genus of hybridising trees. Mol Phylogenet Evol 2009; 52:774-83. [PMID: 19500681 DOI: 10.1016/j.ympev.2009.05.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 04/19/2009] [Accepted: 05/28/2009] [Indexed: 10/20/2022]
Abstract
Pseudopanax (Araliaceae) comprises 12 tree species of diverse morphology and ecology, and is endemic to New Zealand. It is notable for the hybridisation that occurs between P. crassifolius and P. lessonii, which have very different leaves and habits. To provide context for the study of this hybridisation and other investigations, we examined the phylogeny of Pseudopanax using chloroplast DNA sequences (c.5900 base-pairs) and AFLP DNA-fingerprinting. Both approaches resolve two principal groups within Pseudopanax--the Arboreus group and the Crassifolius+Lessonii union--but how they are related to other genera remains unclear. There is, nevertheless, little compelling evidence against the monophyly of Pseudopanax, making unnecessary the recent re-segregation of the Arboreus group as Neopanax. The chloroplast data provided minimal additional resolution, although the position of P. linearis was discordant compared to other data. Analyses of the AFLP data strongly recovered each species, aside from the morphologically heterogeneous P. colensoi, and the two mainland species (P. arboreus and P. crassifolius) that each contained a nested island-endemic (P. kermadecensis and P. chathamicus, respectively). However, relationships amongst species within the two principal groups were poorly resolved. An example was the uncertainty of whether P. crassifolius grouped with P. lessonii and its allies, or the morphologically similar species it had been previously placed with. This in turn raises the issue of how hybridisation might affect phylogenies and the ability to reconstruct them, even when using multiple, independent markers.
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Affiliation(s)
- Leon R Perrie
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.
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