| 1. |
- Sousa, Filipe de, 1982, et al.
(författare)
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Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing
- 2014
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:10
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Tidskriftsartikel (refereegranskat)abstract
- Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research, including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionary history of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylogenies. Identification of the processes causing this genealogical incongruence is essential for the inference of a correct species phylogeny of the genus and requires that more molecular data, preferably from low-copy nuclear genes, are obtained across different species. Here we report the development of 50 novel LCN markers in Medicago and assess the phylogenetic properties of each marker. We used the genomic resources available for Medicago truncatula Gaertn., hybridisation-based gene enrichment (sequence capture) techniques and Next-Generation Sequencing to generate sequences. This alternative proves to be a cost-effective approach to amplicon sequencing in phylogenetic studies at the genus or tribe level and allows for an increase in number and size of targeted loci. Substitution rate estimates for each of the 50 loci are provided, and an overview of the variation in substitution rates among a large number of low-copy nuclear genes in plants is presented for the first time. Aligned sequences of major species lineages of Medicago and its sister genus are made available and can be used in further probe development for sequence-capture of the same markers.
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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
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Tidskriftsartikel (refereegranskat)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 3. |
- Nylinder, Stephan, 1975-, et al.
(författare)
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On the Biogeography of Centipeda: A Species Tree Diffusion Approach
- 2014
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; :63, s. 178-191
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Tidskriftsartikel (refereegranskat)abstract
- Reconstructing the biogeographic history of groups present in continuous arid landscapes is challenging dueto the difficulties in defining discrete areas for analyses, and even more so when species largely overlap both in terms ofgeography and habitat preference. In this study, we use a novel approach to estimate ancestral areas for the small plantgenus Centipeda. We apply continuous diffusion of geography by a relaxed random walk where each species is sampledfrom its extant distribution on an empirical distribution of time-calibrated species-trees. Using a distribution of previouslypublished substitution rates of the internal transcribed spacer (ITS) for Asteraceae, we show how the evolution of Centipedacorrelates with the temporal increase of aridity in the arid zone since the Pliocene. Geographic estimates of ancestral speciesshow a consistent pattern of speciation of early lineages in the Lake Eyre region, with a division in more northerly andsoutherly groups since ∼840 ka. Summarizing the geographic slices of species-trees at the time of the latest speciation event(∼20 ka), indicates no presence of the genus in Australia west of the combined desert belt of the Nullabor Plain, the GreatVictoria Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main continental shelf of Australia. Theresult indicates all western occurrences of the genus to be a result of recent dispersal rather than ancient vicariance. Thisstudy contributes to our understanding of the spatiotemporal processes shaping the flora of the arid zone, and offers asignificant improvement in inference of ancestral areas for any organismal group distributed where it remains difficult todescribe geography in terms of discrete areas.
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| 4. |
- Scheen, Anne-Cathrine, 1972, et al.
(författare)
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Use of allele-specific sequencing primers is an efficient alternative to PCR subcloning of low-copy nuclear genes
- 2012
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 12:1, s. 128-135
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Tidskriftsartikel (refereegranskat)abstract
- Direct Sanger sequencing of polymerase chain reaction (PCR)-amplified nuclear genes leads to polymorphic sequences when allelic variation is present. To overcome this problem, most researchers subclone the PCR products to separate alleles. An alternative is to directly sequence the separate alleles using allele-specific primers. We tested two methods to enhance the specificity of allele-specific primers for use in direct sequencing: using short primers and amplification refractory mutation system (ARMS) technique. By shortening the allele-specific primer to 1513 nucleotides, the single mismatch in the ultimate base of the primer is enough to hinder the amplification of the nontarget allele in direct sequencing and recover only the targeted allele at high accuracy. The deliberate addition of a second mismatch, as implemented in the ARMS technique, was less successful and seems better suited for allele-specific amplification in regular PCR rather than in direct sequencing.
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| 5. |
- Schwartz, Thomas, et al.
(författare)
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The origin of oranges: a multi-locus phylogeny of Rutaceae subfamily Aurantioideae
- 2015
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Ingår i: Systematic Botany. - 0363-6445 .- 1548-2324. ; 40:4
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Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of Rutaceae subfamily Aurantioideae has previously been estimated only using plastid and repetitive nuclear sequences. We added sequences of two low copy nuclear loci to allow further diagnosis of phenomena that may mislead phylogenetic inference. After testing for patterns expected under recombination, positive selection, and hybridization, we excluded data sets or sequences accordingly and then inferred the species tree using the multispecies coalescent. We then reconstructed the ancestral area using parsimony and the dispersal-extinction-cladogenesis model to test the hypothesis that Citrus s. l. may have originated in Australasia and migrated or rafted to Eastern Asia. The ancestral area of Citrus s. l. inferred under either method and several models was west of Wallace’s line. Therefore, Citrus s. l. did not appear to have rafted west on what became the Halmahera Islands (Indonesia). Our findings are also consistent with previously reported ages for the origin of this group that may be too young to have allowed this rafting. The species tree is well resolved and largely consistent with previous molecular phylogenies, especially those using chloroplast sequences.
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| 6. |
- Cosacov, Andrea, et al.
(författare)
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New insights into the phylogenetic relationships, character evolution, and phytogeographic patterns of Calceolaria (Calceolariaceae)
- 2009
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Ingår i: American Journal of Botany. - : Wiley. - 0002-9122. ; 96:12, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- Biogeographical patterns and diversifi cation processes in Andean and Patagonian fl ora are not yet well understood. Calceolaria is a highly diversifi ed genus of these areas, representing one of the most specialized plant – pollinator systems because fl owers produce nonvolatile oils, a very unusual fl oral reward. Phylogenetic analyses with molecular (ITS and matK ) and morphological characters from 103 Calceolaria species were conducted to examine relationships, to understand biogeographic patterns, and to detect evolutionary patterns of fl oral and ecological characters. Total evidence analysis retrieved three major clades, which strongly correspond to the three previously recognized subgenera, although only subgenus Rosula was retrieved as a monophyletic group. A single historical event explains the expansion from the southern to central Andes, while different parallel evolutionary lines show a northward expansion from the central to northern Andes across the Huancabamba Defl ection, an important geographical barrier in northern Peru. Polyploidy, acquisition of elaiophores, and a nototribic pollination mechanism are key aspects of the evolutionary history of Calceolaria . Pollination interactions were more frequently established with Centris than with Chalepoge- nus oil-collecting bee species. The repeated loss of the oil gland and shifts to pollen as the only reward suggest an evolutionary tendency from highly to moderately specialized pollination systems.
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| 7. |
- Havran, J. C., et al.
(författare)
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Taxonomic Reevaluation of Endemic Hawaiian Planchonella (Sapotaceae)
- 2021
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Ingår i: Systematic Botany. - : American Society of Plant Taxonomists. - 0363-6445. ; 46:3, s. 875-888
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Tidskriftsartikel (refereegranskat)abstract
- Planchonella (Sapotaceae) in Hawaii has a complicated taxonomic history that has resulted in considerable confusion among botanists and conservation practitioners. Up to seven different species and several varieties have been described in Hawaii, with the most recent taxonomic evaluation recognizing one species, P. sandwicensis. We have conducted a phylogenetic study of Hawaiian Planchonella using molecular (ETS, ITS, and RPB2) and morphological data to infer whether one or several species can be distinguished. In line with earlier research based on molecular data, we find that Planchonella in Hawaii is comprised of two well-supported clades distinguished by fruit color: yellow or purple. The purple-fruited clade contains individuals with flat leaf blades, long pedicels, and greenish corollas, a species corresponding to P. sandwicensis, distributed on all Hawaiian Islands except the island of Hawaii. The yellow-fruited clade possesses leaves that are frequently longitudinally rolled, wavy or distally deflexed, short pedicels, and yellow or cream (rarely greenish) corollas, a species corresponding to P. spathulata that is distributed on all Hawaiian Islands but is believed rare in Kauai. Both species can set fruit with aborted ovules, resulting in small fruits that look dissimilar to well-developed fruit. The species can occur in sympatry, where P. sandwicensis seems to be better adapted to slightly wetter forests and higher altitudes, whereas P. spathulata usually occurs at lower elevations in mesic to dry forests. Both species exhibit large morphological variation and overlap, resulting in many previous collections with inadequate label information, which has impeded correct taxonomic determinations. We refrain from recognizing infraspecific taxa because there is no morphological coherence, no molecular support, and it is unhelpful for species conservation. Five lectotypes are here designated. Both species are assessed for conservation status according to IUCN guidelines and are tentatively proposed as species of Least Concern.
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| 8. |
- Jardim de Queiroz, Luiz, et al.
(författare)
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Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus.
- 2020
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Ingår i: Molecular phylogenetics and evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 145:April
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Tidskriftsartikel (refereegranskat)abstract
- With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3±1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.
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| 9. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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An open source chimera checker for the fungal ITS region
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-0998 .- 1755-098X. ; 10:6, s. 1076-1081
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Tidskriftsartikel (refereegranskat)abstract
- The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit holds a central position in the pursuit of the taxonomic affiliation of fungi recovered through environmental sampling. Newly generated fungal ITS sequences are typically compared against the International Nucleotide Sequence Databases for a species or genus name using the sequence similarity software suite blast. Such searches are not without complications however, and one of them is the presence of chimeric entries among the query or reference sequences. Chimeras are artificial sequences, generated unintentionally during the polymerase chain reaction step, that feature sequence data from two (or possibly more) distinct species. Available software solutions for chimera control do not readily target the fungal ITS region, but the present study introduces a blast-based open source software package (available at http://www.emerencia.org/chimerachecker.html) to examine newly generated fungal ITS sequences for the presence of potentially chimeric elements in batch mode. We used the software package on a random set of 12 300 environmental fungal ITS sequences in the public sequence databases and found 1.5% of the entries to be chimeric at the ordinal level after manual verification of the results. The proportion of chimeras in the sequence databases can be hypothesized to increase as emerging sequencing technologies drawing from pooled DNA samples are becoming important tools in molecular ecology research.
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| 10. |
- Nylinder, Stephan, 1975, et al.
(författare)
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A dated species-tree approach to the trans-Pacific disjunction of the genus Jovellana (Calceolariaceae, Lamiales)
- 2012
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Ingår i: Taxon. - 0040-0262. ; 61:2, s. 381-391
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Tidskriftsartikel (refereegranskat)abstract
- The genus Jovellana is the sister group to the larger genus Calceolaria, together composing the family Calceolariaceae. Four species are currently recognised, two in New Zealand J. sinclairii, J. repens) and two in Chile (J. punctata, J. violacea). The distribution is disjunct across the Pacific Ocean and has long been believed to be a remnant of an ancient vicariance following the break-up of Gondwana. In this study we infer a species-tree phylogeny of the genus using three chloroplast and four nuclear DNA sequences. By exploring three modes of estimating stem and crown ages of the family Calceolariaceae, a Jovellana species tree could be inferred and dated using a secondary calibration. With this approach we can demonstrate that genetic data, despite slightly different signals from unlinked and linked molecular markers, support the idea that the presence of Jovellana in New Zealand is the result of recent long-distance dispersal across the Pacific Ocean from South America.
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