| 1. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
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In: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
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Journal article (peer-reviewed)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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| 2. |
- Sousa, Filipe de, 1982, et al.
(author)
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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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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:10
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Journal article (peer-reviewed)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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| 3. |
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| 4. |
- Bengtson, Annika, et al.
(author)
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Evolution and diversification related to rainfall regimes : diversification patterns in the South African genus Metalasia (Asteraceae-Gnaphalieae)
- 2015
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In: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 42:1, s. 121-131
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Journal article (peer-reviewed)abstract
- AimThe Cape region is known for its exceptional species richness, although much remains unknown regarding the appearance of the modern Cape flora. One explanation is that floral diversification was influenced by the establishment of winter rainfall/summer arid conditions hypothesized to have occurred towards the end of the Miocene. We studied the evolution and diversification of the plant genus Metalasia (Asteraceae-Gnaphalieae), with the aim of testing whether radiation patterns may have been influenced by the climatic changes. LocationSouth Africa, with emphasis on the south-west. MethodsThe radiation of Metalasia was investigated using two approaches: a species diffusion approach, which estimated the ancestral areas by means of a relaxed random walk while sampling from extant distributions; and a discrete approach, in which distributions were defined according to the phytogeographical centres of the Cape region. Secondarily derived clock rates from an earlier Gnaphalieae study were used for calibration purposes. ResultsOur analyses date Metalasia to approximately 6.9Ma, after the Miocene-Pliocene boundary and the establishment of the winter rainfall/summer arid conditions. Metalasia consists of two sister clades: Clade A and Clade B. Clade B, which is endemic to the winter rainfall area, is estimated to have diversified c. 6.4Ma, whereas Clade A, with a main distribution in the all-year rainfall area, is considerably younger, with a crown group age estimated to 3.3Ma. Diversification rates suggest an early rapid speciation, with rates decreasing through time both for Metalasia and for clades A and B separately. Ancestral area estimations show a possible scenario for the radiation of Metalasia to its current diversity and distribution, with no conflict between results inferred from diffusion or discrete methods. Main conclusionsThe diversification of Metalasia is estimated to have begun after the establishment of the winter rainfall/summer arid conditions, consistent with its radiation having been influenced by changes in the climatic regime.
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| 5. |
- Cosacov, Andrea, et al.
(author)
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New insights into the phylogenetic relationships, character evolution, and phytogeographic patterns of Calceolaria (Calceolariaceae)
- 2009
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In: American Journal of Botany. - : Wiley. - 0002-9122. ; 96:12, s. 1-16
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Journal article (peer-reviewed)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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| 6. |
- de Faria, Aparecida Donisete, et al.
(author)
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Towards a natural classification of Sapotaceae subfamily Chrysophylloideae in the Neotropics
- 2017
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In: Botanical journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 185, s. 27-55
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Journal article (peer-reviewed)abstract
- Generic limits of Chrysophyllum and Pouteria (Chrysophylloideae, Sapotaceae) have been found to be untenable. We here search for natural lineages in Neotropical Chrysophylloideae by sampling 101 terminals for molecular sequences of nuclear ribosomal DNA (external and internal transcribed spacer), the nuclear gene RPB2 and 17 morphological characters. Data were analysed with Bayesian inference and parsimony jackknifing. Morphological traits were finally optimized onto the tree to identify the most coherent characters. The resulting phylogenetic tree suggests that the limits of the well-known genera Chrysophyllum and Pouteria must be amended. Diploon, Ecclinusa and Elaeoluma can be maintained and Chrysophyllum sections Ragala section Prieurella and the satellite gen- era Achrouteria, Cornuella, Martiusella and Nemaluma merit generic resurrection. Lucuma may be restored if the type species belongs to the clade. The accepted genera Chromolucuma, Pradosia and Sarcaulus gain strong clade support, but are embedded in a core clade of Pouteria and may be relegated to the subgeneric level if morphologi- cal studies cannot provide evidence concurring with narrow generic concepts. Circumscriptions of Micropholis and Chrysophyllum sections Chrysophyllum and Villocuspis remain unclear and must be explored by using an extended taxon sampling. We predict that yet-to-be-analysed species of Pouteria sections Franchetella, Gayella, Oxythece and Pouteria and members of the currently accepted genera Chromolucuma, Pradosia and Sarcaulus will fall inside the core clade of Pouteria when analysed.
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| 7. |
- Havran, J. Christopher, et al.
(author)
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Taxonomic Reevaluation of Endemic Hawaiian Planchonella (Sapotaceae)
- 2021
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In: Systematic Botany. - 0363-6445 .- 1548-2324. ; 46, s. 875-888
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Journal article (peer-reviewed)abstract
- Planchonella (Sapotaceae) in Hawaii has a complicated taxonomic history that has resulted in considerable confusion among bota- nists 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 molec- ular (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. |
- Havran, J. C., et al.
(author)
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Taxonomic Reevaluation of Endemic Hawaiian Planchonella (Sapotaceae)
- 2021
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In: Systematic Botany. - : American Society of Plant Taxonomists. - 0363-6445. ; 46:3, s. 875-888
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Journal article (peer-reviewed)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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| 9. |
- Jardim de Queiroz, Luiz, et al.
(author)
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Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus.
- 2020
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In: Molecular phylogenetics and evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 145:April
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Journal article (peer-reviewed)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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| 10. |
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