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33 results for “multi-locus phylogeny”
A multi-locus phylogeny for the Diamesinae (Chironomidae: Diptera) provides new insights into evolution of an amphitropical clade
<p>Aligned FASTA files for each locus, Concatinated Dataset, Input files for MrBayes, IqTree2, PartitionFinder and RASP. Ready trees after MrBayes and BEAST. </p>
Data from: A multi-locus plastid phylogeny of the Aulonemia clade (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) reveals three new genera of bamboo
<p>Arthrostylidiinae (Poaceae: Bambusoideae), a subtribe of Neotropical woody bamboos with diverse morphology, comprises 200 species classified in 16 genera. Previous studies supported monophyly of the subtribe and recovered four major internal clades, however, some genera were found to be polyphyletic while others, like <em>Aulonemia</em> and <em>Colanthelia,</em> were either undersampled or not included. <em>Aulonemia</em> and <em>Colanthelia</em> are complex both in their taxonomy and morphology, and exhibit overlapping morphological characters. Prior morphological and molecular analyses suggested they share a close relationship, with <em>Colanthelia </em>emerging as monophyletic and either nested within <em>Aulonemia</em> or sister to it,<em> </em>but these studies sampled relatively few species of each genus. The aims of this study were to increase taxon sampling to test the monophyly of <em>Aulonemia</em> and <em>Colanthelia, </em>to investigate the relationships within the <em>Aulonemia </em>+ <em>Colanthelia </em>clade, and to revise their classification as appropriate towards a natural classification of the Arthrostylidiinae. We present a multi-locus plastid phylogeny of the Arthrostylidiinae with emphasis on <em>Aulonemia </em>and <em>Colanthelia</em>. We used sequences of seven plastid markers (one coding: <em>ndhF</em>; six non-coding:<em> trnC-rpoB, rps16-trnQ, trnT-trnL, rps16, trnD-trnT, </em>and <em>rpl16</em>) from 67 taxa of Bambusoideae including all genera of Arthrostylidiinae. Phylogenetic trees were inferred using both Bayesian and maximum likelihood methods. <em>Aulonemia</em> was confirmed as polyphyletic and <em>Colanthelia</em> was not supported as monophyletic. The phylogenetic position of <em>Myriocladus </em>within Arthrostylidiinae is resolved for the first time. All species of <em>Colanthelia</em> were recovered within the clade containing most species of <em>Aulonemia</em>. Four species of <em>Aulonemia</em> (<em>A. radiata</em>, <em>A. effusa</em>, <em>A. setosa</em>, and <em>A. setigera</em>) grouped in other clades within the subtribe and these placements combined with morphological evidence support the establishment of three new genera: <em>Quixiume</em>, <em>Stelanemia</em> and <em>Vianaea</em>, to accommodate the four remarkable <em>Aulonemia</em> species. An updated key for the genera of the Arthrostylidiinae is provided, as well as taxonomic treatments for the three new genera, including the description of a new species in <em>Stelanemia</em>.</p>
Data from: A multi-locus plastid phylogeny of the Aulonemia clade (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) reveals three new genera of bamboo
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DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies
<p>Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multigene sequencing (approximately one per simulated genus), the addition of this multigene backbone DNA data for as few as 5–10% of the specimens in the total data set can produce high-quality phylogenies, comparable to those resulting from 100% multigene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen data set of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multigene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for incertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large data sets.</p>
FIGURE 9 in Multi-locus phylogeny and taxonomic revision of Uperoleia toadlets (Anura: Myobatrachidae) from the western arid zone of Australia, with a description of a new species
FIGURE 9. Photos in life (dorsolateral and dorsal views) and after preservation (ventral view) of U. saxatilis sp. nov. holotype (WAM R162877) from Turee Creek, Western Australia. Photos by P. Doughty.
FIGURE 5 in Multi-locus phylogeny and taxonomic revision of Uperoleia toadlets (Anura: Myobatrachidae) from the western arid zone of Australia, with a description of a new species
FIGURE 5. Plot showing results of Principle Components Analysis (top) and Discriminant Function Analysis (bottom) on body proportion variables only, see text for details. Uperoleia micromeles is the most distinct and U. russelli and U. saxatilis sp. nov. are indistinguishable based on these characters, but each is distinct based on genetic, call and other morphological characters.
FIGURE 6 in Multi-locus phylogeny and taxonomic revision of Uperoleia toadlets (Anura: Myobatrachidae) from the western arid zone of Australia, with a description of a new species
FIGURE 6. Oscillographs and spectrograms of (a) U. glandulosa, U. russelli (b) long call and (c) short call, U. talpa (d) long call and (e) short call, and U. saxatilis sp. nov. (f) long call and (g) short call.
FIGURE 1 in Multi-locus phylogeny and taxonomic revision of Uperoleia toadlets (Anura: Myobatrachidae) from the western arid zone of Australia, with a description of a new species
FIGURE 1. Geological regions of the western arid zone of Australia. Solid lines denote geological boundaries and dotted lines represent rivers. Modified from Beard & Webb (1974), Beard (1975, 1979), and Interim Biogeographic Regions of Australia version 6.1 (Commonwealth of Australia 2005).
FIGURE 4 in Multi-locus phylogeny and taxonomic revision of Uperoleia toadlets (Anura: Myobatrachidae) from the western arid zone of Australia, with a description of a new species
FIGURE 4. Molecular phylogeny of the genus Uperoleia based on a combined analysis of five genes including the mtDNA genes 16S and ND2 and the nuclear loci RAG-1, POMC, and BNDF (total 4,152 bp). The phylogeny shown is based on a partitioned Bayesian analysis, see text for details. Values above the branches are Bayesian posterior probabilities and values below are the parsimony bootstrap values.
FIGURE 3 in Multi-locus phylogeny and taxonomic revision of Uperoleia toadlets (Anura: Myobatrachidae) from the western arid zone of Australia, with a description of a new species
FIGURE 3. Molecular phylogeny of the genus Uperoleia based on the mtDNA genes 16S and ND2 (total 2,047 bp), including all tissues available for sequencing from the western arid zone. The phylogeny shown is based on a partitioned Bayesian analysis where each gene represents one partition. Values above the branches are Bayesian posterior probabilities and values below are the parsimony bootstrap values.
FIGURE 2 in Multi-locus phylogeny and taxonomic revision of Uperoleia toadlets (Anura: Myobatrachidae) from the western arid zone of Australia, with a description of a new species
FIGURE 2. Extent of webbing relative to tubercle position on the fourth toe. a) basal webbing, b) webbing extends to the first proximal tubercle, c) webbing extends to halfway between the first and second proximal tubercles, d) webbing extends to the second proximal tubercle.
FIGURE 2 in Multi-locus phylogeny of southern African Acontias aurantiacus (Peters) subspecies (Scincidae: Acontinae) confirms the presence of three genetically, geographically and morphologically discrete taxa
FIGURE 2. Haplotype phylogeny of the South African and nominate subspecies of Acontias aurantiacus inferred from a concatenated cyt b, 16S and RAG1 dataset comprising of 3,159 nucleotides (cyt b = 1,045, 16S = 526 and RAG1 = 1,588 nt) using a Maximum Likelihood algorithm. Maximum Likelihood (ML) bootstrap values ḵ70% (upper) and Bayesian posterior probability (BPP, lower) support values ḵ0.95 are indicated, while nodes with statistical support below these thresholds have no associated support values. Melanistic specimens are indicated with an asterisk and the mottled specimen with a cross.
FIGURE 1 in Multi-locus phylogeny of southern African Acontias aurantiacus (Peters) subspecies (Scincidae: Acontinae) confirms the presence of three genetically, geographically and morphologically discrete taxa
FIGURE 1. Molecular phylogeny of the genus Acontias inferred using a Maximum Likelihood algorithm and a concatenated cyt b, 16S and RAG1 dataset comprising of 2,244 nt. Maximum Likelihood (ML) bootstrap values ḵ70% and Bayesian posterior probability (BPP) support values ḵ0.95 are shown above and below each of the supported nodes, respectively, while unsupported nodes have no associated values. Taxa marked with an asterisk were sourced from GenBank.
FIGURE 4 in Multi-locus phylogeny and morphology of Curvularia isolates associated with leaf spots of corn in northern Algeria unveiled two new species, C. algeriensis sp. nov. and C. boudouaouensis sp. nov., with a new record for C. spicifera
FIGURE 4. Curvularia spicifera (AT-102). a 7-day-old colony on PDA. b symptoms on inoculated corn leaf. c conidiophores with attached conidia on PDA. d–f conidiophores on PDA. g conidia on the host. h, i: germinating conidia on water agar. Scale bars = c–g: 25 µm; h, i: 10 µm.
FIGURE 2 in Multi-locus phylogeny and morphology of Curvularia isolates associated with leaf spots of corn in northern Algeria unveiled two new species, C. algeriensis sp. nov. and C. boudouaouensis sp. nov., with a new record for C. spicifera
FIGURE 2. Curvularia algeriensis (CBS 150506). a 7-day-old colony on PDA. b lesions on inoculated corn leaf. c conidiophores and conidia on the host. d conidiophores with attached conidia on PDA. e conidia on PDA. f chlamydospores. Scale bars = 25 µm.
FIGURE 3 in Multi-locus phylogeny and morphology of Curvularia isolates associated with leaf spots of corn in northern Algeria unveiled two new species, C. algeriensis sp. nov. and C. boudouaouensis sp. nov., with a new record for C. spicifera
FIGURE 3. Curvularia boudouaouensis (CBS 150515). a 7-day-old colony on PDA. b lesions on inoculated corn leaf. c, d conidiophores with attached conidia. e conidia. f chlamydospores. Scale bars = 25 µm.
FIGURE 1 in Multi-locus phylogeny and morphology of Curvularia isolates associated with leaf spots of corn in northern Algeria unveiled two new species, C. algeriensis sp. nov. and C. boudouaouensis sp. nov., with a new record for C. spicifera
FIGURE 1. Phylogenetic tree generated from maximum likelihood (ML) analysis of the combined ITS, GAPDH and TEF1 sequence data of Curvularia species. ML bootstrap support values (BS) ≥ 70% and Bayesian posterior probabilities (PP) ≥ 0.95 are shown near the nodes. The novelties from Algeria are in red and bold and the new record is in bold. The tree is rooted with Bipolaris maydis CBS 136.29 and Exserohilum turcicum CBS 690.71.
FIGURE 4 in Multi-locus phylogeny supports the placement of Endocarpon pulvinatum within Staurothele s. str. (lichenised ascomycetes, Eurotiomycetes, Verrucariaceae)
FIGURE 4. Most likely unrooted tree (with BS values) showing the relationships within the genus Staurothele based on nrLSU. The collection number in bold (BMC 12394) represents E. tortuosum (= E. pulvinatum). The scale bar represents the number of nucleotide substitutions/site.
FIGURE 1 in Multi-locus phylogeny supports the placement of Endocarpon pulvinatum within Staurothele s. str. (lichenised ascomycetes, Eurotiomycetes, Verrucariaceae)
FIGURE 1. General habit of Endocarpon pulvinatum. A. Large thalli found on the nunatak Esjubjörg in southeastern Iceland (LA31862). B. Close-up on specimen SH300 collected near a glacier river in Northern Iceland. Bar = 5 mm. Photos Starri Heiðmarsson.
FIGURE 2 in Multi-locus phylogeny supports the placement of Endocarpon pulvinatum within Staurothele s. str. (lichenised ascomycetes, Eurotiomycetes, Verrucariaceae)
FIGURE 2. Phylogenetic placement of E. pulvinatum within the family Verrucariaceae resulting from a Bayesian analysis of a multi-locus dataset (ITS, nrLSU, mtSSU and mcm7). Support values are reported above or below the branches (posterior probability [PP]/bootstrap support [BS]). Internodes with strong support (1.00 PP and 100% BS) are indicated by a black dot. Only values of PP ≥ 0.95 and of BS ≥ 70% are shown. Two species of Capronia were used as an outgroup.
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