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115 results for “Multi-locus”
Figure S1 in Multi-locus analyses reveal four giraffe species instead of one
Figure S1. Haplotype networks of seven intron sequences. Related to Figure 2 and 3. The networks for 105 giraffe show that numerous single alleles are shared and that for most loci subspecies cannot be easily distinguished. Notable exceptions are intron 52 and 930 that are exclusive for Masai (tippelskirchi, including the formerly recognized
Figure 3 in Multi-locus analyses reveal four giraffe species instead of one
Figure 3. Population Structuring and Giraffe Divergence Times (A) STRUCTURE analysis of seven nuclear loci for 105 individuals. Vertical bars show the membership in a cluster for each individual. Separate colors represent separate clusters. K = 4 has the highest credibility and shows well-resolved groups: blue: southern cluster (South African plus Angolan giraffe); green: Masai giraffe; orange: reticulated giraffe; yellow: northern cluster of the remaining subspecies. K = 5 or higher shows no further resolution. (B) PCA axes 1–2 for four distinct giraffe clusters (1: southern; 2; northern; 3: Masai; 4: reticulated giraffe) according to STRUCTURE clusters (K = 4). The x axis explains 12.5% and the y axis 7.15% of variation. The oval outlines represent 95% confidential intervals and are colored after STRUCTURE clusters. Nonoverlapping frames denote significantly different clusters. Analyses along axes 1–3 (data not shown) produced nearly identical results. (C) Divergence times among giraffe species estimated by BEAST to 1.99, 1.89, and 1.25 mya, respectively. (D) Time-calibrated phylogenomic analysis based on 540,000 bp of protein coding sequences. The divergence time of Giraffidae was estimated at 28.7 mya. See also Figure S3 and Table S2.
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.
FIGURE 3 in Multi-locus phylogeny supports the placement of Endocarpon pulvinatum within Staurothele s. str. (lichenised ascomycetes, Eurotiomycetes, Verrucariaceae)
FIGURE 3. Most likely unrooted tree (with BS values) showing the relationships within the genus Staurothele based on ITS. The collection number in bold (BMC 12394) represents E. tortuosum (= E. pulvinatum). The scale bar represents the number of nucleotide substitutions/site.
FIGURE 3 in Multi-locus phylogeny reveals Phaeodothis mori sp. nov. (Didymosphaeriaceae, Pleosporales) from dead leaves of Morus australis
FIGURE 3. Phaeodothis tricuspidis (SF125876, holotype) a. Herbarium packet and specimen. b. Ascomata on host. c. Close up of ascoma. d, e. Sections through ascomata. f. Peridium comprising hyaline compressed cells. g–j. Mature and immature asci surrounded by pseudoparaphyses. k–n. ascospores. Scale bars: c = 1000 µm, d, e = 100 µm, f = 20 µm, g–j = 30 µm, k–n = 5 µm.
FIGURE 2 in Multi-locus phylogeny reveals Phaeodothis mori sp. nov. (Didymosphaeriaceae, Pleosporales) from dead leaves of Morus australis
FIGURE 2. Phaeodothis mori (holotype, MFLU 18-2612) a, b. Appearance of ascomata on the host. c. Section of ascoma. d. Section of peridium. e. Pseudoparaphyses. f–i. Asci. j–l. Ascospores. m. Ascospores stained in Indian ink showing mucilaginous sheath. n. Germinated ascospore. o. Colony from below. p. Colony from above. Scale bars: c = 50 µm, d = 10 µm, e–i = 20 µm, j–n = 5 µm.
FIGURE 1 in Multi-locus phylogeny reveals Phaeodothis mori sp. nov. (Didymosphaeriaceae, Pleosporales) from dead leaves of Morus australis
FIGURE 1. RAxML tree based on a combined dataset of ITS, LSU, SSU and tef1- α partial sequences of 84 taxa of the family Didymosphaeriaceae. Bootstrap support values for maximum likelihood (ML), maximum parsimony (MP) values higher than 60% and Bayesian posterior probabilities (BYPP) greater than 0.90 are given above each branch respectively. The new isolates are in red. Ex-type strains are in bold. The tree is rooted by Pleospora herbarum (CBS 191.86, IT 956) and P. tarda (CBS 714.68).
Data from: No correlation between multi-locus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour
Correlations between heterozygosity and fitness are frequently found but rarely well understood. Fitness can be affected by single loci of large effect which correlate with neutral markers via linkage disequilibrium, or as a result of variation in genome-wide heterozygosity following inbreeding. We explored these alternatives in the common buzzard, a raptor species in which three colour morphs differ in their lifetime reproductive success. Using 18 polymorphic microsatellite loci, we evaluated potential genetic differences among the morphs which may lead to subpopulation structuring and tested for correlations between three fitness-related traits and heterozygosity, both genome wide and at each locus separately. Despite their assortative mating pattern, the buzzard morphs were found to be genetically undifferentiated. Multilocus heterozygosity was only found to be correlated with a single fitness-related trait, infection with the blood parasite, Leucocytozoon buteonis, and this was via interactions with vole abundance and age. One locus also showed a significant relationship with blood parasite infection and ectoparasite infestation. The vicinity of this locus contains two genes, one of which is potentially implicated in the immune system of birds. We conclude that genome-wide heterozygosity is unlikely to be a major determinant of parasite burden and body condition in the polymorphic common buzzard.
FIGURE 3 in A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny
FIGURE 3. The three different types of palea apices. A1—biapiculate (sinus shallow) palea apex of Yushania niitakayamensis (Hayata) P.-C. Keng (1957: 357) and A2—biapiculate (sinus shallow) palea apex of Bergbambos tessellata; B1—long-divided tips (sinus deep) palea of Arundinaria gigantea and B2—long-divided tips (sinus deep) palea of Fargesia spathacea Franchet (1893: 1067); C1—acute, undivided palea apex of A. debilis and C2—acute, undivided palea apex of Oldeania alpina (K. Schum.) Stapleton (2013: 100).
FIGURE 1. Percentage Potentially Informative Character values for all 11 chloroplast regions. For the regions rps16 in A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny
FIGURE 1. Percentage Potentially Informative Character values for all 11 chloroplast regions. For the regions rps16–trnQ, trnC– rpoB, trnD–trnT, trnT–trnL and ndhF 3' the PIC values include the outgroups. For the regions psbD-trnT, psbJ-petA and ycf6- psbM the PIC values include only the ingroup species.
FIGURE 2 in A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny
FIGURE 2. Strict consensus of 1019 most parsimonious trees based on the five-region cpDNA dataset (rps16–trnQ, trnC–rpoB, trnD–trnT, trnT–trnL, ndhF 3'). Shaded region indicates the well supported Sri Lankan Arundinaria clade. Numbers indicate bootstrap values ≥ 70% from MP and ML analyses and posterior probabilities ≥ 0.95 from the BI analyses, respectively. Note that Clade XI is not shown in the tree because it was unsampled.
Data from: Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs
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Data from: No correlation between multi-locus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour
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Data from: Comparative multi-locus phylogeography of two Palaearctic spruce bark beetles: influence of contrasting ecological strategies on genetic variation
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