Examinando por Materia "Phylogeny"

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Acaulospora aspera, a new fungal species in the Glomeromycetes from rhizosphere soils of the inka nut (Plukenetia volubilis L.) in Peru
(Julius Kühn-Institut, 2019-10-09) Corazon Guivin, Mike Anderson; Cerna Mendoza, Agustín; Guerrero Abad, Juan Carlos; Vallejos Tapullima, Adela; Carballar Hernández, Santos; Alves da Silva, Gladstone; Oehl, Fritz
A new fungal species of the Glomeromycetes, Acaulospora aspera, was isolated from the rhizosphere of the inka nut (Plukenetia volubilis) in San Martín State of Peru (Western Amazonia) and propagated in bait cultures on Sorghum spp., Brachiaria brizantha, Medicago sativa and P. volubilis as host plants. The fungus forms brownish yellow to yellow brown spores, (120-)135-195 × (120-)130 187 μm in diameter. The surface of the structural spore wall layer is crowded with small depressions, 0.4-0.7 μm in diameter, up to 0.8 μm deep, and only 1.1-1.8 apart, giving the spore surface a rough, washboardlike appearance, especially when the outermost, evanescent wall layer has disappeared. Phylogenetically, the new species is close to A. spinosissima, A. excavata and to other morphologically more similar species such as A. spinosa and A. tuberculata, which form spiny or tuberculate projections on the outermost, semi-persistent spore wall layer, or A. herrerae, A. kentinensis, A. scrobiculata and A. minuta, which on the structural spore wall layer all have more pronunced pits than A. aspera. In this study, also the name of A. spinosissima was validated, as it had been preliminary declared invalid because of a typing error in the diagnosis section of its original description.
Characterization of the complete mitochondrial genome of the black Alpaca breed of Vicugna pacos (Mammalia, Artiodactyla, Camelidae) from Puno, Peru
(Taylor & Francis Group, 2020-03-09) Bustamante, Danilo E.; Yalta Macedo, Claudia Esther; Cruz Luis, Juancarlos Alejandro; Maicelo Quintana, Jorge Luis; Guerrero Abad, Juan Carlos; Gutiérrez Reynoso, Dina Lida
The domestic South American camelid Vicugna pacos L. is distributed along Peru, Chile, Bolivia, and Argentina. Here, we contribute to the bioinformatics and evolutionary systematics of the Camelidae by performing high-throughput sequencing analysis on the black Huacaya breed of V. pacos from Puno, Peru. The black Huacaya breed mitogenome is 16,664 base pairs (bp) in length and contains 37 genes (GenBank accession MT044302). The mitogenome shares a high-level of gene synteny to other Camelidae (Camelops, Camelus, Lama, and Vicugna). The mitogenome of the black Huacaya breed of V. pacos situates it in a clade with V. vicugna Molina, sister to Lama. We anticipate that further mitogenome sequencing of different breeds from Vicugna pacos will improve our understanding of the evolutionary history of this taxon.
Decoding the chloroplast genome of the Amazonian fruit Myrciaria dubia (camu-camu): molecular evolution and comparative genomics across the order Myrtales
(Springer Nature, 2026-08-14) Castro, Juan C.; Leonardo, Diego A.; Cobos, Marianela; Vargas, Jhon A.; Paredes, Jae D.; Adrianzén, Pedro M.; Castro, Carlos G.; Imán Correa, Sixto Alfredo; Rodriguez, Hicler N.; Marapara, Jorge L.; Maddox , J. Dylan
Myrciaria dubia (camu-camu) is an economically important Amazonian fruit species with severely limited genomic resources despite growing commercial interest and conservation needs. This study sequenced, assembled, and comprehensively analyzed the complete chloroplast (cp) genome of M. dubia and performed comparative genomic analyses across the order Myrtales, including codon usage, codon decoding mechanisms, repetitive elements, nucleotide diversity, and phylogenetic reconstruction. The cp genome spanned 158,664 bp with a typical quadripartite organization: a large single-copy region (LSC = 87,640 bp), a small single-copy region (SSC = 18,324 bp), and paired inverted repeats (IRA/IRB = 26,350 bp each). Functional annotation identified 135 genomic features, comprising 84 protein-coding genes, 37 tRNA genes, eight rRNA genes, and five pseudogenes. Codon usage analysis revealed a strong AT bias (62.50%), with 30 preferred codons (RSCU >1.0) predominantly ending with A/T nucleotides. Codon decoding analysis assigned all 61 sense codons to five mechanistic categories, collectively achieving complete codon coverage across all 23 Myrtales accessions. Repetitive element analysis identified 69 simple sequence repeats in M. dubia (91.3% mononucleotide, predominantly adenine motifs in LSC intergenic spacers) and 439 long dispersed repeat pairs (97.5% palindromic, concentrated in the inverted repeat regions). Nucleotide diversity varied significantly across structural regions (SSC, mean π = 0.173; LSC, mean π = 0.084; IRA/IRB, mean π = 0.010–0.015), with the highest diversity window (π = 0.240) located in the SSC at approximately 117.7 kb. SWAN analysis of 78 protein-coding genes identified rpl22, ycf1, matK, ndhF, and ndhD as the most variable loci, with no gene exceeding ω = 1.0, indicating a pervasive purifying selection. Comparative analysis across 19 Myrtaceae accessions demonstrated complete gene collinearity and conserved IR boundary arrangement, with divergence concentrated in the SSC intergenic regions. Phylogenetic analysis positioned M. dubia as a sister species to Plinia trunciflora within the Myrteae tribe, nested in a well-supported monophyletic Myrtaceae clade (bootstrap = 100%).
Extended studies of interspecific relationships in Daucus (Apiaceae) using DNA sequences from ten nuclear orthologues
(Oxford University, 2019-09-24) Martínez Flores, Fernando; Crespo, Manuel B.; Geoffriau, Emmanuel; Allender, Charlotte; Ruess, Holly; Arbizu Berrocal, Carlos Irvin; Simon, Philipp W.; Spooner, David M.
Daucus has traditionally been estimated to comprise 21–25 species, but a recent study expanded the genus to c. 40 species. The present study uses ten nuclear orthologues to examine 125 accessions, including 40 collections of 11 species (D. annuus, D. arcanus, D. decipiens, D. durieua, D. edulis, D. gracilis, D. minusculus, D. montanus, D. pumilus, D. setifolius and D. tenuissimus) newly examined with nuclear orthologues. As in previous nuclear orthologue studies, Daucus resolves into two well-defined clades, and groups different accessions of species together. Maximum likelihood and maximum parsimony analyses provide concordant results, but SVD quartets reveals many areas of disagreement of species within these two major clades. With maximum likelihood and maximum parsimony analyses Daucus montanus (hexaploid) is resolved as an allopolyploid between D. pusillus (diploid) and D. glochidiatus (tetraploid), whereas with SVD quartets it is resolved as an allopolyploid between D. glochidiatus and an unknown Daucus sp. We propose the new combination Daucus junceus (Durieua juncea) for a neglected species endemic to the south-western Iberian Peninsula often referred to as D. setifolius, and we place D. arcanus in synonymy with D. pusillus. Three lectotypes are also designated.
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)
(Springer Nature, 2016-10-28) Arbizu Berrocal, Carlos Irvin; Ellison, Shelby L.; Senalik, Douglas; Simon, Philipp W.; Spooner, David M.
Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30% missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10% with a total of 18,565 SNPs, and (ii) rate of missing data 30%, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus
Greatly reduced phylogenetic structure in the cultivated potato clade (Solanum section Petota pro parte)
(John Wiley & Sons, 2018-02-15) Spooner, David M.; Ruess, Holly; Arbizu Berrocal, Carlos Irvin; Rodríguez, Flor; Solís Lemus, Claudia
•Premise of the Study: osible ies boundaries of wild and cultivated potatoes are controversial, with osible the taxonomic problems in the cultivated potato clade. We here provide the first in‐depth phylogenetic study of the cultivated potato clade to explore osible causes of these problems. •Methods: We examined 131 diploid accessions, using 12 nuclear orthologs, producing an aligned data set of 14,072 DNA characters, 2171 of which are parsimony‐informative. We analyzed the data to produce phylogenies and perform concordance analysis and goodness‐of‐fit tests. •Key Results: There is good phylogenetic structure in clades traditionally referred to as clade 1+2 (North and Central American diploid potatoes exclusive of Solanum verrucosum), clade 3, and a newly discovered basal clade, but drastically reduced phylogenetic structure in clade 4, the cultivated potato clade. The results highlight a clade of species in South America not shown before, ‘neocardenasii’, sister to clade 1+2, that possesses key morphological traits typical of diploids in Mexico and Central America. Goodness‐of‐fit tests suggest potential hybridization between some species of the cultivated potato clade. However, we do not have enough phylogenetic signal with the data at hand to explicitly estimate such hybridization events with species networks methods. •Conclusions: We document the close relationships of many of the species in the cultivated potato clade, provide insight into the cause of their taxonomic problems, and support the recent reduction of species in this clade. The discovery of the neocardenasii clade forces a reevaluation of a hypothesis that section Petota originated in Mexico and Central America.