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13 results for “Araucaria angustifolia”
Distinguishing mutations and null alleles from genotyping errors using mother progeny comparisons in Brazilian pine (Araucaria angustifolia)
The use of microsatellite markers provides a window into the evolutionary processes of a given species. As such, these markers are widely used in scientific and applied research and are praised for their practicality and ease of use, however, the unavoidable incidence of genotyping deviations has been broadly neglected in the literature. Therefore, the present study aimed to estimate the rate of null alleles, mutations and genotyping errors in microsatellite loci, using Araucaria angustifolia, a threatened species, as a case study. We estimated the rates of the different types of genotyping deviations using mother-progeny genotype comparison from 50 seed-trees and their respective progeny (seeds). A total of 2336 A. angustifolia samples were genotyped, and we found that the rate of null alleles was 0.045. From the 1972 mother-progeny comparisons, the overall genotype deviation rate was 1.58%, consisting of 145 inconsistences (mutations), 339 null alleles and 210 genotyping errors. In terms of seed numbers, 128 (6.5%) showed inconsistencies in at least one locus, 118 (6.0%) null alleles, and 321 (16.3%) genotyping errors. This is the first study to describe the inconsistences (mutations) between mother-progeny genotypes for A. angustifolia, and the outcome makes it clear that an understanding of these genotyping deviations must be considered in assessing the accuracy of inferences made based on population genetics analyses.
Distinguishing mutations and null alleles from genotyping errors using mother progeny comparisons in Brazilian pine (Araucaria angustifolia)
the rate of null alleles, mutations and genotyping errors in microsatellite loci, using Araucaria angustifolia, a threatened species, as a case study. We estimated the rates of the different types of genotyping deviations using mother-progeny genotype comparison from 50 seed-trees and their respective progeny (seeds). A total of 2336 A. angustifolia samples were genotyped, and we found that the rate of null alleles was 0.045. From the 1972 mother-progeny comparisons, the overall genotype deviation rate was 1.58%, consisting of 145 inconsistences (mutations), 339 null alleles and 210 genotyping errors. In terms of seed numbers, 128 (6.5%) showed inconsistencies in at least one locus, 118 (6.0%) null alleles, and 321 (16.3%) genotyping errors. This is the first study to describe the inconsistences (mutations) between mother-progeny genotypes for A. angustifolia, and the outcome makes it clear that an understanding of these genotyping deviations must be considered in assessing the accuracy of inferences made based on population genetics analyses.
FIGURE 10 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 10. Biogeographic regions and provinces in South America (A), with details of the study area (in dark blue) and sampling sites of Scapteromys meridionalis [For details see Material and Methods] (B); and Araucaria angustifolia Forest habitat (C). Sources: A, adapted from Morrone (2006); C, Photography of Araucaria angustifolia Forest: G.L. Gonçalves.
FIGURE 9 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 9. Occlusal views of upper and lower molar series of Scapteromys meridionalis holotype (FURB 20253). Bar = 1 mm.
FIGURE 6 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 6. Thenar pad of manus (indicated by the red arrow) and its respective morphology in Scapteromys meridionalis (holotype, FURB 20253) (right) and S. tumidus (FURB 20290) (left). Bar = 1 mm.
FIGURE 8 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 8. Hamular process of pterygoid (red square) and its respective shapes in Scapteromys meridionalis (holotype, FURB 20253) (left) and S. tumidus (MCNU 3378) (right).Bar = 1 mm.
FIGURE 5 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 5. Dorsal (upper), ventral (middle) and bottom (bottom) views of skins of (A) Scapteromys meridionalis (holotype, FURB 20253), (B) S. aquaticus (FCM 500) and (C) S. tumidus (FURB 20290). Bar = 10 mm.
FIGURE 7 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 7. (A) Dorsal (left), ventral (middle) and lateral (right) views of skull and labial view of mandible (bottom right) of (A) Scapteromys meridionalis holotype (FURB 20253). (B) S. aquaticus (FCM 489) and (C) S. tumidus (FURB 20289). Bar = 5 mm.
FIGURE 4 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 4. Convex hull for specimens scores of Scapteromys species on the principal components 1 and 2 (A) and 1 and 3 (B) extracted from the variance-covariance matrix of 21 cranial measurements.
FIGURE 3 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 3. Karyotype (conventional Giemsa standing) of Scapteromys sp. n. Above: 2n=34, FNa=40; below: 2n=36, FNa=40.
FIGURE 1 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 1. Distributional range of the three Scapteromys species (Green, Scapteromys sp. n.; light gray, S. aquaticus; dark gray, S. tumidus) and collecting sites of Scapteromys sp. n. (Brazil: 1—Rio Grande do Sul: São Francisco de Paula, 2—Santa Catarina: Campo Belo do Sul, 3—Santa Catarina: Água Doce, 4—Santa Catarina: Doutor Pedrinho, 5—Santa Catarina: Campo Alegre, 6—Santa Catarina: São Domingos, 7—Santa Catarina: Passos Maia, 8—Paraná: São José dos Pinhais, 9—Paraná: São Mateus do Sul, 10—Paraná: Candói). Red solid triangles represent localities with presence of 2n=34, and blue solid triangles indicate the presence of 2n=36. The circled triangle indicates the type locality.
FIGURE 2 in A new species of swamp rat of the genus Scapteromys Waterhouse, 1837 (Rodentia: Sigmodontinae) endemic to Araucaria angustifolia Forest in Southern Brazil
FIGURE 2.Phylogenetic relationships of Scapteromys. A)ML tree of Scapteromys sp. n. haplotypes and relationships within Scapteromys reconstructed using 801 base pairs of cyt-b sequences and rooted with Kunsia tomentosus. Numbers above branches represented bootstrap support (asterisk indicates values <50%) and below indicate genetic divergence based on K2P distances B) Median joining network of the 11 cyt-b haplotypes of Scapteromys sp. n. Areas are proportional to haplotype frequencies. Colors indicate major clades identified from the phylogenetic tree. Small black bars represent nucleotide differences between haplotypes. Small red circles represent missing haplotypes.
Figure 1 in Seed predation of Araucaria angustifolia (Araucariaceae) by small rodents in two areas with contrasting seed densities in the Brazilian Araucaria forest
Figure 1. Survivorship curves for mean number of seeds placed at two areas (27 experimental stations per area) and monitored for 30 days in two periods. These periods corresponded to the time of Araucaria angustifolia seed production (indicated by filled symbols and solid lines) and outside this period (open symbols and broken lines). The area with high density of seeds during time of seed production (planted stand of A. angustifolia) is indicated by circles and the area with low density of seeds throughout the year (planted stand of P. elliottii) is indicated by triangles. Error bars indicate standard errors of the means. Significant differences (p <0.05, log-rank survival tests with sequential Bonferroni correction) are shown by different letters. Statistical comparisons were made only between areas for each season and between seasons for each area.
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