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Rod Peakall - One of the best experts on this subject based on the ideXlab platform.
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A simple method for the detection of size Homoplasy among amplified fragment length polymorphism fragments
Molecular Ecology, 2000Co-Authors: Peter C. O'hanlon, Rod PeakallAbstract:Polymerase chain reaction (PCR)-based methods that produce multilocus DNA profiles such as random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs) have become widely adopted tools for systematic and ecol. applications. However size Homoplasy can result in false interpretations of genetic stability. In this tech. note we introduce and demonstrate a simple and cost effective PCR-based approach for detecting and assessing bias introduced by size Homoplasy using the AFLP method. We tested this approach across different levels of taxonomic divergence within the Carduinae thistles, with known and different levels of chloroplast DNA divergence (GenBank accession nos. AF129824-AF129837) calcd. by percentage no. of nucleotide differences. [on SciFinder(R)]
David B. Wake - One of the best experts on this subject based on the ideXlab platform.
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osteological variation among extreme morphological forms in the mexican salamander genus chiropterotriton amphibia plethodontidae morphological evolution and Homoplasy
PLOS ONE, 2015Co-Authors: David M Darda, David B. WakeAbstract:Osteological variation is recorded among and within four of the most distinctive species of the Mexican salamander genus Chiropterotriton. Analysis of the data is consistent with the monophyletic status of the genus and documents previously unrecorded intraspecific and interspecific variation. Most of the recorded variation involves qualitative and quantitative proportional differences, but four fixed differences constitute autapomorphic states that affirm and diagnose some species (C. dimidiatus, C. magnipes). Osteological variation in 15 characters is analyzed with respect to predictions generated from four hypotheses: 1) phylogeny, 2) adaptation to specific habitats (the four species include cave-dwelling, terrestrial, and arboreal forms), 3) size-free shape, and 4) size. High levels of intraspecific variation suggest that the characters studied are not subject to rigid functional constraints in salamanders, regardless of size. The pattern predicted by the hypothesis based on size differences seen among these four Chiropterotriton species matches most closely the observed pattern of relative skull robustness. Since size change and heterochrony are often associated in plethodontid evolution, it is likely that changes in developmental timing play a role in the morphological transitions among these morphologically diverse taxa. Webbed feet, miniaturization, body shape, and an unusual tarsal arrangement are morphologies exhibited in species of Chiropterotrition that are shown to be homoplastic with other clades of tropical plethodontids. Although extensive Homoplasy in salamanders might be seen as a roadblock to unraveling phylogenetic hypotheses, the homologous developmental systems that appear to underlie such Homoplasy may reveal common and consistent evolutionary processes at work.
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Homoplasy, a Moving Target
Boston Studies in the Philosophy and History of Science, 2014Co-Authors: David B. WakeAbstract:My goal is to present my perspectives on a 50-year exploration of Homoplasy in salamanders, using the 1981 Dahlem conference on Evolution and Development (Bonner 1982) as a centerpiece. I summarize my early work on Homoplasy and show how it was relevant to the planning of the original conference. I then examine how the conference influenced my later studies, and now, with a 30-year retrospective on the original conference, I will attempt to set some future goals. Because I was involved in planning the original conference, I also present some reflections.
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morphological Homoplasy life history evolution and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes
Proceedings of the National Academy of Sciences of the United States of America, 2004Co-Authors: Rachel Lockridge Mueller, David B. Wake, Robert J Macey, Martin Jaekel, Jeffrey L BooreAbstract:The evolutionary history of the largest salamander family (Plethodontidae) is characterized by extreme morphological Homoplasy. Analysis of the mechanisms generating such Homoplasy requires an independent molecular phylogeny. To this end, we sequenced 24 complete mitochondrial genomes (22 plethodontids and two outgroup taxa), added data for three species from GenBank, and performed partitioned and unpartitioned Bayesian, maximum likelihood, and maximum parsimony phylogenetic analyses. We explored four dataset partitioning strategies to account for evolutionary process heterogeneity among genes and codon positions, all of which yielded increased model likelihoods and decreased numbers of supported nodes in the topologies (Bayesian posterior probability >0.95) relative to the unpartitioned analysis. Our phylogenetic analyses yielded congruent trees that contrast with the traditional morphology-based taxonomy; the monophyly of three of four major groups is rejected. Reanalysis of current hypotheses in light of these evolutionary relationships suggests that (i) a larval life history stage reevolved from a direct-developing ancestor multiple times; (ii) there is no phylogenetic support for the “Out of Appalachia” hypothesis of plethodontid origins; and (iii) novel scenarios must be reconstructed for the convergent evolution of projectile tongues, reduction in toe number, and specialization for defensive tail loss. Some of these scenarios imply morphological transformation series that proceed in the opposite direction than was previously thought. In addition, they suggest surprising evolutionary lability in traits previously interpreted to be conservative.
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extreme morphological and ecological Homoplasy in tropical salamanders
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Gabriela Parraolea, David B. WakeAbstract:Fossorial salamanders typically have elongate and attenuated heads and bodies, diminutive limbs, hands and feet, and extremely elongate tails. Batrachoseps from California, Lineatriton from eastern Mexico, and Oedipina from southern Mexico to Ecuador, all members of the family Plethodontidae, tribe Bolitoglossini, resemble one another in external morphology, which has evolved independently. Whereas Oedipina and Batrachoseps are elongate because there are more trunk vertebrae, a widespread Homoplasy (parallelism) in salamanders, the genus Lineatriton is unique in having evolved convergently by an alternate “giraffe-neck” developmental program. Lineatriton has the same number of trunk vertebrae as related, nonelongated taxa, but individual trunk vertebrae are elongated. A robust phylogenetic hypothesis, based on sequences of three mtDNA genes, finds Lineatriton to be deeply nested within a clade characterized by generalized ecology and morphology. Lineatriton lineolus, the only currently recognized taxon in the genus, shows unanticipated genetic diversity. Surprisingly, geographically separated populations of L. lineolus are not monophyletic, but are sister taxa of different species of the morphologically generalized genus Pseudoeurycea. Lineatriton, long thought to be a unique monospecific lineage, is polyphyletic. Accordingly, the specialized morphology of Lineatriton displays Homoplasy at two hierarchical levels: (i) with respect to other elongate lineages in the family (convergence), and (ii) within what is currently recognized as a single taxon (parallelism). These evolutionary events are of adaptive significance because to invade the lowland tropics salamanders must be either arboreal or fossorial; the repeated evolution of elongation and attenuation has led to multiple lowland invasions.
Armando Caballero - One of the best experts on this subject based on the ideXlab platform.
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Homoplasy and distribution of aflp fragments an analysis in silico of the genome of different species
Molecular Biology and Evolution, 2010Co-Authors: Armando Caballero, Humberto QuesadaAbstract:We carried out an in silico analysis of the complete genome sequences of 14 species, including eukaryotes, prokaryotes, and archaea, to investigate the proportion of amplified fragment length polymorphism bands that are homoplasious for the different species, as well as the distribution of fragment lengths. We investigated several possible reasons for the disagreement, previously observed in Arabidopsis thaliana, between the observed fragment length distribution and the null random sequence distribution, which occurs in the direction of a deficit of fragments of small length and an excess of those of large length with respect to the null distribution. We made the following findings: 1) The positive relationship previously found between the percentage of Homoplasy and genome size is a direct consequence of the number of observed bands and the GC content. For the same number of observed bands, the percentage of Homoplasy is independent of the genome size of the species. 2) The disagreement between the observed fragment length distribution and the null random sequence distribution observed in A. thaliana is a phenomenon that also occurs in other species. 3) This disagreement is due neither to the structure of the genomes in isochores nor the possible impact of indels in reducing the number of restriction sites, two hypotheses discussed in the literature. 4) Nor is the disagreement eliminated by using restriction enzymes with balanced motifs. 5) The discrepancy seems to be caused, rather, by the nonrandom distribution of restriction enzyme motifs.
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impact of amplified fragment length polymorphism size Homoplasy on the estimation of population genetic diversity and the detection of selective loci
Genetics, 2008Co-Authors: Armando Caballero, Humberto Quesada, Emilio RolanalvarezAbstract:AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with this technique is the lack of homology of bands with the same electrophoretic mobility, what is known as fragment-size Homoplasy. We carried out a theoretical analysis aimed at quantifying the impact of AFLP Homoplasy on the estimation of within- and between-neutral population genetic diversity in a model of a structured finite population with migration among subpopulations. We also investigated the performance of a currently used method (DFDIST software) to detect selective loci from the comparison between genetic differentiation and heterozygosis of dominant molecular markers, as well as the impact of AFLP Homoplasy on its effectiveness. The results indicate that the biases produced by Homoplasy are: (1) an overestimation of the frequency of the allele determining the presence of the band, (2) an underestimation of the degree of differentiation between subpopulations, and (3) an overestimation or underestimation of the heterozygosis, depending on the allele frequency of the markers. The impact of Homoplasy is quickly diminished by reducing the number of fragments analyzed per primer combination. However, substantial biases on the expected heterozygosity (up to 15–25%) may occur with ∼50–100 fragments per primer combination. The performance of the DFDIST software to detect selective loci from dominant markers is highly dependent on the number of selective loci in the genome and their average effects, the estimate of genetic differentiation chosen to be used in the analysis, and the critical bound probability used to detect outliers. Overall, the results indicate that the software should be used with caution. AFLP Homoplasy can produce a reduction of up to 15% in the power to detect selective loci.
Humberto Quesada - One of the best experts on this subject based on the ideXlab platform.
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Homoplasy and distribution of aflp fragments an analysis in silico of the genome of different species
Molecular Biology and Evolution, 2010Co-Authors: Armando Caballero, Humberto QuesadaAbstract:We carried out an in silico analysis of the complete genome sequences of 14 species, including eukaryotes, prokaryotes, and archaea, to investigate the proportion of amplified fragment length polymorphism bands that are homoplasious for the different species, as well as the distribution of fragment lengths. We investigated several possible reasons for the disagreement, previously observed in Arabidopsis thaliana, between the observed fragment length distribution and the null random sequence distribution, which occurs in the direction of a deficit of fragments of small length and an excess of those of large length with respect to the null distribution. We made the following findings: 1) The positive relationship previously found between the percentage of Homoplasy and genome size is a direct consequence of the number of observed bands and the GC content. For the same number of observed bands, the percentage of Homoplasy is independent of the genome size of the species. 2) The disagreement between the observed fragment length distribution and the null random sequence distribution observed in A. thaliana is a phenomenon that also occurs in other species. 3) This disagreement is due neither to the structure of the genomes in isochores nor the possible impact of indels in reducing the number of restriction sites, two hypotheses discussed in the literature. 4) Nor is the disagreement eliminated by using restriction enzymes with balanced motifs. 5) The discrepancy seems to be caused, rather, by the nonrandom distribution of restriction enzyme motifs.
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impact of amplified fragment length polymorphism size Homoplasy on the estimation of population genetic diversity and the detection of selective loci
Genetics, 2008Co-Authors: Armando Caballero, Humberto Quesada, Emilio RolanalvarezAbstract:AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with this technique is the lack of homology of bands with the same electrophoretic mobility, what is known as fragment-size Homoplasy. We carried out a theoretical analysis aimed at quantifying the impact of AFLP Homoplasy on the estimation of within- and between-neutral population genetic diversity in a model of a structured finite population with migration among subpopulations. We also investigated the performance of a currently used method (DFDIST software) to detect selective loci from the comparison between genetic differentiation and heterozygosis of dominant molecular markers, as well as the impact of AFLP Homoplasy on its effectiveness. The results indicate that the biases produced by Homoplasy are: (1) an overestimation of the frequency of the allele determining the presence of the band, (2) an underestimation of the degree of differentiation between subpopulations, and (3) an overestimation or underestimation of the heterozygosis, depending on the allele frequency of the markers. The impact of Homoplasy is quickly diminished by reducing the number of fragments analyzed per primer combination. However, substantial biases on the expected heterozygosity (up to 15–25%) may occur with ∼50–100 fragments per primer combination. The performance of the DFDIST software to detect selective loci from dominant markers is highly dependent on the number of selective loci in the genome and their average effects, the estimate of genetic differentiation chosen to be used in the analysis, and the critical bound probability used to detect outliers. Overall, the results indicate that the software should be used with caution. AFLP Homoplasy can produce a reduction of up to 15% in the power to detect selective loci.
Peter C. O'hanlon - One of the best experts on this subject based on the ideXlab platform.
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A simple method for the detection of size Homoplasy among amplified fragment length polymorphism fragments
Molecular Ecology, 2000Co-Authors: Peter C. O'hanlon, Rod PeakallAbstract:Polymerase chain reaction (PCR)-based methods that produce multilocus DNA profiles such as random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs) have become widely adopted tools for systematic and ecol. applications. However size Homoplasy can result in false interpretations of genetic stability. In this tech. note we introduce and demonstrate a simple and cost effective PCR-based approach for detecting and assessing bias introduced by size Homoplasy using the AFLP method. We tested this approach across different levels of taxonomic divergence within the Carduinae thistles, with known and different levels of chloroplast DNA divergence (GenBank accession nos. AF129824-AF129837) calcd. by percentage no. of nucleotide differences. [on SciFinder(R)]