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39 results for “Bayesian analyses”
Anatomical partitioning has little influence in topologies from Bayesian phylogenetic analyses of morphological data
<p>Morphological data is a fundamental source of evidence to reconstruct the Tree of Life, and Bayesian phylogenetic methods are increasingly being used for this task, along with, or instead of, traditional parsimony approaches. Bayesian phylogenetic analyses require the use of proper evolutionary models and their performance have been intensively studied in the past few years, with significant improvements to our knowledge regarding their performance. Notwithstanding, it was only recently that partitioned models for morphology received attention in studies of empirical data, but a systematic evaluation of its performances using simulations was never performed. Here we evaluate the influence of partitioned models defined by anatomical criterion in the precision and accuracy of consensus tree topologies, evaluating the possible negative effects of under and overpartitioning. For that, we analysed datasets simulated using parameters and properties of two empirical datasets, using Bayesian phylogenetic analyses in MrBayes. Additionally, we reanalysed 32 empirical datasets for diverse groups of vertebrates, applying unpartitioned and partitioned models. We found that in general, partitioning by anatomy has little to no influences in the performance of Bayesian phylogenetic methods in respect to the metrics studied here, with analyses under alternative partitioning schemes presenting very similar tree precision and accuracy. We discuss the possible reasons for the disagreement between the results obtained here and previous studies for empirical morphological data, and with empirical and simulation studies of molecular data, discussing the adequacy of anatomical partitioning relative to alternative methods to partition morphological datasets and how morphological and molecular partitioning are related.</p>
Prior choice and data requirements of Bayesian multivariate mixed effects models fit to tag-recovery data: The need for power analyses
<p>1. Recent empirical studies have quantified correlation between survival and recovery by estimating these parameters as correlated random effects with hierarchical Bayesian multivariate models fit to tag-recovery data. In these applications, increasingly negative correlation between survival and recovery has been interpreted as evidence for increasingly additive harvest mortality. The power of these hierarchal models to detect non-zero correlations has rarely been evaluated and these few studies have not focused on tag-recovery data, which is a common data type.</p> <p>2. We assessed the power of multivariate hierarchical models to detect negative correlation between annual survival and recovery. Using three priors for multivariate normal distributions, we fit hierarchical effects models to a mallard (<em>Anas</em> <em>platyrhychos</em>) tag-recovery dataset and to simulated data with sample sizes corresponding to different levels of monitoring intensity. We also demonstrate more robust summary statistics for tag-recovery datasets than total individuals tagged.</p> <p>3. Different priors lead to substantially different estimates of correlation from the mallard data. Our power analysis of simulated data indicated most prior distribution and sample size combinations could not estimate strongly negative correlation with useful precision or accuracy. Many correlation estimates spanned the available parameter space (–1,1) and underestimated the magnitude of negative correlation. Only one prior combined with our most intensive monitoring scenario provided reliable results. Underestimating the magnitude of correlation coincided with overestimating the variability of annual survival, but not annual recovery.</p> <p>4. The inadequacy of prior distributions and sample size combinations previously assumed adequate for obtaining robust inference from tag-recovery data represents a concern in the application of Bayesian hierarchical models to tag-recovery data. Our analysis approach provides a means for examining prior influence and sample size on hierarchical models fit to capture-recapture data while emphasizing transferability of results between empirical and simulation studies.</p>
Prior choice and data requirements of Bayesian multivariate mixed effects models fit to tag-recovery data: The need for power analyses
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Anatomical partitioning has little influence in topologies from Bayesian phylogenetic analyses of morphological data
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Figure 2. - Bayesian (GTR+Γ+I and HKY+Γ models) and maximum likelihood 50% majority-rule consensus tree. Numbers in the nodes represent posterior probabilities (GTR+Γ+I and HKY+Γ, respectively), and bootstrap value for maximum likelihood and parsimony analyses, respectively. c1–Bragança, Pará; c2–Santa Maria do Pará, Pará; c3–National Forest of Amapá, Amapá; c4–Belém, Pará; i1–Solimões River, near Manaus, Amazonas; i2–Xingu River, Altamira, Pará; i3 and i4–Itacoatiara, Amazonas. MYBP–million years before present.
Figure 2. - Bayesian (GTR+Γ+I and HKY+Γ models) and maximum likelihood 50% majority-rule consensus tree. Numbers in the nodes represent posterior probabilities (GTR+Γ+I and HKY+Γ, respectively), and bootstrap value for maximum likelihood and parsimony analyses, respectively. c1–Bragança, Pará; c2–Santa Maria do Pará, Pará; c3–National Forest of Amapá, Amapá; c4–Belém, Pará; i1–Solimões River, near Manaus, Amazonas; i2–Xingu River, Altamira, Pará; i3 and i4–Itacoatiara, Amazonas. MYBP–million years before present.
Data from: Bayesian total-evidence dating revisits sloth phylogeny and biogeography: a cautionary tale on morphological clock analyses
<p>Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth <em>Bradypus</em> is consistently recovered as a megatherioid, and <em>Choloepus</em> as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae", whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an <em>a posteriori</em> removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models, and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.</p>
Data for 'Priors and Posteriors in Bayesian Timing of Divergence Analyses: the Age of Butterflies Revisited'
<p>Data and results for Chazot et al. (2018) 'Priors and Posteriors in Bayesian Timing of Divergence Analyses: the Age of Butterflies Revisited.'</p> <p>S1. List of taxa and Genbank accession codes.</p> <p>S2. Molecular matrix for the core analysis (S2a), the reduced dataset (S2b) and the dataset with a mitochondrial fragment (S2c).</p> <p>S3. RAxML topology (S3a) and time-calibrated tree (S3b) obtained from the core analysis. In S3a, numbers at the nodes indicate rapid-bootstrap support values. In S3b, node ages are the median of node age posterior distributions.</p> <p>S4. Tree obtained when using only deep-level fossil calibrations. Node ages are the median of node age posterior distributions.</p> <p>S5. Tree obtained when using only shallow-level fossil calibrations. Node ages are the median of node age posterior distributions.</p> <p>S6. Tree obtained from the reduced dataset. Node ages are the median of node age posterior distributions.</p> <p>S7. Tree obtained when using exponential fossil calibration priors. Node ages are the median of node age posterior distributions.</p> <p>S8. Tree obtained when adding a mitochondrial gene fragment. Node ages are the median of node age posterior distributions.</p> <p>S9. Tree obtained when using fossil information only modeled using lognormal priors. Node ages are the median of node age posterior distributions.</p> <p>S10. Tree obtained when using the host-plant ages obtained from Foster et al. (2017). In S10a node ages are the median of node age posterior distributions, while in S10b the node ages are the mode the mode of the kernel density estimate of the posterior distribution.</p> <p>S11. Tree obtained when using a Yule prior instead of Birth-Death tree prior. Node ages are the median of node age posterior distributions.</p>
Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone
Hybrid zones provide unique opportunities to examine reproductive isolation and introgression in nature. We utilized 45,384 Single Nucleotide Polymorphism (SNP) loci to perform association mapping of 14 floral, vegetative, and ecological traits that differ between Iris hexagona and Iris fulva, and to investigate, using a Bayesian Genomic Cline (BGC) framework, patterns of genomic introgression in a large and phenotypically diverse hybrid zone in southern Louisiana. Many loci of small effect-size were consistently found to be associated with phenotypic variation across all traits, and several individual loci were revealed to influence phenotypic variation across multiple traits. Patterns of genomic introgression were quite heterogeneous throughout the Louisiana Iris genome, with I. hexagona alleles tending to be favored over those of I. fulva. Loci that were found to have exceptional patterns of introgression were also found to be significantly associated with phenotypic variation in a small number of morphological traits. However, this was the exception rather than the rule, as most loci that were associated with morphological trait variation were not significantly associated with excess ancestry. These findings provide insights into the complexity of the genomic architecture of phenotypic differences and are a first step towards identifying loci that are associated with both trait variation and reproductive isolation in nature.
Data for: Evaluating the impact of anatomical partitioning on summary topologies obtained with Bayesian phylogenetic analyses of morphological data
<p>Morphological data are a fundamental source of evidence to reconstruct the Tree of Life, and Bayesian phylogenetic methods are increasingly being used for this task. Bayesian phylogenetic analyses require the use of evolutionary models, which have been intensively studied in the past few years, with significant improvements to our knowledge. Notwithstanding, a systematic evaluation of the performance of partitioned models for morphological data has never been performed. Here we evaluate the influence of partitioned models, defined by anatomical criteria, on the precision and accuracy of summary tree topologies considering the effects of model misspecification. We simulated datasets using partitioning schemes, trees, and other properties obtained from two empirical datasets, and conducted Bayesian phylogenetic analyses. Additionally, we reanalysed 32 empirical datasets for different groups of vertebrates, applying unpartitioned and partitioned models, and, as a focused study case, we reanalysed a dataset including living and fossil armadillos, testing alternative partitioning hypotheses based on functional and ontogenetic modules. We found that, in general, partitioning by anatomy has little influence on summary topologies analysed under alternative partitioning schemes with a varying number of partitions. Nevertheless, models with unlinked branch lengths, which account for heterotachy across partitions, improve topological precision at the cost of reducing accuracy. In some instances, more complex partitioning schemes, led to topological changes, as tested for armadillos, mostly associated with models with unlinked branch lengths. We compare our results with other empirical evaluations of morphological data and those from empirical and simulation studies of partitioning of molecular data, considering the adequacy of anatomical partitioning relative to alternative methods of partitioning morphological datasets.</p>
Data from: Bayesian total-evidence dating revisits sloth phylogeny and biogeography: a cautionary tale on morphological clock analyses
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Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone
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Data for: Evaluating the impact of anatomical partitioning on summary topologies obtained with Bayesian phylogenetic analyses of morphological data
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Data from: Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample
<p>Establishing hypotheses of relationships is a critical prerequisite for any macroevolutionary analysis, but different approaches exist for achieving this goal. Amongst palaeontologists using morphological data the Bayesian approach is increasingly preferred over parsimony, but this shift also alters the way we think about samples of trees. Here we revisit stratigraphic congruence as a comparator between Bayesian and parsimony samples, but in a new visual context: treespace. Such spaces represent an ordination of unique topologies that can also be extended to create a "landscape" where altitude represents some comparative measure (here congruence with stratigraphy). By co-opting existing visualization tools and applying them to a meta-analysis of 128 cladistic data sets we show that there is no consistent favouring of either Bayesian or parsimony according to stratigraphic congruence metrics, and further that empirical treespace visualizations suggest a complex variety of topological landscapes. We conclude by arguing that treespaces should become a standard exploratory tool in phylogenetic analysis.</p>
Data from: Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes
Bayesian clustering methods have been widely used for studying species delimitation and genetic introgression. In order to test the effect of phylogenetic relationships and sampling scheme on the inferred clustering solution and on the performance of Bayesian clustering analysis, I simulated genotypes of the interfertile oak species Quercus robur, Quercus petraea, and Quercus pubescens and I run analyses using two popular software programs, STRUCTURE and BAPS. First, based on purebred simulations, I compared clustering solutions resulting from different sample size configurations. While clustering solution generally reflected the taxonomic relationships when equal samples of each species were included, spurious partition was inferred by STRUCTURE when some species were represented by larger and others by smaller samples. In very unbalanced configurations, STRUCTURE failed to identify the three species, even if three subpopulations were assumed. By contrast, BAPS could properly identify the three species under any sampling scheme. Second, based on simulations of purebreds and hybrids, I tested the performance of individual assignments with variable number of loci. This analysis showed that STRUCTURE can detect introgressed individuals more efficiently than BAPS. However, BAPS could assign purebreds more efficiently with a lower number of loci. Method performance also depended on phylogenetic relationships. In the case of Q. petraea, Q. pubescens, and their hybrids, method performance was lower due to their phylogenetic affinity. Inclusion of three instead of two species into the analysis led to reduction of performance, and to misclassification of hybrids, which often reflected the phylogenetic affinity between Q. petraea and Q. pubescens.
Figure 8. Rooted Bayesian trees from molecular analyses, Table 3 in The systematics of the dusky striped squirrel, Funambulus sublineatus (Waterhouse, 1838) (Rodentia: Sciuridae) and its relationships to Layard's squirrel, Funambulus layardi Blyth, 1849
Figure 8. Rooted Bayesian trees from molecular analyses, Table 3 identifies the specimens. Nodal support values in each phylogenetic tree (BI/ML/MP/NJ) are given on branches.
Figure 1. Bayesian maximum clade credibility tree obtained for 32 in Revision of the higher taxonomy of Neotropical freshwater crabs of the family Pseudothelphusidae, based on multigene and morphological analyses
Figure 1. Bayesian maximum clade credibility tree obtained for 32 genera of the superfamily Pseudothelphusoidea. Values at nodes represent bootstrap values for the Maximum Likelihood analysis (above branches) and posterior probabilities (below branches).
FIGURE. (A) Summary phylogeny showing relations between genera in tribe Phyllantheae from Bayesian and Maximum Likelihood analysis of five markers (ITS, PHYC, accD–psaI, trnS–trnG, matK), modified from Appendix 1. Classification is shown of genera (right column), subgenera (middle column) and sections (except for the genus Phyllanthus. Sections not included in phylogenetic analyses and those for the genus Flueggea were omitted. (B) summary phylogeny of the genus Phyllanthus as envisioned here with subgenera and sections of groups included in phylogenetic studies shown. in A revised phylogenetic classification of tribe Phyllantheae (Phyllanthaceae)
FIGURE. (A) Summary phylogeny showing relations between genera in tribe Phyllantheae from Bayesian and Maximum Likelihood analysis of five markers (ITS, PHYC, accD–psaI, trnS–trnG, matK), modified from Appendix 1. Classification is shown of genera (right column), subgenera (middle column) and sections (except for the genus Phyllanthus. Sections not included in phylogenetic analyses and those for the genus Flueggea were omitted. (B) summary phylogeny of the genus Phyllanthus as envisioned here with subgenera and sections of groups included in phylogenetic studies shown.
FIG. 9. Bayesian tree inferred using D2-D3 28S in Analyses of morphological and molecular characteristics of Telotylenchinae from Iran point at the validity of the genera Bitylenchus and Sauertylenchus
FIG. 9. Bayesian tree inferred using D2-D3 28S rDNA sequences. Posterior probabilities (pp) exceeding 0.65 are given on appropriate clades, bifurcations with pp above 0.95 are considered to be well-supported. Nematode species and GenBank numbers are listed for each taxon. In bold: newly generated D2-D3 28S rDNA sequences. With regard to Telotylenchinae Clades (indicated in Roman figures) we adhered to Handoo et al. (2014)
FIG. 8. Bayesian tree inferred from 18S in Analyses of morphological and molecular characteristics of Telotylenchinae from Iran point at the validity of the genera Bitylenchus and Sauertylenchus
FIG. 8. Bayesian tree inferred from 18S rDNA sequences. Posterior probabilities (pp) exceeding 0.65 are given on appropriate clades, bifurcations with pp above 0.95 are considered to be well-supported. Nematode species and GenBank numbers are listed for each taxon. In bold: newly generated 18S rDNA sequences. With regard to Telotylenchinae Clades (indicated in Roman figures) we adhered to Handoo et al. (2014).
Figure 2. Phylogenetic trees obtained from Parsimony analyses. A, under equal weights. B in Revisiting the phylogeny of the scolebythid wasps (Hymenoptera: Aculeata) through Bayesian model evaluation and parsimony, with description of a new fossil family of Chrysidoidea
Figure 2. Phylogenetic trees obtained from Parsimony analyses. A, under equal weights. B, under implied weighting (k = 3).
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