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68 results for “taxon sampling”
Fig. 3 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 3. Facial markings of didelphid marsupials scored for characters 2–5. Top left, Marmosa robinsoni (dark midrostral stripe absent; circumocular mask present, contrasting with coloration of cheeks and crown; pale spot above each eye absent), score: 0100. Top right, Caluromys lanatus (dark midrostral stripe present; circumocular mask present, contrasting with coloration of cheeks and crown; pale spot above each eye absent), score: 1100. Bottom left, Lutreolina crassicaudata (dark midrostral stripe absent; circumocular mask absent; pale spot above each eye absent), score: 00–0. Bottom right, Philander opossum (dark midrostral stripe absent; circumocular mask present, continuous with dark coronal fur; pale spot above each eye present), score: 0111. Photographs by Pascual Soriano (top left, top right, bottom left) and Nancy B. Simmons (bottom right).
Fig. 14 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 14. Lingual views of anterior mandibular dentition illustrating taxonomic differences in lower incisor morphology. Top, Metachirus nudicaudatus (AMNH 266452) with distinct posterior accessory cusps on i1–i4. Bottom, Lutreolina crassicaudata (AMNH 210424) without distinct posterior accessory cusps on i1–i5.
Fig. 17 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 17. Strict consensus of 2161 equally mostparsimonious trees obtained by a heuristic analysis of nonmolecular characters described in this report (see table 4 for summary dataset characteristics and tree statistics). Bremer support and bootstrap values are provided above and below each branch, respectively. Outgroup taxa are indicated with asterisks.
Fig. 18 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 18. Strict consensus of 252 equally mostparsimonious trees obtained by a heuristic analysis of IRBP sequences described in this report (see table 4 for summary dataset characteristics and tree statistics). Bremer support and bootstrap values are provided above and below each branch, repectively. For simplicity, conspecific sequences (analyzed separately in PAUP*) have been condensed to single terminals in this diagram. Outgroup taxa are indicated with asterisks. All parsimonyequivalent resolutions of the basal ingroup polytomy are shown in figure 19A–E.
Fig. 19 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 19. All equally mostparsimonious resolutions of the basal didelphine polytomy in figures 18 and 21. A, Resolution supported by 72 mostparsimonious trees (MPTs) from the IRBP1 analysis and 6 MPTs from the IRBP2 analysis; B, resolution supported by 72 MPTs from the IRBP1 analysis and 6 MPTs from the IRBP2 analysis; C, resolution supported by 36 MPTs from the IRBP1 analysis and 3 MPTs from the IRBP2 analysis; D, resolution supported by 36 MPTs from the IRBP1 analysis, 6 MPTs from the IRBP2 analysis, and 8 MPTs from the combined analysis; E, resolution supported by 36 MPTs from the IRBP1 analysis, 6 MPTs from the IRBP2 analysis, and 8 MPTs from the combined analysis; F, resolution supported by 18 MPTs from the combined analysis only.
Fig. 13 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 13. Anterolingual views of left M3 illustrating taxonomic differences in cingular morphology. Left, Marmosa murina (AMNH 272870) with preprotocrista and anterolabial cingulum joined to form a continuous shelf along the anterior margin of the tooth crown. Right, Monodelphis adusta (AMNH 272781) with separate crista and cingulum (no continuous shelf).
Impacts of taxon-sampling schemes on Bayesian tip dating under the fossilized birth-death process
<p>Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life.</p>
Data from: Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics
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Impacts of taxon-sampling schemes on Bayesian tip dating under the fossilized birth-death process
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Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling
Deep neural networks (DNNs) are powerful machine learning models that are widely used for classification problems, and have been recently proposed for quartet tree phylogeny estimation (Survorov et al. Systematic Biology 2020 and Zou et al. Molecular Biology and Evolution 2020). Here we present a study evaluating recently trained DNNs (from Zou et al., MBE 2020) in comparison to a collection of standard phylogeny estimation methods, including UPGMA, neighbor joining, maximum parsimony, and maximum likelihood, on a heterogeneous collection of 20-sequence datasets simulated under the same models that were used to train the DNNs, and also under similar conditions but with higher rates of evolution. Our study shows that using DNNs with quartet amalgamation (to combine quartet trees into a tree on the full dataset) is only more accurate than UPGMA, and otherwise is less accurate than all standard phylogeny estimation methods we explore (maximum likelihood, neighbor joining, and maximum parsimony). We further find that while DNNs can provide good quartet tree accuracy, some standard phylogeny estimation methods match or improve on DNNs for quartet accuracy, especially, but not exclusively, when used in a global manner (i.e., the tree on the full dataset is computed and then the induced quartet trees are extracted from the full tree). Thus, our study provides evidence that a major challenge impacting the utility of current DNNs for phylogeny estimation is their restriction to estimating quartet trees which must subsequently be combined into a tree on the full dataset: in contrast, global methods -- i.e., those that estimate trees from the full set of sequences -- are able to benefit from taxon sampling, and hence have higher accuracy on large datasets.
Fig. 23 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 23. Skull of Tlacuatzin canescens, a composite drawing based on USNM 125659 and 511261.
Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling
Abstract The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies.
Data from: Robustness of Felsenstein's versus transfer bootstrap supports with respect to taxon sampling
<p><span>The bootstrap method is based on resampling sequence alignments and re-estimating trees. Felsenstein's bootstrap proportions (FBP) is the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon sampling (i.e., the number of sequences) to hundreds or thousands of taxa, FBP tends to return low supports for deep branches. The Transfer Bootstrap Expectation (TBE) has been recently suggested as an alternative to FBP. TBE is measured using a continuous transfer index in [0,1] for each bootstrap tree, instead of the binary {0,1} index used in FBP to measure the presence/absence of the branch of interest. TBE has been shown to yield higher and more informative supports, while inducing a very low number of falsely supported branches.</span> <span>Nonetheless, it has been argued that TBE must be used with care due to sampling issues, especially in datasets with high number of closely related taxa. In this study, we conduct multiple experiments by varying taxon sampling and comparing FBP and TBE support values on different phylogenetic depth, using empirical datasets. Our results show that the main critique of TBE stands in extreme cases with shallow branches and highly unbalanced sampling among clades, but that TBE is still robust in most cases, while FBP is inescapably negatively impacted by high taxon sampling. We suggest guidelines and good practices in TBE (and FBP) computing and interpretation.</span></p>
Data from: Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling
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Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling
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Data from: Robustness of Felsenstein’s versus transfer bootstrap supports with respect to taxon sampling
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Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling
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Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul
Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by phylogeneticists is likely a product of the scarcity or unavailability of fresh tissue samples for DNA sequencing. Lack of comprehensive phylogenies result in highly discrepant taxonomic arrangements that are based exclusively on morphological data—impressively, these are the only classification schemes available for the group. Here we used high-throughput sequencing and an unprecedented sampling effort of museum specimens to provide the first comprehensive phylogenetic analysis of tree squirrels, with a special emphasis on Neotropical taxa. Results: We gathered mitochondrial genome data from 232 modern and historical samples, representing 40 out of the 43 currently recognized species of Sciurini. We found no correlation between specimen age and completeness of mitogenomes recovered for historical samples. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinctanalytical methods— strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least seven lineages that might represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of pairs of mammae indicated that alternative conditions of both characters must have evolved multiple times along the evolutionary history of tree squirrels. Conclusions: We were able to obtain complete mitogenomes for samples as old as 120 years, reinforcing the potential of historical samples for phylogenetic and evolutionary inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help to explain the incongruence between phylogenetic results and classification schemes presented so far, and we recommend a substantial taxonomic overhaul.
Data from: Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes.
Rodentia is the largest order of placental mammals, with approximately 2,050 species divided into 28 families. It is also one of the most controversial with respect to its monophyly, relationships between families, and divergence dates. Here, we have analyzed and compared the performance of three nuclear genes (von Willebrand Factor, interphotoreceptor retinoid-binding protein, and Alpha 2B adrenergic receptor) for a large taxonomic sampling, covering the whole rodent and placental diversity. The phylogenetic results significantly support rodent monophyly, the association of Rodentia with Lagomorpha (the Glires clade), and a Glires + Euarchonta (Primates, Dermoptera, and Scandentia) clade. The resolution of relationships among rodents is also greatly improved. The currently recognized families are divided here into seven well-defined clades (Anomaluromorpha, Castoridae, Ctenohystrica, Geomyoidea, Gliridae, Myodonta, and Sciuroidea) that can be grouped into three major clades: Ctenohystrica, Gliridae + Sciuroidea, and a mouse-related clade (Anomaluromorpha, Castoridae + Geomyoidea, and Myodonta). Molecular datings based on these three genes suggest that the rodent radiation took place at the transition between Paleocene and Eocene. The divergence between rodents and lagomorphs is placed just at the K-T boundary and the first splits among placentals in the Late Cretaceous. Our results thus tend to reconcile molecular and morphological-paleontological insights.
Data from: Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling
Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth–death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18–0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48–1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89–3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36–1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations" in the sense of convergent morphological and ecological trajectories among species in different clades, these results are consistent with the hypothesis that iteroparity functioned as an adaptive key innovation, providing a mechanism for range expansion and rapid divergence in upper elevation regions across much of the New World.
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International Brain Laboratory public data
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OpenNeuro
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