Find research datasets worth reusing

opencc-by-4.0Jul 2019View details →

Phylogenetic comparative methods are problematic when applied to gene trees with speciation and duplication nodes: correcting for biases in testing the ortholog conjecture

This repository contains “manuscript_dunn.RData” file, which is reproduced by using the files and scripts of Dunn et al. (Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A (2018) Pairwise comparisons across species are problematic when analyzing functional genomic data. Proc Natl Acad Sci U S A 115: E409–E417. <a href="http://dx.doi.org/10.1073/pnas.1707515115">doi:10.1073/pnas.1707515115</a>). In this repository, we also supplied “Data_TMRR_latest.rda” file, containing the results generated by using our own scripts. Our scripts are available on GitHub: <a href="https://github.com/tbegum/Testing_the_ortholog_conjecture">https://github.com/tbegum/Testing_the_ortholog_conjecture</a>.

FIGURE 10 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 10. Phylogenetic hypothesis based on the morphological characters from the Agathemera eggs. a. Unrooted tree considering all the Agathemera species' eggs. b. rooted tree considering just the species in clade 1 (sensu Vera et al. 2012) and A. grylloidea as outgroup. c. Rooted tree considering only the species in clade 2 (sensu Vera et al. 2012) and A. luteola as outgroup. Black circles and their respective numbers indicate synapomorphies. Jacknife/Bootstrap values are shown for each node.

FIGURE 6 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 6. External morphology of the eggs from clade 2 and their respective operculum. a1-c1, dorsal view; a2-c2 operculum. The order of the eggs and operculum from right to left is A. grylloidea, A. elegans, A. mesoauriculae (escale = 1mm).

FIGURE 7 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 7. Ultrastructure surface of the micropylar plate of the eggs from clade 1 and their respective operculum. A1-E1, micropylar plate ultrastructure; A2-E2 ultrastructure surface of the operculum. The order of the micropylar plates and operculum from top to bottom is A. luteola, A. maculafulgens, A. crassa. A. millepunctata, A. claraziana.

FIGURE 8 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 8. Ultrastructure surface of the micropylar plate of the eggs from clade 2 and their respective operculum. A1-C1, micropylar plate ultrastructure; A2-C2 ultrastructure surface of the operculum. The order of the micropylar plates and operculum from top to botom is A. grylloidea, A. elegans, A. mesoauriculae.

FIGURE 9 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 9. Character states reconstruction by maximum parsimony over the molecular phylogeny (sensu Vera et al. 2012). The character states for both the ancestral nodes A-G and actual species (H-O) are represented by color-coded boxes, where numbers indicate the character and colors the state. Besides, examples of the micropylar plate open (A. maculafulgens) and closed (A. elegans) are shown. Note: character numbers are consistent with those throughout the text.

FIGURE 5 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 5. External morphology of the eggs from clade 1 and their respective operculum. a1-e1, dorsal view; a2-e2 operculum. The order of the eggs and operculum from right to left is A. luteola, A. maculafulgens, A. crassa. A. millepunctata, A. claraziana (escale = 1mm).

FIGURE 3 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 3. Principal component analysis for the Agathemera eggs. The percentage of the variance explained by each principal component plotted is in parentheses. Every line connects a data point with its corresponding centroid. a. PCA for the eight Agathemera species; b. PCA for the species from clade 1; c. PCA for species from clade 2.

FIGURE 2 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 2. Distribution of the nine morphometric variables measured. the species are ordered following the phylogenetic relationships. Boxes represent the values between the 25 and 75 percentiles respectively, the horizontal line is the median and the point within each box is the mean and the whiskers indicate the sample range. Light grey boxplots correspond to species from clade 1 and dark grey boxplots correspond to species from clade 2. a. Capsule width; b. Capsule length; c. Capsule height; d. Micropylar plate length; e. Micropylar plate width; f. Operculum length; g. Operculum width; h. Operculum height; i. Opercular angle.

FIGURE 1 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach

FIGURE 1. schematic drawing of an Agathemera egg showing the different variables measured. a. dorsal view. b. lateral view. c. upper view. Abbreviations: w = width; mpl = micropylar plate width; mpl = micropylar plate length; h = capsule height; l = capsule length; opl = operculum length; opa = opercular angle; opw = operculum width; operculum height.

opencc-zeroDec 2015View details →

Data from: The evolution of reproductive diversity in Afrobatrachia: a phylogenetic comparative analysis of an extensive radiation of African frogs

The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co-evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (∼400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift towards using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans.

opencc-zeroDec 2017View details →

Data from: Rethinking phylogenetic comparative methods

As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this paper, we argue that this way of thinking about PCMs is deeply misleading. Not only has this sowed widespread confusion in the literature about what PCMs are doing but has led us to develop methods that are susceptible to the very thing we sought to build defenses against --- unreplicated evolutionary events. Through three Case Studies, we demonstrate that the susceptibility to singular events is indeed a recurring problem in comparative biology that links several seemingly unrelated controversies. In each Case Study we propose a potential solution to the problem. While the details of our proposed solutions differ, they share a common theme: unifying hypothesis testing with data-driven approaches (which we term ``phylogenetic natural history'') to disentangle the impact of singular evolutionary events from that of the factors we are investigating. More broadly, we argue that our field has, at times, been sloppy when weighing evidence in support of causal hypotheses. We suggest that one way to refine our inferences is to re-imagine phylogenies as probabilistic graphical models; adopting this way of thinking will help clarify precisely what we are testing and what evidence supports our claims.

opencc-zeroDec 2016View details →

Data from: A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species

Evaluating trait correlations across species within a lineage via phylogenetic regression is fundamental to comparative evolutionary biology, but when traits of interest are derived from two sets of lineages that co-evolve with one another, methods for evaluating such patterns in a dual-phylogenetic context remain underdeveloped. Here we extend multivariate permutation-based phylogenetic regression to evaluate trait correlations in two sets of interacting species while accounting for their respective phylogenies. This extension is appropriate for both univariate and multivariate response data, and may utilize one or more independent variables, including environmental covariates. Imperfect correspondence between species in the interacting lineages can also be accommodated, such as when species in one lineage associate with multiple species in the other, or when there are unmatched taxa in one or both lineages. For both univariate and multivariate data, the method displays appropriate type I error, and statistical power increases with the strength of the trait covariation and the number of species in the phylogeny. These properties are retained even when there is not a 1:1 correspondence between lineages. Finally, we demonstrate the approach by evaluating the evolutionary correlation between traits in fig species and traits in their agaonid wasp pollinators. R computer code is provided.

opencc-zeroDec 2016View details →

Data from: Multivariate phylogenetic comparative methods: evaluations, comparisons, and recommendations

Recent years have seen increased interest in phylogenetic comparative analyses of multivariate datasets, but to date the varied proposed approaches have not been extensively examined. Here we review the mathematical properties required of any multivariate method, and specifically evaluate existing multivariate phylogenetic comparative methods in this context. Phylogenetic comparative methods based on the full multivariate likelihood are robust to levels of covariation among trait dimensions and are insensitive to the orientation of the dataset, but display increasing model misspecification as the number of trait dimensions increases. This is because the expected evolutionary covariance matrix (V) used in the likelihood calculations becomes more ill-conditioned as trait dimensionality increases, and as evolutionary models become more complex. Thus, these approaches are only appropriate for datasets with few traits and many species. Methods that summarize patterns across trait dimensions treated separately (e.g., SURFACE) incorrectly assume independence among trait dimensions, resulting in nearly a 100% model misspecification rate. Methods using pairwise composite likelihood are highly sensitive to levels of trait covariation, the orientation of the dataset, and the number of trait dimensions. The consequences of these debilitating deficiencies is that a user can arrive at differing statistical conclusions, and therefore biological inferences, simply from a dataspace rotation, like principal component analysis. By contrast, algebraic generalizations of the standard phylogenetic comparative toolkit that use the trace of covariance matrices are insensitive to levels of trait covariation, the number of trait dimensions, and the orientation of the dataset. Further, when appropriate permutation tests are used, these approaches display acceptable Type I error and statistical power. We conclude that methods summarizing information across trait dimensions, as well as pairwise composite likelihood methods should be avoided, while algebraic generalizations of the phylogenetic comparative toolkit provide a useful means of assessing macroevolutionary patterns in multivariate data. Finally, we discuss areas in which multivariate phylogenetic comparative methods are still in need of future development; namely highly multivariate Ornstein-Uhlenbeck models and approaches for multivariate evolutionary model comparisons.

Figure 51. Character states for characters 31 in The comparative osteology and phylogenetic relationships of African and South American lungfishes (Sarcopterygii: Dipnoi)

Figure 51. Character states for characters 31 (contact between pterygoid tooth plates) and 33 (number of ridges on tooth plate). Pterygoid tooth plates in ventral view of: A, Neoceratodus forsteri, AMS I-40438-001; B, †Arganodus atlantis, KU 60708; and C, Protopterus aethiopicus, UF 137272. Anterior is to the top. †Dagger symbol represents extinct taxa. Scale bars: 5 mm.

Figure 50. Character states for character 28 in The comparative osteology and phylogenetic relationships of African and South American lungfishes (Sarcopterygii: Dipnoi)

Figure 50. Character states for character 28 (dorsal process of angular). Left angular in lateral view of: A, †Arganodus atlantis, KU 60710; B, Protopterus annectens, TMM M 1129; C, Lepidosiren paradoxa, CAS 61327. Anterior is to the left. †Dagger symbol represents extinct taxa. Scale bars: 1 mm.

Figure 44 in The comparative osteology and phylogenetic relationships of African and South American lungfishes (Sarcopterygii: Dipnoi)

Figure 44. Lateral view of the computed tomography reconstructions of the left clavicles of extant lungfishes, anterior to the left: A, Lepidosiren paradoxa, CAS 61327; B, Protopterus annectens, TMM M 1129; C, Protopterus dolloi, AMNH 246385; D, Protopterus aethiopicus, UF 137272; E, Protopterus amphibius, CAS 47408; F, Neoceratodus forsteri, AMS I-40438- 001. Scale bar: 5 mm.

Figure 45. Character states for characters 6 in The comparative osteology and phylogenetic relationships of African and South American lungfishes (Sarcopterygii: Dipnoi)

Figure 45. Character states for characters 6 (number of bones in mediolateral series), 12 (lateral parietals), 13 (lateral process of the supraorbital), and 14 (supraorbital articulation). Dorsal view of the skull, mandible, and pectoral girdle of: A, Neoceratodus forsteri, AMS I-40438-001; B, Lepidosiren paradoxa, CAS 61327; and C, Protopterus amphibius, UF 137272. Anterior is to the left. Scale bars: 1 cm.

Figure 41 in The comparative osteology and phylogenetic relationships of African and South American lungfishes (Sarcopterygii: Dipnoi)

Figure 41. Left cleithrum and clavicle of Protopterus annectens, TMM M 2494: A, anterolateral view, anterior to the left; B, posteromedial view, anterior to the right. Scale bar: 5 mm. CL, cleithrum; CLA, clavicle.