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20 results for “phylogenetic congruence”
Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions
<p>Interspecific interactions, including host-symbiont associations, can profoundly affect the evolution of the interacting species. Given the phylogenies of host and symbiont clades and knowledge of which host species interact with which symbiont, two questions are often asked: "Do closely related hosts interact with closely related symbionts?" and "Do host and symbiont phylogenies mirror one another?". These questions are intertwined and can even collapse under specific situations, such that they are often confused one with the other. However, in most situations, a positive answer to the first question, hereafter referred to as "cophylogenetic signal", does not imply a close match between the host and symbiont phylogenies. It suggests only that past evolutionary history has contributed to shaping present-day interactions, which can arise, for example, through present-day trait matching, or from a single ancient vicariance event that increases the probability that closely related species overlap geographically. A positive answer to the second, referred to as "phylogenetic congruence", is more restrictive as it suggests a close match between the two phylogenies, which may happen, for example, if symbiont diversification tracks host diversification or if the diversifications of the two clades were subject to the same succession of vicariance events. Here we apply a set of methods (ParaFit, PACo, and eMPRess), which significance is often interpreted as evidence for phylogenetic congruence, to simulations under three biologically realistic scenarios of trait matching, a single ancient vicariance event, and phylogenetic tracking. The latter is the only scenario that generates phylogenetic congruence, whereas the first two generate a cophylogenetic signal in the absence of phylogenetic congruence. We find that tests of global-fit methods (ParaFit and PACo) are significant under the three scenarios, whereas tests of event-based methods (eMPRess) are only significant under the scenario of phylogenetic tracking. Therefore, significant results from global-fit methods should be interpreted in terms of cophylogenetic signal and not phylogenetic congruence; such significant results can arise under scenarios when hosts and symbionts had independent evolutionary histories. Conversely, significant results from event-based methods suggest a strong form of dependency between hosts and symbionts evolutionary histories. Clarifying the patterns detected by different cophylogenetic methods is key to understanding how interspecific interactions shape and are shaped by evolution.</p>
Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions
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Data from: Strong phylogenetic congruence between Tulasnella fungi and their associated Drakaeinae orchids
<p>The study of congruency between phylogenies of interacting species can provide a powerful approach for understanding the evolutionary history of symbiotic associations. Orchid mycorrhizal fungi can survive independently of orchids making cospeciation unlikely, leading us to predict that any congruence would arise from host-switches to closely related fungal species. The Australasian orchid subtribe Drakaeinae is an iconic group of sexually-deceptive orchids that consists of approximately 66 species. In this study, we investigated the evolutionary relationships between representatives of all six Drakaeinae orchid genera (39 species) and their mycorrhizal fungi. We used an exome capture dataset to generate the first well-resolved phylogeny of the Drakaeinae genera. A total of 10 closely related <em>Tulasnella</em> Operational Taxonomic Units (OTUs) and previously described species were associated with the Drakaeinae orchids. Three of them were shared among orchid genera, with each genus associating with 1–7 <em>Tulasnella</em> lineages. Cophylogenetic analyses show Drakaeinae orchids and their <em>Tulasnella</em> associates exhibit significant congruence (P < 0.001) in the topology of their phylogenetic trees. <span>An event-based method also revealed significant congruence in Drakaeinae-<em>Tulasnella</em> relationships, with duplications (35), losses (25), and failure to diverge (9) the most frequent events, with minimal evidence for cospeciation (1) and host-switches (2). The high number of duplications suggests that the orchids speciate independently from the fungi, and the fungal species association of the ancestral orchid species is typically maintained in the daughter species. </span>For the Drakaeinae-<em>Tulasnella</em> interaction, a pattern of phylogenetic niche conservatism rather than coevolution likely led to the observed phylogenetic congruency in orchid and fungal phylogenies. Given that many orchid genera are characterized by sharing of fungal species between closely related orchid species, we predict that these findings may apply to a wide range of orchid lineages.</p>
Data from: A selective fungal transport organ (mycangium) maintains coarse phylogenetic congruence between fungus-farming ambrosia beetles and their symbionts
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Data from: Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics
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Data from: Strong phylogenetic congruence between Tulasnella fungi and their associated Drakaeinae orchids
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Spatial mismatch and congruence in the taxonomic, functional, and phylogenetic diversities of fish assemblages in China’s water diversion lakes
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Data from: Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective
<p>Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life, but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger datasets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve nine of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can be used to build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups.</p>
Figure 9 in Reconstruction of the pharyngeal corpus of Aphelenchus avenae (Nematoda: Tylenchomorpha), with implications for phylogenetic congruence
Figure 9. Simplified relationships between nematode models with reconstructed sensory anatomies and preliminary mapping of characters based on simple parsimony. Relationships shown are a consensus of published phylogenies inferred from 18S and 28S rRNA sequences (Blaxter et al., 1998; Holterman et al., 2006; Meldal et al., 2007), although placement of the root varies amongst some analyses. Numbers correspond to characters (left of dash) and states (right of dash) drawn from Table 2. *Polarity of character is hypothesized given the state in Myolaimus byersi (suborder Myolaimina; Giblin-Davis et al., 2010), which is a possible outgroup to all nematodes in tree (Nadler et al., 2006).
Figure 7 in Reconstruction of the pharyngeal corpus of Aphelenchus avenae (Nematoda: Tylenchomorpha), with implications for phylogenetic congruence
Figure 7. Diagrammatic representation of the pharyngeal corpus in Caenorhabditis elegans and Aphelenchus avenae, showing hypotheses of homology for radial and marginal cells. The top of each diagram shows the cells lining the cuticle of the pharyngeal lumen dorsally; the bottom shows the cells lining the luminal cuticle ventrally. Colours correspond to those used in reconstruction models in Figures 2, 4, and 6 (with colour key in Fig. 6). Drawing of C. elegans informed by Albertson & Thomson (1976) and De Ley et al. (1995). Abbreviations: dgo, dorsal gland orifice; e1–3, 'epithelial' cells 1–3; mc1–2, marginal cells 1–2; pm1–5, pharyngeal muscle cells 1–5.
Figure 1 in Reconstruction of the pharyngeal corpus of Aphelenchus avenae (Nematoda: Tylenchomorpha), with implications for phylogenetic congruence
Figure 1. Summarized phylogenetic tree of Tylenchomorpha and outgroups, which is a consensus of phylogenies from several phylum-wide analyses (Blaxter et al., 1998; Holterman et al., 2006; Meldal et al., 2007; Bert et al., 2008), although placement of the root varies amongst some analyses. Taxa in boxes belong to Tylenchomorpha; taxa on dashed branches belong to 'Aphelenchoidea'. 'Tylenchids sensu stricto' designates all non-aphelenchid Tylenchomorpha.
Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics
<p>Data for project entitled "Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics" by Marek L. Borowiec</p>
Data from: Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective
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Data from: Testing Phylogenetic Methods with Tree Congruence: Phylogenetic Analysis of Polymorphic Morphological Characters in Phrynosomatid Lizards
Congruence between trees from separately analyzed data sets is a powerful approach for assessing the performance of phylogenetic methods but has been applied primarily to the analysis of molecular data. In this study, different methods for treating polymorphic characters were compared using morphological data from phrynosomatid lizards. Clades were identified that are both traditionally recognized and supported by recent molecular analyses, and species were sampled from these clades to make three RknownS phylogenies of eight species each. The ability of different methods to estimate these "known" phylogenies with a finite sample of characters was tested. The phylogenetic methods included eight parsimony methods for coding polymorphism, three distance approaches (UPGMA, neighbor joining, and Fitch-Margoliash) applied to two genetic distance measures (Nei's and the modified Cavalli-Sforza and Edwards chord distance), and continuous maximum likelihood. The effects of excluding polymorphic characters and character weighting (a priori and successive) were also tested. Among the different parsimony approaches, the fixed-only method (excluding all polymorphic characters) performed relatively poorly, whereas the frequency method (including all polymorphic characters) performed relatively well. However, frequency-based distance methods consistently outperformed parsimony, especially with a small sample size (n= 1 individual per species). These results agree closely with those from recent simulation studies of polymorphic data and argue against the common practices of excluding polymorphic morphological characters, ignoring the frequencies of traits within species, and the exclusive use of parsimony to analyze morphological data.
Data from: Phylogenetic Congruence and Discordance Among One Morphological and Three Molecular Data Sets from Pontederiaceae
A morphological data set and three sources of data from the chloroplast genome (two genes and a restriction-site survey) were used to reconstruct the phylogenetic history of the Pickerelweed family Pontederiaceae. The chloroplast data are converging to a single tree, presumably the true chloroplast phylogeny of the family. Unrooted trees estimated from the three chloroplast data sets were identical or extremely similar in shape to each other, mostly robustly supported and there was no evidence of significant heterogeneity among them. The few topological differences seen among unrooted trees from each chloroplast data set are probably artifacts of sampling error on short branches. Despite well documented differences in rates of evolution for different characters in individual data sets, equally weighted parsimony therefore permits accurate reconstructions of chloroplast relationships in Pontederiaceae. A separate morphology-based data set yielded trees that were very different from the chloroplast trees. While there was substantial support by the morphological evidence for several major clades supported by chloroplast trees, most of the conflicting phylogenetic structure on the morphology trees was not robust. Nonetheless, several statistical tests of incongruence indicate significant heterogeneity between molecules and morphology. The source of this apparent incongruence appears to be a low ratio of phylogenetic signal to noise in the morphological data.
Data from: Testing Phylogenetic Methods with Tree Congruence: Phylogenetic Analysis of Polymorphic Morphological Characters in Phrynosomatid Lizards
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Data from: Phylogenetic Congruence and Discordance Among One Morphological and Three Molecular Data Sets from Pontederiaceae
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Data from: Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test
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Figure 8 in Reconstruction of the pharyngeal corpus of Aphelenchus avenae (Nematoda: Tylenchomorpha), with implications for phylogenetic congruence
Figure 8. Diagrammatic representation of the pharyngeal corpus of Caenorhabditis elegans and three different Tylenchomorpha showing positions of pharyngeal neurone nuclei. Neurone homologies in Aphelenchus avenae are based on similarity to C. elegans in cell body position, dendrite topology, and connectivity. Homologies in Heterodera glycines and Aphelenchoides blastophthorus are proposed based on positions of nuclei as described by Endo (1984) and Shepherd et al. (1984), respectively. The top of each diagram shows dorsal neurone nuclei; the bottom is one of the two subventral rows of nuclei. Diagram of C. elegans redrawn from Chiang et al. (2006); nucleus positions in Aphelenchoides blastophthorus redrawn from Shepherd et al. (1984). Abbreviated names of neurones are consistent with Albertson & Thomson (1976). Abbreviations: I1–3, interneurones 1–3; M1, M3, M4, motor neurones 1, 3, 4; MC, marginal cell neurone; NSM, neurosecretory motor neurone.
Ecol-Lett_Fuzessy-et-al-2021_Phylogenetic_congruence_between_Neotropical_primates_and_plants
<p>Data supporting the results in the Ecology Letters paper DOI: 10.1111/ele.13918:</p> <p>Title: Phylogenetic congruence between Neotropical primates and plants is driven by frugivory</p> <p>Authors: Fuzessy L (lfuzessy@gmail.com), Silveira F A, Culot L, Jordano P, Verdu M.</p> <p>Abstract: Seed dispersal benefits plants and frugivores, and potentially drives co-evolution, with consequences to diversification evidenced for e.g., primates. Evidence for macro-coevolutionary patterns in multi-specific, plant-animal mutualisms is scarce, and the mechanisms driving them remain unexplored. We tested for phylogenetic congruences in primate-plant interactions and showed strong co-phylogenetic signals across Neotropical forests, suggesting that both primates and plants share evolutionary history. Phylogenetic congruence between Platyrrhini and Angiosperms was driven by the most generalist primates, modulated by their functional traits, interacting with a wide-range of Angiosperms. Consistently similar eco-evolutionary dynamics seem to be operating irrespective of local assemblages, since co-phylogenetic signal emerged independently across three Neotropical regions. Our analysis supports the idea that macroevolutionary, coevolved patterns among interacting mutualistic partners are driven by super-generalist taxa. Trait convergence among multiple partners within multi-specific assemblages appears as a mechanism favouring these likely coevolved outcomes.</p>
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