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- Bergsten, Johannes, et al.
(författare)
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Bayesian Tests of Topology Hypotheses with an Example from Diving Beetles
- 2013
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 62:5, s. 660-673
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Tidskriftsartikel (refereegranskat)abstract
- We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.
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- Braga, Mariana P., et al.
(författare)
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Bayesian Inference of Ancestral Host-Parasite Interactions under a Phylogenetic Model of Host Repertoire Evolution
- 2020
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 69:6, s. 1149-1162
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Tidskriftsartikel (refereegranskat)abstract
- Intimate ecological interactions, such as those between parasites and their hosts, may persist over long time spans, coupling the evolutionary histories of the lineages involved. Most methods that reconstruct the coevolutionary history of such interactions make the simplifying assumption that parasites have a single host. Many methods also focus on congruence between host and parasite phylogenies, using cospeciation as the null model. However, there is an increasing body of evidence suggesting that the host ranges of parasites are more complex: that host ranges often include more than one host and evolve via gains and losses of hosts rather than through cospeciation alone. Here, we develop a Bayesian approach for inferring coevolutionary history based on a model accommodating these complexities. Specifically, a parasite is assumed to have a host repertoire, which includes both potential hosts and one or more actual hosts. Over time, potential hosts can be added or lost, and potential hosts can develop into actual hosts or vice versa. Thus, host colonization is modeled as a two-step process that may potentially be influenced by host relatedness. We first explore the statistical behavior of our model by simulating evolution of host-parasite interactions under a range of parameter values. We then use our approach, implemented in the program RevBayes, to infer the coevolutionary history between 34 Nymphalini butterfly species and 25 angiosperm families. Our analysis suggests that host relatedness among angiosperm families influences how easily Nymphalini lineages gain new hosts.
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- Braga, Mariana Pires, 1988-
(författare)
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Evolution of host repertoires and the diversification of butterflies
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- All herbivorous insects are specialized to some extent to their host plants, but the level of specialization varies greatly. Insect-plant coevolution is often invoked to explain the large diversity of herbivorous insects, but the role of specialization during diversification is still controversial. Although well-studied, our understanding of the evolution of species interactions is still improving, and recent theoretical developments have highlighted the role of generalization (via colonization of new hosts) on diversification. In this thesis, various approaches are combined for a detailed study of the origins of macroevolutionary patterns of host use and butterfly diversity. Chapter I provides a mechanistic basis for such patterns through simulations of lineages evolved in silico. By separating the effects of the number of hosts used by a parasite lineage and the diversity of resources they encompass, we found that resource diversity, rather than host range per se, was the main driver of parasite species richness in both simulated and empirical systems. In Chapter II, we combined network and phylogenetic analyses to quantify support for the two main hypothesized drivers of diversification of herbivorous insects. Based on analyses of two butterfly families, Nymphalidae and Pieridae, we found that variability in host use is essential for diversification, while radiation following the colonization of a new host is rare but can produce high diversity. We then reconciled the two alternative hypotheses into a unified process of host-associated diversification where continuous probing of new hosts and retention of the ability to use hosts colonized in the past are the main factors shaping butterfly-plant networks. While network analysis is a powerful tool for investigating patterns of interaction, other methods are necessary to directly test the mechanisms generating the observed patterns. Therefore, in Chapter III we describe a model of host repertoire evolution we developed for Bayesian inference of evolution of host-parasite interactions. The approach was validated with both simulated and empirical data sets. Finally, in Chapter IV we used the method described in Chapter III to explicitly test the predictions made in Chapter II about the evolution of butterfly-plant networks. We found direct evidence for the role of expansion of fundamental host repertoire and phylogenetic conservatism as important drivers of host repertoire evolution. Thus, using three different approaches, we found overall support for the idea that variation in host use accumulated over evolutionary time is essential for butterfly diversification.
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- Braga, Mariana P., et al.
(författare)
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Phylogenetic reconstruction of ancestral ecological networks through time for pierid butterflies and their host plants
- 2021
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 24:10, s. 2134-2145
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Tidskriftsartikel (refereegranskat)abstract
- The study of herbivorous insects underpins much of the theory that concerns the evolution of species interactions. In particular, Pieridae butterflies and their host plants have served as a model system for studying evolutionary arms races. To learn more about the coevolution of these two clades, we reconstructed ancestral ecological networks using stochastic mappings that were generated by a phylogenetic model of host-repertoire evolution. We then measured if, when, and how two ecologically important structural features of the ancestral networks (modularity and nestedness) evolved over time. Our study shows that as pierids gained new hosts and formed new modules, a subset of them retained or recolonised the ancestral host(s), preserving connectivity to the original modules. Together, host-range expansions and recolonisations promoted a phase transition in network structure. Our results demonstrate the power of combining network analysis with Bayesian inference of host-repertoire evolution to understand changes in complex species interactions over time.
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- Cannon, Johanna, 1982-, et al.
(författare)
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Xenacoelomorpha is the sister group to Nephrozoa
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 530, s. 89-93
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Tidskriftsartikel (refereegranskat)abstract
- The position of Xenacoelomorpha in the tree of life remains a major unresolved question in the study of deep animal relationships1. Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella, are bilaterally symmetrical marine worms that lack several features common to most other bilaterians, for example an anus, nephridia, and a circulatory system. Two conflicting hypotheses are under debate: Xenacoelomorpha is the sister group to all remaining Bilateria (= Nephrozoa, namely protostomes and deuterostomes)2,3 or is a clade inside Deuterostomia4. Thus, determining the phylogenetic position of this clade is pivotal for understanding the early evolution of bilaterian features, or as a case of drastic secondary loss of complexity. Here we show robust phylogenomic support for Xenacoelomorpha as the sister taxon of Nephrozoa. Our phylogenetic analyses, based on 11 novel xenacoelomorph transcriptomes and using different models of evolution under maximum likelihood and Bayesian inference analyses, strongly corroborate this result. Rigorous testing of 25 experimental data sets designed to exclude data partitions and taxa potentially prone to reconstruction biases indicates that long- branch attraction, saturation, and missing data do not influence these results. The sister group relationship between Nephrozoa and Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa.
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