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47 results for “Diversification shifts”
Fig. 1 in Species radiation in the Alps: multiple range shifts caused diversification in Ringlet butterflies in the European high mountains
Fig. 1 Sampling locations of all studied species, with Erebia cassioides arvernensis (grey circles), Erebia c. cassioides (black circles), Erebia c. neleus in the Balkan region (black-white circles), Erebia nivalis (white triangles), Erebia tyndarus (white circles) and Erebia ottomana (grey triangles) (a). The detailed map shows the distribution of the samples in the Alps (b). Given numbers coincide with other figures and tables
Data from: Wright's shifting balance theory and the diversification of aposematic signals
Despite accumulating evidence for selection within natural systems, the importance of random genetic drift opposing Wright's and Fisher's views of evolution continue to be a subject of controversy. The geographical diversification of aposematic signals appears to be a suitable system to assess the factors involved in the process of adaptation since both theories were independently proposed to explain this phenomenon. In the present study, the effects of drift and selection were assessed from population genetics and predation experiments on poison-dart frogs, Ranitomaya imitator, of Northern Peru. We specifically focus on the transient zone between two distinct aposematic signals. In contrast to regions where high predation maintains a monomorphic aposematic signal, the transient zones are characterized by lowered selection and a high phenotypic diversity. As a result, the diversification of phenotypes may occur via genetic drift without a significant loss of fitness. These new phenotypes may then colonize alternative habitats if successfully recognized and avoided by predators. This study highlights the interplay between drift and selection as determinant processes in the adaptive diversification of aposematic signals. Results are consistent with the expectations of the Wright's shifting balance theory and represent, to our knowledge, the first empirical demonstration of this highly contested theory in a natural system.
Data from: Niche shifts after island colonization spurred adaptive diversification and speciation in a cosmopolitan bird clade
<p>Islands have long been recognized as key contributors to biodiversity because islands facilitate geographic isolation and ecological divergence from mainland ancestors. However, island colonization has traditionally been considered an evolutionary dead-end process, and its consequences for continental biodiversity remain understudied. Here, we studied the evolutionary radiation of Columbiformes (i.e. pigeons and doves) to examine if ecological niche shifts on islands shaped biological diversification and community composition on continents. We show that the colonization of islands by continental, terrestrial-foraging lineages led to exploitation of a new ecological niche (i.e. arboreal foraging). This transition towards arboreal foraging was associated with evolutionary adaptation towards a new morphological optimum. In addition, arboreal-foraging lineages experienced an increase in speciation rates, which was associated with successful range expansions to other islands as well as back-colonization of continents. Our results provide empirical evidence that diversification on continents can only be fully understood when studying the diversification processes that took place on islands, challenging the view of islands as mere sinks of evolutionary diversity.</p>
Data from: Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae)
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Data from: A radical shift in the taxonomy of Lepraria s.l.: molecular and morphological studies shed new light on the evolution of asexuality and lichen growth form diversification
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Data from: Shifting barriers and phenotypic diversification by hybridisation
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Data from: Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens
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Data from: Wright's shifting balance theory and the diversification of aposematic signals
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Data from: Did pollination shifts drive diversification in southern African Gladiolus? Evaluating the model of pollinator-driven speciation
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Data from: Shifts in diversification rates linked to biogeographic movement into new areas: an example of a recent radiation in the Andes
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Food plant shifts drive the diversification of Sack-bearer moths
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Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)
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Data from: A major shift in diversification rate helps explain macroevolutionary patterns in primate species diversity
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Data from: Niche shifts after island colonization spurred adaptive diversification and speciation in a cosmopolitan bird clade
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Data from: Molecular and morphological phylogenetics of weevils (Coleoptera, Curculionoidea): do niche shifts accompany diversification?
The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil diversification. Phylogenetic relationships among the weevils (Curculionoidea) were inferred from analysis of nucleotide sequences of 18S ribosomal DNA (rDNA; ~2,000 bases) and 115 morphological characters of larval and adult stages. A worldwide sample of 100 species was compiled to maximize representation of weevil morphological and ecological diversity. All families and the main subfamilies of Curculionoidea were represented. The family Curculionidae sensu lato was represented by about 80 species in 30 "subfamilies" of traditional classifications. Phylogenetic reconstruction was accomplished by parsimony analysis of separate and combined molecular and morphological data matrices and Bayesian analysis of the molecular data; tree topology support was evaluated. Results of the combined analysis of 18S rDNA and morphological data indicate that monophyly of and relationships among each of the weevil families are well supported with the topology ((Nemonychidae, Anthribidae) (Belidae (Attelabidae (Caridae (Brentidae, Curculionidae))))). Within the clade Curculionidae sensu lato, the basal positions are occupied by mostly monocot-associated taxa with the primitive type of male genitalia followed by the Curculionidae sensu stricto, which is made up of groups with the derived type of male genitalia. High support values were found for the monophyly of some distinct curculionid groups such as Dryophthorinae (several tribes represented) and Platypodinae (Tesserocerini plus Platypodini), among others. However, the subfamilial relationships in Curculionidae are unresolved or weakly supported. The phylogeny estimate based on combined 18S rDNA and morphological data suggests that diversification in weevils was accompanied by niche shifts in host-plant associations and larval habits. Pronounced conservatism is evident in larval feeding habits, particularly in the host tissue consumed. Multiple shifts to use of angiosperms in Curculionoidea were identified, each time associated with increases in weevil diversity and subsequent shifts back to gymnosperms, particularly in the Curculionidae.
Data from: Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts
Estimates of diversification rates are invaluable for many macroevolutionary studies. Recently, an approach called BAMM (Bayesian Analysis of Macro-evolutionary Mixtures) has become widely used for estimating diversification rates and rate shifts. At the same time, several papers have concluded that estimates of net diversification rates from the method-of-moments (MS) estimators are inaccurate. Yet, no studies have compared the ability of these two methods to accurately estimate clade diversification rates. Here, we use simulations to compare their performance. We found that BAMM yielded relatively weak relationships between true and estimated diversification rates. This occurred because BAMM underestimated the number of rates shifts across each tree, and assigned high rates to small clades with low rates. Errors in both speciation and extinction rates contributed to these errors, showing that using BAMM to estimate only speciation rates is also problematic. In contrast, the MS estimators (particularly using stem group ages), yielded stronger relationships between true and estimated diversification rates, by roughly twofold. Furthermore, the MS approach remained relatively accurate when diversification rates were heterogeneous within clades, despite the widespread assumption that it requires constant rates within clades. Overall, we caution that BAMM may be problematic for estimating diversification rates and rate shifts.
Data from: Bayesian model selection with BAMM: effects of the model prior on the inferred number of diversification shifts
1. Understanding variation in rates of speciation and extinction -- both among lineages and through time -- is critical to the testing of many hypotheses about macroevolutionary processes. BAMM is a flexible Bayesian framework for inferring the number and location of shifts in macroevolutionary rate across phylogenetic trees and has been widely used in empirical studies. BAMM requires that researchers specify a prior probability distribution on the number of diversification rate shifts before conducting an analysis. The consequences of this "model prior" for inference are poorly known but could potentially influence both the probability of accepting models that are more (high error rate) or less (low power) complex than the generating model. 2. The hierarchical Poisson process prior in BAMM reduces to a simple geometric distribution on number of rate shifts and we use this property to increase the efficiency of model selection with Bayes factors. Using BAMM v2.5, we analyzed phylogenies simulated with and without diversification heterogeneity across a broad range of prior parameterizations. We also assessed the impact of the model prior on MCMC convergence times and on diversification rate estimates. 3. For all simulation scenarios, model evidence (Bayes factor support) for the number of shifts is not sensitive to the choice of model prior over the wide range examined here. The best-supported model found using BAMM rarely includes spurious shifts (<2% of all runs) when diversification models are selected using Bayes factors. BAMM was reliably able to infer the true number of diversification rate shifts across prior expectations that varied by three orders of magnitude. However, we find a strong effect of model prior on MCMC convergence properties: a flatter prior distribution (larger expected number of shifts) can dramatically increase the efficiency of the MCMC simulation. 4. Our results support the use of a liberal model prior in BAMM, as it reduces computation time without distorting the evidence for rate heterogeneity.
Data from: Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events
Background and Aims Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. Methods We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of individually analysed 48 tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. Key results Brassicaceae diverged 29.9 Mya during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. Conclusions The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant "pump" for continuous and high species diversification.
Data from: Detecting hidden diversification shifts in models of trait-dependent speciation and extinction
The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.
Data from: Bayesian model selection with BAMM: effects of the model prior on the inferred number of diversification shifts
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