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119 results for “lineage diversification”
Data from: Diversification of Hawaiian Cyrtandra (Gesneriaceae) under the influence of incomplete lineage sorting and hybridization
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Data from: Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. I. Historical biogeography
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Data from: Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage
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Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
Data from: Early diversification trend and Asian origin for extant bat lineages
Bats are a unique mammalian group, which belong to one of the largest and most diverse mammalian radiations, but their early diversification is still poorly understood, and conflicting hypotheses have emerged regarding their biogeographic history. Understanding their diversification is crucial for untangling the enigmatic evolutionary history of bats. In this study, we elucidated the rate of diversification and the biogeographic history of extant bat lineages using genus-level chronograms. The results suggest that a rapid adaptive radiation persisted from the emergence of crown bats until the Early Eocene Climatic Optimum, whereas there was a major deceleration in diversification around 35–49 Ma. There was a positive association between changes in the palaeotemperature and the net diversification rate until 35 Ma, which suggests that the palaeotemperature may have played an important role in the regulation of ecological opportunities. By contrast, there were unexpectedly higher diversification rates around 25–35 Ma during a period characterized by intense and long-lasting global cooling, which implies that intrinsic innovations or adaptations may have released some lineages from the intense selective pressures associated with these severe conditions. Our reconstruction of the ancestral distribution suggests an Asian origin for bats, thereby indicating that the current panglobal but disjunct distribution pattern of extant bats may be related to events involving seriate cross-continental dispersal and local extinction, as well as the influence of geological events and the expansion and contraction of megathermal rainforests during the Tertiary.
Data from: Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms
Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that – at least for these genera with the currently available data – dioecy neither consistently places a strong brake on diversification nor is a strong driver.
Data from: FiSSE: A simple non-parametric test for the effects of a binary character on lineage diversification rates
It is widely assumed that phenotypic traits can influence rates of speciation and extinction, and several statistical approaches have been used to test for correlations between character states and lineage diversification. Recent work suggests that model-based tests of state-dependent speciation and extinction are sensitive to model inadequacy and phylogenetic pseudoreplication. We describe a simple non-parametric statistical test ("FiSSE") to assess the effects of a binary character on lineage diversification rates. The method involves computing a test statistic that compares the distributions of branch lengths for lineages with and without a character state of interest. The value of the test statistic is compared to a null distribution generated by simulating character histories on the observed phylogeny. Our tests show that FiSSE can reliably infer trait-dependent speciation on phylogenies of several hundred tips. The method has low power to detect trait-dependent extinction but can infer state-dependent differences in speciation even when net diversification rates are constant. We assemble a range of macroevolutionary scenarios that are problematic for likelihood-based methods, and we find that FiSSE does not show similarly elevated false positive rates. We suggest that non-parametric statistical approaches, such as FiSSE, provide an important complement to formal process-based models for trait-dependent diversification.
Data from: Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible Onagraceae lineages
A major goal of evolutionary biology is to identify key evolutionary transitions that correspond with shifts in speciation and extinction rates. Stochastic character mapping has become the primary method used to infer the timing, nature, and number of character state transitions along the branches of a phylogeny. The method is widely employed for standard substitution models of character evolution. However, current approaches cannot be used for models that specifically test the association of character state transitions with shifts in diversification rates such as state-dependent speciation and extinction (SSE) models. Here we introduce a new stochastic character mapping algorithm that overcomes these limitations, and apply it to study mating system evolution over a time-calibrated phylogeny of the plant family Onagraceae. Utilizing a hidden state SSE model we tested the association of the loss of self-incompatibility with shifts in diversification rates. Confirming long standing theory, we found that self-compatible lineages have higher extinction rates and lower net diversification rates compared to self-incompatible lineages. Furthermore, these results provide empirical evidence for the "senescing" diversification rates predicted in highly selfing lineages: our mapped character histories show that the loss of self-incompatibility is followed by a short-term spike in speciation rates, which declines after a time lag of several million years resulting in negative net diversification. Lineages that have long been self-compatible such as Fuchsia and Clarkia are in a previously unrecognized and ongoing evolutionary decline. Our results demonstrate that stochastic character mapping of SSE models is a powerful tool for examining the timing and nature of both character state transitions and shifts in diversification rates over the phylogeny.
Fig. 1 in Diversification rates in Tardigrada indicate a decreasing tempo of lineage splitting regardless of reproductive mode
Fig. 1 Number of species/ entities delimited by tree-based and distance-based single-locus delimitation methods used in this study for three tardigrade groups: family Echiniscidae, family Macrobiotidae, genus Milnesium
Supplementary material 6 from: Singh G, Dal Grande FD, Schnitzler J, Pfenninger M, Schmitt I (2018) Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 36: 1-19. https://doi.org/10.3897/mycokeys.36.22548
Results of the linear discrimination analysis :
Supplementary material 4 from: Singh G, Dal Grande FD, Schnitzler J, Pfenninger M, Schmitt I (2018) Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 36: 1-19. https://doi.org/10.3897/mycokeys.36.22548
Global environmental zones of the Protoparmelia and Maronina species :
Supplementary material 5 from: Singh G, Dal Grande FD, Schnitzler J, Pfenninger M, Schmitt I (2018) Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 36: 1-19. https://doi.org/10.3897/mycokeys.36.22548
Results of the linear discrimination analysis :
Supplementary material 3 from: Singh G, Dal Grande FD, Schnitzler J, Pfenninger M, Schmitt I (2018) Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 36: 1-19. https://doi.org/10.3897/mycokeys.36.22548
Genetic characteristics of nuclear loci used in this study :
Supplementary material 2 from: Singh G, Dal Grande FD, Schnitzler J, Pfenninger M, Schmitt I (2018) Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 36: 1-19. https://doi.org/10.3897/mycokeys.36.22548
Voucher information :
Supplementary material 1 from: Singh G, Dal Grande FD, Schnitzler J, Pfenninger M, Schmitt I (2018) Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 36: 1-19. https://doi.org/10.3897/mycokeys.36.22548
Distribution of Protoparmelia and Maronina species. :
Figure 2 from: Singh G, Dal Grande FD, Schnitzler J, Pfenninger M, Schmitt I (2018) Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 36: 1-19. https://doi.org/10.3897/mycokeys.36.22548
Figure 2 Ancestral states in Protoparmelioideae: Chronogram based on a six-locus dataset, dataset 2 (Singh et al. 2017), representing a species tree of Protoparmelioideae showing the ancestral states at nodes of interest. The topology is derived from the *BEAST species tree. A consensus tree was generated in TreeAnnotator. The current substrate of each species is indicated by the coloured circles in front of the name of the species. Polymorphic taxa have more than one coloured circle. Nodes at which ancestral states are reconstructed are numbered from 1 to 5. Pie charts indicate probabilities of each ancestor being in each of the two potential states at nodes of interest. The circles above the node represent bootstrap support for each character state and the circles at the bottom represent the posterior probability. A) Ancestral habitat: cold (blue), warm (red) and B) Ancestral substrate: rock (brown), bark (green).
Figure 1 from: Singh G, Dal Grande FD, Schnitzler J, Pfenninger M, Schmitt I (2018) Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 36: 1-19. https://doi.org/10.3897/mycokeys.36.22548
Figure 1 Time-calibrated phylogeny of the major lineages of Lecanorales (Lecanoraceae, Parmeliaceae, Ramboldiaceae, and Gypsoplacaceae), based on a six-locus dataset, dataset 1 (Singh et al. 2015). Cladoniaceae was used as outgroup (Arup et al. 2007, Singh et al. 2013). Mean node age, 95% highest posterior density (HPD) and posterior probability (PP) were mapped on the maximum clade credibility tree. The red circle indicates the calibration point, i.e. the split between Protoparmelioideae and Parmelioideae. Only the strongly supported nodes were considered for divergence time estimates. Geological times are indicated at the axis of the tree. The number of specimens per species is indicated in brackets in front of the taxon names. The scale at the bottom of the tree represents age in millions of years (Ma). Parmelioideae, Gypsoplacaceae, Cladoniaceae, Ramboldiaceae and Lecanoraceae clades are collapsed. In Parmelioideae, Miriquidica and Protoparmelia s. l. clades are collapsed at the species level.
Figs. 35–36 in Egg Hatch and First Instar of Semijulistus spectabilis (Lewis) (Coleoptera: Rhadalidae) and Diversification of the Ontogenic Development of the Melyrid Lineage
Figs. 35–36. Flow diagrams of growth patterns. 35) Melyrid lineage; 36) Malachiines.
Data from: How well can we detect lineage-specific diversification-rate shifts? A simulation study of sequential AIC methods
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Data from: Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms
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