scholarly journals Detecting hidden diversification shifts in models of trait-dependent speciation and extinction

2015 ◽  
Author(s):  
Jeremy M Beaulieu ◽  
Brian C O'Meara
Keyword(s):  
Empirical Data ◽  
Diversification Rate ◽  
Transition Rates ◽  
Diversification Rates ◽  
Extinction Rates ◽  
State Dependent ◽  
Speciation Rates ◽  
Nuanced Understanding ◽  
Hidden States ◽  
Major Criticism

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 their 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 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 (CID) 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.

scholarly journals How humans drive speciation as well as extinction

2016 ◽  
Vol 283 (1833) ◽  
pp. 20160600 ◽  
Author(s):  
J. W. Bull ◽  
M. Maron
Keyword(s):  
Species Diversity ◽  
Human Activities ◽  
Rapid Evolution ◽  
Novel Ecosystem ◽  
No Net Loss ◽  
Extinction Rates ◽  
Trade Offs ◽  
Speciation Rates ◽  
Nuanced Understanding ◽  
Comparable Magnitude

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation—and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature—considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.

scholarly journals Diversification in Monkeyflowers: An Investigation of the Effects of Elevation and Floral Color in the Genus Mimulus

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Ezgi Ogutcen ◽  
Brooklyn Hamper ◽  
Jana C. Vamosi
Keyword(s):  
High Elevation ◽  
Flowering Plant ◽  
Floral Colour ◽  
Transition Rates ◽  
Extinction Rates ◽  
Floral Color ◽  
Speciation Rates ◽  
Evolutionary Success ◽  
Plant Families ◽  
High Elevations

The vast diversity of floral colours in many flowering plant families, paired with the observation of preferences among pollinators, suggests that floral colour may be involved in the process of speciation in flowering plants. While transitions in floral colour have been examined in numerous genera, we have very little information on the consequences of floral colour transitions to the evolutionary success of a clade. Overlaid upon these patterns is the possibility that certain floral colours are more prevalent in certain environments, with the causes of differential diversification being more directly determined by geographical distribution. Here we examine transition rates to anthocyanin + carotenoid rich (red/orange/fuschia) flowers and examine whether red/orange flowers are associated with differences in speciation and/or extinction rates in Mimulus. Because it has been suggested that reddish flowers are more prevalent at high elevation, we also examine the macroevolutionary evidence for this association and determine if there is evidence for differential diversification at high elevations. We find that, while red/orange clades have equivalent speciation rates, the trait state of reddish flowers reverts more rapidly to the nonreddish trait state. Moreover, there is evidence for high speciation rates at high elevation and no evidence for transition rates in floral colour to differ depending on elevation.

scholarly journals Diatoms diversify and turn over faster in freshwater than marine environments

2018 ◽  
Author(s):  
Teofil Nakov ◽  
Jeremy Michael Beaulieu ◽  
Andrew James Alverson
Keyword(s):  
Turnover Rate ◽  
Turnover Rates ◽  
High Turnover ◽  
Diversification Rates ◽  
Extinction Rates ◽  
State Dependent ◽  
Freshwater Diatoms ◽  
Marine Realm ◽  
Turn Over ◽  
Freshwater Environments

AbstractMany clades that span the marine-freshwater boundary are disproportionately more diverse in the younger, shorter-lived, and scarcer freshwater environments than they are in the marine realm. This disparity is thought to be related to differences in diversification rates between marine and freshwater lineages. However, marine and freshwaters are not ecologically homogeneous, so the study of diversification across the salinity divide should also account for other potentially interacting variables. In diatoms, freshwater and substrate-associated (benthic) lineages are several-fold more diverse than their marine and suspended (planktonic) counterparts. These imbalances provide an excellent system to understand whether these variables interact with diversification. Using multistate hidden-state speciation and extinction models we found that freshwater lineages diversify faster than marine lineages regardless of whether they inhabit the plankton or the benthos. Freshwater lineages also had higher turnover rates (speciation + extinction), suggesting that habitat transitions impact speciation and extinction rates jointly. The plankton-benthos contrast was also consistent with state-dependent diversification, but with modest differences in diversification and turnover rates. Asymmetric, and bidirectional transitions rejected hypotheses about the plankton and freshwaters as absorbing, inescapable habitats. Our results further suggest that the high turnover rate of freshwater diatoms is related to high turnover of freshwater systems themselves.

scholarly journals Hybridizing salamanders experience accelerated diversification

2019 ◽  
Author(s):  
Austin H. Patton ◽  
Mark J. Margres ◽  
Brendan Epstein ◽  
Jon Eastman ◽  
Luke J. Harmon ◽  
...  
Keyword(s):  
Species Diversity ◽  
Strong Evidence ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Speciation Rates ◽  
Evolutionary Role ◽  
Taxonomic Order

ABSTRACTWhether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.

scholarly journals Diversification dynamics of hypermetamorphic blister beetles (Meloidae): Are homoplastic host shifts and phoresy key factors of a rushing forward strategy to escape extinction?

2021 ◽  
Author(s):  
E.K. López-Estrada ◽  
I. Sanmartín ◽  
J.E. Uribe ◽  
S. Abalde ◽  
M. García-París
Keyword(s):  
Life History ◽  
Life Cycle ◽  
Life History Traits ◽  
Complex Life Cycle ◽  
Life Strategies ◽  
Diversification Rates ◽  
Host Shifts ◽  
Extinction Rates ◽  
State Dependent ◽  
History Of

ABSTRACTChanges in life history traits, including reproductive strategies or host shifts, are often considered triggers of speciation, affecting diversification rates. Subsequently, these shifts can have dramatic effects on the evolutionary history of a lineage. In this study, we examine the consequences of changes in life history traits, in particular host-type and phoresy, within the hypermetamorphic clade of blister beetles (Meloidae). This clade exhibits a complex life cycle involving multiple metamorphoses and parasitoidism. Most tribes within the clade are bee-parasitoids, phoretic or non-phoretic, while two tribes feed on grasshopper eggs. Species richness differs greatly between bee and grasshopper specialist clades, and between phoretic and non-phoretic genera. We generated a mitogenomic phylogeny of the hypermetamorphic clade of Meloidae, including 21 newly generated complete mitogenomes. The phylogeny and estimated lineage divergence times were used to explore the association between diversification rates and changes in host specificity and phoresy, using State-Dependent Speciation and Extinction (SSE) models, while accounting for hidden factors and phylogenetic uncertainty within a Bayesian framework. The ancestor of the hypermetamorphic Meloidae was a non-phoretic bee-parasitoid, and independent transitions towards phoretic bee-parasitoidism or grasshopper specialization occurred multiple times. Bee-parasitoid lineages that are non-phoretic have significantly higher relative extinction rates and lower diversification rates than grasshopper specialists or phoretic bee-parasitoids, while no significant differences were found between the latter two strategies. This suggests that these two life strategies contributed independently to the evolutionary success of Nemognathinae and Meloinae, allowing them to escape from the evolutionary constraints imposed by their hypermetamorphic life-cycle, and that the “bee-by-crawling” strategy may be an evolutionary “dead end”. We show how SSE models can be used not only for testing diversification dependence in relation to the focal character but to identify hidden traits contributing to the diversification dynamics. The ability of blister beetles to explore new evolutionary scenarios including the development of homoplastic life strategies, are extraordinary outcomes along the evolution of a single lineage: the hypermetamorphic Meloidae.

scholarly journals Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible Onagraceae lineages

2017 ◽  
Author(s):  
William A. Freyman ◽  
Sebastian Höhna
Keyword(s):  
Time Lag ◽  
State Transitions ◽  
Character State ◽  
Self Incompatibility ◽  
Evolutionary Transitions ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Loss Of Self ◽  
State Dependent ◽  
Character Mapping

AbstractA 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. 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.

scholarly journals A Bayesian Approach for Estimating Branch-Specific Speciation and Extinction Rates

2019 ◽  
Author(s):  
Sebastian Höhna ◽  
William A. Freyman ◽  
Zachary Nolen ◽  
John P. Huelsenbeck ◽  
Michael R. May ◽  
...  
Keyword(s):  
Prior Distribution ◽  
Phylogenetic Trees ◽  
Data Augmentation ◽  
Simulated Data ◽  
Monte Carlo Sampling ◽  
Fixed Number ◽  
Diversification Rate ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Birth Death

AbstractSpecies richness varies considerably among the tree of life which can only be explained by heterogeneous rates of diversification (speciation and extinction). Previous approaches use phylogenetic trees to estimate branch-specific diversification rates. However, all previous approaches disregard diversification-rate shifts on extinct lineages although 99% of species that ever existed are now extinct. Here we describe a lineage-specific birth-death-shift process where lineages, both extant and extinct, may have heterogeneous rates of diversification. To facilitate probability computation we discretize the base distribution on speciation and extinction rates into k rate categories. The fixed number of rate categories allows us to extend the theory of state-dependent speciation and extinction models (e.g., BiSSE and MuSSE) to compute the probability of an observed phylogeny given the set of speciation and extinction rates. To estimate branch-specific diversification rates, we develop two independent and theoretically equivalent approaches: numerical integration with stochastic character mapping and data-augmentation with reversible-jump Markov chain Monte Carlo sampling. We validate the implementation of the two approaches in RevBayes using simulated data and an empirical example study of primates. In the empirical example, we show that estimates of the number of diversification-rate shifts are, unsurprisingly, very sensitive to the choice of prior distribution. Instead, branch-specific diversification rate estimates are less sensitive to the assumed prior distribution on the number of diversification-rate shifts and consistently infer an increased rate of diversification for Old World Monkeys. Additionally, we observe that as few as 10 diversification-rate categories are sufficient to approximate a continuous base distribution on diversification rates. In conclusion, our implementation of the lineage-specific birth-death-shift model in RevBayes provides biologists with a method to estimate branch-specific diversification rates under a mathematically consistent model.

scholarly journals Hidden-state-only speciation and extinction models provide accurate tip estimates of diversification rates

2021 ◽  
Author(s):  
Thais Vasconcelos ◽  
Brian C O'Meara ◽  
Jeremy M. Beaulieu
Keyword(s):  
Model Space ◽  
Comparative Methods ◽  
Character State ◽  
Large Set ◽  
Turnover Rates ◽  
Extinction Rates ◽  
State Dependent ◽  
Related Diversification ◽  
Testing Potential ◽  
Hidden States

1. State-dependent speciation and extinction (SSE) models provide a framework for testing potential correlations between the evolution of an observed trait and speciation and extinction rates. Recent expansions of these models allow for the inclusion of "hidden states" that, among other things, allow for rate heterogeneity often observed among lineages sharing a particular character state. However, in reality, multiple circumstances and interacting traits related to a focal character play a role in changing diversification dynamics of a lineage over time, restricting the use of available SSE models that require trait information to be assigned at the tips. 2. Here we introduce MiSSE, an SSE approach that infers diversification rate differences from hidden states only. It can be used similarly to other trait-free methods to estimate varying speciation, extinction, but also different functions of these parameters such as net-diversification, turnover rates, and extinction fraction. Given the size of the model space, we also describe an algorithm designed for efficiently searching through a reasonably large set of models without having to be exhaustive. 3. We compare the accuracy of rates inferred at the tips of the tree by MiSSE against popular character-free methods and demonstrate that the error associated with tip estimates is generally low. Due to certain characteristics of the SSE models, this method avoids some of the recent concerns with parameter identifiability in diversification analyses and can be used alongside regular phylogenetic comparative methods in trait-related diversification hypotheses. 4. Finally, we apply MiSSE, with a renewed focus on classic comparative methods, to understand processes happening near the present, rather than deep in the past, to examine how variation in plant height has impacted turnover rates in eucalypts, a species-rich lineage of flowering plants.

scholarly journals Diversification rates and the latitudinal gradient of diversity in mammals

2012 ◽  
Vol 279 (1745) ◽  
pp. 4148-4155 ◽  
Author(s):  
Víctor Soria-Carrasco ◽  
Jose Castresana
Keyword(s):  
Species Richness ◽  
Species Distribution ◽  
Phylogenetic Trees ◽  
Latitudinal Gradient ◽  
Diversification Rate ◽  
Independent Contrasts ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Phylogenetically Independent Contrasts ◽  
Distribution Ranges

The latitudinal gradient of species richness has frequently been attributed to higher diversification rates of tropical groups. In order to test this hypothesis for mammals, we used a set of 232 genera taken from a mammalian supertree and, additionally, we reconstructed dated Bayesian phylogenetic trees of 100 genera. For each genus, diversification rate was estimated taking incomplete species sampling into account and latitude was assigned considering the heterogeneity in species distribution ranges. For both datasets, we found that the average diversification rate was similar among all latitudinal bands. Furthermore, when we used phylogenetically independent contrasts, we did not find any significant correlation between latitude and diversification parameters, including different estimates of speciation and extinction rates. Thus, other factors, such as the dynamics of dispersal through time, may be required to explain the latitudinal gradient of diversity in mammals.

scholarly journals How important is it to consider lineage diversification heterogeneity in in macroevolutionary studies: lessons from the lizard family Liolaemidae

2019 ◽  
Author(s):  
Melisa Olave ◽  
Luciano J. Avila ◽  
Jack W. Sites ◽  
Mariana Morando
Keyword(s):  
Diversification Rates ◽  
State Dependent ◽  
The Family ◽  
Problematic Issue ◽  
Speciation Rates ◽  
Potential Risks ◽  
Species Groups ◽  
Extinction Model ◽  
Diversification Pattern ◽  
Lineage Diversification

AbstractMacroevolutionary studies commonly apply multiple models to test state-dependent diversification. These models track the association between states of interest along a phylogeny, but they do not consider whether independent shifts in character states are associated with shifts in diversification rates. This potentially problematic issue has received little theoretical attention, while macroevolutionary studies implementing such models in increasing larger scale studies continue growing. A recent macroevolutionary study has found that Andean orogeny has acted as a species pump driving diversification of the family Liolaemidae, a highly species-rich lizard family native to temperate southern South America.This study approaches a distribution-dependent hypothesis using the Geographic State Speciation and Extinction model (GeoSSE). However, more recent analyses have shown that there is a clear heterogeneous diversification pattern in the Liolaemidae, which likely biased the GeoSSE analysis. Specifically, we show here that there are two shifts to accelered speciation rates involving species groups that were classified as “Andean” in their distributions. We demonstrate that this GeoSSE result is meaningless when heterogeneous diversification rates are included. We use the lizard family Liolaemidae to demonstrate potential risks of ignoring clade-specific differences in diversification rates in macroevolutionary studies.

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