Diversification rates and the latitudinal gradient of diversity in mammals

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.

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

10.1101/555805 ◽

2019 ◽

Cited By ~ 6

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.

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Diversification rates and species richness across the Tree of Life

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.1334 ◽

2016 ◽

Vol 283 (1838) ◽

pp. 20161334 ◽

Cited By ~ 52

Author(s):

Joshua P. Scholl ◽

John J. Wiens

Keyword(s):

Species Richness ◽

Positive Relationship ◽

Tree Of Life ◽

Diversification Rate ◽

Substantial Variation ◽

Diversification Rates ◽

Higher Taxa ◽

Over Time

Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies.

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Freshwater-to-marine transitions may explain the evolution of herbivory in the subgenus Mollienesia (genus Poecilia, mollies and guppies)

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz045 ◽

2019 ◽

Vol 127 (4) ◽

pp. 742-761 ◽

Cited By ~ 1

Author(s):

Jessica L Sanchez ◽

Heather D Bracken-Grissom ◽

Joel C Trexler

Keyword(s):

Independent Contrasts ◽

Diversification Rates ◽

Ecosystem Boundaries ◽

Evolutionary Diversification ◽

Dietary Preferences ◽

Phylogenetically Independent Contrasts ◽

Habitat Transition ◽

Saline Habitats

Abstract The ability of organisms to cross ecosystem boundaries is an important catalyst of evolutionary diversification. The genus Poecilia (mollies and guppies) is an excellent system for studying ecosystem transitions because species display a range of salinity and dietary preferences, with herbivory concentrated in the subgenus Mollienesia. We reconstructed ancestral habitats and diets across a phylogeny of the genus Poecilia, evaluated diversification rates and used phylogenetically independent contrasts to determine whether diet evolved in response to habitat transition in this group. The results suggest that ancestors of subgenus Mollienesia were exclusively herbivorous, whereas ancestral diets of other Poecilia included animals. We found that transitions across euryhaline boundaries occurred at least once in this group, probably after the divergence of the subgenus Mollienesia. Furthermore, increased salinity affiliation explained 24% of the decrease in animals in the gut, and jaw morphology was associated with the percentage of animals in the gut, but not with the percentage of species occupying saline habitats. These findings suggest that in the genus Poecilia, herbivory evolved in association with transitions from fresh to euryhaline habitats, and jaw morphology evolved in response to the appearance of herbivory. These results provide a rare example of increased diet diversification associated with the transition from freshwater to euryhaline habitats.

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Ecological Specialization and Diversification in Birds

10.1101/2020.06.13.142703 ◽

2020 ◽

Author(s):

Nicholas M. A. Crouch ◽

Robert E. Ricklefs ◽

Boris Igić

Keyword(s):

Species Richness ◽

Ecological Specialization ◽

Diversification Rates ◽

Speciation Rate ◽

Extinction Rates ◽

Allopatric Species ◽

Species Formation ◽

Geographic Distributions ◽

Local Ecology ◽

Lineage Diversification

AbstractEcological specialization is widely thought to influence patterns of species richness by affecting rates at which species multiply and perish. Quantifying specialization is challenging, and using only one or a small number of ecological axes could bias estimates of overall specialization. Here, we calculate an index of specialization, based on seven measured traits, and estimate its effect on speciation and extinction rates in a large clade of birds. We find that speciation rate is independent of specialization, suggesting independence of local ecology and the geographic distributions of populations that promote allopatric species formation. Although some analyses suggest that more specialized species have higher extinction rates, leading to negative net diversification, this relationship is not consistently identified across our analyses. Our results suggest that specialization may drive diversification dynamics only on local scales or in specific clades, but is not generally responsible for macroevolutionary disparity in lineage diversification rates.

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Settling down of seasonal migrants promotes bird diversification

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.0473 ◽

2014 ◽

Vol 281 (1784) ◽

pp. 20140473 ◽

Cited By ~ 43

Author(s):

Jonathan Rolland ◽

Frédéric Jiguet ◽

Knud Andreas Jønsson ◽

Fabien L. Condamine ◽

Hélène Morlon

Keyword(s):

Species Richness ◽

Sedentary Behaviour ◽

Evolutionary History ◽

Seasonal Migration ◽

Migratory Behaviour ◽

Migratory Species ◽

Diversification Rates ◽

Extinction Rates ◽

History Of ◽

Daughter Species

How seasonal migration originated and impacted diversification in birds remains largely unknown. Although migratory behaviour is likely to affect bird diversification, previous studies have not detected any effect. Here, we infer ancestral migratory behaviour and the effect of seasonal migration on speciation and extinction dynamics using a complete bird tree of life. Our analyses infer that sedentary behaviour is ancestral, and that migratory behaviour evolved independently multiple times during the evolutionary history of birds. Speciation of a sedentary species into two sedentary daughter species is more frequent than speciation of a migratory species into two migratory daughter species. However, migratory species often diversify by generating a sedentary daughter species in addition to the ancestral migratory one. This leads to an overall higher migratory speciation rate. Migratory species also experience lower extinction rates. Hence, although migratory species represent a minority (18.5%) of all extant birds, they have a higher net diversification rate than sedentary species. These results suggest that the evolution of seasonal migration in birds has facilitated diversification through the divergence of migratory subpopulations that become sedentary, and illustrate asymmetrical diversification as a mechanism by which diversification rates are decoupled from species richness.

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Pulled Diversification Rates, Lineage-Through-Time Plots and Modern Macroevolutionary Modelling

10.1101/2021.01.04.424672 ◽

2021 ◽

Author(s):

Andrew J. Helmstetter ◽

Sylvain Glemin ◽

Jos Käfer ◽

Rosana Zenil-Ferguson ◽

Hervé Sauquet ◽

...

Keyword(s):

Infinite Number ◽

Scientific Community ◽

Phylogenetic Trees ◽

Data Availability ◽

Time Dependent ◽

Evolutionary Processes ◽

Diversification Rates ◽

Extinction Rates ◽

Extant Species ◽

Technical Considerations

AbstractEstimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenies, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineage-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models and inferences to disentangle diversification histories. Using simulations we demonstrate the characteristics of pulled diversification rates and their utility. We recognize the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenies has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.

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

10.1101/016386 ◽

2015 ◽

Cited By ~ 4

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.

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Pulled Diversification Rates, Lineages-Through-Time Plots and Modern Macroevolutionary Modelling

Systematic Biology ◽

10.1093/sysbio/syab083 ◽

2021 ◽

Author(s):

Andrew J Helmstetter ◽

Sylvain Glemin ◽

Jos Käfer ◽

Rosana Zenil-Ferguson ◽

Herv Sauquet ◽

...

Keyword(s):

Infinite Number ◽

Scientific Community ◽

Phylogenetic Trees ◽

Data Availability ◽

Time Dependent ◽

Evolutionary Processes ◽

Diversification Rates ◽

Extinction Rates ◽

Extant Species ◽

Technical Considerations

Abstract Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we illustrate the characteristics of newly-proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community.

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Can net diversification rates account for spatial patterns of species richness?

10.1101/240978 ◽

2017 ◽

Author(s):

Camilo Sanín ◽

Iván Jiménez ◽

Jon Fjeldså ◽

Carsten Rahbek ◽

Carlos Daniel Cadena

Keyword(s):

Species Richness ◽

Spatial Variation ◽

Spatial Patterns ◽

Explanatory Power ◽

Large Family ◽

Diversification Rate ◽

Diversification Rates ◽

Grain Sizes ◽

Time Period ◽

Richness Patterns

ABSTRACTThe diversification rate hypothesis (DRH) proposes that spatial patterns of species richness result from spatial variation in net diversification rates. We developed an approach using a time-calibrated phylogeny and distributional data to estimate the maximum explanatory power of the DRH, over a given time period, to current species richness in an area. We used this approach to study species richness patterns of a large family of suboscine birds across South America. The maximum explanatory power of the DRH increased with the duration of the time period considered and grain size; it ranged from 13 – 37 fold local increases in species richness for T = 33 Ma to less than 2-fold increases for T ≤ 10 Ma. For large grain sizes (≤ 8° × 8°) diversification rate over the last 10 Ma could account for all the spatial variance in species richness, but for smaller grain sizes commonly used in biogeographical studies (1° × 1°), it could only explain < 16% of this variance. Thus, diversification since the Late Miocene, often thought to be a major determinant of Neotropical diversity, had a limited imprint on spatial richness patterns at small grain sizes. Further application of our approach will help determine the role of the DRH in explaining current spatial patterns of species richness.Note to readersThis manuscript has been seen by a few researchers, some of whom suggested that before publishing our work in a peer-reviewed journal we should conduct simulations to demonstrate that our methods properly estimate the contribution of variance in diversification rates to spatial variation in species richness. Although we believe that our approach derives logically from theory and statistics and is therefore valid, we understand that it is rather unique and see why some readers would think that an independent validation is necessary. Unable to complete such validation in the near future, however, we decided to make this manuscript available as a preprint to share our ideas and hopefully stimulate discussion on what we believe is a most interesting topic. We also hope to receive feedback that may enable us to improve our work for publication in a journal at a later date.

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Diversification, sympatry, and the emergence of mega-diverse tropical assemblages

10.1101/238329 ◽

2017 ◽

Author(s):

Jacob B. Socolar ◽

Alexander C. Lees

Keyword(s):

Species Richness ◽

Species Coexistence ◽

Sympatric Species ◽

Latitudinal Gradients ◽

Evolutionary Patterns ◽

Multiple Timescales ◽

Diversification Rates ◽

Evolutionary Diversification ◽

Extinction Rates ◽

High Diversity

ABSTRACTGeographic gradients in species richness, including latitudinal gradients, can arise from geographic variation in any of three mechanisms: the geologic age of habitats, net rates of evolutionary diversification, or rates of sympatry among diversifying lineages. Here we show that variation in rates of sympatry is a dominant force structuring geographic richness gradients in birds. Species-rich sites contain disproportionately high numbers of recently diverged sympatric species but contain lineages with slower-than-average diversification rates. The positive sympatry-diversity relationship consistently overwhelms the negative diversification-diversity relationship, particularly among high-diversity sites (>250 species). These patterns repeat across biomes and continents with striking regularity, and remain consistent across multiple timescales, including the recent evolutionary past. Biogeographic and evolutionary patterns in birds are consistent with a role for ecological conditions in promoting species coexistence, which allows sister species to co-occur and potentially lowers extinction rates.

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