scholarly journals The Evolution of Nest Site Specialization and its Macroevolutionary Consequences in Passerine Birds

2021 ◽  
Author(s):  
Rosana Zenil-Ferguson ◽  
Jay P McEntee ◽  
John Gordon Burleigh ◽  
Renee A Duckworth
Keyword(s):  
Nest Site ◽  
Comparative Methods ◽  
Diversification Rate ◽  
Extinction Rate ◽  
Passerine Birds ◽  
Evolutionary Transitions ◽  
Background Rate ◽  
Diversification Rates ◽  
Resource Specialization ◽  
Dead End

A long-standing hypothesis in evolutionary biology is that the evolution of resource specialization can lead to an evolutionary dead end, where specialists have low diversification rates and limited ability to evolve into generalists. However, in recent years, advances in comparative methods investigating trait-based differences associated with diversification have enabled more robust tests of this idea and have found mixed support. Here we test the evolutionary dead end hypothesis by estimating net diversification rate differences associated with nest site specialization among 3,224 species of passerine birds. In particular, we test whether the adoption of hole-nesting, a nest site specialization that decreases predation, results in reduced diversification rates relative to nesting outside of holes. Further, we examine whether evolutionary transitions to the specialist hole-nesting state have been more frequent than transitions out of hole-nesting. Using diversification models that accounted for background rate heterogeneity and different extinction rate scenarios, we found that hole-nesting specialization was not associated with diversification rate differences. Furthermore, contrary to the assumption that specialists rarely evolve into generalists, we found that transitions out of hole-nesting occur more frequently than transitions into hole-nesting. These results suggest that interspecific competition may limit adoption of hole-nesting, but that such competition does not result in limited diversification of hole-nesters. In conjunction with other recent studies using robust comparative methods, our results add to growing evidence that evolutionary dead ends are not a typical outcome of resource specialization.

scholarly journals Tip rates, phylogenies, and diversification: what are we estimating, and how good are the estimates?

2018 ◽  
Author(s):  
Pascal O. Title ◽  
Daniel L. Rabosky
Keyword(s):  
Diversification Rate ◽  
Rate Variation ◽  
Terminal Branch ◽  
List Type ◽  
Large Set ◽  
Extinction Rate ◽  
Diversification Rates ◽  
Speciation Rate ◽  
Model Based ◽  
Model Free

AbstractSpecies-specific diversification rates, or “tip rates”, can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology, and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait-dependent diversification studies. However, there is substantial confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics across simulated diversification scenarios.We compared the statistical performance of three model-free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model-based approach (BAMM). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes; scenarios included multi-regime time-constant and diversity-dependent trees, as well as trees where the rate of speciation evolves under a diffusion process. We summarized performance in relation to the type of rate variation, the magnitude of rate heterogeneity and rate regime size. We also compared the ability of the metrics to estimate both speciation and net diversification rates.We show decisively that model-free tip rate metrics provide a better estimate of the rate of speciation than of net diversification. Error in net diversification rate estimates increases as a function of the relative extinction rate. In contrast, error in speciation rate estimates is low and relatively insensitive to extinction. Overall, and in particular when relative extinction was high, BAMM inferred the most accurate tip rates and exhibited lower error than non-model-based approaches. DR was highly correlated with true speciation rates but exhibited high error variance, and was the best metric for very small rate regimes.We found that, of the metrics tested, DR and BAMM are the most useful metrics for studying speciation rate dynamics and trait-dependent diversification. Although BAMM was more accurate than DR overall, the two approaches have complementary strengths. Because tip rate metrics are more reliable estimators of speciation rate, we recommend that empirical studies using these metrics exercise caution when drawing biological interpretations in any situation where the distinction between speciation and net diversification is important.

scholarly journals ACDC: Analysis of Congruent Diversification Classes

2022 ◽  
Author(s):  
Sebastian Hoehna ◽  
Bjoern Tore Kopperud ◽  
Andrew F Magee
Keyword(s):  
Congruence Class ◽  
R Package ◽  
Rate Function ◽  
Diversification Rate ◽  
Extinction Rate ◽  
Diversification Rates ◽  
Common Features ◽  
Alternative Hypotheses ◽  
Rate Functions ◽  
Congruence Classes

Diversification rates inferred from phylogenies are not identifiable. There are infinitely many combinations of speciation and extinction rate functions that have the exact same likelihood score for a given phylogeny, building a congruence class. The specific shape and characteristics of such congruence classes have not yet been studied. Whether speciation and extinction rate functions within a congruence class share common features is also not known. Instead of striving to make the diversification rates identifiable, we can embrace their inherent non-identifiable nature. We use two different approaches to explore a congruence class: (i) testing of specific alternative hypotheses, and (ii) randomly sampling alternative rate function within the congruence class. Our methods are implemented in the open-source R package ACDC (https://github.com/afmagee/ACDC). ACDC provides a flexible approach to explore the congruence class and provides summaries of rate functions within a congruence class. The summaries can highlight common trends, i.e. increasing, flat or decreasing rates. Although there are infinitely many equally likely diversification rate functions, these can share common features. ACDC can be used to assess if diversification rate patterns are robust despite non-identifiability. In our example, we clearly identify three phases of diversification rate changes that are common among all models in the congruence class. Thus, congruence classes are not necessarily a problem for studying historical patterns of biodiversity from phylogenies.

scholarly journals Explaining large-scale patterns of vertebrate diversity

2015 ◽  
Vol 11 (7) ◽  
pp. 20150506 ◽  
Author(s):  
John J. Wiens
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Metabolic Rates ◽  
Diversification Rates ◽  
Richness Patterns ◽  
Current Species

The major clades of vertebrates differ dramatically in their current species richness, from 2 to more than 32 000 species each, but the causes of this variation remain poorly understood. For example, a previous study noted that vertebrate clades differ in their diversification rates, but did not explain why they differ. Using a time-calibrated phylogeny and phylogenetic comparative methods, I show that most variation in diversification rates among 12 major vertebrate clades has a simple ecological explanation: predominantly terrestrial clades (i.e. birds, mammals, and lizards and snakes) have higher net diversification rates than predominantly aquatic clades (i.e. amphibians, crocodilians, turtles and all fish clades). These differences in diversification rates are then strongly related to patterns of species richness. Habitat may be more important than other potential explanations for richness patterns in vertebrates (such as climate and metabolic rates) and may also help explain patterns of species richness in many other groups of organisms.

scholarly journals Dynamical analysis of the global elevational diversity gradient in passerine birds reveals a prominent role for highlands as species pumps

2020 ◽  
Author(s):  
Paul van Els ◽  
Leonel Herrera-Alsina ◽  
Alex L. Pigot ◽  
Rampal Etienne
Keyword(s):  
Evolutionary Dynamics ◽  
Strong Support ◽  
High Elevation ◽  
Dynamical Analysis ◽  
Reverse Direction ◽  
Passerine Birds ◽  
Diversification Rates ◽  
Diversity Gradient ◽  
As Species ◽  
Almost All

Abstract Low elevation regions harbor the majority of the world’s species diversity compared to high elevation areas. This global elevational diversity gradient, suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands (either due to higher ecological limits or intrinsically higher diversification rates). However, highlands seem to be cradles of diversity as they contain many young endemics, suggesting that their rates of speciation are exceptionally fast. Here, we use a phylogenetic diversification model that accounts for the dispersal of species between different elevations to examine the evolutionary dynamics of the elevational diversity gradient in passerine birds, a group that has radiated globally to occupy almost all elevations and latitudes. We find strong support for a model where passerines diversify at the same rate in the highlands and the lowlands but where the rate of dispersal from high to low elevations is more than twice as fast as in the reverse direction. This suggests that while there is no consistent trend in diversification across elevations, highland regions act as species pumps because the diversity they generate migrates into the lowlands, thus setting up the observed gradient in passerine diversity. This species pump is particularly strong in the tropics, where the inferred rate of speciation is 1.4 times faster than in the temperate zone. We conclude that despite their lower diversity, highland regions are disproportionally important for maintaining diversity in the adjacent lowlands. The extinction of species in the tropical highlands due to rapid climate change this century could thus have major and long-lasting impacts on global passerine diversity.

scholarly journals Diversification rates and species richness across the Tree of Life

2016 ◽  
Vol 283 (1838) ◽  
pp. 20161334 ◽  
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.

scholarly journals A Bayesian Approach for Detecting Mass-Extinction Events When Rates of Lineage Diversification Vary

2015 ◽  
Author(s):  
Michael R. May ◽  
Sebastian Höhna ◽  
Brian R. Moore
Keyword(s):  
Mass Extinction ◽  
Process Model ◽  
Sequence Data ◽  
Diversification Rate ◽  
Rate Variation ◽  
Specific Rate ◽  
Extinction Rate ◽  
Molecular Sequence Data ◽  
Extinction Events ◽  
Mass Extinction Events

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 mass-extinction events from phylogenies estimated from molecular sequence data. We develop our approach in a Bayesian statistical framework, which enables us to harness prior information on the frequency and magnitude of mass-extinction events. The approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between rate-shift events. We model three types of events: (1) instantaneous tree-wide shifts in speciation rate; (2) instantaneous tree-wide shifts in extinction rate, and; (3) instantaneous tree-wide mass-extinction events. Each of the events is described by a separate compound Poisson process (CPP) model, where the waiting times between each event are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-type specific prior distribution. Parameters of the model are then estimated using a reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events, provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e., below 5%) false discovery rate even in the case of background diversification rate variation. Finally, we provide an empirical application of this approach to conifers, which reveals that this group has experienced two major episodes of mass extinction. This new approach?the CPP on Mass Extinction Times (CoMET) model?provides an effective tool for identifying mass-extinction events from molecular phylogenies, even when the history of those groups includes more prosaic temporal variation in diversification rate.

scholarly journals Seed plant families with diverse mycorrhizal states have higher diversification rates

2019 ◽  
Author(s):  
María Isabel Mujica ◽  
Gustavo Burin ◽  
María Fernanda Pérez ◽  
Tiago Quental
Keyword(s):  
Soil Fungi ◽  
Plant Evolution ◽  
Ancestral State ◽  
Seed Plant ◽  
Plant Family ◽  
Symbiotic Interaction ◽  
Evolutionary Transitions ◽  
Diversification Rates ◽  
Plant Families ◽  
The Relationship

AbstractA crucial innovation in plant evolution was the association with soil fungi during land colonization. Today, this symbiotic interaction is present in most plants species and can be classified in four types: arbuscular (AM), Ecto (EM), Orchid (OM) and Ericoid Mycorrhiza (ER). Since the AM ancestral state, some plants lineages have switched partner (EM, OM and ER) or lost the association (no-association: NM). Evolutionary transitions to a novel mycorrhizal state (MS) might allow plant lineages to access new resources, enhancing diversification rates. However, some clades are not restricted to one MS, and this variability might promote diversification. In this study we address the relationship between MS and diversification rates of seed plant families. For this, we used the recently published FungalRoot database, which compiled data for 14,870 species and their mycorrhizal partners. We assigned a MS to each plant family, calculated the MS heterogeneity and estimated their diversification rates using the method-of-moments. Families with mixed MS had the highest diversification rates and there was a positive relationship between MS heterogeneity and diversification rates. These results support the hypothesis that MS lability promotes diversification and highlight the importance of the association with soil fungi for the diversification of plants.

scholarly journals Shifts in diversification rates and host jump frequencies shaped the diversity of host range amongSclerotiniaceaefungal plant pathogens

2017 ◽  
Author(s):  
Olivier Navaud ◽  
Adelin Barbacci ◽  
Andrew Taylor ◽  
John P. Clarkson ◽  
Sylvain Raffaele
Keyword(s):  
Host Range ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Dominant Mode ◽  
Diversification Rate ◽  
Broad Host Range ◽  
Diversification Rates ◽  
Host Jump ◽  
Duplication Events ◽  
Range Variation

AbstractThe range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within theSclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in theSclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Consistent with previous reports on oomycete parasites, our findings suggest that host jump and radiation, possibly combined with low speciation rates, could associate with the emergence of generalist pathogens. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.

scholarly journals Rapid speciation and karyotype evolution in Orthoptera

2021 ◽  
Author(s):  
Octavio Manuel Palacios-Gimenez
Keyword(s):  
Karyotype Evolution ◽  
Evolutionary Model ◽  
Chromosomal Evolution ◽  
High Rate ◽  
Recent Common Ancestor ◽  
Extinction Rate ◽  
Background Rate ◽  
Speciation Rate ◽  
Most Recent Common Ancestor ◽  
Karyotypic Diversity

To test the hypothesis that high speciation rate in groups is coupled with high rate of karyotype evolution but also that younger groups having a higher rate of karyotypic diversity, I estimated rates of speciation and rates of karyotype evolution in 1,177 species belonging to 26 families in the insect order Orthoptera. Rates of karyotype evolution were estimated using the diploid number and the number of chromosome arms (fundamental number) from published karyotypes of Orthoptera. Rates of speciation were quantified considering the number of species examined karyotypically in each family, the most recent common ancestor of each family and the information about extinction rate. The rate of speciation was strongly correlated with rate of karyotype evolution and the average rates of speciation was nearly ~177 times higher than the background rate estimated for Orthoptera based on acoustic communication using phylogenomic data, as well as 8.4 and 35.6 times higher than the estimated speciation rate in vertebrates and bivalve mollusks respectively, indicating that Orthoptera has evolved very fast at chromosomal level. The findings supported the hypothesis of a high speciation rate in lineages with high rate of chromosomal evolution but there were not evidences that younger groups tended to have higher rate of karyotypic diversity. Furthermore, rates of karyotype evolution most closely fitted the punctuational evolutionary model indicating the existence of long periods of stasis of karyotype change with most karyotype change occurring quickly over short evolutionary times. I discussed genetic drift, divergent selection and meiotic drive as potential biological mechanisms to explain karyotype evolution allowing or impeding for the fixation of chromosomal rearrangements and in turn speciation in orthopterans lineages.

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