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Speciation dynamics during the global radiation of extant bats

Species richness varies widely across extant clades, but the causes of this variation remain poorly understood. We investigate the role of diversification rate heterogeneity in shaping patterns of diversity across families of extant bats. To provide a robust framework for macroevolutionary inference... Full description

Journal Title: Evolution 2015-06, Vol.69 (6), p.1528-1545
Main Author: Shi, Jeff J.
Other Authors: Rabosky, Daniel L.
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: United States: Blackwell Publishing Ltd
ID: ISSN: 0014-3820
Link: https://www.ncbi.nlm.nih.gov/pubmed/25958922
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title: Speciation dynamics during the global radiation of extant bats
format: Article
creator:
  • Shi, Jeff J.
  • Rabosky, Daniel L.
subjects:
  • Analysis
  • Animal behavior
  • Animals
  • BAMM
  • Bats
  • Bayes Theorem
  • Bayesian analysis
  • Behavior
  • Biodiversity
  • Biological diversity
  • Biological taxonomies
  • Chiroptera
  • Chiroptera - classification
  • Chiroptera - genetics
  • diversification rates
  • Ecological genetics
  • Evolution
  • Fossils
  • Genetic aspects
  • Genetic Speciation
  • macroevolution
  • Models, Genetic
  • Origin of species
  • phylogenetic imbalance
  • Phylogenetics
  • Phylogeny
  • Sequence Alignment
  • Speciation
  • Species diversity
  • Taxa
  • Time Factors
ispartof: Evolution, 2015-06, Vol.69 (6), p.1528-1545
description: Species richness varies widely across extant clades, but the causes of this variation remain poorly understood. We investigate the role of diversification rate heterogeneity in shaping patterns of diversity across families of extant bats. To provide a robust framework for macroevolutionary inference, we assemble a time-calibrated, species-level phylogeny using a supermatrix of mitochondrial and nuclear sequence data. We analyze the phylogeny using a Bayesian method for modeling complex evolutionary dynamics. Surprisingly, we find that variation in family richness can largely be explained without invoking heterogeneous diversification dynamics. We document only a single well-supported shift in diversification dynamics across bats, occurring at the base of the subfamily Stenodermatinae. Bat diversity is phylogenetically imbalanced, but—contrary to previous hypotheses—this pattern is unexplained by any simple patterns of diversification rate heterogeneity. This discordance may indicate that diversification dynamics are more complex than can be captured using the statistical tools available for modeling data at this scale. We infer that bats as a whole are almost entirely united into one macroevolutionary cohort, with decelerating speciation through time. There is also a significant relationship between clade age and richness, suggesting that global bat diversity may still be expanding.
language: eng
source:
identifier: ISSN: 0014-3820
fulltext: no_fulltext
issn:
  • 0014-3820
  • 1558-5646
url: Link


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descriptionSpecies richness varies widely across extant clades, but the causes of this variation remain poorly understood. We investigate the role of diversification rate heterogeneity in shaping patterns of diversity across families of extant bats. To provide a robust framework for macroevolutionary inference, we assemble a time-calibrated, species-level phylogeny using a supermatrix of mitochondrial and nuclear sequence data. We analyze the phylogeny using a Bayesian method for modeling complex evolutionary dynamics. Surprisingly, we find that variation in family richness can largely be explained without invoking heterogeneous diversification dynamics. We document only a single well-supported shift in diversification dynamics across bats, occurring at the base of the subfamily Stenodermatinae. Bat diversity is phylogenetically imbalanced, but—contrary to previous hypotheses—this pattern is unexplained by any simple patterns of diversification rate heterogeneity. This discordance may indicate that diversification dynamics are more complex than can be captured using the statistical tools available for modeling data at this scale. We infer that bats as a whole are almost entirely united into one macroevolutionary cohort, with decelerating speciation through time. There is also a significant relationship between clade age and richness, suggesting that global bat diversity may still be expanding.
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languageeng
publisherUnited States: Blackwell Publishing Ltd
subjectAnalysis ; Animal behavior ; Animals ; BAMM ; Bats ; Bayes Theorem ; Bayesian analysis ; Behavior ; Biodiversity ; Biological diversity ; Biological taxonomies ; Chiroptera ; Chiroptera - classification ; Chiroptera - genetics ; diversification rates ; Ecological genetics ; Evolution ; Fossils ; Genetic aspects ; Genetic Speciation ; macroevolution ; Models, Genetic ; Origin of species ; phylogenetic imbalance ; Phylogenetics ; Phylogeny ; Sequence Alignment ; Speciation ; Species diversity ; Taxa ; Time Factors
ispartofEvolution, 2015-06, Vol.69 (6), p.1528-1545
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1Fossil Calibration (Table 2) ReferencesSupplementary Figure 1: An example cohort matrix constructed using a simulated phylogeny of four taxa, separated into two clades A and B.Supplementary Figure 2: The null expectation of a constant rate birth-death process for our operational definition of imbalance and its change through time.Supplementary Figure 3: Support for the ML phylogenetic estimate of 812 extant species of bats based on 29 genetic loci (Table 1). Relevant nodes are labeled in black (70% support) or grey (50% support).Supplementary Figure 4: A set of shift configurations comprising the for most credible shift configurations from our BAMM analysis on the ML phylogeny.Supplementary Figure 5: A cohort matrix (see Fig. 5, Fig. S1) for the variant of our BAMM analysis with halved sampling fractions.Supplementary Figure 6: A plot depicting the relationship between crown family age, in millions of years, and log(richness) for each nonmonotypic family.Supplementary Figure 7: An analysis of phylogenetic imbalance through time, without the exceptional subfamily Stenodermatinae.Supplementary Figure 8: A high-resolution version of the ML, time-calibrated phylogeny (Fig. 2) used for macroevolutionary analyses.Supplementary Table 1: List of taxa removed from the dataset following an initial RAxML search. Supplementary Table 2: Approximate supermatrix sampling percentages (i.e., at least one locus was included per species) for all extant families of bats; these percentages were used to parameterize BAMM analysis and account for incomplete sampling. Supplementary Table 3: Phylogenies simulated under a pure birth model with differing levels of incomplete sampling, and the resulting γ-statistic (Pybus and Harvey ) for each level of sampling.
abstractSpecies richness varies widely across extant clades, but the causes of this variation remain poorly understood. We investigate the role of diversification rate heterogeneity in shaping patterns of diversity across families of extant bats. To provide a robust framework for macroevolutionary inference, we assemble a time-calibrated, species-level phylogeny using a supermatrix of mitochondrial and nuclear sequence data. We analyze the phylogeny using a Bayesian method for modeling complex evolutionary dynamics. Surprisingly, we find that variation in family richness can largely be explained without invoking heterogeneous diversification dynamics. We document only a single well-supported shift in diversification dynamics across bats, occurring at the base of the subfamily Stenodermatinae. Bat diversity is phylogenetically imbalanced, but—contrary to previous hypotheses—this pattern is unexplained by any simple patterns of diversification rate heterogeneity. This discordance may indicate that diversification dynamics are more complex than can be captured using the statistical tools available for modeling data at this scale. We infer that bats as a whole are almost entirely united into one macroevolutionary cohort, with decelerating speciation through time. There is also a significant relationship between clade age and richness, suggesting that global bat diversity may still be expanding.
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