1
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Soewongsono AC, Landis MJ. A Diffusion-Based Approach for Simulating Forward-in-Time State-Dependent Speciation and Extinction Dynamics. Bull Math Biol 2024; 86:101. [PMID: 38970749 DOI: 10.1007/s11538-024-01337-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024]
Abstract
We establish a general framework using a diffusion approximation to simulate forward-in-time state counts or frequencies for cladogenetic state-dependent speciation-extinction (ClaSSE) models. We apply the framework to various two- and three-region geographic-state speciation-extinction (GeoSSE) models. We show that the species range state dynamics simulated under tree-based and diffusion-based processes are comparable. We derive a method to infer rate parameters that are compatible with given observed stationary state frequencies and obtain an analytical result to compute stationary state frequencies for a given set of rate parameters. We also describe a procedure to find the time to reach the stationary frequencies of a ClaSSE model using our diffusion-based approach, which we demonstrate using a worked example for a two-region GeoSSE model. Finally, we discuss how the diffusion framework can be applied to formalize relationships between evolutionary patterns and processes under state-dependent diversification scenarios.
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Affiliation(s)
- Albert C Soewongsono
- Department of Biology, Washington University in St. Louis, Rebstock Hall, St. Louis, MO, 63130, USA.
| | - Michael J Landis
- Department of Biology, Washington University in St. Louis, Rebstock Hall, St. Louis, MO, 63130, USA
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2
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Scott JE. The macroevolutionary dynamics of activity pattern in mammals: Primates in context. J Hum Evol 2023; 184:103436. [PMID: 37741141 DOI: 10.1016/j.jhevol.2023.103436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023]
Abstract
Activity pattern has played a prominent role in discussions of primate evolutionary history. Most primates are either diurnal or nocturnal, but a small number are active both diurnally and nocturnally. This pattern-cathemerality-also occurs at low frequency across mammals. Using a large sample of mammalian species, this study evaluates two macroevolutionary hypotheses proposed to explain why cathemerality is less common than diurnality and nocturnality: 1) that cathemeral lineages have higher extinction probabilities (differential diversification) and 2) that transitions out of cathemerality are more frequent, making it a less persistent state (differential state persistence). Rates of speciation, extinction, and transition between character states were estimated using hidden-rates models applied to a phylogenetic tree containing 3013 mammals classified by activity pattern. The models failed to detect consistent differences in diversification dynamics among activity patterns, but there is strong support for differential state persistence. Transition rates out of cathemerality tend to be much higher than transition rates out of nocturnality. Transition rates out of diurnality are similar to those for cathemerality in most clades, with two important exceptions: diurnality is unusually persistent in anthropoid primates and sciurid rodents. These two groups combine very low rates of transition out of diurnality with high speciation rates. This combination has no parallels among cathemeral lineages, explaining why diurnality has become more common than cathemerality in mammals. Similarly, the combination of rates found in anthropoids is sufficient to explain the low relative frequency of cathemerality in primates, making it unnecessary to appeal to high extinction probabilities in cathemeral lineages in this clade. These findings support the hypothesis that the distribution of activity patterns across mammals has been influenced primarily by differential state persistence, whereas the effect of differential diversification appears to have been more idiosyncratic.
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Affiliation(s)
- Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA.
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3
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Helmstetter AJ, Zenil-Ferguson R, Sauquet H, Otto SP, Méndez M, Vallejo-Marin M, Schönenberger J, Burgarella C, Anderson B, de Boer H, Glémin S, Käfer J. Trait-dependent diversification in angiosperms: Patterns, models and data. Ecol Lett 2023; 26:640-657. [PMID: 36829296 DOI: 10.1111/ele.14170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 02/26/2023]
Abstract
Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesised data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to data set properties - trees that were larger, older or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.
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Affiliation(s)
- Andrew J Helmstetter
- Fondation pour la recherche sur la biodiversité-CEntre de Synthèse et d'Analyse sur la Biodiversité, Montpellier, France
| | | | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Sarah P Otto
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marcos Méndez
- Area of Biodiversity and Conservation, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | | | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Bruce Anderson
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Sylvain Glémin
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- CNRS, Ecosystèmes Biodiversité Evolution (Université de Rennes), Rennes, France
| | - Jos Käfer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
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4
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Friedman ST, Muñoz MM. A latitudinal gradient of deep-sea invasions for marine fishes. Nat Commun 2023; 14:773. [PMID: 36774385 PMCID: PMC9922314 DOI: 10.1038/s41467-023-36501-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
Although the tropics harbor the greatest species richness globally, recent work has demonstrated that, for many taxa, speciation rates are faster at higher latitudes. Here, we explore lability in oceanic depth as a potential mechanism for this pattern in the most biodiverse vertebrates - fishes. We demonstrate that clades with the highest speciation rates also diversify more rapidly along the depth gradient, drawing a fundamental link between evolutionary and ecological processes on a global scale. Crucially, these same clades also inhabit higher latitudes, creating a prevailing latitudinal gradient of deep-sea invasions concentrated in poleward regions. We interpret these findings in the light of classic ecological theory, unifying the latitudinal variation of oceanic features and the physiological tolerances of the species living there. This work advances the understanding of how niche lability sculpts global patterns of species distributions and underscores the vulnerability of polar ecosystems to changing environmental conditions.
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Affiliation(s)
- Sarah T Friedman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA. .,Yale Institute for Biospheric Studies, Yale University, New Haven, CT, 06511, USA.
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
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5
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Scott JE. Variation in macroevolutionary dynamics among extant primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 179:405-416. [PMCID: PMC9826261 DOI: 10.1002/ajpa.24622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/05/2022] [Accepted: 09/03/2022] [Indexed: 09/25/2023]
Abstract
Objectives This study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity. Materials and methods Lineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification. Results Rate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages. Conclusions Recent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.
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Affiliation(s)
- Jeremiah E. Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the PacificWestern University of Health SciencesPomonaCaliforniaUSA
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6
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Hua X, Herdha T, Burden C. Protracted speciation under the state-dependent speciation and extinction approach. Syst Biol 2022; 71:1362-1377. [PMID: 35699529 PMCID: PMC9558848 DOI: 10.1093/sysbio/syac041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 05/16/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
How long does speciation take? The answer to this important question in evolutionary biology lies in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to improve accuracy in inferring evolutionary histories among recently diverged lineages, we now have the lineage-level trees to answer these questions. However, we do not yet have an analytical tool for inferring speciation processes from these trees. What is needed is a model of speciation processes that generates both the trees and species identities of extant lineages. The model should allow calculation of the probability that certain lineages belong to certain species and have an evolutionary history consistent with the tree. Here, we propose such a model and test the model performance on both simulated data and real data. We show that maximum-likelihood estimates of the model are highly accurate and give estimates from real data that generate patterns consistent with observations. We discuss how to extend the model to account for different rates and types of speciation processes across lineages in a species group. By linking evolutionary processes on lineage level to species level, the model provides a new phylogenetic approach to study not just when speciation happened, but how speciation happened. [Micro–macro evolution; Protracted birth–death process; speciation completion rate; SSE approach.]
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Affiliation(s)
- Xia Hua
- Mathematical Sciences Institute, Australian National University, Canberra ACT 0200 Australia
| | - Tyara Herdha
- Mathematical Sciences Institute, Australian National University, Canberra ACT 0200 Australia
| | - Conrad Burden
- Mathematical Sciences Institute, Australian National University, Canberra ACT 0200 Australia
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7
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Moen DS. Improving inference and avoiding overinterpretation of hidden-state diversification models: Specialized plant breeding has no effect on diversification in frogs. Evolution 2021; 76:373-384. [PMID: 34854483 DOI: 10.1111/evo.14406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 11/30/2022]
Abstract
The hidden-state speciation and extinction (HiSSE) model helps avoid spurious results when testing whether a character affects diversification rates. However, care must be taken to optimally analyze models and interpret results. Recently, Tonini et al. (TEA hereafter) studied anuran (frog and toad) diversification with HiSSE methods. They concluded that their focal state, breeding in phytotelmata, increases net diversification rates. Yet this conclusion is counterintuitive, because the state that purportedly increases net diversification rates is 14 times rarer among species than the alternative. Herein, I revisit TEA's analyses and demonstrate problems with inferring model likelihoods, conducting post hoc tests, and interpreting results. I also reevaluate their top models and find that diverse strategies are necessary to reach the parameter values that maximize each model's likelihood. In contrast to TEA, I find no support for an effect of phytotelm breeding on net diversification rates in Neotropical anurans. In particular, even though the most highly supported models include the focal character, averaging parameter estimates over hidden states shows that the focal character does not influence diversification rates. Finally, I suggest ways to better analyze and interpret complex diversification models-both state-dependent and beyond-for future studies in other organisms.
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Affiliation(s)
- Daniel S Moen
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
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8
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MacPherson A, Louca S, McLaughlin A, Joy JB, Pennell MW. Unifying Phylogenetic Birth-Death Models in Epidemiology and Macroevolution. Syst Biol 2021; 71:172-189. [PMID: 34165577 PMCID: PMC8972974 DOI: 10.1093/sysbio/syab049] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/09/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Birth–death stochastic processes are the foundations of many phylogenetic models and are
widely used to make inferences about epidemiological and macroevolutionary dynamics. There
are a large number of birth–death model variants that have been developed; these impose
different assumptions about the temporal dynamics of the parameters and about the sampling
process. As each of these variants was individually derived, it has been difficult to
understand the relationships between them as well as their precise biological and
mathematical assumptions. Without a common mathematical foundation, deriving new models is
nontrivial. Here, we unify these models into a single framework, prove that many
previously developed epidemiological and macroevolutionary models are all special cases of
a more general model, and illustrate the connections between these variants. This
unification includes both models where the process is the same for all lineages and those
in which it varies across types. We also outline a straightforward procedure for deriving
likelihood functions for arbitrarily complex birth–death(-sampling) models that will
hopefully allow researchers to explore a wider array of scenarios than was previously
possible. By rederiving existing single-type birth–death sampling models, we clarify and
synthesize the range of explicit and implicit assumptions made by these models.
[Birth–death processes; epidemiology; macroevolution; phylogenetics; statistical
inference.]
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Affiliation(s)
- Ailene MacPherson
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Stilianos Louca
- Department of Biology, University of Oregon, USA.,Institute of Ecology and Evolution, University of Oregon, USA
| | - Angela McLaughlin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Bioinformatics, University of British Columbia, Vancouver, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Bioinformatics, University of British Columbia, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Matthew W Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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9
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Shafir A, Azouri D, Goldberg EE, Mayrose I. Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates. Evolution 2020; 74:1620-1639. [PMID: 32510165 DOI: 10.1111/evo.14036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/17/2020] [Indexed: 12/01/2022]
Abstract
As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suite of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study, we show that asymmetric rates of sequence evolution lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.
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Affiliation(s)
- Anat Shafir
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Dana Azouri
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel.,School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | | | - Itay Mayrose
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
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10
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11
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Zenil-Ferguson R, Burleigh JG, Freyman WA, Igić B, Mayrose I, Goldberg EE. Interaction among ploidy, breeding system and lineage diversification. THE NEW PHYTOLOGIST 2019; 224:1252-1265. [PMID: 31617595 DOI: 10.1111/nph.16184] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/14/2019] [Indexed: 05/28/2023]
Abstract
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs polyploid states) and breeding system (self-incompatible vs self-compatible states) are both thought to be drivers of differential diversification in angiosperms. We fit 29 diversification models to extensive trait and phylogenetic data in Solanaceae and investigate how speciation and extinction rate differences are associated with ploidy, breeding system, and the interaction between these traits. We show that diversification patterns in Solanaceae are better explained by breeding system and an additional unobserved factor, rather than by ploidy. We also find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization. Comparing multiple stochastic diversification models that include complex trait interactions alongside hidden states enhances our understanding of the macroevolutionary patterns in plant phylogenies.
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Affiliation(s)
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - William A Freyman
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Boris Igić
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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12
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Louca S, Pennell MW. A General and Efficient Algorithm for the Likelihood of Diversification and Discrete-Trait Evolutionary Models. Syst Biol 2019; 69:545-556. [DOI: 10.1093/sysbio/syz055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
As the size of phylogenetic trees and comparative data continue to grow and more complex models are developed to investigate the processes that gave rise to them, macroevolutionary analyses are becoming increasingly limited by computational requirements. Here, we introduce a novel algorithm, based on the “flow” of the differential equations that describe likelihoods along tree edges in backward time, to reduce redundancy in calculations and efficiently compute the likelihood of various macroevolutionary models. Our algorithm applies to several diversification models, including birth–death models and models that account for state- or time-dependent rates, as well as many commonly used models of discrete-trait evolution, and provides an alternative way to describe macroevolutionary model likelihoods. As a demonstration of our algorithm’s utility, we implemented it for a popular class of state-dependent diversification models—BiSSE, MuSSE, and their extensions to hidden-states. Our implementation is available through the R package $\texttt{castor}$. We show that, for these models, our algorithm is one or more orders of magnitude faster than existing implementations when applied to large phylogenies. Our algorithm thus enables the fitting of state-dependent diversification models to modern massive phylogenies with millions of tips and may lead to potentially similar computational improvements for many other macroevolutionary models.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, 1210 University of Oregon, Eugene, OR 97403, USA
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403, USA
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, V6T1Z4 British Columbia, Canada
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, V6T1Z4 British Columbia, Canada
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13
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Scott JE. Macroevolutionary effects on primate trophic evolution and their implications for reconstructing primate origins. J Hum Evol 2019; 133:1-12. [PMID: 31358174 DOI: 10.1016/j.jhevol.2019.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 11/28/2022]
Abstract
The visual-predation hypothesis proposes that certain derived features shared by crown primates reflect an insectivorous ancestry. Critics of this idea have argued that because insectivory is uncommon among extant primates it is unlikely to have been a major influence on early primate evolution. According to this perspective, the low frequency of insectivory indicates that it is an apomorphic deviation from the mostly conserved primate ecological pattern of herbivory. The present study tests two alternative hypotheses that are compatible with an insectivorous ancestor: (1) that trophic evolution was biased, such that herbivory evolved repeatedly with few shifts back to insectivory, and (2) that insectivorous lineages have diversified at a lower rate than herbivorous lineages owing to differential trophic effects on speciation and extinction probabilities. Model-based analysis conducted using trait data for 307 extant primate species indicates that rates of transition into and out of insectivory are similar, rejecting the hypothesis of biased trophic evolution. On the other hand, the hypothesis of asymmetric diversification is supported, with insectivorous lineages having a lower rate of diversification than herbivorous lineages. This correlation is mediated by activity pattern: insectivory occurs mostly in nocturnal lineages, which have a lower diversification rate than diurnal lineages. The frequency of insectivory also appears to have been shaped by repeated transitions into ecological contexts in which insectivory is absent (large body size) or rare (diurnality). These findings suggest that the current distribution of trophic strategies among extant primates is the result of macroevolutionary processes that have favored the proliferation and persistence of herbivory relative to insectivory. This conclusion implies that the low frequency of insectivory is not necessarily evidence against the visual-predation hypothesis.
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Affiliation(s)
- Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E. Second St. Pomona, California, 91766-1854, USA.
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14
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Klaus KV, Matzke NJ. Statistical Comparison of Trait-Dependent Biogeographical Models Indicates That Podocarpaceae Dispersal Is Influenced by Both Seed Cone Traits and Geographical Distance. Syst Biol 2019; 69:61-75. [DOI: 10.1093/sysbio/syz034] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/04/2019] [Indexed: 11/12/2022] Open
Abstract
Abstract
The ability of lineages to disperse long distances over evolutionary timescales may be influenced by the gain or loss of traits adapted to enhance local, ecological dispersal. For example, some species in the southern conifer family Podocarpaceae have fleshy cones that encourage bird dispersal, but it is unknown how this trait has influenced the clade’s historical biogeography, or its importance compared with other predictors of dispersal such as the geographic distance between regions. We answer these questions quantitatively by using a dated phylogeny of 197 species of southern conifers (Podocarpaceae and their sister family Araucariaceae) to statistically compare standard, trait-independent biogeography models with new BioGeoBEARS models where an evolving trait can influence dispersal probability, and trait history, biogeographical history, and model parameters are jointly inferred. We validate the method with simulation-inference experiments. Comparing all models, those that include trait-dependent dispersal accrue 87.5% of the corrected Akaike Information Criterion (AICc) model weight. Averaged across all models, lineages with nonfleshy cones had a dispersal probability multiplier of 0.49 compared with lineages with fleshy cones. Distance is included as a predictor of dispersal in all credible models (100% model weight). However, models with changing geography earned only 22.0% of the model weight, and models submerging New Caledonia/New Zealand earned only 0.01%. The importance of traits and distance suggests that long-distance dispersal over macroevolutionary timespans should not be thought of as a highly unpredictable chance event. Instead, long-distance dispersal can be modeled, allowing statistical model comparison to quantify support for different hypotheses.
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Affiliation(s)
- Kristina V Klaus
- Department of Evolution and Biodiversity of Plants, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Nicholas J Matzke
- Moritz Laboratory, Division of Ecology and Evolution, Centre for Biodiversity Analysis, Research School of Biology, RN Robertson Bldg, Level 2, West Wing (W208), 46 Sullivans Creek Rd, Australian National University, Acton ACT 2601, Australia
- School of Biological Sciences, 3A Symonds Street, The University of Auckland, Auckland 1010, New Zealand
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15
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Esquerré D, Brennan IG, Catullo RA, Torres‐Pérez F, Keogh JS. How mountains shape biodiversity: The role of the Andes in biogeography, diversification, and reproductive biology in South America's most species‐rich lizard radiation (Squamata: Liolaemidae). Evolution 2018; 73:214-230. [DOI: 10.1111/evo.13657] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 11/04/2018] [Accepted: 11/19/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Renee A. Catullo
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
- School of Science & Health and Hawkesbury Institute for the EnvironmentWestern Sydney University 2751 Perth New South Wales Australia
| | - Fernando Torres‐Pérez
- Instituto de BiologíaPontificia Universidad Católica de Valparaíso 2950 Valparaíso Chile
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
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16
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Freyman WA, Höhna S. Stochastic Character Mapping of State-Dependent Diversification Reveals the Tempo of Evolutionary Decline in Self-Compatible Onagraceae Lineages. Syst Biol 2018; 68:505-519. [DOI: 10.1093/sysbio/syy078] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- William A Freyman
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, CA 94720, USA
| | - Sebastian Höhna
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
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17
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Ng J, Smith SD. Why are red flowers so rare? Testing the macroevolutionary causes of tippiness. J Evol Biol 2018; 31:1863-1875. [PMID: 30256485 DOI: 10.1111/jeb.13381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 01/05/2023]
Abstract
Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches and differ between recently diverged sister species. This phylogenetic pattern has classically been attributed to the trait being an evolutionary dead end, where the trait arises due to some short-term evolutionary advantage, but it ultimately leads species to extinction. While the higher extinction rate associated with a dead end trait could produce such a tippy pattern, a similar pattern could appear if lineages with the trait speciated slower than other lineages, or if the trait was lost more often that it was gained. In this study, we quantify the degree of tippiness of red flowers in the tomato family, Solanaceae, and investigate the macroevolutionary processes that could explain the sparse phylogenetic distribution of this trait. Using a suite of metrics, we confirm that red-flowered lineages are significantly overdispersed across the tree and form smaller clades than expected under a null model. Next, we fit 22 alternative models using HiSSE (Hidden State Speciation and Extinction), which accommodates asymmetries in speciation, extinction and transition rates that depend on observed and unobserved (hidden) character states. Results of the model fitting indicated significant variation in diversification rates across the family, which is best explained by the inclusion of hidden states. Our best fitting model differs between the maximum clade credibility tree and when incorporating phylogenetic uncertainty, suggesting that the extreme tippiness and rarity of red Solanaceae flowers makes it difficult to distinguish among different underlying processes. However, both of the best models strongly support a bias towards the loss of red flowers. The best fitting HiSSE model when incorporating phylogenetic uncertainty lends some support to the hypothesis that lineages with red flowers exhibit reduced diversification rates due to elevated extinction rates. Future studies employing simulations or targeting population-level processes may allow us to determine whether red flowers in Solanaceae or other angiosperms clades are rare and tippy due to a combination of processes, or asymmetrical transitions alone.
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Affiliation(s)
- Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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18
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Caetano DS, O'Meara BC, Beaulieu JM. Hidden state models improve state-dependent diversification approaches, including biogeographical models. Evolution 2018; 72:2308-2324. [DOI: 10.1111/evo.13602] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/20/2018] [Accepted: 08/27/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Daniel S. Caetano
- Department of Biological Sciences; University of Arkansas; Fayetteville Arkansas 72701
| | - Brian C. O'Meara
- Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville Tennessee 37996-1610
| | - Jeremy M. Beaulieu
- Department of Biological Sciences; University of Arkansas; Fayetteville Arkansas 72701
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19
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Sauquet H, Magallón S. Key questions and challenges in angiosperm macroevolution. THE NEW PHYTOLOGIST 2018; 219:1170-1187. [PMID: 29577323 DOI: 10.1111/nph.15104] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/05/2018] [Indexed: 05/26/2023]
Abstract
Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid diversification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm diversification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day biodiversity. We present six key questions that explore the origin and diversification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include diversification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for sampling bias and heterogeneity of macroevolutionary processes through time and among lineages; (2) the need for large and standardized synthetic databases of morphological variation; and (3) continuous effort on sampling the fossil record, but with a revolution in current paleobotanical practice.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS, UMR 8079, Orsay, 91405, France
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacán, México City, 04510, México
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20
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Scott JE. Reevaluating cases of trait-dependent diversification in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:244-256. [DOI: 10.1002/ajpa.23621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/23/2018] [Accepted: 05/12/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Jeremiah E. Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific; Western University of Health Sciences; Pomona California 91766
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21
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Kodandaramaiah U, Murali G. What affects power to estimate speciation rate shifts? PeerJ 2018; 6:e5495. [PMID: 30155369 PMCID: PMC6108317 DOI: 10.7717/peerj.5495] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 07/30/2018] [Indexed: 02/04/2023] Open
Abstract
The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rate, and three modelling methods-BiSSE, MEDUSA and BAMM-have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (speciation rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide suggestions to users of these methods.
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Affiliation(s)
- Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, India
| | - Gopal Murali
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, India
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22
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Simpson AG, Wagner PJ, Wing SL, Fenster CB. Binary-state speciation and extinction method is conditionally robust to realistic violations of its assumptions. BMC Evol Biol 2018; 18:69. [PMID: 29739313 PMCID: PMC5941815 DOI: 10.1186/s12862-018-1174-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/10/2018] [Indexed: 11/26/2022] Open
Abstract
Background Phylogenetic comparative methods allow us to test evolutionary hypotheses without the benefit of an extensive fossil record. These methods, however, make simplifying assumptions, among them that clades are always increasing or stable in diversity, an assumption we know to be false. This study simulates hypothetical clades to test whether the Binary State Speciation and Extinction (BiSSE) method can be used to correctly detect relative differences in diversification rate between ancestral and derived character states even as net diversification rates are declining overall. We simulate clades with declining but positive diversification rates, as well those in which speciation rates decline below extinction rates so that they are losing richness for part of their history. We run these analyses both with simulated symmetric and asymmetric speciation rates to test whether BiSSE can be used to detect them correctly. Results For simulations with a neutral character, the fit for a BiSSE model with a neutral character is better than alternative models so long as net diversification rates remain positive. Once net diversification rates become negative, the BiSSE model with the greatest likelihood often has a non-neutral character, even though there is no such character in the simulation. BiSSE’s usefulness in detecting real asymmetry in speciation rates improves with clade age, even well after net diversification rates have become negative. Conclusions BiSSE is most useful in analyzing clades of intermediate age, before they have reached peak diversity and gone into decline. After this point, users of BiSSE risk incorrectly inferring differential evolutionary rates when none exist. Fortunately, most studies using BiSSE and similar models focus on rapid, recent diversifications, and are less likely to encounter the biases BiSSE models are subject to for older clades. For extant groups that were once more diverse than now, however, caution should be taken in inferring past diversification patterns without fossil data. Electronic supplementary material The online version of this article (10.1186/s12862-018-1174-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew G Simpson
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington D.C., USA. .,Program in Behavior, Ecology, Evolution, and Systematics, University of Maryland, College Park, USA.
| | - Peter J Wagner
- Department of Earth & Atmospheric Sciences and School of Biological Sciences, University of Nebraska, Lincoln, USA
| | - Scott L Wing
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington D.C., USA.,Program in Behavior, Ecology, Evolution, and Systematics, University of Maryland, College Park, USA
| | - Charles B Fenster
- Department of Biology and Microbiology, South Dakota State University, Brookings, USA
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23
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Vamosi JC, Magallón S, Mayrose I, Otto SP, Sauquet H. Macroevolutionary Patterns of Flowering Plant Speciation and Extinction. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:685-706. [PMID: 29489399 DOI: 10.1146/annurev-arplant-042817-040348] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Species diversity is remarkably unevenly distributed among flowering plant lineages. Despite a growing toolbox of research methods, the reasons underlying this patchy pattern have continued to perplex plant biologists for the past two decades. In this review, we examine the present understanding of transitions in flowering plant evolution that have been proposed to influence speciation and extinction. In particular, ploidy changes, transitions between tropical and nontropical biomes, and shifts in floral form have received attention and have offered some surprises in terms of which factors influence speciation and extinction rates. Mating systems and dispersal characteristics once predominated as determining factors, yet recent evidence suggests that these changes are not as influential as previously thought or are important only when paired with range shifts. Although range extent is an important correlate of speciation, it also influences extinction and brings an applied focus to diversification research. Recent studies that find that past diversification can predict present-day extinction risk open an exciting avenue for future research to help guide conservation prioritization.
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Affiliation(s)
- Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada;
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sarah P Otto
- Department of Zoology and the Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Hervé Sauquet
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS UMR 8079, 91405 Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
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24
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Hua X, Lanfear R. The influence of non‐random species sampling on macroevolutionary and macroecological inference from phylogenies. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.12982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Xia Hua
- Ecology and Evolution Research School of Biology Australian National University Canberra ACT Australia
| | - Robert Lanfear
- Ecology and Evolution Research School of Biology Australian National University Canberra ACT Australia
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25
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Ingram T, Harrison A, Mahler DL, Castañeda MDR, Glor RE, Herrel A, Stuart YE, Losos JB. Comparative tests of the role of dewlap size in Anolis lizard speciation. Proc Biol Sci 2017; 283:rspb.2016.2199. [PMID: 28003450 DOI: 10.1098/rspb.2016.2199] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 11/17/2016] [Indexed: 02/01/2023] Open
Abstract
Phenotypic traits may be linked to speciation in two distinct ways: character values may influence the rate of speciation or diversification in the trait may be associated with speciation events. Traits involved in signal transmission, such as the dewlap of Anolis lizards, are often involved in the speciation process. The dewlap is an important visual signal with roles in species recognition and sexual selection, and dewlaps vary among species in relative size as well as colour and pattern. We compile a dataset of relative dewlap size digitized from photographs of 184 anole species from across the genus' geographical range. We use phylogenetic comparative methods to test two hypotheses: that larger dewlaps are associated with higher speciation rates, and that relative dewlap area diversifies according to a speciational model of evolution. We find no evidence of trait-dependent speciation, indicating that larger signals do not enhance any role the dewlap has in promoting speciation. Instead, we find a signal of mixed speciational and gradual trait evolution, with a particularly strong signal of speciational change in the dewlaps of mainland lineages. This indicates that dewlap size diversifies in association with the speciation process, suggesting that divergent selection may play a role in the macroevolution of this signalling trait.
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Affiliation(s)
- Travis Ingram
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Alexis Harrison
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - D Luke Mahler
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, 3031, Toronto, Ontario, Canada M5S 3B2
| | - María Del Rosario Castañeda
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Richard E Glor
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Anthony Herrel
- Département d'Ecologie et de Gestion de la Biodiversité, UMR 7179 C.N.R.S/M.N.H.N., 57 rue Cuvier, Case postale 55, 75231 Paris Cedex 5, France
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, One University Station C0990, Austin, TX 78712, USA
| | - Jonathan B Losos
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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26
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Huang D, Goldberg EE, Chou LM, Roy K. The origin and evolution of coral species richness in a marine biodiversity hotspot. Evolution 2017; 72:288-302. [PMID: 29178128 DOI: 10.1111/evo.13402] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 10/30/2017] [Accepted: 11/12/2017] [Indexed: 12/25/2022]
Abstract
The Coral Triangle (CT) region of the Indo-Pacific realm harbors an extraordinary number of species, with richness decreasing away from this biodiversity hotspot. Despite multiple competing hypotheses, the dynamics underlying this regional diversity pattern remain poorly understood. Here, we use a time-calibrated evolutionary tree of living reef coral species, their current geographic ranges, and model-based estimates of regional rates of speciation, extinction, and geographic range shifts to show that origination rates within the CT are lower than in surrounding regions, a result inconsistent with the long-standing center of origin hypothesis. Furthermore, endemism of coral species in the CT is low, and the CT endemics are older than relatives found outside this region. Overall, our model results suggest that the high diversity of reef corals in the CT is largely due to range expansions into this region of species that evolved elsewhere. These findings strongly support the notion that geographic range shifts play a critical role in generating species diversity gradients. They also show that preserving the processes that gave rise to the striking diversity of corals in the CT requires protecting not just reefs within the hotspot, but also those in the surrounding areas.
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Affiliation(s)
- Danwei Huang
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
| | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108
| | - Loke Ming Chou
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, California 92093
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27
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Pereira EB, Pinto-Ledezma JN, de Freitas CG, Villalobos F, Collevatti RG, Maciel NM. Evolution of the anuran foam nest: trait conservatism and lineage diversification. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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28
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Abstract
Evolutionary theory has been extended almost continually since the evolutionary synthesis (ES), but except for the much greater importance afforded genetic drift, the principal tenets of the ES have been strongly supported. Adaptations are attributable to the sorting of genetic variation by natural selection, which remains the only known cause of increase in fitness. Mutations are not adaptively directed, but as principal authors of the ES recognized, the material (structural) bases of biochemistry and development affect the variety of phenotypic variations that arise by mutation and recombination. Against this historical background, I analyse major propositions in the movement for an 'extended evolutionary synthesis'. 'Niche construction' is a new label for a wide variety of well-known phenomena, many of which have been extensively studied, but (as with every topic in evolutionary biology) some aspects may have been understudied. There is no reason to consider it a neglected 'process' of evolution. The proposition that phenotypic plasticity may engender new adaptive phenotypes that are later genetically assimilated or accommodated is theoretically plausible; it may be most likely when the new phenotype is not truly novel, but is instead a slight extension of a reaction norm already shaped by natural selection in similar environments. However, evolution in new environments often compensates for maladaptive plastic phenotypic responses. The union of population genetic theory with mechanistic understanding of developmental processes enables more complete understanding by joining ultimate and proximate causation; but the latter does not replace or invalidate the former. Newly discovered molecular phenomena have been easily accommodated in the past by elaborating orthodox evolutionary theory, and it appears that the same holds today for phenomena such as epigenetic inheritance. In several of these areas, empirical evidence is needed to evaluate enthusiastic speculation. Evolutionary theory will continue to be extended, but there is no sign that it requires emendation.
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Affiliation(s)
- Douglas J. Futuyma
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
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29
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Rabosky DL, Goldberg EE. FiSSE: A simple nonparametric test for the effects of a binary character on lineage diversification rates. Evolution 2017; 71:1432-1442. [DOI: 10.1111/evo.13227] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/06/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan 48103
| | - Emma E. Goldberg
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul Minnesota 55108
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30
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Harrington S, Reeder TW. Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification. J Evol Biol 2016; 30:313-325. [DOI: 10.1111/jeb.13004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/24/2016] [Accepted: 10/24/2016] [Indexed: 11/29/2022]
Affiliation(s)
- S. Harrington
- Department of Biology; San Diego State University; San Diego CA USA
- Department of Biology; University of California; Riverside CA USA
| | - T. W. Reeder
- Department of Biology; San Diego State University; San Diego CA USA
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31
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Hunt G, Slater G. Integrating Paleontological and Phylogenetic Approaches to Macroevolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-112414-054207] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With proliferation of molecular phylogenies and advances in statistical modeling, phylogeneticists can now address macroevolutionary questions that had traditionally been the purview of paleontology. Interest has focused on three areas at the intersection of phylogenetic and paleontological research: time-scaling phylogenies, understanding trait evolution, and modeling species diversification. Fossil calibrations have long been crucial for scaling phylogenies to absolute time, but recent advances allow more equal integration of extinct taxa. Simulation and empirical studies have shown that fossil data can markedly improve inferences about trait evolution, especially for models with heterogeneous temporal dynamics and in clades for which the living forms are unrepresentative remnants of their larger clade. Recent years have also seen a productive cross-disciplinary conversation about the nature and uncertainties of inferring diversification dynamics. Challenges remain, but the present time represents a flowering of interest in integrating these two views on the history of life.
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Affiliation(s)
- Gene Hunt
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Graham Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois 60637
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32
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Hardy NB, Peterson DA, Normark BB. Nonadaptive radiation: Pervasive diet specialization by drift in scale insects? Evolution 2016; 70:2421-2428. [DOI: 10.1111/evo.13036] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/29/2016] [Accepted: 07/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Nate B. Hardy
- Department of Entomology and Plant Pathology, 301 Funchess Hall Auburn University Auburn Alabama 36849
| | - Daniel A. Peterson
- Graduate Program in Organismic & Evolutionary Biology, Department of Biology University of Massachusetts Amherst Massachusetts 01003
| | - Benjamin B. Normark
- Graduate Program in Organismic & Evolutionary Biology, Department of Biology University of Massachusetts Amherst Massachusetts 01003
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33
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Zhan SH, Drori M, Goldberg EE, Otto SP, Mayrose I. Phylogenetic evidence for cladogenetic polyploidization in land plants. AMERICAN JOURNAL OF BOTANY 2016; 103:1252-1258. [PMID: 27466054 DOI: 10.3732/ajb.1600108] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation". Whether polyploidization is associated with the formation of new species (cladogenesis) or simply occurs over time within a lineage (anagenesis), however, has never been assessed systematically. METHODS We tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. KEY RESULTS Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. CONCLUSIONS Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera.
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Affiliation(s)
- Shing H Zhan
- Department of Zoology, 4200-6270 University Boulevard, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - Michal Drori
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, P. O. Box 39040, Tel Aviv 69978, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution, & Behavior, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, Minnesota 55108 USA
| | - Sarah P Otto
- Department of Zoology, 4200-6270 University Boulevard, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, P. O. Box 39040, Tel Aviv 69978, Israel
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34
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O'Meara BC, Beaulieu JM. Past, future, and present of state-dependent models of diversification. AMERICAN JOURNAL OF BOTANY 2016; 103:792-795. [PMID: 27208347 DOI: 10.3732/ajb.1600012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 03/25/2016] [Indexed: 06/05/2023]
Affiliation(s)
- Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996-1610 USA
| | - Jeremy M Beaulieu
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996-1610 USA
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35
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Rankin BD, Fox JW, Barrón-Ortiz CR, Chew AE, Holroyd PA, Ludtke JA, Yang X, Theodor JM. The extended Price equation quantifies species selection on mammalian body size across the Palaeocene/Eocene Thermal Maximum. Proc Biol Sci 2016. [PMID: 26224712 DOI: 10.1098/rspb.2015.1097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Species selection, covariation of species' traits with their net diversification rates, is an important component of macroevolution. Most studies have relied on indirect evidence for its operation and have not quantified its strength relative to other macroevolutionary forces. We use an extension of the Price equation to quantify the mechanisms of body size macroevolution in mammals from the latest Palaeocene and earliest Eocene of the Bighorn and Clarks Fork Basins of Wyoming. Dwarfing of mammalian taxa across the Palaeocene/Eocene Thermal Maximum (PETM), an intense, brief warming event that occurred at approximately 56 Ma, has been suggested to reflect anagenetic change and the immigration of small bodied-mammals, but might also be attributable to species selection. Using previously reconstructed ancestor-descendant relationships, we partitioned change in mean mammalian body size into three distinct mechanisms: species selection operating on resident mammals, anagenetic change within resident mammalian lineages and change due to immigrants. The remarkable decrease in mean body size across the warming event occurred through anagenetic change and immigration. Species selection also was strong across the PETM but, intriguingly, favoured larger-bodied species, implying some unknown mechanism(s) by which warming events affect macroevolution.
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Affiliation(s)
- Brian D Rankin
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Canada AB T2N 1N4 Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA 94720, USA
| | - Jeremy W Fox
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Canada AB T2N 1N4
| | - Christian R Barrón-Ortiz
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Canada AB T2N 1N4
| | - Amy E Chew
- Department of Anatomy, Western University of Health Sciences, 309 E. Second Street, Pomona, CA 91766, USA
| | - Patricia A Holroyd
- Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA 94720, USA
| | - Joshua A Ludtke
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Canada AB T2N 1N4
| | - Xingkai Yang
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Canada AB T2N 1N4
| | - Jessica M Theodor
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Canada AB T2N 1N4
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36
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Kühnert D, Stadler T, Vaughan TG, Drummond AJ. Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data. Mol Biol Evol 2016; 33:2102-16. [PMID: 27189573 PMCID: PMC4948704 DOI: 10.1093/molbev/msw064] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth-death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters.We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group.
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Affiliation(s)
- Denise Kühnert
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland Department of Computer Science, University of Auckland, Auckland, New Zealand Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Timothy G Vaughan
- Department of Computer Science, University of Auckland, Auckland, New Zealand
| | - Alexei J Drummond
- Department of Computer Science, University of Auckland, Auckland, New Zealand
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37
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Day EH, Hua X, Bromham L. Is specialization an evolutionary dead end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists. J Evol Biol 2016; 29:1257-67. [DOI: 10.1111/jeb.12867] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/29/2016] [Accepted: 03/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- E. H. Day
- Centre for Macroevolution & Macroecology; Division of Ecology, Evolution and Genetics; Research School of Biology; Australian National University; Canberra ACT Australia
| | - X. Hua
- Centre for Macroevolution & Macroecology; Division of Ecology, Evolution and Genetics; Research School of Biology; Australian National University; Canberra ACT Australia
| | - L. Bromham
- Centre for Macroevolution & Macroecology; Division of Ecology, Evolution and Genetics; Research School of Biology; Australian National University; Canberra ACT Australia
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38
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Beaulieu JM, O'Meara BC. Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction. Syst Biol 2016; 65:583-601. [PMID: 27016728 DOI: 10.1093/sysbio/syw022] [Citation(s) in RCA: 297] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/08/2016] [Indexed: 01/21/2023] Open
Abstract
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 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 (Binary State Speciation and Extinction) 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 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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Affiliation(s)
- Jeremy M Beaulieu
- National Institute for Biological and Mathematical Synthesis, University of Tennessee, Knoxville, TN 37996, USA Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-1610, USA
| | - Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-1610, USA
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39
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Chevin LM. Species selection and random drift in macroevolution. Evolution 2016; 70:513-25. [PMID: 26880617 DOI: 10.1111/evo.12879] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 11/28/2022]
Abstract
Species selection resulting from trait-dependent speciation and extinction is increasingly recognized as an important mechanism of phenotypic macroevolution. However, the recent bloom in statistical methods quantifying this process faces a scarcity of dynamical theory for their interpretation, notably regarding the relative contributions of deterministic versus stochastic evolutionary forces. I use simple diffusion approximations of birth-death processes to investigate how the expected and random components of macroevolutionary change depend on phenotype-dependent speciation and extinction rates, as can be estimated empirically. I show that the species selection coefficient for a binary trait, and selection differential for a quantitative trait, depend not only on differences in net diversification rates (speciation minus extinction), but also on differences in species turnover rates (speciation plus extinction), especially in small clades. The randomness in speciation and extinction events also produces a species-level equivalent to random genetic drift, which is stronger for higher turnover rates. I then show how microevolutionary processes including mutation, organismic selection, and random genetic drift cause state transitions at the species level, allowing comparison of evolutionary forces across levels. A key parameter that would be needed to apply this theory is the distribution and rate of origination of new optimum phenotypes along a phylogeny.
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Affiliation(s)
- Luis-Miguel Chevin
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919 route de Mende, F-34293 Montpellier, CEDEX 5, France.
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40
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Looney BP, Ryberg M, Hampe F, Sánchez-García M, Matheny PB. Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi. Mol Ecol 2016; 25:630-47. [PMID: 26642189 DOI: 10.1111/mec.13506] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/10/2015] [Accepted: 11/22/2015] [Indexed: 01/30/2023]
Abstract
Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the 'generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms.
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Affiliation(s)
- Brian P Looney
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA
| | - Martin Ryberg
- Department of Organismal Biology, Uppsala University, Evolutionsbiologiskt Centrum, Norbyv. 18D, 75236, Uppsala, Sweden
| | - Felix Hampe
- Department of Biology, Gent University, K.L. Ledeganckstraat 35, 9000, Gent, Belgium
| | - Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA
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41
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Krug PJ, Vendetti JE, Ellingson RA, Trowbridge CD, Hirano YM, Trathen DY, Rodriguez AK, Swennen C, Wilson NG, Valdés ÁA. Species Selection Favors Dispersive Life Histories in Sea Slugs, but Higher Per-Offspring Investment Drives Shifts to Short-Lived Larvae. Syst Biol 2015; 64:983-99. [PMID: 26163664 PMCID: PMC4794617 DOI: 10.1093/sysbio/syv046] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 07/02/2015] [Indexed: 01/27/2023] Open
Abstract
For 40 years, paleontological studies of marine gastropods have suggested that species selection favors lineages with short-lived (lecithotrophic) larvae, which are less dispersive than long-lived (planktotrophic) larvae. Although lecithotrophs appeared to speciate more often and accumulate over time in some groups, lecithotrophy also increased extinction rates, and tests for state-dependent diversification were never performed. Molecular phylogenies of diverse groups instead suggested lecithotrophs accumulate without diversifying due to frequent, unidirectional character change. Although lecithotrophy has repeatedly originated in most phyla, no adult trait has been correlated with shifts in larval type. Thus, both the evolutionary origins of lecithotrophy and its consequences for patterns of species richness remain poorly understood. Here, we test hypothesized links between development mode and evolutionary rates using likelihood-based methods and a phylogeny of 202 species of gastropod molluscs in Sacoglossa, a clade of herbivorous sea slugs. Evolutionary quantitative genetics modeling and stochastic character mapping supported 27 origins of lecithotrophy. Tests for correlated evolution revealed lecithotrophy evolved more often in lineages investing in extra-embryonic yolk, the first adult trait associated with shifts in development mode across a group. However, contrary to predictions from paleontological studies, species selection actually favored planktotrophy; most extant lecithotrophs originated through recent character change, and did not subsequently diversify. Increased offspring provisioning in planktotrophs thus favored shifts to short-lived larvae, which led to short-lived lineages over macroevolutionary time scales. These findings challenge long-standing assumptions about the effects of alternative life histories in the sea. Species selection can explain the long-term persistence of planktotrophy, the ancestral state in most clades, despite frequent transitions to lecithotrophy.
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Affiliation(s)
- Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA;
| | - Jann E Vendetti
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Ryan A Ellingson
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Cynthia D Trowbridge
- Oregon Institute of Marine Biology, University of Oregon, PO Box 5389, Charleston, OR 97420, USA
| | - Yayoi M Hirano
- Coastal Branch of Natural History Museum and Institute, Chiba, 123 Yoshio, Katsuura, 299-5242, Japan
| | - Danielle Y Trathen
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Albert K Rodriguez
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Cornelis Swennen
- Faculty of Science and Technology, Prince of Songkla University, Pattani 94000, Thailand
| | - Nerida G Wilson
- Western Australian Museum, Kew Street, Welshpool, Perth, WA 6106, Australia; and
| | - Ángel A Valdés
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
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42
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Hardy NB, Otto SP. Specialization and generalization in the diversification of phytophagous insects: tests of the musical chairs and oscillation hypotheses. Proc Biol Sci 2015; 281:rspb.2013.2960. [PMID: 25274368 DOI: 10.1098/rspb.2013.2960] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evolutionary biologists have often assumed that ecological generalism comes at the expense of less intense exploitation of specific resources and that this trade-off will promote the evolution of ecologically specialized daughter species. Using a phylogenetic comparative approach with butterflies as a model system, we test hypotheses that incorporate changes in niche breadth and location into explanations of the taxonomic diversification of insect herbivores. Specifically, we compare the oscillation hypothesis, where speciation is driven by host-plant generalists giving rise to specialist daughter species, to the musical chairs hypothesis, where speciation is driven by host-plant switching, without changes in niche breadth. Contrary to the predictions of the oscillation hypothesis, we recover a negative relationship between host-plant breadth and diversification rate and find that changes in host breadth are seldom coupled to speciation events. By contrast, we present evidence for a positive relationship between rates of host switching and butterfly diversification, consonant with the musical chairs hypothesis. These results suggest that the costs of trophic generalism in plant-feeding insects may have been overvalued and that transitions from generalists to ecological specialists may not be an important driver of speciation in general.
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Affiliation(s)
- Nate B Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Sarah P Otto
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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43
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Bromham L, Hua X, Cardillo M. Detecting Macroevolutionary Self-Destruction from Phylogenies. Syst Biol 2015; 65:109-27. [PMID: 26454872 DOI: 10.1093/sysbio/syv062] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 08/18/2015] [Indexed: 12/14/2022] Open
Abstract
Phylogenetic analyses have lent support to the concept of lineage selection: that biological lineages can have heritable traits that influence their capacity to persist and diversify, and thereby affect their representation in biodiversity. While many discussions have focused on "positive" lineage selection, where stably heritable properties of lineages enhance their diversification rate, there are also intriguing examples that seem to represent "negative" lineage selection, where traits reduce the likelihood that a lineage will persist or speciate. In this article, we test whether a particular pattern of negative lineage selection is detectable from the distributions of the trait on a phylogeny. "Self-destructive" traits are those that arise often but then disappear again because they confer either a raised extinction rate or they are prone to a high rate of trait loss. For such a trait, the reconstructed origins will tend to be dispersed across the tips of the phylogeny, rather than defining large clades of related lineages that all share the trait. We examine the utility of four possible measures of "tippiness" as potential indicators of macroevolutionary self-destruction, applying them to phylogenies on which trait evolution has been simulated under different combinations of parameters for speciation, extinction, trait gain, and trait loss. We use an efficient simulation approach that starts with the required number of tips with and without the trait and uses a model to work "backwards" to construct different possible trees that result in that set of tips. We then apply these methods to a number of case studies: salt tolerance in grasses, color polymorphism in birds of prey, and selfing in nightshades. We find that the relative age of species, measured from tip length, can indicate a reduced speciation rate but does not identify traits that increase the extinction rate or the trait loss rate. We show that it is possible to detect cases of macroevolutionary self-destruction by considering the number of tips with the trait that arise from each inferred origin, and the degree to which the trait is scattered across the phylogeny. These metrics, and the methods we present, may be useful for testing macroevolutionary hypotheses from phylogenetic patterns.
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Affiliation(s)
- Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Ecology, Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Xia Hua
- Centre for Macroevolution and Macroecology, Division of Ecology, Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Marcel Cardillo
- Centre for Macroevolution and Macroecology, Division of Ecology, Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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44
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Rabosky DL, Huang H. A Robust Semi-Parametric Test for Detecting Trait-Dependent Diversification. Syst Biol 2015; 65:181-93. [DOI: 10.1093/sysbio/syv066] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 09/09/2015] [Indexed: 12/15/2022] Open
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45
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The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift. Proc Natl Acad Sci U S A 2015; 112:11600-5. [PMID: 26324894 DOI: 10.1073/pnas.1507072112] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Adaptive radiations play key roles in the generation of biodiversity and biological novelty, and therefore understanding the factors that drive them remains one of the most important challenges of evolutionary biology. Although both intrinsic innovations and extrinsic ecological opportunities contribute to diversification bursts, few studies have looked at the synergistic effect of such factors. Here we investigate the Teloschistales (Ascomycota), a group of >1,000 lichenized species with variation in species richness and phenotypic traits that hinted at a potential adaptive radiation. We found evidence for a dramatic increase in diversification rate for one of four families within this order--Teloschistaceae--which occurred ∼ 100 Mya (Late Cretaceous) and was associated with a switch from bark to rock and from shady to sun-exposed habitats. This adaptation to sunny habitats is likely to have been enabled by a contemporaneous key novel phenotypic innovation: the production in both vegetative structure (thallus) and fruiting body (apothecia) of anthraquinones, secondary metabolites known to protect against UV light. We found that the two ecological factors (sun exposure and rock substrate) and the phenotypic innovation (anthraquinones in the thallus) were all significant when testing for state-dependent shifts in diversification rates, and together they seem likely to be responsible for the success of the Teloschistaceae, one of the largest lichen-forming fungal lineages. Our results support the idea that adaptive radiations are driven not by a single factor or key innovation, but require a serendipitous combination of both intrinsic biotic and extrinsic abiotic and ecological factors.
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46
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Brunet TDP, Doolittle WF. Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements. Genome Biol Evol 2015; 7:2445-57. [PMID: 26253318 PMCID: PMC4558868 DOI: 10.1093/gbe/evv152] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
One of several issues at play in the renewed debate over “junk DNA” is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to “speed evolution” or as an “evolutionary repository” could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness—or are instead junk— is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class.
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Affiliation(s)
- Tyler D P Brunet
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - W Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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47
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Neutral Theory Overestimates Extinction Times in Nonhuman Primates. INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9854-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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48
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Reyes E, Morlon H, Sauquet H. Presence in Mediterranean hotspots and floral symmetry affect speciation and extinction rates in Proteaceae. THE NEW PHYTOLOGIST 2015; 207:401-410. [PMID: 25537140 DOI: 10.1111/nph.13244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/24/2014] [Indexed: 06/04/2023]
Abstract
The Proteaceae is a large angiosperm family displaying the common pattern of uneven distribution of species among genera. Previous studies have shown that this disparity is a result of variation in diversification rates across lineages, but the reasons for this variation are still unclear. Here, we tested the impact of floral symmetry and occurrence in Mediterranean climate regions on speciation and extinction rates in the Proteaceae. A rate shift analysis was conducted on dated genus-level phylogenetic trees of the Proteaceae. Character-dependent analyses were used to test for differences in diversification rates between actinomorphic and zygomorphic lineages and between lineages located within or outside Mediterranean climate regions. The rate shift analysis identified 5-10 major diversification rate shifts in the Proteaceae tree. The character-dependent analyses showed that speciation rates, extinction rates and net diversification rates of the Proteaceae were significantly higher for lineages occurring in Mediterranean hotspots. Higher speciation and extinction rates were also detected for zygomorphic species, but net diversification rates appeared to be similar in actinomorphic and zygomorphic Proteaceae. Presence in Mediterranean hotspots favors Proteaceae diversification. In contrast with observations at the scale of angiosperms, floral symmetry is not a trait that strongly influences their evolutionary success.
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Affiliation(s)
- Elisabeth Reyes
- Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
- CMAP, École Polytechnique, CNRS UMR 7641, Route de Saclay, 91128, Palaiseau, France
| | - Hélène Morlon
- CMAP, École Polytechnique, CNRS UMR 7641, Route de Saclay, 91128, Palaiseau, France
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197, 46 rue d'Ulm, 75005, Paris, France
| | - Hervé Sauquet
- Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
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49
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Soulebeau A, Aubriot X, Gaudeul M, Rouhan G, Hennequin S, Haevermans T, Dubuisson JY, Jabbour F. The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0220-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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50
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Gascuel F, Ferriere R, Aguilee R, Lambert A. How Ecology and Landscape Dynamics Shape Phylogenetic Trees. Syst Biol 2015; 64:590-607. [DOI: 10.1093/sysbio/syv014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 03/09/2015] [Indexed: 01/21/2023] Open
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