1
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Quintero I, Lartillot N, Morlon H. Imbalanced speciation pulses sustain the radiation of mammals. Science 2024; 384:1007-1012. [PMID: 38815022 DOI: 10.1126/science.adj2793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
The evolutionary histories of major clades, including mammals, often comprise changes in their diversification dynamics, but how these changes occur remains debated. We combined comprehensive phylogenetic and fossil information in a new "birth-death diffusion" model that provides a detailed characterization of variation in diversification rates in mammals. We found an early rising and sustained diversification scenario, wherein speciation rates increased before and during the Cretaceous-Paleogene (K-Pg) boundary. The K-Pg mass extinction event filtered out more slowly speciating lineages and was followed by a subsequent slowing in speciation rates rather than rebounds. These dynamics arose from an imbalanced speciation process, with separate lineages giving rise to many, less speciation-prone descendants. Diversity seems to have been brought about by these isolated, fast-speciating lineages, rather than by a few punctuated innovations.
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Affiliation(s)
- Ignacio Quintero
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Nicolas Lartillot
- Université Claude Bernard Lyon 1, CNRS, VetAgroSup, LBBE, UMR 5558, F-69100 Villeurbanne, France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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2
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Caetano DS, Quental TB. How Important Is Budding Speciation for Comparative Studies? Syst Biol 2023; 72:1443-1453. [PMID: 37586404 DOI: 10.1093/sysbio/syad050] [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: 05/30/2022] [Revised: 07/26/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023] Open
Abstract
The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with 3 or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here, we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here, we show that many PCMs assume that divergence happens as a symmetric split, even if these methods do not explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We discuss the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.
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Affiliation(s)
- Daniel S Caetano
- Department of Biological Sciences, Towson University, 8000 York Road, Towson, MD 21252, USA
- Department of Ecology, University of São Paulo, Rua do Matão, 321 - Trav. 14, São Paulo, SP, 05508-090, Brazil
| | - Tiago B Quental
- Department of Ecology, University of São Paulo, Rua do Matão, 321 - Trav. 14, São Paulo, SP, 05508-090, Brazil
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3
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Patterson CW, Drury JP. Interspecific behavioural interference and range dynamics: current insights and future directions. Biol Rev Camb Philos Soc 2023; 98:2012-2027. [PMID: 37364865 DOI: 10.1111/brv.12993] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023]
Abstract
Novel biotic interactions in shifting communities play a key role in determining the ability of species' ranges to track suitable habitat. To date, the impact of biotic interactions on range dynamics have predominantly been studied in the context of interactions between different trophic levels or, to a lesser extent, exploitative competition between species of the same trophic level. Yet, both theory and a growing number of empirical studies show that interspecific behavioural interference, such as interspecific territorial and mating interactions, can slow down range expansions, preclude coexistence, or drive local extinction, even in the absence of resource competition. We conducted a systematic review of the current empirical research into the consequences of interspecific behavioural interference on range dynamics. Our findings demonstrate there is abundant evidence that behavioural interference by one species can impact the spatial distribution of another. Furthermore, we identify several gaps where more empirical work is needed to test predictions from theory robustly. Finally, we outline several avenues for future research, providing suggestions for how interspecific behavioural interference could be incorporated into existing scientific frameworks for understanding how biotic interactions influence range expansions, such as species distribution models, to build a stronger understanding of the potential consequences of behavioural interference on the outcome of future range dynamics.
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Affiliation(s)
| | - Jonathan P Drury
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
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4
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Quintero I, Landis MJ, Jetz W, Morlon H. The build-up of the present-day tropical diversity of tetrapods. Proc Natl Acad Sci U S A 2023; 120:e2220672120. [PMID: 37159475 PMCID: PMC10194011 DOI: 10.1073/pnas.2220672120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/04/2023] [Indexed: 05/11/2023] Open
Abstract
The extraordinary number of species in the tropics when compared to the extra-tropics is probably the most prominent and consistent pattern in biogeography, suggesting that overarching processes regulate this diversity gradient. A major challenge to characterizing which processes are at play relies on quantifying how the frequency and determinants of tropical and extra-tropical speciation, extinction, and dispersal events shaped evolutionary radiations. We address this question by developing and applying spatiotemporal phylogenetic and paleontological models of diversification for tetrapod species incorporating paleoenvironmental variation. Our phylogenetic model results show that area, energy, or species richness did not uniformly affect speciation rates across tetrapods and dispute expectations of a latitudinal gradient in speciation rates. Instead, both neontological and fossil evidence coincide in underscoring the role of extra-tropical extinctions and the outflow of tropical species in shaping biodiversity. These diversification dynamics accurately predict present-day levels of species richness across latitudes and uncover temporal idiosyncrasies but spatial generality across the major tetrapod radiations.
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Affiliation(s)
- Ignacio Quintero
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université Paris Science & Lettres, Paris75005, France
| | - Michael J. Landis
- Landis Lab, Department of Biology, Washington University in St. Louis, St. Louis, MO63130
| | - Walter Jetz
- Jetz Lab, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT06511
- Center for Biodiversity and Global Change, Yale University, New Haven, CT06511
| | - Hélène Morlon
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université Paris Science & Lettres, Paris75005, France
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5
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Vasconcelos T. A trait-based approach to determining principles of plant biogeography. AMERICAN JOURNAL OF BOTANY 2023; 110:e16127. [PMID: 36648370 DOI: 10.1002/ajb2.16127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Lineage-specific traits determine how plants interact with their surrounding environment. Unrelated species may evolve similar phenotypic characteristics to tolerate, persist in, and invade environments with certain characteristics, resulting in some traits becoming relatively more common in certain types of habitats. Analyses of these general patterns of geographical trait distribution have led to the proposal of general principles to explain how plants diversify in space over time. Trait-environment correlation analyses quantify to what extent unrelated lineages have similar evolutionary responses to a given type of habitat. In this synthesis, I give a short historical overview on trait-environment correlation analyses, from some key observations from classic naturalists to modern approaches using trait evolution models, large phylogenies, and massive data sets of traits and distributions. I discuss some limitations of modern approaches, including the need for more realistic models, the lack of data from tropical areas, and the necessary focus on trait scoring that goes beyond macromorphology. Overcoming these limitations will allow the field to explore new questions related to trait lability and niche evolution and to better identify generalities and exceptions in how plants diversify in space over time.
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Affiliation(s)
- Thais Vasconcelos
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
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6
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Bird Communities in a Changing World: The Role of Interspecific Competition. DIVERSITY 2022. [DOI: 10.3390/d14100857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Significant changes in the environment have the potential to affect bird species abundance and distribution, both directly, through a modification of the landscape, habitats, and climate, and indirectly, through a modification of biotic interactions such as competitive interactions. Predicting and mitigating the consequences of global change thus requires not only a sound understanding of the role played by biotic interactions in current ecosystems, but also the recognition and study of the complex and intricate effects that result from the perturbation of these ecosystems. In this review, we emphasize the role of interspecific competition in bird communities by focusing on three main predictions derived from theoretical and empirical considerations. We provide numerous examples of population decline and displacement that appeared to be, at least in part, driven by competition, and were amplified by environmental changes associated with human activities. Beyond a shift in relative species abundance, we show that interspecific competition may have a negative impact on species richness, ecosystem services, and endangered species. Despite these findings, we argue that, in general, the role played by interspecific competition in current communities remains poorly understood due to methodological issues and the complexity of natural communities. Predicting the consequences of global change in these communities is further complicated by uncertainty regarding future environmental conditions and the speed and efficacy of plastic and evolutionary responses to fast-changing environments. Possible directions of future research are highlighted.
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7
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Gates TA, Cai H, Hu Y, Han X, Griffith E, Burgener L, Hyland E, Zanno LE. Estimating ancient biogeographic patterns with statistical model discrimination. Anat Rec (Hoboken) 2022. [PMID: 36151605 DOI: 10.1002/ar.25067] [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: 05/20/2022] [Revised: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 11/06/2022]
Abstract
The geographic ranges in which species live is a function of many factors underlying ecological and evolutionary contingencies. Observing the geographic range of an individual species provides valuable information about these historical contingencies for a lineage, determining the distribution of many distantly related species in tandem provides information about large-scale constraints on evolutionary and ecological processes generally. We present a linear regression method that allows for the discrimination of various hypothetical biogeographical models for determining which landscape distributional pattern best matches data from the fossil record. The linear regression models used in the discrimination rely on geodesic distances between sampling sites (typically geologic formations) as the independent variable and three possible dependent variables: Dice/Sorensen similarity; Euclidean distance; and phylogenetic community dissimilarity. Both the similarity and distance measures are useful for full-community analyses without evolutionary information, whereas the phylogenetic community dissimilarity requires phylogenetic data. Importantly, the discrimination method uses linear regression residual error to provide relative measures of support for each biogeographical model tested, not absolute answers or p-values. When applied to a recently published dataset of Campanian pollen, we find evidence that supports two plant communities separated by a transitional zone of unknown size. A similar case study of ceratopsid dinosaurs using phylogenetic community dissimilarity provided no evidence of a biogeographical pattern, but this case study suffers from a lack of data to accurately discriminate and/or too much temporal mixing. Future research aiming to reconstruct the distribution of organisms across a landscape has a statistical-based method for determining what biogeographic distributional model best matches the available data.
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Affiliation(s)
- Terry A Gates
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
| | - Hengrui Cai
- Department of Statistics, University of California Irvine, Irvine, California, USA
| | - Yifei Hu
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Xu Han
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Emily Griffith
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Ethan Hyland
- Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Lindsay E Zanno
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
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8
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Quintero I, Suchard MA, Jetz W. Macroevolutionary dynamics of climatic niche space. Proc Biol Sci 2022; 289:20220091. [PMID: 35611527 PMCID: PMC9130784 DOI: 10.1098/rspb.2022.0091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
How and why lineages evolve along with niche space as they diversify and adapt to different environments is fundamental to evolution. Progress has been hampered by the difficulties of linking a robust empirical characterization of species niches with flexible evolutionary models that describe their evolution. Consequently, the relative influence of abiotic and biotic factors remains poorly understood. Here, we characterize species' two-dimensional temperature and precipitation niche space occupied (i.e. species niche envelope) as complex geometries and assess their evolution across all Aves using a model that captures heterogeneous evolutionary rates on time-calibrated phylogenies. We find that extant birds coevolved from warm, mesic climatic niches into colder and drier environments and responded to the Cretaceous-Palaeogene (K-Pg) boundary with a dramatic increase in disparity. Contrary to expectations of subsiding rates of niche evolution, our results show that overall rates have increased steadily, with some lineages experiencing exceptionally high evolutionary rates, associated with the colonization of novel niche spaces, and others showing niche stasis. Both competition- and environmental change-driven niche evolution transpire and result in highly heterogeneous rates near the present. Our findings highlight the growing ecological and conservation insights arising from the model-based integration of comprehensive environmental and phylogenetic information.
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Affiliation(s)
- Ignacio Quintero
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Marc A. Suchard
- Department of Human Genetics, University of California, Los Angeles, 695 Charles E. Young Dr., Los Angeles, CA 90095, USA,Department of Biostatistics, University of California, Los Angeles, 695 Charles E. Young Dr., Los Angeles, CA 90095, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA,Center for Biodiversity and Global Change, Yale University, New Haven, CT 06511, USA
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9
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Abstract
SignificanceGeography molds how species evolve in space. Strong geographical barriers to movement, for instance, both inhibit dispersal between regions and allow isolated populations to diverge as new species. Weak barriers, by contrast, permit species range expansion and persistence. These factors present a conundrum: How strong must a barrier be before between-region speciation outpaces dispersal? We designed a phylogenetic model of dispersal, extinction, and speciation that allows regional features to influence rates of biogeographic change and applied it to the neotropical radiation of Anolis lizards. Separation by water induces a threefold steeper barrier to movement than equivalent distances over land. Our model will help biologists detect relationships between evolutionary processes and the spatial contexts in which they operate.
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10
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Abstract
Technologies, from molecular genetics to precision agriculture, are outpacing theory, which is becoming a bottleneck for crop improvement. Here, we outline theoretical insights on the wheat phenotype from the perspective of three evolutionary and ecologically important relations-mother-offspring, plant-insect and plant-plant. The correlation between yield and grain number has been misinterpreted as cause-and-effect; an evolutionary perspective shows a striking similarity between crop and fishes. Both respond to environmental variation through offspring number; seed and egg size are conserved. The offspring of annual plants and semelparous fishes, lacking parental care, are subject to mother-offspring conflict and stabilizing selection. Labile reserve carbohydrates do not fit the current model of wheat yield; they can stabilize grain size, but involve trade-offs with root growth and grain number, and are at best neutral for yield. Shifting the focus from the carbon balance to an ecological role, we suggest that labile carbohydrates may disrupt aphid osmoregulation, and thus contribute to wheat agronomic adaptation. The tight association between high yield and low competitive ability justifies the view of crop yield as a population attribute whereby the behaviour of the plant becomes subordinated within that of the population, with implications for genotyping, phenotyping and plant breeding.
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Affiliation(s)
- Victor O Sadras
- South Australian Research and Development Institute, and School of Agriculture, Food and Wine, The University of Adelaide, Australia
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11
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Hackel J, Sanmartín I. Modelling the tempo and mode of lineage dispersal. Trends Ecol Evol 2021; 36:1102-1112. [PMID: 34462154 DOI: 10.1016/j.tree.2021.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
Lineage dispersal is a basic macroevolutionary process shaping the distribution of biodiversity. Probabilistic approaches in biogeography, epidemiology, and macroecology often model dispersal as a background process to explain extant or infer past distributions. We propose framing questions around the mode, timing, rate, and direction of lineage dispersal itself, from a lineage- or geography-centric perspective. We review available methods for modelling lineage dispersal. Likelihood- and simulation-based approaches to modelling dispersal have made progress in accounting for the variation of lineage dispersal over space, time, and branches of a phylogeny and its interaction with diversification. Methodological improvements, guided by a focus on model adequacy, will lead to more realistic models that can answer fundamental questions about the tempo and mode of lineage dispersal.
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Affiliation(s)
- Jan Hackel
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, UK.
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12
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Drury JP, Clavel J, Tobias JA, Rolland J, Sheard C, Morlon H. Tempo and mode of morphological evolution are decoupled from latitude in birds. PLoS Biol 2021; 19:e3001270. [PMID: 34428214 PMCID: PMC8384433 DOI: 10.1371/journal.pbio.3001270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/07/2021] [Indexed: 12/17/2022] Open
Abstract
The latitudinal diversity gradient is one of the most striking patterns in nature, yet its implications for morphological evolution are poorly understood. In particular, it has been proposed that an increased intensity of species interactions in tropical biota may either promote or constrain trait evolution, but which of these outcomes predominates remains uncertain. Here, we develop tools for fitting phylogenetic models of phenotypic evolution in which the impact of species interactions-namely, competition-can vary across lineages. Deploying these models on a global avian trait dataset to explore differences in trait divergence between tropical and temperate lineages, we find that the effect of latitude on the mode and tempo of morphological evolution is weak and clade- or trait dependent. Our results indicate that species interactions do not disproportionately impact morphological evolution in tropical bird families and question the validity of previously reported patterns of slower trait evolution in the tropics.
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Affiliation(s)
- Jonathan P. Drury
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Julien Clavel
- Natural History Museum, London, United Kingdom
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023, LEHNA, Villeurbanne, France
| | - Joseph A. Tobias
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Jonathan Rolland
- Zoology Department, University of British Columbia, Vancouver, Canada
| | - Catherine Sheard
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Hélène Morlon
- Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, Paris, France
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13
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Maliet O, Morlon H. Fast and accurate estimation of species-specific diversification rates using data augmentation. Syst Biol 2021; 71:353-366. [PMID: 34228799 DOI: 10.1093/sysbio/syab055] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 06/10/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Diversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversification rates have proven particularly useful for understanding clades diversification. Recently, we introduced the cladogenetic diversification rate shift model (ClaDS), which allows inferring multiple rate changes of small magnitude across lineages. Here we present a new inference technique for this model that considerably reduces computation time through the use of data augmentation and provide an implementation of this method in Julia. In addition to drastically reducing computation time, this new inference approach provides a posterior distribution of the augmented data, that is the tree with extinct and unsampled lineages as well as associated diversification rates. In particular, this allows extracting the distribution through time of both the mean rate and the number of lineages. We assess the statistical performances of our approach using simulations and illustrate its application on the entire bird radiation.
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Affiliation(s)
- Odile Maliet
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Hélène Morlon
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
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14
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Character displacement drives trait divergence in a continental fauna. Proc Natl Acad Sci U S A 2021; 118:2021209118. [PMID: 33963076 DOI: 10.1073/pnas.2021209118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coexisting (sympatric) pairs of closely related species are often characterized by exaggerated trait differences. This widespread pattern is consistent with adaptation for reduced similarity due to costly interactions (i.e., "character displacement")-a classic hypothesis in evolutionary theory. But it is equally consistent with a community assembly bias in which lineages with greater trait differences are more likely to establish overlapping ranges in the first place (i.e., "species sorting"), as well as with null expectations of trait divergence through time. Few comparative analyses have explicitly modeled these alternatives, and it remains unclear whether trait divergence is a general prerequisite for sympatry or a consequence of interactions between sympatric species. Here, we develop statistical models that allow us to distinguish the signature of these processes based on patterns of trait divergence in closely related lineage pairs. We compare support for each model using a dataset of bill shape differences in 207 pairs of New World terrestrial birds representing 30 avian families. We find that character displacement models are overwhelmingly supported over species sorting and null expectations, indicating that exaggerated bill shape differences in sympatric pairs result from enhanced divergent selection in sympatry. We additionally detect a latitudinal gradient in character displacement, which appears strongest in the tropics. Our analysis implicates costly species interactions as powerful drivers of trait divergence in a major vertebrate fauna. These results help substantiate a long-standing but equivocally supported linchpin of evolutionary theory.
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15
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Duchen P, Alfaro ML, Rolland J, Salamin N, Silvestro D. On the Effect of Asymmetrical Trait Inheritance on Models of Trait Evolution. Syst Biol 2021; 70:376-388. [PMID: 32681798 PMCID: PMC7875446 DOI: 10.1093/sysbio/syaa055] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 11/25/2022] Open
Abstract
Current phylogenetic comparative methods modeling quantitative trait evolution generally assume that, during speciation, phenotypes are inherited identically between the two daughter species. This, however, neglects the fact that species consist of a set of individuals, each bearing its own trait value. Indeed, because descendent populations after speciation are samples of a parent population, we can expect their mean phenotypes to randomly differ from one another potentially generating a "jump" of mean phenotypes due to asymmetrical trait inheritance at cladogenesis. Here, we aim to clarify the effect of asymmetrical trait inheritance at speciation on macroevolutionary analyses, focusing on model testing and parameter estimation using some of the most common models of quantitative trait evolution. We developed an individual-based simulation framework in which the evolution of phenotypes is determined by trait changes at the individual level accumulating across generations, and cladogenesis occurs then by separation of subsets of the individuals into new lineages. Through simulations, we assess the magnitude of phenotypic jumps at cladogenesis under different modes of trait inheritance at speciation. We show that even small jumps can strongly alter both the results of model selection and parameter estimations, potentially affecting the biological interpretation of the estimated mode of evolution of a trait. Our results call for caution when interpreting analyses of trait evolution, while highlighting the importance of testing a wide range of alternative models. In the light of our findings, we propose that future methodological advances in comparative methods should more explicitly model the intraspecific variability around species mean phenotypes and how it is inherited at speciation.
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Affiliation(s)
- Pablo Duchen
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Michael L Alfaro
- University of California Los Angeles (UCLA). College Life Sciences - Ecology and Evolutionary Biology. Los Angeles, CA, USA
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
- Department of Zoology, University of British Columbia, #4200-6270 University Blvd, Vancouver, BC, Canada
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland Nicolas Salamin and Daniele Silvestro contributed equally to this article
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16
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Tobias JA, Ottenburghs J, Pigot AL. Avian Diversity: Speciation, Macroevolution, and Ecological Function. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-025023] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The origin, distribution, and function of biological diversity are fundamental themes of ecology and evolutionary biology. Research on birds has played a major role in the history and development of these ideas, yet progress was for many decades limited by a focus on patterns of current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from a recent wave of integrative studies combining comprehensive phylogenetic, environmental, and functional trait data at unprecedented scales. We review these empirical advances and describe how they are reshaping our understanding of global patterns of bird diversity and the processes by which it arises, with implications for avian biogeography and functional ecology. Further expansion and integration of data sets may help to resolve longstanding debates about the evolutionary origins of biodiversity and offer a framework for understanding and predicting the response of ecosystems to environmental change.
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Affiliation(s)
- Joseph A. Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot SL5 7PY, United Kingdom
| | - Jente Ottenburghs
- Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Alex L. Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
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Braga MP, Landis MJ, Nylin S, Janz N, Ronquist F. Bayesian Inference of Ancestral Host-Parasite Interactions under a Phylogenetic Model of Host Repertoire Evolution. Syst Biol 2020; 69:1149-1162. [PMID: 32191324 PMCID: PMC7584141 DOI: 10.1093/sysbio/syaa019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 02/27/2020] [Accepted: 03/15/2020] [Indexed: 11/12/2022] Open
Abstract
Intimate ecological interactions, such as those between parasites and their hosts, may persist over long time spans, coupling the evolutionary histories of the lineages involved. Most methods that reconstruct the coevolutionary history of such interactions make the simplifying assumption that parasites have a single host. Many methods also focus on congruence between host and parasite phylogenies, using cospeciation as the null model. However, there is an increasing body of evidence suggesting that the host ranges of parasites are more complex: that host ranges often include more than one host and evolve via gains and losses of hosts rather than through cospeciation alone. Here, we develop a Bayesian approach for inferring coevolutionary history based on a model accommodating these complexities. Specifically, a parasite is assumed to have a host repertoire, which includes both potential hosts and one or more actual hosts. Over time, potential hosts can be added or lost, and potential hosts can develop into actual hosts or vice versa. Thus, host colonization is modeled as a two-step process that may potentially be influenced by host relatedness. We first explore the statistical behavior of our model by simulating evolution of host-parasite interactions under a range of parameter values. We then use our approach, implemented in the program RevBayes, to infer the coevolutionary history between 34 Nymphalini butterfly species and 25 angiosperm families. Our analysis suggests that host relatedness among angiosperm families influences how easily Nymphalini lineages gain new hosts. [Ancestral hosts; coevolution; herbivorous insects; probabilistic modeling.].
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Affiliation(s)
- Mariana P Braga
- Department of Zoology, Stockholm University, Stockholm, SE-10691, Sweden
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael J Landis
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Sören Nylin
- Department of Zoology, Stockholm University, Stockholm, SE-10691, Sweden
| | - Niklas Janz
- Department of Zoology, Stockholm University, Stockholm, SE-10691, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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18
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Jarzyna MA, Quintero I, Jetz W. Global functional and phylogenetic structure of avian assemblages across elevation and latitude. Ecol Lett 2020; 24:196-207. [PMID: 33124188 DOI: 10.1111/ele.13631] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/06/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
Mountain systems are exceptionally species rich, yet the associated elevational gradients in functional and phylogenetic diversity and their consistency across latitude remain little understood. Here, we document how avian functional and phylogenetic diversity and structure vary along all major elevational gradients worldwide and uncover strong latitudinal differences. Assemblages in warm tropical lowlands and cold temperate highlands are marked by high functional overdispersion and distinctiveness, whereas tropical highlands and temperate lowlands appear strongly functionally clustered and redundant. We additionally find strong geographic variation in the interplay of phylogenetic and functional structure, with strongest deviations between the two in temperate highlands. This latitudinal and elevational variation in assemblage functional structure is underpinned by nuanced shifts in the position, shape and composition of multivariate trait space. We find that, independent of latitude, high-elevation assemblages emerge as exceptionally susceptible to functional change.
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Affiliation(s)
- Marta A Jarzyna
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Laboratory, Columbus, OH, 43210, USA.,Translational Data Analytics Institute, The Ohio State University, 1760 Neil Avenue, 175 Pomerene Hall, Columbus, OH, 43210, USA.,Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
| | - Ignacio Quintero
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.,Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.,Center for Biodiversity and Global Change, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
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19
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Fraser D, Soul LC, Tóth AB, Balk MA, Eronen JT, Pineda-Munoz S, Shupinski AB, Villaseñor A, Barr WA, Behrensmeyer AK, Du A, Faith JT, Gotelli NJ, Graves GR, Jukar AM, Looy CV, Miller JH, Potts R, Lyons SK. Investigating Biotic Interactions in Deep Time. Trends Ecol Evol 2020; 36:61-75. [PMID: 33067015 DOI: 10.1016/j.tree.2020.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.
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Affiliation(s)
- Danielle Fraser
- Palaeobiology, Canadian Museum of Nature, Ottawa, ON, Canada; Biology and Earth Sciences, Carleton University, Ottawa, ON, Canada; Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA.
| | - Laura C Soul
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Anikó B Tóth
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, NSW, Australia
| | - Meghan A Balk
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Jussi T Eronen
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; Helsinki Institute of Sustainability Science, Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland; BIOS research Unit, Helsinki, Finland
| | - Silvia Pineda-Munoz
- Department of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Amelia Villaseñor
- Department of Anthropology, University of Arkansas, Fayetteville, AR, USA
| | - W Andrew Barr
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Anna K Behrensmeyer
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Andrew Du
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, Salt Lake City, UT,USA; Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Gary R Graves
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Advait M Jukar
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Cindy V Looy
- Department of Integrative Biology, Museum of Paleontology, University and Jepson Herbaria, University of California-Berkeley, Berkeley, CA , USA
| | - Joshua H Miller
- Department of Geology, University of Cincinnati, Cincinnati, OH, USA
| | - Richard Potts
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC , USA
| | - S Kathleen Lyons
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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20
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Brennan IG, Lemmon AR, Lemmon EM, Portik DM, Weijola V, Welton L, Donnellan SC, Keogh JS. Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity. Syst Biol 2020; 70:120-132. [PMID: 32521014 DOI: 10.1093/sysbio/syaa046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here, we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragon Varanus komodoensis and the smallest Australian dwarf goannas, Varanus length and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. Incorporating both exon-capture molecular and morphological data sets we use a combined evidence approach to estimate the relationships among living and extinct varaniform lizards. Our results suggest that communities of Australian Varanus show high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.[Character displacement; comparative methods; phylogenetics; trait evolution; Varanus.].
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alan R Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Daniel M Portik
- Department of Ecology and Evolution, University of Arizona, Biosciences West Rm 310, 1041 E. Lowell St, Tucson, AZ 85745 USA
| | - Valter Weijola
- Zoological Museum, Biodiversity Unit, FI-20014 University of Turku, Finland
| | - Luke Welton
- Univeristy of Kansas Biodiversity Institute & Natural History Museum, 1345 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Stephen C Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide SA 5000 Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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