1
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Rakotoarivelo AR, Rambuda T, Taron UH, Stalder G, O'Donoghue P, Robovský J, Hartmann S, Hofreiter M, Moodley Y. Complex patterns of gene flow and convergence in the evolutionary history of the spiral-horned antelopes (Tragelaphini). Mol Phylogenet Evol 2024; 198:108131. [PMID: 38909875 DOI: 10.1016/j.ympev.2024.108131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/19/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
The Tragelaphini, also known as spiral-horned antelope, is a phenotypically diverse mammalian tribe comprising a single genus, Tragelaphus. The evolutionary history of this tribe has attracted the attention of taxonomists and molecular geneticists for decades because its diversity is characterised by conflicts between morphological and molecular data as well as between mitochondrial, nuclear and chromosomal DNA. These inconsistencies point to a complex history of ecological diversification, coupled by either phenotypic convergence or introgression. Therefore, to unravel the phylogenetic relationships among spiral-horned antelopes, and to further investigate the role of divergence and gene flow in trait evolution, we sequenced genomes for all nine accepted species of the genus Tragelaphus, including a genome each for the highly divergent bushbuck lineages (T. s. scriptus and T. s. sylvaticus). We successfully reconstructed the Tragelaphus species tree, providing genome-level support for the early Pliocene divergence and monophyly of the nyala (T. angasii) and lesser kudu (T. imberbis), the monophyly of the two eland species (T. oryx and T. derbianus) and, importantly, the monophyly of kéwel (T. s. scriptus) and imbabala (T. s. sylvaticus) bushbuck. We found strong evidence for gene flow in at least four of eight nodes on the species tree. Among the six phenotypic traits assessed here, only habitat type mapped onto the species tree without homoplasy, showing that trait evolution was the result of complex patterns of divergence, introgression and convergent evolution.
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Affiliation(s)
- Andrinajoro R Rakotoarivelo
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa; Department of Zoology and Entomology, University of the Free State: QwaQwa Campus, Private Bag X13, Phuthaditjhaba 9866, Republic of South Africa
| | - Thabelo Rambuda
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa; Department of Genetics, University of Pretoria, Private Bag X20, Hatfield 0028, Republic of South Africa
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Gabrielle Stalder
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstraße 1, A-1160 Wien, Austria
| | | | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Stefanie Hartmann
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa.
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2
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Lambert S, Voznica J, Morlon H. Deep Learning from Phylogenies for Diversification Analyses. Syst Biol 2023; 72:1262-1279. [PMID: 37556735 DOI: 10.1093/sysbio/syad044] [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: 10/03/2022] [Revised: 06/20/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
Birth-death (BD) models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood formula must be established each time a new model is proposed; for some models, such a formula is not even tractable. Deep learning can bring solutions in such situations, as deep neural networks can be trained to learn the relation between simulations and parameter values as a regression problem. In this paper, we adapt a recently developed deep learning method from pathogen phylodynamics to the case of diversification inference, and we extend its applicability to the case of the inference of state-dependent diversification models from phylogenies associated with trait data. We demonstrate the accuracy and time efficiency of the approach for the time-constant homogeneous BD model and the Binary-State Speciation and Extinction model. Finally, we illustrate the use of the proposed inference machinery by reanalyzing a phylogeny of primates and their associated ecological role as seed dispersers. Deep learning inference provides at least the same accuracy as likelihood-based inference while being faster by several orders of magnitude, offering a promising new inference approach for the deployment of future models in the field.
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Affiliation(s)
- Sophia Lambert
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, 46 Rue d'Ulm, 75005 Paris, France
- Institute of Ecology and Evolution, Department of Biology, 5289 University of Oregon, Eugene, OR 97403, USA
| | - Jakub Voznica
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, 25-28 Rue du Dr Roux, 75015 Paris, France
- Unité de Biologie Computationnelle, USR 3756 CNRS, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, 46 Rue d'Ulm, 75005 Paris, France
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3
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Gómez-Llano M, Boys WA, Ping T, Tye SP, Siepielski AM. Interactions between fitness components across the life cycle constrain competitor coexistence. J Anim Ecol 2023; 92:2297-2308. [PMID: 37087690 DOI: 10.1111/1365-2656.13927] [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: 01/06/2023] [Accepted: 03/22/2023] [Indexed: 04/24/2023]
Abstract
Numerous mechanisms can promote competitor coexistence. Yet, these mechanisms are often considered in isolation from one another. Consequently, whether multiple mechanisms shaping coexistence combine to promote or constrain species coexistence remains an open question. Here, we aim to understand how multiple mechanisms interact within and between life stages to determine frequency-dependent population growth, which has a key role stabilizing local competitor coexistence. We conducted field experiments in three lakes manipulating relative frequencies of two Enallagma damselfly species to evaluate demographic contributions of three mechanisms affecting different fitness components across the life cycle: the effect of resource competition on individual growth rate, predation shaping mortality rates, and mating harassment determining fecundity. We then used a demographic model that incorporates carry-over effects between life stages to decompose the relative effect of each fitness component generating frequency-dependent population growth. This decomposition showed that fitness components combined to increase population growth rates for one species when rare, but they combined to decrease population growth rates for the other species when rare, leading to predicted exclusion in most lakes. Because interactions between fitness components within and between life stages vary among populations, these results show that local coexistence is population specific. Moreover, we show that multiple mechanisms do not necessarily increase competitor coexistence, as they can also combine to yield exclusion. Identifying coexistence mechanisms in other systems will require greater focus on determining contributions of different fitness components across the life cycle shaping competitor coexistence in a way that captures the potential for population-level variation.
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Affiliation(s)
- Miguel Gómez-Llano
- Department of Environmental and Life Sciences, Karlstad University, Karlstad, 65188, Sweden
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Wade A Boys
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Taylor Ping
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Simon P Tye
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Adam M Siepielski
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
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4
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Henao-Diaz LF, Pennell M. The Major Features of Macroevolution. Syst Biol 2023; 72:1188-1198. [PMID: 37248967 DOI: 10.1093/sysbio/syad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/02/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the "major features of macroevolution." By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.
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Affiliation(s)
- L Francisco Henao-Diaz
- Department of Ecology and Evolution, University of Chicago, Chicago, USA
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Matt Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, USA
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5
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Pantel JH, Becks L. Statistical methods to identify mechanisms in studies of eco-evolutionary dynamics. Trends Ecol Evol 2023; 38:760-772. [PMID: 37437547 DOI: 10.1016/j.tree.2023.03.011] [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: 08/18/2022] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 07/14/2023]
Abstract
While the reciprocal effects of ecological and evolutionary dynamics are increasingly recognized as an important driver for biodiversity, detection of such eco-evolutionary feedbacks, their underlying mechanisms, and their consequences remains challenging. Eco-evolutionary dynamics occur at different spatial and temporal scales and can leave signatures at different levels of organization (e.g., gene, protein, trait, community) that are often difficult to detect. Recent advances in statistical methods combined with alternative hypothesis testing provides a promising approach to identify potential eco-evolutionary drivers for observed data even in non-model systems that are not amenable to experimental manipulation. We discuss recent advances in eco-evolutionary modeling and statistical methods and discuss challenges for fitting mechanistic models to eco-evolutionary data.
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Affiliation(s)
- Jelena H Pantel
- Ecological Modelling, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 2, 45117 Essen, Germany.
| | - Lutz Becks
- University of Konstanz, Aquatic Ecology and Evolution, Limnological Institute University of Konstanz Mainaustraße 252 78464, Konstanz/Egg, Germany
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6
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Platania L, Gómez-Zurita J. Analysis of intrinsic evolutionary factors leading to microendemic distributions in New Caledonian leaf beetles. Sci Rep 2023; 13:6909. [PMID: 37106022 PMCID: PMC10140066 DOI: 10.1038/s41598-023-34104-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/24/2023] [Indexed: 04/29/2023] Open
Abstract
Microendemicity, or the condition of some species having local ranges, is a relatively common pattern in nature. However, the factors that lead to this pattern are still largely unknown. Most studies addressing this issue tend to focus on extrinsic factors associated with microendemic distributions, such as environmental conditions, hypothesising a posteriori about underlying potential speciation mechanisms, linked or not to these conditions. Here, we use a multi-faceted approach mostly focusing on intrinsic factors instead, namely diversification dynamics and speciation modes in two endemic sibling genera of leaf beetles with microendemic distributions, Taophila and Tricholapita, in a microendemicity hotspot, New Caledonia. Results suggest that the diversification rate in this lineage slowed down through most of the Neogene and consistently with a protracted speciation model possibly combined with several ecological and environmental factors potentially adding rate-slowing effects through time. In turn, species accumulated following successive allopatric speciation cycles, possibly powered by marked geological and climatic changes in the region in the last 25 million years, with daughter species ranges uncorrelated with the time of speciation. In this case, microendemicity seems to reflect a mature state for the system, rather than a temporary condition for recent species, as suggested for many microendemic organisms.
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Affiliation(s)
- Leonardo Platania
- Botanical Institute of Barcelona (CSIC-Ajuntament Barcelona), Pg. del Migdia S/N, 08038, Barcelona, Spain
- Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Jesús Gómez-Zurita
- Botanical Institute of Barcelona (CSIC-Ajuntament Barcelona), Pg. del Migdia S/N, 08038, Barcelona, Spain.
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7
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Jiménez-Ortega D, Valente L, Dugo-Cota Á, Rabosky DL, Vilà C, Gonzalez-Voyer A. Diversification dynamics in Caribbean rain frogs ( Eleutherodactylus) are uncoupled from the anuran community and consistent with adaptive radiation. Proc Biol Sci 2023; 290:20222171. [PMID: 36629104 PMCID: PMC9832552 DOI: 10.1098/rspb.2022.2171] [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: 10/28/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
Adaptive radiation is proposed to play a key role in generating differences in species richness among lineages and geographical regions. Due to the importance of ecological divergence in adaptive radiation, species richness is predicted to be influenced by equilibrium diversity dynamics, although the concept continues to generate much debate. An additional important question is whether radiating clades have intrinsic biological characteristics that make them particularly prone to diversify. We tackle these questions by analysing (i) the temporal patterns of diversification of Caribbean Eleutherodactylus frogs, and (ii) assembly of the complete native anuran community of the Caribbean archipelago (197 species), testing for the presence of equilibrium dynamics and whether diversification patterns of Eleutherodactylus differ from those of the rest of the Caribbean anurans. Diversification rates follow the predicted pattern of rapid diversification early in the radiation which gradually decreases towards the present. Eleutherodactylus diversification is significantly faster than that of the Caribbean anuran community, and although equilibrium dynamics influence richness of all Caribbean anurans, Eleutherodactylus shows higher carrying capacity. Our results indicate that ecological opportunity per se is not sufficient for adaptive radiation and that diverse lineages present intrinsic characteristics that enable them to make the most of available opportunity.
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Affiliation(s)
- Dante Jiménez-Ortega
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Luis Valente
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Álvaro Dugo-Cota
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| | - Daniel L. Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
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8
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Schachat SR, Goldstein PZ, Desalle R, Bobo DM, Boyce CK, Payne JL, Labandeira CC. Illusion of flight? Absence, evidence and the age of winged insects. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abstract
The earliest fossils of winged insects (Pterygota) are mid-Carboniferous (latest Mississippian, 328–324 Mya), but estimates of their age based on fossil-calibrated molecular phylogenetic studies place their origin at 440–370 Mya during the Silurian or Devonian. This discrepancy would require that winged insects evaded fossilization for at least the first ~50 Myr of their history. Here, we examine the plausibility of such a gap in the fossil record, and possible explanations for it, based on comparisons with the fossil records of other arthropod groups, the distribution of first occurrence dates of pterygote families, phylogenetically informed simulations of the fossilization of Palaeozoic insects, and re-analysis of data presented by Misof and colleagues using updated fossil calibrations under a variety of prior probability settings. We do not find support for the mechanisms previously suggested to account for such an extended gap in the pterygote fossil record, including sampling bias, preservation bias, and body size. We suggest that inference of an early origin of Pterygota long prior to their first appearance in the fossil record is probably an analytical artefact of taxon sampling and choice of fossil calibration points, possibly compounded by heterogeneity in rates of sequence evolution or speciation, including radiations or ‘bursts’ during their early history.
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Affiliation(s)
- Sandra R Schachat
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Paul Z Goldstein
- Systematic Entomology Laboratory, USDA, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Rob Desalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics , New York, NY , USA
| | - Dean M Bobo
- American Museum of Natural History, Sackler Institute for Comparative Genomics , New York, NY , USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University , New York, NY , USA
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Jonathan L Payne
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Conrad C Labandeira
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
- Department of Entomology and Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park , MD , USA
- Capital Normal University, School of Life Sciences , Beijing , China
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9
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Esquerré D, Brennan IG, Donnellan S, Keogh JS. Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons. Biol Lett 2022; 18:20220360. [PMID: 36541096 PMCID: PMC9768648 DOI: 10.1098/rsbl.2022.0360] [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: 08/04/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
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10
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Utami CY, Sholihah A, Condamine FL, Thébaud C, Hubert N. Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses. Proc Biol Sci 2022; 289:20221335. [PMID: 36382998 PMCID: PMC9667750 DOI: 10.1098/rspb.2022.1335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/26/2022] [Indexed: 12/02/2023] Open
Abstract
Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are now available. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporating DNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdowns when cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecological models received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.
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Affiliation(s)
- C. Y. Utami
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
- UMR 5174 EDB (CNRS, Université Paul Sabatier, IRD), 31062 Toulouse Cedex 9, France
| | - A. Sholihah
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung 40132, Indonesia
| | - F. L. Condamine
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - C. Thébaud
- UMR 5174 EDB (CNRS, Université Paul Sabatier, IRD), 31062 Toulouse Cedex 9, France
| | - N. Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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11
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Velasco JA, Pinto-Ledezma JN. Mapping species diversification metrics in macroecology: Prospects and challenges. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.951271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The intersection of macroecology and macroevolution is one of today’s most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.
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12
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Skeels A, Bach W, Hagen O, Jetz W, Pellissier L. Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations. Syst Biol 2022:6637530. [PMID: 35809070 DOI: 10.1093/sysbio/syac048] [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] [Received: 10/08/2021] [Revised: 06/21/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Biodiversity varies predictably with environmental energy around the globe, but the underlaying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental kinetic energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modelled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modelling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - W Bach
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - O Hagen
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.,Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
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13
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Louca S, Henao-Diaz LF, Pennell M. The scaling of diversification rates with age is likely explained by sampling bias. Evolution 2022; 76:1625-1637. [PMID: 35567800 DOI: 10.1111/evo.14515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/07/2022] [Indexed: 01/22/2023]
Abstract
Numerous phylogenetic studies reported the existence of a pervasive scaling relationship between the ages of extant eukaryotic clades and their estimated diversification rates. The causes of this age-rate-scaling (ARS), whether biological and/or artifactual, remain unresolved. Here we fit diversification models to thousands of eukaryotic time-calibrated phylogenies to explore multiple potential causes of the ARS including parameter non-identifiability, model inadequacy, biases in taxonomic practice, and an important and ubiquitous form of sampling bias-preferentially analyzing larger extant clades. We distinguish between two mechanism by which such sampling biases can cause an ARS: First, by favoring clades that happen to be unusually large merely by chance (i.e., due to the stochastic nature of the cladogenic process), thus leading to rate overestimation, and second, by favoring clades that have truly higher diversification rates. We find that, of the proposed explanations, only sampling biases are likely to contribute to the observed ARS. We develop methods for fully correcting for sampling bias mechanism 1, and find that despite these corrections a substantial ARS remains. We then confirm using simulations that preferring trees with truly higher rates (mechanism 2) likely explains this residual ARS. Since we do not have a completely unbiased sample of clades, including extinct ones, for phylogenetic analyses, it is difficult to demonstrate unambiguously that sampling biases are the sole cause of the ARS. Sampling biases are, however, a parsimonious and plausible explanation for this widely observed macroevolutionary pattern, and this has implications for how we interpret the distribution of diversification rate estimates in extant clades.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - L Francisco Henao-Diaz
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Matt Pennell
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
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14
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Chaparro‐Pedraza PC, Roth G, Seehausen O. The enrichment paradox in adaptive radiations: Emergence of predators hinders diversification in resource rich environments. Ecol Lett 2022; 25:802-813. [PMID: 35032146 PMCID: PMC9303570 DOI: 10.1111/ele.13955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/25/2021] [Accepted: 12/08/2021] [Indexed: 12/18/2022]
Abstract
Adaptive radiations are known for rapid niche diversification in response to ecological opportunity. While most resources usually exist prior to adaptive radiation, novel niches associated with novel resources can be created as a clade diversifies. For example, in African lake cichlid radiations some species prey upon other species of the clade (intraclade consumers). Using a trait-based eco-evolutionary model, we investigate the evolution of intraclade consumers in adaptive radiations and the effect of this novel trophic interaction on the diversification process of the radiating clade. We find that the evolutionary emergence of intraclade consumers halts the diversification processes of other ecomorphs as a result of increased top-down control of density. Because high productivity enables earlier evolution of intraclade consumers, highly productive environments come to harbour less species-rich radiations than comparable radiations in less productive environments. Our results reveal how macroevolutionary and community patterns can emerge from ecological and microevolutionary processes.
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Affiliation(s)
- P. Catalina Chaparro‐Pedraza
- Aquatic Ecology and EvolutionInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology and EvolutionSwiss Federal Institute of Aquatic Science and Technology (EAWAG)KastanienbaumSwitzerland
- Department Systems Analysis, Integrated Assessment and ModellingSwiss Federal Institute of Aquatic Science and Technology (EAWAG)DübendorfSwitzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Ole Seehausen
- Aquatic Ecology and EvolutionInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology and EvolutionSwiss Federal Institute of Aquatic Science and Technology (EAWAG)KastanienbaumSwitzerland
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15
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Siepielski AM, Gómez-Llano M, McPeek MA. Environmental Conditions during Development Affect Sexual Selection through Trait-Fitness Relationships. Am Nat 2022; 199:34-50. [DOI: 10.1086/717294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Harmon LJ, Pennell MW, Henao-Diaz LF, Rolland J, Sipley BN, Uyeda JC. Causes and Consequences of Apparent Timescaling Across All Estimated Evolutionary Rates. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-011921-023644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including rates of molecular evolution, trait evolution, and lineage diversification, share a similar scaling pattern with time: The highest rates are those measured over the shortest time interval. This creates a disconnect between micro- and macroevolution, although the pattern is the opposite of what some might expect: Patterns of change over short timescales predict that evolution has tremendous potential to create variation and that potential is barely tapped by macroevolution. In this review, we discuss this shared scaling pattern across evolutionary rates. We break down possible explanations for scaling into two categories, estimation error and model misspecification, and discuss how both apply to each type of rate. We also discuss the consequences of this ubiquitous pattern, which can lead to unexpected results when comparing ratesover different timescales. Finally, after addressing purely statistical concerns, we explore a few possibilities for a shared unifying explanation across the three types of rates that results from a failure to fully understand and account for how biological processes scale over time.
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Affiliation(s)
- Luke J. Harmon
- Institute for Bioinformatics and Evolutionary Studies (IBEST) and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA
| | - Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - L. Francisco Henao-Diaz
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jonathan Rolland
- Laboratoire Evolution et Diversité Biologique, CNRS, UMR5174, Université Toulouse III–Paul Sabatier, 31062 Toulouse, France
| | - Breanna N. Sipley
- Program for Bioinformatics and Computational Biology, University of Idaho, Moscow, Idaho 83844, USA
| | - Josef C. Uyeda
- Department of Biological Sciences, Virginia Tech University, Blacksburg, Virginia 24061, USA
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17
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Multiple paths to morphological diversification during the origin of amniotes. Nat Ecol Evol 2021; 5:1243-1249. [PMID: 34312521 DOI: 10.1038/s41559-021-01516-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Early terrestrial vertebrates (amniotes) provide a classic example of diversification following adaptive zone invasion. The initial terrestrialization of vertebrates was closely followed by dietary diversification, as evidenced by a proliferation of craniomandibular and dental adaptations. However, morphological evolution of early amniotes has received limited study, in analyses with restricted taxonomic scope, leaving substantial questions about the dynamics of this important terrestrial radiation. We use novel analyses of discrete characters to quantify variation in evolutionary rates and constraints during diversification of the amniote feeding apparatus. We find evidence for an early burst, comprising high rates of anatomical change that decelerated through time, giving way to a background of saturated morphological evolution. Subsequent expansions of phenotypic diversity were not associated with increased evolutionary rates. Instead, variation in the mode of evolution became important, with groups representing independent origins of herbivory evolving distinctive, group-specific morphologies and thereby exploring novel character-state spaces. Our findings indicate the importance of plant-animal interactions in structuring the earliest radiation of amniotes and demonstrate the importance of variation in modes of phenotypic divergence during a major evolutionary radiation.
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18
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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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19
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Petrosky AL, Rowsey DM, Heaney LR. Molecular assessment of dietary niche partitioning in an endemic island radiation of tropical mammals. Mol Ecol 2021; 30:5858-5873. [PMID: 34460971 DOI: 10.1111/mec.16158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 07/27/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023]
Abstract
Island radiations represent unique evolutionary histories in unique ecological contexts. These radiations provide opportunities to investigate ecological diversification in groups that typically exhibit niche partitioning among their constituents, including partitioning of food resources. DNA metabarcoding produces finer levels of diet identification than traditional methods, allowing us to examine dietary niche partitioning in communities or clades in which species share superficially similar diets. Here, we use DNA metabarcoding to investigate dietary niche partitioning in an endemic radiation of mammals in the Philippines. Our data reveal niche partitioning as well as phylogenetically-uncorrelated adaptive evolution in this small mammal community. Because 70% of the focal species belong to the tribe Chrotomyini, an endemic Philippine radiation of murid rodents that feed extensively on earthworms, this study sheds light on dietary adaptation and its role in the co-occurrence of closely related species. Our results reveal fine-scale resource partitioning within this community; our data provide compelling evidence for niche partitioning of diet that was masked by previous diet categories and will help in further dissecting the model adaptive radiation of endemic small mammals on Luzon. This study reinforces the notion that DNA metabarcoding can be a valuable tool for investigating both ecological relationships and evolutionary ecology at the community and phylogenetic level, respectively.
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Affiliation(s)
- Anna L Petrosky
- Field Museum of Natural History, Chicago, Illinois, USA.,Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
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20
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Vankan M, Ho SYW, Duchêne DA. Evolutionary Rate Variation Among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference. Syst Biol 2021; 71:490-500. [PMID: 34255084 PMCID: PMC8830059 DOI: 10.1093/sysbio/syab051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/18/2021] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help to inform the choice of data for phylogenomic analysis. We investigated this in an analysis of 30 phylogenomic data sets. For each data set, we examined the association between several branch-length characteristics of gene trees and the distance between these gene trees and the corresponding species trees. We found that the distance of each gene tree to the species tree inferred from the full data set was positively associated with variation in root-to-tip distances and negatively associated with mean branch support. However, no such associations were found for gene-tree length, a measure of the overall substitution rate at each locus. We further explored the usefulness of the best-performing branch-based characteristics for selecting loci for phylogenomic analyses. We found that loci that yield gene trees with high variation in root-to-tip distances have a disproportionately distant signal of tree topology compared with the complete data sets. These results suggest that rate variation across lineages should be taken into consideration when exploring and even selecting loci for phylogenomic analysis.[Branch support; data filtering; nucleotide substitution model; phylogenomics; substitution rate; summary coalescent methods.]
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Affiliation(s)
- Mezzalina Vankan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.,Research School of Biology, Australian National University, ACT 2601, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - David A Duchêne
- Research School of Biology, Australian National University, ACT 2601, Australia.,Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1352, Denmark
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21
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Stireman JO, Cerretti P, O’hara JE, Moulton JK. Extraordinary diversification of the “bristle flies” (Diptera: Tachinidae) and its underlying causes. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The family Tachinidae (“bristle flies”) is the most diverse and ecologically important group of insect parasitoids outside the parasitic wasps. It is among the most species rich families of flies (Diptera) and has experienced a recent adaptive radiation across the globe. We make use of a molecular phylogeny of the family to examine its rapid radiation and explore the traits of tachinid lineages that may have contributed to variation in their diversification. We apply a range of diversification analyses to assess the consistency and robustness of effects. We find that the Tachinidae are among the most rapidly diversifying families of animals. Six to eight clades of bristle flies, distributed across the phylogeny, exhibit strong evidence of accelerated diversification. Our results suggest that the use of holometabolous insect larvae, and specifically caterpillars (Lepidoptera), as hosts, is associated with increased diversification rates. However, these effects were inconsistent across analyses. We detected little influence of oviposition strategy (egg type) or host feeding habit, and we recovered evidence that unmeasured “hidden” traits may explain greater variance in diversification. We evaluated the strengths and weaknesses of different Maximum Likelihood and Bayesian approaches for analysing diversification and the potential for extrinsic factors, such as geography, to influence patterns of richness and diversification. In general, we conclude that although certain traits may provide opportunities for diversification, whether this is capitalized on may depend on additional traits and/or historical contingency.
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Affiliation(s)
- John O Stireman
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Pierfilippo Cerretti
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, ‘Sapienza’ Università di Roma, Piazzale A. Moro 5, Rome, Italy
- Australian National Insect Collection, CSIRO National Facilities and Collections, Black Mountain, Canberra, Australia
| | - James E O’hara
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - John K Moulton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
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22
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Sholihah A, Delrieu-Trottin E, Condamine FL, Wowor D, Rüber L, Pouyaud L, Agnèse JF, Hubert N. Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots. Syst Biol 2021; 70:940-960. [PMID: 33560439 DOI: 10.1093/sysbio/syab006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 01/23/2023] Open
Abstract
Pleistocene Climatic Fluctuations (PCF) are frequently highlighted as important evolutionary engines that triggered cycles of biome expansion and contraction. While there is ample evidence of the impact of PCF on biodiversity of continental biomes, the consequences in insular systems depend on the geology of the islands and the ecology of the taxa inhabiting them. The idiosyncratic aspects of insular systems are exemplified by the islands of the Sunda Shelf in Southeast Asia (Sundaland), where PCF-induced eustatic fluctuations had complex interactions with the geology of the region, resulting in high species diversity and endemism. Emergent land in Southeast Asia varied drastically with sea level fluctuations during the Pleistocene. Climate-induced fluctuations in sea level caused temporary connections between insular and continental biodiversity hotspots in Southeast Asia. These exposed lands likely had freshwater drainage systems that extended between modern islands: the Paleoriver Hypothesis. Built upon the assumption that aquatic organisms are among the most suitable models to trace ancient river boundaries and fluctuations of landmass coverage, the present study aims to examine the evolutionary consequences of PCF on the dispersal of freshwater biodiversity in Southeast Asia. Time-calibrated phylogenies of DNA-delimited species were inferred for six species-rich freshwater fish genera in Southeast Asia (Clarias, Channa, Glyptothorax, Hemirhamphodon, Dermogenys, Nomorhamphus). The results highlight rampant cryptic diversity and the temporal localization of most speciation events during the Pleistocene, with 88% of speciation events occurring during this period. Diversification analyses indicate that sea level-dependent diversification models poorly account for species proliferation patterns for all clades excepting Channa. Ancestral area estimations point to Borneo as the most likely origin for most lineages, with two waves of dispersal to Sumatra and Java during the last 5 Myr. Speciation events are more frequently associated with boundaries of the paleoriver watersheds, with 60%, than islands boundaries, with 40%. In total, one-third of speciation events are inferred to have occured within paleorivers on a single island, suggesting that habitat heterogeneity and factors other than allopatry between islands substantially affected diversification of Sundaland fishes. Our results suggest that species proliferation in Sundaland is not wholly reliant on Pleistocene sea-level fluctuations isolating populations on different islands.
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Affiliation(s)
- Arni Sholihah
- Institut Teknologi Bandung, School of Life Sciences and Technology, Jalan Ganesha 10, Bandung 40132, Indonesia.,UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Erwan Delrieu-Trottin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung an der Humboldt-Universität zu Berlin
| | - Fabien L Condamine
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Daisy Wowor
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong 16911, Indonesia
| | - Lukas Rüber
- Naturhistorisches Museum Bern, Bernastrasse 15, 3005 Bern, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Jean-François Agnèse
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
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23
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Villastrigo A, Abellán P, Ribera I. Habitat preference and diversification rates in a speciose lineage of diving beetles. Mol Phylogenet Evol 2021; 159:107087. [PMID: 33545273 DOI: 10.1016/j.ympev.2021.107087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/24/2022]
Abstract
The long-term geological stability of aquatic habitats has been demonstrated to be a determinant in the evolution of macroinvertebrate fauna, with species in running (lotic) waters having lower dispersal abilities, smaller ranges and higher gene flow between populations than species in standing (lentic) environments. Lotic species have been hypothesized to be more specialised, but the diversification dynamics of both habitat types have not been studied in detail. Using a speciose lineage of water beetles we test here whether diversification rates are related to the habitat preference of the species and its consequences on turnover, which we expect to be higher for lotic taxa. Moreover, we tested whether life in lotic environments is acting as an evolutionary dead-end as it is considered an ecological specialisation. We built a comprehensive molecular phylogeny with 473 terminals representing 421 of the 689 known species of the tribe Hydroporini (Coleoptera, Dytiscidae), using a combination of sequences from four mitochondrial and two nuclear genes plus 69 mitogenomes obtained with NGS. We found a general pattern of gradual acceleration of diversification rate with time, with 2-3 significant diversification shifts. However, habitat is not the main factor driving diversification in Hydroporini based on SecSSE analyses. The most recent common ancestor of Hydroporini was reconstructed as a lotic species, with multiple shifts to lentic environments. Most frequent transitions were estimated from lentic and lotic habitats to the category "both", followed by transitions from lotic to lentic and lentic to lotic respectively, although with very similar rates. Contrary to expectations, we found little evidence for differences in diversification dynamics between habitats, with lotic environments clearly not acting as evolutionary dead-ends in Hydroporini.
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Affiliation(s)
- Adrián Villastrigo
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| | | | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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24
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Machac A. The Dynamics of Bird Diversity in the New World. Syst Biol 2021; 69:1180-1199. [PMID: 32333771 PMCID: PMC7584135 DOI: 10.1093/sysbio/syaa028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/12/2020] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
Three prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (i) time for speciation, (ii) diversification rates, and (iii) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and geographic information systems, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon. [Biogeography; community; competition; macroevolution; phylogenetics; richness gradient.]
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Affiliation(s)
- Antonin Machac
- Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver V6T 1Z4, Canada.,Center for Theoretical Study, Charles University, Jilska 1, 110 00 Praha 1, Czech Republic.,Department of Ecology, Charles University, Vinicna 7, 12844 Praha 2, Czech Republic.,Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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25
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Pannetier T, Martinez C, Bunnefeld L, Etienne RS. Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification. Evolution 2020; 75:25-38. [PMID: 33205832 PMCID: PMC7898657 DOI: 10.1111/evo.14124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 10/06/2020] [Accepted: 10/10/2020] [Indexed: 01/08/2023]
Abstract
One of the primary goals of macroevolutionary biology has been to explain general trends in long‐term diversity patterns, including whether such patterns correspond to an upscaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity‐dependent (DD) diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time dependence without diversity dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time‐dependent, but diversity‐independent model that matches the expected diversity through time of a DD model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity dependence. We advocate that tests encompassing additional data, for example, traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.
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Affiliation(s)
- Théo Pannetier
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands.,Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - César Martinez
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands
| | - Lynsey Bunnefeld
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands
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26
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Hua X, Bromham L. Modeling colonization rates over time: Generating null models and testing model adequacy in phylogenetic analyses of species assemblages*. Evolution 2020; 74:2605-2616. [DOI: 10.1111/evo.14086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 07/06/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Xia Hua
- Mathematical Sciences Institute Australian National University Canberra ACT 2601 Australia
- Division of Ecology and Evolution Research School of Biology Australian National University Canberra ACT 2601 Australia
| | - Lindell Bromham
- Division of Ecology and Evolution Research School of Biology Australian National University Canberra ACT 2601 Australia
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27
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Kröger B, Penny A. Skeletal marine animal biodiversity is built by families with long macroevolutionary lag times. Nat Ecol Evol 2020; 4:1410-1415. [PMID: 32747774 DOI: 10.1038/s41559-020-1265-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022]
Abstract
The clade dynamics of marine animals have changed markedly over the Phanerozoic. Long-term diversification is associated with decreasing origination and extinction rates, and with increasing taxon longevity. Here we use the diversification trajectories of skeletal non-colonial marine families to infer the mechanisms that generated these trends. Suggested mechanisms behind these trends include stochastic extinction of taxa with high evolutionary volatility and selection for traits that buffer against extinction. We find an increasing predominance of Phanerozoic families with long lag times between first appearance and peak diversity, over those with 'early burst' diversification trajectories. Long-lag families persisted for longer and had lower evolutionary volatilities, higher genus-level occupancies and genera with larger niche breadths than early burst families. However, they do not preferentially show ecological modes known to protect against extinction. We interpret the rise of the long-lag families as reflecting an intensification of ecosystem-level mechanisms supporting both long-term coexistence and transient dynamics, which increased the capacity of marine ecosystems to accommodate highly diverse communities.
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Affiliation(s)
- Björn Kröger
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
| | - Amelia Penny
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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28
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Nürk NM, Linder HP, Onstein RE, Larcombe MJ, Hughes CE, Piñeiro Fernández L, Schlüter PM, Valente L, Beierkuhnlein C, Cutts V, Donoghue MJ, Edwards EJ, Field R, Flantua SGA, Higgins SI, Jentsch A, Liede‐Schumann S, Pirie MD. Diversification in evolutionary arenas-Assessment and synthesis. Ecol Evol 2020; 10:6163-6182. [PMID: 32607221 PMCID: PMC7319112 DOI: 10.1002/ece3.6313] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/30/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions, and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b), and clade-specific phenotypes or traits (c); thus, d ~ a,b,c. We refer to the four components (a-d) and their interactions collectively as the "Evolutionary Arena." We outline analytical approaches to this framework and present a case study on conifers, for which we parameterize the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.
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Affiliation(s)
- Nicolai M. Nürk
- Department of Plant SystematicsBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - H. Peter Linder
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Renske E. Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | | | - Colin E. Hughes
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Laura Piñeiro Fernández
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
- Department of BotanyUniversity of HohenheimStuttgartGermany
| | | | - Luis Valente
- Naturalis Biodiversity CenterUnderstanding Evolution GroupLeidenThe Netherlands
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Carl Beierkuhnlein
- Department of BiogeographyBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Vanessa Cutts
- School of GeographyUniversity of NottinghamNottinghamUK
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Erika J. Edwards
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Richard Field
- School of GeographyUniversity of NottinghamNottinghamUK
| | | | | | - Anke Jentsch
- Department of Disturbance EcologyBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Sigrid Liede‐Schumann
- Department of Plant SystematicsBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Michael D. Pirie
- Johannes Gutenberg‐UniversitätMainzGermany
- University MuseumUniversity of BergenBergenNorway
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29
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Changing Only Slowly: The Role of Phylogenetic Niche Conservatism in Caviidae (Rodentia) Speciation. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09501-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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Penny A, Kröger B. Impacts of spatial and environmental differentiation on early Palaeozoic marine biodiversity. Nat Ecol Evol 2019; 3:1655-1660. [PMID: 31740841 DOI: 10.1038/s41559-019-1035-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/10/2019] [Indexed: 11/09/2022]
Abstract
The unprecedented diversifications in the fossil record of the early Palaeozoic (541-419 million years ago) increased both within-sample (α) and global (γ) diversity, generating considerable ecological complexity. Faunal difference (β diversity), including spatial heterogeneity, is thought to have played a major role in early Palaeozoic marine diversification, although α diversity is the major determinant of γ diversity through the Phanerozoic. Drivers for this Phanerozoic shift from β to α diversity are not yet resolved. Here, we evaluate the impacts of environmental and faunal heterogeneity on diversity patterns using a global spatial grid. We present early Palaeozoic genus-level α, β and γ diversity curves for molluscs, brachiopods, trilobites and echinoderms and compare them with measures of spatial lithological heterogeneity, which is our proxy for environmental heterogeneity. We find that α and β diversity are associated with increased lithological heterogeneity, and that β diversity declines over time while α increases. We suggest that the enhanced dispersal of marine taxa from the Middle Ordovician onwards facilitated increases in α diversity by encouraging the occupation of narrow niches and increasing the prevalence of transient species, simultaneously reducing spatial β diversity. This may have contributed to a shift from β to α diversity as the major determinant of γ diversity increase over this critical evolutionary interval.
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Affiliation(s)
- Amelia Penny
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
| | - Björn Kröger
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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31
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Harvey MG, Singhal S, Rabosky DL. Beyond Reproductive Isolation: Demographic Controls on the Speciation Process. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024701] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of speciation typically investigate the evolution of reproductive isolation between populations, but several other processes can serve as key steps limiting the formation of species. In particular, the probability of successful speciation can be influenced by factors that affect the frequency with which population isolates form as well as their persistence through time. We suggest that population isolation and persistence have an inherently spatial dimension that can be profitably studied using a conceptual framework drawn from metapopulation ecology. We discuss models of speciation that incorporate demographic processes and highlight the need for a broader application of phylogenetic comparative approaches to evaluate the general importance of population isolation, persistence, and reproductive isolation in speciation. We review diverse and nontraditional data sources that can be leveraged to study isolation and persistence in a comparative framework. This incorporation of spatial demographic information facilitates the integration of perspectives on speciation across disciplines and timescales.
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Affiliation(s)
- Michael G. Harvey
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, California 90747, USA
| | - Daniel L. Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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32
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Lajmi A, Verma A, Karanth KP. Repeated evolution of terrestrial lineages in a continental lizard radiation. J Evol Biol 2019; 33:57-66. [PMID: 31541555 DOI: 10.1111/jeb.13544] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/23/2022]
Abstract
The "early-burst" model of adaptive radiation predicts an early increase in phenotypic disparity concurrent with lineage diversification. Although most studies report a lack of this coupled pattern, the underlying processes are not identified. The continental radiation of Hemidactylus geckos from Peninsular India includes morphologically diverse species that occupy various microhabitats. This radiation began diversifying ~36 Mya with an early increase in lineage diversification. Here, we test the "early-burst" hypothesis by investigating the presence of ecomorphs and examining the pattern of morphological diversification in a phylogenetic framework. Two ecomorphs-terrestrial and scansorial species-that vary significantly in body size and toepad size were identified. Unlike the prediction of the "early-burst" model, we find that disparity in toepad morphology accumulated more recently ~14 Mya and fit the Ornstein-Ulhenbeck model. Ancestral state reconstruction of the two ecomorphs demonstrates that terrestrial lineages evolved independently at least five times from scansorial ancestors, with the earliest diversification in terrestrial lineages 19-12 Mya. Our study demonstrates a delayed increase in morphological disparity as a result of the evolution of terrestrial ecomorphs. The diversification of terrestrial lineages is concurrent with the establishment of open habitat and grasslands in Peninsular India, suggesting that the appearance of this novel resource led to the adaptive diversification.
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Affiliation(s)
- Aparna Lajmi
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India.,Institute of Evolution, Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Anjali Verma
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - K Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
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33
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Aristide L, Morlon H. Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification. Ecol Lett 2019; 22:2006-2017. [PMID: 31507039 DOI: 10.1111/ele.13385] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/12/2019] [Accepted: 08/19/2019] [Indexed: 02/05/2023]
Abstract
Competition can drive macroevolutionary change, for example during adaptive radiations. However, we still lack a clear understanding of how it shapes diversification processes and patterns. To better understand the macroevolutionary consequences of competition, as well as the signal left on phylogenetic data, we developed a model linking trait evolution and species diversification in an ecological context. We find four main results: first, competition spurs trait diversity but not necessarily species richness; second, competition produces slowdowns in species diversification even in the absence of explicit ecological limits, but not in phenotypic diversification even in the presence of such limits; third, early burst patterns do not provide a reliable way of testing for adaptive radiations; and fourth, looking for phylogenetic signal in trait data and support for phenotypic models incorporating competition is a better alternative. Our results clarify the macroevolutionary consequences of competition and could help design more powerful tests of adaptive radiations in nature.
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Affiliation(s)
- Leandro Aristide
- École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS, UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Hélène Morlon
- École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS, UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
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34
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Condamine FL, Rolland J, Morlon H. Assessing the causes of diversification slowdowns: temperature‐dependent and diversity‐dependent models receive equivalent support. Ecol Lett 2019; 22:1900-1912. [DOI: 10.1111/ele.13382] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/20/2019] [Accepted: 08/12/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Fabien L. Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier Place Eugène Bataillon 34095Montpellier France
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
| | - Jonathan Rolland
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
- Department of Computational Biology, Biophore University of Lausanne Lausanne 1015Switzerland
- Department of Zoology University of British Columbia University Blvd #4200‐6270Vancouver B.C Canada
| | - Hélène Morlon
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University F‐75005Paris France
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35
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Lorenzo-Carballa MO, Torres-Cambas Y, Heaton K, Hurst GDD, Charlat S, Sherratt TN, Van Gossum H, Cordero-Rivera A, Beatty CD. Widespread Wolbachia infection in an insular radiation of damselflies (Odonata, Coenagrionidae). Sci Rep 2019; 9:11933. [PMID: 31417112 PMCID: PMC6695491 DOI: 10.1038/s41598-019-47954-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022] Open
Abstract
Wolbachia is one of the most common endosymbionts found infecting arthropods. Theory predicts symbionts like Wolbachia will be more common in species radiations, as host shift events occur with greatest frequency between closely related species. Further, the presence of Wolbachia itself may engender reproductive isolation, and promote speciation of their hosts. Here we screened 178 individuals belonging to 30 species of the damselfly genera Nesobasis and Melanesobasis - species radiations endemic to the Fiji archipelago in the South Pacific - for Wolbachia, using multilocus sequence typing to characterize bacterial strains. Incidence of Wolbachia was 71% in Nesobasis and 40% in Melanesobasis, and prevalence was also high, with an average of 88% in the Nesobasis species screened. We identified a total of 25 Wolbachia strains, belonging to supergroups A, B and F, with some epidemic strains present in multiple species. The occurrence of Wolbachia in both males and females, and the similar global prevalence found in both sexes rules out any strong effect of Wolbachia on the primary sex-ratio, but are compatible with the phenotype of cytoplasmic incompatibility. Nesobasis has higher species richness than most endemic island damselfly genera, and we discuss the potential for endosymbiont-mediated speciation within this group.
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Affiliation(s)
- M O Lorenzo-Carballa
- ECOEVO Lab, EE Forestal, Campus Universitario A Xunqueira s/n, 36005, Pontevedra, Spain. .,Institute of Integrative Biology, University of Liverpool, Crown Street, L69 7ZB, Liverpool, United Kingdom.
| | - Y Torres-Cambas
- Departamento de Biología y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Oriente, Avda. Patricio Lumumba s/n, Santiago de Cuba, 90500, Cuba
| | - K Heaton
- Institute of Integrative Biology, University of Liverpool, Crown Street, L69 7ZB, Liverpool, United Kingdom
| | - G D D Hurst
- Institute of Integrative Biology, University of Liverpool, Crown Street, L69 7ZB, Liverpool, United Kingdom
| | - S Charlat
- Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 16, rue Raphael Dubois, 69622, Villeurbanne, France
| | - T N Sherratt
- Department of Biology, Carleton University 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - H Van Gossum
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1 D.D.136 2610, Wilrijk Antwerp, Belgium
| | - A Cordero-Rivera
- ECOEVO Lab, EE Forestal, Campus Universitario A Xunqueira s/n, 36005, Pontevedra, Spain
| | - C D Beatty
- Department of Ecology & Evolutionary Biology, Cornell University, E149 Corson Hall, 215 Tower Road, Ithaca, NY, 08053, United States of America
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36
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Czekanski-Moir JE, Rundell RJ. The Ecology of Nonecological Speciation and Nonadaptive Radiations. Trends Ecol Evol 2019; 34:400-415. [DOI: 10.1016/j.tree.2019.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 01/08/2023]
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37
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Soltis PS, Folk RA, Soltis DE. Darwin review: angiosperm phylogeny and evolutionary radiations. Proc Biol Sci 2019; 286:20190099. [PMCID: PMC6452062 DOI: 10.1098/rspb.2019.0099] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/05/2019] [Indexed: 08/17/2023] Open
Abstract
Darwin's dual interests in evolution and plants formed the basis of evolutionary botany, a field that developed following his publications on both topics. Here, we review his many contributions to plant biology—from the evolutionary origins of angiosperms to plant reproduction, carnivory, and movement—and note that he expected one day there would be a ‘true’ genealogical tree for plants. This view fuelled the field of plant phylogenetics. With perhaps nearly 400 000 species, the angiosperms have diversified rapidly since their origin in the Early Cretaceous, often through what appear to be rapid radiations. We describe these evolutionary patterns, evaluate possible drivers of radiations, consider how new approaches to studies of diversification can contribute to our understanding of angiosperm diversity, and suggest new directions for further insight into plant evolution.
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Affiliation(s)
- Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Ryan A. Folk
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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38
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Crouch NMA, Ricklefs RE. Speciation Rate Is Independent of the Rate of Evolution of Morphological Size, Shape, and Absolute Morphological Specialization in a Large Clade of Birds. Am Nat 2019; 193:E78-E91. [PMID: 30912971 DOI: 10.1086/701630] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Whether ecological differences between species evolve in parallel with lineage diversification is a fundamental issue in evolutionary biology. These processes might be connected if conditions that favor the proliferation of species, such as release from competitors, facilitate the evolution of novel ecological relationships. Despite this, phylogenetic studies do not consistently identify such a connection. Conversely, if higher diversity caused species to become increasingly specialized ecologically, then lineage diversification might become dissociated from ecological diversification. In this analysis, we ask whether the rate of lineage diversification in a large clade of birds is correlated with morphological specialization and with rates of morphological evolution. We find that morphological variation is related to species richness within clades but that rates of morphological evolution are decoupled from the rate of lineage diversification. Additionally, morphological specialization within lineages is independent of the rate at which lineages diversify, with the results apparently robust against false negative inference. This dissociation is likely a consequence of the major ecomorphological differences between avian clades arising early in their evolutionary history, with comparatively little variation added subsequently, while avian diversification has been driven predominantly by geographic isolation and sexual selection. Accordingly, biodiversity appears to be limited by the extent to which taxa can subdivide exploited regions of ecological space and not just overall ecological opportunity.
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39
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40
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Adeoba MI, Yessoufou K. Analysis of temporal diversification of African Cyprinidae (Teleostei, Cypriniformes). Zookeys 2018:141-161. [PMID: 30588160 PMCID: PMC6302146 DOI: 10.3897/zookeys.806.25844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 10/02/2018] [Indexed: 11/12/2022] Open
Abstract
Recent evidence that freshwater fishes diversify faster than marine fishes signifies that the evolutionary history of biodiversity in freshwater system is of particular interest. Here, the evolutionary diversification events of African Cyprinidae, a freshwater fish family with wide geographic distribution, were reconstructed and analysed. The overall diversification rate of African Cyprinidae is 0.08 species per million year (when extinction rate is very high, i.e., ε = 0.9) and 0.11 species per million year (when ε = 0). This overall rate is lower than the rate reported for African Cichlids, suggesting that African freshwaters might be less conducive for a rapid diversification of Cyprinidae. However, the observed diversification events of African Cyprinidae occurred in the last 10 million years. The temporal pattern of these events follows a non-constant episodic birth-death model (Bayes Factor > 28) and the rate-constant model never outperformed any of the non-constant models tested. The fact that most diversification events occurred in the last 10 million years supports the pattern reported for Cyprinidae in other continent, e.g., Asia, perhaps pointing to concomitant diversification globally. However, the diversification events coincided with major geologic and paleo-climatic events in Africa, suggesting that geological and climatic events may have mediated the diversification patterns of Cyprinidae on the continent.
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Affiliation(s)
- Mariam I Adeoba
- Department of Zoology, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, South Africa University of Johannesburg Johannesburg South Africa
| | - Kowiyou Yessoufou
- Department of Geography, Environmental management and Energy studies, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, South Africa University of Johannesburg Johannesburg South Africa
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41
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Costa CLN, Lemos-Costa P, Marquitti FMD, Fernandes LD, Ramos MF, Schneider DM, Martins AB, de Aguiar MAM. Signatures of Microevolutionary Processes in Phylogenetic Patterns. Syst Biol 2018; 68:131-144. [PMID: 29939352 DOI: 10.1093/sysbio/syy049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem, we analyzed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.
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Affiliation(s)
- Carolina L N Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Paula Lemos-Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Flavia M D Marquitti
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Lucas D Fernandes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900 Piracicaba, SP, Brazil
| | - Marlon F Ramos
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - David M Schneider
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Ayana B Martins
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Department of Fish Ecology & Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
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42
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Smissen PJ, Rowe KC. Repeated biome transitions in the evolution of Australian rodents. Mol Phylogenet Evol 2018; 128:182-191. [DOI: 10.1016/j.ympev.2018.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/26/2018] [Accepted: 07/16/2018] [Indexed: 12/31/2022]
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43
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Larcombe MJ, Jordan GJ, Bryant D, Higgins SI. The dimensionality of niche space allows bounded and unbounded processes to jointly influence diversification. Nat Commun 2018; 9:4258. [PMID: 30323199 PMCID: PMC6189034 DOI: 10.1038/s41467-018-06732-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/17/2018] [Indexed: 11/18/2022] Open
Abstract
There are two prominent and competing hypotheses that disagree about the effect of competition on diversification processes. The first, the bounded hypothesis, suggests that species diversity is limited (bounded) by competition between species for finite ecological niche space. The second, the unbounded hypothesis, proposes that innovations associated with evolution render competition unimportant over macroevolutionary timescales. Here we use phylogenetically structured niche modelling to show that processes consistent with both of these diversification models drive species accumulation in conifers. In agreement with the bounded hypothesis, niche competition constrained diversification, and in line with the unbounded hypothesis, niche evolution and partitioning promoted diversification. We then analyse niche traits to show that these diversification enhancing and inhibiting processes can occur simultaneously on different niche dimensions. Together these results suggest a new hypothesis for lineage diversification based on the multi-dimensional nature of ecological niches that can accommodate both bounded and unbounded evolutionary processes.
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Affiliation(s)
- Matthew J Larcombe
- Department of Botany, University of Otago, PO Box 56,, Dunedin, 9054, New Zealand.
| | - Gregory J Jordan
- Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, PO Box 56,, Dunedin, 9054, New Zealand
| | - Steven I Higgins
- Department of Botany, University of Otago, PO Box 56,, Dunedin, 9054, New Zealand.
- Plant Ecology, University of Bayreuth, Universitätstraße 30, 95447, Bayreuth, Germany.
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44
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Start D. Predator macroevolution drives trophic cascades and ecosystem functioning. Proc Biol Sci 2018; 285:20180384. [PMID: 30051862 PMCID: PMC6083245 DOI: 10.1098/rspb.2018.0384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/03/2018] [Indexed: 01/08/2023] Open
Abstract
Biologists now recognize that ecology can drive evolution, and that evolution in turn produces ecological patterns. I extend this thinking to include longer time scales, suggesting that macroevolutionary transitions can create phenotypic differences among species, which then have predictable impacts on species interactions, community assembly and ecosystem functioning. Repeated speciation can exacerbate these patterns by creating communities with similar phenotypes and hence ecological impacts. Here, I use several experiments to test these ideas in dragonfly larvae that occupy ponds with fish, ponds without fish, or both. I show that macroevolutionary transitions between habitats cause fishless pond species to be more active relative to fish pond specialists, reducing prey abundance, shifting prey community composition and creating stronger trophic cascades. These effects scale up to the community level with predictable consequences for ecosystem multi-functioning. I suggest that macroevolutionary history can have predictable impacts on phenotypic traits, with consequences for interacting species and ecosystems.
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Affiliation(s)
- Denon Start
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada
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Burin G, Alencar LRV, Chang J, Alfaro ME, Quental TB. How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline? Syst Biol 2018; 68:47-62. [DOI: 10.1093/sysbio/syy037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/09/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- Gustavo Burin
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Laura R V Alencar
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Tiago B Quental
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
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46
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Gunderson AR, Mahler DL, Leal M. Thermal niche evolution across replicated Anolis lizard adaptive radiations. Proc Biol Sci 2018; 285:20172241. [PMID: 29669895 PMCID: PMC5936720 DOI: 10.1098/rspb.2017.2241] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/27/2018] [Indexed: 11/12/2022] Open
Abstract
Elucidating how ecological and evolutionary mechanisms interact to produce and maintain biodiversity is a fundamental problem in evolutionary ecology. Here, we focus on how physiological evolution affects performance and species coexistence along the thermal niche axis in replicated radiations of Anolis lizards best known for resource partitioning based on morphological divergence. We find repeated divergence in thermal physiology within these radiations, and that this divergence significantly affects performance within natural thermal environments. Morphologically similar species that co-occur invariably differ in their thermal physiology, providing evidence that physiological divergence facilitates species coexistence within anole communities. Despite repeated divergence, phylogenetic comparative analyses indicate that physiological traits have evolved more slowly than key morphological traits related to the structural niche. Phylogenetic analyses also reveal that physiological divergence is correlated with divergence in broad-scale habitat climatic features commonly used to estimate thermal niche evolution, but that the latter incompletely predicts variation in the former. We provide comprehensive evidence for repeated adaptive evolution of physiological divergence within Anolis adaptive radiations, including the complementary roles of physiological and morphological divergence in promoting community-level diversity. We recommend greater integration of performance-based traits into analyses of climatic niche evolution, as they facilitate a more complete understanding of the phenotypic and ecological consequences of climatic divergence.
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Affiliation(s)
- Alex R Gunderson
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720-3140, USA
| | - D Luke Mahler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Manuel Leal
- Division of Biological Sciences, University of Missouri, 105 Tucker Hall, Columbia, MO 65211, USA
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47
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Maliet O, Gascuel F, Lambert A. Ranked Tree Shapes, Nonrandom Extinctions, and the Loss of Phylogenetic Diversity. Syst Biol 2018; 67:1025-1040. [DOI: 10.1093/sysbio/syy030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 04/08/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Odile Maliet
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- ED 227, Sorbonne Universités, Paris, France
| | - Fanny Gascuel
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- ED 227, Sorbonne Universités, Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
- Laboratoire Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS, Paris, France
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48
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Storch D, Bohdalková E, Okie J. The more-individuals hypothesis revisited: the role of community abundance in species richness regulation and the productivity-diversity relationship. Ecol Lett 2018; 21:920-937. [PMID: 29659144 DOI: 10.1111/ele.12941] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/09/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022]
Abstract
Species richness increases with energy availability, yet there is little consensus as to the exact processes driving this species-energy relationship. The most straightforward explanation is the more-individuals hypothesis (MIH). It states that higher energy availability promotes a higher total number of individuals in a community, which consequently increases species richness by allowing for a greater number of species with viable populations. Empirical support for the MIH is mixed, partially due to the lack of proper formalisation of the MIH and consequent confusion as to its exact predictions. Here, we review the evidence of the MIH and evaluate the reliability of various predictions that have been tested. There is only limited evidence that spatial variation in species richness is driven by variation in the total number of individuals. There are also problems with measures of energy availability, with scale-dependence, and with the direction of causality, as the total number of individuals may sometimes itself be driven by the number of species. However, even in such a case the total number of individuals may be involved in diversity regulation. We propose a formal theory that encompasses these processes, clarifying how the different factors affecting diversity dynamics can be disentangled.
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Affiliation(s)
- David Storch
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, Praha, Czech Republic.,Department of Ecology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Eliška Bohdalková
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, Praha, Czech Republic.,Department of Ecology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Jordan Okie
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA.,School for the Future of Innovation in Society, Arizona State University, Tempe, AZ, USA
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49
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Abstract
Background Much evolutionary theory predicts that diversity arises via both adaptive radiation (diversification driven by selection against niche-overlap within communities) and divergence of geographically isolated populations. We focus on tropical fruit flies (Blepharoneura, Tephritidae) that reveal unexpected patterns of niche-overlap within local communities. Throughout the Neotropics, multiple sympatric non-interbreeding populations often share the same highly specialized patterns of host use (e.g., flies are specialists on flowers of a single gender of a single species of host plants). Lineage through time (LTT) plots can help distinguish patterns of diversification consistent with ecologically limited adaptive radiation from those predicted by ecologically neutral theories. Here, we use a time-calibrated phylogeny of Blepharoneura to test the hypothesis that patterns of Blepharoneura diversification are consistent with an “ecologically neutral” model of diversification that predicts that diversification is primarily a function of time and space. Results The Blepharoneura phylogeny showed more cladogenic divergence associated with geography than with shifts in host-use. Shifts in host-use were associated with ~ 20% of recent splits (< 3 Ma), but > 60% of older splits (> 3 Ma). In the overall tree, gamma statistic and maximum likelihood model fitting showed no evidence of diversification rate changes though there was a weak signature of slowing diversification rate in one of the component clades. Conclusions Overall patterns of Blepharoneura diversity are inconsistent with a traditional explanation of adaptive radiation involving decreases in diversification rates associated with niche-overlap. Sister lineages usually use the same host-species and host-parts, and multiple non-interbreeding sympatric populations regularly co-occur on the same hosts. We suggest that most lineage origins (phylogenetic splits) occur in allopatry, usually without shifts in host-use, and that subsequent dispersal results in assembly of communities composed of multiple sympatric non-interbreeding populations of flies that share the same hosts. Electronic supplementary material The online version of this article (10.1186/s12862-018-1146-9) contains supplementary material, which is available to authorized users.
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50
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Rojas D, Ramos Pereira MJ, Fonseca C, Dávalos LM. Eating down the food chain: generalism is not an evolutionary dead end for herbivores. Ecol Lett 2018; 21:402-410. [DOI: 10.1111/ele.12911] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/11/2017] [Accepted: 12/12/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Danny Rojas
- Department of Natural Sciences and Mathematics Pontificia Universidad Javeriana Cali Colombia
- Department of Biology and Centre for Environmental and Marine Studies University of Aveiro 3810‐193 Aveiro Portugal
| | - Maria João Ramos Pereira
- Department of Biology and Centre for Environmental and Marine Studies University of Aveiro 3810‐193 Aveiro Portugal
- Institute of Biosciences Universidade Federal do Rio Grande do Sul Porto Alegre RS Brazil
| | - Carlos Fonseca
- Department of Biology and Centre for Environmental and Marine Studies University of Aveiro 3810‐193 Aveiro Portugal
| | - Liliana M. Dávalos
- Department of Ecology and Evolution Stony Brook University 650 Life Sciences Building, Stony Brook NY11794 USA
- Consortium for Inter‐Disciplinary Environmental Research School of Marine and Atmospheric Sciences Stony Brook University 129 Dana Hall Stony Brook NY11794 USA
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