1
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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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2
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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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3
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Neubauer TA, Hauffe T, Silvestro D, Scotese CR, Stelbrink B, Albrecht C, Delicado D, Harzhauser M, Wilke T. Drivers of diversification in freshwater gastropods vary over deep time. Proc Biol Sci 2022; 289:20212057. [PMID: 35105242 PMCID: PMC8808086 DOI: 10.1098/rspb.2021.2057] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Unravelling the drivers of species diversification through geological time is of crucial importance for our understanding of long-term evolutionary processes. Numerous studies have proposed different sets of biotic and abiotic controls of speciation and extinction rates, but typically they were inferred for a single, long geological time frame. However, whether the impact of biotic and abiotic controls on diversification changes over time is poorly understood. Here, we use a large fossil dataset, a multivariate birth-death model and a comprehensive set of biotic and abiotic predictors, including a new index to quantify tectonic complexity, to estimate the drivers of diversification for European freshwater gastropods over the past 100 Myr. The effects of these factors on origination and extinction are estimated across the entire time frame as well as within sequential time windows of 20 Myr each. Our results find support for temporal heterogeneity in the factors associated with changes in diversification rates. While the factors impacting speciation and extinction rates vary considerably over time, diversity-dependence and topography are consistently important. Our study highlights that a high level of heterogeneity in diversification rates is best captured by incorporating time-varying effects of biotic and abiotic factors.
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Affiliation(s)
- Thomas A. Neubauer
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
- Marine Biodiversity, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
| | - Christopher R. Scotese
- Department of Earth and Planetary Sciences, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Björn Stelbrink
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
| | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
| | - Diana Delicado
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
| | - Mathias Harzhauser
- Geological-Paleontological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
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4
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Mikami T, Iwasaki W. The flipping
t
‐ratio test: Phylogenetically informed assessment of the Pareto theory for phenotypic evolution. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tomoyuki Mikami
- Department of Biological Sciences Graduate School of Science The University of Tokyo Tokyo Japan
| | - Wataru Iwasaki
- Department of Biological Sciences Graduate School of Science The University of Tokyo Tokyo Japan
- Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Kashiwa Japan
- Atmosphere and Ocean Research Institute The University of Tokyo Kashiwa Japan
- Institute for Quantitative Biosciences The University of Tokyo Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
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5
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Lewitus E, Aristide L, Morlon H. Characterizing and Comparing Phylogenetic Trait Data from Their Normalized Laplacian Spectrum. Syst Biol 2020; 69:234-248. [PMID: 31529071 DOI: 10.1093/sysbio/syz061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 09/02/2019] [Accepted: 09/10/2019] [Indexed: 11/13/2022] Open
Abstract
The dissection of the mode and tempo of phenotypic evolution is integral to our understanding of global biodiversity. Our ability to infer patterns of phenotypes across phylogenetic clades is essential to how we infer the macroevolutionary processes governing those patterns. Many methods are already available for fitting models of phenotypic evolution to data. However, there is currently no comprehensive nonparametric framework for characterizing and comparing patterns of phenotypic evolution. Here, we build on a recently introduced approach for using the phylogenetic spectral density profile (SDP) to compare and characterize patterns of phylogenetic diversification, in order to provide a framework for nonparametric analysis of phylogenetic trait data. We show how to construct the SDP of trait data on a phylogenetic tree from the normalized graph Laplacian. We demonstrate on simulated data the utility of the SDP to successfully cluster phylogenetic trait data into meaningful groups and to characterize the phenotypic patterning within those groups. We furthermore demonstrate how the SDP is a powerful tool for visualizing phenotypic space across traits and for assessing whether distinct trait evolution models are distinguishable on a given empirical phylogeny. We illustrate the approach in two empirical data sets: a comprehensive data set of traits involved in song, plumage, and resource-use in tanagers, and a high-dimensional data set of endocranial landmarks in New World monkeys. Considering the proliferation of morphometric and molecular data collected across the tree of life, we expect this approach will benefit big data analyses requiring a comprehensive and intuitive framework.
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Affiliation(s)
- Eric Lewitus
- Ecole Normale Superieure Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS) CNRS UMR 8197 INSERM U1024 46rue d'Ulm,F-75005, Paris, France.,Henry M. Jackson Foundation in support of the US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Leandro Aristide
- Ecole Normale Superieure Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS) CNRS UMR 8197 INSERM U1024 46rue d'Ulm,F-75005, Paris, France
| | - Hélène Morlon
- Ecole Normale Superieure Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'Ecole Normale Superieure (IBENS) CNRS UMR 8197 INSERM U1024 46rue d'Ulm,F-75005, Paris, France
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6
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Lewitus E, Rolland M. A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity. Virus Evol 2019; 5:vez044. [PMID: 31700680 PMCID: PMC6826062 DOI: 10.1093/ve/vez044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Phylogenetics is a powerful tool for understanding the diversification dynamics of viral pathogens. Here we present an extension of the spectral density profile of the modified graph Laplacian, which facilitates the characterization of within-host molecular evolution of viruses and the direct comparison of diversification dynamics between hosts. This approach is non-parametric and therefore fast and model-free. We used simulations of within-host evolutionary scenarios to evaluate the efficiency of our approach and to demonstrate the significance of interpreting a viral phylogeny by its spectral density profile in terms of diversification dynamics. The key features that are captured by the profile are positive selection on the viral gene (or genome), temporal changes in substitution rates, mutational fitness, and time between sampling. Using sequences from individuals infected with HIV-1, we showed the utility of this approach for characterizing within-host diversification dynamics, for comparing dynamics between hosts, and for charting disease progression in infected individuals sampled over multiple years. We furthermore propose a heuristic test for assessing founder heterogeneity, which allows us to classify infections with single and multiple HIV-1 founder viruses. This non-parametric approach can be a valuable complement to existing parametric approaches.
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Affiliation(s)
- Eric Lewitus
- U.S. Military HIV Research Program (MHRP), WRAIR, 503 Robert Grant Avenue, Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr, Bethesda, MD, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program (MHRP), WRAIR, 503 Robert Grant Avenue, Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr, Bethesda, MD, USA
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7
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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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8
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Abstract
For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an incredible variety of organismal traits. Here we analyze a large collection of phylogenetic trees and fossil time series and describe a hidden generality among these seemingly idiosyncratic results: speciation and extinction rates follow a scaling law in which both depend on the age of the group in which they are measured, with the fastest rates in the youngest clades. Using a series of simulations and sensitivity analyses, we demonstrate that the time dependency is unlikely to be a result of simple statistical artifacts. As such, this time scaling is likely a genuine feature of the tree of life, hinting that the dynamics of biodiversity over deep time may be driven in part by surprisingly simple and general principles.
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9
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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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10
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Hegde S, Pai SR, Bhagwat RM, Saini A, Rathore PK, Jalalpure SS, Hegde HV, Sugunan AP, Gupta VS, Kholkute SD, Roy S. Genetic and phytochemical investigations for understanding population variability of the medicinally important tree Saraca asoca to help develop conservation strategies. PHYTOCHEMISTRY 2018; 156:43-54. [PMID: 30189346 DOI: 10.1016/j.phytochem.2018.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 08/02/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Saraca asoca (Roxb.) De Wilde (Caesalpiniaceae) is a highly traded IUCN red listed tree species used in Ayurvedic medicines for the treatment of various disorders, especially gynaecological problems. However, information about the genetic variations between populations and corresponding variation in specialized metabolites of S. asoca remains unclear. To address this issue, we analysed 11 populations of S. asoca with 106 accessions collected from Western Ghats of India using ISSR markers along with selected phytocompounds using RP-HPLC. Twenty primers were screened, out of which seven were selected for further analysis based on generation of clear polymorphic banding patterns. These seven ISSR primers produced 74 polymorphic loci. AMOVA showed 43% genetic variation within populations and 57% among the populations of S. asoca. To estimate the genetic relationships among S. asoca populations, UPGMA and Bayesian Models were constructed, which revealed two clusters of similar grouping patterns. However, excluding minor deviations, UPGMA and dissimilarity analysis showed close association of genotypes according to their geographical locations. Catechin (CAT), epicatechin (EPI) and gallic acid (GA) were quantified from bark and leaf samples of corresponding genotypes collected from 106 accessions. ROC plots depicted the sensitivity and specificity of the concentrations of tested phytocompounds at various cut-off points. Although, multiple logistic regression analysis predicted some association between few loci with GA, EPI and CAT, but PCA for phytochemical data failed to distinguish the populations. Overall, there were no significant trends observed to distinguish the populations based on these phytocompounds. Furthermore, the study advocates the delineate provenance regions of S. asoca genotypes/chemotype snapshots for in-situ conservation and ex-situ cultivation.
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Affiliation(s)
- Satisha Hegde
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India; KLE Academy of Higher Education and Research (Deemed-to-be-University), Dr. Prabhakar Kore Basic Science Research Center, Belagavi, Karnataka, 590010, India
| | - Sandeep Ramchandra Pai
- Amity Institute of Biotechnology, Amity University, Mumbai - Pune Expressway, Bhatan, Post - Somathne, Panvel, Mumbai, Maharashtra, 410206, India
| | - Rasika M Bhagwat
- Plant Molecular Biology Group, Division of Biochemical Sciences, CSIR - National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Archana Saini
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India
| | - Poonam Kanwar Rathore
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India
| | - Sunil Satyappa Jalalpure
- KLE Academy of Higher Education and Research (Deemed-to-be-University), Dr. Prabhakar Kore Basic Science Research Center, Belagavi, Karnataka, 590010, India; Department of Pharmacognosy and Phytochemistry, College of Pharmacy, KLE Academy of Higher Education and Research (Deemed-to-be-University), Belagavi, Karnataka, 590010, India
| | - Harsha Vasudev Hegde
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India
| | - Attayoor Purushottaman Sugunan
- Division of Epidemiology, RMRC-NIE-LRU, National Institute of Epidemiology, Indian Council of Medical Research, Department of Health Research, Government of India, Chennai, Tamil Nadu, 600 077, India
| | - Vidya S Gupta
- Plant Molecular Biology Group, Division of Biochemical Sciences, CSIR - National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Sanjiva D Kholkute
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India
| | - Subarna Roy
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India.
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11
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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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12
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Burress ED, Tan M. Ecological opportunity alters the timing and shape of adaptive radiation. Evolution 2017; 71:2650-2660. [PMID: 28895124 DOI: 10.1111/evo.13362] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/18/2017] [Accepted: 08/27/2017] [Indexed: 12/14/2022]
Abstract
The uneven distribution of diversity is a conspicuous phenomenon across the tree of life. Ecological opportunity is a prominent catalyst of adaptive radiation and therefore may alter patterns of diversification. We evaluated the distribution of shifts in diversification rates across the cichlid phylogeny and the distribution of major clades across phylogenetic space. We also tested if ecological opportunity influenced these patterns. Colonization-associated ecological opportunity altered the tempo and mode of diversification during the adaptive radiation of cichlid fishes. Clades that arose following colonization events diversified faster than other clades. Speciation rate shifts were nonrandomly distributed across the phylogeny such that they were disproportionally concentrated around nodes that corresponded with colonization events (i.e., of continents, river basins, or lakes). Young clades tend to expand faster than older clades; however, colonization-associated ecological opportunity accentuated this pattern. There was an interaction between clade age and ecological opportunity that explained the trajectory of clades through phylogenetic space over time. Our results indicate that ecological opportunities afforded by continental and ecosystem-scale colonization events explain the dramatic speciation rate heterogeneity and phylogenetic imbalance that arose during the evolutionary history of cichlid fishes.
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Affiliation(s)
- Edward D Burress
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama
| | - Milton Tan
- Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia
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13
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Lewitus É, Morlon H. [The rules of biodiversity in deep time]. Med Sci (Paris) 2017; 33:123-126. [PMID: 28240199 DOI: 10.1051/medsci/20173302003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Éric Lewitus
- Institut de Biologie, École Normale Supérieure, 46, rue d'Ulm, 75005 Paris, France
| | - Hélène Morlon
- Institut de Biologie, École Normale Supérieure, 46, rue d'Ulm, 75005 Paris, France
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14
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Abstract
Biodiversity today is huge, and it has a long history. Identifying rules for the heterogeneity of modern biodiversity—the high to low species richness of different clades—has been hard. There are measurable biodiversity differences between land and sea and between the tropics and temperate-polar regions. Some analyses suggest that the net age of a clade can determine its extinction risk, but this is equivocal. New work shows that, through geological time, clades pass through different diversification regimes, and those regimes constrain the balance of tree size and the nature of branching events.
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Affiliation(s)
- Michael J. Benton
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail:
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