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Caetano-Anollés G, Janko R. The rise of hierarchy and modularity in biological networks explained by empedocles’ double tale ∼2,400 years before darwin and systems biology. Front Genet 2022; 13:973233. [PMID: 36061206 PMCID: PMC9428273 DOI: 10.3389/fgene.2022.973233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, C.R. Woese Institute for Genomic Biology, and Illinois Informatics Institute, University of Illinois, Urbana, IL, United States
- *Correspondence: Gustavo Caetano-Anollés,
| | - Richard Janko
- Department of Classical Studies, University of Michigan, Ann Arbor, MI, United States
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2
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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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3
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Simpson AG, Wing SL, Fenster CB. Diversification in the Rosales is influenced by dispersal, geographic range size, and pre-existing species richness. AMERICAN JOURNAL OF BOTANY 2022; 109:922-938. [PMID: 35446437 DOI: 10.1002/ajb2.1855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Biodiversity results from origination and extinction, justifying interest in identifying traits that influence this balance. Traits implicated in the success or failure of lineages include dispersal, colonization ability, and geographic range size. We investigated the impact of dispersal and range size on contemporary diversity in the Rosales. METHODS We used the multiple-state speciation and extinction (MuSSE) method to explore the effects on genus-level diversification of two genus-level traits (geographic range size and within-genus proclivity to speciate) and two species traits (seed dispersal and growth habit) and the multiple hidden-state speciation and extinction (MuHiSSE) method for species-level associations. Finally, we conducted a PGLS (phylogenetic least-squares) analysis to distinguish between speciation within genera versus origination of new genera. RESULTS At the species level, animal dispersal enhances diversification rate in both woody and herbaceous lineages, while woody lineages without animal dispersal have higher extinction rates than speciation rates. At the genus level, herbaceous taxa have positive diversification rates regardless of other character states. Diversification rate variation is also explained by two interactions: (1) a three-way interaction between large geographic range, animal-mediated dispersal, and high within-genus species richness, whereby genera possessing all three traits have high diversification rates, and (2) a four-way interaction by which the three-way interaction is stronger in woody genera than in herbaceous genera. CONCLUSIONS Colonization ability may underlie the relationship between dispersal type and range size and may influence past diversification rates by decreasing extinction rates during late Cenozoic climate volatility. Thus, colonization ability could be used to predict future extinction risk to aid conservation.
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Affiliation(s)
- Andrew G Simpson
- Program in Behavior, Ecology, Evolution, Systematics, University of Maryland, College Park, MD, USA
| | - Scott L Wing
- Program in Behavior, Ecology, Evolution, Systematics, University of Maryland, College Park, MD, USA
| | - Charles B Fenster
- Program in Behavior, Ecology, Evolution, Systematics, University of Maryland, College Park, MD, USA
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4
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Hembry DH, Bennett G, Bess E, Cooper I, Jordan S, Liebherr J, Magnacca KN, Percy DM, Polhemus DA, Rubinoff D, Shaw KL, O’Grady PM. Insect Radiations on Islands: Biogeographic Pattern and Evolutionary Process in Hawaiian Insects. THE QUARTERLY REVIEW OF BIOLOGY 2021. [DOI: 10.1086/717787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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5
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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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6
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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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7
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Close RA, Benson RBJ, Alroy J, Carrano MT, Cleary TJ, Dunne EM, Mannion PD, Uhen MD, Butler RJ. The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases. Proc Biol Sci 2020; 287:20200372. [PMID: 32259471 PMCID: PMC7209054 DOI: 10.1098/rspb.2020.0372] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 60 859 fossil occurrences, we show that the spatial extent of the worldwide terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic. Changes in spatial sampling explain up to 67% of the change in known fossil species counts, and these changes are decoupled from variation in habitable land area that existed through time. Spatial sampling therefore represents a real and profound sampling bias that cannot be explained as redundancy. To address this bias, we estimate terrestrial tetrapod diversity for palaeogeographical regions of approximately equal size. We find that regional-scale diversity was constrained over timespans of tens to hundreds of millions of years, and similar patterns are recovered for major subgroups, such as dinosaurs, mammals and squamates. Although the Cretaceous/Palaeogene mass extinction catalysed an abrupt two- to three-fold increase in regional diversity 66 million years ago, no further increases occurred, and recent levels of regional diversity do not exceed those of the Palaeogene. These results parallel those recovered in analyses of local community-level richness. Taken together, our findings strongly contradict past studies that suggested unbounded diversity increases at local and regional scales over the last 100 million years.
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Affiliation(s)
- Roger A Close
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roger B J Benson
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
| | - John Alroy
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Matthew T Carrano
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Terri J Cleary
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Emma M Dunne
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Philip D Mannion
- Department of Earth Sciences, University College London, London WC1E 6BT, UK
| | - Mark D Uhen
- Department of Atmospheric, Oceanic, and Earth Sciences, George Mason University, Fairfax, VA 22030, USA
| | - Richard J Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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8
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Huang XC, German DA, Koch MA. Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events. ANNALS OF BOTANY 2020; 125:29-47. [PMID: 31314080 PMCID: PMC6948214 DOI: 10.1093/aob/mcz123] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/16/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. METHODS We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. KEY RESULTS Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. CONCLUSIONS The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant 'pump' for continuous and high species diversification.
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Affiliation(s)
- Xiao-Chen Huang
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Dmitry A German
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
- For correspondence. E-mail
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9
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Nyman T, Onstein RE, Silvestro D, Wutke S, Taeger A, Wahlberg N, Blank SM, Malm T. The early wasp plucks the flower: disparate extant diversity of sawfly superfamilies (Hymenoptera: ‘Symphyta’) may reflect asynchronous switching to angiosperm hosts. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder ‘Symphyta’, which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the ‘Symphyta’, with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes – and back – have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms.
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Affiliation(s)
- Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, Germany
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg and Gothenburg Global Biodiversity Centre, Sweden
| | - Saskia Wutke
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Andreas Taeger
- Senckenberg Deutsches Entomologisches Institut Müncheberg, Germany
| | | | - Stephan M Blank
- Senckenberg Deutsches Entomologisches Institut Müncheberg, Germany
| | - Tobias Malm
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
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10
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Starko S, Soto Gomez M, Darby H, Demes KW, Kawai H, Yotsukura N, Lindstrom SC, Keeling PJ, Graham SW, Martone PT. A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem. Mol Phylogenet Evol 2019; 136:138-150. [PMID: 30980936 DOI: 10.1016/j.ympev.2019.04.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 12/24/2022]
Abstract
Reconstructing phylogenetic topologies and divergence times is essential for inferring the timing of radiations, the appearance of adaptations, and the historical biogeography of key lineages. In temperate marine ecosystems, kelps (Laminariales) drive productivity and form essential habitat but an incomplete understanding of their phylogeny has limited our ability to infer their evolutionary origins and the spatial and temporal patterns of their diversification. Here, we reconstruct the diversification of habitat-forming kelps using a global genus-level phylogeny inferred primarily from organellar genome datasets, and investigate the timing of kelp radiation. We resolve several important phylogenetic features, including relationships among the morphologically simple kelp families and the broader radiation of complex kelps, demonstrating that the initial radiation of the latter resulted from an increase in speciation rate around the Eocene-Oligocene boundary. This burst in speciation rate is consistent with a possible role of recent climatic cooling in triggering the kelp radiation and pre-dates the origin of benthic-foraging carnivores. Historical biogeographical reconstructions point to a northeast Pacific origin of complex kelps, with subsequent colonization of new habitats likely playing an important role in driving their ecological diversification. We infer that complex morphologies associated with modern kelp forests (e.g. branching, pneumatocysts) evolved several times over the past 15-20 MY, highlighting the importance of morphological convergence in establishing modern upright kelp forests. Our phylogenomic findings provide new insights into the geographical and ecological proliferation of kelps and provide a timeline along which feedbacks between kelps and their food-webs could have shaped the structure of temperate ecosystems.
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Affiliation(s)
- Samuel Starko
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Bamfield Marine Sciences Centre, 100 Pachena Rd., Bamfield V0R 1B0, Canada; Hakai Institute, Heriot Bay, Quadra Island, Canada.
| | - Marybel Soto Gomez
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Hayley Darby
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Kyle W Demes
- Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Hiroshi Kawai
- Department of Biology, Kobe University, Rokkodaicho 657-8501, Japan
| | - Norishige Yotsukura
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo 060-0809, Japan
| | - Sandra C Lindstrom
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Patrick T Martone
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Bamfield Marine Sciences Centre, 100 Pachena Rd., Bamfield V0R 1B0, Canada; Hakai Institute, Heriot Bay, Quadra Island, Canada
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11
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Sclavi B, Herrick J. Genome size variation and species diversity in salamanders. J Evol Biol 2019; 32:278-286. [DOI: 10.1111/jeb.13412] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/14/2018] [Accepted: 12/20/2018] [Indexed: 12/13/2022]
Affiliation(s)
| | - John Herrick
- Department of Physics; Simon Fraser University; Burnaby British Columbia Canada
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12
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Budd GE, Mann RP. History is written by the victors: The effect of the push of the past on the fossil record. Evolution 2018; 72:2276-2291. [PMID: 30257040 PMCID: PMC6282550 DOI: 10.1111/evo.13593] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 09/01/2018] [Indexed: 02/05/2023]
Abstract
Survivorship biases can generate remarkable apparent rate heterogeneities through time in otherwise homogeneous birth‐death models of phylogenies. They are a potential explanation for many striking patterns seen in the fossil record and molecular phylogenies. One such bias is the “push of the past”: clades that survived a substantial length of time are likely to have experienced a high rate of early diversification. This creates the illusion of a secular rate slow‐down through time that is, rather, a reversion to the mean. An extra effect increasing early rates of lineage generation is also seen in large clades. These biases are important but relatively neglected influences on many aspects of diversification patterns in the fossil record and elsewhere, such as diversification spikes after mass extinctions and at the origins of clades; they also influence rates of fossilization, changes in rates of phenotypic evolution and even molecular clocks. These inevitable features of surviving and/or large clades should thus not be generalized to the diversification process as a whole without additional study of small and extinct clades, and raise questions about many of the traditional explanations of the patterns seen in the fossil record.
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Affiliation(s)
- Graham E Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala, SE 752 36, Sweden
| | - Richard P Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, United Kingdom
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13
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Abdelkrim J, Aznar-Cormano L, Fedosov AE, Kantor YI, Lozouet P, Phuong MA, Zaharias P, Puillandre N. Exon-Capture-Based Phylogeny and Diversification of the Venomous Gastropods (Neogastropoda, Conoidea). Mol Biol Evol 2018; 35:2355-2374. [DOI: 10.1093/molbev/msy144] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Jawad Abdelkrim
- Outils et Méthodes de la Systématique Intégrative (OMSI) UMS 2700, Muséum National d’Histoire Naturelle, Paris, France
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Laetitia Aznar-Cormano
- Outils et Méthodes de la Systématique Intégrative (OMSI) UMS 2700, Muséum National d’Histoire Naturelle, Paris, France
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Alexander E Fedosov
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Yuri I Kantor
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Pierre Lozouet
- Muséum National d’Histoire Naturelle, Direction des Collections, 55, rue Buffon, 75005 Paris, France
| | - Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
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14
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Insights into global planktonic diatom diversity: The importance of comparisons between phylogenetically equivalent units that account for time. ISME JOURNAL 2018; 12:2807-2810. [PMID: 30013161 DOI: 10.1038/s41396-018-0221-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/16/2018] [Accepted: 06/11/2018] [Indexed: 11/09/2022]
Abstract
Metabarcoding has offered unprecedented insights into microbial diversity. In many studies, short DNA sequences are binned into consecutively lower Linnaean ranks, and ranked groups (e.g., genera) are the units of biodiversity analyses. These analyses assume that Linnaean ranks are biologically meaningful and that identically ranked groups are comparable. We used a metabarcode dataset for marine planktonic diatoms to illustrate the limits of this approach. We found that the 20 most abundant marine planktonic diatom genera ranged in age from 4 to 134 million years, indicating the non-equivalence of genera because some have had more time to diversify than others. However, species richness was largely independent of genus age, suggesting that disparities in species richness among genera were better explained by variation in rates of speciation and extinction. Taxonomic classifications often do not reflect phylogeny, so genus-level analyses can include phylogenetically nested genera, further confounding rank-based analyses. These results underscore the indispensable role of phylogeny in understanding patterns of microbial diversity.
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15
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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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16
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Sánchez-Reyes LL, Morlon H, Magallón S. Uncovering Higher-Taxon Diversification Dynamics from Clade Age and Species-Richness Data. Syst Biol 2018; 66:367-378. [PMID: 28003532 DOI: 10.1093/sysbio/syw088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 09/26/2016] [Indexed: 11/14/2022] Open
Abstract
The relationship between clade age and species richness has been increasingly used in macroevolutionary studies as evidence for ecologically versus time-dependent diversification processes. However, theory suggests that phylogenetic structure, age type (crown or stem age), and taxonomic delimitation can affect estimates of the age-richness correlation (ARC) considerably. We currently lack an integrative understanding of how these different factors affect ARCs, which in turn, obscures further interpretations. To assess its informative breadth, we characterize ARC behavior with simulated and empirical phylogenies, considering phylogenetic structure and both crown and stem ages. First, we develop a two-state birth-death model to simulate phylogenies including the origin of higher taxa and a hierarchical taxonomy to determine ARC expectations under ecologically and time-dependent diversification processes. Then, we estimate ARCs across various taxonomic ranks of extant amphibians, squamate reptiles, mammals, birds, and flowering plants. We find that our model reproduces the general ARC trends of a wide range of biological systems despite the particularities of taxonomic practice within each, suggesting that the model is adequate to establish a framework of ARC null expectations for different diversification processes when taxa are defined with a hierarchical taxonomy. ARCs estimated with crown ages were positive in all the scenarios we studied, including ecologically dependent processes. Negative ARCs were only found at less inclusive taxonomic ranks, when considering stem age, and when rates varied among clades. This was the case both in ecologically and time-dependent processes. Together, our results warn against direct interpretations of single ARC estimates and advocate for a more integrative use of ARCs across age types and taxonomic ranks in diversification studies. [Birth-Death models; crown age; diversity dependence; extinction; phylogenetic structure; speciation; stem age; taxonomy; time dependence; tree simulations.].
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Affiliation(s)
- Luna L Sánchez-Reyes
- Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, Ciudad de México 04510, México
| | - Hélène Morlon
- École Normale Supérieure, UMR 8197 CNRS, 46 rue d'Ulm, 75005, Paris, France
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
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17
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Meyer ALS, Wiens JJ. Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts. Evolution 2017; 72:39-53. [DOI: 10.1111/evo.13378] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Andreas L. S. Meyer
- Graduate Program in Zoology Universidade Federal do Paraná Curitiba Paraná 81531 Brazil
- Department of Ecology and Evolution University of Arizona Tucson Arizona 85721
| | - John J. Wiens
- Department of Ecology and Evolution University of Arizona Tucson Arizona 85721
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18
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Moen DS, Wiens JJ. Microhabitat and Climatic Niche Change Explain Patterns of Diversification among Frog Families. Am Nat 2017; 190:29-44. [DOI: 10.1086/692065] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Harvey MG, Seeholzer GF, Smith BT, Rabosky DL, Cuervo AM, Brumfield RT. Positive association between population genetic differentiation and speciation rates in New World birds. Proc Natl Acad Sci U S A 2017; 114:6328-6333. [PMID: 28559330 PMCID: PMC5474768 DOI: 10.1073/pnas.1617397114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from 173 New World bird species (>17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity.
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Affiliation(s)
- Michael G Harvey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803;
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Glenn F Seeholzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
| | - Brian Tilston Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
- Department of Ornithology, American Museum of Natural History, New York, NY 10024
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Andrés M Cuervo
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118
| | - Robb T Brumfield
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
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20
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Zhao RL, Li GJ, Sánchez-Ramírez S, Stata M, Yang ZL, Wu G, Dai YC, He SH, Cui BK, Zhou JL, Wu F, He MQ, Moncalvo JM, Hyde KD. A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0381-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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21
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Arbour JH, Santana SE. A major shift in diversification rate helps explain macroevolutionary patterns in primate species diversity. Evolution 2017; 71:1600-1613. [PMID: 28346661 DOI: 10.1111/evo.13237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/12/2017] [Indexed: 01/11/2023]
Abstract
Primates represent one of the most species rich, wide ranging, and ecologically diverse clades of mammals. What major macroevolutionary factors have driven their diversification and contributed to the modern distribution of primate species remains widely debated. We employed phylogenetic comparative methods to examine the role of clade age and evolutionary rate heterogeneity in the modern distribution of species diversity of Primates. Primate diversification has accelerated since its origin, with decreased extinction leading to a shift to even higher evolutionary rates in the most species rich family (Cercopithecidae). Older primate clades tended to be more diverse, however a shift in evolutionary rate was necessary to adequately explain the imbalance in species diversity. Species richness was also poorly explained by geographic distribution, especially once clade age and evolutionary rate shifts were accounted for, and may relate instead to other ecological factors. The global distribution of primate species diversity appears to have been strongly impacted by heterogeneity in evolutionary rates.
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Affiliation(s)
- Jessica H Arbour
- Department of Biology, University of Washington, Seattle, Washington, 98195
| | - Sharlene E Santana
- Department of Biology, University of Washington, Seattle, Washington, 98195.,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195
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22
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Smith BT, Seeholzer GF, Harvey MG, Cuervo AM, Brumfield RT. A latitudinal phylogeographic diversity gradient in birds. PLoS Biol 2017; 15:e2001073. [PMID: 28406905 PMCID: PMC5390966 DOI: 10.1371/journal.pbio.2001073] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 03/10/2017] [Indexed: 01/06/2023] Open
Abstract
High tropical species diversity is often attributed to evolutionary dynamics over long timescales. It is possible, however, that latitudinal variation in diversification begins when divergence occurs within species. Phylogeographic data capture this initial stage of diversification in which populations become geographically isolated and begin to differentiate genetically. There is limited understanding of the broader implications of intraspecific diversification because comparative analyses have focused on species inhabiting and evolving in restricted regions and environments. Here, we scale comparative phylogeography up to the hemisphere level and examine whether the processes driving latitudinal differences in species diversity are also evident within species. We collected genetic data for 210 New World bird species distributed across a broad latitudinal gradient and estimated a suite of metrics characterizing phylogeographic history. We found that lower latitude species had, on average, greater phylogeographic diversity than higher latitude species and that intraspecific diversity showed evidence of greater persistence in the tropics. Factors associated with species ecologies, life histories, and habitats explained little of the variation in phylogeographic structure across the latitudinal gradient. Our results suggest that the latitudinal gradient in species richness originates, at least partly, from population-level processes within species and are consistent with hypotheses implicating age and environmental stability in the formation of diversity gradients. Comparative phylogeographic analyses scaled up to large geographic regions and hundreds of species can show connections between population-level processes and broad-scale species-richness patterns.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, New York, United States of America
| | - Glenn F. Seeholzer
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Michael G. Harvey
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrés M. Cuervo
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, United States of America
| | - Robb T. Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
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23
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Clapham ME, Karr JA, Nicholson DB, Ross AJ, Mayhew PJ. Ancient origin of high taxonomic richness among insects. Proc Biol Sci 2017; 283:rspb.2015.2476. [PMID: 26842567 DOI: 10.1098/rspb.2015.2476] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Insects are a hyper-diverse group, comprising nearly three-quarters of all named animal species on the Earth, but the environmental drivers of their richness and the roles of ecological interactions and evolutionary innovations remain unclear. Previous studies have argued that family-level insect richness increased continuously over the evolutionary history of the group, but inclusion of extant family records artificially inflated the relative richness of younger time intervals. Here we apply sampling-standardization methods to a species-level database of fossil insect occurrences, removing biases present in previous richness curves. We show that insect family-richness peaked 125 Ma and that Recent values are only 1.5-3 times as high as the Late Palaeozoic. Rarefied species-richness data also tentatively suggest little or no net increase in richness over the past 125 Myr. The Cretaceous peak in family richness was coincident with major radiations within extant groups but occurred prior to extinctions within more basal groups. Those extinctions may in part be linked to mid-Cretaceous floral turnover following the evolution of flowering plants. Negligible net richness change over the past 125 Myr implies that major radiations within extant groups were offset by reduced richness within groups that are now relict or extinct.
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Affiliation(s)
- Matthew E Clapham
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Jered A Karr
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA 95064, USA
| | - David B Nicholson
- Department of Biology, University of York, York YO10 5YW, UK Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK Department of Natural Sciences, National Museum of Scotland, Chambers Street, Edinburgh, Midlothian EH1 1JF, UK
| | - Andrew J Ross
- Department of Natural Sciences, National Museum of Scotland, Chambers Street, Edinburgh, Midlothian EH1 1JF, UK
| | - Peter J Mayhew
- Department of Biology, University of York, York YO10 5YW, UK
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24
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Harris LW, Davies TJ. A Complete Fossil-Calibrated Phylogeny of Seed Plant Families as a Tool for Comparative Analyses: Testing the 'Time for Speciation' Hypothesis. PLoS One 2016; 11:e0162907. [PMID: 27706173 PMCID: PMC5051821 DOI: 10.1371/journal.pone.0162907] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/30/2016] [Indexed: 01/17/2023] Open
Abstract
Explaining the uneven distribution of species richness across the branches of the tree of life has been a major challenge for evolutionary biologists. Advances in phylogenetic reconstruction, allowing the generation of large, well-sampled, phylogenetic trees have provided an opportunity to contrast competing hypotheses. Here, we present a new time-calibrated phylogeny of seed plant families using Bayesian methods and 26 fossil calibrations. While there are various published phylogenetic trees for plants which have a greater density of species sampling, we are still a long way from generating a complete phylogeny for all ~300,000+ plants. Our phylogeny samples all seed plant families and is a useful tool for comparative analyses. We use this new phylogenetic hypothesis to contrast two alternative explanations for differences in species richness among higher taxa: time for speciation versus ecological limits. We calculated net diversification rate for each clade in the phylogeny and assessed the relationship between clade age and species richness. We then fit models of speciation and extinction to individual branches in the tree to identify major rate-shifts. Our data suggest that the majority of lineages are diversifying very slowly while a few lineages, distributed throughout the tree, are diversifying rapidly. Diversification is unrelated to clade age, no matter the age range of the clades being examined, contrary to both the assumption of an unbounded lineage increase through time, and the paradigm of fixed ecological limits. These findings are consistent with the idea that ecology plays a role in diversification, but rather than imposing a fixed limit, it may have variable effects on per lineage diversification rates through time.
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Affiliation(s)
- Liam W. Harris
- Department of Biology, McGill University, 1205 Docteur-Penfield Avenue, Montreal, Quebec, Canada, H3A 1B1
| | - T. Jonathan Davies
- Department of Biology, McGill University, 1205 Docteur-Penfield Avenue, Montreal, Quebec, Canada, H3A 1B1
- African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa
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25
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Hamm CA, Fordyce JA. Greater host breadth still not associated with increased diversification rate in the Nymphalidae-A response to Janz et al. Evolution 2016; 70:1156-60. [PMID: 27061297 DOI: 10.1111/evo.12914] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 12/18/2022]
Abstract
In their technical comment, Janz et al. take issue with our recent study examining the association between host breadth and diversification rates in the brush-footed butterflies (Lepidoptera: Nymphalidae) (Hamm and Fordyce 2015). Specifically, they are concerned that we misrepresent their "oscillation hypothesis" (OH) (Janz et al. 2006; Janz and Nylin 2008) and that one of our models was inadequate to test hypotheses regarding host breadth and diversification rate. Given our mutual interests in the macroevolutionary patterns of herbivorous insects, we appreciate the opportunity to respond to their concerns.
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Affiliation(s)
- Christopher A Hamm
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045.
| | - James A Fordyce
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996
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26
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Towards standardizing taxonomic ranks using divergence times – a case study for reconstruction of the Agaricus taxonomic system. FUNGAL DIVERS 2016. [DOI: 10.1007/s13225-016-0357-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Near-Stasis in the Long-Term Diversification of Mesozoic Tetrapods. PLoS Biol 2016; 14:e1002359. [PMID: 26807777 PMCID: PMC4726655 DOI: 10.1371/journal.pbio.1002359] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/15/2015] [Indexed: 11/21/2022] Open
Abstract
How did evolution generate the extraordinary diversity of vertebrates on land? Zero species are known prior to ~380 million years ago, and more than 30,000 are present today. An expansionist model suggests this was achieved by large and unbounded increases, leading to substantially greater diversity in the present than at any time in the geological past. This model contrasts starkly with empirical support for constrained diversification in marine animals, suggesting different macroevolutionary processes on land and in the sea. We quantify patterns of vertebrate standing diversity on land during the Mesozoic–early Paleogene interval, applying sample-standardization to a global fossil dataset containing 27,260 occurrences of 4,898 non-marine tetrapod species. Our results show a highly stable pattern of Mesozoic tetrapod diversity at regional and local levels, underpinned by a weakly positive, but near-zero, long-term net diversification rate over 190 million years. Species diversity of non-flying terrestrial tetrapods less than doubled over this interval, despite the origins of exceptionally diverse extant groups within mammals, squamates, amphibians, and dinosaurs. Therefore, although speciose groups of modern tetrapods have Mesozoic origins, rates of Mesozoic diversification inferred from the fossil record are slow compared to those inferred from molecular phylogenies. If high speciation rates did occur in the Mesozoic, then they seem to have been balanced by extinctions among older clades. An apparent 4-fold expansion of species richness after the Cretaceous/Paleogene (K/Pg) boundary deserves further examination in light of potential taxonomic biases, but is consistent with the hypothesis that global environmental disturbances such as mass extinction events can rapidly adjust limits to diversity by restructuring ecosystems, and suggests that the gradualistic evolutionary diversification of tetrapods was punctuated by brief but dramatic episodes of radiation. A large-scale examination of the fossil record reveals slow diversification rates in tetrapods across the 190-million-year Mesozoic era, followed by a possible rapid and abrupt 4-fold increase in species richness after the Cretaceous-Paleogene mass extinction event. Vertebrates invaded the land more than 360 million years ago. Since then, they diversified to more than 30,000 tetrapod species today, including birds, mammals, squamates, and amphibians. The fossil record provides our best window onto diversification across such long spans of time, but is unevenly sampled. Previous studies counted observed families of fossil tetrapods and supported an expansionist model, entailing large and unbounded diversity increases through time. We applied methods that correct for differences in sampling through time and space to a comprehensive species-level database of Mesozoic to early Cenozoic fossil tetrapods. We find strong evidence that tetrapod diversity increased during the Mesozoic, but that the long-term net rate of diversification was low; species richness only doubled or tripled over 190 million years. This is enigmatic because today’s high biodiversity could not have been realised at such a slow rate. Diversification rates must have been much higher during other intervals, or rapid diversification might have been concentrated during brief episodes such as the earliest Cenozoic. Patterns of diversification on geological timescales and their relationships to hypothesised drivers such as ecological opportunity and environmental volatility must receive renewed scrutiny if we are to understand how land vertebrates and other animals attained the high biodiversity seen today.
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28
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Paradis E. The distribution of branch lengths in phylogenetic trees. Mol Phylogenet Evol 2015; 94:136-45. [PMID: 26277061 DOI: 10.1016/j.ympev.2015.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/05/2015] [Accepted: 08/08/2015] [Indexed: 10/23/2022]
Abstract
A lot of effort has been devoted to analyze the distribution of branching times observed in a phylogenetic tree. On the other hand, the distribution of branch lengths has not received similar attention. In this paper, the distribution of branch lengths is studied. It is shown that different types of branches within a tree have distinct distributions. Some equations to predict these distributions are derived with respect to diversification parameters and whether the size of the tree is known or not. A simulation study validated these predictions. The inferred distributions are used to develop graphical and statistical tools to assess the goodness-of-fit of diversification models. An application is presented on a recently published dated phylogeny of Carnivora. Some future developments are discussed.
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Affiliation(s)
- Emmanuel Paradis
- Institut des Sciences de l'Évolution, Université Montpellier, CNRS, IRD, EPHE, CC 064, Place Eugène Bataillon, F-34095 Montpellier Cédex 05, France.
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29
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30
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Harte J, Rominger A, Zhang W. Integrating macroecological metrics and community taxonomic structure. Ecol Lett 2015; 18:1068-77. [DOI: 10.1111/ele.12489] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/17/2015] [Accepted: 07/10/2015] [Indexed: 11/26/2022]
Affiliation(s)
- John Harte
- Energy and Resources Group; University of California at Berkeley; Berkeley CA 94720 USA
| | - Andrew Rominger
- Department of Environmental Science, Policy and Management; University of California at Berkeley; Berkeley CA 94720 USA
| | - Wenyu Zhang
- Department of Statistical Science; Cornell University; Ithaca NY 14850 USA
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31
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Tank DC, Eastman JM, Pennell MW, Soltis PS, Soltis DE, Hinchliff CE, Brown JW, Sessa EB, Harmon LJ. Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. THE NEW PHYTOLOGIST 2015; 207:454-467. [PMID: 26053261 DOI: 10.1111/nph.13491] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 05/01/2015] [Indexed: 05/18/2023]
Abstract
Our growing understanding of the plant tree of life provides a novel opportunity to uncover the major drivers of angiosperm diversity. Using a time-calibrated phylogeny, we characterized hot and cold spots of lineage diversification across the angiosperm tree of life by modeling evolutionary diversification using stepwise AIC (MEDUSA). We also tested the whole-genome duplication (WGD) radiation lag-time model, which postulates that increases in diversification tend to lag behind established WGD events. Diversification rates have been incredibly heterogeneous throughout the evolutionary history of angiosperms and reveal a pattern of 'nested radiations' - increases in net diversification nested within other radiations. This pattern in turn generates a negative relationship between clade age and diversity across both families and orders. We suggest that stochastically changing diversification rates across the phylogeny explain these patterns. Finally, we demonstrate significant statistical support for the WGD radiation lag-time model. Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time. These diversification shifts are only rarely perfectly associated with WGD events, but commonly follow them after a lag period.
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Affiliation(s)
- David C Tank
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Jonathan M Eastman
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Matthew W Pennell
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Pamela S Soltis
- 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
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Cody E Hinchliff
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph W Brown
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Luke J Harmon
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
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Shi JJ, Rabosky DL. Speciation dynamics during the global radiation of extant bats. Evolution 2015; 69:1528-1545. [DOI: 10.1111/evo.12681] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 05/04/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Jeff J. Shi
- Department of Ecology and Evolutionary Biology and Museum of Zoology; University of Michigan; Ann Arbor Michigan 48109
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology; University of Michigan; Ann Arbor Michigan 48109
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Harmon LJ, Harrison S. Species diversity is dynamic and unbounded at local and continental scales. Am Nat 2015; 185:584-93. [PMID: 25905502 DOI: 10.1086/680859] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We argue that biotas at scales from local communities to entire continents are nearly always open to new species and that their diversities are far from any ecological limits. We show that the fossil, phylogenetic, and morphological evidence that has been used to suggest that ecological processes set limits to diversity in evolutionary time is weak and inconsistent. At the same time, ecological evidence from biological invasions, experiments, and diversity analyses strongly supports the openness of communities to new species. We urge evolutionary biologists to recognize that ecology has largely moved beyond simple notions of equilibrium at a carrying capacity and toward a richer view of communities as highly dynamic in space and time.
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Affiliation(s)
- Luke J Harmon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83843
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Betancur-R R, Ortí G, Pyron RA. Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes. Ecol Lett 2015; 18:441-50. [PMID: 25808114 DOI: 10.1111/ele.12423] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/20/2014] [Accepted: 01/29/2015] [Indexed: 11/30/2022]
Abstract
The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies.
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Affiliation(s)
- Ricardo Betancur-R
- Department of Biology, University of Puerto Rico - Río Piedras, P.O. Box 23360, San Juan, Puerto Rico, 00931; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013, USA
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