1
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Faurby S, Silvestro D, Werdelin L, Antonelli A. Reliable biogeography requires fossils: insights from a new species-level phylogeny of extinct and living carnivores. Proc Biol Sci 2024; 291:20240473. [PMID: 39106959 DOI: 10.1098/rspb.2024.0473] [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: 02/27/2024] [Accepted: 05/21/2024] [Indexed: 08/09/2024] Open
Abstract
A central objective of historical biogeography is to understand where clades originated and how they moved across space and over time. However, given the dynamic history of ecosystem changes in response to climate change and geological events, the manifold long-distance dispersals over evolutionary timescales, and regional and global extinctions, it remains uncertain how reliable inferences based solely on extant taxa can be achieved. Using a novel species-level phylogeny of all known extant and extinct species of the mammalian order Carnivora and related extinct groups, we show that far more precise and accurate ancestral areas can be estimated by fully integrating extinct species into the analyses, rather than solely relying on extant species or identifying ancestral areas only based on the geography of the oldest fossils. Through a series of simulations, we further show that this conclusion is robust under realistic scenarios in which the unknown extinct taxa represent a biased subset of all extinct species. Our results highlight the importance of integrating fossil taxa into a phylogenetic framework to further improve our understanding of historical biogeography and reveal the dynamic dispersal and diversification history of carnivores.
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Affiliation(s)
- Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 40530 Gothenburg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 40530 Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 40530 Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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2
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Quintero I, Lartillot N, Morlon H. Imbalanced speciation pulses sustain the radiation of mammals. Science 2024; 384:1007-1012. [PMID: 38815022 DOI: 10.1126/science.adj2793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
The evolutionary histories of major clades, including mammals, often comprise changes in their diversification dynamics, but how these changes occur remains debated. We combined comprehensive phylogenetic and fossil information in a new "birth-death diffusion" model that provides a detailed characterization of variation in diversification rates in mammals. We found an early rising and sustained diversification scenario, wherein speciation rates increased before and during the Cretaceous-Paleogene (K-Pg) boundary. The K-Pg mass extinction event filtered out more slowly speciating lineages and was followed by a subsequent slowing in speciation rates rather than rebounds. These dynamics arose from an imbalanced speciation process, with separate lineages giving rise to many, less speciation-prone descendants. Diversity seems to have been brought about by these isolated, fast-speciating lineages, rather than by a few punctuated innovations.
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Affiliation(s)
- Ignacio Quintero
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Nicolas Lartillot
- Université Claude Bernard Lyon 1, CNRS, VetAgroSup, LBBE, UMR 5558, F-69100 Villeurbanne, France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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3
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Mendes FK, Landis MJ. PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571907. [PMID: 38168278 PMCID: PMC10760140 DOI: 10.1101/2023.12.15.571907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, through its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This paper describes the features of PhyloJunction - which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models - and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.
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Affiliation(s)
- Fábio K. Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO
| | - Michael J. Landis
- Department of Biology, Washington University in St. Louis, St. Louis, MO
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4
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Morinaga G, Wiens JJ, Moen DS. The radiation continuum and the evolution of frog diversity. Nat Commun 2023; 14:7100. [PMID: 37925440 PMCID: PMC10625520 DOI: 10.1038/s41467-023-42745-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Most of life's vast diversity of species and phenotypes is often attributed to adaptive radiation. Yet its contribution to species and phenotypic diversity of a major group has not been examined. Two key questions remain unresolved. First, what proportion of clades show macroevolutionary dynamics similar to adaptive radiations? Second, what proportion of overall species richness and phenotypic diversity do these adaptive-radiation-like clades contain? We address these questions with phylogenetic and morphological data for 1226 frog species across 43 families (which represent >99% of all species). Less than half of frog families resembled adaptive radiations (with rapid diversification and morphological evolution). Yet, these adaptive-radiation-like clades encompassed ~75% of both morphological and species diversity, despite rapid rates in other clades (e.g., non-adaptive radiations). Overall, we support the importance of adaptive-radiation-like evolution for explaining diversity patterns and provide a framework for characterizing macroevolutionary dynamics and diversity patterns in other groups.
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Affiliation(s)
- Gen Morinaga
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, 74078, USA
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Daniel S Moen
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA.
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5
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Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. Ancient segmentally duplicated LCORL retrocopies in equids. PLoS One 2023; 18:e0286861. [PMID: 37289743 PMCID: PMC10249811 DOI: 10.1371/journal.pone.0286861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant perissodactyls. The majority of LCORL transcripts in horses and donkeys originate from the retrocopies. The initial LCORL retrotransposition occurred 18 million years ago (17-19 95% CI), which is coincident with the increase in body size, reduction in digit number, and changes in dentition that characterized equid evolution. Evolutionary conservation of the LCORL retrocopy segmental amplification in the Equidae family, high expression levels and the ancient timeline for LCORL retrotransposition support a functional role for this structural variant.
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Affiliation(s)
- Kevin Batcher
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
| | - Scarlett Varney
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Matthew Jevit
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Peter Dickinson
- Department of Surgical and Radiological Sciences, University of California Davis, Davis, CA, United States of America
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
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6
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Vincelette AR, Renders E, Scott KM, Falkingham PL, Janis CM. Hipparion tracks and horses' toes: the evolution of the equid single hoof. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230358. [PMID: 37351494 PMCID: PMC10282582 DOI: 10.1098/rsos.230358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023]
Abstract
The traditional story of the evolution of the horse (family Equidae) has been in large part about the evolution of their feet. How did modern horses come to have a single toe (digit III), with the hoof bearing a characteristic V-shaped keratinous frog on the sole, and what happened to the other digits? While it has long been known that the proximal portions of digits II and IV are retained as the splint bones, a recent hypothesis suggested that the distal portion of these digits have also been retained as part of the frog, drawing upon the famous Laetoli footprints of the tridactyl (three-toed) equid Hipparion as part of the evidence. We show here that, while there is good anatomical and embryological evidence for the proximal portions of all the accessory digits (i.e. I and V, as well as II and IV) being retained in the feet of modern horses, evidence is lacking for the retention of any distal portions of these digits. There is also good ichnological evidence that many tridactyl equids possessed a frog, and that the frog has been part of the equid foot for much of equid evolutionary history.
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Affiliation(s)
| | - Elise Renders
- Department of Functional Morphology, Faculty of Veterinary Medicine, Utrecht University (Ret.), Utrecht, 3584 CM, The Netherlands
| | - Kathleen M. Scott
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, 08854, NJ, USA
| | - Peter L. Falkingham
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Christine M. Janis
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
- Department of Ecology and Evolutionary Biology, Brown University, Providence, 02912, RI, USA
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7
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Sanisidro O, Mihlbachler MC, Cantalapiedra JL. A macroevolutionary pathway to megaherbivory. Science 2023; 380:616-618. [PMID: 37167399 DOI: 10.1126/science.ade1833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
Several scenarios have been proposed to explain rapid net size increases in some early Cenozoic mammalian lineages: sustained and gradual directional change, successive occupation of adaptive zones associated with progressively larger body sizes, and nondirectional evolution associated with branching events in combination with higher diversification potential of the larger lineages. We test these hypotheses in brontotheres, which are among the first radiations of mammals that consistently evolved multitonne sizes. Body-mass evolution in brontotheres mainly occurred during speciation and had no preferential direction. Long-term directional change stemmed from the higher survival of larger lineages in less-saturated herbivore guilds. Our study emphasizes the role of differential species proliferation in explaining the long-term phenotypic trends observed in the fossil record, which are more than an accumulation of steady microevolutionary changes.
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Affiliation(s)
- Oscar Sanisidro
- Global Change Ecology and Evolution Research Group (GloCEE), Department of Life Sciences, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain
| | - Matthew C Mihlbachler
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY 11568, USA
- Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA
| | - Juan L Cantalapiedra
- Global Change Ecology and Evolution Research Group (GloCEE), Department of Life Sciences, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain
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8
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A Late Devonian actinopterygian suggests high lineage survivorship across the end-Devonian mass extinction. Nat Ecol Evol 2023; 7:10-19. [PMID: 36396970 DOI: 10.1038/s41559-022-01919-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/29/2022] [Indexed: 11/18/2022]
Abstract
Many accounts of the early history of actinopterygians (ray-finned fishes) posit that the end-Devonian mass extinction had a major influence on their evolution. Existing phylogenies suggest this episode could have acted as a bottleneck, paring the early diversity of the group to a handful of survivors. This picture, coupled with increases in taxonomic and morphological diversity in the Carboniferous, contributes to a model of explosive post-extinction radiation. However, most actinopterygians from within a roughly 20-million year (Myr) window surrounding the extinction are poorly known, contributing to uncertainty about the meaning of these patterns. Here, we report an exceptionally preserved fossil from 7 Myr before the extinction that reveals unexpected anatomical features. Palaeoneiros clackorum gen. et sp. nov. nests within a clade of post-Devonian species and, in an expanded phylogenetic analysis, draws multiple lineages of Carboniferous actinopterygians into the Devonian. This suggests cryptic but extensive lineage diversification in the latest Devonian, followed by more conspicuous feeding and locomotor structure diversification in the Carboniferous. Our revised model matches more complex patterns of divergence, survival and diversification around the Devonian/Carboniferous boundary in other vertebrate clades. It also fundamentally recalibrates the onset of diversification early in the history of this major radiation.
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9
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Esquerré D, Brennan IG, Donnellan S, Keogh JS. Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons. Biol Lett 2022; 18:20220360. [PMID: 36541096 PMCID: PMC9768648 DOI: 10.1098/rsbl.2022.0360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
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10
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Gamboa S, Condamine FL, Cantalapiedra JL, Varela S, Pelegrín JS, Menéndez I, Blanco F, Hernández Fernández M. A phylogenetic study to assess the link between biome specialization and diversification in swallowtail butterflies. GLOBAL CHANGE BIOLOGY 2022; 28:5901-5913. [PMID: 35838418 PMCID: PMC9543414 DOI: 10.1111/gcb.16344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The resource-use hypothesis, proposed by E.S. Vrba, states that habitat fragmentation caused by climatic oscillations would affect particularly biome specialists (species inhabiting only one biome), which might show higher speciation and extinction rates than biome generalists. If true, lineages would accumulate biome-specialist species. This effect would be particularly exacerbated for biomes located at the periphery of the global climatic conditions, namely, biomes that have high/low precipitation and high/low temperature such as rainforest (warm-humid), desert (warm-dry), steppe (cold-dry) and tundra (cold-humid). Here, we test these hypotheses in swallowtail butterflies, a clade with more than 570 species, covering all the continents but Antarctica, and all climatic conditions. Swallowtail butterflies are among the most studied insects, and they are a model group for evolutionary biology and ecology studies. Continental macroecological rules are normally tested using vertebrates, this means that there are fewer examples exploring terrestrial invertebrate patterns at global scale. Here, we compiled a large Geographic Information System database on swallowtail butterflies' distribution maps and used the most complete time-calibrated phylogeny to quantify diversification rates (DRs). In this paper, we aim to answer the following questions: (1) Are there more biome-specialist swallowtail butterflies than biome generalists? (2) Is DR related to biome specialization? (3) If so, do swallowtail butterflies inhabiting extreme biomes show higher DRs? (4) What is the effect of species distribution area? Our results showed that swallowtail family presents a great number of biome specialists which showed substantially higher DRs compared to generalists. We also found that biome specialists are unevenly distributed across biomes. Overall, our results are consistent with the resource-use hypothesis, species climatic niche and biome fragmentation as key factors promoting isolation.
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Affiliation(s)
- Sara Gamboa
- Centro de Investigación Mariña (CIM)Universidade de Vigo, Grupo de Ecoloxía Animal (GEA), MAPAS LabVigoPontevedraSpain
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
- CNRSUMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier)MontpellierFrance
| | - Fabien L. Condamine
- CNRSUMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier)MontpellierFrance
| | - Juan L. Cantalapiedra
- Departamento de Ciencias de la Vida, Edificio de Ciencias Campus Científico‐TecnológicoUniversidad de AlcaláAlcalá de HenaresSpain
| | - Sara Varela
- Centro de Investigación Mariña (CIM)Universidade de Vigo, Grupo de Ecoloxía Animal (GEA), MAPAS LabVigoPontevedraSpain
| | - Jonathan S. Pelegrín
- Área de Biología y Ciencias Ambientales Facultades de Ciencias Básicas y EducaciónUniversidad Santiago de CaliSantiago de CaliValle del CaucaColombia
- Departamento de Biología, Facultad de Ciencias Naturales y ExactasUniversidad del Valle, Campus MeléndezSantiago de CaliValle del CaucaColombia
| | - Iris Menéndez
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
| | - Fernando Blanco
- Museum für Naturkunde, Leibniz‐Institut für Evolutions und BiodiversitätsforschungBerlinGermany
| | - Manuel Hernández Fernández
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
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11
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Giles SAW, Arbuckle K. Diversification dynamics of chameleons (Chamaeleonidae). J Zool (1987) 2022. [DOI: 10.1111/jzo.13019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. A. W. Giles
- Department of Biosciences, Faculty of Science and Engineering Swansea University Swansea UK
| | - K. Arbuckle
- Department of Biosciences, Faculty of Science and Engineering Swansea University Swansea UK
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12
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Ruiz-García M, Pinedo-Castro M, Shostell JM. Comparative phylogeography among eight Neotropical wild cat species: no single evolutionary pattern. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blab170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The felid species of South America are thought to have arrived on the continent during the Great American Biotic Interchange (GABI) in the Pleistocene. However, molecular and palaeontological data do not agree on how this event affected speciation in felids. Here, we determine both the number of colonization events and the period when felines first migrated from North America to South America. In addition, we evaluate whether similar evolutionary events could have affected the eight Neotropical cat species in their levels of genetic diversity, spatial genetic structure and demographic changes. We analysed four concatenated mitochondrial genes of the jaguar, ocelot, margay, tigrina, pampas cat, Andean cat, puma and jaguarundi. The samples were representative of a wide distribution of these species in Central and South America. Our analysis suggests either three or four colonization events from North America to South America over the past 3 Myr, followed by subsequent speciation events and the attainment of high or very high genetic diversity levels for seven of the species. No unique evolutionary process was detected for any of the current Neotropical cat species.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No. 43-82, Bogotá DC, Colombia
| | - Myreya Pinedo-Castro
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No. 43-82, Bogotá DC, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, 2900 University Avenue, Crookston, MN 56716, USA
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13
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Morphological volatility precedes ecological innovation in early echinoderms. Nat Ecol Evol 2022; 6:263-272. [PMID: 35145267 DOI: 10.1038/s41559-021-01656-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/20/2021] [Indexed: 11/08/2022]
Abstract
Origins of higher taxonomic groups entail dramatic and nearly simultaneous changes in morphology and ecological function, limiting our ability to disentangle the drivers of evolutionary diversification. Here we phylogenetically compare the anatomy and life habits of Cambrian-Ordovician echinoderms to test which facet better facilitates future success. Rates of morphological evolution are faster and involve more volatile trait changes, allowing morphological disparity to accrue faster and earlier in the Cambrian. However, persistent life-habit evolution throughout the early Palaeozoic, combined with iterative functional convergence within adaptive strategies, results in major expansion of ecospace and functional diversity. The interactions between tempo, divergence and convergence demonstrate not only that anatomical novelty precedes ecological success, but also that ecological innovation is constrained, even during a phylum's origin.
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14
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Upham NS, Esselstyn JA, Jetz W. Molecules and fossils tell distinct yet complementary stories of mammal diversification. Curr Biol 2021; 31:4195-4206.e3. [PMID: 34329589 DOI: 10.1016/j.cub.2021.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 07/07/2021] [Indexed: 11/25/2022]
Abstract
Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to "pull" speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (n = 5,911 species, ∼70% from DNA) to those in fossil genus durations (n = 5,320). We use fossil extinction rates to correct or "push" the timetree-based (pulled) speciation-rate estimates, finding a surge of speciation during the Paleocene (∼66-56 million years ago, Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, about two-thirds of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is likely undetectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ∼10 Ma and are equal at the present day when recent evolutionary processes can be estimated without bias using species-specific "tip" rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade's extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.
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Affiliation(s)
- Nathan S Upham
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Center for Biodiversity and Global Change, Yale University, New Haven, CT 06511, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Jacob A Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Center for Biodiversity and Global Change, Yale University, New Haven, CT 06511, USA.
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15
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Benson RBJ, Butler R, Close RA, Saupe E, Rabosky DL. Biodiversity across space and time in the fossil record. Curr Biol 2021; 31:R1225-R1236. [PMID: 34637736 DOI: 10.1016/j.cub.2021.07.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fossil record is the primary source of information on how biodiversity has varied in deep time, providing unique insight on the long-term dynamics of diversification and their drivers. However, interpretations of fossil record diversity patterns have been much debated, with a traditional focus on global diversity through time. Problems arise because the fossil record is spatially and temporally patchy, so 'global' diversity estimates actually represent the summed diversity across a set of geographically and environmentally distinct regions that vary substantially in number and identity through time. Furthermore, a focus on global diversity lumps the signal of ecological drivers at local and regional scales with the signal of global-scale processes, including variation in the distribution of environments and in provincialism (the extent of subdivision into distinct biogeographic regions). These signals cannot be untangled by studying global diversity measures alone. These conceptual and empirical concerns necessitate a shift away from the study of 'biodiversity through time' and towards the study of 'biodiversity across time and space'. Spatially explicit investigations, including analyses of local- and regional-scale datasets, are central to achieving this and allow analysis of geographic scale, location and the environmental parameters directly experienced by organisms. So far, research in this area has revealed the stability of species richness variation among environments through time, and the potential climatic and Earth-system drivers of changing biodiversity. Ultimately, this research program promises to address key questions regarding the assembly of biodiversity, and the contributions of local-, regional- and global-scale processes to the diversification of life on Earth.
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Affiliation(s)
- Roger B J Benson
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK.
| | - Richard Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roger A Close
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Erin Saupe
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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16
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The rise and fall of proboscidean ecological diversity. Nat Ecol Evol 2021; 5:1266-1272. [PMID: 34211141 DOI: 10.1038/s41559-021-01498-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023]
Abstract
Proboscideans were keystone Cenozoic megaherbivores and present a highly relevant case study to frame the timing and magnitude of recent megafauna extinctions against long-term macroevolutionary patterns. By surveying the entire proboscidean fossil history using model-based approaches, we show that the dramatic Miocene explosion of proboscidean functional diversity was triggered by their biogeographical expansion beyond Africa. Ecomorphological innovations drove niche differentiation; communities that accommodated several disparate proboscidean species in sympatry became commonplace. The first burst of extinctions took place in the late Miocene, approximately 7 million years ago (Ma). Importantly, this and subsequent extinction trends showed high ecomorphological selectivity and went hand in hand with palaeoclimate dynamics. The global extirpation of proboscideans began escalating from 3 Ma with further extinctions in Eurasia and then a dramatic increase in African extinctions at 2.4 Ma. Overhunting by humans may have served as a final double jeopardy in the late Pleistocene after climate-triggered extinction trends that began long before hominins evolved suitable hunting capabilities.
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17
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Simões TR, Pierce SE. Sustained high rates of morphological evolution during the rise of tetrapods. Nat Ecol Evol 2021; 5:1403-1414. [PMID: 34426679 DOI: 10.1038/s41559-021-01532-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022]
Abstract
The fish-to-tetrapod transition is one of the most iconic events in vertebrate evolution, yet fundamental questions regarding the dynamics of this transition remain unresolved. Here, we use advances in Bayesian morphological clock modelling to reveal the evolutionary dynamics of early tetrapodomorphs (tetrapods and their closest fish relatives). We show that combining osteological and ichnological calibration data results in major shifts on the time of origin of all major groups of tetrapodomorphs (up to 25 million years) and that low rates of net diversification, not fossilization, explain long ghost lineages in the early tetrapodomorph fossil record. Further, our findings reveal extremely low rates of morphological change for most early tetrapodomorphs, indicating widespread stabilizing selection upon their 'fish' morphotype. This pattern was broken only by elpistostegalians (including early tetrapods), which underwent sustained high rates of morphological evolution for ~30 Myr during the deployment of the tetrapod body plan.
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Affiliation(s)
- Tiago R Simões
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Stephanie E Pierce
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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18
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Moen DS, Ravelojaona RN, Hutter CR, Wiens JJ. Testing for adaptive radiation: A new approach applied to Madagascar frogs. Evolution 2021; 75:3008-3025. [PMID: 34396527 DOI: 10.1111/evo.14328] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 07/17/2021] [Indexed: 11/27/2022]
Abstract
Adaptive radiation is a key topic at the intersection of ecology and evolutionary biology. Yet the definition and identification of adaptive radiation both remain contentious. Here, we introduce a new approach for identifying adaptive radiations that combines key aspects of two widely used definitions. Our approach compares evolutionary rates in morphology, performance, and diversification between the candidate radiation and other clades. We then apply this approach to a putative adaptive radiation of frogs from Madagascar (Mantellidae). We present new data on morphology and performance from mantellid frogs, then compare rates of diversification and multivariate evolution of size, shape, and performance between mantellids and other frogs. We find that mantellids potentially pass our test for accelerated rates of evolution for shape, but not for size, performance, or diversification. Our results demonstrate that clades can have accelerated phenotypic evolution without rapid diversification (dubbed "adaptive non-radiation"). We also highlight general issues in testing for adaptive radiation, including taxon sampling and the problem of including another adaptive radiation among the comparison clades. Finally, we suggest that similar tests should be conducted on other putative adaptive radiations on Madagascar, comparing their evolutionary rates to those of related clades outside Madagascar. Based on our results, we speculate that older Madagascar clades may show evolutionary patterns more similar to those on a continent than an island.
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Affiliation(s)
- Daniel S Moen
- Department of Integrative Biology, 501 Life Sciences West, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Rojo N Ravelojaona
- Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Carl R Hutter
- Museum of Natural Science and Department of Biological Sciences, Lousiana State University, Baton Rouge, Louisiana, 70803, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
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19
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de Alencar LRV, Quental TB. Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale. Ecol Evol 2021; 11:5828-5843. [PMID: 34141187 PMCID: PMC8207422 DOI: 10.1002/ece3.7511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 11/05/2022] Open
Abstract
Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource-partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the microscale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the microscale and macroscale, and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader's attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect microevolution and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data.
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Affiliation(s)
| | - Tiago Bosisio Quental
- Departamento de EcologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrazil
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20
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Cirilli O, Pandolfi L, Rook L, Bernor RL. Evolution of Old World Equus and origin of the zebra-ass clade. Sci Rep 2021; 11:10156. [PMID: 33980921 PMCID: PMC8114910 DOI: 10.1038/s41598-021-89440-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022] Open
Abstract
Evolution of the genus Equus has been a matter of long debate with a multitude of hypotheses. Currently, there is no consensus on either the taxonomic content nor phylogeny of Equus. Some hypotheses segregate Equus species into three genera, Plesippus, Allohippus and Equus. Also, the evolutionary role of European Pleistocene Equus stenonis in the origin of the zebra-ass clade has been debated. Studies based on skull, mandible and dental morphology suggest an evolutionary relationship between North American Pliocene E. simplicidens and European and African Pleistocene Equus. In this contribution, we assess the validity of the genera Plesippus, Allohippus and Equus by cladistic analysis combined with morphological and morphometrical comparison of cranial anatomy. Our cladistic analysis, based on cranial and postcranial elements (30 taxa, 129 characters), supports the monophyly of Equus, denies the recognition of Plesippus and Allohippus and supports the derivation of Equus grevyi and members of the zebra-ass clade from European stenonine horses. We define the following evolutionary steps directly relevant to the phylogeny of extant zebras and asses: E. simplicidens–E. stenonis–E. koobiforensis–E. grevyi -zebra-ass clade. The North American Pliocene species Equus simplicidens represents the ancestral stock of Old World Pleistocene Equus and the zebra-ass clade. Our phylogenetic results uphold the most recent genomic outputs which indicate an age of 4.0–4.5 Ma for the origin and monophyly of Equus.
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Affiliation(s)
- Omar Cirilli
- Dottorato Regionale Pegaso in Scienze della Terra, Università di Pisa, Via S. Maria 53, 56126, Pisa, Italy. .,Dipartimento di Scienze della Terra, Paleo[Fab]Lab, Università degli Studi di Firenze, Via G. La Pira 4, 50121, Firenze, Italy.
| | - Luca Pandolfi
- Dipartimento di Scienze della Terra, Paleo[Fab]Lab, Università degli Studi di Firenze, Via G. La Pira 4, 50121, Firenze, Italy.
| | - Lorenzo Rook
- Dipartimento di Scienze della Terra, Paleo[Fab]Lab, Università degli Studi di Firenze, Via G. La Pira 4, 50121, Firenze, Italy
| | - Raymond L Bernor
- Laboratory of Evolutionary Biology, Department of Anatomy, College of Medicine, 520 W St. N.W, Washington, DC, 20059, USA.,Department of Anthropology, Human Origins Program, Smithsonian Institution, Washington, DC, 20560, USA
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21
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Saarinen J, Cirilli O, Strani F, Meshida K, Bernor RL. Testing Equid Body Mass Estimate Equations on Modern Zebras—With Implications to Understanding the Relationship of Body Size, Diet, and Habitats of Equus in the Pleistocene of Europe. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622412] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The monodactyl horses of the genus Equus originated in North America during the Pliocene, and from the beginning of the Pleistocene, they have been an essential part of the large ungulate communities of Europe, North America and Africa. Understanding how body size of Equus species evolved and varied in relation to changes in environments and diet thus forms an important part of understanding the dynamics of ungulate body size variation in relation to Pleistocene paleoenvironmental changes. Here we test previously published body mass estimation equations for the family Equidae by investigating how accurately different skeletal and dental measurements estimate the mean body mass (and body mass range) reported for extant Grevy's zebra (Equus grevyi) and Burchell's zebra (Equus quagga). Based on these tests and information on how frequently skeletal elements occur in the fossil record, we construct a hierarchy of best practices for the selection of body mass estimation equations in Equus. As a case study, we explore body size variation in Pleistocene European Equus paleopopulations in relation to diet and vegetation structure in their paleoenvironments. We show a relationship between diet and body size in Equus: very large-sized species tend to have more browse-dominated diets than small and medium-sized species, and paleovegetation proxies indicate on average more open and grass-rich paleoenvironments for small-sized, grazing species of Equus. When more than one species of Equus co-occur sympatrically, the larger species tend to be less abundant and have more browse-dominated diets than the smaller species. We suggest that body size variation in Pleistocene Equus was driven by a combined effect of resource quality and availability, partitioning of habitats and resources between species, and the effect of environmental openness and group size on the body size of individuals.
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22
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MacLaren JA. Biogeography a key influence on distal forelimb variation in horses through the Cenozoic. Proc Biol Sci 2021; 288:20202465. [PMID: 33434465 DOI: 10.1098/rspb.2020.2465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Locomotion in terrestrial tetrapods is reliant on interactions between distal limb bones (e.g. metapodials and phalanges). The metapodial-phalangeal joint in horse (Equidae) limbs is highly specialized, facilitating vital functions (shock absorption; elastic recoil). While joint shape has changed throughout horse evolution, potential drivers of these modifications have not been quantitatively assessed. Here, I examine the morphology of the forelimb metacarpophalangeal (MCP) joint of horses and their extinct kin (palaeotheres) using geometric morphometrics and disparity analyses, within a phylogenetic context. I also develop a novel alignment protocol that explores the magnitude of shape change through time, correlated against body mass and diet. MCP shape was poorly correlated with mass or diet proxies, although significant temporal correlations were detected at 0-1 Myr intervals. A clear division was recovered between New and Old World hipparionin MCP morphologies. Significant changes in MCP disparity and high rates of shape divergence were observed during the Great American Biotic Interchange, with the MCP joint becoming broad and robust in two separate monodactyl lineages, possibly exhibiting novel locomotor behaviour. This large-scale study of MCP joint shape demonstrates the apparent capacity for horses to rapidly change their distal limb morphology to overcome discrete locomotor challenges in new habitats.
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Affiliation(s)
- Jamie A MacLaren
- Evolution and Diversity Dynamics Laboratory, Department of Geology, Université de Liege, Building B18, Allée du Six Août 14, Sart-Tillman Campus, Liege 4000, Belgium.,Functional Morphology Laboratory, Department of Biology, Universiteit Antwerpen, Antwerpen 2610, Belgium
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23
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Abstract
The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.
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Affiliation(s)
- Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
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24
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Heterogeneous relationships between rates of speciation and body size evolution across vertebrate clades. Nat Ecol Evol 2020; 5:101-110. [PMID: 33106601 DOI: 10.1038/s41559-020-01321-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 09/04/2020] [Indexed: 01/09/2023]
Abstract
Several theories predict that rates of phenotypic evolution should be related to the rate at which new lineages arise. However, drawing general conclusions regarding the coupling between these fundamental evolutionary rates has been difficult due to the inconsistent nature of previous results combined with uncertainty over the most appropriate methodology with which to investigate such relationships. Here we propose and compare the performance of several different approaches for testing associations between lineage-specific rates of speciation and phenotypic evolution using phylogenetic data. We then use the best-performing method to test relationships between rates of speciation and body size evolution in five major vertebrate clades (amphibians, birds, mammals, ray-finned fish and squamate reptiles) at two phylogenetic scales. Our results provide support for the long-standing view that rates of speciation and morphological evolution are generally positively related at broad macroevolutionary scales, but they also reveal a substantial degree of heterogeneity in the strength and direction of these associations at finer scales across the vertebrate tree of life.
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25
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Fraser D, Soul LC, Tóth AB, Balk MA, Eronen JT, Pineda-Munoz S, Shupinski AB, Villaseñor A, Barr WA, Behrensmeyer AK, Du A, Faith JT, Gotelli NJ, Graves GR, Jukar AM, Looy CV, Miller JH, Potts R, Lyons SK. Investigating Biotic Interactions in Deep Time. Trends Ecol Evol 2020; 36:61-75. [PMID: 33067015 DOI: 10.1016/j.tree.2020.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.
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Affiliation(s)
- Danielle Fraser
- Palaeobiology, Canadian Museum of Nature, Ottawa, ON, Canada; Biology and Earth Sciences, Carleton University, Ottawa, ON, Canada; Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA.
| | - Laura C Soul
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Anikó B Tóth
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, NSW, Australia
| | - Meghan A Balk
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Jussi T Eronen
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; Helsinki Institute of Sustainability Science, Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland; BIOS research Unit, Helsinki, Finland
| | - Silvia Pineda-Munoz
- Department of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Amelia Villaseñor
- Department of Anthropology, University of Arkansas, Fayetteville, AR, USA
| | - W Andrew Barr
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Anna K Behrensmeyer
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Andrew Du
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, Salt Lake City, UT,USA; Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Gary R Graves
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Advait M Jukar
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Cindy V Looy
- Department of Integrative Biology, Museum of Paleontology, University and Jepson Herbaria, University of California-Berkeley, Berkeley, CA , USA
| | - Joshua H Miller
- Department of Geology, University of Cincinnati, Cincinnati, OH, USA
| | - Richard Potts
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC , USA
| | - S Kathleen Lyons
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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26
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Menéndez I, Gómez Cano AR, Cantalapiedra JL, Peláez‐Campomanes P, Álvarez‐Sierra MÁ, Hernández Fernández M. A multi‐layered approach to the diversification of squirrels. Mamm Rev 2020. [DOI: 10.1111/mam.12215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Iris Menéndez
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas Universidad Complutense de Madrid C/ José Antonio Novais 12 Madrid28040 Spain
- Departamento de Cambio Medioambiental Instituto de Geociencias (UCM, CSIC) C/Severo Ochoa 7 Madrid28040 Spain
| | | | - Juan L. Cantalapiedra
- Departamento de Ciencias de la Vida, GloCEE Global Change Ecology and Evolution Research Group Universidad de Alcalá Plaza de San Diego s/n, Alcalá de Henares Madrid28801 Spain
| | - Pablo Peláez‐Campomanes
- Departameto de Paleobiología Museo Nacional de Ciencias Naturales, MNCN‐CSIC C/ José Gutiérrez Abascal, 2 Madrid28006 Spain
| | - María Ángeles Álvarez‐Sierra
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas Universidad Complutense de Madrid C/ José Antonio Novais 12 Madrid28040 Spain
- Departamento de Cambio Medioambiental Instituto de Geociencias (UCM, CSIC) C/Severo Ochoa 7 Madrid28040 Spain
| | - Manuel Hernández Fernández
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas Universidad Complutense de Madrid C/ José Antonio Novais 12 Madrid28040 Spain
- Departamento de Cambio Medioambiental Instituto de Geociencias (UCM, CSIC) C/Severo Ochoa 7 Madrid28040 Spain
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27
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Whalen CD, Hull PM, Briggs DEG. Paleozoic ammonoid ecomorphometrics test ecospace availability as a driver of morphological diversification. SCIENCE ADVANCES 2020; 6:eabc2365. [PMID: 32917688 PMCID: PMC11206447 DOI: 10.1126/sciadv.abc2365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
The early burst model suggests that disparity rises rapidly to fill empty ecospace following clade origination or in the aftermath of a mass extinction. Early bursts are considered common features of fossil data, but neontological studies have struggled to identify them. Furthermore, tests have proven difficult because factors besides ecology can drive changes in morphology. Here, we document the ecomorphometric evolution of the extinct Ammonoidea at 1-million-year resolution, from their origination in the Early Devonian (Emsian) to the Early Triassic (Induan), over ~156 million years. This time interval encompasses six global extinction events, including two of the Big Five, and incorporates multiple ammonoid radiations. However, we find no evidence for early bursts of ecomorphological disparity. This contradicts arguments that the temporal scope, or traits measured in genomic data, conceal evidence of early bursts. Rather, early bursts may be less prevalent in fossil data than is often assumed.
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Affiliation(s)
- Christopher D Whalen
- Department of Earth and Planetary Sciences, Yale University, 210 Whitney Ave., New Haven, CT 06511, USA.
| | - Pincelli M Hull
- Department of Earth and Planetary Sciences, Yale University, 210 Whitney Ave., New Haven, CT 06511, USA
- Peabody Museum of Natural History, Yale University, 170 Whitney Ave., New Haven, CT 06511, USA
| | - Derek E G Briggs
- Department of Earth and Planetary Sciences, Yale University, 210 Whitney Ave., New Haven, CT 06511, USA
- Peabody Museum of Natural History, Yale University, 170 Whitney Ave., New Haven, CT 06511, USA
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28
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Simões TR, Vernygora O, Caldwell MW, Pierce SE. Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles. Nat Commun 2020; 11:3322. [PMID: 32620878 PMCID: PMC7335191 DOI: 10.1038/s41467-020-17190-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 06/17/2020] [Indexed: 11/18/2022] Open
Abstract
The origin of phenotypic diversity among higher clades is one of the most fundamental topics in evolutionary biology. However, due to methodological challenges, few studies have assessed rates of evolution and phenotypic disparity across broad scales of time to understand the evolutionary dynamics behind the origin and early evolution of new clades. Here, we provide a total-evidence dating approach to this problem in diapsid reptiles. We find major chronological gaps between periods of high evolutionary rates (phenotypic and molecular) and expansion in phenotypic disparity in reptile evolution. Importantly, many instances of accelerated phenotypic evolution are detected at the origin of major clades and body plans, but not concurrent with previously proposed periods of adaptive radiation. Furthermore, strongly heterogenic rates of evolution mark the acquisition of similarly adapted functional types, and the origin of snakes is marked by the highest rates of phenotypic evolution in diapsid history.
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Affiliation(s)
- Tiago R Simões
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
| | - Oksana Vernygora
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Michael W Caldwell
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Stephanie E Pierce
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
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29
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McHorse BK, Biewener AA, Pierce SE. The Evolution of a Single Toe in Horses: Causes, Consequences, and the Way Forward. Integr Comp Biol 2020; 59:638-655. [PMID: 31127281 DOI: 10.1093/icb/icz050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Horses are a classic example of macroevolution in three major traits-large body size, tall-crowned teeth (hypsodonty), and a single toe (monodactyly)-but how and why monodactyly evolved is still poorly understood. Existing hypotheses usually connect digit reduction in horses to the spread and eventual dominance of open-habitat grasslands, which took over from forests during the Cenozoic; digit reduction has been argued to be an adaptation for speed, locomotor economy, stability, and/or increased body size. In this review, we assess the evidence for these (not necessarily mutually exclusive) hypotheses from a variety of related fields, including paleoecology, phylogenetic comparative methods, and biomechanics. Convergent evolution of digit reduction, including in litopterns and artiodactyls, is also considered. We find it unlikely that a single evolutionary driver was responsible for the evolution of monodactyly, because changes in body size, foot posture, habitat, and substrate are frequently found to influence one another (and to connect to broader potential drivers, such as changing climate). We conclude with suggestions for future research to help untangle the complex dynamics of this remarkable morphological change in extinct horses. A path forward should combine regional paleoecology studies, quantitative biomechanical work, and make use of convergence and modern analogs to estimate the relative contributions of potential evolutionary drivers for digit reduction.
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Affiliation(s)
- Brianna K McHorse
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Concord Field Station, Harvard University, Bedford, MA 01730, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Andrew A Biewener
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Concord Field Station, Harvard University, Bedford, MA 01730, USA
| | - Stephanie E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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30
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Hedrick BP, Dickson BV, Dumont ER, Pierce SE. The evolutionary diversity of locomotor innovation in rodents is not linked to proximal limb morphology. Sci Rep 2020; 10:717. [PMID: 31959908 PMCID: PMC6970985 DOI: 10.1038/s41598-019-57144-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/11/2019] [Indexed: 01/08/2023] Open
Abstract
Rodents are the most species-rich order within Mammalia and have evolved disparate morphologies to accommodate numerous locomotor niches, providing an excellent opportunity to understand how locomotor innovation can drive speciation. To evaluate the connection between the evolutionary success of rodents and the diversity of rodent locomotor ecologies, we used a large dataset of proximal limb CT scans from across Myomorpha and Geomyoidea to examine internal and external limb shape. Only fossorial rodents displayed a major reworking of their proximal limbs in either internal or external morphology, with other locomotor modes plotting within a generalist morphospace. Fossorial rodents were also the only locomotor mode to consistently show increased rates of humerus/femur morphological evolution. We propose that these rodent clades were successful at spreading into ecological niches due to high behavioral plasticity and small body sizes, allowing them to modify their locomotor mode without requiring major changes to their proximal limb morphology.
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Affiliation(s)
- Brandon P Hedrick
- Department of Cell Biology and Anatomy, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA. .,Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. .,Department of Earth Sciences, University of Oxford, Oxford, UK.
| | - Blake V Dickson
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Elizabeth R Dumont
- School of Natural Sciences, University of California-Merced, Merced, CA, 95343, USA
| | - Stephanie E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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31
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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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32
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Cantalapiedra JL, Aze T, Cadotte MW, Dalla Riva GV, Huang D, Mazel F, Pennell MW, Ríos M, Mooers AØ. Conserving evolutionary history does not result in greater diversity over geological time scales. Proc Biol Sci 2019; 286:20182896. [PMID: 31161910 PMCID: PMC6571466 DOI: 10.1098/rspb.2018.2896] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alternative prioritization strategies have been proposed to safeguard biodiversity over macroevolutionary time scales. The first prioritizes the most distantly related species—maximizing phylogenetic diversity (PD)—in the hopes of capturing at least some lineages that will successfully diversify into the future. The second prioritizes lineages that are currently speciating, in the hopes that successful lineages will continue to generate species into the future. These contrasting schemes also map onto contrasting predictions about the role of slow diversifiers in the production of biodiversity over palaeontological time scales. We consider the performance of the two schemes across 10 dated species-level palaeo-phylogenetic trees ranging from Foraminifera to dinosaurs. We find that prioritizing PD for conservation generally led to fewer subsequent lineages, while prioritizing diversifiers led to modestly more subsequent diversity, compared with random sets of lineages. Importantly for conservation, the tree shape when decisions are made cannot predict which scheme will be most successful. These patterns are inconsistent with the notion that long-lived lineages are the source of new species. While there may be sound reasons for prioritizing PD for conservation, long-term species production might not be one of them.
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Affiliation(s)
- J L Cantalapiedra
- 1 Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung , Invalidenstraße 43, Berlin 10115 , Germany.,2 Departamento de Ciencias de la Vida, Universidad de Alcalá , 28805 Alcalá de Henares, Madrid , Spain
| | - T Aze
- 3 School of Earth and Environment, The University of Leeds , Leeds LS2 9JT , UK
| | - M W Cadotte
- 4 Department of Biological Sciences, University of Toronto-Scarborough , 1265 Military Trail, Toronto, Ontario , Canada M1C 1A4.,5 Department of Ecology and Evolutionary Biology, University of Toronto , 25 Wilcocks Street, Toronto, Ontario , Canada M5S 3B2
| | - G V Dalla Riva
- 6 Department of Statistics, University of British Columbia , 4200-6270 University Boulevard, Vancouver, BC , Canada V6T 1Z4.,9 School of Mathematics and Statistics, University of Canterbury , Private Bag 4800, Christchurch 8140 , New Zealand
| | - D Huang
- 10 Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore , 16 Science Drive 4 , Singapore 117558 , Singapore
| | - F Mazel
- 7 Department of Botany, University of British Columbia , 4200-6270 University Boulevard, Vancouver, BC , Canada V6T 1Z4.,11 Department of Biological Sciences, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia , Canada V5A 1S6
| | - M W Pennell
- 8 Department of Zoology, University of British Columbia , 4200-6270 University Boulevard, Vancouver, BC , Canada V6T 1Z4
| | - M Ríos
- 12 Departamento de Paleobiología, Museo Nacional de Ciencias Naturales (CSIC) , José Gutiérrez Abascal 2, 28006 Madrid , Spain
| | - A Ø Mooers
- 11 Department of Biological Sciences, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia , Canada V5A 1S6
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33
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Janis CM, Bernor RL. The Evolution of Equid Monodactyly: A Review Including a New Hypothesis. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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34
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Shan S, Kovalsky SZ, Winchester JM, Boyer DM, Daubechies I. ariaDNE: A robustly implemented algorithm for Dirichlet energy of the normal. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13148] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Shan Shan
- Department of Mathematics Duke University Durham North Carolina
| | | | - Julie M. Winchester
- Department of Evolutionary Anthropology Duke University Durham North Carolina
| | - Doug M. Boyer
- Department of Evolutionary Anthropology Duke University Durham North Carolina
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35
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Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change with and within phylogenetic trees including extinct species. PLoS One 2019; 14:e0210101. [PMID: 30682060 PMCID: PMC6347132 DOI: 10.1371/journal.pone.0210101] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022] Open
Abstract
Recognizing evolutionary trends in phenotypic means and rates requires the application of phylogenetic comparative methods (PCMs). Most PCMs are unsuited to make full use of fossil information, which is a drawback, given the inclusion of such data improves, and in some cases even corrects, the proper understanding of trait evolution. Here we present a new computer application, written in R, that allows the simultaneous computation of temporal trends in phenotypic mean and evolutionary rate along a phylogeny, and to contrast such patterns among different clades within the tree. By using simulation experiments, we show the new implementation, names search.trend is as powerful as existing PCM tools in discerning macroevolutionary patterns in phenotypic means and rates, but differently from any other PCM allows comparing individual clades to each other, and provides rich information about trait evolution for all lineages in the tree.
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36
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López-Estrada EK, Sanmartín I, García-París M, Zaldívar-Riverón A. High extinction rates and non-adaptive radiation explains patterns of low diversity and extreme morphological disparity in North American blister beetles (Coleoptera, Meloidae). Mol Phylogenet Evol 2019; 130:156-168. [DOI: 10.1016/j.ympev.2018.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/24/2018] [Accepted: 09/22/2018] [Indexed: 10/28/2022]
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37
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Mitchell JS, Etienne RS, Rabosky DL. Inferring Diversification Rate Variation From Phylogenies With Fossils. Syst Biol 2018; 68:1-18. [PMID: 29788398 DOI: 10.1093/sysbio/syy035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification-extinction rates in particular-can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of extant and extinct species. The model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree. We implemented the model in BAMM, a computational framework that uses reversible jump Markov chain Monte Carlo to simulate a posterior distribution of macroevolutionary rate regimes conditional on the branching times and topology of a phylogeny. The implementation, we describe can be applied to paleontological phylogenies, neontological phylogenies, and to phylogenies that include both extant and extinct taxa. We evaluate performance of the model on data sets simulated under a range of diversification scenarios. We find that speciation rates are reliably inferred in the absence of paleontological data. However, the inclusion of fossil observations substantially increases the accuracy of extinction rate estimates. We demonstrate that inferences are relatively robust to at least some violations of model assumptions, including heterogeneity in preservation rates and misspecification of the number of occurrences in paleontological data sets.
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Affiliation(s)
- Jonathan S Mitchell
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
- Department of Biology, West Virginia University Institute of Technology, 410 Neville Street, Beckley, WV 25801, USA
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
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38
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Dornburg A, Su Z, Townsend JP. Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets. Syst Biol 2018; 68:145-156. [PMID: 29939341 DOI: 10.1093/sysbio/syy047] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/13/2018] [Indexed: 02/02/2023] Open
Abstract
With the rise of genome-scale data sets, there has been a call for increased data scrutiny and careful selection of loci that are appropriate to use in an attempt to resolve a phylogenetic problem. Such loci should maximize phylogenetic information content while minimizing the risk of homoplasy. Theory posits the existence of characters that evolve at an optimum rate, and efforts to determine optimal rates of inference have been a cornerstone of phylogenetic experimental design for over two decades. However, both theoretical and empirical investigations of optimal rates have varied dramatically in their conclusions: spanning no relationship to a tight relationship between the rate of change and phylogenetic utility. Herein, we synthesize these apparently contradictory views, demonstrating both empirical and theoretical conditions under which each is correct. We find that optimal rates of characters-not genes-are generally robust to most experimental design decisions. Moreover, consideration of site rate heterogeneity within a given locus is critical to accurate predictions of utility. Factors such as taxon sampling or the targeted number of characters providing support for a topology are additionally critical to the predictions of phylogenetic utility based on the rate of character change. Further, optimality of rates and predictions of phylogenetic utility are not equivalent, demonstrating the need for further development of comprehensive theory of phylogenetic experimental design. [Divergence time; GC bias; homoplasy; incongruence; information content; internode length; optimal rates; phylogenetic informativeness; phylogenetic theory; phylogenetic utility; phylogenomics; signal and noise; subtending branch length; state space; taxon and character sampling.].
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Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, 1671 Goldstar Drive, NC 27601, USA
| | - Zhuo Su
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, 165 Prospect Street, CT 06525, USA
| | - Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, 165 Prospect Street, CT 06525, USA
- Department of Biostatistics, Yale University, New Haven, 60 College Street, CT 06510, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, 300 George Street, CT 06511, USA
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39
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Kergoat GJ, Condamine FL, Toussaint EFA, Capdevielle-Dulac C, Clamens AL, Barbut J, Goldstein PZ, Le Ru B. Opposite macroevolutionary responses to environmental changes in grasses and insects during the Neogene grassland expansion. Nat Commun 2018; 9:5089. [PMID: 30504767 PMCID: PMC6269479 DOI: 10.1038/s41467-018-07537-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 11/08/2018] [Indexed: 11/11/2022] Open
Abstract
The rise of Neogene C4 grasslands is one of the most drastic changes recently experienced by the biosphere. A central - and widely debated - hypothesis posits that Neogene grasslands acted as a major adaptive zone for herbivore lineages. We test this hypothesis with a novel model system, the Sesamiina stemborer moths and their associated host-grasses. Using a comparative phylogenetic framework integrating paleoenvironmental proxies we recover a negative correlation between the evolutionary trajectories of insects and plants. Our results show that paleoenvironmental changes generated opposing macroevolutionary dynamics in this insect-plant system and call into question the role of grasslands as a universal adaptive cradle. This study illustrates the importance of implementing environmental proxies in diversification analyses to disentangle the relative impacts of biotic and abiotic drivers of macroevolutionary dynamics.
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Affiliation(s)
- Gael J Kergoat
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, 755 Avenue du campus Agropolis, 34988, Montferrier-sur-Lez, France.
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | | | - Claire Capdevielle-Dulac
- UMR EGCE (Evolution, Génome, Comportement, Ecologie), CNRS-IRD-Univ. Paris-Sud, IDEEV, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Anne-Laure Clamens
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, 755 Avenue du campus Agropolis, 34988, Montferrier-sur-Lez, France
| | - Jérôme Barbut
- MNHN, Muséum national d'Histoire naturelle (Entomologie), 57 rue Cuvier, 75005, Paris, France
| | - Paul Z Goldstein
- USDA, Systematic Entomology Laboratory, Smithsonian Institution, National Museum of Natural History, PO Box 37012, Washington DC, USA
| | - Bruno Le Ru
- UMR EGCE (Evolution, Génome, Comportement, Ecologie), CNRS-IRD-Univ. Paris-Sud, IDEEV, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
- IRD c/o ICIPE, NSBB Project, PO Box 30772, Nairobi, Kenya
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40
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Bone histology provides insights into the life history mechanisms underlying dwarfing in hipparionins. Sci Rep 2018; 8:17203. [PMID: 30464210 PMCID: PMC6249282 DOI: 10.1038/s41598-018-35347-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 11/01/2018] [Indexed: 02/02/2023] Open
Abstract
Size shifts may be a by-product of alterations in life history traits driven by natural selection. Although this approach has been proposed for islands, it has not yet been explored in continental faunas. The trends towards size decrease experienced by some hipparionins constitute a good case study for the application of a life history framework to understand the size shifts on the continent. Here, we analysed bone microstructure to reconstruct the growth of some different-sized hipparionins from Greece and Spain. The two dwarfed lineages studied show different growth strategies. The Greek hipparions ceased growth early at a small size thus advancing maturity, whilst the slower-growing Spanish hipparion matured later at a small size. Based on predictive life history models, we suggest that high adult mortality was the likely selective force behind early maturity and associated size decrease in the Greek lineage. Conversely, we infer that resource limitation accompanied by high juvenile mortality triggered decrease in growth rate and a relative late maturity in the Spanish lineage. Our results provide evidence that different selective pressures can precipitate different changes in life history that lead to similar size shifts.
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41
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Multi-scale interplays of biotic and abiotic drivers shape mammalian sub-continental diversity over millions of years. Sci Rep 2018; 8:13413. [PMID: 30194335 PMCID: PMC6128930 DOI: 10.1038/s41598-018-31699-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/23/2018] [Indexed: 11/20/2022] Open
Abstract
The reconstruction of deep-time diversity trends is key to understanding current and future species richness. Studies that statistically evaluate potential factors affecting paleodiversity have focused on continental and global, clade-wide datasets, and thus we ignore how community species richness build-up to generate large-scale patterns over geological timescales. If community diversity is shaped by biotic interactions and continental and global diversities are governed by abiotic events, which are the modulators of diversity in subcontinental regions? To address this question, we model Iberian mammalian species richness over 13 million years (15 to 2 Ma) using exhaustive fossil evidence for subcontinental species’ ecomorphology, environmental context, and biogeographic affinities, and quantitatively evaluate their impact on species richness. We find that the diversity of large Iberian mammals has been limited over time, with species richness showing marked fluctuations, undergoing substantial depletions as diversity surpasses a critical limit where a significant part of the niches is unviable. The strength of such diversity-dependence has also shifted. Large faunal dispersals and environmental heterogeneity increased the system’s critical diversity limit. Diversity growth rate (net migration and diversification) also oscillated, mainly modulated by functional saturation, patchiness of canopy cover, and local temperature and aridity. Our study provides quantitative support for subcontinental species pools being complex and dynamic systems where diversity is perpetually imbalanced over geological timescales. Subcontinental diversity-dependence dynamics are mainly modulated by a multi-scale interplay of biotic and abiotic factors, with abiotic factors playing a more relevant role.
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42
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First Radiological Study of a Complete Dental Ontogeny Sequence of an Extinct Equid: Implications for Equidae Life History and Taphonomy. Sci Rep 2018; 8:8507. [PMID: 29855587 PMCID: PMC5981301 DOI: 10.1038/s41598-018-26817-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/16/2018] [Indexed: 11/09/2022] Open
Abstract
The sequence of cheek teeth mineralization, eruption, and replacement of an extinct horse species is here documented with radiological techniques for the first time thanks to the exceptional preservation of Hipparion sp. mandibles from Cerro de los Batallones (Madrid Basin, Spain). The sequence of dental ontogeny in mammals provides valuable insights about life history traits, such as the pace of growth, and about the mode of formation of fossiliferous assemblages. We have determined that the order of permanent cheek teeth mineralization and eruption of hipparionine horses is m1, m2, (p2, p3), p4, m3. Cheek teeth mineralization timing of hipparionine horses coincides with the one observed in modern equids. In turn, there are differences in the eruption timing of the p4 and m3 between horses belonging to the Anchitheriinae and Hipparionini compared to equids of the Equus genus that might be related to the shorter durability of the deciduous tooth dp4 in anchitheriine and hipparionine horses and, more broadly, to an increased durability of equid teeth through their evolutionary history. Based on the dental eruption sequence, hipparionine horses are slow-growing, long-living mammals. The Hipparion sp. assemblage from Batallones-10 conforms to an attritional model, as individuals more vulnerable to natural mortality predominate.
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43
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McLean BS, Helgen KM, Goodwin HT, Cook JA. Trait‐specific processes of convergence and conservatism shape ecomorphological evolution in ground‐dwelling squirrels. Evolution 2018; 72:473-489. [DOI: 10.1111/evo.13422] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/18/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Bryan S. McLean
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico 87131
- Florida Museum of Natural History University of Florida Gainesville Florida 32611
| | - Kristofer M. Helgen
- School of Biological Sciences University of Adelaide Adelaide SA 5005 Australia
| | - H. Thomas Goodwin
- Department of Biology Andrews University Berrien Springs Michigan 49104
| | - Joseph A. Cook
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico 87131
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44
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Hirasawa T, Kuratani S. Evolution of the muscular system in tetrapod limbs. ZOOLOGICAL LETTERS 2018; 4:27. [PMID: 30258652 PMCID: PMC6148784 DOI: 10.1186/s40851-018-0110-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/04/2018] [Indexed: 05/16/2023]
Abstract
While skeletal evolution has been extensively studied, the evolution of limb muscles and brachial plexus has received less attention. In this review, we focus on the tempo and mode of evolution of forelimb muscles in the vertebrate history, and on the developmental mechanisms that have affected the evolution of their morphology. Tetrapod limb muscles develop from diffuse migrating cells derived from dermomyotomes, and the limb-innervating nerves lose their segmental patterns to form the brachial plexus distally. Despite such seemingly disorganized developmental processes, limb muscle homology has been highly conserved in tetrapod evolution, with the apparent exception of the mammalian diaphragm. The limb mesenchyme of lateral plate mesoderm likely plays a pivotal role in the subdivision of the myogenic cell population into individual muscles through the formation of interstitial muscle connective tissues. Interactions with tendons and motoneuron axons are involved in the early and late phases of limb muscle morphogenesis, respectively. The mechanism underlying the recurrent generation of limb muscle homology likely resides in these developmental processes, which should be studied from an evolutionary perspective in the future.
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Affiliation(s)
- Tatsuya Hirasawa
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047 Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo 650-0047 Japan
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45
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Nacarino-Meneses C, Jordana X, Orlandi-Oliveras G, Köhler M. Reconstructing molar growth from enamel histology in extant and extinct Equus. Sci Rep 2017; 7:15965. [PMID: 29162890 PMCID: PMC5698294 DOI: 10.1038/s41598-017-16227-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/09/2017] [Indexed: 11/26/2022] Open
Abstract
The way teeth grow is recorded in dental enamel as incremental marks. Detailed analysis of tooth growth is known to provide valuable insights into the growth and the pace of life of vertebrates. Here, we study the growth pattern of the first lower molar in several extant and extinct species of Equus and explore its relationship with life history events. Our histological analysis shows that enamel extends beyond the molar’s cervix in these mammals. We identified three different crown developmental stages (CDS) in the first lower molars of equids characterised by different growth rates and likely to be related to structural and ontogenetic modifications of the tooth. Enamel extension rate, which ranges from ≈400 μm/d at the beginning of crown development to rates of ≈30 μm/d near the root, and daily secretion rate (≈17 μm/d) have been shown to be very conservative within the genus. From our results, we also inferred data of molar wear rate for these equids that suggest higher wear rates at early ontogenetic stages (13 mm/y) than commonly assumed. The results obtained here provide a basis for future studies of equid dentition in different scientific areas, involving isotope, demographic and dietary studies.
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Affiliation(s)
- Carmen Nacarino-Meneses
- Institut Català de Paleontologia Miquel Crusafont (ICP), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Xavier Jordana
- Unitat d'Antropologia Biològica, BABVE department, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Guillem Orlandi-Oliveras
- Institut Català de Paleontologia Miquel Crusafont (ICP), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Meike Köhler
- Institut Català de Paleontologia Miquel Crusafont (ICP), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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Seed size and its rate of evolution correlate with species diversification across angiosperms. PLoS Biol 2017; 15:e2002792. [PMID: 28723902 PMCID: PMC5536390 DOI: 10.1371/journal.pbio.2002792] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/31/2017] [Accepted: 06/29/2017] [Indexed: 11/19/2022] Open
Abstract
Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, which can subsequently influence speciation and extinction. The rate at which seed mass changes across the angiosperm phylogeny may also be linked to diversification by increasing reproductive isolation and allowing access to novel ecological niches. However, the magnitude and direction of the association between seed mass and diversification has not been assessed across the angiosperm phylogeny. Here, we show that absolute seed size and the rate of change in seed size are both associated with variation in diversification rates. Based on the largest available angiosperm phylogenetic tree, we found that smaller-seeded plants had higher rates of diversification, possibly due to improved colonisation potential. The rate of phenotypic change in seed size was also strongly positively correlated with speciation rates, providing rare, large-scale evidence that rapid morphological change is associated with species divergence. Our study now reveals that variation in morphological traits and, importantly, the rate at which they evolve can contribute to explaining the extremely uneven distribution of diversity across the ToL. Why are some groups of flowering plants extremely diverse while others are very poor in species? Are the traits of species and the rate at which they evolve important in generating this uneven distribution of biodiversity? By using the largest available phylogenetic tree of plants coupled with an unparalleled trait dataset, we analysed how seed size and its rate of change across the phylogeny are correlated with the rate of species formation. Seed size is crucial to plant evolution because it is related to adaptation to environment and influences many aspects of plant life history, including dispersal, resistance to damage and colonisation potential. We found that faster rates of seed size change were associated with faster rates of speciation, probably by fostering the appearance of reproductive barriers between lineages. We also found that smaller seeded species speciated faster than larger seeded ones. These results underscore the importance of morphological traits, and particularly their rate of evolution, in promoting species divergence across one of the largest radiations of organisms on the planet.
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Dunning LT, Lundgren MR, Moreno-Villena JJ, Namaganda M, Edwards EJ, Nosil P, Osborne CP, Christin PA. Introgression and repeated co-option facilitated the recurrent emergence of C 4 photosynthesis among close relatives. Evolution 2017; 71:1541-1555. [PMID: 28395112 PMCID: PMC5488178 DOI: 10.1111/evo.13250] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/04/2017] [Indexed: 01/16/2023]
Abstract
The origins of novel traits are often studied using species trees and modeling phenotypes as different states of the same character, an approach that cannot always distinguish multiple origins from fewer origins followed by reversals. We address this issue by studying the origins of C4 photosynthesis, an adaptation to warm and dry conditions, in the grass Alloteropsis. We dissect the C4 trait into its components, and show two independent origins of the C4 phenotype via different anatomical modifications, and the use of distinct sets of genes. Further, inference of enzyme adaptation suggests that one of the two groups encompasses two transitions to a full C4 state from a common ancestor with an intermediate phenotype that had some C4 anatomical and biochemical components. Molecular dating of C4 genes confirms the introgression of two key C4 components between species, while the inheritance of all others matches the species tree. The number of origins consequently varies among C4 components, a scenario that could not have been inferred from analyses of the species tree alone. Our results highlight the power of studying individual components of complex traits to reconstruct trajectories toward novel adaptations.
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Affiliation(s)
- Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Jose J Moreno-Villena
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | | | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, 02912
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
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