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Marion AFP, Condamine FL, Guinot G. Sequential trait evolution did not drive deep-time diversification in sharks. Evolution 2024; 78:1405-1425. [PMID: 38745524 DOI: 10.1093/evolut/qpae070] [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: 11/21/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/16/2024]
Abstract
Estimating how traits evolved and impacted diversification across the tree of life represents a critical topic in ecology and evolution. Although there has been considerable research in comparative biology, large parts of the tree of life remain underexplored. Sharks are an iconic clade of marine vertebrates, and key components of marine ecosystems since the early Mesozoic. However, few studies have addressed how traits evolved or whether they impacted their extant diversity patterns. Our study aimed to fill this gap by reconstructing the largest time-calibrated species-level phylogeny of sharks and compiling an exhaustive database for ecological (diet, habitat) and biological (reproduction, maximum body length) traits. Using state-of-the-art models of evolution and diversification, we outlined the major character shifts and modes of trait evolution across shark species. We found support for sequential models of trait evolution and estimated a small to medium-sized lecithotrophic and coastal-dwelling most recent common ancestor for extant sharks. However, our exhaustive hidden traits analyses do not support trait-dependent diversification for any examined traits, challenging previous works. This suggests that the role of traits in shaping sharks' diversification dynamics might have been previously overestimated and should motivate future macroevolutionary studies to investigate other drivers of diversification in this clade.
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Affiliation(s)
- Alexis F P Marion
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Guillaume Guinot
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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2
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Nicolaï MPJ, Van Hecke B, Rogalla S, Debruyn G, Bowie RCK, Matzke NJ, Hackett SJ, D'Alba L, Shawkey MD. The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae). Syst Biol 2024; 73:343-354. [PMID: 38289860 DOI: 10.1093/sysbio/syae006] [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: 08/31/2022] [Revised: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 02/01/2024] Open
Abstract
How and why certain groups become speciose is a key question in evolutionary biology. Novel traits that enable diversification by opening new ecological niches are likely important mechanisms. However, ornamental traits can also promote diversification by opening up novel sensory niches and thereby creating novel inter-specific interactions. More specifically, ornamental colors may enable more precise and/or easier species recognition and may act as key innovations by increasing the number of species-specific patterns and promoting diversification. While the influence of coloration on diversification is well-studied, the influence of the mechanisms that produce those colors (e.g., pigmentary, nanostructural) is less so, even though the ontogeny and evolution of these mechanisms differ. We estimated a new phylogenetic tree for 121 sunbird species and combined color data of 106 species with a range of phylogenetic tools to test the hypothesis that the evolution of novel color mechanisms increases diversification in sunbirds, one of the most colorful bird clades. Results suggest that: (1) the evolution of novel color mechanisms expands the visual sensory niche, increasing the number of achievable colors, (2) structural coloration diverges more readily across the body than pigment-based coloration, enabling an increase in color complexity, (3) novel color mechanisms might minimize trade-offs between natural and sexual selection such that color can function both as camouflage and conspicuous signal, and (4) despite structural colors being more colorful and mobile, only melanin-based coloration is positively correlated with net diversification. Together, these findings explain why color distances increase with an increasing number of sympatric species, even though packing of color space predicts otherwise.
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Affiliation(s)
- Michaël P J Nicolaï
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Bert Van Hecke
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Svana Rogalla
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
- Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena, 48940 Leioa, Spain
| | - Gerben Debruyn
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Shannon J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Liliana D'Alba
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Matthew D Shawkey
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
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3
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Liu J, Lindstrom AJ, Gong Y, Dong S, Liu YC, Zhang S, Gong X. Eco-evolutionary evidence for the global diversity pattern of Cycas (Cycadaceae). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1170-1191. [PMID: 38477647 DOI: 10.1111/jipb.13638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/04/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
The evolution of the latitudinal diversity gradient (LDG), characterized by a peak in diversity toward the tropics, has captured significant attention in evolutionary biology and ecology. However, the inverse LDG (i-LDG) mechanism, wherein species richness increases toward the poles, remains inadequately explored. Cycads are among one of the oldest lineages of extant seed plants and have undergone extensive diversification in the tropics. Intriguingly, the extant cycad abundance exhibits an i-LDG pattern, and the underlying causes for this phenomenon remain largely elusive. Here, using 1,843 nuclear genes from a nearly complete sampling, we conducted comprehensive phylogenomic analyses to establish a robust species-level phylogeny for Cycas, the largest genus within cycads. We then reconstructed the spatial-temporal dynamics and integrated global environmental data to evaluate the roles of species ages, diversification rates, contemporary environment, and conservatism to ancestral niches in shaping the i-LDG pattern. We found Cycas experienced decreased diversification rates, coupled with the cooling temperature since its origin in the Eocene from continental Asia. Different regions have distinctively contributed to the formation of i-LDG for Cycas, with the northern hemisphere acting as evolutionary museums and the southern hemisphere serving as cradles. Moreover, water-related climate variables, specifically precipitation seasonality and potential evapotranspiration, were identified as paramount factors constraining Cycas species richness in the rainforest biome near the equator. Notably, the adherence to ancestral monsoonal climates emerges as a critical factor in sustaining the diversity pattern. This study underscores the imperative of integrating both evolutionary and ecological approaches to comprehensively unravel the mechanisms underpinning global biodiversity patterns.
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Affiliation(s)
- Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Anders J Lindstrom
- Global Biodiversity Conservancy, 144/124 Moo3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi, 20250, Thailand
| | - Yiqing Gong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yusheng Chris Liu
- Department of Earth and Environmental Sciences, Indiana University-Indianapolis, Indianapolis, 46202, IN, USA
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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Dixit NM, Guicking D. Exploring the evolutionary dynamics of myrmecophytism: Perspectives from the Southeast Asian Macaranga ant-plant symbiosis. Mol Phylogenet Evol 2024; 194:108028. [PMID: 38342161 DOI: 10.1016/j.ympev.2024.108028] [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: 11/08/2023] [Revised: 01/31/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Myrmecophytic plants utilise defensive services offered by obligate ant partners nesting in their domatia in a novel means of survival in tropical habitats. Although much is known about the ecology of myrmecophytism, there aren't enough empirical examples to demonstrate whether it substantially influences evolutionary patterns in host plant lineages. In this study, we make use of the species-rich Macaranga (Euphorbiaceae) ant-plant symbiosis distributed in the Southeast Asian Sundaland to delve into the evolutionary dynamics of myrmecophytism in host plants. We generated the most comprehensive dated phylogeny of myrmecophytic Macaranga till date using genotyping-by-sequencing (GBS). With this in hand, we traced the evolutionary history of myrmecophytism in Macaranga using parametric biogeography and ancestral state reconstruction. Diversification rate analysis methods were employed to determine if myrmecophytism enhanced diversification rates in the genus. Our results demonstrate that myrmecophytism is labile and easily lost. Ancestral state reconstruction supported a single origin of myrmecophytism in Macaranga ∼18 mya on Borneo followed by multiple losses. Diversification rate analysis methods did not yield sufficient evidence to support the hypothesis that myrmecophytism enhanced diversification rates in Macaranga; we found that topographical features on Borneo may have played a more direct role in the divergence of clades instead. Our study provides evidence that while the acquisition of domatia clearly functions as a key innovation that has enabled host plants to exploit the environment in novel ways, it may not necessarily enhance diversification rates. In fact, we hypothesise that overly specialised cases of myrmecophytism may even be an evolutionary dead end.
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Affiliation(s)
- Nadi M Dixit
- Department of Botany, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany.
| | - Daniela Guicking
- Department of Botany, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany.
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Shen ZY, Terada T, Landry JF, Hoare RJB, Kuo LY, Chou MH, Hsu YF, Huang JP. Systematics and evolutionary dynamics of insect-fern interactions in the specialized fern-spore feeding Cuprininae (Lepidoptera, Stathmopodidae). Mol Phylogenet Evol 2024; 194:108040. [PMID: 38395320 DOI: 10.1016/j.ympev.2024.108040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
Fern-spore-feeding (FSF) is rare and found in only four families of Lepidoptera. Stathmopodidae is the most speciose family that contains FSF species, and its subfamily Cuprininae exclusively specializes on FSF. However, three species of Stathmopodinae also specialize on FSF. To better understand the evolutionary history of FSF and, more generally, the significance of specialization on a peculiar host, a phylogenetic and taxonomic revision for this group is necessary. We reconstructed the most comprehensive molecular phylogeny, including one mitochondrial and four nuclear genes, of Stathmopodidae to date, including 137 samples representing 62 species, with a particular focus on the FSF subfamily, Cuprininae, including 33 species (41% of named species) from 6 of the 7 Cuprininae genera. Species from two other subfamilies, Stathmopodinae and Atkinsoniinae, were also included. We found that FSF evolved only once in Stathmopodidae and that the previous hypothesis of multiple origins of FSF was misled by inadequate taxonomy. Moreover, we showed that (1) speciation/extinction rates do not differ significantly between FSF and non-FSF groups and that (2) oligophage is the ancestral character state in Cuprininae. We further revealed that a faster rate of accumulating specialists over time, and thus a higher number of specialists, was achieved by a higher transition rate from oligophagages to specialists compared to the transition rate in the opposite direction. We finish by describing three new genera, Trigonodagen. nov., Petalagen. nov., and Pediformisgen. nov., and revalidating five genera: Cuprina, Calicotis, Thylacosceles, Actinoscelis, Thylacosceloides in Cuprininae, and we provide an updated taxonomic key to genera and a revised global checklist of Cuprininae.
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Affiliation(s)
- Zong-Yu Shen
- Biodiversity Research Center, Academic Sinica, Taipei, Taiwan; Department of Life Science, National Taiwan Normal University, Taipei, Taiwan; Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Takeshi Terada
- Okayama Prefectural Environmental Conservation Foundation, Inc., Okayama, Japan
| | - Jean-François Landry
- Canadian National Collection of Insects, Arachnids, and Nematodes, Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, C.E.F., Ottawa, Ontario, Canada
| | - Robert J B Hoare
- New Zealand Arthropod Collection, Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, New Zealand
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Hsun Chou
- Department of Biological Sciences, Northern Arizona University, AZ, USA
| | - Yu-Feng Hsu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.
| | - Jen-Pan Huang
- Biodiversity Research Center, Academic Sinica, Taipei, Taiwan.
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6
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Li W, Wang R, Liu MF, Folk RA, Xue B, Saunders RMK. Climatic and biogeographic processes underlying the diversification of the pantropical flowering plant family Annonaceae. FRONTIERS IN PLANT SCIENCE 2024; 15:1287171. [PMID: 38525154 PMCID: PMC10957689 DOI: 10.3389/fpls.2024.1287171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
Tropical forests harbor the richest biodiversity among terrestrial ecosystems, but few studies have addressed the underlying processes of species diversification in these ecosystems. We use the pantropical flowering plant family Annonaceae as a study system to investigate how climate and biogeographic events contribute to diversification. A super-matrix phylogeny comprising 835 taxa (34% of Annonaceae species) based on eight chloroplast regions was used in this study. We show that global temperature may better explain the recent rapid diversification in Annonaceae than time and constant models. Accelerated accumulation of niche divergence (around 15 Ma) lags behind the increase of diversification rate (around 25 Ma), reflecting a heterogeneous transition to recent diversity increases. Biogeographic events are related to only two of the five diversification rate shifts detected. Shifts in niche evolution nevertheless appear to be associated with increasingly seasonal environments. Our results do not support the direct correlation of any particular climatic niche shifts or historical biogeographical event with shifts in diversification rate. Instead, we suggest that Annonaceae diversification can lead to later niche divergence as a result of increasing interspecific competition arising from species accumulation. Shifts in niche evolution appear to be associated with increasingly seasonal environments. Our results highlight the complexity of diversification in taxa with long evolutionary histories.
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Affiliation(s)
- Weixi Li
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Runxi Wang
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ming-Fai Liu
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ryan A. Folk
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Bine Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Richard M. K. Saunders
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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7
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Wacker KS, Winger BM. An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates. Am Nat 2024; 203:362-381. [PMID: 38358813 DOI: 10.1086/728598] [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] [Indexed: 02/17/2024]
Abstract
AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.
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8
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Tian Q, Stull GW, Kellermann J, Medan D, Nge FJ, Liu SY, Kates HR, Soltis DE, Soltis PS, Guralnick RP, Folk RA, Onstein RE, Yi TS. Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales. THE NEW PHYTOLOGIST 2024; 241:1851-1865. [PMID: 38229185 DOI: 10.1111/nph.19504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.
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Affiliation(s)
- Qin Tian
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jürgen Kellermann
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Diego Medan
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Ave San Martín 4453, C1417DSE, Buenos Aires, Argentina
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- IRD - Institut de Recherche pour le Développement, Ave Agropolis BP 64501, Montpellier, 34394, France
| | - Shui-Yin Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
| | - Heather R Kates
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi, MS, 39762, USA
| | - Renske E Onstein
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Leipzig University, Leipzig, 04013, Germany
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
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9
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Scott JE. The macroevolutionary dynamics of activity pattern in mammals: Primates in context. J Hum Evol 2023; 184:103436. [PMID: 37741141 DOI: 10.1016/j.jhevol.2023.103436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023]
Abstract
Activity pattern has played a prominent role in discussions of primate evolutionary history. Most primates are either diurnal or nocturnal, but a small number are active both diurnally and nocturnally. This pattern-cathemerality-also occurs at low frequency across mammals. Using a large sample of mammalian species, this study evaluates two macroevolutionary hypotheses proposed to explain why cathemerality is less common than diurnality and nocturnality: 1) that cathemeral lineages have higher extinction probabilities (differential diversification) and 2) that transitions out of cathemerality are more frequent, making it a less persistent state (differential state persistence). Rates of speciation, extinction, and transition between character states were estimated using hidden-rates models applied to a phylogenetic tree containing 3013 mammals classified by activity pattern. The models failed to detect consistent differences in diversification dynamics among activity patterns, but there is strong support for differential state persistence. Transition rates out of cathemerality tend to be much higher than transition rates out of nocturnality. Transition rates out of diurnality are similar to those for cathemerality in most clades, with two important exceptions: diurnality is unusually persistent in anthropoid primates and sciurid rodents. These two groups combine very low rates of transition out of diurnality with high speciation rates. This combination has no parallels among cathemeral lineages, explaining why diurnality has become more common than cathemerality in mammals. Similarly, the combination of rates found in anthropoids is sufficient to explain the low relative frequency of cathemerality in primates, making it unnecessary to appeal to high extinction probabilities in cathemeral lineages in this clade. These findings support the hypothesis that the distribution of activity patterns across mammals has been influenced primarily by differential state persistence, whereas the effect of differential diversification appears to have been more idiosyncratic.
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Affiliation(s)
- Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA.
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10
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Wiens JJ. Trait-based species richness: ecology and macroevolution. Biol Rev Camb Philos Soc 2023; 98:1365-1387. [PMID: 37015839 DOI: 10.1111/brv.12957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/06/2023]
Abstract
Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, USA
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11
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Murali G, Meiri S, Roll U. Chemical signaling glands are unlinked to species diversification in lizards. Evolution 2023; 77:1829-1841. [PMID: 37279331 DOI: 10.1093/evolut/qpad101] [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: 09/04/2022] [Revised: 05/17/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023]
Abstract
Sexual selection has long been thought to increase species diversification. Sexually selected traits, such as sexual signals that contribute to reproductive isolation, were thought to promote diversification. However, studies exploring links between sexually selected traits and species diversification have thus far primarily focused on visual or acoustic signals. Many animals often employ chemical signals (i.e., pheromones) for sexual communications, but large-scale analyses on the role of chemical communications in driving species diversification have been missing. Here, for the first time, we investigate whether traits associated with chemical communications-the presence of follicular epidermal glands-promote diversification across 6,672 lizard species. In most analyses, we found no strong association between the presence of follicular epidermal glands and species diversification rates, either across all lizard species or at lower phylogenetic scales. Previous studies suggest that follicular gland secretions act as species recognition signals that prevent hybridization during speciation in lizards. However, we show that geographic range overlap was no different in sibling species pairs with and without follicular epidermal glands. Together, these results imply that either follicular epidermal glands do not primarily function in sexual communications or sexually selected traits in general (here chemical communication) have a limited effect on species diversification. In our additional analysis accounting for sex-specific differences in glands, we again found no detectable effect of follicular epidermal glands on species diversification rates. Thus, our study challenges the general role of sexually selected traits in broad-scale species diversification patterns.
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Affiliation(s)
- Gopal Murali
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Mitrani Department of Desert Ecology, The Swiss Institute for Dryland Environments and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Shai Meiri
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Beersheva, Sede-Boqer Campus, 8499000, Israel
| | - Uri Roll
- Mitrani Department of Desert Ecology, The Swiss Institute for Dryland Environments and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
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12
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Loeffler-Henry K, Kang C, Sherratt TN. Evolutionary transitions from camouflage to aposematism: Hidden signals play a pivotal role. Science 2023; 379:1136-1140. [PMID: 36927015 DOI: 10.1126/science.ade5156] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The initial evolution of warning signals in unprofitable prey, termed aposematism, is often seen as a paradox because any new conspicuous mutant would be easier to detect than its cryptic conspecifics and not readily recognized by naïve predators as defended. One possibility is that permanent aposematism first evolved through species using hidden warning signals, which are only exposed to would-be predators on encounter. Here, we present a large-scale analysis of evolutionary transitions in amphibian antipredation coloration and demonstrate that the evolutionary transition from camouflage to aposematism is rarely direct but tends to involve an intermediary stage, namely cryptic species that facultatively reveal conspicuous coloration. Accounting for this intermediate step can resolve the paradox and thereby advance our understanding of the evolution of aposematism.
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Affiliation(s)
| | - Changku Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Thomas N Sherratt
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
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13
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Vasconcelos T. A trait-based approach to determining principles of plant biogeography. AMERICAN JOURNAL OF BOTANY 2023; 110:e16127. [PMID: 36648370 DOI: 10.1002/ajb2.16127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Lineage-specific traits determine how plants interact with their surrounding environment. Unrelated species may evolve similar phenotypic characteristics to tolerate, persist in, and invade environments with certain characteristics, resulting in some traits becoming relatively more common in certain types of habitats. Analyses of these general patterns of geographical trait distribution have led to the proposal of general principles to explain how plants diversify in space over time. Trait-environment correlation analyses quantify to what extent unrelated lineages have similar evolutionary responses to a given type of habitat. In this synthesis, I give a short historical overview on trait-environment correlation analyses, from some key observations from classic naturalists to modern approaches using trait evolution models, large phylogenies, and massive data sets of traits and distributions. I discuss some limitations of modern approaches, including the need for more realistic models, the lack of data from tropical areas, and the necessary focus on trait scoring that goes beyond macromorphology. Overcoming these limitations will allow the field to explore new questions related to trait lability and niche evolution and to better identify generalities and exceptions in how plants diversify in space over time.
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Affiliation(s)
- Thais Vasconcelos
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
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14
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Mellado-Mansilla D, Testo W, Sundue MA, Zotz G, Kreft H, Coiro M, Kessler M. The relationship between chlorophyllous spores and mycorrhizal associations in ferns: evidence from an evolutionary approach. AMERICAN JOURNAL OF BOTANY 2022; 109:2068-2081. [PMID: 36310350 DOI: 10.1002/ajb2.16094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Approximately 14% of all fern species have physiologically active chlorophyllous spores that are much more short-lived than the more common and dormant achlorophyllous spores. Most chlorophyllous-spored species (70%) are epiphytes and account for almost 37% of all epiphytic ferns. Chlorophyllous-spored ferns are also overrepresented among fern species in habitats with waterlogged soils, of which nearly 60% have chlorophyllous spores. Ferns in these disparate habitat types also have a low incidence of mycorrhizal associations. We therefore hypothesized that autotrophic chlorophyllous spores represent an adaptation of ferns to habitats with scarce mycorrhizal associations. METHODS We evaluated the coevolution of chlorophyllous spores and mycorrhizal associations in ferns and their relation to habitat type using phylogenetic comparative methods. RESULTS Although we did not find support for the coevolution of spore type and mycorrhizal associations, we did find that chlorophyllous spores and the absence of mycorrhizal associations have coevolved with epiphytic and waterlogged habitats. Transition rates to epiphytic and waterlogged habitats were significantly higher in species with chlorophyllous spores compared to achlorophyllous lineages. CONCLUSIONS Spore type and mycorrhizal associations appear to play important roles in the radiation of ferns into different habitat types. Future work should focus on clarifying the functional significance of these associations.
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Affiliation(s)
- Daniela Mellado-Mansilla
- Department of Biodiversity, Macroecology and Biogeography, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Göttingen, Germany
- Institute for Biology and Environmental Sciences, AG Functional Ecology, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Weston Testo
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Michael A Sundue
- The Pringle Herbarium, Department of Plant Biology, University of Vermont, Burlington, VT, USA
| | - Gerhard Zotz
- Institute for Biology and Environmental Sciences, AG Functional Ecology, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Smithsonian Tropical Research Institute, Panama
| | - Holger Kreft
- Department of Biodiversity, Macroecology and Biogeography, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Göttingen, Germany
| | - Mario Coiro
- Department of Paleontology, University of Vienna, Vienna, Austria
- Ronin Institute for Independent Scholarship, Montclair, NJ, USA
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
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15
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Yuan ML, Westeen EP, Wogan GOU, Wang IJ. Female dewlap ornaments are evolutionarily labile and associated with increased diversification rates in Anolis lizards. Proc Biol Sci 2022; 289:20221871. [PMID: 36382524 PMCID: PMC9667357 DOI: 10.1098/rspb.2022.1871] [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: 09/20/2022] [Accepted: 10/26/2022] [Indexed: 12/02/2023] Open
Abstract
The evolution of costly signalling traits has largely focused on male ornaments. However, our understanding of ornament evolution is necessarily incomplete without investigating the causes and consequences of variation in female ornamentation. Here, we study the Anolis lizard dewlap, a trait extensively studied as a male secondary sexual characteristic but present in females of several species. We characterized female dewlaps for 339 species to test hypotheses about their evolution. Our results did not support the hypothesis that female dewlaps are selected against throughout the anole phylogeny. Rather, we found that female dewlaps were evolutionary labile. We also did not find support for the adaptive hypothesis that interspecific competition drove the evolution of female dewlaps. However, we did find support for the pleiotropy hypothesis as species with larger females and reduced sexual size dimorphism were more likely to possess female dewlaps. Lastly, we found that female dewlap presence influenced diversification rates in anoles, but only secondarily to a hidden state. Our results demonstrate that female ornamentation is widespread in anoles and the traditional hypothesis of divergent selection between the sexes does not fully explain their evolution. Instead, female ornamentation is likely to be subject to complex adaptive and non-adaptive evolutionary forces.
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Affiliation(s)
- Michael L. Yuan
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Erin P. Westeen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Guinevere O. U. Wogan
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ian J. Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
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16
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Iglesias‐Carrasco M, Tobias JA, Duchêne DA. Bird lineages colonizing urban habitats have diversified at high rates across deep time. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2022; 31:1784-1793. [PMID: 36246452 PMCID: PMC9540638 DOI: 10.1111/geb.13558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 06/16/2023]
Abstract
Aim Urbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human-made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long-term patterns of diversification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood. Location World. Time period Current. Major taxa studied Passerine birds. Methods We applied macroevolutionary models to a large dataset of passerine birds to compare the evolutionary history of urban-tolerant species with that of urban-avoidant species. Specifically, we examined models of state-dependent speciation and extinction to assess the macroevolution of urban tolerance as a binary trait, in addition to models of quantitative trait-dependent diversification based on relative urban abundance. We also ran simulation-based model assessments to explore potential sources of bias. Results We provide evidence that historically, species with traits promoting urban colonization have undergone faster diversification than urban-avoidant species, indicating that urbanization favours clades with a historical tendency towards rapid speciation or reduced extinction. In addition, we find that past transitions towards states that currently impede urban colonization by passerines have been more frequent than in the opposite direction. Furthermore, we find a portion of urban-avoidant passerines to be recent and to undergo fast diversification. All highly supported models give this result consistently. Main conclusions Urbanization is mainly associated with the loss of lineages that are inherently more vulnerable to extinction over deep time, whereas cities tend to be colonized by less vulnerable lineages, for which urbanization might be neutral or positive in terms of longer-term diversification. Urban avoidance is associated with high rates of recent diversification for some clades occurring in regions with relatively intact natural ecosystems and low current levels of urbanization.
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Affiliation(s)
| | | | - David A. Duchêne
- Centre for Evolutionary HologenomicsUniversity of CopenhagenCopenhagenDenmark
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17
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Román-Palacios C, Moraga-López D, Wiens JJ. The origins of global biodiversity on land, sea and freshwater. Ecol Lett 2022; 25:1376-1386. [PMID: 35334149 DOI: 10.1111/ele.13999] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/06/2022] [Accepted: 02/16/2022] [Indexed: 11/28/2022]
Abstract
Many biodiversity studies focus on explaining high tropical species richness, but an equally dramatic yet understudied pattern involves the divergent richness of land, sea and freshwater. Here, we reveal the origins of these richness differences among habitats across animals and plants. Most plant and animal species are terrestrial, although these habitats cover only ~28% of Earth's surface. Marine habitats have fewer species over a larger area (~70%). Freshwater habitats have relatively high richness and exceptional phylogenetic diversity given their tiny area (2%). The relative richness of habitats is related to variation in diversification rates. Based on ancestral reconstructions of habitat, we find that most marine species are descended from marine ancestors and most terrestrial species from freshwater ancestors. Yet, most extant animal richness in freshwater is derived from terrestrial ancestors. Overall, our results reveal the origins of fundamental but neglected biodiversity patterns, and highlight the conservation importance of freshwater habitats.
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Affiliation(s)
| | - Daniela Moraga-López
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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18
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Dale EE, Foest JJ, Hacket-Pain A, Bogdziewicz M, Tanentzap AJ. Macroevolutionary consequences of mast seeding. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200372. [PMID: 34657467 PMCID: PMC8520783 DOI: 10.1098/rstb.2020.0372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/05/2022] Open
Abstract
Masting characterizes large, intermittent and highly synchronous seeding events among individual plants and is found throughout the plant Tree of Life (ToL). Although masting can increase plant fitness, little is known about whether it results in evolutionary changes across entire clades, such as by promoting speciation or enhanced trait selection. Here, we tested if masting has macroevolutionary consequences by combining the largest existing dataset of population-level reproductive time series and time-calibrated phylogenetic tree of vascular plants. We found that the coefficient of variation (CVp) of reproductive output for 307 species covaried with evolutionary history, and more so within clades than expected by random. Speciation rates estimated at the species level were highest at intermediate values of CVp and regional-scale synchrony (Sr) in seed production, that is, there were unimodal correlations. There was no support for monotonic correlations between either CVp or Sr and rates of speciation or seed size evolution. These results were robust to different sampling decisions, and we found little bias in our dataset compared with the wider plant ToL. While masting is often adaptive and encompasses a rich diversity of reproductive behaviours, we suggest it may have few consequences beyond the species level. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.
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Affiliation(s)
- Esther E. Dale
- Manaaki Whenua - Landcare Research, Dunedin, New Zealand
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Jessie J. Foest
- Department of Geography and Planning, School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Andrew Hacket-Pain
- Department of Geography and Planning, School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Michał Bogdziewicz
- Department of Systematic Zoology, Faculty of Biology, Adam Mickiewicz University, Ul. Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
- INRAE, LESSEM, University Grenoble Alpes, Saint-Martin-d'Heres, France
| | - Andrew J. Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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19
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Moen DS. Improving inference and avoiding overinterpretation of hidden-state diversification models: Specialized plant breeding has no effect on diversification in frogs. Evolution 2021; 76:373-384. [PMID: 34854483 DOI: 10.1111/evo.14406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 11/30/2022]
Abstract
The hidden-state speciation and extinction (HiSSE) model helps avoid spurious results when testing whether a character affects diversification rates. However, care must be taken to optimally analyze models and interpret results. Recently, Tonini et al. (TEA hereafter) studied anuran (frog and toad) diversification with HiSSE methods. They concluded that their focal state, breeding in phytotelmata, increases net diversification rates. Yet this conclusion is counterintuitive, because the state that purportedly increases net diversification rates is 14 times rarer among species than the alternative. Herein, I revisit TEA's analyses and demonstrate problems with inferring model likelihoods, conducting post hoc tests, and interpreting results. I also reevaluate their top models and find that diverse strategies are necessary to reach the parameter values that maximize each model's likelihood. In contrast to TEA, I find no support for an effect of phytotelm breeding on net diversification rates in Neotropical anurans. In particular, even though the most highly supported models include the focal character, averaging parameter estimates over hidden states shows that the focal character does not influence diversification rates. Finally, I suggest ways to better analyze and interpret complex diversification models-both state-dependent and beyond-for future studies in other organisms.
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Affiliation(s)
- Daniel S Moen
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
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20
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Miller EC. Comparing diversification rates in lakes, rivers, and the sea. Evolution 2021; 75:2055-2073. [PMID: 34181244 DOI: 10.1111/evo.14295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 05/29/2021] [Accepted: 06/06/2021] [Indexed: 12/23/2022]
Abstract
The diversity of species inhabiting freshwater relative to marine habitats is striking, given that freshwater habitats encompass <1% of Earth's water. The most commonly proposed explanation for this pattern is that freshwater habitats are more fragmented than marine habitats, allowing more opportunities for allopatric speciation and thus increased diversification rates in freshwater. However, speciation may be generally faster in sympatry than in allopatry, as illustrated by lacustrine radiations such as African cichlids. Such differences between rivers and lakes may be important to consider when comparing diversification broadly among freshwater and marine groups. Here I compared diversification rates of teleost fishes in marine, riverine and lacustrine habitats. I found that lakes had faster speciation and net diversification rates than other aquatic habitats. However, most freshwater diversity arose in rivers. Surprisingly, riverine and marine habitats had similar rates of net diversification on average. Biogeographic models suggest that lacustrine habitats are evolutionarily unstable, explaining the dearth of lacustrine species in spite of their rapid diversification. Collectively, these results suggest that strong diversification rate differences are unlikely to explain the freshwater paradox. Instead, this pattern may be attributable to the comparable amount of time spent in riverine and marine habitats over the 200-million-year history of teleosts.
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21
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Twining CW, Bernhardt JR, Derry AM, Hudson CM, Ishikawa A, Kabeya N, Kainz MJ, Kitano J, Kowarik C, Ladd SN, Leal MC, Scharnweber K, Shipley JR, Matthews B. The evolutionary ecology of fatty-acid variation: Implications for consumer adaptation and diversification. Ecol Lett 2021; 24:1709-1731. [PMID: 34114320 DOI: 10.1111/ele.13771] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/20/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022]
Abstract
The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.
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Affiliation(s)
- Cornelia W Twining
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Limnological Institute, University of Konstanz, Konstanz-Egg, Germany
| | - Joey R Bernhardt
- Department of Biology, McGill University, Montréal, QC, Canada.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Alison M Derry
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Cameron M Hudson
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology (TUMSAT, Tokyo, Japan
| | - Martin J Kainz
- WasserCluster Lunz-Inter-university Center for Aquatic Ecosystems Research, Lunz am See, Austria
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Carmen Kowarik
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Sarah Nemiah Ladd
- Ecosystem Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Miguel C Leal
- ECOMARE and CESAM - Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Kristin Scharnweber
- Department of Ecology and Genetics; Limnology, Uppsala University, Uppsala, Sweden.,University of Potsdam, Plant Ecology and Nature Conservation, Potsdam-Golm, Germany
| | - Jeremy R Shipley
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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22
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Miller EC, Mesnick SL, Wiens JJ. Sexual Dichromatism Is Decoupled from Diversification over Deep Time in Fishes. Am Nat 2021; 198:232-252. [PMID: 34260865 DOI: 10.1086/715114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractSexually selected traits have long been thought to drive diversification, but support for this hypothesis has been persistently controversial. In fishes, sexually dimorphic coloration is associated with assortative mating and speciation among closely related species, as shown in classic studies. However, it is unclear whether these results can generalize to explain diversity patterns across ray-finned fishes, which contain the majority of vertebrate species and 96% of fishes. Here, we use phylogenetic approaches to test for an association between sexual dichromatism and diversification rates (speciation minus extinction) in ray-finned fishes. We assembled dichromatism data for 10,898 species, a data set of unprecedented size. We found no difference in diversification rates between monochromatic and dichromatic species when including all ray-finned fishes. However, at lower phylogenetic scales (within orders and families), some intermediate-sized clades did show an effect of dichromatism on diversification. Surprisingly, dichromatism could significantly increase or decrease diversification rates. Moreover, we found no effect in many of the clades initially used to link dichromatism to speciation in fishes (e.g., cichlids) or an effect only at shallow scales (within subclades). Overall, we show how the effects of dichromatism on diversification are highly variable in direction and restricted to certain clades and phylogenetic scales.
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23
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Basava K, Zhang H, Mace R. A phylogenetic analysis of revolution and afterlife beliefs. Nat Hum Behav 2021; 5:604-611. [PMID: 33398146 DOI: 10.1038/s41562-020-01013-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/12/2020] [Indexed: 01/28/2023]
Abstract
Beliefs about the fate of humanity and the soul after death may structure behaviours of religious groups. Here we test theories from religious studies: that belief in an imminent apocalypse co-evolved with and facilitated revolutionary violence, whereas belief in reincarnation caused people to acquiesce to existing social orders and withdraw from political activism. We test these hypotheses by building a cultural phylogeny of historical Islamic sects and schools from the seventh to twentieth centuries and use phylogenetic comparative methods to show that these two types of belief display distinct relationships with intergroup violence. There is substantial evidence that apocalyptic beliefs co-evolved with revolutionary violence, whereas reincarnation beliefs were evolutionarily stable in peaceful groups. In both cases, violence precedes the emergence of beliefs, which suggests that conditions that generate revolutionary violence changed beliefs rather than beliefs generating violence. We also found that apocalyptic beliefs are associated with accelerated group extinction, although causal relationships cannot be determined.
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Affiliation(s)
- Kiran Basava
- Dept of Anthropology, University College London, London, UK.,Institute of Cognitive and Evolutionary Anthropology, University of Oxford, Oxford, UK
| | - Hanzhi Zhang
- Dept of Anthropology, University College London, London, UK.
| | - Ruth Mace
- Dept of Anthropology, University College London, London, UK
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24
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Turk E, Kralj-Fišer S, Kuntner M. Exploring diversification drivers in golden orbweavers. Sci Rep 2021; 11:9248. [PMID: 33927261 PMCID: PMC8084975 DOI: 10.1038/s41598-021-88555-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/14/2021] [Indexed: 11/08/2022] Open
Abstract
Heterogeneity in species diversity is driven by the dynamics of speciation and extinction, potentially influenced by organismal and environmental factors. Here, we explore macroevolutionary trends on a phylogeny of golden orbweavers (spider family Nephilidae). Our initial inference detects heterogeneity in speciation and extinction, with accelerated extinction rates in the extremely sexually size dimorphic Nephila and accelerated speciation in Herennia, a lineage defined by highly derived, arboricolous webs, and pronounced island endemism. We evaluate potential drivers of this heterogeneity that relate to organisms and their environment. Primarily, we test two continuous organismal factors for correlation with diversification in nephilids: phenotypic extremeness (female and male body length, and sexual size dimorphism as their ratio) and dispersal propensity (through range sizes as a proxy). We predict a bell-shaped relationship between factor values and speciation, with intermediate phenotypes exhibiting highest diversification rates. Analyses using SSE-class models fail to support our two predictions, suggesting that phenotypic extremeness and dispersal propensity cannot explain patterns of nephilid diversification. Furthermore, two environmental factors (tropical versus subtropical and island versus continental species distribution) indicate only marginal support for higher speciation in the tropics. Although our results may be affected by methodological limitations imposed by a relatively small phylogeny, it seems that the tested organismal and environmental factors play little to no role in nephilid diversification. In the phylogeny of golden orbweavers, the recent hypothesis of universal diversification dynamics may be the simplest explanation of macroevolutionary patterns.
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Affiliation(s)
- Eva Turk
- Evolutionary Zoology Laboratory, Institute of Biology, ZRC SAZU, Ljubljana, Slovenia.
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia.
| | - Simona Kralj-Fišer
- Evolutionary Zoology Laboratory, Institute of Biology, ZRC SAZU, Ljubljana, Slovenia
| | - Matjaž Kuntner
- Evolutionary Zoology Laboratory, Institute of Biology, ZRC SAZU, Ljubljana, Slovenia
- Evolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei, China
- University of Ljubljana, Ljubljana, Slovenia
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25
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Emberts Z, Wiens JJ. Do sexually selected weapons drive diversification? Evolution 2021; 75:2411-2424. [PMID: 33738793 DOI: 10.1111/evo.14212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/16/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022]
Abstract
Sexual selection is often thought to promote speciation. This expectation is largely driven by the fact that sexually selected traits can influence mating patterns and contribute to reproductive isolation. Indeed, some comparative studies have shown that clades with sexually selected traits have increased rates of speciation and diversification. However, these studies have almost exclusively focused on one mechanism of sexual selection: female choice. Another widespread mechanism is male-male competition. Few empirical studies (if any) have investigated the role of this alternative mechanism in driving diversification. Nevertheless, recent reviews have suggested that male-male competition can increase speciation rates. Here, we investigated whether traits associated with precopulatory male-male competition (i.e., sexually selected weapons) have promoted speciation and diversification in insects. We focused on three clades with both weapons and suitable phylogenies: leaf-footed and broad-headed bugs (Coreidae+Alydidae; ∼2850 species), stick insects and relatives (Phasmatodea; ∼3284 species), and scarab beetles (Scarabaeoidea; ∼39,717 species). We found no evidence that weapon-bearing lineages in these clades have higher rates of speciation or diversification than their weaponless relatives. Thus, our results suggest that precopulatory male-male competition may not have strong, general effects on speciation and diversification in insects, a group encompassing ∼60% of all described species.
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Affiliation(s)
- Zachary Emberts
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721
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26
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Cally JG, Stuart-Fox D, Holman L, Dale J, Medina I. Male-biased sexual selection, but not sexual dichromatism, predicts speciation in birds. Evolution 2021; 75:931-944. [PMID: 33559135 DOI: 10.1111/evo.14183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/13/2021] [Indexed: 01/04/2023]
Abstract
Sexual selection is thought to shape phylogenetic diversity by affecting speciation or extinction rates. However, the net effect of sexual selection on diversification is hard to predict because many of the hypothesized effects on speciation or extinction have opposing signs and uncertain magnitudes. Theoretical work also suggests that the net effect of sexual selection on diversification should depend strongly on ecological factors, though this prediction has seldom been tested. Here, we test whether variation in sexual selection can predict speciation and extinction rates across passerine birds (up to 5812 species, covering most genera) and whether this relationship is mediated by environmental factors. Male-biased sexual selection, and specifically sexual size dimorphism, predicted two of the three measures of speciation rates that we examined. The link we observed between sexual selection and speciation was independent of environmental variability, though species with smaller ranges had higher speciation rates. There was no association between any proxies of sexual selection and extinction rate. Our findings support the view that male-biased sexual selection, as measured by frequent predictors of male-male competition, has shaped diversification in the largest radiation of birds.
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Affiliation(s)
- Justin G Cally
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Devi Stuart-Fox
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Luke Holman
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - James Dale
- School of Natural and Computational Sciences, Massey University (Albany Campus), Auckland, 0632, New Zealand
| | - Iliana Medina
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
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27
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Thacker CE, Shelley JJ, McCraney WT, Unmack PJ, McGee MD. Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock. Syst Biol 2021; 71:13-23. [PMID: 33682001 PMCID: PMC8677556 DOI: 10.1093/sysbio/syab014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
Adaptive radiations are generally thought to occur soon after a lineage invades a region offering high levels of ecological opportunity. However, few adaptive radiations beyond a handful of exceptional examples are known, so a comprehensive understanding of their dynamics is still lacking. Here, we present a novel case of an island species flock of freshwater fishes with a radically different tempo of adaptive history than that found in many popular evolutionary model systems. Using a phylogenomic data set combined with simultaneous Bayesian estimation of divergence times and trait-based speciation and extinction models, we show that the New Zealand Gobiomorphus gudgeons comprise a monophyletic assemblage, but surprisingly, the radiation did not fully occupy freshwater habitats and explosively speciate until more than 10 myr after the lineage invaded the islands. This shift in speciation rate was not accompanied by an acceleration in the rate of morphological evolution in the freshwater crown clade relative to the other species, but is correlated with a reduction in head pores and scales as well as an increase in egg size. Our results challenge the notion that clades always rapidly exploit ecological opportunities in the absence of competing lineages. Instead, we demonstrate that adaptive radiation can experience a slow start before undergoing accelerated diversification and that lineage and phenotypic diversification may be uncoupled in young radiations. [Adaptive radiation; Eleotridae; freshwater; Gobiomorphus; New Zealand.]
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Affiliation(s)
- Christine E Thacker
- Vertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara CA USA.,Research and Collections, Section of Ichthyology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA USA
| | - James J Shelley
- National Institute of Water and Atmospheric Research, Gate 10 Silverdale Road Hillcrest, 3216 Hamilton, New Zealand
| | - W Tyler McCraney
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 612 Charles E. Young Drive South, Box 957246, Los Angeles, CA 90095-7246 USA
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra Canberra ACT 2601, Australia
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
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28
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Allio R, Nabholz B, Wanke S, Chomicki G, Pérez-Escobar OA, Cotton AM, Clamens AL, Kergoat GJ, Sperling FAH, Condamine FL. Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nat Commun 2021; 12:354. [PMID: 33441560 PMCID: PMC7806994 DOI: 10.1038/s41467-020-20507-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/03/2020] [Indexed: 01/29/2023] Open
Abstract
The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic insect-plant interaction between swallowtail butterflies and the highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient host-plant shifts. This evolutionary framework provides a valuable opportunity for repeated tests of genomic signatures of macroevolutionary changes and estimation of diversification rates across their phylogeny. We find that host-plant shifts in butterflies are associated with both genome-wide adaptive molecular evolution (more genes under positive selection) and repeated bursts of speciation rates, contributing to an increase in global diversification through time. Our study links ecological changes, genome-wide adaptations and macroevolutionary consequences, lending support to the importance of ecological interactions as evolutionary drivers over long time periods.
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Affiliation(s)
- Rémi Allio
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Benoit Nabholz
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - Guillaume Chomicki
- Department of Bioscience, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | | | - Adam M Cotton
- 86/2 Moo 5, Tambon Nong Kwai, Hang Dong, Chiang Mai, Thailand
| | - Anne-Laure Clamens
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Gaël J Kergoat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada
| | - Fabien L Condamine
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada.
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29
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Bromham L, Hua X, Cardillo M. Macroevolutionary and macroecological approaches to understanding the evolution of stress tolerance in plants. PLANT, CELL & ENVIRONMENT 2020; 43:2832-2846. [PMID: 32705700 DOI: 10.1111/pce.13857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/26/2020] [Accepted: 07/05/2020] [Indexed: 05/24/2023]
Abstract
Environmental stress response in plants has been studied using a wide range of approaches, from lab-based investigation of biochemistry and genetics, to glasshouse studies of physiology and growth rates, to field-based trials and ecological surveys. It is also possible to investigate the evolution of environmental stress responses using macroevolutionary and macroecological analyses, analysing data from many different species, providing a new perspective on the way that environmental stress shapes the evolution and distribution of biodiversity. "Macroevoeco" approaches can produce intriguing results and new ways of looking at old problems. In this review, we focus on studies using phylogenetic analysis to illuminate macroevolutionary patterns in the evolution of environmental stress tolerance in plants. We follow a particular thread from our own research-evolution of salt tolerance-as a case study that illustrates a macroevolutionary way of thinking that opens up a range of broader questions on the evolution of environmental stress tolerances. We consider some potential future applications of macroevolutionary and macroecological analyses to understanding how diverse groups of plants evolve in response to environmental stress, which may allow better prediction of current stress tolerance and a way of predicting the capacity of species to adapt to changing environmental stresses over time.
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Affiliation(s)
- Lindell Bromham
- Macroevolution & Macroecology, Research School of Biology, Australian National University, Canberra, Australia
| | - Xia Hua
- Macroevolution & Macroecology, Research School of Biology, Australian National University, Canberra, Australia
- Mathematical Sciences Institute, Australian National University, Canberra, Australia
| | - Marcel Cardillo
- Macroevolution & Macroecology, Research School of Biology, Australian National University, Canberra, Australia
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30
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S Meseguer A, Condamine FL. Ancient tropical extinctions at high latitudes contributed to the latitudinal diversity gradient. Evolution 2020; 74:1966-1987. [PMID: 32246727 DOI: 10.1111/evo.13967] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 03/04/2020] [Accepted: 03/21/2020] [Indexed: 01/15/2023]
Abstract
Global biodiversity currently peaks at the equator and decreases toward the poles. Growing fossil evidence suggest this hump-shaped latitudinal diversity gradient (LDG) has not been persistent through time, with similar diversity across latitudes flattening out the LDG during past greenhouse periods. However, when and how diversity declined at high latitudes to generate the modern LDG remains an open question. Although diversity-loss scenarios have been proposed, they remain mostly undemonstrated. We outline the "asymmetric gradient of extinction and dispersal" framework that contextualizes previous ideas behind the LDG under a time-variable scenario. Using phylogenies and fossils of Testudines, Crocodilia, and Lepidosauria, we find that the hump-shaped LDG could be explained by (1) disproportionate extinctions of high-latitude tropical-adapted clades when climate transitioned from greenhouse to icehouse, and (2) equator-ward biotic dispersals tracking their climatic preferences when tropical biomes became restricted to the equator. Conversely, equivalent diversification rates across latitudes can account for the formation of an ancient flat LDG. The inclusion of fossils in macroevolutionary studies allows revealing time-dependent extinction rates hardly detectable from phylogenies only. This study underscores that the prevailing evolutionary processes generating the LDG during greenhouses differed from those operating during icehouses.
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Affiliation(s)
- Andrea S Meseguer
- INRA, UMR 1062 Centre de Biologie pour la Gestion des Populations (INRA | IRD | CIRAD | Montpellier SupAgro), Montferrier-sur-Lez, France
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Montpellier, France
- Real Jardín Botánico de Madrid (RJB-CSIC), Madrid, Spain
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Montpellier, France
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31
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Burridge CP, Waters JM. Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes. Evolution 2020; 74:1954-1965. [DOI: 10.1111/evo.14066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022]
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32
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de Vos JM, Augustijnen H, Bätscher L, Lucek K. Speciation through chromosomal fusion and fission in Lepidoptera. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190539. [PMID: 32654638 DOI: 10.1098/rstb.2019.0539] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Changes in chromosome numbers may strongly affect reproductive barriers, because individuals heterozygous for distinct karyotypes are typically expected to be at least partially sterile or to show reduced recombination. Therefore, several classic speciation models are based on chromosomal changes. One import mechanism generating variation in chromosome numbers is fusion and fission of existing chromosomes, which is particularly likely in species with holocentric chromosomes, i.e. chromosomes that lack a single centromere. Holocentric chromosomes evolved repeatedly across the tree of life, including in Lepidoptera. Although changes in chromosome numbers are hypothesized to be an important driver of the spectacular diversification of Lepidoptera, comparative studies across the order are lacking. We performed the first comprehensive literature survey of karyotypes for Lepidoptera species since the 1970s and tested if, and how, chromosomal variation might affect speciation. Even though a meta-analysis of karyological differences between closely related taxa did not reveal an effect on the degree of reproductive isolation, phylogenetic diversification rate analyses across the 16 best-covered genera indicated a strong, positive association of rates of chromosome number evolution and speciation. These findings suggest a macroevolutionary impact of varying chromosome numbers in Lepidoptera and likely apply to other taxonomic groups, especially to those with holocentric chromosomes. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Jurriaan M de Vos
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Hannah Augustijnen
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Livio Bätscher
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
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33
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Shafir A, Azouri D, Goldberg EE, Mayrose I. Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates. Evolution 2020; 74:1620-1639. [PMID: 32510165 DOI: 10.1111/evo.14036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/17/2020] [Indexed: 12/01/2022]
Abstract
As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suite of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study, we show that asymmetric rates of sequence evolution lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.
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Affiliation(s)
- Anat Shafir
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Dana Azouri
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel.,School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | | | - Itay Mayrose
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
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34
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Holland BR, Ketelaar-Jones S, O'Mara AR, Woodhams MD, Jordan GJ. Accuracy of ancestral state reconstruction for non-neutral traits. Sci Rep 2020; 10:7644. [PMID: 32376845 PMCID: PMC7203120 DOI: 10.1038/s41598-020-64647-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/09/2020] [Indexed: 12/05/2022] Open
Abstract
The assumptions underpinning ancestral state reconstruction are violated in many evolutionary systems, especially for traits under directional selection. However, the accuracy of ancestral state reconstruction for non-neutral traits is poorly understood. To investigate the accuracy of ancestral state reconstruction methods, trees and binary characters were simulated under the BiSSE (Binary State Speciation and Extinction) model using a wide range of character-state-dependent rates of speciation, extinction and character-state transition. We used maximum parsimony (MP), BiSSE and two-state Markov (Mk2) models to reconstruct ancestral states. Under each method, error rates increased with node depth, true number of state transitions, and rates of state transition and extinction; exceeding 30% for the deepest 10% of nodes and highest rates of extinction and character-state transition. Where rates of character-state transition were asymmetrical, error rates were greater when the rate away from the ancestral state was largest. Preferential extinction of species with the ancestral character state also led to higher error rates. BiSSE outperformed Mk2 in all scenarios where either speciation or extinction was state dependent and outperformed MP under most conditions. MP outperformed Mk2 in most scenarios except when the rates of character-state transition and/or extinction were highly asymmetrical and the ancestral state was unfavoured.
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Affiliation(s)
- Barbara R Holland
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tas, 7001, Australia.
| | - Saan Ketelaar-Jones
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tas, 7001, Australia
| | - Aidan R O'Mara
- School of Health Sciences, University of Tasmania, Private Bag 121, Hobart, Tas, 7001, Australia
| | - Michael D Woodhams
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tas, 7001, Australia
| | - Gregory J Jordan
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tas, 7001, Australia
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35
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Modica MV, Gorson J, Fedosov AE, Malcolm G, Terryn Y, Puillandre N, Holford M. Macroevolutionary Analyses Suggest That Environmental Factors, Not Venom Apparatus, Play Key Role in Terebridae Marine Snail Diversification. Syst Biol 2020; 69:413-430. [PMID: 31504987 PMCID: PMC7164365 DOI: 10.1093/sysbio/syz059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
How species diversification occurs remains an unanswered question in predatory marine invertebrates, such as sea snails of the family Terebridae. However, the anatomical disparity found throughput the Terebridae provides a unique perspective for investigating diversification patterns in venomous predators. In this study, a new dated molecular phylogeny of the Terebridae is used as a framework for investigating diversification of the family through time, and for testing the putative role of intrinsic and extrinsic traits, such as shell size, larval ecology, bathymetric distribution, and anatomical features of the venom apparatus, as drivers of terebrid species diversification. Macroevolutionary analysis revealed that when diversification rates do not vary across Terebridae clades, the whole family has been increasing its global diversification rate since 25 Ma. We recovered evidence for a concurrent increase in diversification of depth ranges, while shell size appeared to have undergone a fast divergence early in terebrid evolutionary history. Our data also confirm that planktotrophy is the ancestral larval ecology in terebrids, and evolutionary modeling highlighted that shell size is linked to larval ecology of the Terebridae, with species with long-living pelagic larvae tending to be larger and have a broader size range than lecithotrophic species. Although we recovered patterns of size and depth trait diversification through time and across clades, the presence or absence of a venom gland (VG) did not appear to have impacted Terebridae diversification. Terebrids have lost their venom apparatus several times and we confirm that the loss of a VG happened in phylogenetically clustered terminal taxa and that reversal is extremely unlikely. Our findings suggest that environmental factors, and not venom, have had more influence on terebrid evolution.
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Affiliation(s)
- Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- UMR5247, Université de Montpellier CC 1703, Place Eugène Bataillon 34095 Montpellier, France
| | - Juliette Gorson
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
| | - Alexander E Fedosov
- Institute of Ecology and Evolution of Russian Academy of Sciences, Leninskiy Prospect, 33, Moscow 119071, Russia
| | - Gavin Malcolm
- Bird Hill, Barnes Lane, Milford on Sea, Hampshire, UK
| | - Yves Terryn
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
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36
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Patton AH, Margres MJ, Epstein B, Eastman J, Harmon LJ, Storfer A. Hybridizing salamanders experience accelerated diversification. Sci Rep 2020; 10:6566. [PMID: 32300150 PMCID: PMC7162952 DOI: 10.1038/s41598-020-63378-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/23/2020] [Indexed: 11/09/2022] Open
Abstract
Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.
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Affiliation(s)
- Austin H Patton
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.
| | - Mark J Margres
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.,Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, 02138, USA
| | - Brendan Epstein
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.,University of Minnesota, College of Biological Sciences, Saint Paul, MN, 55108, USA
| | | | - Luke J Harmon
- University of Idaho, Department of Biological Sciences and IBEST, Moscow, ID, 83844, USA
| | - Andrew Storfer
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA
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37
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Moen DS. What Determines the Distinct Morphology of Species with a Particular Ecology? The Roles of Many-to-One Mapping and Trade-Offs in the Evolution of Frog Ecomorphology and Performance. Am Nat 2019; 194:E81-E95. [DOI: 10.1086/704736] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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38
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Nyman T, Onstein RE, Silvestro D, Wutke S, Taeger A, Wahlberg N, Blank SM, Malm T. The early wasp plucks the flower: disparate extant diversity of sawfly superfamilies (Hymenoptera: ‘Symphyta’) may reflect asynchronous switching to angiosperm hosts. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder ‘Symphyta’, which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the ‘Symphyta’, with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes – and back – have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms.
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Affiliation(s)
- Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, Germany
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg and Gothenburg Global Biodiversity Centre, Sweden
| | - Saskia Wutke
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Andreas Taeger
- Senckenberg Deutsches Entomologisches Institut Müncheberg, Germany
| | | | - Stephan M Blank
- Senckenberg Deutsches Entomologisches Institut Müncheberg, Germany
| | - Tobias Malm
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
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39
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Scott JE. Macroevolutionary effects on primate trophic evolution and their implications for reconstructing primate origins. J Hum Evol 2019; 133:1-12. [PMID: 31358174 DOI: 10.1016/j.jhevol.2019.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 11/28/2022]
Abstract
The visual-predation hypothesis proposes that certain derived features shared by crown primates reflect an insectivorous ancestry. Critics of this idea have argued that because insectivory is uncommon among extant primates it is unlikely to have been a major influence on early primate evolution. According to this perspective, the low frequency of insectivory indicates that it is an apomorphic deviation from the mostly conserved primate ecological pattern of herbivory. The present study tests two alternative hypotheses that are compatible with an insectivorous ancestor: (1) that trophic evolution was biased, such that herbivory evolved repeatedly with few shifts back to insectivory, and (2) that insectivorous lineages have diversified at a lower rate than herbivorous lineages owing to differential trophic effects on speciation and extinction probabilities. Model-based analysis conducted using trait data for 307 extant primate species indicates that rates of transition into and out of insectivory are similar, rejecting the hypothesis of biased trophic evolution. On the other hand, the hypothesis of asymmetric diversification is supported, with insectivorous lineages having a lower rate of diversification than herbivorous lineages. This correlation is mediated by activity pattern: insectivory occurs mostly in nocturnal lineages, which have a lower diversification rate than diurnal lineages. The frequency of insectivory also appears to have been shaped by repeated transitions into ecological contexts in which insectivory is absent (large body size) or rare (diurnality). These findings suggest that the current distribution of trophic strategies among extant primates is the result of macroevolutionary processes that have favored the proliferation and persistence of herbivory relative to insectivory. This conclusion implies that the low frequency of insectivory is not necessarily evidence against the visual-predation hypothesis.
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Affiliation(s)
- Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E. Second St. Pomona, California, 91766-1854, USA.
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40
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Caetano DS, Harmon LJ. Estimating Correlated Rates of Trait Evolution with Uncertainty. Syst Biol 2019; 68:412-429. [PMID: 30329124 DOI: 10.1093/sysbio/syy067] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 11/14/2022] Open
Abstract
Correlated evolution among traits, which can happen due to genetic constraints, ontogeny, and selection, can have an important impact on the trajectory of phenotypic evolution. For example, shifts in the pattern of evolutionary integration may allow the exploration of novel regions of the morphospace by lineages. Here, we use phylogenetic trees to study the pace of evolution of several traits and their pattern of evolutionary correlation across clades and over time. We use regimes mapped to the branches of the phylogeny to test for shifts in evolutionary integration while incorporating the uncertainty related to trait evolution and ancestral regimes with joint estimation of all parameters of the model using Bayesian Markov chain Monte Carlo. We implemented the use of summary statistics to test for regime shifts based on a series of attributes of the model that can be directly relevant to biological hypotheses. In addition, we extend Felsenstein's pruning algorithm to the case of multivariate Brownian motion models with multiple rate regimes. We performed extensive simulations to explore the performance of the method under a series of scenarios. Finally, we provide two test cases; the evolution of a novel buccal morphology in fishes of the family Centrarchidae and a shift in the trajectory of evolution of traits during the radiation of anole lizards to and from the Caribbean islands. [Anolis; Centrarchidae; comparative methods; evolutionary integration; evolutionary rates; modularity; pruning algorithm.].
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Affiliation(s)
- D S Caetano
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83843, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - L J Harmon
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83843, USA
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41
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Onstein RE, Baker WJ, Couvreur TLP, Faurby S, Herrera-Alsina L, Svenning JC, Kissling WD. To adapt or go extinct? The fate of megafaunal palm fruits under past global change. Proc Biol Sci 2019; 285:rspb.2018.0882. [PMID: 29899077 PMCID: PMC6015859 DOI: 10.1098/rspb.2018.0882] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/17/2018] [Indexed: 01/03/2023] Open
Abstract
Past global change may have forced animal-dispersed plants with megafaunal fruits to adapt or go extinct, but these processes have remained unexplored at broad spatio-temporal scales. Here, we combine phylogenetic, distributional and fruit size data for more than 2500 palm (Arecaceae) species in a time-slice diversification analysis to quantify how extinction and adaptation have changed over deep time. Our results indicate that extinction rates of palms with megafaunal fruits have increased in the New World since the onset of the Quaternary (2.6 million years ago). In contrast, Old World palms show a Quaternary increase in transition rates towards evolving small fruits from megafaunal fruits. We suggest that Quaternary climate oscillations and concurrent habitat fragmentation and defaunation of megafaunal frugivores in the New World have reduced seed dispersal distances and geographical ranges of palms with megafaunal fruits, resulting in their extinction. The increasing adaptation to smaller fruits in the Old World could reflect selection for seed dispersal by ocean-crossing frugivores (e.g. medium-sized birds and bats) to colonize Indo-Pacific islands against a background of Quaternary sea-level fluctuations. Our macro-evolutionary results suggest that megafaunal fruits are increasingly being lost from tropical ecosystems, either due to extinctions or by adapting to smaller fruit sizes.
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Affiliation(s)
- Renske E Onstein
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090 GE Amsterdam, The Netherlands
| | | | | | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
| | - Leonel Herrera-Alsina
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Bioscience, Aarhus University, Aarhus, Denmark.,Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090 GE Amsterdam, The Netherlands
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42
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Soltis PS, Folk RA, Soltis DE. Darwin review: angiosperm phylogeny and evolutionary radiations. Proc Biol Sci 2019; 286:20190099. [PMCID: PMC6452062 DOI: 10.1098/rspb.2019.0099] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/05/2019] [Indexed: 08/17/2023] Open
Abstract
Darwin's dual interests in evolution and plants formed the basis of evolutionary botany, a field that developed following his publications on both topics. Here, we review his many contributions to plant biology—from the evolutionary origins of angiosperms to plant reproduction, carnivory, and movement—and note that he expected one day there would be a ‘true’ genealogical tree for plants. This view fuelled the field of plant phylogenetics. With perhaps nearly 400 000 species, the angiosperms have diversified rapidly since their origin in the Early Cretaceous, often through what appear to be rapid radiations. We describe these evolutionary patterns, evaluate possible drivers of radiations, consider how new approaches to studies of diversification can contribute to our understanding of angiosperm diversity, and suggest new directions for further insight into plant evolution.
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Affiliation(s)
- Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Ryan A. Folk
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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43
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Hernández-Vera G, Toševski I, Caldara R, Emerson BC. Evolution of host plant use and diversification in a species complex of parasitic weevils (Coleoptera: Curculionidae). PeerJ 2019; 7:e6625. [PMID: 30918760 PMCID: PMC6431137 DOI: 10.7717/peerj.6625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/14/2019] [Indexed: 01/24/2023] Open
Abstract
Weevils (Coleoptera: Curculionoidea) represent one of the most diverse groups of organisms on Earth; interactions with their host plants have been recognized to play a central role in their remarkable diversity, yet the exact mechanisms and factors still remain poorly understood. Using phylogenetic comparative analyses, here we investigate the evolution of host use and its possible role in diversification processes of Rhinusa and Gymnetron, two closely related groups of weevils that feed and develop inside plant tissues of hosts within the families Scrophulariaceae and Plantaginaceae. We found strong evidence for phylogenetic conservatism of host use at the plant family level, most likely due to substantial differences in the chemical composition of hosts, reducing the probability of shifts between host families. In contrast, the use of different plant organs represents a more labile ecological trait and ecological niche expansion that allows a finer partitioning of resources. Rhinusa and Gymnetron weevils initially specialized on plants within Scrophulariaceae and then shifted to the closely related Plantaginaceae; likewise, a gall inducing behavior evolved from non-galler weevils, possibly in response to resource competition, as galls facilitate larval development by providing enhanced nutrition and a favorable microhabitat. Results from trait-dependent diversification analyses suggest that both use of hosts within Plantaginaceae and parasitism on fruits and seed capsules are associated with enhanced diversification of Rhinusa and Gymnetron via low extinction rates. Our study provides quantitative evidence and insights on the ecological factors that can promote diversification in phytophagous insects that feed and develop inside plant tissues.
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Affiliation(s)
- Gerardo Hernández-Vera
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK.,Instituto de Botánica, Departamento de Botánica y Zoología. Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Jalisco, México
| | - Ivo Toševski
- CABI Switzerland, Delémont, Switzerland.,Department of Plant Pests, Institute for Plant Protection and Environment, Zemun, Serbia
| | - Roberto Caldara
- Center of Alpine Entomology, University of Milan, Milan, Italy
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Canary Islands, Spain
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44
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O'Hara TD, Hugall AF, Woolley SNC, Bribiesca-Contreras G, Bax NJ. Contrasting processes drive ophiuroid phylodiversity across shallow and deep seafloors. Nature 2019; 565:636-639. [PMID: 30675065 DOI: 10.1038/s41586-019-0886-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 12/14/2018] [Indexed: 11/09/2022]
Abstract
Our knowledge of the distribution and evolution of deep-sea life is limited, impeding our ability to identify priority areas for conservation1. Here we analyse large integrated phylogenomic and distributional datasets of seafloor fauna from the sea surface to the abyss and from equator to pole of the Southern Hemisphere for an entire class of invertebrates (Ophiuroidea). We find that latitudinal diversity gradients are assembled through contrasting evolutionary processes for shallow (0-200 m) and deep (>200 m) seas. The shallow-water tropical-temperate realm broadly reflects a tropical diversification-driven process that shows exchange of lineages in both directions. Diversification rates are reversed for the realm that contains the deep sea and Antarctica; the diversification rates are highest at polar and lowest at tropical latitudes, and net exchange occurs from high to low latitudes. The tropical upper bathyal (200-700 m deep), with its rich ancient phylodiversity, is characterized by relatively low diversification and moderate immigration rates. Conversely, the young, specialized Antarctic fauna is inferred to be rebounding from regional extinctions that are associated with the rapid cooling of polar waters during the mid-Cenozoic era.
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Affiliation(s)
| | | | - Skipton N C Woolley
- Museums Victoria, Melbourne, Victoria, Australia.,CSIRO Oceans and Atmosphere, Hobart, Tasmania, Australia
| | - Guadalupe Bribiesca-Contreras
- Museums Victoria, Melbourne, Victoria, Australia.,Biosciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Nicholas J Bax
- CSIRO Oceans and Atmosphere, Hobart, Tasmania, Australia.,Institute for Marine and Antarctic Science, University of Tasmania, Hobart, Tasmania, Australia
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45
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Lambert JW, Reichard M, Pincheira-Donoso D. Live fast, diversify non-adaptively: evolutionary diversification of exceptionally short-lived annual killifishes. BMC Evol Biol 2019; 19:10. [PMID: 30626330 PMCID: PMC6327596 DOI: 10.1186/s12862-019-1344-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/02/2019] [Indexed: 11/17/2022] Open
Abstract
Background Adaptive radiations are triggered by ecological opportunity – the access to novel niche domains with abundant available resources that facilitate the formation of new ecologically divergent species. Therefore, as new species saturate niche space, clades experience a diversity-dependent slowdown of diversification over time. At the other extreme of the radiation continuum, non-adaptively radiating lineages undergo diversification with minimal niche differentiation when ‘spatial opportunity’ (i.e. areas with suitable ‘ancestral’ ecological conditions) is available. Traditionally, most research has focused on adaptive radiations, while empirical studies on non-adaptive radiations remain lagging behind. A prolific clade of African fish with extremely short lifespan (Nothobranchius killifish), show the key evolutionary features of a candidate non-adaptive radiation – primarily allopatric species with minimal niche and phenotypic divergence. Here, we test the hypothesis that Nothobranchius killifish have non-adaptively diversified. We employ phylogenetic modelling to investigate the tempo and mode of macroevolutionary diversification of these organisms. Results Nothobranchius diversification has proceeded with minor niche differentiation and minimal morphological disparity among allopatric species. Additionally, we failed to identify evidence for a role of body size or biogeography in influencing diversification rates. Diversification has been homogeneous within this genus, with the only hotspot of species-richness not resulting from rapid diversification. However, species in sympatry show higher disparity, which may have been caused by character displacement among coexisting species. Conclusions Nothobranchius killifish have proliferated following the tempo and mode of a non-adaptive radiation. Our study confirms that this exceptionally short-lived group have diversified with minimal divergent niche adaptation, while one group of coexisting species seems to have facilitated spatial overlap among these taxa via the evolution of ecological character displacement. Electronic supplementary material The online version of this article (10.1186/s12862-019-1344-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua W Lambert
- School of Life Sciences, Joseph Banks Laboratories, Brayford Campus, University of Lincoln, Lincoln, LN6 7DL, UK
| | - Martin Reichard
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic
| | - Daniel Pincheira-Donoso
- MacroBiodiversity Lab, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK.
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46
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Legendre F, Condamine FL. When Darwin's Special Difficulty Promotes Diversification in Insects. Syst Biol 2018; 67:873-887. [PMID: 29481653 DOI: 10.1093/sysbio/syy014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 02/14/2018] [Indexed: 01/22/2023] Open
Abstract
Eusociality, Darwin's special difficulty, has been widely investigated but remains a topic of great debate in organismal biology. Eusocial species challenge existing theories, and the impact of highly integrated societies on diversification dynamics is controversial with opposing assertions and hypotheses in the literature. Here, using phylogenetic approaches in termites-the first group that has evolved eusociality-we assessed the fundamental prediction that eusocial lineages have higher diversification rates than non-eusocial clades. We found multiple lines of evidence that eusociality provided higher diversification as compared to non-eusociality. This is particularly exacerbated for eusocial species with "true" workers as compared to species with "false" workers. Because most species with "true" workers have an entirely prokaryotic microbiota, the latter feature is also related to higher diversification rates, but it should be investigated further, notably in relation to angiosperm diversification. Overall, this study suggests that societies with "true" workers are not only more successful at ecological timescales but also over millions of years, which further implies that both organism- and species-level traits act on species selection.
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Affiliation(s)
- Frédéric Legendre
- Muséum national d'Histoire naturelle, UMR 7205 Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Sorbonne Universités, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier), Place Eugène Bataillon, 34095 Montpellier, France
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47
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Singhal S, Huang H, Grundler MR, Marchán-Rivadeneira MR, Holmes I, Title PO, Donnellan SC, Rabosky DL. Does Population Structure Predict the Rate of Speciation? A Comparative Test across Australia’s Most Diverse Vertebrate Radiation. Am Nat 2018; 192:432-447. [DOI: 10.1086/699515] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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48
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Landis JB, Bell CD, Hernandez M, Zenil-Ferguson R, McCarthy EW, Soltis DE, Soltis PS. Evolution of floral traits and impact of reproductive mode on diversification in the phlox family (Polemoniaceae). Mol Phylogenet Evol 2018; 127:878-890. [DOI: 10.1016/j.ympev.2018.06.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/20/2018] [Accepted: 06/20/2018] [Indexed: 01/19/2023]
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49
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Ng J, Freitas LB, Smith SD. Stepwise evolution of floral pigmentation predicted by biochemical pathway structure. Evolution 2018; 72:2792-2802. [PMID: 30187462 DOI: 10.1111/evo.13589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/11/2018] [Accepted: 08/18/2018] [Indexed: 02/06/2023]
Abstract
Developmental pathways play a major role in influencing the distribution of naturally occurring phenotypes. For example, pathway structure and regulation could make some phenotypes inaccessible or restrict the routes through which phenotypes evolve. In this study, we examine floral anthocyanin pigments across the Solanaceae family and test whether patterns of phenotypic variation are consistent with predicted constraints based on the structure of the flavonoid biosynthetic pathway. We find that anthocyanin evolution occurs in a stepwise manner whereby transitions between the production of red mono hydroxylated pelargonidin pigments and blue trihydroxylated delphinidin pigments first passes through an intermediate step of producing purple dihydroxylated cyanidin pigments. Although the transitions between these three pigment types differ in frequency, we infer that these shifts are often reversible, suggesting that the functionality of the underlying biochemical pathway is generally conserved. Furthermore, our study finds that some pigment combinations are never observed, pointing to additional constraints on naturally occurring phenotypes. Overall, our findings provide insights into how the structure of an angiosperm-wide biochemical pathway has shaped macroevolutionary variation in floral pigmentation.
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Affiliation(s)
- Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 91501, Brazil
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
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50
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Sauquet H, Magallón S. Key questions and challenges in angiosperm macroevolution. THE NEW PHYTOLOGIST 2018; 219:1170-1187. [PMID: 29577323 DOI: 10.1111/nph.15104] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/05/2018] [Indexed: 05/26/2023]
Abstract
Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid diversification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm diversification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day biodiversity. We present six key questions that explore the origin and diversification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include diversification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for sampling bias and heterogeneity of macroevolutionary processes through time and among lineages; (2) the need for large and standardized synthetic databases of morphological variation; and (3) continuous effort on sampling the fossil record, but with a revolution in current paleobotanical practice.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS, UMR 8079, Orsay, 91405, France
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacán, México City, 04510, México
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