1
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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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2
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Halabi K, Shafir A, Mayrose I. PloiDB: the plant ploidy database. THE NEW PHYTOLOGIST 2023; 240:918-927. [PMID: 37337836 DOI: 10.1111/nph.19057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/16/2023] [Indexed: 06/21/2023]
Abstract
See also the Commentary on this article by Spoelhof et al., 240: 909–911.
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Affiliation(s)
- Keren Halabi
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, 69978, Israel
| | - Anat Shafir
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, 69978, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, 69978, Israel
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3
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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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4
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Meseguer AS, Carrillo R, Graham SW, Sanmartín I. Macroevolutionary dynamics in the transition of angiosperms to aquatic environments. THE NEW PHYTOLOGIST 2022; 235:344-355. [PMID: 35292979 PMCID: PMC9320795 DOI: 10.1111/nph.18100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Angiosperm lineages in aquatic environments are characterized by high structural and functional diversity, and wide distributions. A long-standing evolutionary riddle is what processes have caused the relatively low diversity of aquatic angiosperms compared to their terrestrial relatives. We use diversification and ancestral reconstruction models with a comprehensive > 10 000 genus angiosperm phylogeny to elucidate the macroevolutionary dynamics associated with transitions of terrestrial plants to water. Our study reveals that net diversification rates are significantly lower in aquatic than in terrestrial angiosperms due to lower speciation and higher extinction. Shifts from land to water started early in angiosperm evolution, but most events were concentrated during the last c. 25 million years. Reversals to a terrestrial habitat started only 40 million years ago, but occurred at much higher rates. Within aquatic angiosperms, the estimated pattern is one of gradual accumulation of lineages, and relatively low and constant diversification rates throughout the Cenozoic. Low diversification rates, together with infrequent water transitions, account for the low diversity of aquatic angiosperms today. The stressful conditions and small global surface of the aquatic habitat available for angiosperms are hypothesized to explain this pattern.
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Affiliation(s)
| | - Rubén Carrillo
- Real Jardín Botánico de Madrid (RJB)CSIC28014MadridSpain
| | - Sean W. Graham
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
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5
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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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6
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Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction. PLoS Biol 2021; 19:e3001414. [PMID: 34648487 PMCID: PMC8516226 DOI: 10.1371/journal.pbio.3001414] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022] Open
Abstract
The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs as well as to long-term physiographic changes that created new biogeographic theaters and new habitats. Snakes underwent massive ecological diversification during this period, repeatedly evolving novel dietary adaptations and prey preferences. The evolutionary tempo and mode of these trophic ecological changes remain virtually unknown, especially compared with co-radiating lineages of birds and mammals that are simultaneously predators and prey of snakes. Here, we assemble a dataset on snake diets (34,060 observations on the diets of 882 species) to investigate the history and dynamics of the multidimensional trophic niche during the global radiation of snakes. Our results show that per-lineage dietary niche breadths remained remarkably constant even as snakes diversified to occupy disparate outposts of dietary ecospace. Rapid increases in dietary diversity and complexity occurred in the early Cenozoic, and the overall rate of ecospace expansion has slowed through time, suggesting a potential response to ecological opportunity in the wake of the end-Cretaceous mass extinction. Explosive bursts of trophic innovation followed colonization of the Nearctic and Neotropical realms by a group of snakes that today comprises a majority of living snake diversity. Our results indicate that repeated transformational shifts in dietary ecology are important drivers of adaptive radiation in snakes and provide a framework for analyzing and visualizing the evolution of complex ecological phenotypes on phylogenetic trees. The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs and long-term physiographic changes. This phylogenetic natural history study offers new insights into the evolution of snake ecological diversity after the end-Cretaceous mass extinction, as they took advantage of these new opportunities.
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Cássia-Silva C, Freitas CG, Jardim L, Bacon CD, Collevatti RG. In situ radiation explains the frequency of dioecious palms on islands. ANNALS OF BOTANY 2021; 128:205-215. [PMID: 33949659 PMCID: PMC8324027 DOI: 10.1093/aob/mcab056] [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: 01/30/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Dioecy has evolved up to 5000 times in angiosperms, despite the potentially high intrinsic costs to unisexuality. Dioecy prevents inbreeding, which is especially relevant on isolated islands when gene pools are small. Dioecy is also associated with certain dispersal traits, such as fruit size and type. However, the influence of dioecy on other life history traits and island distribution remains poorly understood. Here, we test the effect of dioecy on palm (Arecaceae) speciation rates, fruit size and frequency on islands. METHODS We used phylogenetic comparative methods to estimate the ancestral state of the sexual system and its impact on speciation rates and fruit size. Frequency of sexual systems, effect of insularity on the probability of being dioecious, and phylogenetic clustering of island dioecious vs. mainland species were inferred. Lastly, we determined the interplay of insularity and sexual system on speciation rates. KEY RESULTS Palms repeatedly evolved different sexual systems (dioecy, monoecy and polygamy) from a hermaphrodite origin. Differences in speciation rates and fruit size among the different sexual systems were not identified. An effect of islands on the probability of the palms being dioecious was also not found. However, we found a high frequency and phylogenetic clustering of dioecious palms on islands, which were not correlated with higher speciation rates. CONCLUSIONS The high frequency and phylogenetic clustering may be the result of in situ radiation and suggest an 'island effect' for dioecious palms, which was not explained by differential speciation rates. This island effect also cannot be attributed to long-distance dispersal due to the lack of fruit size difference among sexual systems, and particularly because palm dispersal to islands is highly constrained by the interaction between the sizes of fruit and frugivores. Taken together, we suggest that trait flexibility in sexual system evolution and the in situ radiation of dioecious lineages are the underlying causes of the outstanding distribution of palms on islands.
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Affiliation(s)
- Cibele Cássia-Silva
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Cíntia G Freitas
- Pós-Graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Lucas Jardim
- Laboratório de Ecologia Teórica e Síntese, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
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8
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Moreira MO, Fonseca C, Rojas D. Parthenogenesis is self-destructive for scaled reptiles. Biol Lett 2021; 17:20210006. [PMID: 33975486 PMCID: PMC8113917 DOI: 10.1098/rsbl.2021.0006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/20/2021] [Indexed: 11/12/2022] Open
Abstract
Parthenogenesis is rare in nature. With 39 described true parthenogens, scaled reptiles (Squamata) are the only vertebrates that evolved this reproductive strategy. Parthenogenesis is ecologically advantageous in the short term, but the young age and rarity of parthenogenetic species indicate it is less advantageous in the long term. This suggests parthenogenesis is self-destructive: it arises often but is lost due to increased extinction rates, high rates of reversal or both. However, this role of parthenogenesis as a self-destructive trait remains unknown. We used a phylogeny of Squamata (5388 species), tree metrics, null simulations and macroevolutionary scenarios of trait diversification to address the factors that best explain the rarity of parthenogenetic species. We show that parthenogenesis can be considered as self-destructive, with high extinction rates mainly responsible for its rarity in nature. Since these parthenogenetic species occur, this trait should be ecologically relevant in the short term.
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Affiliation(s)
- Matthew Owen Moreira
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carlos Fonseca
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
- ForestWISE - Collaborative Laboratory for Integrated Forest and Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Danny Rojas
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cali, Colombia
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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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10
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Chen ZH, Soltis DE. Evolution of environmental stress responses in plants. PLANT, CELL & ENVIRONMENT 2020; 43:2827-2831. [PMID: 33103798 DOI: 10.1111/pce.13922] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
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11
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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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12
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Tonini JFR, Ferreira RB, Pyron RA. Specialized breeding in plants affects diversification trajectories in Neotropical frogs. Evolution 2020; 74:1815-1825. [PMID: 32510580 DOI: 10.1111/evo.14037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/15/2020] [Accepted: 05/30/2020] [Indexed: 11/30/2022]
Abstract
Many animals breed exclusively in plants that accumulate rainwater (phytotelma; e.g., bromeliad, bamboo, fruit husk, and tree hole), to which they are either physiologically or behaviorally specialized for this microhabitat. Of the numerous life-history modes observed in frogs, few are as striking or potentially consequential as the transition from pond- or stream-breeding to the deposition of eggs or larvae in phytotelmata. Such specialization can increase offspring survivorship due to reduced competition and predation, representing potential ecological opportunity for adaptive radiation, yet few lineages of phytotelma-breeding frogs appear to have diversified extensively after such a transition, at least in the New World. We use a phylogeny of Neotropical frogs and data on breeding microhabitat to understand the evolutionary transitions involved with specialized phytotelma-breeding. First, we find that phytotelma-breeding is present in at least 168 species in 10 families of frogs. Across the phylogeny, we estimate 14 origins of phytotelma-breeding and 115 reversals, showing that phytotelma-breeding is a highly labile character. Second, phytotelma-breeding lineages overall have higher net diversification than nonphytotelma-breeding ones. This specialization represents an ecological opportunity resulting in increased diversification in most families with phytotelma-breeding lineages, whereas phytotelma-breeding toads have restricted diversification histories.
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Affiliation(s)
- João Filipe Riva Tonini
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, 20052.,Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138
| | - Rodrigo Barbosa Ferreira
- Projeto Bromeligenous, Instituto de Pesquisa, Ensino e Preservação Ambiental Marcos Daniel, Vitória, ES 29056-020, Brazil
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, 20052
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Dinnage R, Skeels A, Cardillo M. Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as threats in a hotspot plant genus. Proc Biol Sci 2020; 287:20192817. [PMID: 32370670 DOI: 10.1098/rspb.2019.2817] [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] [Indexed: 11/12/2022] Open
Abstract
Comparative models used to predict species threat status can help identify the diagnostic features of species at risk. Such models often combine variables measured at the species level with spatial variables, causing multiple statistical challenges, including phylogenetic and spatial non-independence. We present a novel Bayesian approach for modelling threat status that simultaneously deals with both forms of non-independence and estimates their relative contribution, and we apply the approach to modelling threat status in the Australian plant genus Hakea. We find that after phylogenetic and spatial effects are accounted for, species with greater evolutionary distinctiveness and a shorter annual flowering period are more likely to be threatened. The model allows us to combine information on evolutionary history, species biology and spatial data, calculate latent extinction risk (potential for non-threatened species to become threatened), estimate the most important drivers of risk for individual species and map spatial patterns in the effects of different predictors on extinction risk. This could be of value for proactive conservation decision-making based on the early identification of species and regions of potential conservation concern.
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Affiliation(s)
- Russell Dinnage
- Macroevolution and Macroecology Group, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Alexander Skeels
- Macroevolution and Macroecology Group, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Marcel Cardillo
- Macroevolution and Macroecology Group, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
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14
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Wessinger CA, Rausher MD, Hileman LC. Adaptation to hummingbird pollination is associated with reduced diversification in Penstemon. Evol Lett 2019; 3:521-533. [PMID: 31636944 PMCID: PMC6791294 DOI: 10.1002/evl3.130] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/12/2019] [Accepted: 07/12/2019] [Indexed: 12/24/2022] Open
Abstract
A striking characteristic of the Western North American flora is the repeated evolution of hummingbird pollination from insect-pollinated ancestors. This pattern has received extensive attention as an opportunity to study repeated trait evolution as well as potential constraints on evolutionary reversibility, with little attention focused on the impact of these transitions on species diversification rates. Yet traits conferring adaptation to divergent pollinators potentially impact speciation and extinction rates, because pollinators facilitate plant reproduction and specify mating patterns between flowering plants. Here, we examine macroevolutionary processes affecting floral pollination syndrome diversity in the largest North American genus of flowering plants, Penstemon. Within Penstemon, transitions from ancestral bee-adapted flowers to hummingbird-adapted flowers have frequently occurred, although hummingbird-adapted species are rare overall within the genus. We inferred macroevolutionary transition and state-dependent diversification rates and found that transitions from ancestral bee-adapted flowers to hummingbird-adapted flowers are associated with reduced net diversification rate, a finding based on an estimated 17 origins of hummingbird pollination in our sample. Although this finding is congruent with hypotheses that hummingbird adaptation in North American Flora is associated with reduced species diversification rates, it contrasts with studies of neotropical plant families where hummingbird pollination has been associated with increased species diversification. We further used the estimated macroevolutionary rates to predict the expected pattern of floral diversity within Penstemon over time, assuming stable diversification and transition rates. Under these assumptions, we find that hummingbird-adapted species are expected to remain rare due to their reduced diversification rates. In fact, current floral diversity in the sampled Penstemon lineage, where less than one-fifth of species are hummingbird adapted, is consistent with predicted levels of diversity under stable macroevolutionary rates.
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Affiliation(s)
- Carolyn A Wessinger
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas 66045
| | - Mark D Rausher
- Department of Biology Duke University Durham North Carolina 27708
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas 66045
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15
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A model with many small shifts for estimating species-specific diversification rates. Nat Ecol Evol 2019; 3:1086-1092. [DOI: 10.1038/s41559-019-0908-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 04/26/2019] [Indexed: 01/23/2023]
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Davies TJ. The macroecology and macroevolution of plant species at risk. THE NEW PHYTOLOGIST 2019; 222:708-713. [PMID: 30485443 DOI: 10.1111/nph.15612] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/12/2018] [Indexed: 05/19/2023]
Abstract
Contents Summary 708 I. Introduction 708 II. Fossils and phylogenies: learning from our past 708 III. Threatened species and Red Lists 710 IV. The geography of threat 710 V. The taxonomy of threat 710 VI. Predicting species at risk 711 VII. Conclusion 711 Acknowledgements 712 References 712 SUMMARY: Current rates of extinction are unprecedented in human history. The fossil record and newer molecular phylogenies illuminate historical patterns of speciation and extinction. They reveal both spectacular radiations and the characteristic features of mass extinction events in our geological past. The IUCN Red List provides insight into present-day species declines. There is emerging synthesis that species at risk are nonrandomly distributed across space and phylogeny. This pattern may be explained by geographical variation in driver intensity and species differential sensitivities. However, traits that confer resistance to one global change driver may increase susceptibility to a different driver. A complete understanding of extinction risk requires consideration of the interaction between extinction drivers, ecological traits, and species' evolutionary histories.
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Affiliation(s)
- T Jonathan Davies
- Departments of Botany, Forest & Conservation Sciences, Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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17
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Title PO, Rabosky DL. Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates? Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13153] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pascal O. Title
- Department of Ecology and Evolutionary Biology and Museum of ZoologyUniversity of Michigan Ann Arbor Michigan
- Environmental Resilience InstituteIndiana University Bloomington Indiana
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of ZoologyUniversity of Michigan Ann Arbor Michigan
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18
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Zhang Q, Onstein RE, Little SA, Sauquet H. Estimating divergence times and ancestral breeding systems in Ficus and Moraceae. ANNALS OF BOTANY 2019; 123:191-204. [PMID: 30202847 PMCID: PMC6344110 DOI: 10.1093/aob/mcy159] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 08/06/2018] [Indexed: 05/30/2023]
Abstract
Background and Aims Although dioecy, which characterizes only 6 % of angiosperm species, has been considered an evolutionary dead end, recent studies have demonstrated that this is not necessarily the case. Moraceae (40 genera, 1100 spp., including Ficus, 750 spp.) are particularly diverse in breeding systems (including monoecy, gynodioecy, androdioecy and dioecy) and thus represent a model clade to study macroevolution of dioecy. Methods Ancestral breeding systems of Ficus and Moraceae were inferred. To do so, a new dated phylogenetic tree of Ficus and Moraceae was first reconstructed by combining a revised 12-fossil calibration set and a densely sampled molecular data set of eight markers and 320 species. Breeding system evolution was then reconstructed using both parsimony and model-based (maximum likelihood and Bayesian) approaches with this new time scale. Key Results The crown group ages of Ficus and Moraceae were estimated in the Eocene (40.6-55.9 Ma) and Late Cretaceous (73.2-84.7 Ma), respectively. Strong support was found for ancestral dioecy in Moraceae. Although the ancestral state of Ficus remained particularly sensitive to model selection, the results show that monoecy and gynodioecy evolved from dioecy in Moraceae, and suggest that gynodioecy probably evolved from monoecy in Ficus. Conclusions Dioecy was found not to be an evolutionary dead end in Moraceae. This study provides a new time scale for the phylogeny and a new framework of breeding system evolution in Ficus and Moraceae.
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Affiliation(s)
- Qian Zhang
- Laboratoire Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Renske E Onstein
- Laboratoire Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐Leipzig, Leipzig, Germany
| | - Stefan A Little
- Laboratoire Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Hervé Sauquet
- Laboratoire Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, Australia
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19
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Ng J, Smith SD. Why are red flowers so rare? Testing the macroevolutionary causes of tippiness. J Evol Biol 2018; 31:1863-1875. [PMID: 30256485 DOI: 10.1111/jeb.13381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 01/05/2023]
Abstract
Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches and differ between recently diverged sister species. This phylogenetic pattern has classically been attributed to the trait being an evolutionary dead end, where the trait arises due to some short-term evolutionary advantage, but it ultimately leads species to extinction. While the higher extinction rate associated with a dead end trait could produce such a tippy pattern, a similar pattern could appear if lineages with the trait speciated slower than other lineages, or if the trait was lost more often that it was gained. In this study, we quantify the degree of tippiness of red flowers in the tomato family, Solanaceae, and investigate the macroevolutionary processes that could explain the sparse phylogenetic distribution of this trait. Using a suite of metrics, we confirm that red-flowered lineages are significantly overdispersed across the tree and form smaller clades than expected under a null model. Next, we fit 22 alternative models using HiSSE (Hidden State Speciation and Extinction), which accommodates asymmetries in speciation, extinction and transition rates that depend on observed and unobserved (hidden) character states. Results of the model fitting indicated significant variation in diversification rates across the family, which is best explained by the inclusion of hidden states. Our best fitting model differs between the maximum clade credibility tree and when incorporating phylogenetic uncertainty, suggesting that the extreme tippiness and rarity of red Solanaceae flowers makes it difficult to distinguish among different underlying processes. However, both of the best models strongly support a bias towards the loss of red flowers. The best fitting HiSSE model when incorporating phylogenetic uncertainty lends some support to the hypothesis that lineages with red flowers exhibit reduced diversification rates due to elevated extinction rates. Future studies employing simulations or targeting population-level processes may allow us to determine whether red flowers in Solanaceae or other angiosperms clades are rare and tippy due to a combination of processes, or asymmetrical transitions alone.
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Affiliation(s)
- Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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20
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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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21
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Vamosi JC, Magallón S, Mayrose I, Otto SP, Sauquet H. Macroevolutionary Patterns of Flowering Plant Speciation and Extinction. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:685-706. [PMID: 29489399 DOI: 10.1146/annurev-arplant-042817-040348] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Species diversity is remarkably unevenly distributed among flowering plant lineages. Despite a growing toolbox of research methods, the reasons underlying this patchy pattern have continued to perplex plant biologists for the past two decades. In this review, we examine the present understanding of transitions in flowering plant evolution that have been proposed to influence speciation and extinction. In particular, ploidy changes, transitions between tropical and nontropical biomes, and shifts in floral form have received attention and have offered some surprises in terms of which factors influence speciation and extinction rates. Mating systems and dispersal characteristics once predominated as determining factors, yet recent evidence suggests that these changes are not as influential as previously thought or are important only when paired with range shifts. Although range extent is an important correlate of speciation, it also influences extinction and brings an applied focus to diversification research. Recent studies that find that past diversification can predict present-day extinction risk open an exciting avenue for future research to help guide conservation prioritization.
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Affiliation(s)
- Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada;
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sarah P Otto
- Department of Zoology and the Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Hervé Sauquet
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS UMR 8079, 91405 Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
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22
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Cyriac VP, Kodandaramaiah U. Digging their own macroevolutionary grave: fossoriality as an evolutionary dead end in snakes. J Evol Biol 2018; 31:587-598. [DOI: 10.1111/jeb.13248] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/23/2018] [Indexed: 01/13/2023]
Affiliation(s)
- V. P. Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology; Indian Institute of Science Education and Research Thiruvananthapuram; Thiruvananthapuram India
| | - U. Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology; Indian Institute of Science Education and Research Thiruvananthapuram; Thiruvananthapuram India
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23
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Hanschen ER, Herron MD, Wiens JJ, Nozaki H, Michod RE. Repeated evolution and reversibility of self-fertilization in the volvocine green algae. Evolution 2018; 72:386-398. [PMID: 29134623 PMCID: PMC5796843 DOI: 10.1111/evo.13394] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022]
Abstract
Outcrossing and self-fertilization are fundamental strategies of sexual reproduction, each with different evolutionary costs and benefits. Self-fertilization is thought to be an evolutionary "dead-end" strategy, beneficial in the short term but costly in the long term, resulting in self-fertilizing species that occupy only the tips of phylogenetic trees. Here, we use volvocine green algae to investigate the evolution of self-fertilization. We use ancestral-state reconstructions to show that self-fertilization has repeatedly evolved from outcrossing ancestors and that multiple reversals from selfing to outcrossing have occurred. We use three phylogenetic metrics to show that self-fertilization is not restricted to the tips of the phylogenetic tree, a finding inconsistent with the view of self-fertilization as a dead-end strategy. We also find no evidence for higher extinction rates or lower speciation rates in selfing lineages. We find that self-fertilizing species have significantly larger colonies than outcrossing species, suggesting the benefits of selfing may counteract the costs of increased size. We speculate that our macroevolutionary results on self-fertilization (i.e., non-tippy distribution, no decreased diversification rates) may be explained by the haploid-dominant life cycle that occurs in volvocine algae, which may alter the costs and benefits of selfing.
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Affiliation(s)
- Erik R. Hanschen
- Department of Ecology and Evolutionary Biology, University of Arizona
| | | | - John J. Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona
| | | | - Richard E. Michod
- Department of Ecology and Evolutionary Biology, University of Arizona
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24
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Vincent AM. Digest: Going solo: Self-fertilization in haploid algae may not lead to evolutionary decline. Evolution 2018; 72:409-410. [PMID: 29315523 DOI: 10.1111/evo.13420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/20/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Alan M Vincent
- Division of Ecology and Evolution. Research School of Biology, The Australian National University, Canberra, Australia
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25
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Harvey MG, Rabosky DL. Continuous traits and speciation rates: Alternatives to state‐dependent diversification models. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12949] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael G. Harvey
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
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26
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Jablonski D. Approaches to Macroevolution: 2. Sorting of Variation, Some Overarching Issues, and General Conclusions. Evol Biol 2017; 44:451-475. [PMID: 29142334 PMCID: PMC5661022 DOI: 10.1007/s11692-017-9434-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/04/2017] [Indexed: 11/08/2022]
Abstract
Approaches to macroevolution require integration of its two fundamental components, within a hierarchical framework. Following a companion paper on the origin of variation, I here discuss sorting within an evolutionary hierarchy. Species sorting-sometimes termed species selection in the broad sense, meaning differential origination and extinction owing to intrinsic biological properties-can be split into strict-sense species selection, in which rate differentials are governed by emergent, species-level traits such as geographic range size, and effect macroevolution, in which rates are governed by organism-level traits such as body size; both processes can create hitchhiking effects, indirectly causing the proliferation or decline of other traits. Several methods can operationalize the concept of emergence, so that rigorous separation of these processes is increasingly feasible. A macroevolutionary tradeoff, underlain by the intrinsic traits that influence evolutionary dynamics, causes speciation and extinction rates to covary in many clades, resulting in evolutionary volatility of some clades and more subdued behavior of others; the few clades that break the tradeoff can achieve especially prolific diversification. In addition to intrinsic biological traits at multiple levels, extrinsic events can drive the waxing and waning of clades, and the interaction of traits and events are difficult but important to disentangle. Evolutionary trends can arise in many ways, and at any hierarchical level; descriptive models can be fitted to clade trajectories in phenotypic or functional spaces, but they may not be diagnostic regarding processes, and close attention must be paid to both leading and trailing edges of apparent trends. Biotic interactions can have negative or positive effects on taxonomic diversity within a clade, but cannot be readily extrapolated from the nature of such interactions at the organismic level. The relationships among macroevolutionary currencies through time (taxonomic richness, morphologic disparity, functional variety) are crucial for understanding the nature of evolutionary diversification. A novel approach to diversity-disparity analysis shows that taxonomic diversifications can lag behind, occur in concert with, or precede, increases in disparity. Some overarching issues relating to both the origin and sorting of clades and phenotypes include the macroevolutionary role of mass extinctions, the potential differences between plant and animal macroevolution, whether macroevolutionary processes have changed through geologic time, and the growing human impact on present-day macroevolution. Many challenges remain, but progress is being made on two of the key ones: (a) the integration of variation-generating mechanisms and the multilevel sorting processes that act on that variation, and (b) the integration of paleontological and neontological approaches to historical biology.
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Affiliation(s)
- David Jablonski
- Department of Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637 USA
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27
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Miller EC, Wiens JJ. Extinction and time help drive the marine‐terrestrial biodiversity gradient: is the ocean a deathtrap? Ecol Lett 2017; 20:911-921. [DOI: 10.1111/ele.12783] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/11/2017] [Accepted: 04/23/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Elizabeth C. Miller
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ85721–0088 USA
| | - John J. Wiens
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ85721–0088 USA
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28
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Phylogenetic Paleoecology: Tree-Thinking and Ecology in Deep Time. Trends Ecol Evol 2017; 32:452-463. [DOI: 10.1016/j.tree.2017.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/04/2017] [Accepted: 03/06/2017] [Indexed: 01/26/2023]
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29
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Rabosky DL, Goldberg EE. FiSSE: A simple nonparametric test for the effects of a binary character on lineage diversification rates. Evolution 2017; 71:1432-1442. [DOI: 10.1111/evo.13227] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/06/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan 48103
| | - Emma E. Goldberg
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul Minnesota 55108
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30
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Gamisch A. Notes on the Statistical Power of the Binary State Speciation and Extinction (BiSSE) Model. Evol Bioinform Online 2016; 12:165-74. [PMID: 27486297 PMCID: PMC4962954 DOI: 10.4137/ebo.s39732] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 02/07/2023] Open
Abstract
The Binary State Speciation and Extinction (BiSSE) method is one of the most popular tools for investigating the rates of diversification and character evolution. Yet, based on previous simulation studies, it is commonly held that the BiSSE method requires phylogenetic trees of fairly large sample sizes (>300 taxa) in order to distinguish between the different models of speciation, extinction, or transition rate asymmetry. Here, the power of the BiSSE method is reevaluated by simulating trees of both small and large sample sizes (30, 60, 90, and 300 taxa) under various asymmetry models and root state assumptions. Results show that the power of the BiSSE method can be much higher, also in trees of small sample size, for detecting differences in speciation rate asymmetry than anticipated earlier. This, however, is not a consequence of any conceptual or mathematical flaw in the method per se but rather of assumptions about the character state at the root of the simulated trees and thus the underlying macroevolutionary model, which led to biased results and conclusions in earlier power assessments. As such, these earlier simulation studies used to determine the power of BiSSE were not incorrect but biased, leading to an overestimation of type-II statistical error for detecting differences in speciation rate but not for extinction and transition rates.
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Affiliation(s)
- Alexander Gamisch
- Department of Ecology and Evolution, University of Salzburg, Salzburg, Austria
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31
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O'Meara BC, Beaulieu JM. Past, future, and present of state-dependent models of diversification. AMERICAN JOURNAL OF BOTANY 2016; 103:792-795. [PMID: 27208347 DOI: 10.3732/ajb.1600012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 03/25/2016] [Indexed: 06/05/2023]
Affiliation(s)
- Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996-1610 USA
| | - Jeremy M Beaulieu
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996-1610 USA
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32
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Day EH, Hua X, Bromham L. Is specialization an evolutionary dead end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists. J Evol Biol 2016; 29:1257-67. [DOI: 10.1111/jeb.12867] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/29/2016] [Accepted: 03/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- E. H. Day
- Centre for Macroevolution & Macroecology; Division of Ecology, Evolution and Genetics; Research School of Biology; Australian National University; Canberra ACT Australia
| | - X. Hua
- Centre for Macroevolution & Macroecology; Division of Ecology, Evolution and Genetics; Research School of Biology; Australian National University; Canberra ACT Australia
| | - L. Bromham
- Centre for Macroevolution & Macroecology; Division of Ecology, Evolution and Genetics; Research School of Biology; Australian National University; Canberra ACT Australia
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33
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Hua X, Bromham L. PHYLOMETRICS: an R package for detecting macroevolutionary patterns, using phylogenetic metrics and backward tree simulation. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12531] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xia Hua
- Division of Evolution, Ecology and Genetics Research School of Biology Australian National University Canberra ACT 0200 Australia
| | - Lindell Bromham
- Division of Evolution, Ecology and Genetics Research School of Biology Australian National University Canberra ACT 0200 Australia
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