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Yu Y, Fan MY, Zhou HX, Song YQ. The global pattern of epiphytic liverwort disparity: insights from Frullania. BMC Ecol Evol 2024; 24:63. [PMID: 38741051 DOI: 10.1186/s12862-024-02254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
The geographical and ecological patterns of morphological disparity are crucial to understand how species are assembled within communities in the context of the evolutionary history, morphological evolution and ecological interactions. However, with limited exceptions, rather few studies have been conducted on the global pattern of disparity, particularly in early land plants. Here we explored the spatial accumulation of disparity in a morphologically variable and species rich liverwort genus Frullania in order to test the hypothesis of latitude disparity gradient. We compiled a morphological data set consisting of eight continuous traits for 244 currently accepted species, and scored the species distribution into 19 floristic regions worldwide. By reconstructing the morphospace of all defined regions and comparisons, we identified a general Gondwana-Laurasia pattern of disparity in Frullania. This likely results from an increase of ecological opportunities and / or relaxed constraints towards low latitudes. The lowest disparity occurred in arid tropical regions, largely due to a high extinction rate as a consequence of paleoaridification. There was weak correlation between species diversity and disparity at different spatial scales. Furthermore, long-distance dispersal may have partially shaped the present-day distribution of Frullania disparity, given its frequency and the great contribution of widely distributed species to local morphospace. This study not only highlighted the crucial roles of paleoenvironmental changes, ecological opportunities, and efficient dispersal on the global pattern of plant disparity, but also implied its dependence on the ecological and physiological function of traits.
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Affiliation(s)
- Ying Yu
- College of Life and Environmental Sciences, Huangshan University, Huangshan, 245041, China.
| | - Mei-Ying Fan
- College of Life and Environmental Sciences, Huangshan University, Huangshan, 245041, China
| | - Hong-Xia Zhou
- College of Life and Environmental Sciences, Huangshan University, Huangshan, 245041, China
| | - Yue-Qin Song
- College of Life and Environmental Sciences, Huangshan University, Huangshan, 245041, China
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2
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Kopper C, Schönenberger J, Dellinger AS. High floral disparity without pollinator shifts in buzz-bee-pollinated Melastomataceae. THE NEW PHYTOLOGIST 2024. [PMID: 38634161 DOI: 10.1111/nph.19735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024]
Abstract
Shifts among functional pollinator groups are commonly regarded as sources of floral morphological diversity (disparity) through the formation of distinct pollination syndromes. While pollination syndromes may be used for predicting pollinators, their predictive accuracy remains debated, and they are rarely used to test whether floral disparity is indeed associated with pollinator shifts. We apply classification models trained and validated on 44 functional floral traits across 252 species with empirical pollinator observations and then use the validated models to predict pollinators for 159 species lacking observations. In addition, we employ multivariate statistics and phylogenetic comparative analyses to test whether pollinator shifts are the main source of floral disparity in Melastomataceae. We find strong support for four well-differentiated pollination syndromes ('buzz-bee', 'nectar-foraging vertebrate', 'food-body-foraging vertebrate', 'generalist'). While pollinator shifts add significantly to floral disparity, we find that the most species-rich 'buzz-bee' pollination syndrome is most disparate, indicating that high floral disparity may evolve without pollinator shifts. Also, relatively species-poor clades and geographic areas contributed substantially to total disparity. Finally, our results show that machine-learning approaches are a powerful tool for evaluating the predictive accuracy of the pollination syndrome concept as well as for predicting pollinators where observations are missing.
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Affiliation(s)
- Constantin Kopper
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, 1030, Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, 1030, Austria
| | - Agnes S Dellinger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, 1030, Austria
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3
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Coiro M, Seyfullah LJ. Disparity of cycad leaves dispels the living fossil metaphor. Commun Biol 2024; 7:328. [PMID: 38485767 PMCID: PMC10940627 DOI: 10.1038/s42003-024-06024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test of this hypothesis exists. Here, we use a recent phylogenetic framework and an improved character matrix to reconstruct the Disparity Through Time for cycad leaves using a Principal Coordinate Analysis and employing Pre-Ordination Ancestral State Reconstruction to test the impact of sampling on the results. Our analysis shows that the cycad leaf morsphospace expanded up to the present, with numerous shifts in its general positioning, independently of sampling biases. Moreover, they also show that Zamiaceae expanded rapidly in the Early Cretaceous and continued to expand up to the present, while now-extinct clades experienced a slow contraction from their peak in the Triassic. We also show that rates of evolution were constantly high up to the Early Cretaceous, and then experienced a slight decrease in the Paleogene, followed by a Neogene acceleration. These results show a much more dynamic history for cycads, and suggest that the 'living fossil' metaphor is actually a hindrance to our understanding of their macroevolution.
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Affiliation(s)
- Mario Coiro
- Department of Palaeontology, University of Vienna, Vienna, Austria.
- Ronin Institute for Independent Scholarship, Montclair, NJ, USA.
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4
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López‐Martínez AM, Magallón S, von Balthazar M, Schönenberger J, Sauquet H, Chartier M. Angiosperm flowers reached their highest morphological diversity early in their evolutionary history. THE NEW PHYTOLOGIST 2024; 241:1348-1360. [PMID: 38029781 PMCID: PMC10952840 DOI: 10.1111/nph.19389] [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: 08/28/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Abstract
Flowers are the complex and highly diverse reproductive structures of angiosperms. Because of their role in sexual reproduction, the evolution of flowers is tightly linked to angiosperm speciation and diversification. Accordingly, the quantification of floral morphological diversity (disparity) among angiosperm subgroups and through time may give important insights into the evolutionary history of angiosperms as a whole. Based on a comprehensive dataset focusing on 30 characters describing floral structure across angiosperms, we used 1201 extant and 121 fossil flowers to measure floral disparity and explore patterns of floral evolution through time and across lineages. We found that angiosperms reached their highest floral disparity in the Early Cretaceous. However, decreasing disparity toward the present likely has not precluded the innovation of other complex traits at other morphological levels, which likely played a key role in the outstanding angiosperm species richness. Angiosperms occupy specific regions of the theoretical morphospace, indicating that only a portion of the possible floral trait combinations is observed in nature. The ANA grade, the magnoliids, and the early-eudicot grade occupy large areas of the morphospace (higher disparity), whereas nested groups occupy narrower regions (lower disparity).
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Affiliation(s)
- Andrea M. López‐Martínez
- Posgrado en Ciencias Biológicas, Instituto de BiologíaUniversidad Nacional Autónoma de México, 3er Circuito de Ciudad UniversitariaCoyoacánCiudad de México04510Mexico
- Departamento de Botánica, Instituto de BiologíaUniversidad Nacional Autónoma de México, 3er Circuito de Ciudad UniversitariaCoyoacánCiudad de México04510Mexico
| | - Susana Magallón
- Departamento de Botánica, Instituto de BiologíaUniversidad Nacional Autónoma de México, 3er Circuito de Ciudad UniversitariaCoyoacánCiudad de México04510Mexico
| | - Maria von Balthazar
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14ViennaA‐1030Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14ViennaA‐1030Austria
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW)Royal Botanic Gardens and Domain TrustSydneyNSW2000Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South Wales, Biological Sciences North (D26)SydneyNSW2052Australia
| | - Marion Chartier
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14ViennaA‐1030Austria
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5
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Huntsman SV, Leslie AB. The ontogeny of disparity in Cupressaceae seed cones. THE NEW PHYTOLOGIST 2023. [PMID: 38148572 DOI: 10.1111/nph.19482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/25/2023] [Indexed: 12/28/2023]
Abstract
Ontogenetic shape change has long been recognized to be important in generating patterns of morphological diversity and may be especially important in plant reproductive structures. We explore how seed cone disparity in Cupressaceae changes over ontogeny by comparing pollination-stage and mature cones. We sampled cones at pollen and seed release and measured cone scales using basic morphometric shape variables. We used multivariate statistical methods, particularly hypervolume overlap calculations, to measure morphospace occupation and disparity. Cone scales at both pollination and maturity exhibit substantial variability, although the disparity is greater at maturity. Mature cone scales are also more clustered in trait space, showing less overlap with other taxa than at pollination. These patterns reflect two growth strategies that generate closed cones over maturation, either through thin laminar scales or relatively thick, peltate scales, resulting in two distinct regions of morphospace occupation. Disparity patterns in Cupressaceae seed cones change over ontogeny, reflecting shifting functional demands that require specific patterns of cone scale growth. The evolution of Cupressaceae reproductive disparity therefore represents selection for trajectories of ontogenetic shape change, a phenomenon that should be widespread across seed plants.
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Affiliation(s)
- Stepfan V Huntsman
- Department of Earth and Planetary Sciences, Stanford University, 450 Jane Stanford Way, Building 320, Room 118, Stanford, CA, 94305, USA
| | - Andrew B Leslie
- Department of Earth and Planetary Sciences, Stanford University, 450 Jane Stanford Way, Building 320, Room 118, Stanford, CA, 94305, USA
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6
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Clark JW, Hetherington AJ, Morris JL, Pressel S, Duckett JG, Puttick MN, Schneider H, Kenrick P, Wellman CH, Donoghue PCJ. Evolution of phenotypic disparity in the plant kingdom. NATURE PLANTS 2023; 9:1618-1626. [PMID: 37666963 PMCID: PMC10581900 DOI: 10.1038/s41477-023-01513-x] [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: 04/15/2023] [Accepted: 08/07/2023] [Indexed: 09/06/2023]
Abstract
The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, the extinction of evolutionary intermediates and lineage-specific evolution. Phenotypic complexity correlates not with disparity but with ploidy history, reflecting the role of genome duplication in plant macroevolution. Overall, the plant kingdom exhibits a pattern of episodically increasing disparity throughout its evolutionary history that mirrors the evolutionary floras and reflects ecological expansion facilitated by reproductive innovations. This pattern also parallels that seen in the animal and fungal kingdoms, suggesting a general pattern for the evolution of multicellular bodyplans.
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Affiliation(s)
- James W Clark
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK.
| | - Alexander J Hetherington
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - Jennifer L Morris
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | | | - Mark N Puttick
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Harald Schneider
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
- The Natural History Museum, London, UK
- Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | | | | | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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7
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Deregnaucourt I, Bardin J, Villier L, Julliard R, Béthoux O. Disparification and extinction trade-offs shaped the evolution of Permian to Jurassic Odonata. iScience 2023; 26:107420. [PMID: 37583549 PMCID: PMC10424082 DOI: 10.1016/j.isci.2023.107420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/10/2023] [Accepted: 07/13/2023] [Indexed: 08/17/2023] Open
Abstract
Owing to their prevalence in nowadays terrestrial ecosystems, insects are a relevant group to assess the impact of mass extinctions on emerged land. However, limitations of the insect fossil record make it difficult to assess the impact of such events based on taxonomic diversity alone. Therefore, we documented trends in morphological diversity, i.e., disparity, using wings of Permian to Jurassic Odonata as model. Our results show a decreasing trend in disparity while species richness increased. Both the Permian-Triassic and Triassic-Jurassic transitions are revealed as important events, associated with strong morphospace restructuring due to selective extinction. In each case, a recovery was assured by the diversification of new forms compensating the loss of others. Early representatives of Odonata continuously evolved new shapes, a pattern contrasting with the classical assertion of a morphospace fulfilled early and followed by selective extinctions and specialization within it.
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Affiliation(s)
- Isabelle Deregnaucourt
- Centre de Recherche en Paléontologie - Paris (CR2P), Sorbonne Université, MNHN, CNRS, 57 rue Cuvier, CP38, F-75005 Paris, France
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Sorbonne Université, MNHN, CNRS, 43 rue Buffon, 75005 Paris, France
| | - Jérémie Bardin
- Centre de Recherche en Paléontologie - Paris (CR2P), Sorbonne Université, MNHN, CNRS, 57 rue Cuvier, CP38, F-75005 Paris, France
| | - Loïc Villier
- Centre de Recherche en Paléontologie - Paris (CR2P), Sorbonne Université, MNHN, CNRS, 57 rue Cuvier, CP38, F-75005 Paris, France
| | - Romain Julliard
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Sorbonne Université, MNHN, CNRS, 43 rue Buffon, 75005 Paris, France
| | - Olivier Béthoux
- Centre de Recherche en Paléontologie - Paris (CR2P), Sorbonne Université, MNHN, CNRS, 57 rue Cuvier, CP38, F-75005 Paris, France
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8
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Li Y, Brinkworth A, Green E, Oyston J, Wills M, Ruta M. Divergent vertebral formulae shape the evolution of axial complexity in mammals. Nat Ecol Evol 2023; 7:367-381. [PMID: 36878987 PMCID: PMC9998275 DOI: 10.1038/s41559-023-01982-5] [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: 01/31/2022] [Accepted: 01/03/2023] [Indexed: 03/08/2023]
Abstract
Complexity, defined as the number of parts and their degree of differentiation, is a poorly explored aspect of macroevolutionary dynamics. The maximum anatomical complexity of organisms has undoubtedly increased through evolutionary time. However, it is unclear whether this increase is a purely diffusive process or whether it is at least partly driven, occurring in parallel in most or many lineages and with increases in the minima as well as the means. Highly differentiated and serially repeated structures, such as vertebrae, are useful systems with which to investigate these patterns. We focus on the serial differentiation of the vertebral column in 1,136 extant mammal species, using two indices that quantify complexity as the numerical richness and proportional distribution of vertebrae across presacral regions and a third expressing the ratio between thoracic and lumbar vertebrae. We address three questions. First, we ask whether the distribution of complexity values in major mammal groups is similar or whether clades have specific signatures associated with their ecology. Second, we ask whether changes in complexity throughout the phylogeny are biased towards increases and whether there is evidence of driven trends. Third, we ask whether evolutionary shifts in complexity depart from a uniform Brownian motion model. Vertebral counts, but not complexity indices, differ significantly between major groups and exhibit greater within-group variation than recognized hitherto. We find strong evidence of a trend towards increasing complexity, where higher values propagate further increases in descendant lineages. Several increases are inferred to have coincided with major ecological or environmental shifts. We find support for multiple-rate models of evolution for all complexity metrics, suggesting that increases in complexity occurred in stepwise shifts, with evidence for widespread episodes of recent rapid divergence. Different subclades evolve more complex vertebral columns in different configurations and probably under different selective pressures and constraints, with widespread convergence on the same formulae. Further work should therefore focus on the ecological relevance of differences in complexity and a more detailed understanding of historical patterns.
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Affiliation(s)
- Yimeng Li
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.,Nanjing Institute of Geology and Palaeontology, CAS, Nanjing, China
| | - Andrew Brinkworth
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Emily Green
- Joseph Banks Laboratories, Department of Life Sciences, University of Lincoln, Lincoln, UK
| | - Jack Oyston
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Matthew Wills
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
| | - Marcello Ruta
- Joseph Banks Laboratories, Department of Life Sciences, University of Lincoln, Lincoln, UK.
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9
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Zuo (左胜) S, Guo (郭新异) X, Mandáková T, Edginton M, Al-Shehbaz IA, Lysak MA. Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution. PLANT PHYSIOLOGY 2022; 190:403-420. [PMID: 35670733 PMCID: PMC9434143 DOI: 10.1093/plphys/kiac268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/09/2022] [Indexed: 05/20/2023]
Abstract
Angiosperm genome evolution was marked by many clade-specific whole-genome duplication events. The Microlepidieae is one of the monophyletic clades in the mustard family (Brassicaceae) formed after an ancient allotetraploidization. Postpolyploid cladogenesis has resulted in the extant c. 17 genera and 60 species endemic to Australia and New Zealand (10 species). As postpolyploid genome diploidization is a trial-and-error process under natural selection, it may proceed with different intensity and be associated with speciation events. In Microlepidieae, different extents of homoeologous recombination between the two parental subgenomes generated clades marked by slow ("cold") versus fast ("hot") genome diploidization. To gain a deeper understanding of postpolyploid genome evolution in Microlepidieae, we analyzed phylogenetic relationships in this tribe using complete chloroplast sequences, entire 35S rDNA units, and abundant repetitive sequences. The four recovered intra-tribal clades mirror the varied diploidization of Microlepidieae genomes, suggesting that the intrinsic genomic features underlying the extent of diploidization are shared among genera and species within one clade. Nevertheless, even congeneric species may exert considerable morphological disparity (e.g. in fruit shape), whereas some species within different clades experience extensive morphological convergence despite the different pace of their genome diploidization. We showed that faster genome diploidization is positively associated with mean morphological disparity and evolution of chloroplast genes (plastid-nuclear genome coevolution). Higher speciation rates in perennials than in annual species were observed. Altogether, our results confirm the potential of Microlepidieae as a promising subject for the analysis of postpolyploid genome diploidization in Brassicaceae.
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Affiliation(s)
| | | | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Mark Edginton
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Mt Coot-tha Road, Toowong, QLD 4066, Australia
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10
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Bippus AC, Flores JR, Hyvönen J, Tomescu AMF. The role of paleontological data in bryophyte systematics. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4273-4290. [PMID: 35394022 DOI: 10.1093/jxb/erac137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
Systematics reconstructs tempo and mode in biological evolution by resolving the phylogenetic fabric of biodiversity. The staggering duration and complexity of evolution, coupled with loss of information (extinction), render exhaustive reconstruction of the evolutionary history of life unattainable. Instead, we sample its products-phenotypes and genotypes-to generate phylogenetic hypotheses, which we sequentially reassess and update against new data. Current consensus in evolutionary biology emphasizes fossil integration in total-evidence analyses, requiring in-depth understanding of fossils-age, phenotypes, and systematic affinities-and a detailed morphological framework uniting fossil and extant taxa. Bryophytes present a special case: deep evolutionary history but sparse fossil record and phenotypic diversity encompassing small dimensional scales. We review how these peculiarities shape fossil inclusion in bryophyte systematics. Paucity of the bryophyte fossil record, driven primarily by phenotypic (small plant size) and ecological constraints (patchy substrate-hugging populations), and incomplete exploration, results in many morphologically isolated, taxonomically ambiguous fossil taxa. Nevertheless, instances of exquisite preservation and pioneering studies demonstrate the feasibility of including bryophyte fossils in evolutionary inference. Further progress will arise from developing extensive morphological matrices for bryophytes, continued exploration of the fossil record, re-evaluation of previously described fossils, and training specialists in identification and characterization of bryophyte fossils, and in bryophyte morphology.
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Affiliation(s)
- Alexander C Bippus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Department of Biological Sciences, California State Polytechnic University-Humboldt, Arcata, CA, USA
| | - Jorge R Flores
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Viikki Plant Science Center & Organismal & Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University-Humboldt, Arcata, CA, USA
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11
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Abstract
AbstractEvolvability is best addressed from a multi-level, macroevolutionary perspective through a comparative approach that tests for among-clade differences in phenotypic diversification in response to an opportunity, such as encountered after a mass extinction, entering a new adaptive zone, or entering a new geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers to recognize intrinsic differences in evolvability, aiming for a macroevolutionary analog of a common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining differences among extant populations that can be hypothesized to generate large-scale, long-term contrasts in evolvability among clades; or observing large-scale differences among clade histories that can by hypothesized to reflect contrasts in genetics and development observed directly in extant populations. However, many comparative analyses can be informative on their own, as explored in this overview. Differences in clade-level evolvability can be visualized in diversity-disparity plots, which can quantify positive and negative departures of phenotypic productivity from stochastic expectations scaled to taxonomic diversification. Factors that evidently can promote evolvability include modularity—when selection aligns with modular structure or with morphological integration patterns; pronounced ontogenetic changes in morphology, as in allometry or multiphase life cycles; genome size; and a variety of evolutionary novelties, which can also be evaluated using macroevolutionary lags between the acquisition of a trait and phenotypic diversification, and dead-clade-walking patterns that may signal a loss of evolvability when extrinsic factors can be excluded. High speciation rates may indirectly foster phenotypic evolvability, and vice versa. Mechanisms are controversial, but clade evolvability may be higher in the Cambrian, and possibly early in the history of clades at other times; in the tropics; and, for marine organisms, in shallow-water disturbed habitats.
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12
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Jardine PE, Palazzesi L, Tellería MC, Barreda VD. Why does pollen morphology vary? Evolutionary dynamics and morphospace occupation in the largest angiosperm order (Asterales). THE NEW PHYTOLOGIST 2022; 234:1075-1087. [PMID: 35147224 DOI: 10.1111/nph.18024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Morphological diversity (disparity) is a key component of biodiversity and increasingly a focus of botanical research. Despite the wide range of morphologies represented by pollen grains, to date there are few studies focused on the controls on pollen disparity and morphospace occupation, and fewer still considering these parameters in a phylogenetic framework. Here, we analyse morphospace occupation, disparity and rates of morphological evolution in Asterales pollen, in a phylogenetic context. We use a dataset comprising 113 taxa from across the Asterales phylogeny, with pollen morphology described using 28 discrete characters. The Asterales pollen morphospace is phylogenetically structured around groups of related taxa, consistent with punctuated bursts of morphological evolution at key points in the Asterales phylogeny. There is no substantial difference in disparity among these groups of taxa, despite large differences in species richness and biogeographic range. There is also mixed evidence for whole-genome duplication as a driver of Asterales pollen morphological evolution. Our results highlight the importance of evolutionary history for structuring pollen morphospace. Our study is consistent with others that have shown a decoupling of biodiversity parameters, and reinforces the need to focus on disparity as a key botanical metric in its own right.
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Affiliation(s)
- Phillip E Jardine
- Institute of Geology and Palaeontology, University of Münster, Münster, 48149, Germany
| | - Luis Palazzesi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405DJR, Buenos Aires, Argentina
- Sección Paleopalinología, Museo Argentino de Ciencias Naturales 'Bernardino Rivadavia', C1405DJR, Buenos Aires, Argentina
| | - M Cristina Tellería
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405DJR, Buenos Aires, Argentina
- Laboratorio de Sistemática y Biología Evolutiva, Museo de La Plata, B1900FWA, La Plata, Argentina
| | - Viviana D Barreda
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405DJR, Buenos Aires, Argentina
- Sección Paleopalinología, Museo Argentino de Ciencias Naturales 'Bernardino Rivadavia', C1405DJR, Buenos Aires, Argentina
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13
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Multiple paths to morphological diversification during the origin of amniotes. Nat Ecol Evol 2021; 5:1243-1249. [PMID: 34312521 DOI: 10.1038/s41559-021-01516-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Early terrestrial vertebrates (amniotes) provide a classic example of diversification following adaptive zone invasion. The initial terrestrialization of vertebrates was closely followed by dietary diversification, as evidenced by a proliferation of craniomandibular and dental adaptations. However, morphological evolution of early amniotes has received limited study, in analyses with restricted taxonomic scope, leaving substantial questions about the dynamics of this important terrestrial radiation. We use novel analyses of discrete characters to quantify variation in evolutionary rates and constraints during diversification of the amniote feeding apparatus. We find evidence for an early burst, comprising high rates of anatomical change that decelerated through time, giving way to a background of saturated morphological evolution. Subsequent expansions of phenotypic diversity were not associated with increased evolutionary rates. Instead, variation in the mode of evolution became important, with groups representing independent origins of herbivory evolving distinctive, group-specific morphologies and thereby exploring novel character-state spaces. Our findings indicate the importance of plant-animal interactions in structuring the earliest radiation of amniotes and demonstrate the importance of variation in modes of phenotypic divergence during a major evolutionary radiation.
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14
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Singh S, Singh A. A prescient evolutionary model for genesis, duplication and differentiation of MIR160 homologs in Brassicaceae. Mol Genet Genomics 2021; 296:985-1003. [PMID: 34052911 DOI: 10.1007/s00438-021-01797-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/21/2021] [Indexed: 12/18/2022]
Abstract
MicroRNA160 is a class of nitrogen-starvation responsive genes which governs establishment of root system architecture by down-regulating AUXIN RESPONSE FACTOR genes (ARF10, ARF16 and ARF17) in plants. The high copy number of MIR160 variants discovered by us from land plants, especially polyploid crop Brassicas, posed questions regarding genesis, duplication, evolution and function. Absence of studies on impact of whole genome and segmental duplication on retention and evolution of MIR160 homologs in descendent plant lineages prompted us to undertake the current study. Herein, we describe ancestry and fate of MIR160 homologs in Brassicaceae in context of polyploidy driven genome re-organization, copy number and differentiation. Paralogy amongst Brassicaceae MIR160a, MIR160b and MIR160c was inferred using phylogenetic analysis of 468 MIR160 homologs from land plants. The evolutionarily distinct MIR160a was found to represent ancestral form and progenitor of MIR160b and MIR160c. Chronology of evolutionary events resulting in origin and diversification of genomic loci containing MIR160 homologs was delineated using derivatives of comparative synteny. A prescient model for causality of segmental duplications in establishment of paralogy in Brassicaceae MIR160, with whole genome duplication accentuating the copy number increase, is being posited in which post-segmental duplication events viz. differential gene fractionation, gene duplications and inversions are shown to drive divergence of chromosome segments. While mutations caused the diversification of MIR160a, MIR160b and MIR160c, duplicated segments containing these diversified genes suffered gene rearrangements via gene loss, duplications and inversions. Yet the topology of phylogenetic and phenetic trees were found congruent suggesting similar evolutionary trajectory. Over 80% of Brassicaceae genomes and subgenomes showed a preferential retention of single copy each of MIR160a, MIR160b and MIR160c suggesting functional relevance. Thus, our study provides a blue-print for reconstructing ancestry and phylogeny of MIRNA gene families at genomics level and analyzing the impact of polyploidy on organismal complexity. Such studies are critical for understanding the molecular basis of agronomic traits and deploying appropriate candidates for crop improvement.
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Affiliation(s)
- Swati Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, 110070, India.,Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Plot no. 32-34, Knowledge Park III, Greater Noida, Uttar Pradesh, 201310, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, 110070, India.
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15
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Perkovich C, Ward D. Herbivore-induced defenses are not under phylogenetic constraints in the genus Quercus (oak): Phylogenetic patterns of growth, defense, and storage. Ecol Evol 2021; 11:5187-5203. [PMID: 34026000 PMCID: PMC8131805 DOI: 10.1002/ece3.7409] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/05/2021] [Accepted: 02/12/2021] [Indexed: 11/30/2022] Open
Abstract
The evolution of plant defenses is often constrained by phylogeny. Many of the differences between competing plant defense theories hinge upon the differences in the location of meristem damage (apical versus auxiliary) and the amount of tissue removed. We analyzed the growth and defense responses of 12 Quercus (oak) species from a well-resolved molecular phylogeny using phylogenetically independent contrasts. Access to light is paramount for forest-dwelling tree species, such as many members of the genus Quercus. We therefore predicted a greater investment in defense when apical meristem tissue was removed. We also predicted a greater investment in defense when large amounts of tissue were removed and a greater investment in growth when less tissues were removed. We conducted five simulated herbivory treatments including a control with no damage and alterations of the location of meristem damage (apical versus auxiliary shoots) and intensity (25% versus 75% tissue removal). We measured growth, defense, and nutrient re-allocation traits in response to simulated herbivory. Phylomorphospace models were used to demonstrate the phylogenetic nature of trade-offs between characteristics of growth, chemical defenses, and nutrient re-allocation. We found that growth-defense trade-offs in control treatments were under phylogenetic constraints, but phylogenetic constraints and growth-defense trade-offs were not common in the simulated herbivory treatments. Growth-defense constraints exist within the Quercus genus, although there are adaptations to herbivory that vary among species.
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Affiliation(s)
| | - David Ward
- Department of Biological SciencesKent State UniversityKentOHUSA
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16
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Chartier M, von Balthazar M, Sontag S, Löfstrand S, Palme T, Jabbour F, Sauquet H, Schönenberger J. Global patterns and a latitudinal gradient of flower disparity: perspectives from the angiosperm order Ericales. THE NEW PHYTOLOGIST 2021; 230:821-831. [PMID: 33454991 PMCID: PMC8048689 DOI: 10.1111/nph.17195] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 12/13/2020] [Indexed: 05/29/2023]
Abstract
Morphological diversity (disparity) is an essential but often neglected aspect of biodiversity. Hence, it seems timely and promising to re-emphasize morphology in modern evolutionary studies. Disparity is a good proxy for the diversity of functions and interactions with the environment of a group of taxa. In addition, geographical and ecological patterns of disparity are crucial to understand organismal evolution and to guide biodiversity conservation efforts. Here, we analyse floral disparity across latitudinal intervals, growth forms, climate types, types of habitats, and regions for a large and representative sample of the angiosperm order Ericales. We find a latitudinal gradient of floral disparity and a decoupling of disparity from species richness. Other factors investigated are intercorrelated, and we find the highest disparity for tropical trees growing in African and South American forests. Explanations for the latitudinal gradient of floral disparity may involve the release of abiotic constraints and the increase of biotic interactions towards tropical latitudes, allowing tropical lineages to explore a broader area of the floral morphospace. Our study confirms the relevance of biodiversity parameters other than species richness and is consistent with the importance of species interactions in the tropics, in particular with respect to angiosperm flowers and their pollinators.
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Affiliation(s)
- Marion Chartier
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
| | - Maria von Balthazar
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
| | - Susanne Sontag
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
| | - Stefan Löfstrand
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
| | - Thomas Palme
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
| | - Florian Jabbour
- Institut de Systématique, Evolution, BiodiversitéMuséum National d'Histoire NaturelleCNRSSorbonne UniversitéEPHEUniversité des Antilles57 rue Cuvier, CP39Paris75005France
| | - Hervé Sauquet
- National Herbarium of New South WalesRoyal Botanic Gardens and Domain TrustMrs Macquaries RoadSydneyNSW2000Australia
- Evolution and Ecology Research CentreSchool of Biological, Earth and Environmental SciencesUniversity of New South WalesKensingtonNSW2033Australia
| | - Jürg Schönenberger
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
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17
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Puttick MN, Guillerme T, Wills MA. The complex effects of mass extinctions on morphological disparity. Evolution 2020; 74:2207-2220. [PMID: 32776526 DOI: 10.1111/evo.14078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 07/23/2020] [Accepted: 07/31/2020] [Indexed: 01/01/2023]
Abstract
Studies of biodiversity through deep time have been a staple for biologists and paleontologists for over 60 years. Investigations of species richness (diversity) revealed that at least five mass extinctions punctuated the last half billion years, each seeing the rapid demise of a large proportion of contemporary taxa. In contrast to diversity, the response of morphological diversity (disparity) to mass extinctions is unclear. Generally, diversity and disparity are decoupled, such that diversity may decline as morphological disparity increases, and vice versa. Here, we develop simulations to model disparity changes across mass extinctions using continuous traits and birth-death trees. We find no simple null for disparity change following a mass extinction but do observe general patterns. The range of trait values decreases following either random or trait-selective mass extinctions, whereas variance and the density of morphospace occupation only decline following trait-selective events. General trends may differentiate random and trait-selective mass extinctions, but methods struggle to identify trait selectivity. Long-term effects of mass extinction trait selectivity change support for phylogenetic comparative methods away from the simulated Brownian motion toward Ornstein-Uhlenbeck and Early Burst models. We find that morphological change over mass extinction is best studied by quantifying multiple aspects of morphospace occupation.
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Affiliation(s)
- Mark N Puttick
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom
| | - Thomas Guillerme
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Matthew A Wills
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom
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18
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Walden N, German DA, Wolf EM, Kiefer M, Rigault P, Huang XC, Kiefer C, Schmickl R, Franzke A, Neuffer B, Mummenhoff K, Koch MA. Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae. Nat Commun 2020. [PMID: 32732942 DOI: 10.1038/s41467-020-1760.5-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Angiosperms have become the dominant terrestrial plant group by diversifying for ~145 million years into a broad range of environments. During the course of evolution, numerous morphological innovations arose, often preceded by whole genome duplications (WGD). The mustard family (Brassicaceae), a successful angiosperm clade with ~4000 species, has been diversifying into many evolutionary lineages for more than 30 million years. Here we develop a species inventory, analyze morphological variation, and present a maternal, plastome-based genus-level phylogeny. We show that increased morphological disparity, despite an apparent absence of clade-specific morphological innovations, is found in tribes with WGDs or diversification rate shifts. Both are important processes in Brassicaceae, resulting in an overall high net diversification rate. Character states show frequent and independent gain and loss, and form varying combinations. Therefore, Brassicaceae pave the way to concepts of phylogenetic genome-wide association studies to analyze the evolution of morphological form and function.
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Affiliation(s)
- Nora Walden
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Dmitry A German
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
- South-Siberian Botanical Garden, Altai State University, Lenina Ave. 61, 656049, Barnaul, Russia
| | - Eva M Wolf
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Markus Kiefer
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Philippe Rigault
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
- GYDLE, 1135 Grande Allée Ouest, Québec, QC, G1S 1E7, Canada
| | - Xiao-Chen Huang
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
- School of Life Sciences, Nanchang University, 330031, Nanchang, China
| | - Christiane Kiefer
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czech Republic
| | - Andreas Franzke
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Barbara Neuffer
- Department of Biology, Systematic Botany, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Klaus Mummenhoff
- Department of Biology, Systematic Botany, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Marcus A Koch
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.
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19
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Walden N, German DA, Wolf EM, Kiefer M, Rigault P, Huang XC, Kiefer C, Schmickl R, Franzke A, Neuffer B, Mummenhoff K, Koch MA. Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae. Nat Commun 2020; 11:3795. [PMID: 32732942 PMCID: PMC7393125 DOI: 10.1038/s41467-020-17605-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 07/09/2020] [Indexed: 01/24/2023] Open
Abstract
Angiosperms have become the dominant terrestrial plant group by diversifying for ~145 million years into a broad range of environments. During the course of evolution, numerous morphological innovations arose, often preceded by whole genome duplications (WGD). The mustard family (Brassicaceae), a successful angiosperm clade with ~4000 species, has been diversifying into many evolutionary lineages for more than 30 million years. Here we develop a species inventory, analyze morphological variation, and present a maternal, plastome-based genus-level phylogeny. We show that increased morphological disparity, despite an apparent absence of clade-specific morphological innovations, is found in tribes with WGDs or diversification rate shifts. Both are important processes in Brassicaceae, resulting in an overall high net diversification rate. Character states show frequent and independent gain and loss, and form varying combinations. Therefore, Brassicaceae pave the way to concepts of phylogenetic genome-wide association studies to analyze the evolution of morphological form and function.
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Affiliation(s)
- Nora Walden
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Dmitry A German
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
- South-Siberian Botanical Garden, Altai State University, Lenina Ave. 61, 656049, Barnaul, Russia
| | - Eva M Wolf
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Markus Kiefer
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Philippe Rigault
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
- GYDLE, 1135 Grande Allée Ouest, Québec, QC, G1S 1E7, Canada
| | - Xiao-Chen Huang
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
- School of Life Sciences, Nanchang University, 330031, Nanchang, China
| | - Christiane Kiefer
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czech Republic
| | - Andreas Franzke
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Barbara Neuffer
- Department of Biology, Systematic Botany, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Klaus Mummenhoff
- Department of Biology, Systematic Botany, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Marcus A Koch
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.
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20
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Li Y, Ruta M, Wills MA. Craniodental and Postcranial Characters of Non-Avian Dinosauria Often Imply Different Trees. Syst Biol 2020; 69:638-659. [PMID: 31769837 PMCID: PMC7302058 DOI: 10.1093/sysbio/syz077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/08/2019] [Accepted: 11/18/2019] [Indexed: 12/28/2022] Open
Abstract
Despite the increasing importance of molecular sequence data, morphology still makes an important contribution to resolving the phylogeny of many groups, and is the only source of data for most fossils. Most systematists sample morphological characters as broadly as possible on the principle of total evidence. However, it is not uncommon for sampling to be focused on particular aspects of anatomy, either because characters therein are believed to be more informative, or because preservation biases restrict what is available. Empirically, the optimal trees from partitions of morphological data sets often represent significantly different hypotheses of relationships. Previous work on hard-part versus soft-part characters across animal phyla revealed significant differences in about a half of sampled studies. Similarly, studies of the craniodental versus postcranial characters of vertebrates revealed significantly different trees in about one-third of cases, with the highest rates observed in non-avian dinosaurs. We test whether this is a generality here with a much larger sample of 81 published data matrices across all major dinosaur groups. Using the incongruence length difference test and two variants of the incongruence relationship difference test, we found significant incongruence in about 50% of cases. Incongruence is not uniformly distributed across major dinosaur clades, being highest (63%) in Theropoda and lowest (25%) in Thyreophora. As in previous studies, our partition tests show some sensitivity to matrix dimensions and the amount and distribution of missing entries. Levels of homoplasy and retained synapomorphy are similar between partitions, such that incongruence must partly reflect differences in patterns of homoplasy between partitions, which may itself be a function of modularity and mosaic evolution. Finally, we implement new tests to determine which partition yields trees most similar to those from the entire matrix. Despite no bias across dinosaurs overall, there are striking differences between major groups. The craniodental characters of Ornithischia and the postcranial characters of Saurischia yield trees most similar to the "total evidence" trees derived from the entire matrix. Trees from these same character partitions also tend to be most stratigraphically congruent: a mutual consilience suggesting that those partitions yield more accurate trees. [Dinosauria; homoplasy; partition homogeneity.].
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Affiliation(s)
- Yimeng Li
- Department of Biology & Biochemistry, The Milner Centre for Evolution, The University of Bath, The Avenue, Claverton Down, Bath BA2 7AY, UK
| | - Marcello Ruta
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln LN6 7DL, UK
| | - Matthew A Wills
- Department of Biology & Biochemistry, The Milner Centre for Evolution, The University of Bath, The Avenue, Claverton Down, Bath BA2 7AY, UK
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21
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Brinkworth AR, Sansom R, Wills MA. Phylogenetic incongruence and homoplasy in the appendages and bodies of arthropods: why broad character sampling is best. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Notwithstanding the rapidly increasing sampling density of molecular sequence data, morphological characters still make an important contribution to our understanding of the evolutionary relationships of arthropod groups. In many clades, characters relating to the number and morphological specialization of appendages are ascribed particular phylogenetic significance and may be preferentially sampled. However, previous studies have shown that partitions of morphological character matrices often imply significantly different phylogenies. Here, we ask whether a similar incongruence is observed in the appendage and non-appendage characters of arthropods. We apply tree length (incongruence length difference, ILD) and tree distance (incongruence relationship difference, IRD) tests to these partitions in an empirical sample of 53 published neontological datasets for arthropods. We find significant incongruence about one time in five: more often than expected, but markedly less often than in previous partition studies. We also find similar levels of homoplasy in limb and non-limb characters, both in terms of internal consistency and consistency relative to molecular trees. Taken together, these findings imply that sampled limb and non-limb characters are of similar phylogenetic utility and quality, and that a total evidence approach to their analysis is preferable.
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Affiliation(s)
- Andrew R Brinkworth
- The Milner Centre for Evolution, Department of Biology and Biochemistry, The University of Bath, Claverton Down, Bath, UK
| | - Robert Sansom
- School of Earth and Environmental Science, The University of Manchester, Manchester, UK
| | - Matthew A Wills
- The Milner Centre for Evolution, Department of Biology and Biochemistry, The University of Bath, Claverton Down, Bath, UK
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22
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Signatures of echolocation and dietary ecology in the adaptive evolution of skull shape in bats. Nat Commun 2019; 10:2036. [PMID: 31048713 PMCID: PMC6497661 DOI: 10.1038/s41467-019-09951-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 04/10/2019] [Indexed: 11/20/2022] Open
Abstract
Morphological diversity may arise rapidly as a result of adaptation to novel ecological opportunities, but early bursts of trait evolution are rarely observed. Rather, models of discrete shifts between adaptive zones may better explain macroevolutionary dynamics across radiations. To investigate which of these processes underlie exceptional levels of morphological diversity during ecological diversification, we use modern phylogenetic tools and 3D geometric morphometric datasets to examine adaptive zone shifts in bat skull shape. Here we report that, while disparity was established early, bat skull evolution is best described by multiple adaptive zone shifts. Shifts are partially decoupled between the cranium and mandible, with cranial evolution more strongly driven by echolocation than diet. Phyllostomidae, a trophic adaptive radiation, exhibits more adaptive zone shifts than all other families combined. This pattern was potentially driven by ecological opportunity and facilitated by a shift to intermediate cranial shapes compared to oral-emitters and other nasal emitters. What drives changes in morphological diversity? Here, Arbour et al. analyse skull 3D shape evolution across the bat radiation using µCT scan data, finding two phases of skull shape diversification, early adaptive shifts related to echolocation, and more recent shifts related to diet transitions.
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23
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Developmental Bias and Evolution: A Regulatory Network Perspective. Genetics 2018; 209:949-966. [PMID: 30049818 DOI: 10.1534/genetics.118.300995] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/19/2018] [Indexed: 01/12/2023] Open
Abstract
Phenotypic variation is generated by the processes of development, with some variants arising more readily than others-a phenomenon known as "developmental bias." Developmental bias and natural selection have often been portrayed as alternative explanations, but this is a false dichotomy: developmental bias can evolve through natural selection, and bias and selection jointly influence phenotypic evolution. Here, we briefly review the evidence for developmental bias and illustrate how it is studied empirically. We describe recent theory on regulatory networks that explains why the influence of genetic and environmental perturbation on phenotypes is typically not uniform, and may even be biased toward adaptive phenotypic variation. We show how bias produced by developmental processes constitutes an evolving property able to impose direction on adaptive evolution and influence patterns of taxonomic and phenotypic diversity. Taking these considerations together, we argue that it is not sufficient to accommodate developmental bias into evolutionary theory merely as a constraint on evolutionary adaptation. The influence of natural selection in shaping developmental bias, and conversely, the influence of developmental bias in shaping subsequent opportunities for adaptation, requires mechanistic models of development to be expanded and incorporated into evolutionary theory. A regulatory network perspective on phenotypic evolution thus helps to integrate the generation of phenotypic variation with natural selection, leaving evolutionary biology better placed to explain how organisms adapt and diversify.
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24
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Clark JW, Donoghue PCJ. Whole-Genome Duplication and Plant Macroevolution. TRENDS IN PLANT SCIENCE 2018; 23:933-945. [PMID: 30122372 DOI: 10.1016/j.tplants.2018.07.006] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/29/2018] [Accepted: 07/12/2018] [Indexed: 05/18/2023]
Abstract
Whole-genome duplication (WGD) is characteristic of almost all fundamental lineages of land plants. Unfortunately, the timings of WGD events are loosely constrained and hypotheses of evolutionary consequence are poorly formulated, making them difficult to test. Using examples from across the plant kingdom, we show that estimates of timing can be improved through the application of molecular clock methodology to multigene datasets. Further, we show that phenotypic change can be quantified in morphospaces and that relative phenotypic disparity can be compared in the light of WGD. Together, these approaches facilitate tests of hypotheses on the role of WGD in plant evolution, underscoring the potential of plants as a model system for investigating the role WGD in macroevolution.
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Affiliation(s)
- James W Clark
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TH, UK.
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TH, UK.
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25
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Flores JR, Catalano SA, Muñoz J, Suárez GM. Combined phylogenetic analysis of the subclass Marchantiidae (Marchantiophyta): towards a robustly diagnosed classification. Cladistics 2018; 34:517-541. [PMID: 34706484 DOI: 10.1111/cla.12225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 11/26/2022] Open
Abstract
The most extensive combined phylogenetic analyses of the subclass Marchantiidae yet undertaken was conducted on the basis of morphological and molecular data. The morphological data comprised 126 characters and 56 species. Taxonomic sampling included 35 ingroup species with all genera and orders of Marchantiidae sampled, and 21 outgroup species with two genera of Blasiidae (Marchantiopsida), 15 species of Jungermanniopsida (the three subclasses represented) and the three genera of Haplomitriopsida. Takakia ceratophylla (Bryophyta) was employed to root the trees. Character sampling involved 92 gametophytic and 34 sporophytic traits, supplemented with ten continuous characters. Molecular data included 11 molecular markers: one nuclear ribosomal (26S), three mitochondrial genes (nad1, nad5, rps3) and seven chloroplast regions (atpB, psbT-psbH, rbcL, ITS, rpoC1, rps4, psbA). Searches were performed under extended implied weighting, weighting the character blocks against the average homoplasy. Clade stability was assessed across three additional weighting schemes (implied weighting corrected for missing entries, standard implied weighting and equal weighting) in three datasets (molecular, morphological and combined). The contribution from different biological phases regarding node recovery and diagnosis was evaluated. Our results agree with many of the previous studies but cast doubt on some relationships, mainly at the family and interfamily level. The combined analyses underlined the fact that, by combining data, taxonomic enhancements could be achieved regarding taxon delimitation and quality of diagnosis. Support values for many clades of previous molecular studies were improved by the addition of morphological data. The long-held assumption that morphology may render spurious or low-quality results in this taxonomic group is challenged. The morphological trends previously proposed are re-evaluated in light of the new phylogenetic scheme.
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Affiliation(s)
- Jorge R Flores
- Unidad Ejecutora Lillo (UEL; FML-CONICET), Miguel Lillo 251, S.M. de Tucumán, 4000, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, S.M. de Tucumán, 4000, Argentina
| | - Santiago A Catalano
- Unidad Ejecutora Lillo (UEL; FML-CONICET), Miguel Lillo 251, S.M. de Tucumán, 4000, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, S.M. de Tucumán, 4000, Argentina
| | - Jesus Muñoz
- Real Jardín Botánico (RJB - CSIC), Plaza de Murillo 2, Madrid, 28014, Spain
| | - Guillermo M Suárez
- Unidad Ejecutora Lillo (UEL; FML-CONICET), Miguel Lillo 251, S.M. de Tucumán, 4000, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, S.M. de Tucumán, 4000, Argentina
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Chartier M, Löfstrand S, von Balthazar M, Gerber S, Jabbour F, Sauquet H, Schönenberger J. How (much) do flowers vary? Unbalanced disparity among flower functional modules and a mosaic pattern of morphospace occupation in the order Ericales. Proc Biol Sci 2017; 284:20170066. [PMID: 28381623 PMCID: PMC5394665 DOI: 10.1098/rspb.2017.0066] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/03/2017] [Indexed: 12/21/2022] Open
Abstract
The staggering diversity of angiosperms and their flowers has fascinated scientists for centuries. However, the quantitative distribution of floral morphological diversity (disparity) among lineages and the relative contribution of functional modules (perianth, androecium and gynoecium) to total floral disparity have rarely been addressed. Focusing on a major angiosperm order (Ericales), we compiled a dataset of 37 floral traits scored for 381 extant species and nine fossils. We conducted morphospace analyses to explore phylogenetic, temporal and functional patterns of disparity. We found that the floral morphospace is organized as a continuous cloud in which most clades occupy distinct regions in a mosaic pattern, that disparity increases with clade size rather than age, and that fossils fall in a narrow portion of the space. Surprisingly, our study also revealed that among functional modules, it is the androecium that contributes most to total floral disparity in Ericales. We discuss our findings in the light of clade history, selective regimes as well as developmental and functional constraints acting on the evolution of the flower and thereby demonstrate that quantitative analyses such as the ones used here are a powerful tool to gain novel insights into the evolution and diversity of flowers.
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Affiliation(s)
- Marion Chartier
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Stefan Löfstrand
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Maria von Balthazar
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Sylvain Gerber
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, 57 rue Cuvier, CP 39, 75005 Paris, France
| | - Florian Jabbour
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, 57 rue Cuvier, CP 39, 75005 Paris, France
| | - Hervé Sauquet
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS UMR 8079, 91405 Orsay, France
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
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Fernández-Mazuecos M, Glover BJ. The evo-devo of plant speciation. Nat Ecol Evol 2017; 1:110. [DOI: 10.1038/s41559-017-0110] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/07/2017] [Indexed: 11/09/2022]
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Mander L. A combinatorial approach to angiosperm pollen morphology. Proc Biol Sci 2016; 283:20162033. [PMID: 27881756 PMCID: PMC5136598 DOI: 10.1098/rspb.2016.2033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/28/2016] [Indexed: 11/12/2022] Open
Abstract
Angiosperms (flowering plants) are strikingly diverse. This is clearly expressed in the morphology of their pollen grains, which are characterized by enormous variety in their shape and patterning. In this paper, I approach angiosperm pollen morphology from the perspective of enumerative combinatorics. This involves generating angiosperm pollen morphotypes by algorithmically combining character states and enumerating the results of these combinations. I use this approach to generate 3 643 200 pollen morphotypes, which I visualize using a parallel-coordinates plot. This represents a raw morphospace. To compare real-world and theoretical morphologies, I map the pollen of 1008 species of Neotropical angiosperms growing on Barro Colorado Island (BCI), Panama, onto this raw morphospace. This highlights that, in addition to their well-documented taxonomic diversity, Neotropical rainforests also represent an enormous reservoir of morphological diversity. Angiosperm pollen morphospace at BCI has been filled mostly by pollen morphotypes that are unique to single plant species. Repetition of pollen morphotypes among higher taxa at BCI reflects both constraint and convergence. This combinatorial approach to morphology addresses the complexity that results from large numbers of discrete character combinations and could be employed in any situation where organismal form can be captured by discrete morphological characters.
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Affiliation(s)
- Luke Mander
- Department of Environment, Earth and Ecosystems, The Open University, Milton Keynes MK7 6AA, UK
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Lamsdell JC, Selden PA. From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis. Evolution 2016; 71:95-110. [PMID: 27783385 DOI: 10.1111/evo.13106] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 10/12/2016] [Accepted: 10/21/2016] [Indexed: 01/03/2023]
Abstract
Mass extinctions have altered the trajectory of evolution a number of times over the Phanerozoic. During these periods of biotic upheaval a different selective regime appears to operate, although it is still unclear whether consistent survivorship rules apply across different extinction events. We compare variations in diversity and disparity across the evolutionary history of a major Paleozoic arthropod group, the Eurypterida. Using these data, we explore the group's transition from a successful, dynamic clade to a stagnant persistent lineage, pinpointing the Devonian as the period during which this evolutionary regime shift occurred. The late Devonian biotic crisis is potentially unique among the "Big Five" mass extinctions in exhibiting a drop in speciation rates rather than an increase in extinction. Our study reveals eurypterids show depressed speciation rates throughout the Devonian but no abnormal peaks in extinction. Loss of morphospace occupation is random across all Paleozoic extinction events; however, differential origination during the Devonian results in a migration and subsequent stagnation of occupied morphospace. This shift appears linked to an ecological transition from euryhaline taxa to freshwater species with low morphological diversity alongside a decrease in endemism. These results demonstrate the importance of the Devonian biotic crisis in reshaping Paleozoic ecosystems.
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Affiliation(s)
- James C Lamsdell
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024.,Department of Geology and Geography, West Virginia University, 98 Beechurst Avenue, Brooks Hall, Morgantown, West Virginia, 26506
| | - Paul A Selden
- Paleontological Institute and Department of Geology, University of Kansas, 1475 Jayhawk Boulevard, Lawrence, Kansas, 66045.,Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
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Melzer R, Theißen G. The significance of developmental robustness for species diversity. ANNALS OF BOTANY 2016; 117:725-32. [PMID: 26994100 PMCID: PMC4845805 DOI: 10.1093/aob/mcw018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/05/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND The origin of new species and of new forms is one of the fundamental characteristics of evolution. However, the mechanisms that govern the diversity and disparity of lineages remain poorly understood. Particularly unclear are the reasons why some taxa are vastly more species-rich than others and the manner in which species diversity and morphological disparity are interrelated. SCOPE AND CONCLUSIONS Evolutionary innovations and ecological opportunities are usually cited as among the major factors promoting the evolution of species diversity. In many cases it is likely that these factors are positively reinforcing, with evolutionary innovations creating ecological opportunities that in turn foster the origin of new innovations. However, we propose that a third factor, developmental robustness, is very often essential for this reinforcement to be effective. Evolutionary innovations need to be stably and robustly integrated into the developmental genetic programme of an organism to be a suitable substrate for selection to 'explore' ecological opportunities and morphological 'design' space (morphospace). In particular, we propose that developmental robustness of the bauplan is often a prerequisite for the exploration of morphospace and to enable the evolution of further novelties built upon this bauplan Thus, while robustness may reduce the morphological disparity at one level, it may be the basis for increased morphological disparity and for evolutionary innovations at another level, thus fostering species diversity.
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Affiliation(s)
- Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland and
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
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Theißen G, Melzer R. Robust views on plasticity and biodiversity. ANNALS OF BOTANY 2016; 117:693-697. [PMCID: PMC4845811 DOI: 10.1093/aob/mcw066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 02/28/2016] [Accepted: 03/03/2016] [Indexed: 06/09/2023]
Abstract
Background How the diversity of life on our planet originated is not completely understood and many questions are still open. Especially, the role of developmental robustness in evolution is an often neglected topic. Scope Considering diverse groups of plants and animals, and employing different concepts and approaches, the authors of articles in this Special Issue try to understand better the impact of developmental robustness, phenotypic plasticity and variance on species diversity, evolution and morphological disparity. Conclusions Several lines of theoretical considerations as well as case studies show that developmental robustness supports rather than prevents the evolution of species diversity, at least under certain circumstances. Among the possible mechanisms is the scenario that developmental robustness facilitates the synorganization of body parts, which may enable the origin of complex novelties; this then may set the ground for species radiation.
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Affiliation(s)
- Günter Theißen
- Friedrich-Schiller-University Jena, Department of Genetics, Philosophenweg 12, D-07743 Jena, Germany
| | - Rainer Melzer
- University College Dublin, School of Biology and Environmental Science, Belfield, Dublin 4, Ireland
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