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Phylogenomics and diversification drivers of the Eastern Asian – Eastern North American disjunct Podophylloideae. Mol Phylogenet Evol 2022; 169:107427. [DOI: 10.1016/j.ympev.2022.107427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/02/2021] [Accepted: 12/25/2021] [Indexed: 11/17/2022]
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Loureiro LO, Engstrom MD, Lim BK. Does evolution of echolocation calls and morphology in Molossus result from convergence or stasis? PLoS One 2020; 15:e0238261. [PMID: 32970683 PMCID: PMC7514107 DOI: 10.1371/journal.pone.0238261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022] Open
Abstract
Although many processes of diversification have been described to explain variation of morphological traits within clades that have obvious differentiation among taxa, not much is known about these patterns in complexes of cryptic species. Molossus is a genus of bats that is mainly Neotropical, occurring from the southeastern United States to southern Argentina, including the Caribbean islands. Molossus comprises some groups of species that are morphologically similar but phylogenetically divergent, and other groups of species that are genetically similar but morphologically distinct. This contrast allows investigation of unequal trait diversification and the evolution of morphological and behavioural characters. In this study, we assessed the role of phylogenetic history in a genus of bat with three cryptic species complexes, and evaluated if morphology and behavior are evolving concertedly. The Genotype by Sequence genomic approach was used to build a species-level phylogenetic tree for Molossus and to estimate the ancestral states of morphological and echolocation call characters. We measured the correlation of phylogenetic distances to morphological and echolocation distances, and tested the relationship between morphology and behavior when the effect of phylogeny is removed. Morphology evolved via a mosaic of convergence and stasis, whereas call design was influenced exclusively through local adaptation and convergent evolution. Furthermore, the frequency of echolocation calls is negatively correlated with the size of the bat, but other characters do not seem to be evolving in concert. We hypothesize that slight variation in both morphology and behaviour among species of the genus might result from niche specialization, and that traits evolve to avoid competition for resources in similar environments.
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Affiliation(s)
- Livia O. Loureiro
- Hospital for Sick Children SickKids Learning Institute, The Centre for Applied Genomics, Toronto, Ontario, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Mark D. Engstrom
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Burton K. Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
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Loiseau O, Weigand A, Noben S, Rolland J, Silvestro D, Kessler M, Lehnert M, Salamin N. Slowly but surely: gradual diversification and phenotypic evolution in the hyper-diverse tree fern family Cyatheaceae. ANNALS OF BOTANY 2020; 125:93-103. [PMID: 31562744 PMCID: PMC6948215 DOI: 10.1093/aob/mcz145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 09/26/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS The tremendously unbalanced distribution of species richness across clades in the tree of life is often interpreted as the result of variation in the rates of diversification, which may themselves respond to trait evolution. Even though this is likely a widespread pattern, not all diverse groups of organisms exhibit heterogeneity in their dynamics of diversification. Testing and characterizing the processes driving the evolution of clades with steady rates of diversification over long periods of time are of importance in order to have a full understanding of the build-up of biodiversity through time. METHODS We studied the macroevolutionary history of the species-rich tree fern family Cyatheaceae and inferred a time-calibrated phylogeny of the family including extinct and extant species using the recently developed fossilized birth-death method. We tested whether the high diversity of Cyatheaceae is the result of episodes of rapid diversification associated with phenotypic and ecological differentiation or driven by stable but low rates of diversification. We compared the rates of diversification across clades, modelled the evolution of body size and climatic preferences and tested for trait-dependent diversification. KEY RESULTS This ancient group diversified at a low and constant rate during its long evolutionary history. Morphological and climatic niche evolution were found to be overall highly conserved, although we detected several shifts in the rates of evolution of climatic preferences, linked to changes in elevation. The diversification of the family occurred gradually, within limited phenotypic and ecological boundaries, and yet resulted in a remarkable species richness. CONCLUSIONS Our study indicates that Cyatheaceae is a diverse clade which slowly accumulated morphological, ecological and taxonomic diversity over a long evolutionary period and provides a compelling example of the tropics as a museum of biodiversity.
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Affiliation(s)
- Oriane Loiseau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Weigand
- Institute for Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
| | - Sarah Noben
- Institute for Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Zoology, University of British Columbia, #4200-6270 University Blvd, Vancouver, B.C., Canada
| | - Daniele Silvestro
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Global Gothenburg Biodiversity Center, Gothenburg, Sweden
| | - Michael Kessler
- Institute for Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
| | - Marcus Lehnert
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
- Department of Geobotany and Botanical Garden, Herbarium, Martin-Luther-University Halle-Wittenberg, Neuwerk 21, 06108 Halle, Germany
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
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Dong S, Xiao Y, Kong H, Feng C, Harris A, Yan Y, Kang M. Nuclear loci developed from multiple transcriptomes yield high resolution in phylogeny of scaly tree ferns (Cyatheaceae) from China and Vietnam. Mol Phylogenet Evol 2019; 139:106567. [DOI: 10.1016/j.ympev.2019.106567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/10/2019] [Accepted: 07/18/2019] [Indexed: 11/27/2022]
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Halliday TJD, dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z, Goswami A. Rapid morphological evolution in placental mammals post-dates the origin of the crown group. Proc Biol Sci 2019; 286:20182418. [PMID: 30836875 PMCID: PMC6458320 DOI: 10.1098/rspb.2018.2418] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/12/2019] [Indexed: 12/28/2022] Open
Abstract
Resolving the timing and pattern of early placental mammal evolution has been confounded by conflict among divergence date estimates from interpretation of the fossil record and from molecular-clock dating studies. Despite both fossil occurrences and molecular sequences favouring a Cretaceous origin for Placentalia, no unambiguous Cretaceous placental mammal has been discovered. Investigating the differing patterns of evolution in morphological and molecular data reveals a possible explanation for this conflict. Here, we quantified the relationship between morphological and molecular rates of evolution. We show that, independent of divergence dates, morphological rates of evolution were slow relative to molecular evolution during the initial divergence of Placentalia, but substantially increased during the origination of the extant orders. The rapid radiation of placentals into a highly morphologically disparate Cenozoic fauna is thus not associated with the origin of Placentalia, but post-dates superordinal origins. These findings predict that early members of major placental groups may not be easily distinguishable from one another or from stem eutherians on the basis of skeleto-dental morphology. This result supports a Late Cretaceous origin of crown placentals with an ordinal-level adaptive radiation in the early Paleocene, with the high relative rate permitting rapid anatomical change without requiring unreasonably fast molecular evolutionary rates. The lack of definitive Cretaceous placental mammals may be a result of morphological similarity among stem and early crown eutherians, providing an avenue for reconciling the fossil record with molecular divergence estimates for Placentalia.
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Affiliation(s)
- Thomas J. D. Halliday
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
- School of Geography, Earth, and Environmental Science, University of Birmingham, Edgbaston B15 2TT, UK
| | - Mario dos Reis
- School of Biological and Chemical Sciences, Queen Mary University London, Mile End Road, London E1 4NS, UK
| | - Asif U. Tamuri
- Research IT Services, University College London, Gower Street, London WC1E 6BT, UK
- European Molecular Biology Laboratory, European Bioinformatics, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Henry Ferguson-Gow
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ziheng Yang
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Anjali Goswami
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, UK
- Faculty of Life Sciences, Natural History Museum, Cromwell Road, London SW9 5DJ, UK
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Culumber ZW, Tobler M. Correlated evolution of thermal niches and functional physiology in tropical freshwater fishes. J Evol Biol 2018; 31:722-734. [DOI: 10.1111/jeb.13260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/13/2018] [Accepted: 02/23/2018] [Indexed: 11/30/2022]
Affiliation(s)
| | - Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
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Testo WL, Sundue MA. Are rates of species diversification and body size evolution coupled in the ferns? AMERICAN JOURNAL OF BOTANY 2018; 105:525-535. [PMID: 29637539 DOI: 10.1002/ajb2.1044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/09/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Understanding the relationship between phenotypic evolution and lineage diversification is a central goal of evolutionary biology. To extend our understanding of the role morphological evolution plays in the diversification of plants, we examined the relationship between leaf size evolution and lineage diversification across ferns. METHODS We tested for an association between body size evolution and lineage diversification using a comparative phylogenetic approach that combined a time-calibrated phylogeny and leaf size data set for 2654 fern species. Rates of leaf size change and lineage diversification were estimated using BAMM, and rate correlations were performed for rates obtained for all families and individual species. Rates and patterns of rate-rate correlation were also analyzed separately for terrestrial and epiphytic taxa. KEY RESULTS We find no significant correlation between rates of leaf area change and lineage diversification, nor was there a difference in this pattern when growth habit is considered. Our results are consistent with the findings of an earlier study that reported decoupled rates of body size evolution and diversification in the Polypodiaceae, but conflict with a recent study that reported a positive correlation between body size evolution and lineage diversification rates in the tree fern family Cyatheaceae. CONCLUSIONS Our findings indicate that lineage diversification in ferns is largely decoupled from shifts in body size, in contrast to several other groups of organisms. Speciation in ferns appears to be primarily driven by hybridization and isolation along elevational gradients, rather than adaptive radiations featuring prominent morphological restructuring. The exceptional diversity of leaf morphologies in ferns appears to reflect a combination of ecophysiological constraints and adaptations that are not key innovations.
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Affiliation(s)
- Weston L Testo
- The Pringle Herbarium, University of Vermont, 27 Colchester Drive, Burlington, VT, 05405, USA
| | - Michael A Sundue
- The Pringle Herbarium, University of Vermont, 27 Colchester Drive, Burlington, VT, 05405, USA
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Rates of morphological evolution, asymmetry and morphological integration of shell shape in scallops. BMC Evol Biol 2017; 17:248. [PMID: 29216839 PMCID: PMC5721563 DOI: 10.1186/s12862-017-1098-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022] Open
Abstract
Background Rates of morphological evolution vary across different taxonomic groups, and this has been proposed as one of the main drivers for the great diversity of organisms on Earth. Of the extrinsic factors pertaining to this variation, ecological hypotheses feature prominently in observed differences in phenotypic evolutionary rates across lineages. But complex organisms are inherently modular, comprising distinct body parts that can be differentially affected by external selective pressures. Thus, the evolution of trait covariation and integration in modular systems may also play a prominent role in shaping patterns of phenotypic diversity. Here we investigate the role ecological diversity plays in morphological integration, and the tempo of shell shape evolution and of directional asymmetry in bivalved scallops. Results Overall, the shape of both valves and the magnitude of asymmetry of the whole shell (difference in shape between valves) are traits that are evolving fast in ecomorphs under strong selective pressures (gliders, recessers and nestling), compared to low rates observed in other ecomorphs (byssal-attaching, free-living and cementing). Given that different parts of an organism can be under different selective pressures from the environment, we also examined the degree of evolutionary integration between the valves as it relates to ecological shifts. We find that evolutionary morphological integration is consistent and surprisingly high across species, indicating that while the left and right valves of a scallop shell are diversifying in accordance with ecomorphology, they are doing so in a concerted fashion. Conclusions Our study on scallops adds another strong piece of evidence that ecological shifts play an important role in the tempo and mode of morphological evolution. Strong selective pressures from the environment, inferred from the repeated evolution of distinct ecomorphs, have influenced the rate of morphological evolution in valve shape and the magnitude of asymmetry between valves. Our observation that morphological integration of the valves making up the shell is consistently strong suggests tight developmental pathways are responsible for the concerted evolution of these structures while environmental pressures are driving whole shell shape. Finally, our study shows that directional asymmetry in shell shape among species is an important aspect of scallop macroevolution. Electronic supplementary material The online version of this article (10.1186/s12862-017-1098-5) contains supplementary material, which is available to authorized users.
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Mason NA, Burns KJ, Tobias JA, Claramunt S, Seddon N, Derryberry EP. Song evolution, speciation, and vocal learning in passerine birds. Evolution 2017; 71:786-796. [DOI: 10.1111/evo.13159] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 12/17/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York 14853
- Fuller Evolutionary Biology Program Cornell Lab of Ornithology Ithaca New York 14850
| | - Kevin J. Burns
- Department of Biology San Diego State University San Diego California 92182
| | - Joseph A. Tobias
- Department of Life Sciences Imperial College London Silwood Park Ascot SL5 7PY United Kingdom
| | - Santiago Claramunt
- Department of Ornithology American Museum of Natural History New York New York 10024
| | - Nathalie Seddon
- Edward Grey Institute, Department of Zoology University of Oxford Oxford OX1 3PS United Kingdom
| | - Elizabeth P. Derryberry
- Department of Ecology and Evolutionary Biology Tulane University New Orleans Louisiana 70118
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Sosa V, Ornelas JF, Ramírez-Barahona S, Gándara E. Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica. PeerJ 2016; 4:e2696. [PMID: 27896030 PMCID: PMC5119233 DOI: 10.7717/peerj.2696] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 10/18/2016] [Indexed: 12/27/2022] Open
Abstract
Background Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Methods Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Results Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant variables or elevation. For elevational shifts, we found repeated change from low to high elevations. Conclusions Our data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recentrly from their ancestors.
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Affiliation(s)
- Victoria Sosa
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Etelvina Gándara
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico.,Instituto de Ciencias/Herbario y Jardín Botánico, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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