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Stayton CT. Performance Surface Analysis Identifies Consistent Functional Patterns across 10 Morphologically Divergent Terrestrial Turtle Lineages. Integr Comp Biol 2019; 59:346-357. [DOI: 10.1093/icb/icz072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abstract
Newly-developed methods for utilizing performance surfaces—multivariate representations of the relationship between phenotype and functional performance—allow researchers to test hypotheses about adaptive landscapes and evolutionary diversification with explicit attention to functional factors. Here, information from performance surfaces of three turtle shell functions—shell strength, hydrodynamics, and self-righting—is used to test the hypothesis that turtle lineages transitioning from aquatic to terrestrial habitats show patterns of shell shape evolution consistent with decreased importance of hydrodynamic performance. Turtle shells are excellent model systems for evolutionary functional analysis. The evolution of terrestriality is an interesting test case for the efficacy of these methods because terrestrial turtles do not show a straightforward pattern of morphological convergence in shell shape: many terrestrial lineages show increased shell height, typically assumed to decrease hydrodynamic performance, but there are also several lineages where the evolution of terrestriality was accompanied by shell flattening. Performance surface analyses allow exploration of these complex patterns and explicit quantitative analysis of the functional implications of changes in shell shape. Ten lineages were examined. Nearly all terrestrial lineages, including those which experienced decreased shell height, are associated with morphological changes consistent with a decrease in the importance of shell hydrodynamics. This implies a common selective pattern across lineages showing divergent morphological patterns. Performance studies such as these hold great potential for integrating adaptive and performance data in macroevolutionary studies.
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Affiliation(s)
- C Tristan Stayton
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA
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102
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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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103
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Dupin J, Smith SD. Integrating historical biogeography and environmental niche evolution to understand the geographic distribution of Datureae. AMERICAN JOURNAL OF BOTANY 2019; 106:667-678. [PMID: 31059141 DOI: 10.1002/ajb2.1281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
PREMISE The distributions of plant clades are shaped by abiotic and biotic factors as well as historical aspects such as center of origin. Dispersals between distant areas may lead to niche evolution when lineages are established in new environments. Alternatively, dispersing lineages may exhibit niche conservatism, moving between areas with similar environmental conditions. Here we test these contrasting hypotheses in the Datureae clade (Solanaceae). METHODS We used maximum likelihood methods to estimate the ancestral range of Datureae along with the history of biogeographic events. We then characterized the niche of each taxon using climatic and soil variables and tested for shifts in environmental niche optima. Finally, we examined how these shifts relate to the niche breadth of taxa and clades within Datureae and the degree of overlap between them. RESULTS Datureae originated in the Andes and subsequently expanded its range to North America and non-Andean regions of South America. The ancestral niche, and that of most Datura and Trompettia species, is dry, while Brugmansia species likely shifted toward a more mesic environment. Nonetheless, most Datureae present moderate to high overlap in niche breadth today. CONCLUSIONS The expansion of Datureae into North America was associated with niche conservatism, with dispersal into similarly dry areas as occupied by the ancestral lineage. Subsequent niche evolution, including the apparent shift to a mesic niche in Brugmansia, diversified the range of habitats occupied by species in the tribe Datureae but also led to significant niche overlap among the three genera.
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Affiliation(s)
- Julia Dupin
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, Colorado, 80309, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, Colorado, 80309, USA
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104
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Barrett CF, McKain MR, Sinn BT, Ge XJ, Zhang Y, Antonelli A, Bacon CD. Ancient Polyploidy and Genome Evolution in Palms. Genome Biol Evol 2019; 11:1501-1511. [PMID: 31028709 PMCID: PMC6535811 DOI: 10.1093/gbe/evz092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2019] [Indexed: 12/23/2022] Open
Abstract
Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
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Affiliation(s)
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Yuqu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Royal Botanical Gardens Kew, Richmond, United Kingdom
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
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105
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Bernardi M, Couette S, Chateau Smith C, Montuire S. Middle ear pneumatization in nonhuman primates: A comparative analysis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:540-556. [DOI: 10.1002/ajpa.23848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 12/03/2018] [Accepted: 04/16/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Margot Bernardi
- EPHEPSL Research University Paris Paris France
- Biogéosciences, UMR 6282 CNRSUniversité Bourgogne Franche‐Comté Dijon France
| | - Sébastien Couette
- EPHEPSL Research University Paris Paris France
- Biogéosciences, UMR 6282 CNRSUniversité Bourgogne Franche‐Comté Dijon France
| | | | - Sophie Montuire
- EPHEPSL Research University Paris Paris France
- Biogéosciences, UMR 6282 CNRSUniversité Bourgogne Franche‐Comté Dijon France
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106
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Kriebel R, Drew BT, Drummond CP, González‐Gallegos JG, Celep F, Mahdjoub MM, Rose JP, Xiang C, Hu G, Walker JB, Lemmon EM, Lemmon AR, Sytsma KJ. Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data. AMERICAN JOURNAL OF BOTANY 2019; 106:573-597. [PMID: 30986330 PMCID: PMC6850103 DOI: 10.1002/ajb2.1268] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/31/2019] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia. METHODS A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared. KEY RESULTS A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade. CONCLUSIONS Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.
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Affiliation(s)
- Ricardo Kriebel
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Bryan T. Drew
- Department of BiologyUniversity of Nebraska at KearneyKearneyNE68849USA
| | - Chloe P. Drummond
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | | | - Ferhat Celep
- Mehmet Akif Ersoy mah. 269. cad. Urankent Prestij KonutlarıC16 Blok, No. 53DemetevlerAnkaraTurkey
| | - Mohamed M. Mahdjoub
- Research Laboratory of Ecology and EnvironmentDepartment of Environment Biological SciencesFaculty of Nature and Life SciencesUniversité de BejaiaTarga Ouzemmour06000BejaiaAlgeria
| | - Jeffrey P. Rose
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Chun‐Lei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China
| | - Guo‐Xiong Hu
- College of Life SciencesGuizhou UniversityGuiyang550025GuizhouChina
| | | | - Emily M. Lemmon
- Department of Biological ScienceFlorida State UniversityTallahasseeFL32306USA
| | - Alan R. Lemmon
- Department of Scientific ComputingFlorida State UniversityTallahasseeFL32306USA
| | - Kenneth J. Sytsma
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
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107
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Oliver PM, Ashman LG, Bank S, Laver RJ, Pratt RC, Tedeschi LG, Moritz CC. On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation. BMC Evol Biol 2019; 19:81. [PMID: 30894117 PMCID: PMC6427882 DOI: 10.1186/s12862-019-1408-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/04/2019] [Indexed: 12/17/2022] Open
Abstract
Background Congruent patterns in the distribution of biodiversity between regions or habitats suggest that key factors such as climatic and topographic variation may predictably shape evolutionary processes. In a number of tropical and arid biomes, genetic analyses are revealing deeper and more localised lineage diversity in rocky ranges than surrounding habitats. Two potential drivers of localised endemism in rocky areas are refugial persistence through climatic change, or ecological diversification and specialisation. Here we examine how patterns of lineage and phenotypic diversity differ across two broad habitat types (rocky ranges and open woodlands) in a small radiation of gecko lizards in the genus Gehyra (the australis group) from the Australian Monsoonal Tropics biome. Results Using a suite of approaches for delineating evolutionarily independent lineages, we find between 26 and 41 putative evolutionary units in the australis group (versus eight species currently recognised). Rocky ranges are home to a greater number of lineages that are also relatively more restricted in distribution, while lineages in open woodland habitats are fewer, more widely distributed, and, in one case, show evidence of range expansion. We infer at least two shifts out of rocky ranges and into surrounding woodlands. Phenotypic divergence between rocky ranges specialist and more generalist taxa is detected, but no convergent evolutionary regimes linked to ecology are inferred. Conclusions In climatically unstable biomes such as savannahs, rocky ranges have functioned as zones of persistence, generators of diversity and a source of colonists for surrounding areas. Phenotypic divergence can also be linked to the use of differing habitat types, however, the extent to which ecological specialisation is a primary driver or secondary outcome of localised diversification remains uncertain. Electronic supplementary material The online version of this article (10.1186/s12862-019-1408-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul M Oliver
- Environmental Futures Research Institute, Griffith University, 170 Kessels Rd, Nathan, Queensland, 4111, Australia. .,Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101, Australia. .,Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia.
| | - Lauren G Ashman
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Sarah Bank
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia.,Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Rebecca J Laver
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Renae C Pratt
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Leonardo G Tedeschi
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Craig C Moritz
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
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108
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Dugo-Cota Á, Vilà C, Rodríguez A, Gonzalez-Voyer A. Ecomorphological convergence in Eleutherodactylus frogs: a case of replicate radiations in the Caribbean. Ecol Lett 2019; 22:884-893. [PMID: 30868693 DOI: 10.1111/ele.13246] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/25/2018] [Accepted: 01/16/2019] [Indexed: 11/28/2022]
Abstract
Replicate radiations, the repeated multiplication of species associated with ecological divergence, have attracted much attention and generated as much debate. Due to the few well-studied cases, it remains unclear whether replicate radiations are an exceptional result of evolution or a relatively common example of the power of adaptation by natural selection. We examined the case of Eleutherodactylus frogs, which radiated in the Caribbean islands resulting in more than 160 species that occupy very diverse habitats. A time-calibrated phylogeny revealed that these frogs independently diversified on all larger islands producing species that occupy a broad range of microhabitats in different islands. Using phylogenetic comparative methods, we found an association between morphological traits and particular microhabitats, and for most microhabitats detected significant morphological convergence. Our results indicate Caribbean Eleutherodactylus are a novel example of replicate radiations, and highlight the predictability of evolutionary processes, as similar ecological opportunities can lead to similar outcomes.
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Affiliation(s)
- Álvaro Dugo-Cota
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Av. Américo Vespucio 26, 41092, Sevilla, España
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Av. Américo Vespucio 26, 41092, Sevilla, España
| | - Ariel Rodríguez
- Institut für Zoologie, Stiftung Tierärztliche Hochschule Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Alejandro Gonzalez-Voyer
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. México, 04510, México
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109
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Stayton CT. Performance in three shell functions predicts the phenotypic distribution of hard-shelled turtles. Evolution 2019; 73:720-734. [PMID: 30820948 DOI: 10.1111/evo.13709] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/28/2019] [Indexed: 01/30/2023]
Abstract
Adaptive landscapes have served as fruitful guides to evolutionary research for nearly a century. Current methods guided by landscape frameworks mostly utilize evolutionary modeling (e.g., fitting data to Ornstein-Uhlenbeck models) to make inferences about adaptive peaks. Recent alternative methods utilize known relationships between phenotypes and functional performance to derive information about adaptive landscapes; this information can then help explain the distribution of species in phenotypic space and help infer the relative importance of various functions for guiding diversification. Here, data on performance for three turtle shell functions-strength, hydrodynamic efficiency, and self-righting ability-are used to develop a set of predicted performance optima in shell shape space. The distribution of performance optima shows significant similarity to the distribution of existing turtle species and helps explain the absence of shells in otherwise anomalously empty regions of morphospace. The method outperforms a modeling-based approach in inferring the location of reasonable adaptive peaks and in explaining the shape of the phenotypic distributions of turtle shells. Performance surface-based methods allow researchers to more directly connect functional performance with macroevolutionary diversification, and to explain the distribution of species (including presences and absences) across phenotypic space.
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Affiliation(s)
- C Tristan Stayton
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, 17837
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110
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Didier G, Chabrol O, Laurin M. Parsimony-based test for identifying changes in evolutionary trends for quantitative characters: implications for the origin of the amniotic egg. Cladistics 2019; 35:576-599. [DOI: 10.1111/cla.12371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Gilles Didier
- IMAG; Univ Montpellier; CNRS; Montpellier France
- Aix Marseille Univ; CNRS; Centrale Marseille; I2M; Marseille France
| | - Olivier Chabrol
- Aix Marseille Univ; CNRS; Centrale Marseille; I2M; Marseille France
| | - Michel Laurin
- CR2P; CNRS/MNHN/Sorbonne Université; Muséum National d'Histoire Naturelle; 75005 Paris France
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111
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Slater GJ, Friscia AR. Hierarchy in adaptive radiation: A case study using the Carnivora (Mammalia). Evolution 2019; 73:524-539. [DOI: 10.1111/evo.13689] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 01/13/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Graham J. Slater
- Department of the Geophysical SciencesUniversity of ChicagoChicago Illinois 60637
| | - Anthony R. Friscia
- Department of Integrative Biology and PhysiologyUniversity of CaliforniaLos Angeles California 90095
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112
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Multiple Components of Phylogenetic Non-stationarity in the Evolution of Brain Size in Fossil Hominins. Evol Biol 2019. [DOI: 10.1007/s11692-019-09471-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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113
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Lambert JW, Reichard M, Pincheira-Donoso D. Live fast, diversify non-adaptively: evolutionary diversification of exceptionally short-lived annual killifishes. BMC Evol Biol 2019; 19:10. [PMID: 30626330 PMCID: PMC6327596 DOI: 10.1186/s12862-019-1344-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/02/2019] [Indexed: 11/17/2022] Open
Abstract
Background Adaptive radiations are triggered by ecological opportunity – the access to novel niche domains with abundant available resources that facilitate the formation of new ecologically divergent species. Therefore, as new species saturate niche space, clades experience a diversity-dependent slowdown of diversification over time. At the other extreme of the radiation continuum, non-adaptively radiating lineages undergo diversification with minimal niche differentiation when ‘spatial opportunity’ (i.e. areas with suitable ‘ancestral’ ecological conditions) is available. Traditionally, most research has focused on adaptive radiations, while empirical studies on non-adaptive radiations remain lagging behind. A prolific clade of African fish with extremely short lifespan (Nothobranchius killifish), show the key evolutionary features of a candidate non-adaptive radiation – primarily allopatric species with minimal niche and phenotypic divergence. Here, we test the hypothesis that Nothobranchius killifish have non-adaptively diversified. We employ phylogenetic modelling to investigate the tempo and mode of macroevolutionary diversification of these organisms. Results Nothobranchius diversification has proceeded with minor niche differentiation and minimal morphological disparity among allopatric species. Additionally, we failed to identify evidence for a role of body size or biogeography in influencing diversification rates. Diversification has been homogeneous within this genus, with the only hotspot of species-richness not resulting from rapid diversification. However, species in sympatry show higher disparity, which may have been caused by character displacement among coexisting species. Conclusions Nothobranchius killifish have proliferated following the tempo and mode of a non-adaptive radiation. Our study confirms that this exceptionally short-lived group have diversified with minimal divergent niche adaptation, while one group of coexisting species seems to have facilitated spatial overlap among these taxa via the evolution of ecological character displacement. Electronic supplementary material The online version of this article (10.1186/s12862-019-1344-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua W Lambert
- School of Life Sciences, Joseph Banks Laboratories, Brayford Campus, University of Lincoln, Lincoln, LN6 7DL, UK
| | - Martin Reichard
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic
| | - Daniel Pincheira-Donoso
- MacroBiodiversity Lab, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK.
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114
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Marburger S, Alexandrou MA, Taggart JB, Creer S, Carvalho G, Oliveira C, Taylor MI. Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes. Proc Biol Sci 2019; 285:rspb.2017.2732. [PMID: 29445022 PMCID: PMC5829208 DOI: 10.1098/rspb.2017.2732] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/25/2018] [Indexed: 01/12/2023] Open
Abstract
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.
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Affiliation(s)
- Sarah Marburger
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Markos A Alexandrou
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,Wildlands Conservation Science, LLC PO Box 1846, Lompoc, CA 93438, USA
| | - John B Taggart
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências/UNESP, Rua Professor Doutor Antonio Celso Wagner Zanin, s/n°18618-689 Botucatu, São Paulo, Brazil
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Smaers JB, Mongle CS, Safi K, Dechmann DK. Allometry, evolution and development of neocortex size in mammals. PROGRESS IN BRAIN RESEARCH 2019; 250:83-107. [DOI: 10.1016/bs.pbr.2019.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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117
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Clavel J, Aristide L, Morlon H. A Penalized Likelihood Framework for High-Dimensional Phylogenetic Comparative Methods and an Application to New-World Monkeys Brain Evolution. Syst Biol 2018; 68:93-116. [PMID: 29931145 DOI: 10.1093/sysbio/syy045] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 06/13/2018] [Indexed: 01/03/2023] Open
Abstract
Working with high-dimensional phylogenetic comparative data sets is challenging because likelihood-based multivariate methods suffer from low statistical performances as the number of traits $p $ approaches the number of species $n $ and because some computational complications occur when $p $ exceeds $n$. Alternative phylogenetic comparative methods have recently been proposed to deal with the large $p $ small $n $ scenario but their use and performances are limited. Herein, we develop a penalized likelihood (PL) framework to deal with high-dimensional comparative data sets. We propose various penalizations and methods for selecting the intensity of the penalties. We apply this general framework to the estimation of parameters (the evolutionary trait covariance matrix and parameters of the evolutionary model) and model comparison for the high-dimensional multivariate Brownian motion (BM), Early-burst (EB), Ornstein-Uhlenbeck (OU), and Pagel's lambda models. We show using simulations that our PL approach dramatically improves the estimation of evolutionary trait covariance matrices and model parameters when $p$ approaches $n$, and allows for their accurate estimation when $p$ equals or exceeds $n$. In addition, we show that PL models can be efficiently compared using generalized information criterion (GIC). We implement these methods, as well as the related estimation of ancestral states and the computation of phylogenetic principal component analysis in the R package RPANDA and mvMORPH. Finally, we illustrate the utility of the new proposed framework by evaluating evolutionary models fit, analyzing integration patterns, and reconstructing evolutionary trajectories for a high-dimensional 3D data set of brain shape in the New World monkeys. We find a clear support for an EB model suggesting an early diversification of brain morphology during the ecological radiation of the clade. PL offers an efficient way to deal with high-dimensional multivariate comparative data.
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Affiliation(s)
- Julien Clavel
- École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France
| | - Leandro Aristide
- École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France
| | - Hélène Morlon
- École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France
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118
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Santibáñez-López CE, Kriebel R, Ballesteros JA, Rush N, Witter Z, Williams J, Janies DA, Sharma PP. Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions. PeerJ 2018; 6:e5902. [PMID: 30479892 PMCID: PMC6240337 DOI: 10.7717/peerj.5902] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale datasets. Disagreements over scorpion higher-level systematics have also incurred challenges to previous interpretations of venom families as ancestral or derived. To redress these gaps, we assessed the phylogenomic relationships of scorpions using the most comprehensive taxonomic sampling to date. We surveyed genomic resources for the incidence of calcins (a type of calcium channel toxin), which were previously known only from 16 scorpion species. Here, we show that calcins are diverse, but phylogenetically restricted only to parvorder Iurida, one of the two basal branches of scorpions. The other branch of scorpions, Buthida, bear the related LKTx toxins (absent in Iurida), but lack calcins entirely. Analysis of sequences and molecular models demonstrates remarkable phylogenetic inertia within both calcins and LKTx genes. These results provide the first synapomorphies (shared derived traits) for the recently redefined clades Buthida and Iurida, constituting the only known case of such traits defined from the morphology of molecules.
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Affiliation(s)
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Jesús A. Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nathaniel Rush
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary Witter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - John Williams
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
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119
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Bastide P, Ané C, Robin S, Mariadassou M. Inference of Adaptive Shifts for Multivariate Correlated Traits. Syst Biol 2018; 67:662-680. [PMID: 29385556 DOI: 10.1093/sysbio/syy005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/23/2018] [Indexed: 11/14/2022] Open
Abstract
To study the evolution of several quantitative traits, the classical phylogenetic comparative framework consists of a multivariate random process running along the branches of a phylogenetic tree. The Ornstein-Uhlenbeck (OU) process is sometimes preferred to the simple Brownian motion (BM) as it models stabilizing selection toward an optimum. The optimum for each trait is likely to be changing over the long periods of time spanned by large modern phylogenies. Our goal is to automatically detect the position of these shifts on a phylogenetic tree, while accounting for correlations between traits, which might exist because of structural or evolutionary constraints. We show that, in the presence of shifts, phylogenetic Principal Component Analysis fails to decorrelate traits efficiently, so that any method aiming at finding shifts needs to deal with correlation simultaneously. We introduce here a simplification of the full multivariate OU model, named scalar OU, which allows for noncausal correlations and is still computationally tractable. We extend the equivalence between the OU and a BM on a rescaled tree to our multivariate framework. We describe an Expectation-Maximization (EM) algorithm that allows for a maximum likelihood estimation of the shift positions, associated with a new model selection criterion, accounting for the identifiability issues for the shift localization on the tree. The method, freely available as an R-package (PhylogeneticEM) is fast, and can deal with missing values. We demonstrate its efficiency and accuracy compared to another state-of-the-art method ($\ell$1ou) on a wide range of simulated scenarios and use this new framework to reanalyze recently gathered data sets on New World Monkeys and Anolis lizards.
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Affiliation(s)
- Paul Bastide
- Unité Mixte de Recherche Mathématiques et Informatique Appliquées (MIA - Paris), AgroParisTech, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, 16 rue Claude Bernard, 75005 Paris, France.,Unité de Recherche Mathématiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - Cécile Ané
- Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA.,Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Stéphane Robin
- Unité Mixte de Recherche Mathématiques et Informatique Appliquées (MIA - Paris), AgroParisTech, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, 16 rue Claude Bernard, 75005 Paris, France
| | - Mahendra Mariadassou
- Unité de Recherche Mathématiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Domaine de Vilvert, 78352 Jouy-en-Josas, France
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120
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Bastide P, Solís-Lemus C, Kriebel R, William Sparks K, Ané C. Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations. Syst Biol 2018; 67:800-820. [PMID: 29701821 DOI: 10.1093/sysbio/syy033] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/20/2018] [Indexed: 12/29/2022] Open
Abstract
The goal of phylogenetic comparative methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's $\lambda$ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a data set of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.
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Affiliation(s)
- Paul Bastide
- Unité Mixte de Recherche Mathématiques et Informatique Appliquées (MIA - Paris), AgroParisTech, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, 16 rue Claude Bernard, 75005 Paris, France.,Unité de Recherche Mathématiques et Informatique Appliquées du Génome ál'Environnement (MaIAGE), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - Claudia Solís-Lemus
- Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - K William Sparks
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Cécile Ané
- Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA.,Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
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121
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Aristide L, Bastide P, Dos Reis SF, Pires Dos Santos TM, Lopes RT, Perez SI. Multiple factors behind early diversification of skull morphology in the continental radiation of New World monkeys. Evolution 2018; 72:2697-2711. [PMID: 30246282 DOI: 10.1111/evo.13609] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 09/03/2018] [Indexed: 01/24/2023]
Abstract
Understanding the origin of diversity is a fundamental problem in evolutionary biology. The null expectation for the evolutionary diversification is that all changes in biological diversity are the result of random processes. Adaptive radiations depart from this expectation as ecological factors and natural selection are supposed to play a central role in driving exceptional diversification. However, it is not well understood how large-scale continental radiations, given their characteristics, fit to these opposing theoretical models. Here, we used phylogenetic comparative methods and geometric morphometrics to study the evolutionary process of cranial diversification in the continental radiation of New World monkeys. Particularly, we tested several alternative evolutionary scenarios for morphological evolution in the clade. Results indicated that despite the platyrrhine radiation being old and geographically widespread, the formative patterns arising from the initial stages of diversification probably associated with an adaptive radiation can still be recognized today. We also show that no single explored factor (e.g., ecological or allometric) can be invoked as a complete explanation for the observed phenotypic diversity patterns in the clade and, moreover, that different cranial regions exhibit particular macroevolutionary patterns. Together, our results highlight the evident complexity behind large-scale evolutionary radiations.
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Affiliation(s)
- Leandro Aristide
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Buenos Aires, Argentina.,École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Paul Bastide
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49 box 1030 BE-3000, Leuven, Belgium
| | - Sergio Furtado Dos Reis
- Departamento de Biologia Animal, Universidade Estadual de Campinas, CEP 13.083-862 Campinas, São Paulo, Brazil
| | - Thaís M Pires Dos Santos
- Laboratório de Instrumentação Nuclear, Centro de Tecnologia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, CEP 21949-900, Rio de Janeiro, Brazil
| | - Ricardo T Lopes
- Laboratório de Instrumentação Nuclear, Centro de Tecnologia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, CEP 21949-900, Rio de Janeiro, Brazil
| | - S Ivan Perez
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Buenos Aires, Argentina
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122
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Liedtke HC, Gower DJ, Wilkinson M, Gomez-Mestre I. Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate. Nat Ecol Evol 2018; 2:1792-1799. [PMID: 30250158 DOI: 10.1038/s41559-018-0674-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 08/17/2018] [Indexed: 11/09/2022]
Abstract
The evolution and great diversity of genome size has been of long-standing interest to biologists, but has seldom been investigated on a broad phylogenetic scale. Here we present a comparative quantitative analysis of factors shaping genome size evolution in amphibians, the extant class of vertebrates with the largest variation in genome size. We find that amphibian genomes have undergone saltations in size, although these are rare and the evolutionary history of genome size in amphibians has otherwise been one of gradual, time-dependent variation (that is, Brownian motion). This macroevolutionary homogeneity is remarkable given the evolutionary and ecological diversity of most other aspects of the natural history of amphibians. Contrary to previous claims, we find no evidence for associations between life cycle complexity and genome size despite the high diversity of reproductive modes and the multiple events of independent evolution of divergent life cycles in the group. Climate (temperature and humidity) affects genome size indirectly, at least in frogs, as a consequence of its effect on premetamorphic developmental period, although directionality of the relationship between developmental period and genome size is not unequivocal.
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Affiliation(s)
- H Christoph Liedtke
- Ecology, Evolution and Developmental Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - David J Gower
- Department of Life Sciences, Natural History Museum, London, UK
| | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - Ivan Gomez-Mestre
- Ecology, Evolution and Developmental Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain.
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123
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Divergence, Convergence and Phenotypic Diversity of Neotropical Frugivorous Bats. DIVERSITY 2018. [DOI: 10.3390/d10030100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Knowing how adaptation shapes morphological evolution is fundamental to understanding the processes that promote biological diversity. However, there is a lack of empirical evidence on the effects of adaptive radiations on phenotypic diversity, which is related to processes that promote phenotypic divergence and convergence. We applied comparative methods to identify shifts in adaptive peaks and to detect divergence and convergence in skull morphology of frugivorous bats (Phyllostomidae: Stenodermatinae and Carollinae), an ecologically diverse group with strong association between skull morphology, feeding performance and diet that suggests adaptive diversification through morphological innovation. We found divergence and convergence for skull morphology. Fifteen peak shifts were found for jaws, which result in four convergent and four divergent regimes. For skull, nine peak shifts were detected that result in three convergent and three divergent regimes. Furthermore, convergence was significant and strong for skull morphology since distantly related organisms converged to the same adaptive optima. Results suggest that convergence indicates the effect of restriction on phenotypes to keep the advantages provided by the skull phenotype that played a central role in the evolution of strict frugivory in phyllostomids. We conclude that convergence has limited phenotypic diversity of functional traits related to feeding in phyllostomid frugivores.
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124
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Hutchinson MC, Gaiarsa MP, Stouffer DB. Contemporary Ecological Interactions Improve Models of Past Trait Evolution. Syst Biol 2018; 67:861-872. [PMID: 29471501 DOI: 10.1093/sysbio/syy012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 02/10/2018] [Indexed: 11/12/2022] Open
Abstract
Despite the fact that natural selection underlies both traits and interactions, evolutionary models often neglect that ecological interactions may, and in many cases do, influence the evolution of traits. Herein, we explore the interdependence of ecological interactions and functional traits in the pollination associations of hawkmoths and flowering plants. Specifically, we develop an adaptation of the Ornstein-Uhlenbeck model of trait evolution that allows us to study the influence of plant corolla depth and observed hawkmoth-plant interactions on the evolution of hawkmoth proboscis length. Across diverse modelling scenarios, we find that the inclusion of contemporary interactions can provide a better description of trait evolution than the null expectation. Moreover, we show that the pollination interactions provide more-likely models of hawkmoth trait evolution when interactions are considered at increasingly fine-scale groups of hawkmoths. Finally, we demonstrate how the results of best-fit modeling approaches can implicitly support the association between interactions and trait evolution that our method explicitly examines. In showing that contemporary interactions can provide insight into the historical evolution of hawkmoth proboscis length, we demonstrate the clear utility of incorporating additional ecological information to models designed to study past trait evolution.
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Affiliation(s)
- Matthew C Hutchinson
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Marília P Gaiarsa
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.,Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, 11294, 05422-970 São Paulo, Brazil
| | - Daniel B Stouffer
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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125
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Abstract
The primate foot functions as a grasping organ. As such, its bones, soft tissues, and joints evolved to maximize power and stability in a variety of grasping configurations. Humans are the obvious exception to this primate pattern, with feet that evolved to support the unique biomechanical demands of bipedal locomotion. Of key functional importance to bipedalism is the morphology of the joints at the forefoot, known as the metatarsophalangeal joints (MTPJs), but a comprehensive analysis of hominin MTPJ morphology is currently lacking. Here we present the results of a multivariate shape and Bayesian phylogenetic comparative analyses of metatarsals (MTs) from a broad selection of anthropoid primates (including fossil apes and stem catarrhines) and most of the early hominin pedal fossil record, including the oldest hominin for which good pedal remains exist, Ardipithecus ramidus Results corroborate the importance of specific bony morphologies such as dorsal MT head expansion and "doming" to the evolution of terrestrial bipedalism in hominins. Further, our evolutionary models reveal that the MT1 of Ar. ramidus shifts away from the reconstructed optimum of our last common ancestor with apes, but not necessarily in the direction of modern humans. However, the lateral rays of Ar. ramidus are transformed in a more human-like direction, suggesting that they were the digits first recruited by hominins into the primary role of terrestrial propulsion. This pattern of evolutionary change is seen consistently throughout the evolution of the foot, highlighting the mosaic nature of pedal evolution and the emergence of a derived, modern hallux relatively late in human evolution.
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126
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Catalán A, Macias-Muñoz A, Briscoe AD. Evolution of Sex-Biased Gene Expression and Dosage Compensation in the Eye and Brain of Heliconius Butterflies. Mol Biol Evol 2018; 35:2120-2134. [DOI: 10.1093/molbev/msy111] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ana Catalán
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
- Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians Universität, Planegg-Martinsried, Germany
| | - Aide Macias-Muñoz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
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127
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Smaers JB, Turner AH, Gómez-Robles A, Sherwood CC. A cerebellar substrate for cognition evolved multiple times independently in mammals. eLife 2018; 7:e35696. [PMID: 29809137 PMCID: PMC6003771 DOI: 10.7554/elife.35696] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/21/2018] [Indexed: 12/21/2022] Open
Abstract
Given that complex behavior evolved multiple times independently in different lineages, a crucial question is whether these independent evolutionary events coincided with modifications to common neural systems. To test this question in mammals, we investigate the lateral cerebellum, a neurobiological system that is novel to mammals, and is associated with higher cognitive functions. We map the evolutionary diversification of the mammalian cerebellum and find that relative volumetric changes of the lateral cerebellar hemispheres (independent of cerebellar size) are correlated with measures of domain-general cognition in primates, and are characterized by a combination of parallel and convergent shifts towards similar levels of expansion in distantly related mammalian lineages. Results suggest that multiple independent evolutionary occurrences of increased behavioral complexity in mammals may at least partly be explained by selection on a common neural system, the cerebellum, which may have been subject to multiple independent neurodevelopmental remodeling events during mammalian evolution.
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Affiliation(s)
- Jeroen B Smaers
- Department of AnthropologyStony Brook UniversityNew YorkUnited States
- Center for the Advanced Study of Human PaleobiologyStony Brook UniversityNew YorkUnited States
| | - Alan H Turner
- Department of Anatomical SciencesStony Brook UniversityNew YorkUnited States
| | - Aida Gómez-Robles
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUnited Kingdom
- Department of AnthropologyThe George Washington UniversityWashingtonUnited States
| | - Chet C Sherwood
- Department of AnthropologyThe George Washington UniversityWashingtonUnited States
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128
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Uyeda JC, Zenil-Ferguson R, Pennell MW. Rethinking phylogenetic comparative methods. Syst Biol 2018; 67:1091-1109. [DOI: 10.1093/sysbio/syy031] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/17/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Josef C Uyeda
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061 USA
| | - Rosana Zenil-Ferguson
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844 USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108 USA
| | - Matthew W Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, #4200-6700 University Blvd., Vancouver, BC V6T 1Z4, Canada
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129
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Voje KL, Starrfelt J, Liow LH. Model Adequacy and Microevolutionary Explanations for Stasis in the Fossil Record. Am Nat 2018; 191:509-523. [DOI: 10.1086/696265] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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130
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Racimo F, Berg JJ, Pickrell JK. Detecting Polygenic Adaptation in Admixture Graphs. Genetics 2018; 208:1565-1584. [PMID: 29348143 PMCID: PMC5887149 DOI: 10.1534/genetics.117.300489] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/16/2018] [Indexed: 01/09/2023] Open
Abstract
An open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred. To address this, we created a method to detect polygenic adaptation in an admixture graph, which is a representation of the historical divergences and admixture events relating different populations through time. We developed a Markov chain Monte Carlo (MCMC) algorithm to infer branch-specific parameters reflecting the strength of selection in each branch of a graph. Additionally, we developed a set of summary statistics that are fast to compute and can indicate which branches are most likely to have experienced polygenic adaptation. We show via simulations that this method-which we call PolyGraph-has good power to detect polygenic adaptation, and applied it to human population genomic data from around the world. We also provide evidence that variants associated with several traits, including height, educational attainment, and self-reported unibrow, have been influenced by polygenic adaptation in different populations during human evolution.
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Affiliation(s)
- Fernando Racimo
- New York Genome Center, New York, New York 10013
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350, Denmark
| | - Jeremy J Berg
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Joseph K Pickrell
- New York Genome Center, New York, New York 10013
- Department of Biological Sciences, Columbia University, New York, New York 10027
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131
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Puttick MN. Mixed evidence for early bursts of morphological evolution in extant clades. J Evol Biol 2018; 31:502-515. [PMID: 29285828 PMCID: PMC6849586 DOI: 10.1111/jeb.13236] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 12/08/2017] [Accepted: 12/20/2017] [Indexed: 01/23/2023]
Abstract
Macroevolutionary theory predicts high rates of evolution should occur early in a clade's history as species exploit ecological opportunity. Evidence from the fossil record has shown a high prevalence of early bursts in morphological evolution, but recent work has provided little evidence for early high rates in the evolution of extant clades. Here, I test the prevalence of early bursts in extant data using phylogenetic comparative methods. Existing models are extended to allow a shift from a background Brownian motion (BM) process to an early burst process within subclades of phylogenies, rather than an early burst being applied to an entire phylogenetic tree. This nested early burst model is compared to other modes of evolution that can occur within subclades, such as evolution with a constraint (Ornstein-Uhlenbeck model) and nested BM rate shift models. These relaxed models are validated using simulations and then are applied to body size evolution of three major clades of amniotes (mammals, squamates and aves) at different levels of taxonomic organization (order, family). Applying these unconstrained models greatly increases the support for early bursts within nested subclades, and so early bursts are the most common model of evolution when only one shift is analysed. However, the relative fit of early burst models is worse than models that allow for multiple shifts of the BM or OU process. No single-shift or homogenous model is superior to models of multiple shifts in BM or OU evolution, but the patterns shown by these multirate models are generally congruent with patterns expected from early bursts.
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Affiliation(s)
- M. N. Puttick
- School of Earth SciencesBristolUK
- Department of Life SciencesNatural History MuseumLondonUK
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132
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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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133
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Davis AM, Betancur-R R. Widespread ecomorphological convergence in multiple fish families spanning the marine-freshwater interface. Proc Biol Sci 2018; 284:rspb.2017.0565. [PMID: 28515206 DOI: 10.1098/rspb.2017.0565] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/19/2017] [Indexed: 11/12/2022] Open
Abstract
The theoretical definition and quantification of convergence is an increasingly topical focus in evolutionary research, with particular growing interest on study scales spanning deep phylogenetic divergences and broad geographical areas. While much progress has recently been made in understanding the role of convergence in driving terrestrial (e.g. anole lizards) and aquatic (e.g. cichlids) radiations, little is known about its macroevolutionary effects across environmental gradients. This study uses a suite of recently developed comparative approaches integrating diverse aspects of morphology, dietary data, habitat affiliation and phylogeny to assess convergence across several well-known tropical-temperate fish families in the percomorph suborder Terapontoidei, a clade with considerable phenotypic and ecological diversity radiating in both marine and freshwater environments. We demonstrate significant widespread convergence across many lineages occupying equivalent trophic niches, particularly feeding habits such as herbivory and biting of attached prey off hard substrates. These include several examples of convergent morphotypes evolving independently in marine and freshwater clades, separated by deep evolutionary divergences (tens of millions of years). The Terapontoidei present a new example of the macroevolutionary dynamics of morphological and ecological coevolution in relation to habitat and trophic preferences, at a greater phylogenetic and habitat scale than most well-studied adaptive radiations.
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Affiliation(s)
- Aaron M Davis
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), and School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia .,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 159, Washington, DC 20013-7012, USA
| | - Ricardo Betancur-R
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 159, Washington, DC 20013-7012, USA.,Department of Biology, University of Puerto Rico, Río Piedras, PO Box 23360, San Juan, Puerto Rico 00931, USA
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134
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Smith SD, Kriebel R. Convergent evolution of floral shape tied to pollinator shifts in Iochrominae (Solanaceae)*. Evolution 2018; 72:688-697. [DOI: 10.1111/evo.13416] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/01/2017] [Accepted: 12/08/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Stacey D. Smith
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado 80305
| | - Ricardo Kriebel
- Department of Botany University of Wisconsin – Madison Madison Wisconsin 53706
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135
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Hipp AL, Manos PS, González-Rodríguez A, Hahn M, Kaproth M, McVay JD, Avalos SV, Cavender-Bares J. Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity. THE NEW PHYTOLOGIST 2018; 217:439-452. [PMID: 28921530 DOI: 10.1111/nph.14773] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/29/2017] [Indexed: 05/21/2023]
Abstract
Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks. Our highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates. The two major American oak clades arose in what is now the boreal zone and radiated, in parallel, from eastern North America into Mexico and Central America. Oaks adapted rapidly to niche transitions. The Mexican oaks are particularly numerous, not because Mexico is a center of origin, but because of high rates of lineage diversification associated with high rates of evolution along moisture gradients and between the evergreen and deciduous leaf habits. Sympatric parallel diversification in the oaks has shaped the diversity of North American forests.
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Affiliation(s)
- Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
| | | | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex Hacienda de Sán José de la Huerta, Morelia, Michoacán, 58190, México
| | - Marlene Hahn
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
| | - Matthew Kaproth
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Biological Sciences, Minnesota State University, Mankato, MN 56001, USA
| | | | - Susana Valencia Avalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Circuito Exterior, s.n., Ciudad Universitaria, Coyoacán, CP, 04510, México City, México
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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136
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Boucher FC, Démery V, Conti E, Harmon LJ, Uyeda J. A General Model for Estimating Macroevolutionary Landscapes. Syst Biol 2017; 67:304-319. [DOI: 10.1093/sysbio/syx075] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 09/08/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Florian C Boucher
- Department of Systematic and Evolutionary Botany (ISEB), University of Zurich, Zurich, Switzerland
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Vincent Démery
- Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, France
| | - Elena Conti
- Department of Systematic and Evolutionary Botany (ISEB), University of Zurich, Zurich, Switzerland
| | - Luke J Harmon
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA
- Department of Fish Ecology and Evolution, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Center for Ecology, Evolution, and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Josef Uyeda
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA
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137
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Bartoszek K, Glémin S, Kaj I, Lascoux M. Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations. J Theor Biol 2017; 429:35-45. [PMID: 28619246 DOI: 10.1016/j.jtbi.2017.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/08/2017] [Accepted: 06/09/2017] [Indexed: 11/15/2022]
Abstract
The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes random perturbations and stabilizing selection and assumes that species evolve independently. However, evolving species may interact through various ecological process and also exchange genes especially in plants. This is particularly true if we want to study phenotypic evolution among diverging populations within species. In this work we present a straightforward statistical approach with analytical solutions that allows for the inclusion of adaptation and migration in a common phylogenetic framework, which can also be useful for studying local adaptation among populations within the same species. We furthermore present a detailed simulation study that clearly indicates the adverse effects of ignoring migration. Similarity between species due to migration could be misinterpreted as very strong convergent evolution without proper correction for these additional dependencies. Finally, we show that our model can be interpreted in terms of ecological interactions between species, providing a general framework for the evolution of traits between "interacting" species or populations.
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Affiliation(s)
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 752 36, Sweden; UMR 5554 ISEM, CNRS-Université de Montpellier-IRD-EPHE, Montpellier, France.
| | - Ingemar Kaj
- Department of Mathematics, Uppsala University, Uppsala, 751 06, Sweden.
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 752 36, Sweden.
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138
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Waller JT, Svensson EI. Body size evolution in an old insect order: No evidence for Cope's Rule in spite of fitness benefits of large size. Evolution 2017; 71:2178-2193. [DOI: 10.1111/evo.13302] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 06/03/2017] [Accepted: 06/20/2017] [Indexed: 01/18/2023]
Affiliation(s)
- John T. Waller
- Evolutionary Ecology Unit, Department of Biology; Lund University; SE-223 62 Lund Sweden
| | - Erik I. Svensson
- Evolutionary Ecology Unit, Department of Biology; Lund University; SE-223 62 Lund Sweden
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139
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Mahler DL, Weber MG, Wagner CE, Ingram T. Pattern and Process in the Comparative Study of Convergent Evolution. Am Nat 2017; 190:S13-S28. [DOI: 10.1086/692648] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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140
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Sex-specific evolution during the diversification of live-bearing fishes. Nat Ecol Evol 2017; 1:1185-1191. [DOI: 10.1038/s41559-017-0233-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 06/05/2017] [Indexed: 11/09/2022]
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141
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Smaers JB, Mongle CS. On the accuracy and theoretical underpinnings of the multiple variance Brownian motion approach for estimating variable rates and inferring ancestral states. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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142
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Evans KM, Waltz B, Tagliacollo V, Chakrabarty P, Albert JS. Why the short face? Developmental disintegration of the neurocranium drives convergent evolution in neotropical electric fishes. Ecol Evol 2017; 7:1783-1801. [PMID: 28331588 PMCID: PMC5355199 DOI: 10.1002/ece3.2704] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/13/2016] [Accepted: 11/20/2016] [Indexed: 01/07/2023] Open
Abstract
Convergent evolution is widely viewed as strong evidence for the influence of natural selection on the origin of phenotypic design. However, the emerging evo‐devo synthesis has highlighted other processes that may bias and direct phenotypic evolution in the presence of environmental and genetic variation. Developmental biases on the production of phenotypic variation may channel the evolution of convergent forms by limiting the range of phenotypes produced during ontogeny. Here, we study the evolution and convergence of brachycephalic and dolichocephalic skull shapes among 133 species of Neotropical electric fishes (Gymnotiformes: Teleostei) and identify potential developmental biases on phenotypic evolution. We plot the ontogenetic trajectories of neurocranial phenotypes in 17 species and document developmental modularity between the face and braincase regions of the skull. We recover a significant relationship between developmental covariation and relative skull length and a significant relationship between developmental covariation and ontogenetic disparity. We demonstrate that modularity and integration bias the production of phenotypes along the brachycephalic and dolichocephalic skull axis and contribute to multiple, independent evolutionary transformations to highly brachycephalic and dolichocephalic skull morphologies.
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Affiliation(s)
- Kory M Evans
- Department of Biology University of Louisiana at Lafayette Lafayette LA USA
| | - Brandon Waltz
- Department of Biology University of Louisiana at Lafayette Lafayette LA USA
| | - Victor Tagliacollo
- Universidade Federal do Tocantins Programa de Pós-graduação Ciências do Ambiente (CIAMB) Palmas Tocantins 77001-090 Brazil
| | | | - James S Albert
- Department of Biology University of Louisiana at Lafayette Lafayette LA USA
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143
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Smaers JB, Gómez-Robles A, Parks AN, Sherwood CC. Exceptional Evolutionary Expansion of Prefrontal Cortex in Great Apes and Humans. Curr Biol 2017; 27:714-720. [PMID: 28162899 DOI: 10.1016/j.cub.2017.01.020] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/05/2016] [Accepted: 01/11/2017] [Indexed: 01/09/2023]
Abstract
One of the enduring questions that has driven neuroscientific enquiry in the last century has been the nature of differences in the prefrontal cortex of humans versus other animals [1]. The prefrontal cortex has drawn particular interest due to its role in a range of evolutionarily specialized cognitive capacities such as language [2], imagination [3], and complex decision making [4]. Both cytoarchitectonic [5] and comparative neuroimaging [6] studies have converged on the conclusion that the proportion of prefrontal cortex in the human brain is greatly increased relative to that of other primates. However, considering the tremendous overall expansion of the neocortex in human evolution, it has proven difficult to ascertain whether this extent of prefrontal enlargement follows general allometric growth patterns, or whether it is exceptional [1]. Species' adherence to a common allometric relationship suggests conservation through phenotypic integration, while species' deviations point toward the occurrence of shifts in genetic and/or developmental mechanisms. Here we investigate prefrontal cortex scaling across anthropoid primates and find that great ape and human prefrontal cortex expansion are non-allometrically derived features of cortical organization. This result aligns with evidence for a developmental heterochronic shift in human prefrontal growth [7, 8], suggesting an association between neurodevelopmental changes and cortical organization on a macroevolutionary scale. The evolutionary origin of non-allometric prefrontal enlargement is estimated to lie at the root of great apes (∼19-15 mya), indicating that selection for changes in executive cognitive functions characterized both great ape and human cortical organization.
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Affiliation(s)
- Jeroen B Smaers
- Department of Anthropology, Stony Brook University, Circle Road, Stony Brook, NY 11794-4364, USA.
| | - Aida Gómez-Robles
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, 800 22(nd) St NW, Washington, DC 20052, USA
| | - Ashley N Parks
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Circle Road, Stony Brook, NY 11794-4364, USA
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, 800 22(nd) St NW, Washington, DC 20052, USA
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144
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Zelditch ML, Ye J, Mitchell JS, Swiderski DL. Rare ecomorphological convergence on a complex adaptive landscape: Body size and diet mediate evolution of jaw shape in squirrels (Sciuridae). Evolution 2017; 71:633-649. [PMID: 28075012 DOI: 10.1111/evo.13168] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 12/30/2016] [Indexed: 11/28/2022]
Abstract
Convergence is widely regarded as compelling evidence for adaptation, often being portrayed as evidence that phenotypic outcomes are predictable from ecology, overriding contingencies of history. However, repeated outcomes may be very rare unless adaptive landscapes are simple, structured by strong ecological and functional constraints. One such constraint may be a limitation on body size because performance often scales with size, allowing species to adapt to challenging functions by modifying only size. When size is constrained, species might adapt by changing shape; convergent shapes may therefore be common when size is limiting and functions are challenging. We examine the roles of size and diet as determinants of jaw shape in Sciuridae. As expected, size and diet have significant interdependent effects on jaw shape and ecomorphological convergence is rare, typically involving demanding diets and limiting sizes. More surprising is morphological without ecological convergence, which is equally common between and within dietary classes. Those cases, like rare ecomorphological convergence, may be consequences of evolving on an adaptive landscape shaped by many-to-many relationships between ecology and function, many-to-one relationships between form and performance, and one-to-many relationships between functionally versatile morphologies and ecology. On complex adaptive landscapes, ecological selection can yield different outcomes.
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Affiliation(s)
| | - Ji Ye
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, 48109
| | - Jonathan S Mitchell
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109
| | - Donald L Swiderski
- Kresge Hearing Research Institute and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109
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145
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Johnson AE, Mitchell JS, Brown MB. Convergent evolution in social swallows (Aves: Hirundinidae). Ecol Evol 2017; 7:550-560. [PMID: 28116052 PMCID: PMC5243784 DOI: 10.1002/ece3.2641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 12/03/2022] Open
Abstract
Behavioral shifts can initiate morphological evolution by pushing lineages into new adaptive zones. This has primarily been examined in ecological behaviors, such as foraging, but social behaviors may also alter morphology. Swallows and martins (Hirundinidae) are aerial insectivores that exhibit a range of social behaviors, from solitary to colonial breeding and foraging. Using a well-resolved phylogenetic tree, a database of social behaviors, and morphological measurements, we ask how shifts from solitary to social breeding and foraging have affected morphological evolution in the Hirundinidae. Using a threshold model of discrete state evolution, we find that shifts in both breeding and foraging social behavior are common across the phylogeny of swallows. Solitary swallows have highly variable morphology, while social swallows show much less absolute variance in all morphological traits. Metrics of convergence based on both the trajectory of social lineages through morphospace and the overall morphological distance between social species scaled by their phylogenetic distance indicate strong convergence in social swallows, especially socially foraging swallows. Smaller physical traits generally observed in social species suggest that social species benefit from a distinctive flight style, likely increasing maneuverability and foraging success and reducing in-flight collisions within large flocks. These results highlight the importance of sociality in species evolution, a link that had previously been examined only in eusocial insects and primates.
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Affiliation(s)
| | - Jonathan S. Mitchell
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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146
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