1
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Tsai WLE, Escalona M, Garrett KL, Terrill RS, Sahasrabudhe R, Nguyen O, Beraut E, Seligmann W, Fairbairn CW, Harrigan RJ, McCormack JE, Alfaro ME, Smith TB, Bay RA. A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia). J Hered 2024; 115:317-325. [PMID: 38401156 PMCID: PMC11081134 DOI: 10.1093/jhered/esae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.
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Affiliation(s)
- Whitney L E Tsai
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States
| | - Kimball L Garrett
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, United States
| | - Ryan S Terrill
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - Ryan J Harrigan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - John E McCormack
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, CA 95616, United States
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2
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Dornburg A, Zapfe KL, Williams R, Alfaro ME, Morris R, Adachi H, Flores J, Santini F, Near TJ, Frédérich B. Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae). Syst Biol 2024:syae014. [PMID: 38490727 DOI: 10.1093/sysbio/syae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Indexed: 03/17/2024] Open
Abstract
Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that differ from their adult forms in morphology and ecology. Focusing disproportionately on the evolution of adult forms unnecessarily hinders our understanding of the pressures shaping evolution over time. Non-adult disparity patterns are particularly important to consider for coastal ray-finned fishes, which often have juvenile phases with distinct phenotypes. These juvenile forms are often associated with sheltered nursery environments, with phenotypic shifts between adults and juvenile stages that are readily apparent in locomotor morphology. Whether this ontogenetic variation in locomotor morphology reflects a decoupling of diversification dynamics between life stages remains unknown. Here we investigate the evolutionary dynamics of locomotor morphology between adult and juvenile triggerfishes. We integrate a time-calibrated phylogenetic framework with geometric morphometric approaches and measurement data of fin aspect ratio and incidence, and reveal a mismatch between morphospace occupancy, the evolution of morphological disparity, and the tempo of trait evolution between life stages. Collectively, our results illuminate how the heterogeneity of morpho-functional adaptations can decouple the mode and tempo of morphological diversification between ontogenetic stages.
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Affiliation(s)
- Alex Dornburg
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Richard Morris
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Haruka Adachi
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Joseph Flores
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Francesco Santini
- Associazione Italiana per lo Studio della Biodiversità, Pisa, 56100, Italy
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Bruno Frédérich
- Laboratory of Evolutionary Ecology, FOCUS, University of Liège, Liège, Belgium
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3
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Smith JE, Natterson-Horowitz B, Mueller MM, Alfaro ME. Mechanisms of equality and inequality in mammalian societies. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220307. [PMID: 37381860 DOI: 10.1098/rstb.2022.0307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/09/2023] [Indexed: 06/30/2023] Open
Abstract
The extent of (in)equality is highly diverse across species of social mammals, but we have a poor understanding of the factors that produce or inhibit equitable social organizations. Here, we adopt a comparative evolutionary perspective to test whether the evolution of social dominance hierarchies, a measure of social inequality in animals, exhibits phylogenetic conservatism and whether interspecific variation in these traits can be explained by sex, age or captivity. We find that hierarchy steepness and directional consistency evolve rapidly without any apparent constraint from evolutionary history. Given this extraordinary variability, we next consider multiple factors that have evolved to mitigate social inequality. Social networks, coalitionary support and knowledge transfer advantage to privilege some individuals over others. Nutritional access and prenatal stressors can impact the development of offspring, generating health disparities with intergenerational consequences. Intergenerational transfer of material resources (e.g. stone tools, food stashes, territories) advantage those who receive. Nonetheless, many of the same social species that experience unequal access to food (survival) and mates (reproduction) engage in levelling mechanisms such as food sharing, adoption, revolutionary coalitions, forgiveness and inequity aversion. Taken together, mammals rely upon a suite of mechanisms of (in)equality to balance the costs and benefits of group living. This article is part of the theme issue 'Evolutionary ecology of inequality'.
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Affiliation(s)
- Jennifer E Smith
- Biology Department, University of Wisconsin Eau Claire, 105 Garfield Avenue, Eau Claire, WI 54702, USA
| | - Barbara Natterson-Horowitz
- School of Medicine, Division of Cardiology, University of California, 650 Charles Young Drive South, A2-237 CHS, Los Angeles, CA 90095, USA
| | - Maddison M Mueller
- Biology Department, University of Wisconsin Eau Claire, 105 Garfield Avenue, Eau Claire, WI 54702, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 2149 Terasaki Life Sciences Building, 612 Charles E. Young Drive South, Box 957246, Los Angeles, CA 90095-7246, USA
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4
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Abstract
Boxfish (Ostraciidae) have peculiar body shapes, with conspicuous keels formed by their bony carapaces. Previous studies have proposed various hydrodynamic roles for these keels, including reducing drag during swimming, contributing to passive stabilization of the swimming course, or providing resistance against roll rotations. Here, we tested these hypotheses using computational fluid dynamics simulations of five species of Ostraciidae with a range of carapace shapes. The hydrodynamic performance of the original carapace surface models, obtained from laser scanning of museum specimens, was compared with models where the keels had been digitally reduced. The original carapaces showed no reduced drag or increased passive stability against pitch and yaw compared to the reduced-keel carapaces. However, consistently for all studied species, a strong increase in roll drag and roll-added mass was observed for the original carapaces compared to the reduced-keel carapaces, despite the relatively small differences in keel height. In particular, the damping of roll movement by resistive drag torques increased considerably by the presence of keels. Our results suggest that the shape of the boxfish carapace is important in enabling the observed roll-free forward swimming of boxfish and may facilitate the control of manoeuvres.
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Affiliation(s)
- Merel J W Van Gorp
- Department of Biology, Universiteit Antwerpen, Universiteitsplein 1, 2610 Antwerpen, Belgium
| | - Jana Goyens
- Department of Biology, Universiteit Antwerpen, Universiteitsplein 1, 2610 Antwerpen, Belgium
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 2154 Terasaki Life Sciences Building, Los Angeles, CA 90095, USA
| | - Sam Van Wassenbergh
- Department of Biology, Universiteit Antwerpen, Universiteitsplein 1, 2610 Antwerpen, Belgium
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5
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Abstract
Abstract
Wealth inequality is widespread across human societies, from pastoral and small-scale agricultural groups to large modern social structures. The intergenerational transfer of wealth privileges some individuals over others through the transmission of resources external to an individual organism. Privileged access to household wealth (e.g., land, shelter, silver) positively influences the destinies of some (and their descendants) over others in human societies. Strikingly parallel phenomena exist in animal societies. Inheritance of nongenetic commodities (e.g., a nest, territory, tool) external to an individual also contributes greatly to direct fitness in animals. Here, we illustrate the evolutionary diversity of privilege and its disparity-generating effects on the evolutionary trajectories of lineages across the Tree of Life. We propose that integration of approaches used to study these patterns in humans may offer new insights into a core principle from behavioral ecology—differential access to inherited resources—and help to establish a broad, comparative framework for studying inequality in animals.
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Affiliation(s)
| | - B Natterson-Horowitz
- School of Medicine, Division of Cardiology, University of California, Los Angeles, CA, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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6
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Affiliation(s)
- Shawn T. Schwartz
- Department of Ecology and Evolutionary Biology University of California Los Angeles California USA
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology University of California Los Angeles California USA
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7
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Melo BF, Sidlauskas BL, Near TJ, Roxo FF, Ghezelayagh A, Ochoa LE, Stiassny MLJ, Arroyave J, Chang J, Faircloth BC, MacGuigan DJ, Harrington RC, Benine RC, Burns MD, Hoekzema K, Sanches NC, Maldonado-Ocampo JA, Castro RMC, Foresti F, Alfaro ME, Oliveira C. Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes. Syst Biol 2021; 71:78-92. [PMID: 34097063 DOI: 10.1093/sysbio/syab040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.
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Affiliation(s)
- Bruno F Melo
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Brian L Sidlauskas
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Thomas J Near
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Fabio F Roxo
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Ava Ghezelayagh
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Luz E Ochoa
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil.,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Palmira, Valle del Cauca, 763547, Colombia
| | - Melanie L J Stiassny
- Dept of Ichthyology, American Museum of Natural History, New York, NY, 10024, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Jonathan Chang
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Brant C Faircloth
- Dept of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Daniel J MacGuigan
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Richard C Harrington
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Ricardo C Benine
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell University Museum of Vertebrates, Ithaca, NY, 14850, USA
| | - Kendra Hoekzema
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Natalia C Sanches
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Javier A Maldonado-Ocampo
- Dept de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia (in memoriam)
| | - Ricardo M C Castro
- Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Fausto Foresti
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Michael E Alfaro
- Dept of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudio Oliveira
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
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8
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Stiller J, da Fonseca RR, Alfaro ME, Faircloth BC, Wilson NG, Rouse GW. Using ultraconserved elements to track the influence of sea-level change on leafy seadragon populations. Mol Ecol 2021; 30:1364-1380. [PMID: 33217068 DOI: 10.1111/mec.15744] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/08/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022]
Abstract
During the Last Glacial Maximum (LGM), global sea levels were 120-130 m lower than today, resulting in the emergence of most continental shelves and extirpation of subtidal organisms from these areas. During the interglacial periods, rapid inundation of shelf regions created a dynamic environment for coastal organisms, such as the charismatic leafy seadragon (Phycodurus eques, Syngnathidae), a brooder with low dispersal ability inhabiting kelp beds in temperate Australia. Reconstructions of the palaeoshoreline revealed that the increase of shallow areas since the LGM was not uniform across the species' range and we investigated the effects of these asymmetries on genetic diversity and structuring. Using targeted capture of 857 variable ultraconserved elements (UCEs, 2,845 single nucleotide polymorphisms) in 68 individuals, we found that the regionally different shelf topographies were paralleled by contrasting population genetic patterns. In the west, populations may not have persisted through sea-level lows because shallow seabed was very limited. Shallow genetic structure, weak expansion signals and a westward cline in genetic diversity indicate a postglacial recolonization of the western part of the range from a more eastern location following sea-level rise. In the east, shallow seabed persisted during the LGM and increased considerably after the flooding of large bays, which resulted in strong demographic expansions, deeper genetic structure and higher genetic diversity. This study suggests that postglacial flooding with rising sea levels produced locally variable signatures in colonizing populations.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
- Centre for Biodiversity Genomics, Section for Ecology and Evolution, University of Copenhagen, Kobenhavn, Denmark
| | | | | | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
- Collections & Research, Western Australian Museum, Welshpool and School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
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9
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Chang J, Rabosky DL, Alfaro ME. Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions. Syst Biol 2020; 69:602-611. [PMID: 31804691 DOI: 10.1093/sysbio/syz081] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/12/2019] [Accepted: 12/01/2019] [Indexed: 11/13/2022] Open
Abstract
Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on "sampling fractions" can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (Taxonomic Addition for Complete Trees [TACT]) that uses birth-death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling. [Birth-death process; diversification; incomplete sampling; phylogenetic uncertainty; rate heterogeneity; rate shifts; stochastic polytomy resolution.].
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Affiliation(s)
- Jonathan Chang
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Melbourne, VIC 3800, Australia.,Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, USA.,Department of Ecology and Evolutionary Biology, University of California, 612 Charles E Young Dr S, Los Angeles, CA 90095, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E Young Dr S, Los Angeles, CA 90095, USA
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10
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McCraney WT, Thacker CE, Alfaro ME. Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria. Mol Phylogenet Evol 2020; 151:106862. [DOI: 10.1016/j.ympev.2020.106862] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 05/06/2020] [Accepted: 05/21/2020] [Indexed: 01/04/2023]
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11
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Campbell MA, Buser TJ, Alfaro ME, López JA. Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships. PeerJ 2020; 8:e9389. [PMID: 32685284 PMCID: PMC7337038 DOI: 10.7717/peerj.9389] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven challenging to resolve in molecular phylogenetics studies in part due to ancestral autopolyploidy contributing to conflicting gene trees. We examine a sequence capture dataset from salmonids and use alternative strategies to accommodate the effects of gene tree conflict based on aspects of salmonid genome history and the multispecies coalescent. We investigate in detail three uncertain relationships: (1) subfamily branching, (2) monophyly of Coregonus and (3) placement of Parahucho. Coregoninae and Thymallinae are resolved as sister taxa, although conflicting topologies are found across analytical strategies. We find inconsistent and generally low support for the monophyly of Coregonus, including in results of analyses with the most extensive dataset and complex model. The most consistent placement of Parahucho is as sister lineage of Salmo.
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Affiliation(s)
- Matthew A. Campbell
- University of Alaska Museum, University of Alaska—Fairbanks, Fairbanks, AK, USA
| | - Thaddaeus J. Buser
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - J. Andrés López
- University of Alaska Museum, University of Alaska—Fairbanks, Fairbanks, AK, USA
- College of Fisheries and Ocean Sciences, University of Alaska—Fairbanks, Fairbanks, AK, USA
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12
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Gjesfjeld E, Silvestro D, Chang J, Koch B, Foster JG, Alfaro ME. A quantitative workflow for modeling diversification in material culture. PLoS One 2020; 15:e0227579. [PMID: 32027685 PMCID: PMC7004301 DOI: 10.1371/journal.pone.0227579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
Questions about the evolution of material culture are widespread in the humanities and social sciences. Statistical modeling of long-term changes in material culture is less common due to a lack of appropriate frameworks. Our goal is to close this gap and provide robust statistical methods for examining changes in the diversity of material culture. We provide an open-source and quantitative workflow for estimating rates of origination, extinction, and preservation, as well as identifying key shift points in the diversification histories of material culture. We demonstrate our approach using two distinct kinds of data: age ranges for the production of American car models, and radiocarbon dates associated with archaeological cultures of the European Neolithic. Our approach improves on existing frameworks by disentangling the relative contributions of origination and extinction to diversification. Our method also permits rigorous statistical testing of competing hypotheses to explain changes in diversity. Finally, we stress the value of a flexible approach that can be applied to data in various forms; this flexibility allows scholars to explore commonalities between forms of material culture and ask questions about the general properties of cultural change.
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Affiliation(s)
- Erik Gjesfjeld
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, England, United Kingdom
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jonathan Chang
- School of Biological Sciences, Monash University, Melbourne, Australia.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America
| | - Bernard Koch
- Department of Sociology, University of California, Los Angeles, CA, United States of America
| | - Jacob G Foster
- Department of Sociology, University of California, Los Angeles, CA, United States of America
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America.,Institute for Society and Genetics, University of California, Los Angeles, CA, United States of America
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13
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Faircloth BC, Alda F, Hoekzema K, Burns MD, Oliveira C, Albert JS, Melo BF, Ochoa LE, Roxo FF, Chakrabarty P, Sidlauskas BL, Alfaro ME. A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes. COPEIA 2020. [DOI: 10.1643/cg-18-139] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Brant C. Faircloth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; (BCF) ; and (PC) . Send reprint requests to BCF
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403;
| | - Kendra Hoekzema
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Michael D. Burns
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - James S. Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana 70503;
| | - Bruno F. Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - Luz E. Ochoa
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - Fábio F. Roxo
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil;
| | - Prosanta Chakrabarty
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; (BCF) ; and (PC) . Send reprint requests to BCF
| | - Brian L. Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095;
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14
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Friedman M, Feilich KL, Beckett HT, Alfaro ME, Faircloth BC, Černý D, Miya M, Near TJ, Harrington RC. A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean. Proc Biol Sci 2019; 286:20191502. [PMID: 31506051 PMCID: PMC6742994 DOI: 10.1098/rspb.2019.1502] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/14/2019] [Indexed: 11/12/2022] Open
Abstract
The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide a time-calibrated phylogeny for this widely distributed clade. Some inferred relationships have clear precedents (e.g. the monophyly of 'core' Stromateoidei, and a clade comprising 'Gempylidae' and Trichiuridae), but others are unexpected despite strong support (e.g. Chiasmodontidae + Tetragonurus). Relaxed molecular clock analysis using node-based fossil calibrations estimates a latest Cretaceous origin for Pelagiaria, with crown-group families restricted to the Cenozoic. Estimated mean speciation rates decline from the origin of the group in the latest Cretaceous, although credible intervals for root and tip rates are broad and overlap in most cases, and there is higher-than-expected partitioning of body shape diversity (measured as fineness ratio) between clades concentrated during the Palaeocene-Eocene. By contrast, more direct measures of ecology show either no substantial deviation from a null model of diversification (diet) or patterns consistent with evolutionary constraint or high rates of recent change (depth habitat). Collectively, these results indicate a mosaic model of diversification. Pelagiarians show high morphological disparity and modest species richness compared to better-studied fish radiations in contrasting environments. However, this pattern is also apparent in other clades in open-ocean or deep-sea habitats, and suggests that comparative study of such groups might provide a more inclusive model of the evolution of diversity in fishes.
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Affiliation(s)
- Matt Friedman
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Kara L. Feilich
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
| | | | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Brant C. Faircloth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - David Černý
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Masaki Miya
- Natural History Museum and Institute, Chiba, Aoba-cho, Chuo-ku, Chiba, Japan
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Peabody Museum, Yale University, New Haven, CT, USA
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15
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Phuong MA, Alfaro ME, Mahardika GN, Marwoto RM, Prabowo RE, von Rintelen T, Vogt PWH, Hendricks JR, Puillandre N. Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails. Syst Biol 2019; 68:781-796. [PMID: 30816949 PMCID: PMC6934442 DOI: 10.1093/sysbio/syz016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 12/29/2022] Open
Abstract
Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or the intrinsic capacity of lineages for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, $>$900 spp.) provide a unique opportunity to test this prediction because their toxin genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, we did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though detection of a signal depended on the dataset and the method. If our results remain true with increased taxonomic sampling in future studies, they suggest that the rapid evolution of conid venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.
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Affiliation(s)
- Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Gusti N Mahardika
- Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University Bali, Jl Sesetan-Markisa 6, Denpasar, Bali 80225, Indonesia
| | - Ristiyanti M Marwoto
- Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, LIPI, Km.46, Jl. Raya Bogor, Cibinong, Bogor, West Java 16911, Indonesia
| | - Romanus Edy Prabowo
- Aquatic Biology Laboratory, Faculty of Biology, Universitas Jenderal Soedirman, Jalan dr. Suparno 63 Grendeng, Purwokerto, Indonesia, 53122
| | - Thomas von Rintelen
- Museum für Naturkunde—Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Philipp W H Vogt
- Museum für Naturkunde—Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | | | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, 1259 Trumansburg Road, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
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16
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Abstract
Abstract
Coral reef fishes constitute one of the most diverse assemblages of vertebrates on the planet. Color patterns are known to serve a number of functions including intra- and inter-specific signaling, camouflage, mimicry, and defense. However, the relative importance of these and other factors in shaping color pattern evolution is poorly understood. Here we conduct a comparative phylogenetic analysis of color pattern evolution in the butterflyfishes (Chaetodontidae). Using recently developed tools for quantifying color pattern geometry as well as machine learning approaches, we investigate the tempo of evolution of color pattern elements and test whether ecological variables relating to defense, depth, and social behavior predict color pattern evolution. Butterflyfishes exhibit high diversity in measures of chromatic conspicuousness and the degrees of fine versus gross scale color patterning. Surprisingly, most diversity in color pattern was not predicted by any of the measures of ecology in our study, although we did find a significant but weak relationship between the level of fine scale patterning and some aspects of defensive morphology. We find that the tempo of color pattern diversification in butterflyfishes has increased toward the present and suggest that rapid evolution, presumably in response to evolutionary pressures surrounding speciation and lineage divergence, has effectively decoupled color pattern geometry from some aspects of ecology. Machine learning classification of color pattern appears to rely on a set of features that are weakly correlated with current color pattern geometry descriptors, but that may be better suited for the detection of discrete components of color pattern. A key challenge for future studies lies in determining whether rapid evolution has generally decoupled color patterns from ecology, or whether convergence in function produces convergence in color pattern at phylogenetic scales.
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Affiliation(s)
- Michael E Alfaro
- Department of Ecology and Evolutionary Biology, Terasaki 2149, University of California, Los Angeles, CA 90095, USA
| | - Elizabeth A Karan
- Department of Ecology and Evolutionary Biology, Terasaki 2149, University of California, Los Angeles, CA 90095, USA
| | - Shawn T Schwartz
- Department of Ecology and Evolutionary Biology, Terasaki 2149, University of California, Los Angeles, CA 90095, USA
| | - Allison J Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
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17
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Roxo FF, Ochoa LE, Sabaj MH, Lujan NK, Covain R, Silva GS, Melo BF, Albert JS, Chang J, Foresti F, Alfaro ME, Oliveira C. Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements. Mol Phylogenet Evol 2019; 135:148-165. [DOI: 10.1016/j.ympev.2019.02.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/09/2019] [Accepted: 02/18/2019] [Indexed: 12/15/2022]
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18
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Chang J, Rabosky DL, Smith SA, Alfaro ME. An
r
package and online resource for macroevolutionary studies using the ray‐finned fish tree of life. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13182] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jonathan Chang
- School of Biological Sciences Monash University Clayton VIC Australia
| | - Daniel L. Rabosky
- Museum of Zoology Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI
| | - Stephen A. Smith
- Museum of Zoology Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCA
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19
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Hulsey CD, Alfaro ME, Zheng J, Meyer A, Holzman R. Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi cichlids. Proc Biol Sci 2019; 286:20182358. [PMID: 30963830 PMCID: PMC6408893 DOI: 10.1098/rspb.2018.2358] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Complexity in how mechanistic variation translates into ecological novelty could be critical to organismal diversification. For instance, when multiple distinct morphologies can generate the same mechanical or functional phenotype, this could mitigate trade-offs and/or provide alternative ways to meet the same ecological challenge. To investigate how this type of complexity shapes diversity in a classic adaptive radiation, we tested several evolutionary consequences of the anterior jaw four-bar linkage for Lake Malawi cichlid trophic diversification. Using a novel phylogenetic framework, we demonstrated that different mechanical outputs of the same four jaw elements are evolutionarily associated with both jaw protrusion distance and jaw protrusion angle. However, these two functional aspects of jaw protrusion have evolved independently. Additionally, although four-bar morphology showed little evidence for attraction to optima, there was substantial evidence of adaptive peaks for emergent four-bar linkage mechanics and jaw protrusion abilities among Malawi feeding guilds. Finally, we highlighted a clear case of two cichlid species that have -independently evolved to graze algae in less than 2 Myr and have converged on similar jaw protrusion abilities as well as four-bar linkage mechanics, but have evolved these similarities via non-convergent four-bar morphologies.
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Affiliation(s)
- C. Darrin Hulsey
- Department of Biology, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Michael E. Alfaro
- Department of Ecology & Evolutionary Biology, University of California-Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095-7246, USA
| | - Jimmy Zheng
- Department of Ecology & Evolutionary Biology, University of California-Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095-7246, USA
| | - Axel Meyer
- Department of Biology, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Roi Holzman
- Department of Zoology, Tel Aviv University and the Inter-University Institute for Marine Sciences, PO Box 469, Eilat 88103, Israel
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20
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Lutzoni F, Nowak MD, Alfaro ME, Reeb V, Miadlikowska J, Krug M, Arnold AE, Lewis LA, Swofford DL, Hibbett D, Hilu K, James TY, Quandt D, Magallón S. Contemporaneous radiations of fungi and plants linked to symbiosis. Nat Commun 2018; 9:5451. [PMID: 30575731 PMCID: PMC6303338 DOI: 10.1038/s41467-018-07849-9] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 11/20/2018] [Indexed: 12/26/2022] Open
Abstract
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma), likely facilitating terrestriality through endomycorrhizal and possibly endophytic symbioses. The largest radiation of fungi (Leotiomyceta), the origin of arbuscular mycorrhizae, and the diversification of extant embryophytes occurred ca. 480 Ma. This was followed by the origin of extant lichens. Saprotrophic mushrooms diversified in the Late Paleozoic as forests of seed plants started to dominate the landscape. The subsequent diversification and explosive radiation of Agaricomycetes, and eventually of ectomycorrhizal mushrooms, were associated with the evolution of Pinaceae in the Mesozoic, and establishment of angiosperm-dominated biomes in the Cretaceous. Plants and fungi interact widely and in diverse ways, from mutualism to parasitism and decomposition. Here, Lutzoni et al. analyse the timing of plant and fungal evolutionary radiations and identify four major periods in which plant-fungal interactions likely drove lineage diversification.
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Affiliation(s)
| | - Michael D Nowak
- Natural History Museum, University of Oslo, NO-0318, Oslo, Norway
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Valérie Reeb
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | | | - Michael Krug
- Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität, 53115, Bonn, Germany
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - David L Swofford
- Department of Biology, Duke University, Durham, NC, 27708, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - David Hibbett
- Department of Biology, Clark University, Worcester, MA, 01610, USA
| | - Khidir Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dietmar Quandt
- Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität, 53115, Bonn, Germany
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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21
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Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P. Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting. Syst Biol 2018; 68:573-593. [DOI: 10.1093/sysbio/syy085] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Fernando Alda
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Victor A Tagliacollo
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Ipirianga, 04263-000, São Paulo, São Paulo, Brazil
| | - Maxwell J Bernt
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - Brandon T Waltz
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - William B Ludt
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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22
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Darrin Hulsey C, Zheng J, Holzman R, Alfaro ME, Olave M, Meyer A. Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes? BMC Evol Biol 2018; 18:179. [PMID: 30486792 PMCID: PMC6263179 DOI: 10.1186/s12862-018-1296-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 11/16/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Phylogenies provide critical information about convergence during adaptive radiation. To test whether there have been multiple origins of a distinctive trophic phenotype in one of the most rapidly radiating groups known, we used ultra-conserved elements (UCEs) to examine the evolutionary affinities of Lake Malawi cichlids lineages exhibiting greatly hypertrophied lips. RESULTS The hypertrophied lip cichlids Cheilochromis euchilus, Eclectochromis ornatus, Placidochromis "Mbenji fatlip", and Placidochromis milomo are all nested within the non-mbuna clade of Malawi cichlids based on both concatenated sequence and single nucleotide polymorphism (SNP) inferred phylogenies. Lichnochromis acuticeps that exhibits slightly hypertrophied lips also appears to have evolutionary affinities to this group. However, Chilotilapia rhoadesii that lacks hypertrophied lips was recovered as nested within the species Cheilochromis euchilus. Species tree reconstructions and analyses of introgression provided largely ambiguous patterns of Malawi cichlid evolution. CONCLUSIONS Contrary to mitochondrial DNA phylogenies, bifurcating trees based on our 1024 UCE loci supported close affinities of Lake Malawi lineages with hypertrophied lips. However, incomplete lineage sorting in Malawi tends to render these inferences more tenuous. Phylogenomic analyses will continue to provide powerful inferences about whether phenotypic novelties arose once or multiple times during adaptive radiation.
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Affiliation(s)
- C. Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jimmy Zheng
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA USA
| | - Roi Holzman
- Department of Zoology, Tel Aviv University and the Inter-University Institute for Marine Sciences in Eilat, 88103 Eilat, Israel
| | - Michael E. Alfaro
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA USA
| | - Melisa Olave
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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23
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DiBattista JD, Alfaro ME, Sorenson L, Choat JH, Hobbs JA, Sinclair‐Taylor TH, Rocha LA, Chang J, Luiz OJ, Cowman PF, Friedman M, Berumen ML. Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot. Ecol Evol 2018; 8:10989-11008. [PMID: 30519422 PMCID: PMC6262737 DOI: 10.1002/ece3.4566] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 08/19/2018] [Accepted: 08/29/2018] [Indexed: 01/19/2023] Open
Abstract
For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e., Red Sea to Arabian Gulf) and their close relatives. Bayesian tree building methods produced a well-resolved phylogeny that elucidated the origins of butterflyfishes in this hotspots of endemism. We show that UCEs, often used to resolve deep evolutionary relationships, represent an important tool to assess the mechanisms underlying recently diverged taxa. Our analyses indicate that unique environmental conditions in the coastal waters of the Arabian Peninsula probably contributed to the formation of endemic butterflyfishes. Older endemic species are also associated with narrow versus broad depth ranges, suggesting that adaptation to deeper coral reefs in this region occurred only recently (<1.75 Ma). Even though deep reef environments were drastically reduced during the extreme low sea level stands of glacial ages, shallow reefs persisted, and as such there was no evidence supporting mass extirpation of fauna in this region.
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Affiliation(s)
- Joseph D. DiBattista
- Red Sea Research Center, Division of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Australian Museum Research Institute, Australian MuseumSydneyNew South WalesAustralia
- School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCalifornia
| | - Laurie Sorenson
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCalifornia
| | - John H. Choat
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Jean‐Paul A. Hobbs
- School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Tane H. Sinclair‐Taylor
- Red Sea Research Center, Division of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Luiz A. Rocha
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCalifornia
| | - Jonathan Chang
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCalifornia
| | - Osmar J. Luiz
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Peter F. Cowman
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Matt Friedman
- Department of Earth SciencesUniversity of OxfordOxfordUK
- Museum of Paleontology and Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMichigan
| | - Michael L. Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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24
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Abstract
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that generates model residuals or the traits themselves. For high-dimensional traits, inferring all pair-wise correlations within the multivariate diffusion is limiting. To circumvent this problem, we propose phylogenetic factor analysis (PFA) that assumes a small unknown number of independent evolutionary factors arise along the phylogeny and these factors generate clusters of dependent traits. Set in a Bayesian framework, PFA provides measures of uncertainty on the factor number and groupings, combines both continuous and discrete traits, integrates over missing measurements and incorporates phylogenetic uncertainty with the help of molecular sequences. We develop Gibbs samplers based on dynamic programming to estimate the PFA posterior distribution, over 3-fold faster than for multivariate diffusion and a further order-of-magnitude more efficiently in the presence of latent traits. We further propose a novel marginal likelihood estimator for previously impractical models with discrete data and find that PFA also provides a better fit than multivariate diffusion in evolutionary questions in columbine flower development, placental reproduction transitions and triggerfish fin morphometry.
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Affiliation(s)
- Max R Tolkoff
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, 650 Charles E. Young Dr. South Los Angeles, CA 90095-1772, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South Los Angeles, CA 90095-1606, USA
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroederstraat 10 BE-3000 Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroederstraat 10 BE-3000 Leuven, Belgium
| | - Marc A Suchard
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, 650 Charles E. Young Dr. South Los Angeles, CA 90095-1772, USA.,Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, 650 Charles E. Young Dr., South Los Angeles, CA 90095-1766, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, 695 Charles E. Young Drive South Los Angeles, CA 90095-7088, USA
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25
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Gilbert PS, Wu J, Simon MW, Sinsheimer JS, Alfaro ME. Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements. Mol Phylogenet Evol 2018; 126:116-128. [PMID: 29626666 PMCID: PMC6217972 DOI: 10.1016/j.ympev.2018.03.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/20/2018] [Accepted: 03/29/2018] [Indexed: 02/06/2023]
Abstract
Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps to resolve key nodes in the Neoaves tree of life. We find that our analysis of data sets filtered for high signal to noise ratio results in topologies that are inconsistent with unfiltered results but that are congruent with whole-genome analyses. These relationships include the Columbea + Passerea sister relationship and the Phaethontimorphae + Aequornithia sister relationship. We also find increased statistical support for more recent nodes (i.e. the Pelecanidae + Ardeidae sister relationship, the Eucavitaves clade, and the Otidiformes + Musophagiformes sister relationship). We also find instances where support is reduced for well-established clades, possibly due to the removal of sites with moderate signal-to-noise ratio. Our results suggest that filtering on the basis of signal to noise ratio is a useful tool for resolving problematic splits in phylogenomic data sets.
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Affiliation(s)
- Princess S Gilbert
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.
| | - Jing Wu
- Henry Samueli School of Engineering and Applied Science, Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Margaret W Simon
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Janet S Sinsheimer
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Michael E Alfaro
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.
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Burin G, Alencar LRV, Chang J, Alfaro ME, Quental TB. How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline? Syst Biol 2018; 68:47-62. [DOI: 10.1093/sysbio/syy037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/09/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- Gustavo Burin
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Laura R V Alencar
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Tiago B Quental
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
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Lima MGM, Silva-Júnior JDSE, Černý D, Buckner JC, Aleixo A, Chang J, Zheng J, Alfaro ME, Martins A, Di Fiore A, Boubli JP, Lynch Alfaro JW. A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America. Mol Phylogenet Evol 2018; 124:137-150. [PMID: 29545109 DOI: 10.1016/j.ympev.2018.02.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 01/06/2018] [Accepted: 02/23/2018] [Indexed: 11/30/2022]
Abstract
Phylogenetic relationships amongst the robust capuchin monkeys (genus Sapajus) are poorly understood. Morphology-based taxonomies have recognized anywhere from one to twelve different species. The current IUCN (2017) classification lists eight robust capuchins: S. xanthosternos, S. nigritus, S. robustus, S. flavius, S. libidinosus, S. cay, S. apella and S. macrocephalus. Here, we assembled the first phylogenomic data set for Sapajus using ultra-conserved elements (UCEs) to reconstruct a capuchin phylogeny. All phylogenomic analyses strongly supported a deep divergence of Sapajus and Cebus clades within the capuchin monkeys, and provided support for Sapajus nigritus, S. robustus and S. xanthosternos as distinct species. However, the UCE phylogeny lumped the putative species S. cay, S. libidinosus, S. apella, S. macrocephalus, and S. flavius together as a single widespread lineage. A SNP phylogeny constructed from the UCE data was better resolved and recovered S. flavius and S. libidinosus as sister species; however, S. apella, S. macrocephalus, and S. cay individuals were recovered in two geographic clades, from northeastern and southwestern Amazon, rather than clustering by currently defined morphospecies. STRUCTURE analysis of population clustering revealed widespread admixture among Sapajus populations within the Amazon and even into the Cerrado and Atlantic Forest. Difficulty in assigning species by morphology may be a result of widespread population admixture facilitated through frequent movement across major rivers and even ecosystems by robust capuchin monkeys.
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Affiliation(s)
- Marcela G M Lima
- Institute for Society and Genetics, University of California, Los Angeles, CA, USA; Curso de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil.
| | - José de Sousa E Silva-Júnior
- Curso de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - David Černý
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Janet C Buckner
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Alexandre Aleixo
- Curso de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Jimmy Zheng
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Amely Martins
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA; Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, ICMBio, MMA, Brazil
| | - Anthony Di Fiore
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | - Jean P Boubli
- School of Environment and Life Sciences, University of Salford, UK
| | - Jessica W Lynch Alfaro
- Institute for Society and Genetics, University of California, Los Angeles, CA, USA; Department of Anthropology, UCLA, Los Angeles, CA, USA.
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Chakrabarty P, Faircloth BC, Alda F, Ludt WB, Mcmahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME. Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes. Syst Biol 2018; 66:881-895. [PMID: 28334176 DOI: 10.1093/sysbio/syx038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/24/2016] [Indexed: 12/30/2022] Open
Abstract
Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5 million base pairs collected across 35 representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher level (interordinal) relationships among ostariophysan fishes, focusing on the monophyly of the Characiformes-one of the most contentiously debated groups in fish systematics. As with most previous molecular studies, we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophysan clades than to each other. We also explore incongruence between results from different UCE data sets, issues of orthology, and the use of morphological characters in combination with our molecular data. [Conserved sequence; ichthyology; massively parallel sequencing; morphology; next-generation sequencing; UCEs.].
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Affiliation(s)
- Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Fernando Alda
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - William B Ludt
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Caleb D Mcmahan
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.,The Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL 60605, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
| | - James S Albert
- Department of Biology, University of Louisiana, Lafayette, LA 70504, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Laurie Sorenson
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.,Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Yound Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Yound Drive South, Los Angeles, CA 90095, USA
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Campbell MA, Alfaro ME, Belasco M, López JA. Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences. PeerJ 2017; 5:e3548. [PMID: 28929008 PMCID: PMC5592902 DOI: 10.7717/peerj.3548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/15/2017] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.
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Affiliation(s)
- Matthew A Campbell
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, United States of America.,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States of America
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Max Belasco
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, United States of America
| | - J Andrés López
- School of Fisheries and Ocean Sciencs, University of Alaska Fairbanks, Fairbanks, AK, United States of America.,University of Alaska Museum, Fairbanks, AK, United States of America
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Hulsey CD, Zheng J, Faircloth BC, Meyer A, Alfaro ME. Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit. Mol Phylogenet Evol 2017; 114:40-48. [DOI: 10.1016/j.ympev.2017.05.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/14/2017] [Accepted: 05/30/2017] [Indexed: 01/05/2023]
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Frédérich B, Santini F, Konow N, Schnitzler J, Lecchini D, Alfaro ME. Body shape convergence driven by small size optimum in marine angelfishes. Biol Lett 2017; 13:20170154. [PMID: 28615351 PMCID: PMC5493737 DOI: 10.1098/rsbl.2017.0154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/22/2017] [Indexed: 11/12/2022] Open
Abstract
Convergent evolution of small body size occurs across many vertebrate clades and may reflect an evolutionary response to shared selective pressures. However it remains unclear if other aspects of phenotype undergo convergent evolution in miniaturized lineages. Here we present a comparative analysis of body size and shape evolution in marine angelfishes (Pomacanthidae), a reef fish family characterized by repeated transitions to small body size. We ask if lineages that evolve small sizes show convergent evolution in body shape. Our results reveal that angelfish lineages evolved three different stable size optima with one corresponding to the group of pygmy angelfishes (Centropyge). Then, we test if the observed shifts in body size are associated with changes to new adaptive peaks in shape. Our data suggest that independent evolution to small size optima have induced repeated convergence upon deeper body and steeper head profile in Centropyge These traits may favour manoeuvrability and visual awareness in these cryptic species living among corals, illustrating that functional demands on small size may be related to habitat specialization and predator avoidance. The absence of shape convergence in large marine angelfishes also suggests that more severe requirements exist for small than for large size optima.
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Affiliation(s)
- Bruno Frédérich
- Laboratoire de Morphologie Fonctionnelle et Evolutive, Université de Liège, Liège, Belgium
| | | | - Nicolai Konow
- Department of Biological Sciences, UMass, Lowell, MA, USA
| | - Joseph Schnitzler
- Institute for Terrestrial and Aquatic Wildlife Research, TiHo Hannover, Büsum, Germany
| | - David Lecchini
- USR 3278, PSL, Labex 'Corail', CRIOBE, Moorea, French Polynesia
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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Harrington RC, Faircloth BC, Eytan RI, Smith WL, Near TJ, Alfaro ME, Friedman M. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evol Biol 2016; 16:224. [PMID: 27769164 PMCID: PMC5073739 DOI: 10.1186/s12862-016-0786-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/30/2016] [Indexed: 11/26/2022] Open
Abstract
Background Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than 1,000 ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes. Results We present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0–23.03 Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.97 million years. Conclusions The longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0786-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard C Harrington
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK. .,Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, 06520, USA.
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Ron I Eytan
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77553, USA
| | - W Leo Smith
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, 06520, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Matt Friedman
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK.,Museum of Paleontology and Department of Earth and Environmental Science, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48109-1079, USA
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33
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McGee MD, Faircloth BC, Borstein SR, Zheng J, Darrin Hulsey C, Wainwright PC, Alfaro ME. Replicated divergence in cichlid radiations mirrors a major vertebrate innovation. Proc Biol Sci 2016; 283:rspb.2015.1413. [PMID: 26763694 DOI: 10.1098/rspb.2015.1413] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Decoupling of the upper jaw bones--jaw kinesis--is a distinctive feature of the ray-finned fishes, but it is not clear how the innovation is related to the extraordinary diversity of feeding behaviours and feeding ecology in this group. We address this issue in a lineage of ray-finned fishes that is well known for its ecological and functional diversity--African rift lake cichlids. We sequenced ultraconserved elements to generate a phylogenomic tree of the Lake Tanganyika and Lake Malawi cichlid radiations. We filmed a diverse array of over 50 cichlid species capturing live prey and quantified the extent of jaw kinesis in the premaxillary and maxillary bones. Our combination of phylogenomic and kinematic data reveals a strong association between biting modes of feeding and reduced jaw kinesis, suggesting that the contrasting demands of biting and suction feeding have strongly influenced cranial evolution in both cichlid radiations.
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Affiliation(s)
- Matthew D McGee
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Samuel R Borstein
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jimmy Zheng
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Peter C Wainwright
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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Abstract
A new study finds that the evolution of bioluminescent sexual displays drives high species richness across animal lineages, providing a crucial link between microevolutionary and macroevolutionary explanations of biodiversity.
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Affiliation(s)
- Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA.
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35
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Phuong MA, Mahardika GN, Alfaro ME. Dietary breadth is positively correlated with venom complexity in cone snails. BMC Genomics 2016; 17:401. [PMID: 27229931 PMCID: PMC4880860 DOI: 10.1186/s12864-016-2755-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/19/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. We tested these hypotheses under a comparative phylogenetic framework using ecological data from past studies in conjunction with venom duct transcriptomes sequenced from 12 phylogenetically disparate cone snail species, including 10 vermivores (worm-eating), one molluscivore, and one generalist. RESULTS We discovered 2223 unique conotoxin precursor peptides that encoded 1864 unique mature toxins across all species, >90 % of which are new to this study. In addition, we identified two novel gene superfamilies and 16 novel cysteine frameworks. Each species exhibited unique venom profiles, with venom composition and expression patterns among species dominated by a restricted set of gene superfamilies and mature toxins. In contrast with the dominant paradigm for interpreting Conidae venom evolution, prey taxonomic class did not predict venom composition patterns among species. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity. CONCLUSIONS The poor performance of prey taxonomic class in predicting venom components suggests that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type (i.e., worms, mollusc, or fish) and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also show that species with more generalized diets tend to have more complex venoms and utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.
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Affiliation(s)
- Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
| | - Gusti N Mahardika
- Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University Bali, Jl Sesetan-Markisa 6, Denpasar, Bali, 80225, Indonesia
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
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36
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Affiliation(s)
- Jonathan Chang
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
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Blumstein DT, Buckner J, Shah S, Patel S, Alfaro ME, Natterson-Horowitz B. A clinical research pathway towards developing new insights into cardiomyopathy. Evol Med Public Health 2015; 2015:280. [PMID: 26415642 PMCID: PMC4606057 DOI: 10.1093/emph/eov024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 11/21/2022]
Affiliation(s)
- Daniel T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA and
| | - Janet Buckner
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA and
| | - Sajan Shah
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA and
| | - Shane Patel
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA and
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA and
| | - Barbara Natterson-Horowitz
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA and David Geffen School of Medicine at UCLA, Division of Cardiology, 650 Charles E. Young Drive South, A2-237, Los Angeles, CA 90095, USA
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Van Wassenbergh S, van Manen K, Marcroft TA, Alfaro ME, Stamhuis EJ. Boxfish swimming paradox resolved: forces by the flow of water around the body promote manoeuvrability. J R Soc Interface 2015; 12:rsif.2014.1146. [PMID: 25505133 DOI: 10.1098/rsif.2014.1146] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The shape of the carapace protecting the body of boxfishes has been attributed an important hydrodynamic role in drag reduction and in providing automatic, flow-direction realignment and is therefore used in bioinspired design of cars. However, tight swimming-course stabilization is paradoxical given the frequent, high-performance manoeuvring that boxfishes display in their spatially complex, coral reef territories. Here, by performing flow-tank measurements of hydrodynamic drag and yaw moments together with computational fluid dynamics simulations, we reverse several assumptions about the hydrodynamic role of the boxfish carapace. Firstly, despite serving as a model system in aerodynamic design, drag-reduction performance was relatively low compared with more generalized fish morphologies. Secondly, the current theory of course stabilization owing to flow over the boxfish carapace was rejected, as destabilizing moments were found consistently. This solves the boxfish swimming paradox: destabilizing moments enhance manoeuvrability, which is in accordance with the ecological demands for efficient turning and tilting.
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Affiliation(s)
- S Van Wassenbergh
- Department of Biology, Universiteit Antwerpen, Universiteitsplein 1, 2610 Antwerpen, Belgium Evolutionar Morphology of Vertebrates, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - K van Manen
- Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 7, AG Groningen 9747, The Netherlands
| | - T A Marcroft
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 2154 Terasaki Life Sciences Building, Los Angeles, CA 90095, USA
| | - M E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 2154 Terasaki Life Sciences Building, Los Angeles, CA 90095, USA
| | - E J Stamhuis
- Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 7, AG Groningen 9747, The Netherlands Bionik Innovations Centrum, Hochschule Bremen, Neustadtswall 30, 28199 Bremen, Germany
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Blumstein DT, Buckner J, Shah S, Patel S, Alfaro ME, Natterson-Horowitz B. The evolution of capture myopathy in hooved mammals: a model for human stress cardiomyopathy? Evol Med Public Health 2015. [PMID: 26198189 PMCID: PMC4538952 DOI: 10.1093/emph/eov015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background and objectives: Capture myopathy (CM) syndromes in wildlife may be a model for human stress cardiomyopathy, including Takotsubo cardiomyopathy. Emotional stress or grief may trigger heart attack-like symptoms, and occasionally, sudden death in some humans. Similarly, wildlife exposed to predatory stresses, chase, or capture occasionally results in sudden death. To better understand the nature of vulnerability to stress-induced sudden death, we studied cases of CM in hooved mammals—ungulates—and hypothesized that CM would be associated with a syndrome of longevity-related traits. Methodology: We reconstructed the evolution of CM in ungulates then determined how a set of life history traits explained variation in the likelihood that CM was reported. Results: CM is broadly reported, but not in all genera, and phylogenetic analyses suggest that it is an evolutionarily labile trait. We found that the following traits were significantly associated with reports of CM: greater brain mass, faster maximum running speed, greater minimum group size and greater maximum longevity. Conclusions and implications: CM may be an unavoidable consequence of adaptations to reduce predation risk that include increased running speed, sociality and having larger brains. Moreover, longer-lived species seem to be more likely to be susceptible to CM. Exploring variable susceptibility to CM highlights the evolutionary origins of the disorder, potential basic mechanisms that underlie vulnerability to the phenomenon, and the potential for reduction of risk through modification of life history trajectory.
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Affiliation(s)
- Daniel T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA;
| | - Janet Buckner
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Sajan Shah
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Shane Patel
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Barbara Natterson-Horowitz
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA; David Geffen School of Medicine at UCLA, Division of Cardiology, 650 Charles E. Young Drive South, A2-237, Los Angeles, CA 90095, USA
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Gilbert PS, Chang J, Pan C, Sobel EM, Sinsheimer JS, Faircloth BC, Alfaro ME. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes. Mol Phylogenet Evol 2015; 92:140-6. [PMID: 26079130 DOI: 10.1016/j.ympev.2015.05.027] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/13/2015] [Accepted: 05/26/2015] [Indexed: 02/04/2023]
Abstract
Ultraconserved elements (UCEs) have become popular markers in phylogenomic studies because of their cost effectiveness and their potential to resolve problematic phylogenetic relationships. Although UCE datasets typically contain a much larger number of loci and sites than more traditional datasets of PCR-amplified, single-copy, protein coding genes, a fraction of UCE sites are expected to be part of a nearly invariant core, and the relative performance of UCE datasets versus protein coding gene datasets is poorly understood. Here we use phylogenetic informativeness (PI) to compare the resolving power of multi-locus and UCE datasets in a sample of percomorph fishes with sequenced genomes (genome-enabled). We compare three data sets: UCE core regions, flanking sequence adjacent to the UCE core and a set of ten protein coding genes commonly used in fish systematics. We found the net informativeness of UCE core and flank regions to be roughly ten-fold and 100-fold more informative than that of the protein coding genes. On a per locus basis UCEs and protein coding genes exhibited similar levels of phylogenetic informativeness. Our results suggest that UCEs offer enormous potential for resolving relationships across the percomorph tree of life.
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Affiliation(s)
- Princess S Gilbert
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.
| | - Jonathan Chang
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Calvin Pan
- Department of Medicine, University of California, Los Angeles, CA, USA
| | - Eric M Sobel
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Janet S Sinsheimer
- Department of Biomathematics, University of California, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, CA, USA; Department of Biostatistics, University of California, Los Angeles, CA, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Michael E Alfaro
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.
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41
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Boubli JP, Ribas C, Lynch Alfaro JW, Alfaro ME, da Silva MNF, Pinho GM, Farias IP. Spatial and temporal patterns of diversification on the Amazon: A test of the riverine hypothesis for all diurnal primates of Rio Negro and Rio Branco in Brazil. Mol Phylogenet Evol 2015; 82 Pt B:400-12. [DOI: 10.1016/j.ympev.2014.09.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 08/27/2014] [Accepted: 09/09/2014] [Indexed: 11/16/2022]
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Lynch Alfaro JW, Boubli JP, Paim FP, Ribas CC, Silva MNFD, Messias MR, Röhe F, Mercês MP, Silva Júnior JS, Silva CR, Pinho GM, Koshkarian G, Nguyen MT, Harada ML, Rabelo RM, Queiroz HL, Alfaro ME, Farias IP. Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate. Mol Phylogenet Evol 2015; 82 Pt B:436-54. [DOI: 10.1016/j.ympev.2014.09.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 08/02/2014] [Accepted: 09/09/2014] [Indexed: 12/15/2022]
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Frédérich B, Olivier D, Litsios G, Alfaro ME, Parmentier E. Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes. Proc Biol Sci 2014; 281:20141047. [PMID: 24990683 PMCID: PMC4100519 DOI: 10.1098/rspb.2014.1047] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/09/2014] [Indexed: 11/12/2022] Open
Abstract
Trait decoupling, wherein evolutionary release of constraints permits specialization of formerly integrated structures, represents a major conceptual framework for interpreting patterns of organismal diversity. However, few empirical tests of this hypothesis exist. A central prediction, that the tempo of morphological evolution and ecological diversification should increase following decoupling events, remains inadequately tested. In damselfishes (Pomacentridae), a ceratomandibular ligament links the hyoid bar and lower jaws, coupling two main morphofunctional units directly involved in both feeding and sound production. Here, we test the decoupling hypothesis by examining the evolutionary consequences of the loss of the ceratomandibular ligament in multiple damselfish lineages. As predicted, we find that rates of morphological evolution of trophic structures increased following the loss of the ligament. However, this increase in evolutionary rate is not associated with an increase in trophic breadth, but rather with morphofunctional specialization for the capture of zooplanktonic prey. Lineages lacking the ceratomandibular ligament also shows different acoustic signals (i.e. higher variation of pulse periods) from others, resulting in an increase of the acoustic diversity across the family. Our results support the idea that trait decoupling can increase morphological and behavioural diversity through increased specialization rather than the generation of novel ecotypes.
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Affiliation(s)
- Bruno Frédérich
- Laboratoire de Morphologie Fonctionnelle et Evolutive, Applied and Fundamental Fish Research Center, Université de Liège, 4000 Liège, Belgium
| | - Damien Olivier
- Laboratoire de Morphologie Fonctionnelle et Evolutive, Applied and Fundamental Fish Research Center, Université de Liège, 4000 Liège, Belgium
| | - Glenn Litsios
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Génopode, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Eric Parmentier
- Laboratoire de Morphologie Fonctionnelle et Evolutive, Applied and Fundamental Fish Research Center, Université de Liège, 4000 Liège, Belgium
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Collar DC, Reece JS, Alfaro ME, Wainwright PC, Mehta RS. Imperfect Morphological Convergence: Variable Changes in Cranial Structures Underlie Transitions to Durophagy in Moray Eels. Am Nat 2014; 183:E168-84. [DOI: 10.1086/675810] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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45
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Buckner JC, Lynch Alfaro JW, Rylands AB, Alfaro ME. Biogeography of the marmosets and tamarins (Callitrichidae). Mol Phylogenet Evol 2014; 82 Pt B:413-25. [PMID: 24857784 DOI: 10.1016/j.ympev.2014.04.031] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 04/09/2014] [Accepted: 04/15/2014] [Indexed: 11/26/2022]
Abstract
The marmosets and tamarins, Family Callitrichidae, are Neotropical primates with over 60 species and subspecies that inhabit much of South America. Although callitrichids exhibit a remarkable widespread distribution, attempts to unravel their biogeographic history have been limited by taxonomic confusion and the lack of an appropriate statistical biogeographic framework. Here, we construct a time-calibrated multi-locus phylogeny from GenBank data and the callitrichid literature for 38 taxa. We use this framework to conduct statistical biogeographic analyses of callitrichids using BioGeoBEARS. The DIVAj model is the best supported reconstruction of biogeographic history among our analyses and suggests that the most recent common ancestor to the callitrichids was widespread across forested regions c. 14 Ma. There is also support for multiple colonizations of the Atlantic forest region from the Amazon basin, first by Leontopithecus c. 11 Ma and later by Callithrix c. 5 Ma. Our results show support for a 9 million year old split between a small-bodied group and large-bodied group of tamarins. These phylogenetic data, in concert with the consistent difference in body size between the two groups and geographical patterns (small-bodied tamarins and large-bodied tamarins have an unusually high degree of geographic overlap for congeners) lend support to our suggestion to split Saguinus into two genera, and we propose the use of distinct generic names; Leontocebus and Saguinus, respectively.
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Affiliation(s)
- Janet C Buckner
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.
| | - Jessica W Lynch Alfaro
- Institute for Society and Genetics, University of California, Los Angeles, CA 90095, USA; Department of Anthropology, University of California, Los Angeles, CA 90095, USA
| | | | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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Pennell MW, Eastman JM, Slater GJ, Brown JW, Uyeda JC, FitzJohn RG, Alfaro ME, Harmon LJ. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. ACTA ACUST UNITED AC 2014; 30:2216-8. [PMID: 24728855 DOI: 10.1093/bioinformatics/btu181] [Citation(s) in RCA: 467] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
SUMMARY Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0, a complete overhaul of the popular R package geiger. We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types. AVAILABILITY AND IMPLEMENTATION This R package is available on the CRAN repository http://cran.r-project.org/web/packages/geiger/. All source code is also available on github http://github.com/mwpennell/geiger-v2. geiger v2.0 depends on the ape package. CONTACT mwpennell@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew W Pennell
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jonathan M Eastman
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Graham J Slater
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joseph W Brown
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Josef C Uyeda
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Richard G FitzJohn
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Luke J Harmon
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Santana SE, Alfaro JL, Noonan A, Alfaro ME. Adaptive response to sociality and ecology drives the diversification of facial colour patterns in catarrhines. Nat Commun 2013; 4:2765. [DOI: 10.1038/ncomms3765] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 10/14/2013] [Indexed: 11/09/2022] Open
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Walker JA, Alfaro ME, Noble MM, Fulton CJ. Body fineness ratio as a predictor of maximum prolonged-swimming speed in coral reef fishes. PLoS One 2013; 8:e75422. [PMID: 24204575 PMCID: PMC3799785 DOI: 10.1371/journal.pone.0075422] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022] Open
Abstract
The ability to sustain high swimming speeds is believed to be an important factor affecting resource acquisition in fishes. While we have gained insights into how fin morphology and motion influences swimming performance in coral reef fishes, the role of other traits, such as body shape, remains poorly understood. We explore the ability of two mechanistic models of the causal relationship between body fineness ratio and endurance swimming-performance to predict maximum prolonged-swimming speed (Umax ) among 84 fish species from the Great Barrier Reef, Australia. A drag model, based on semi-empirical data on the drag of rigid, submerged bodies of revolution, was applied to species that employ pectoral-fin propulsion with a rigid body at U max. An alternative model, based on the results of computer simulations of optimal shape in self-propelled undulating bodies, was applied to the species that swim by body-caudal-fin propulsion at Umax . For pectoral-fin swimmers, Umax increased with fineness, and the rate of increase decreased with fineness, as predicted by the drag model. While the mechanistic and statistical models of the relationship between fineness and Umax were very similar, the mechanistic (and statistical) model explained only a small fraction of the variance in Umax . For body-caudal-fin swimmers, we found a non-linear relationship between fineness and Umax , which was largely negative over most of the range of fineness. This pattern fails to support either predictions from the computational models or standard functional interpretations of body shape variation in fishes. Our results suggest that the widespread hypothesis that a more optimal fineness increases endurance-swimming performance via reduced drag should be limited to fishes that swim with rigid bodies.
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Affiliation(s)
- Jeffrey A. Walker
- Department of Biological Sciences, University of Southern Maine, Portland, Maine, United States of America
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Mae M. Noble
- ARC Centre of Excellence for Coral Reef Studies, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Christopher J. Fulton
- ARC Centre of Excellence for Coral Reef Studies, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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Santini F, Sorenson L, Alfaro ME. A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes). Mol Phylogenet Evol 2013; 69:165-76. [DOI: 10.1016/j.ympev.2013.05.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/19/2013] [Accepted: 05/20/2013] [Indexed: 12/01/2022]
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Santini F, Kong X, Sorenson L, Carnevale G, Mehta RS, Alfaro ME. A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes). Mol Phylogenet Evol 2013; 69:884-94. [PMID: 23831455 DOI: 10.1016/j.ympev.2013.06.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 05/21/2013] [Accepted: 06/24/2013] [Indexed: 11/25/2022]
Abstract
Anguilliformes are an ecologically diverse group of predominantly marine fishes whose members are easily recognized by their extremely elongate bodies, and universal lack of pelvic fins. Recent studies based on mitochondrial loci, including full mitogenomes, have called into question the monophyly of both the Anguilliformes, which appear to be paraphyletic without the inclusion of the Saccopharyngiformes (gulper eels and allies), as well as other more commonly known eel families (e.g., Congridae, Serrivomeridae). However, no study to date has investigated anguilliform interrelationships using nuclear loci. Here we present a new phylogenetic hypothesis for the Anguilliformes based on five markers (the nuclear loci Early Growth Hormone 3, Myosin Heavy Polypeptide 6 and Recombinase Activating Gene 1, as well as the mitochondrial genes Cytochrome b and Cytochrome Oxidase I). Our sampling spans 148 species and includes 19 of the 20 extant families of anguilliforms and saccopharyngiforms. Maximum likelihood analysis reveals that saccopharyngiform eels are deeply nested within the anguilliforms, and supports the non-monophyly of Congridae and Nettastomatidae, as well as that of Derichthyidae and Chlopsidae. Our analyses suggest that Protanguilla may be the sister group of the Synaphobranchidae, though the recent hypothesis that this species is the sister group to all other anguilliforms cannot be rejected. The molecular phylogeny, time-calibrated using a Bayesian relaxed clock approach and seven fossil calibration points, reveals a Late Cretaceous origin of this expanded anguilliform clade (stem age ~116 Ma, crown age ~99 Ma). Most major (family level) lineages originated between the end of the Cretaceous and Early Eocene, suggesting that anguilliform radiation may have been facilitated by the recovery of marine ecosystems following the KP extinction.
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Affiliation(s)
- Francesco Santini
- University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA; Università degli Studi di Torino, Dipartimento di Scienze della Terra, Via Valperga Caluso 35, 10125 Torino, Italy.
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