1
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Hay EM, McGee MD, White CR, Chown SL. Body size shapes song in honeyeaters. Proc Biol Sci 2024; 291:20240339. [PMID: 38654649 PMCID: PMC11040244 DOI: 10.1098/rspb.2024.0339] [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: 02/08/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
Birdsongs are among the most distinctive animal signals. Their evolution is thought to be shaped simultaneously by habitat structure and by the constraints of morphology. Habitat structure affects song transmission and detectability, thus influencing song (the acoustic adaptation hypothesis), while body size and beak size and shape necessarily constrain song characteristics (the morphological constraint hypothesis). Yet, support for the acoustic adaptation and morphological constraint hypotheses remains equivocal, and their simultaneous examination is infrequent. Using a phenotypically diverse Australasian bird clade, the honeyeaters (Aves: Meliphagidae), we compile a dataset consisting of song, environmental, and morphological variables for 163 species and jointly examine predictions of these two hypotheses. Overall, we find that body size constrains song frequency and pace in honeyeaters. Although habitat type and environmental temperature influence aspects of song, that influence is indirect, likely via effects of environmental variation on body size, with some evidence that elevation constrains the evolution of song peak frequency. Our results demonstrate that morphology has an overwhelming influence on birdsong, in support of the morphological constraint hypothesis, with the environment playing a secondary role generally via body size rather than habitat structure. These results suggest that changing body size (a consequence of both global effects such as climate change and local effects such as habitat transformation) will substantially influence the nature of birdsong.
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Affiliation(s)
- Eleanor M. Hay
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Matthew D. McGee
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Craig R. White
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Steven L. Chown
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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2
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Tims AR, Unmack PJ, Hammer MP, Brown C, Adams M, McGee MD. Museum genomics reveals the hybrid origin of an extinct crater lake endemic. Syst Biol 2024:syae017. [PMID: 38597146 DOI: 10.1093/sysbio/syae017] [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: 10/25/2023] [Indexed: 04/11/2024] Open
Abstract
Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.
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Affiliation(s)
- Amy R Tims
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Peter J Unmack
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
- Institute for Applied Ecology, Centre for Applied Water Science, University of Canberra, Australian Capital Territory 2601, Australia
| | - Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory 0801, Australia
| | - Culum Brown
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Mark Adams
- South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew D McGee
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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3
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Eastment RV, Wong BBM, McGee MD. Convergent genomic signatures associated with vertebrate viviparity. BMC Biol 2024; 22:34. [PMID: 38331819 PMCID: PMC10854053 DOI: 10.1186/s12915-024-01837-w] [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: 08/29/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Viviparity-live birth-is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes? RESULTS We reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes-be it at the nucleotide or protein level-common to all viviparous lineages. CONCLUSIONS Our results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.
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Affiliation(s)
- Rhiannon V Eastment
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia.
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
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4
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Meier JI, McGee MD, Marques DA, Mwaiko S, Kishe M, Wandera S, Neumann D, Mrosso H, Chapman LJ, Chapman CA, Kaufman L, Taabu-Munyaho A, Wagner CE, Bruggmann R, Excoffier L, Seehausen O. Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science 2023; 381:eade2833. [PMID: 37769075 DOI: 10.1126/science.ade2833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/21/2023] [Indexed: 09/30/2023]
Abstract
Although some lineages of animals and plants have made impressive adaptive radiations when provided with ecological opportunity, the propensities to radiate vary profoundly among lineages for unknown reasons. In Africa's Lake Victoria region, one cichlid lineage radiated in every lake, with the largest radiation taking place in a lake less than 16,000 years old. We show that all of its ecological guilds evolved in situ. Cycles of lineage fusion through admixture and lineage fission through speciation characterize the history of the radiation. It was jump-started when several swamp-dwelling refugial populations, each of which were of older hybrid descent, met in the newly forming lake, where they fused into a single population, resuspending old admixture variation. Each population contributed a different set of ancient alleles from which a new adaptive radiation assembled in record time, involving additional fusion-fission cycles. We argue that repeated fusion-fission cycles in the history of a lineage make adaptive radiation fast and predictable.
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Affiliation(s)
- Joana I Meier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D McGee
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Natural History Museum Basel, Basel, Switzerland
| | - Salome Mwaiko
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Mary Kishe
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Sylvester Wandera
- National Fisheries Resources Research Institute (NAFIRRI), Jinja, Uganda
| | - Dirk Neumann
- Leipniz Institute for Biodiversity Change, Hamburg, Germany
| | - Hilary Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Colin A Chapman
- Wilson Center, Washington, DC, USA
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Les Kaufman
- Boston University Marine Program, Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
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5
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Abstract
Abstract
Background
Darwin and others proposed that a species’ geographic range size positively influences speciation likelihood, with the relationship potentially dependent on the mode of speciation and other contributing factors, including geographic setting and species traits. Several alternative proposals for the influence of range size on speciation rate have also been made (e.g. negative or a unimodal relationship with speciation). To examine Darwin’s proposal, we use a range of phylogenetic comparative methods, focusing on a large Australasian bird clade, the honeyeaters (Aves: Meliphagidae).
Results
We consider the influence of range size, shape, and position (latitudinal and longitudinal midpoints, island or continental species), and consider two traits known to influence range size: dispersal ability and body size. Applying several analytical approaches, including phylogenetic Bayesian path analysis, spatiophylogenetic models, and state-dependent speciation and extinction models, we find support for both the positive relationship between range size and speciation rate and the influence of mode of speciation.
Conclusions
Honeyeater speciation rate differs considerably between islands and the continental setting across the clade’s distribution, with range size contributing positively in the continental setting, while dispersal ability influences speciation regardless of setting. These outcomes support Darwin’s original proposal for a positive relationship between range size and speciation likelihood, while extending the evidence for the contribution of dispersal ability to speciation.
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6
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Thompson KA, Peichel CL, Rennison DJ, McGee MD, Albert AYK, Vines TH, Greenwood AK, Wark AR, Brandvain Y, Schumer M, Schluter D. Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent. PLoS Biol 2022; 20:e3001469. [PMID: 35007278 PMCID: PMC8746713 DOI: 10.1371/journal.pbio.3001469] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/04/2021] [Indexed: 12/25/2022] Open
Abstract
Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
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Affiliation(s)
- Ken A. Thompson
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
| | - Catherine L. Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diana J. Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Matthew D. McGee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Timothy H. Vines
- DataSeer Research Data Services, Vancouver, British Columbia, Canada
| | | | - Abigail R. Wark
- Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Maryland, United States of America
| | - Dolph Schluter
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
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7
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Thacker CE, Shelley JJ, McCraney WT, Unmack PJ, McGee MD. Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock. Syst Biol 2021; 71:13-23. [PMID: 33682001 PMCID: PMC8677556 DOI: 10.1093/sysbio/syab014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/21/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
Adaptive radiations are generally thought to occur soon after a lineage invades a region offering high levels of ecological opportunity. However, few adaptive radiations beyond a handful of exceptional examples are known, so a comprehensive understanding of their dynamics is still lacking. Here, we present a novel case of an island species flock of freshwater fishes with a radically different tempo of adaptive history than that found in many popular evolutionary model systems. Using a phylogenomic data set combined with simultaneous Bayesian estimation of divergence times and trait-based speciation and extinction models, we show that the New Zealand Gobiomorphus gudgeons comprise a monophyletic assemblage, but surprisingly, the radiation did not fully occupy freshwater habitats and explosively speciate until more than 10 myr after the lineage invaded the islands. This shift in speciation rate was not accompanied by an acceleration in the rate of morphological evolution in the freshwater crown clade relative to the other species, but is correlated with a reduction in head pores and scales as well as an increase in egg size. Our results challenge the notion that clades always rapidly exploit ecological opportunities in the absence of competing lineages. Instead, we demonstrate that adaptive radiation can experience a slow start before undergoing accelerated diversification and that lineage and phenotypic diversification may be uncoupled in young radiations. [Adaptive radiation; Eleotridae; freshwater; Gobiomorphus; New Zealand.]
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Affiliation(s)
- Christine E Thacker
- Vertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara CA USA.,Research and Collections, Section of Ichthyology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA USA
| | - James J Shelley
- National Institute of Water and Atmospheric Research, Gate 10 Silverdale Road Hillcrest, 3216 Hamilton, New Zealand
| | - W Tyler McCraney
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 612 Charles E. Young Drive South, Box 957246, Los Angeles, CA 90095-7246 USA
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra Canberra ACT 2601, Australia
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
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8
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Feller AF, Selz OM, McGee MD, Meier JI, Mwaiko S, Seehausen O. Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids. Ecol Evol 2020; 10:7445-7462. [PMID: 32760540 PMCID: PMC7391563 DOI: 10.1002/ece3.6471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 01/28/2020] [Revised: 05/15/2020] [Accepted: 05/16/2020] [Indexed: 01/25/2023] Open
Abstract
The East African cichlid radiations are characterized by repeated and rapid diversification into many distinct species with different ecological specializations and by a history of hybridization events between nonsister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second-generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialized on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialized on sand sifting. We combined experimental behavioral and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behavior related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioral traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behavior in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behavior, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.
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Affiliation(s)
- Anna F. Feller
- Division of Aquatic Ecology and EvolutionInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
| | - Oliver M. Selz
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
| | - Matthew D. McGee
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Joana I. Meier
- Division of Aquatic Ecology and EvolutionInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Department of ZoologyUniversity of CambridgeCambridgeUK
- St John’s CollegeUniversity of CambridgeCambridgeUK
| | - Salome Mwaiko
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
| | - Ole Seehausen
- Division of Aquatic Ecology and EvolutionInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
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9
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Schmid DW, McGee MD, Best RJ, Seehausen O, Matthews B. Rapid Divergence of Predator Functional Traits Affects Prey Composition in Aquatic Communities. Am Nat 2019; 193:331-345. [PMID: 30794448 DOI: 10.1086/701784] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Identifying traits that underlie variation in individual performance of consumers (i.e., trait utility) can help reveal the ecological causes of population divergence and the subsequent consequences for species interactions and community structure. Here, we document a case of rapid divergence (over the past 100 generations, or ∼150 years) in foraging traits and feeding efficiency between a lake and stream population pair of threespine stickleback. Building on predictions from functional trait models of fish feeding, we analyzed foraging experiments with a Bayesian path analysis and elucidated the traits explaining variation in foraging performance and the species composition of ingested prey. Despite extensive previous research on the divergence of foraging traits among populations and ecotypes of stickleback, our results provide novel experimental evidence of trait utility for jaw protrusion, gill raker length, and gill raker spacing when foraging on a natural zooplankton assemblage. Furthermore, we discuss how these traits might contribute to the differential effects of lake and stream stickleback on their prey communities, observed in both laboratory and mesocosm conditions. More generally, our results illustrate how the rapid divergence of functional foraging traits of consumers can impact the biomass, species composition, and trophic structure of prey communities.
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10
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Tang HYH, Shin DS, Hura GL, Yang Y, Hu X, Lightstone FC, McGee MD, Padgett HS, Yannone SM, Tainer JA. Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase. Biochemistry 2018; 57:6688-6700. [PMID: 30376300 DOI: 10.1021/acs.biochem.8b00963] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein engineering to alter recognition underlying ligand binding and activity has enormous potential. Here, ligand binding for Escherichia coli phosphoenolpyruvate carboxykinase (PEPCK), which converts oxaloacetate into CO2 and phosphoenolpyruvate as the first committed step in gluconeogenesis, was engineered to accommodate alternative ligands as an exemplary system with structural information. From our identification of bicarbonate binding in the PEPCK active site at the supposed CO2 binding site, we probed binding of nonnative ligands with three oxygen atoms arranged to resemble the bicarbonate geometry. Crystal structures of PEPCK and point mutants with bound nonnative ligands thiosulfate and methanesulfonate along with strained ATP and reoriented oxaloacetate intermediates and unexpected bicarbonate were determined and analyzed. The mutations successfully altered the bound ligand position and orientation and its specificity: mutated PEPCKs bound either thiosulfate or methanesulfonate but never both. Computational calculations predicted a methanesulfonate binding mutant and revealed that release of the active site ordered solvent exerts a strong influence on ligand binding. Besides nonnative ligand binding, one mutant altered the Mn2+ coordination sphere: instead of the canonical octahedral ligand arrangement, the mutant in question had an only five-coordinate arrangement. From this work, critical features of ligand binding, position, and metal ion cofactor geometry required for all downstream events can be engineered with small numbers of mutations to provide insights into fundamental underpinnings of protein-ligand recognition. Through structural and computational knowledge, the combination of designed and random mutations aids in the robust design of predetermined changes to ligand binding and activity to engineer protein function.
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Affiliation(s)
- Henry Y H Tang
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - David S Shin
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Biochemistry and Chemistry , University of California , Santa Cruz , California 95064 , United States
| | - Yue Yang
- Biosciences and Biotechnology Division , Lawrence Livermore National Laboratory , Livermore , California 94550 , United States
| | - Xiaoyu Hu
- Department of Chemical Engineering , Tsinghua University , Beijing 100084 , China
| | - Felice C Lightstone
- Biosciences and Biotechnology Division , Lawrence Livermore National Laboratory , Livermore , California 94550 , United States
| | - Matthew D McGee
- Novici Biotech LLC , Vacaville , California 95688 , United States
| | - Hal S Padgett
- Novici Biotech LLC , Vacaville , California 95688 , United States
| | - Steven M Yannone
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Molecular and Cellular Oncology , The University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
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11
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Martinez CM, McGee MD, Borstein SR, Wainwright PC. Feeding ecology underlies the evolution of cichlid jaw mobility. Evolution 2018; 72:1645-1655. [PMID: 29920668 DOI: 10.1111/evo.13518] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 01/31/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 12/25/2022]
Abstract
The fish feeding apparatus is among the most diverse functional systems in vertebrates. While morphological and mechanical variations of feeding systems are well studied, we know far less about the diversity of the motions that they produce. We explored patterns of feeding movements in African cichlids from Lakes Malawi and Tanganyika, asking whether the degree of kinesis is associated with dietary habits of species. We used geometric morphometrics to measure feeding kinesis as trajectories of shape change, based on 326 high-speed videos in 56 species. Cranial morphology was significantly related to feeding movements, both of which were distributed along a dietary axis associated with prey evasiveness. Small-mouthed cichlids that feed by scraping algae and detritus from rocks had low kinesis strikes, while large-mouthed species that eat large, evasive prey (fishes and shrimps) generated the greatest kinesis. Despite having higher overall kinesis, comparisons of trajectory shape (linearity) revealed that cichlids that eat mobile prey also displayed more kinematically conserved, or efficient, feeding motions. Our work indicates that prey evasiveness is strongly related to the evolution of cichlid jaw mobility, suggesting that this same relationship may explain the origins and diversity of highly kinetic jaws that characterize the super-radiation of spiny-rayed fishes.
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Affiliation(s)
| | - Matthew D McGee
- School of Biological Sciences, Monash University, 3800 Victoria, Australia
| | - Samuel R Borstein
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Peter C Wainwright
- Department of Evolution and Ecology, University of California, Davis, California 95616
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12
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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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McGee MD, Neches RY, Seehausen O. Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations. Mol Ecol 2016; 25:260-8. [PMID: 26558354 DOI: 10.1111/mec.13463] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 05/29/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 01/22/2023]
Abstract
Comparative genomic studies of closely related species typically focus on single species pairs at one given stage of divergence. That makes it difficult to infer the continuum of evolutionary process during speciation and beyond. Here, we use whole-genome resequencing to examine genomic patterns of divergence in three sympatric cichlid species pairs with very similar functional and ecological differentiation, but different ages. We find a strong signature of increasing genomic divergence with time in both the mitochondrial genome and the nuclear genome. In contrast to many other systems, we find that in these cichlids, regions of elevated relative differentiation also exhibit increased absolute differentiation. We detect a signature of convergent evolution in a comparison of outlier regions across all three species pair comparisons, but the extent of it is modest, and regions that are strongly divergent in any one pair tend to be only slightly elevated in the other pairs, consistent with a repeatable but polygenic basis of traits that characterize the ecomorphs. Our results suggest that strong functional phenotypic differentiation, as seen in all three species pairs, is generally associated with a clear signature of genomic divergence, even in the youngest species pair.
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Affiliation(s)
- Matthew D McGee
- Institute of Ecology and Evolution, University of Bern, Bern, CH-3012, Switzerland.,Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, CH-6047, Switzerland
| | - Russell Y Neches
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA, 95616, USA
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, CH-3012, Switzerland.,Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, CH-6047, Switzerland
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McGee MD, Borstein SR, Neches RY, Buescher HH, Seehausen O, Wainwright PC. A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids. Science 2015; 350:1077-9. [PMID: 26612951 DOI: 10.1126/science.aab0800] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Evolutionary innovations, traits that give species access to previously unoccupied niches, may promote speciation and adaptive radiation. Here, we show that such innovations can also result in competitive inferiority and extinction. We present evidence that the modified pharyngeal jaws of cichlid fishes and several marine fish lineages, a classic example of evolutionary innovation, are not universally beneficial. A large-scale analysis of dietary evolution across marine fish lineages reveals that the innovation compromises access to energy-rich predator niches. We show that this competitive inferiority shaped the adaptive radiation of cichlids in Lake Tanganyika and played a pivotal and previously unrecognized role in the mass extinction of cichlid fishes in Lake Victoria after Nile perch invasion.
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Affiliation(s)
- Matthew D McGee
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA. Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland. Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland.
| | - Samuel R Borstein
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Russell Y Neches
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Heinz H Buescher
- Zoological Institute, University of Basel, CH-4051 Basel, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland. Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
| | - Peter C Wainwright
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
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McGee MD, Reustle JW, Oufiero CE, Wainwright PC. Intermediate Kinematics Produce Inferior Feeding Performance in a Classic Case of Natural Hybridization. Am Nat 2015; 186:807-14. [DOI: 10.1086/683464] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Martin RA, McGee MD, Langerhans RB. Predicting ecological and phenotypic differentiation in the wild: a case of piscivorous fish in a fishless environment. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12449] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Ryan A. Martin
- Department of Biological Sciences; W. M. Keck Center for Behavioral Biology; North Carolina State University; Raleigh NC 27695 USA
- Department of Biology; Case Western Reserve University; Cleveland OH 44106-7060 USA
| | - Matthew D. McGee
- Department of Evolution and Ecology; University of California, Davis; One Shields Avenue Davis CA 95616 USA
| | - R. Brian Langerhans
- Department of Biological Sciences; W. M. Keck Center for Behavioral Biology; North Carolina State University; Raleigh NC 27695 USA
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Longo SJ, McGee MD, Oufiero CE, Waltzek TB, Wainwright PC. Body ram, not suction, is the primary axis of suction feeding diversity in spiny-rayed fishes. J Exp Biol 2015; 219:119-28. [DOI: 10.1242/jeb.129015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/04/2015] [Indexed: 11/20/2022]
Abstract
Suction feeding fishes exhibit diverse prey capture strategies that vary in their relative use of suction and predator approach (ram), which is often referred to as the ram-suction continuum. Previous research has found that ram varies more than suction distances among species, such that ram accounts for most differences in prey capture behaviors. To determine whether these findings hold at broad evolutionary scales, we collected high-speed videos of 40 species of spiny-rayed fishes (Acanthomorpha) feeding on live prey. For each strike, we calculated the contributions of suction, body ram (swimming), and jaw ram (mouth movement relative to the body) to closing the distance between predator and prey. We confirm that the contribution of suction distance is limited even in this phylogenetically and ecologically broad sample of species, with the extreme suction area of prey capture space conspicuously unoccupied. Instead of a continuum from suction to ram, we find that variation in body ram is the major factor underlying the diversity of prey-capture strategies among suction-feeding fishes. Independent measurement of the contribution of jaw ram revealed that it is an important component of diversity among spiny-rayed fishes, with a number of ecomorphologies relying heavily on jaw ram, including pivot feeding in syngnathiforms, extreme jaw protruders, and benthic sit-and-wait ambush predators. A combination of morphological and behavioral innovations have allowed fish to invade the extreme jaw ram area of prey capture space. We caution that while two-species comparisons may support a ram-suction trade-off, these patterns do not speak to broader patterns across spiny-rayed fishes
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Affiliation(s)
- Sarah J. Longo
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Matthew D. McGee
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland 3012
| | | | - Thomas B. Waltzek
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, USA
| | - Peter C. Wainwright
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Arnegard ME, McGee MD, Matthews B, Marchinko KB, Conte GL, Kabir S, Bedford N, Bergek S, Chan YF, Jones FC, Kingsley DM, Peichel CL, Schluter D. Genetics of ecological divergence during speciation. Nature 2014; 511:307-11. [PMID: 24909991 PMCID: PMC4149549 DOI: 10.1038/nature13301] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [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: 06/04/2013] [Accepted: 04/01/2014] [Indexed: 01/15/2023]
Abstract
Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context.
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Affiliation(s)
- Matthew E Arnegard
- 1] Fred Hutchinson Cancer Research Center, Human Biology and Basic Sciences Divisions, 1100 Fairview Avenue North, Seattle, Washington 98109, USA [2] University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Matthew D McGee
- University of California at Davis, Department of Evolution and Ecology, One Shields Avenue, Davis, California 95616, USA
| | - Blake Matthews
- EAWAG, Department of Aquatic Ecology, Center for Ecology, Evolution, and Biogeochemistry, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Kerry B Marchinko
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Gina L Conte
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sahriar Kabir
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nicole Bedford
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sara Bergek
- 1] Uppsala University, Department of Animal Ecology, Evolutionary Biology Centre (EBC), Norbyvägen 18D, SE-75236 Uppsala, Sweden [2] Swedish University of Agricultural Sciences, Department of Aquatic Resources, Stångholmsvägen 2, SE-17893 Drottningholm, Sweden
| | - Yingguang Frank Chan
- Stanford University School of Medicine, Department of Developmental Biology and Howard Hughes Medical Institute, 279 Campus Drive, Stanford, California 94305, USA
| | - Felicity C Jones
- Stanford University School of Medicine, Department of Developmental Biology and Howard Hughes Medical Institute, 279 Campus Drive, Stanford, California 94305, USA
| | - David M Kingsley
- Stanford University School of Medicine, Department of Developmental Biology and Howard Hughes Medical Institute, 279 Campus Drive, Stanford, California 94305, USA
| | - Catherine L Peichel
- Fred Hutchinson Cancer Research Center, Human Biology and Basic Sciences Divisions, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
| | - Dolph Schluter
- University of British Columbia, Biodiversity Research Centre and Zoology Department, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
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McGee MD, Schluter D, Wainwright PC. Functional basis of ecological divergence in sympatric stickleback. BMC Evol Biol 2013; 13:277. [PMID: 24380474 PMCID: PMC3890603 DOI: 10.1186/1471-2148-13-277] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [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: 09/14/2013] [Accepted: 12/04/2013] [Indexed: 11/10/2022] Open
Abstract
Background The evolution of ecological divergence in closely related species is a key component of adaptive radiation. However, in most examples of adaptive radiation the mechanistic basis of ecological divergence remains unclear. A classic example is seen in the young benthic and limnetic stickleback species pairs of British Columbia. In each pair the benthic species feeds on littoral macroinvertebrates whereas the limnetic feeds on pelagic zooplankton. Previous studies indicate that in both short-term feeding trials and long-term enclosure studies, benthics and limnetics exhibit enhanced performance on their own resource but fare more poorly on the other species’ resource. We examined the functional basis of ecological divergence in the stickleback species pair from Paxton Lake, BC, using biomechanical models of fish feeding applied to morphological traits. We examined the consequences of morphological differences using high speed video of feeding fish. Results Benthic stickleback possess morphological traits that predict high suction generation capacity, including greatly hypertrophied epaxial musculature. In contrast, limnetic stickleback possess traits thought to enhance capture of evasive planktonic prey, including greater jaw protrusion than benthics and greater displacement advantage in both the lower jaw-opening lever system and the opercular four-bar linkage. Kinematic data support the expectations from the morphological analysis that limnetic stickleback exhibit faster strikes and greater jaw protrusion than benthic fish, whereas benthics exert greater suction force on attached prey. Conclusions We reveal a previously unknown suite of complex morphological traits that affect rapid ecological divergence in sympatric stickleback. These results indicate that postglacial divergence in stickleback involves many functional systems and shows the value of investigating the functional consequences of phenotypic divergence in adaptive radiation.
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Affiliation(s)
- Matthew D McGee
- Department of Evolution and Ecology, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA.
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20
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Abstract
SUMMARY
Sexual dimorphism is common in nature and has the potential to increase intraspecific variation in performance and patterns of resource use. We sought to determine whether anadromous threespine stickleback, Gasterosteus aculeatus, exhibit sexual dimorphism in feeding kinematics. We filmed four males and four females consuming live prey in a total of 51 sequences filmed at 500 Hz, then tested for differences in cranial kinematics using a combination of principal component analysis and linear mixed models. We document, for the first time in fishes, divergence between males and females in both the timing of key movements and the magnitude of excursions reached by the hyoid, jaws and neurocranium during prey capture. Some of the largest differences are in jaw protrusion, with males exhibiting faster time to peak jaw protrusion but females exhibiting greater maximum jaw protrusion. Measurements of morphological jaw protrusion on cleared and stained specimens significantly predict jaw protrusion in kinematics. This morphological divergence could reflect ecological divergence between the sexes, or the demands of nest building and territory defense compromising male feeding performance. Remarkably, the morphological jaw protrusion divergence in anadromous males and females is similar to jaw protrusion divergence between ecomorphs in a benthic–limnetic species pair, with limnetics exhibiting female-like patterns of protrusion and benthics exhibiting male-like patterns. These results suggest that sexual dimorphism in feeding functional morphology exists in nature and may have played an important role in the radiation of threespine stickleback.
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Affiliation(s)
- Matthew D. McGee
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Peter C. Wainwright
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Schmitz L, Motani R, Oufiero CE, Martin CH, McGee MD, Gamarra AR, Lee JJ, Wainwright PC. Allometry indicates giant eyes of giant squid are not exceptional. BMC Evol Biol 2013; 13:45. [PMID: 23418818 PMCID: PMC3661360 DOI: 10.1186/1471-2148-13-45] [Citation(s) in RCA: 9] [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: 09/23/2012] [Accepted: 02/11/2013] [Indexed: 11/30/2022] Open
Abstract
Background The eyes of giant and colossal squid are among the largest eyes in the history of life. It was recently proposed that sperm whale predation is the main driver of eye size evolution in giant squid, on the basis of an optical model that suggested optimal performance in detecting large luminous visual targets such as whales in the deep sea. However, it is poorly understood how the eye size of giant and colossal squid compares to that of other aquatic organisms when scaling effects are considered. Results We performed a large-scale comparative study that included 87 squid species and 237 species of acanthomorph fish. While squid have larger eyes than most acanthomorphs, a comparison of relative eye size among squid suggests that giant and colossal squid do not have unusually large eyes. After revising constants used in a previous model we found that large eyes perform equally well in detecting point targets and large luminous targets in the deep sea. Conclusions The eyes of giant and colossal squid do not appear exceptionally large when allometric effects are considered. It is probable that the giant eyes of giant squid result from a phylogenetically conserved developmental pattern manifested in very large animals. Whatever the cause of large eyes, they appear to have several advantages for vision in the reduced light of the deep mesopelagic zone.
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Affiliation(s)
- Lars Schmitz
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
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Abstract
Convergent evolution, in which populations produce similar phenotypes in response to similar selection pressure, is strong evidence for the role of natural selection in shaping biological diversity. In some cases, closely related populations can produce functionally similar but phenotypically divergence forms in response to selection. Functional convergence with morphological divergence has been observed in laboratory selection experiments and computer simulations, but while potentially common, is rarely recognized in nature. Here, we present data from the North Pacific threespine stickleback radiation showing that ecologically and functionally similar, but morphologically divergent phenotypes rapidly evolved when an ancestral population colonized freshwater benthic habitats in parallel. In addition, we show that in this system, functional convergence substantially increases morphospace occupation relative to ancestral phenotypes, which suggests that convergent evolution may, paradoxically, be an important and previously underappreciated source of morphological diversity.
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Affiliation(s)
- Matthew D McGee
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California 95616, USA.
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Schmitz L, Motani R, Oufiero CE, Martin CH, McGee MD, Wainwright PC. Potential enhanced ability of giant squid to detect sperm whales is an exaptation tied to their large body size. BMC Evol Biol 2013; 13:226. [PMID: 24127991 PMCID: PMC3852725 DOI: 10.1186/1471-2148-13-226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 11/10/2022] Open
Abstract
It has been hypothesized that sperm whale predation is the driver of eye size evolution in giant squid. Given that the eyes of giant squid have the size expected for a squid this big, it is likely that any enhanced ability of giant squid to detect whales is an exaptation tied to their body size. Future studies should target the mechanism behind the evolution of large body size, not eye size. Reconstructions of the evolutionary history of selective regime, eye size, optical performance, and body size will improve the understanding of the evolution of large eyes in large ocean animals.
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Abstract
The roundworm C. elegans is widely used as an aging model, with hundreds of genes identified that modulate aging (Kaeberlein et al., 2002. Mech. Ageing Dev.123, 1115-1119). The development and bodyplan of the 959 cells comprising the adult have been well described and established for more than 25 years (Sulston & Horvitz, 1977. Dev. Biol.56, 110-156; Sulston et al., 1983. Dev. Biol.100, 64-119.). However, morphological changes with age in this optically transparent animal are less well understood, with only a handful of studies investigating the pathobiology of aging. Age-related changes in muscle (Herndon et al., 2002. Nature419, 808-814), neurons (Herndon et al., 2002), intestine and yolk granules (Garigan et al., 2002. Genetics161, 1101-1112; Herndon et al., 2002), nuclear architecture (Haithcock et al., 2005. Proc. Natl Acad. Sci. USA102, 16690-16695), tail nuclei (Golden et al., 2007. Aging Cell6, 179-188), and the germline (Golden et al., 2007) have been observed via a variety of traditional relatively low-throughput methods. We report here a number of novel approaches to study the pathobiology of aging C. elegans. We combined histological staining of serial-sectioned tissues, transmission electron microscopy, and confocal microscopy with 3D volumetric reconstructions and characterized age-related morphological changes in multiple wild-type individuals at different ages. This enabled us to identify several novel pathologies with age in the C. elegans intestine, including the loss of critical nuclei, the degradation of intestinal microvilli, changes in the size, shape, and cytoplasmic contents of the intestine, and altered morphologies caused by ingested bacteria. The three-dimensional models we have created of tissues and cellular components from multiple individuals of different ages represent a unique resource to demonstrate global heterogeneity of a multicellular organism.
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Affiliation(s)
- Matthew D McGee
- Buck Institute for Age Research, 8001 Redwood Blvd., Novato, CA 94945, USA
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Abstract
Klarsicht, ANC-1 and Syne homology (KASH) proteins localize to the outer nuclear membrane where they connect the nucleus to the cytoskeleton. KASH proteins interact with Sad1-UNC-84 (SUN) proteins to transfer forces across the nuclear envelope to position nuclei or move chromosomes. A new KASH protein, KDP-1, was identified in a membrane yeast two-hybrid screen of a Caenorhabditis elegans library using the SUN protein UNC-84 as bait. KDP-1 also interacted with SUN-1. KDP-1 was enriched at the nuclear envelope in a variety of tissues and required SUN-1 for nuclear envelope localization in the germline. Genetic analyses showed that kdp-1 was essential for embryonic viability, larval growth and germline development. kdp-1(RNAi) delayed the entry into mitosis in embryos, led to a small mitotic zone in the germline, and caused an endomitotic phenotype. Aspects of these phenotypes were similar to those seen in sun-1(RNAi), suggesting that KDP-1 functions with SUN-1 in the germline and early embryo. The data suggest that KDP-1 is a novel KASH protein that functions to ensure the timely progression of the cell cycle between the end of S phase and the entry into mitosis.
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Affiliation(s)
- Matthew D McGee
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
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McGee MD, Rillo R, Anderson AS, Starr DA. UNC-83 IS a KASH protein required for nuclear migration and is recruited to the outer nuclear membrane by a physical interaction with the SUN protein UNC-84. Mol Biol Cell 2006; 17:1790-801. [PMID: 16481402 PMCID: PMC1415293 DOI: 10.1091/mbc.e05-09-0894] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
UNC-84 is required to localize UNC-83 to the nuclear envelope where it functions during nuclear migration. A KASH domain in UNC-83 was identified. KASH domains are conserved in the nuclear envelope proteins Syne/nesprins, Klarsicht, MSP-300, and ANC-1. Caenorhabditis elegans UNC-83 was shown to localize to the outer nuclear membrane and UNC-84 to the inner nuclear membrane in transfected mammalian cells, suggesting the KASH and SUN protein targeting mechanisms are conserved. Deletion of the KASH domain of UNC-83 blocked nuclear migration and localization to the C. elegans nuclear envelope. Some point mutations in the UNC-83 KASH domain disrupted nuclear migration, even if they localized normally. At least two separable portions of the C-terminal half of UNC-84 were found to interact with the UNC-83 KASH domain in a membrane-bound, split-ubiquitin yeast two-hybrid system. However, the SUN domain was essential for UNC-84 function and UNC-83 localization in vivo. These data support the model that KASH and SUN proteins bridge the nuclear envelope, connecting the nuclear lamina to cytoskeletal components. This mechanism seems conserved across eukaryotes and is the first proposed mechanism to target proteins specifically to the outer nuclear membrane.
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Affiliation(s)
- Matthew D McGee
- The Center for Genetics and Development and the Section of Molecular and Cellular Biology, University of California-Davis, Davis, CA 95616, USA
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Russell JM, Early TS, Patterson JC, Martin JL, Villanueva-Meyer J, McGee MD. Temporal lobe perfusion asymmetries in schizophrenia. J Nucl Med 1997; 38:607-12. [PMID: 9098211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
UNLABELLED Structural and functional neuroimaging techniques have consistently demonstrated that abnormal lateralization of temporal lobes may be important in identifying the pathophysiologic processes in schizophrenia. The exact nature of these reported abnormalities has not been consistent. METHODS We examined temporal lobe perfusion using HMPAO-SPECT in 22 individuals with schizophrenia in an effort to establish whether temporal lobe perfusion asymmetry is seen in these individuals, as compared to a group of 22 age- and sex-matched controls. RESULTS We found that the asymmetry index, a measure of perfusion differences between two homologous compared areas, was lower (more negative) in schizophrenic individuals. The asymmetry indices of patients considered with the results from globally corrected ROI means indicated that the left temporal lobes of individuals with schizophrenia were significantly hypoperfused when compared to controls. This finding does not appear to be caused by medication effects, demographic variables, handedness, imaging artifacts or analysis techniques. CONCLUSION In our sample, patients with schizophrenia appear to have significant left hypoperfusion relative to right of their temporal lobes. Abnormal lateralization of temporal lobe blood flow may have important clinical implications by assisting with diagnosis and appropriate treatment for individuals with schizophrenia.
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Affiliation(s)
- J M Russell
- Department of Psychiatry and Behavioral Science, University of Texas Medical Branch, Galveston 77555-0428, USA
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Abstract
The improvements in both clinical and fiscal outcomes necessary for prosperity in the current healthcare environment require a rethinking of our conceptual approaches to patient assessment, treatment planning, and service delivery. Conventional practice rests in part on the Level of Care concept, which assigns intensities of both clinical services and treatment settings in a linked manner according to impairment severity. Although this approach has resulted in more efficient matching of resources to needs, it is overly restrictive, and does not speak directly to the need to match both healthcare and social services (including treatment setting) to human needs for treatment to be successful. The Human Service Matrix model presented in this article delinks clinical from social services and creates a conceptual framework for integrating social and healthcare services in the cure of patients with addictions. Our experience with this model suggests it has heuristic value in promoting cost and outcome effective treatment.
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Affiliation(s)
- M D McGee
- Massachusetts Merit Behavioral Care, Cambridge, USA
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Abstract
Advances in computer technology have made databases more widespread and accessible, bringing both opportunities and benefits to psychiatrists. Their increasing usefulness has also resulted in increased expectations by others, such as accrediting agencies and payers, that psychiatrists have the capacity to manage outcome and utilization data as well as other information. This paper provides an overview of the uses of databases in psychiatry, describes basic principles and features of relational databases, and reviews some of the features of currently available database-development packages.
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Affiliation(s)
- M D McGee
- Cambridge Hospital, Massachusetts 02139
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Cavens TR, Miller RR, Bowen DA, McGee MD. Utilization of a hospital rotation system in an offic practice. Easing the burden of nighttime and office practice. Clin Pediatr (Phila) 1975; 14:268-9, 272. [PMID: 1116317 DOI: 10.1177/000992287501400315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A four-man pediatric group in private practice instituted a rotation system whereby one of the four worked entirely in the hospital for a week at a time. That physician also took all emergency nighttime calls. The program was evaluated for patient acceptance and for income production.
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McGee MD. Rhododendron ingestion. Bull Natl Clgh Poison Control Cent 1973:1-2. [PMID: 4742238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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