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Trait variation in a successful global invader: a large-scale analysis of morphological variance and integration in the brown trout. Biol Invasions 2023. [DOI: 10.1007/s10530-023-03003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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2
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Simon MN, Rothier PS, Donihue CM, Herrel A, Kolbe JJ. Can extreme climatic events induce shifts in adaptive potential? A conceptual framework and empirical test with Anolis lizards. J Evol Biol 2023; 36:195-208. [PMID: 36357963 DOI: 10.1111/jeb.14115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/04/2022] [Accepted: 09/10/2022] [Indexed: 11/12/2022]
Abstract
Multivariate adaptation to climatic shifts may be limited by trait integration that causes genetic variation to be low in the direction of selection. However, strong episodes of selection induced by extreme climatic pressures may facilitate future population-wide responses if selection reduces trait integration and increases adaptive potential (i.e., evolvability). We explain this counter-intuitive framework for extreme climatic events in which directional selection leads to increased evolvability and exemplify its use in a case study. We tested this hypothesis in two populations of the lizard Anolis scriptus that experienced hurricane-induced selection on limb traits. We surveyed populations immediately before and after the hurricane as well as the offspring of post-hurricane survivors, allowing us to estimate both selection and response to selection on key functional traits: forelimb length, hindlimb length, and toepad area. The direct selection was parallel in both islands and strong in several limb traits. Even though overall limb integration did not change after the hurricane, both populations showed a non-significant tendency toward increased evolvability after the hurricane despite the direction of selection not being aligned with the axis of most variance (i.e., body size). The population with comparably lower between-limb integration showed a less constrained response to selection. Hurricane-induced selection, not aligned with the pattern of high trait correlations, likely conflicts with selection occurring during normal ecological conditions that favours functional coordination between limb traits, and would likely need to be very strong and more persistent to elicit a greater change in trait integration and evolvability. Future tests of this hypothesis should use G-matrices in a variety of wild organisms experiencing selection due to extreme climatic events.
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Affiliation(s)
- Monique N Simon
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | | | - Colin M Donihue
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Anthony Herrel
- UMR 7179, Centre National de la Recherche Scientifique/Muséum National d'Histoire Naturelle, Paris, France.,Functional Morphology Lab, Department of Biology, University of Antwerp, Wilrijk, Belgium.,Evolutionary Morphology of Vertebrates, Ghent University, Ghent, Belgium
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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3
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Assis APA, Galetti M, Maia KP, Guimarães PR. Reduced evolutionary potential of a frugivorous bird species in fragmented forests. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.804138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Morphological attributes are important in determining the success of ecological interactions, such as the interactions between fleshy fruited plants and their seed dispersers. Morphological traits can present high levels of intraspecific variation both within and across populations. Such variation will not only mediate which interactions can be established locally but also the potential for populations to respond to perturbations and selective pressure. Here, we investigated patterns of morphological variation (body weight and beaks’ traits) among different populations of blue manakin (Chiroxiphia caudata), in the highly fragmented Atlantic Forest, Brazil, both in terms of mean trait values – that might mediate interactions locally – and in their habitat-level variation which influences their evolutionary potential. Using metrics of evolutionary potential derived from quantitative genetics theory, we hypothesized that ecological stress would lead to a decline in the overall evolutionary potential in manakin populations. We found that populations differ slightly in their mean morphological attributes, with the exception of a population that occurs in temperate Araucaria forests. Nevertheless, we found a striking difference in the evolutionary potential of populations from different vegetation types. Specifically, populations that occur in ecological stress areas, Araucaria forests, and forest fragments immersed in savanna presented a smaller overall and conditional evolvability, suggesting their lower ability to respond in the direction of selection. This pattern might have important implications for the role of this species as seed disperser, as populations under stress may lack morphological variation (and covariation) that can be important to allow a given population to disperse seeds of multiple types of fruits. Moreover, a smaller evolvability might impact the potential of these populations to persist and perform their ecosystem services in face of environmental changes.
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4
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A method to predict the response to directional selection using a Kalman filter. Proc Natl Acad Sci U S A 2022; 119:e2117916119. [PMID: 35867739 DOI: 10.1073/pnas.2117916119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Predicting evolution remains challenging. The field of quantitative genetics provides predictions for the response to directional selection through the breeder's equation, but these predictions can have errors. The sources of these errors include omission of traits under selection, inaccurate estimates of genetic variance, and nonlinearities in the relationship between genetic and phenotypic variation. Previous research showed that the expected value of these prediction errors is often not zero, so predictions are systematically biased. Here, we propose that this bias, rather than being a nuisance, can be used to improve the predictions. We use this to develop a method to predict evolution, which is built on three key innovations. First, the method predicts change as the breeder's equation plus a bias term. Second, the method combines information from the breeder's equation and from the record of past changes in the mean to predict change using a Kalman filter. Third, the parameters of the filter are fitted in each generation using a learning algorithm on the record of past changes. We compare the method to the breeder's equation in two artificial selection experiments, one using the wing of the fruit fly and another using simulations that include a complex mapping of genotypes to phenotypes. The proposed method outperforms the breeder's equation, particularly when traits under selection are omitted from the analysis, when data are noisy, and when additive genetic variance is estimated inaccurately or not estimated at all. The proposed method is easy to apply, requiring only the trait means over past generations.
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5
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McGlothlin JW, Kobiela ME, Wright HV, Kolbe JJ, Losos JB, III EDB. Conservation and Convergence of Genetic Architecture in the Adaptive Radiation of Anolis Lizards. Am Nat 2022; 200:E207-E220. [DOI: 10.1086/721091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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Tensen L, Power J, Camacho G, Godinho R, Jansen van Vuuren B, Fischer K. Molecular tracking and prevalence of the red colour morph restricted to a harvested leopard population in South Africa. Evol Appl 2022; 15:1028-1041. [PMID: 35782007 PMCID: PMC9234631 DOI: 10.1111/eva.13423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 12/02/2022] Open
Abstract
The red leopard (Panthera pardus) colour morph is a colour variant that occurs only in South Africa, where it is confined to the Central Bushveld bioregion. Red leopards have been spreading over the past 40 years, which raises the speculation that the prevalence of this phenotype is related to low dispersal of young individuals owing to high off-take in the region. Intensive selective hunting tends to remove large resident male leopards from the breeding population, which gives young male leopards the chance to mate with resident female leopards that are more likely to be their relatives, eventually increasing the frequency of rare genetic variants. To investigate the genetic mechanisms underlying the red coat colour morph in leopards, and whether its prevalence in South Africa relates to an increase in genetic relatedness in the population, we sequenced exons of six coat colour-associated genes and 20 microsatellite loci in twenty Wild-type and four red leopards. The results were combined with demographic data available from our study sites. We found that red leopards own a haplotype in homozygosity identified by two SNPs and a 1 bp deletion that causes a frameshift in the tyrosinase-related protein 1 (TYRP1), a gene known to be involved in the biosynthesis of melanin. Microsatellite analyses indicate clear signs of a population bottleneck and a relatedness of 0.11 among all pairwise relationships, eventually supporting our hypothesis that a rare colour morph in the wild has increased its local frequency due to low natal dispersal, while subject to high human-induced mortality rate.
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Affiliation(s)
- Laura Tensen
- Institute for Integrated Natural Sciences, ZoologyUniversity of Koblenz‐LandauKoblenzGermany
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - John Power
- Directorate of Biodiversity Management, Department of Economic Development, Environment, Conservation and TourismNorth West Provincial GovernmentMmabathoSouth Africa
| | - Gerrie Camacho
- Mpumalanga Tourism and Parks AgencyNelspruitSouth Africa
| | - Raquel Godinho
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório AssociadoCampus de Vairão, Universidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO, Campus de VairãoVairãoPortugal
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, ZoologyUniversity of Koblenz‐LandauKoblenzGermany
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7
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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8
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Ramírez-Valiente JA, Solé-Medina A, Pyhäjärvi T, Savolainen O, Cervantes S, Kesälahti R, Kujala ST, Kumpula T, Heer K, Opgenoorth L, Siebertz J, Danusevicius D, Notivol E, Benavides R, Robledo-Arnuncio JJ. Selection patterns on early-life phenotypic traits in Pinus sylvestris are associated with precipitation and temperature along a climatic gradient in Europe. THE NEW PHYTOLOGIST 2021; 229:3009-3025. [PMID: 33098590 DOI: 10.1111/nph.17029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Understanding the dynamics of selection is key to predicting the response of tree species to new environmental conditions in the current context of climate change. However, selection patterns acting on early recruitment stages and their climatic drivers remain largely unknown in most tree species, despite being a critical period of their life cycle. We measured phenotypic selection on Pinus sylvestris seed mass, emergence time and early growth rate over 2 yr in four common garden experiments established along the latitudinal gradient of the species in Europe. Significant phenotypic plasticity and among-population genetic variation were found for all measured phenotypic traits. Heat and drought negatively affected fitness in the southern sites, but heavy rainfalls also decreased early survival in middle latitudes. Climate-driven directional selection was found for higher seed mass and earlier emergence time, while the form of selection on seedling growth rates differed among sites and populations. Evidence of adaptive and maladaptive phenotypic plasticity was found for emergence time and early growth rate, respectively. Seed mass, emergence time and early growth rate have an adaptive role in the early stages of P. sylvestris and climate strongly influences the patterns of selection on these fitness-related traits.
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Affiliation(s)
| | - Aida Solé-Medina
- Department of Forest Ecology & Genetics, INIA-CIFOR, Ctra. de la Coruña km 7.5, Madrid, 28040, Spain
- Escuela Internacional de Doctorado, Universidad Rey Juan Carlos, C/ Tulipán s/n, Móstoles, 28933, Spain
| | - Tanja Pyhäjärvi
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
- Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
| | - Sandra Cervantes
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
- Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland
| | - Robert Kesälahti
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
| | - Sonja T Kujala
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
- Natural Resources Institute Finland (Luke), Jokioinen, 90570, Finland
| | - Timo Kumpula
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
| | - Katrin Heer
- Conservation Biology, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Jan Siebertz
- Plant Ecology and Geobotany, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
| | - Darius Danusevicius
- Faculty of Forest Science and Ecology, Vytautas Magnus University, Studentų str. 11, Akademija, Kaunas, LT-53361, Lithuania
| | - Eduardo Notivol
- Unidad de Recursos Forestales, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, Zaragoza, 50059, Spain
| | - Raquel Benavides
- Department of Biogeography and Global Change, LINCGlobal, Museo Nacional de Ciencias Naturales, CSIC, C/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
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9
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Benham PM, Bowie RCK. The influence of spatially heterogeneous anthropogenic change on bill size evolution in a coastal songbird. Evol Appl 2021; 14:607-624. [PMID: 33664798 PMCID: PMC7896719 DOI: 10.1111/eva.13144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 12/25/2022] Open
Abstract
Natural history collections provide an unparalleled resource for documenting population responses to past anthropogenic change. However, in many cases, traits measured on specimens may vary temporally in response to a number of different anthropogenic pressures or demographic processes. While teasing apart these different drivers is challenging, approaches that integrate analyses of spatial and temporal series of specimens can provide a robust framework for examining whether traits exhibit common responses to ecological variation in space and time. We applied this approach to analyze bill morphology variation in California Savannah Sparrows (Passerculus sandwichensis). We found that bill surface area increased in birds from higher salinity tidal marshes that are hotter and drier. Only the coastal subspecies, alaudinus, exhibited a significant increase in bill size through time. As with patterns of spatial variation, alaudinus populations occupying higher salinity tidal marshes that have become warmer and drier over the past century exhibited the greatest increases in bill surface area. We also found a significant negative correlation between bill surface area and total evaporative water loss (TEWL) and estimated that observed increases in bill size could result in a reduction of up to 16.2% in daily water losses. Together, these patterns of spatial and temporal variation in bill size were consistent with the hypothesis that larger bills are favored in freshwater-limited environments as a mechanism of dissipating heat, reducing reliance on evaporative cooling, and increasing water conservation. With museum collections increasingly being leveraged to understand past responses to global change, this work highlights the importance of considering the influence of many different axes of anthropogenic change and of integrating spatial and temporal analyses to better understand the influence of specific human impacts on population change over time.
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Affiliation(s)
- Phred M. Benham
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeley, BerkeleyCAUSA
| | - Rauri C. K. Bowie
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeley, BerkeleyCAUSA
- Department of Integrative BiologyUniversity of CaliforniaBerkeley, BerkeleyCAUSA
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10
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Melo D, Marroig G, Wolf JB. Genomic Perspective on Multivariate Variation, Pleiotropy, and Evolution. J Hered 2020; 110:479-493. [PMID: 30986303 DOI: 10.1093/jhered/esz011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/13/2019] [Indexed: 11/14/2022] Open
Abstract
Multivariate quantitative genetics provides a powerful framework for understanding patterns and processes of phenotypic evolution. Quantitative genetics parameters, like trait heritability or the G-matrix for sets of traits, can be used to predict evolutionary response or to understand the evolutionary history of a population. These population-level approaches have proven to be extremely successful, but the underlying genetics of multivariate variation and evolutionary change typically remain a black box. Establishing a deeper empirical understanding of how individual genetic effects lead to genetic (co)variation is then crucial to our understanding of the evolutionary process. To delve into this black box, we exploit an experimental population of mice composed from lineages derived by artificial selection. We develop an approach to estimate the multivariate effect of loci and characterize these vectors of effects in terms of their magnitude and alignment with the direction of evolutionary divergence. Using these estimates, we reconstruct the traits in the ancestral populations and quantify how much of the divergence is due to genetic effects. Finally, we also use these vectors to decompose patterns of genetic covariation and examine the relationship between these components and the corresponding distribution of pleiotropic effects. We find that additive effects are much larger than dominance effects and are more closely aligned with the direction of selection and divergence, with larger effects being more aligned than smaller effects. Pleiotropic effects are highly variable but are, on average, modular. These results are consistent with pleiotropy being partly shaped by selection while reflecting underlying developmental constraints.
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Affiliation(s)
- Diogo Melo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Gabriel Marroig
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Jason B Wolf
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
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11
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Puckett EE, Sherratt E, Combs M, Carlen EJ, Harcourt‐Smith W, Munshi‐South J. Variation in brown rat cranial shape shows directional selection over 120 years in New York City. Ecol Evol 2020; 10:4739-4748. [PMID: 32551057 PMCID: PMC7297766 DOI: 10.1002/ece3.6228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 01/22/2023] Open
Abstract
Urbanization exposes species to novel environments and selection pressures that may change morphological traits within a population. We investigated how the shape and size of crania and mandibles changed over time within a population of brown rats (Rattus norvegicus) living in Manhattan, New York, USA, a highly urbanized environment. We measured 3D landmarks on the cranium and mandible of 62 adult individuals sampled in the 1890s and 2010s. Static allometry explained approximately 22% of shape variation in crania and mandible datasets, while time accounted for approximately 14% of variation. We did not observe significant changes in skull size through time or between the sexes. Estimating the P-matrix revealed that directional selection explained temporal change of the crania but not the mandible. Specifically, rats from the 2010s had longer noses and shorter upper molar tooth rows, traits identified as adaptive to colder environments and higher quality or softer diets, respectively. Our results highlight the continual evolution to selection pressures. We acknowledge that urban selection pressures impacting cranial shape likely began in Europe prior to the introduction of rats to Manhattan. Yet, our study period spanned changes in intensity of artificial lighting, human population density, and human diet, thereby altering various aspects of rat ecology and hence pressures on the skull.
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Affiliation(s)
- Emily E. Puckett
- Department of Biological SciencesUniversity of MemphisMemphisTNUSA
- Department of Biological SciencesLouis Calder Center‐Biological Field StationFordham UniversityArmonkNYUSA
| | - Emma Sherratt
- Department of Ecology and Evolutionary BiologySchool of Biological SciencesThe University of AdelaideAdelaideSAAustralia
| | - Matthew Combs
- Department of Biological SciencesLouis Calder Center‐Biological Field StationFordham UniversityArmonkNYUSA
- Present address:
Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNYUSA
| | - Elizabeth J. Carlen
- Department of Biological SciencesLouis Calder Center‐Biological Field StationFordham UniversityArmonkNYUSA
| | - William Harcourt‐Smith
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of AnthropologyThe Graduate CenterCity University of New YorkNew YorkNYUSA
- Lehman CollegeCity University of New YorkBronxNYUSA
| | - Jason Munshi‐South
- Department of Biological SciencesLouis Calder Center‐Biological Field StationFordham UniversityArmonkNYUSA
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12
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Acevedo CR, Riecke TV, Leach AG, Lohman MG, Williams PJ, Sedinger JS. Long-term research and hierarchical models reveal consistent fitness costs of being the last egg in a clutch. J Anim Ecol 2020; 89:1978-1987. [PMID: 32248534 PMCID: PMC7497156 DOI: 10.1111/1365-2656.13232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/12/2020] [Indexed: 02/03/2023]
Abstract
Maintenance of phenotypic heterogeneity in the face of strong selection is an important component of evolutionary ecology, as are the consequences of such heterogeneity. Organisms may experience diminishing returns of increased reproductive allocation as clutch or litter size increases, affecting current and residual reproductive success. Given existing uncertainty regarding trade‐offs between the quantity and quality of offspring, we sought to examine the potential for diminishing returns on increased reproductive allocation in a long‐lived species of goose, with a particular emphasis on the effect of position in the laying sequence on offspring quality. To better understand the effects of maternal allocation on offspring survival and growth, we estimated the effects of egg size, timing of breeding, inter‐ and intra‐annual variation, and position in the laying sequence on gosling survival and growth rates of black brant Branta bernicla nigricans breeding in western Alaska from 1987 to 2007. We found that gosling growth rates and survival decreased with position in the laying sequence, regardless of clutch size. Mean egg volume of the clutch a gosling originated from had a positive effect on gosling survival (β = 0.095, 95% CRI: 0.024, 0.165) and gosling growth rates (β = 0.626, 95% CRI: 0.469, 0.738). Gosling survival (β = −0.146, 95% CRI: −0.214, −0.079) and growth rates (β = −1.286, 95% CRI: −1.435, −1.132) were negatively related to hatching date. These findings indicate substantial heterogeneity in offspring quality associated with their position in the laying sequence. They also potentially suggest a trade‐off mechanism for females whose total reproductive investment is governed by pre‐breeding state.
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Affiliation(s)
- Cheyenne R Acevedo
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, USA
| | - Thomas V Riecke
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
| | - Alan G Leach
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
| | - Madeleine G Lohman
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, USA
| | - Perry J Williams
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, USA
| | - James S Sedinger
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, USA
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13
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Hu X, Carver BF, Powers C, Yan L, Zhu L, Chen C. Effectiveness of Genomic Selection by Response to Selection for Winter Wheat Variety Improvement. THE PLANT GENOME 2019; 12:1-15. [PMID: 33016592 DOI: 10.3835/plantgenome2018.11.0090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/11/2019] [Indexed: 06/11/2023]
Abstract
Prediction performance for winter wheat grain yield and end-use quality traits. Prediction accuracies evaluated by cross-validations are significantly overestimated. Nonparametric algorithms outperform the parametric alternatives in cross-year predictions. Strategically designing training population improves response to selection. Response to selection varies across growing seasons and environments. Considering the practicality of applying genomic selection (GS) in the line development stage of a hard red winter (HRW) wheat (Triticum aestivum L.) variety development program (VDP), the effectiveness of GS was evaluated by prediction accuracy and by the response to selection across field seasons that demonstrated challenges for crop improvement under significant climate variability. Important breeding targets for wheat improvement in the southern Great Plains of the United States, including grain yield, kernel weight, wheat protein content, and sodium dodecyl sulfate (SDS) sedimentation volume as a rapid test for predicting bread-making quality, were used to estimate the effectiveness of GS across harvest years from 2014 (drought) to 2016 (normal). In general, nonparametric algorithms reproducing kernel Hilbert space (RKHS) and random forest (RF) produced higher accuracies in both same-year cross-validations (CVs) and cross-year predictions for the purpose of line selection. Further, the stability of GS performance was greatest for SDS sedimentation volume but least for wheat protein content. To ensure long-term genetic gain, our study on selection response suggested that across this sample of environmental variability, and though there are cases where phenotypic selection (PS) might be still preferred, training conducted under drought or in suboptimal conditions could provide an encouraging prediction outcome when selection decisions were made in normal conditions. However, it is not advisable to use training information collected from a normal season to predict trait performance under drought conditions. Finally, the superiority of response to selection was most evident if the training population (TP) can be optimized.
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Affiliation(s)
- Xiaowei Hu
- Dep. of Statistics, Oklahoma State Univ., 301 MSCS, Stillwater, OK, 74078
| | - Brett F Carver
- Dep. of Plant and Soil Sciences, Oklahoma State Univ., 371 Agriculture Hall, Stillwater, OK, 74078
| | - Carol Powers
- Dep. of Plant and Soil Sciences, Oklahoma State Univ., 371 Agriculture Hall, Stillwater, OK, 74078
| | - Liuling Yan
- Dep. of Plant and Soil Sciences, Oklahoma State Univ., 371 Agriculture Hall, Stillwater, OK, 74078
| | - Lan Zhu
- Dep. of Statistics, Oklahoma State Univ., 301 MSCS, Stillwater, OK, 74078
| | - Charles Chen
- Dep. of Biochemistry and Molecular Biology, Oklahoma State Univ., 246 Nobel Research Center, Stillwater, OK, 74078
- Dep. of Plant and Soil Sciences, Oklahoma State Univ., 371 Agriculture Hall, Stillwater, OK, 74078
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14
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Machado FA, Hubbe A, Melo D, Porto A, Marroig G. Measuring the magnitude of morphological integration: The effect of differences in morphometric representations and the inclusion of size. Evolution 2019; 73:2518-2528. [PMID: 31595985 DOI: 10.1111/evo.13864] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/03/2019] [Indexed: 12/21/2022]
Abstract
The magnitude of morphological integration is a major aspect of multivariate evolution, providing a simple measure of the intensity of association between morphological traits. Studies concerned with morphological integration usually translate phenotypes into morphometric representations to quantify how different morphological elements covary. Geometric and classic morphometric representations translate biological form in different ways, raising the question if magnitudes of morphological integration estimates obtained from different morphometric representations are compatible. Here we sought to answer this question using the relative eigenvalue variance of the covariance matrix obtained for both geometric and classical representations of empirical and simulated datasets. We quantified the magnitude of morphological integration for both shape and form and compared results between representations. Furthermore, we compared integration values between shape and form to evaluate the effect of the inclusion or not of size on the quantification of the magnitude of morphological integration. Results show that the choice of morphological representation has significant impact on the integration magnitude estimate, either for shape or form. Despite this, ordination of the integration values within representations is relatively the same, allowing for similar conclusions to be reached using different methods. However, the inclusion of size in the dataset significantly changes the estimates of magnitude of morphological integration, hindering the comparison of this statistic obtained from different spaces. Morphometricians should be aware of these differences and must consider how biological hypothesis translate into predictions about integration in each particular choice of representation.
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Affiliation(s)
- Fabio A Machado
- Department of Biology, University of Massachusetts, Boston, Massachusetts, 02125.,División Mastozoología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia,", Av. Ángel Gallardo 470 (C1405DJR), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alex Hubbe
- Departamento de Oceanografia, Instituto de Geociências, Universidade Federal da Bahia, R. Barão de Jeremoabo, S/N - Ondina, Salvador, Bahia 40170-110, Brazil
| | - Diogo Melo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Rua do Matão, 277 Universidade de São Paulo, São Paulo, São Paulo 05508-090, Brazil
| | - Arthur Porto
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0315, Oslo, Norway
| | - Gabriel Marroig
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Rua do Matão, 277 Universidade de São Paulo, São Paulo, São Paulo 05508-090, Brazil
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15
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Affiliation(s)
- David Jablonski
- Department of Geophysical Sciences University of Chicago Chicago Illinois
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16
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Bi K, Linderoth T, Singhal S, Vanderpool D, Patton JL, Nielsen R, Moritz C, Good JM. Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PLoS Genet 2019; 15:e1008119. [PMID: 31050681 PMCID: PMC6519841 DOI: 10.1371/journal.pgen.1008119] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 05/15/2019] [Accepted: 04/01/2019] [Indexed: 12/12/2022] Open
Abstract
Many species have experienced dramatic changes in their abundance and distribution during recent climate change, but it is often unclear whether such ecological responses are accompanied by evolutionary change. We used targeted exon sequencing of 294 museum specimens (160 historic, 134 modern) to generate independent temporal genomic contrasts spanning a century of climate change (1911-2012) for two co-distributed chipmunk species: an endemic alpine specialist (Tamias alpinus) undergoing severe range contraction and a stable mid-elevation species (T. speciosus). Using a novel analytical approach, we reconstructed the demographic histories of these populations and tested for evidence of recent positive directional selection. Only the retracting species showed substantial population genetic fragmentation through time and this was coupled with positive selection and substantial shifts in allele frequencies at a gene, Alox15, involved in regulation of inflammation and response to hypoxia. However, these rapid population and gene-level responses were not detected in an analogous temporal contrast from another area where T. alpinus has also undergone severe range contraction. Collectively, these results highlight that evolutionary responses may be variable and context dependent across populations, even when they show seemingly synchronous ecological shifts. Our results demonstrate that temporal genomic contrasts can be used to detect very recent evolutionary responses within and among contemporary populations, even in the face of complex demographic changes. Given the wealth of specimens archived in natural history museums, comparative analyses of temporal population genomic data have the potential to improve our understanding of recent and ongoing evolutionary responses to rapidly changing environments.
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Affiliation(s)
- Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, United States of America
| | - Tyler Linderoth
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Sonal Singhal
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - James L. Patton
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, Australia
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Wildlife Biology Program, University of Montana, Missoula, MT, United States of America
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17
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Rossoni DM, Costa BMA, Giannini NP, Marroig G. A multiple peak adaptive landscape based on feeding strategies and roosting ecology shaped the evolution of cranial covariance structure and morphological differentiation in phyllostomid bats. Evolution 2019; 73:961-981. [DOI: 10.1111/evo.13715] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/15/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Daniela M. Rossoni
- Department of Genetics and Evolutionary Biology, Biosciences InstituteUniversity of São Paulo São Paulo Brazil
| | - Bárbara M. A. Costa
- Department of Genetics and Evolutionary Biology, Biosciences InstituteUniversity of São Paulo São Paulo Brazil
| | - Norberto P. Giannini
- Unidad Ejecutora Lillo‐CONICETUniversidad Nacional de Tucumán San Miguel de Tucumán Argentina
| | - Gabriel Marroig
- Department of Genetics and Evolutionary Biology, Biosciences InstituteUniversity of São Paulo São Paulo Brazil
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18
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Stange M, Núñez-León D, Sánchez-Villagra MR, Jensen P, Wilson LAB. Morphological variation under domestication: how variable are chickens? ROYAL SOCIETY OPEN SCIENCE 2018; 5:180993. [PMID: 30225085 PMCID: PMC6124038 DOI: 10.1098/rsos.180993] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/04/2018] [Indexed: 05/08/2023]
Abstract
The process of domestication has long fascinated evolutionary biologists, yielding insights into the rapidity with which selection can alter behaviour and morphology. Previous studies on dogs, cattle and pigeons have demonstrated that domesticated forms show greater magnitudes of morphological variation than their wild ancestors. Here, we quantify variation in skull morphology, modularity and integration in chickens and compare those to the wild fowl using three-dimensional geometric morphometrics and multivariate statistics. Similar to other domesticated species, chickens exhibit a greater magnitude of variation in shape compared with their ancestors. The most variable part of the chicken skull is the cranial vault, being formed by dermal and neural crest-derived bones, its form possibly related to brain shape variation in chickens, especially in crested breeds. Neural crest-derived portions of the skull exhibit a higher amount of variation. Further, we find that the chicken skull is strongly integrated, confirming previous studies in birds, in contrast to the presence of modularity and decreased integration in mammals.
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Affiliation(s)
- Madlen Stange
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, 8006 Zürich, Switzerland
- Authors for correspondence: Madlen Stange e-mail:
| | - Daniel Núñez-León
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, 8006 Zürich, Switzerland
| | | | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 581 83 Linköping, Sweden
| | - Laura A. B. Wilson
- Palaeontology, Geobiology and Earth Archives Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
- Authors for correspondence: Laura A. B. Wilson e-mail:
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Machado FA, Zahn TMG, Marroig G. Evolution of morphological integration in the skull of Carnivora (Mammalia): Changes in Canidae lead to increased evolutionary potential of facial traits. Evolution 2018; 72:1399-1419. [PMID: 29803199 DOI: 10.1111/evo.13495] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/20/2018] [Indexed: 12/14/2022]
Abstract
Morphological integration refers to the fact that different phenotypic traits of organisms are not fully independent from each other, and tend to covary to different degrees. The covariation among traits is thought to reflect properties of the species' genetic architecture and thus can have an impact on evolutionary responses. Furthermore, if morphological integration changes along the history of a group, inferences of past selection regimes might be problematic. Here, we evaluated the stability and evolution of the morphological integration of skull traits in Carnivora by using evolutionary simulations and phylogenetic comparative methods. Our results show that carnivoran species are able to respond to natural selection in a very similar way. Our comparative analyses show that the phylogenetic signal for pattern of integration is lower than that observed for morphology (trait averages), and that integration was stable throughout the evolution of the group. That notwithstanding, Canidae differed from other families by having higher integration, evolvability, flexibility, and allometric coefficients on the facial region. These changes might have allowed canids to rapidly adapt to different food sources, helping to explain not only the phenotypic diversification of the family, but also why humans were able to generate such a great diversity of dog breeds through artificial selection.
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Affiliation(s)
- Fabio Andrade Machado
- División Mastozoologa, Museo Argentino de Ciencias Naturales, "Bernardino Rivadavia". Av. Ángel Gallardo 470 (C1405DJR), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Thiago Macek Gonçalves Zahn
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP 05508-090, Brazil
| | - Gabriel Marroig
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP 05508-090, Brazil
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20
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Penna A, Melo D, Bernardi S, Oyarzabal MI, Marroig G. The evolution of phenotypic integration: How directional selection reshapes covariation in mice. Evolution 2017; 71:2370-2380. [PMID: 28685813 PMCID: PMC5655774 DOI: 10.1111/evo.13304] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/10/2017] [Indexed: 02/03/2023]
Abstract
Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection.
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Affiliation(s)
- Anna Penna
- Laboratório de Evolução de Mamíferos, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Diogo Melo
- Laboratório de Evolução de Mamíferos, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Sandra Bernardi
- Cátedra de Histología y Embriología Básica. Facultad de Ciencias Veterinarias, Universidad Nacional de Rosario, Argentina
| | - Maria Inés Oyarzabal
- Cátedra de Producción de Bovinos para Carne, Facultad de Ciencias Veterinarias y Consejo de Investigaciones, Universidad Nacional de Rosario, Argentina
| | - Gabriel Marroig
- Laboratório de Evolução de Mamíferos, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
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21
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Assis APA, Patton JL, Hubbe A, Marroig G. Directional selection effects on patterns of phenotypic (co)variation in wild populations. Proc Biol Sci 2016; 283:20161615. [PMID: 27881744 PMCID: PMC5136582 DOI: 10.1098/rspb.2016.1615] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 11/12/2022] Open
Abstract
Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus an important gap in evolutionary theory. Here, we documented changes in the phenotypic (co)variation structure in two separate natural populations in each of two chipmunk species (Tamias alpinus and T. speciosus) undergoing directional selection. In populations where selection was strongest (those of T. alpinus), we observed changes, at least for one population, in phenotypic (co)variation that matched theoretical expectations, namely an increase of both phenotypic integration and (co)variance in the direction of selection and a re-alignment of the major axis of variation with the selection gradient.
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Affiliation(s)
- A P A Assis
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo 05508-090, Brazil
| | - J L Patton
- Museum of Vertebrate Zoology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - A Hubbe
- Departamento de Oceanografia, Instituto de Geociências, Universidade Federal da Bahia, Salvador, Bahia 40170-020, Brazil
| | - G Marroig
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo 05508-090, Brazil
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