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Bourrat P, Deaven K, Villegas C. Evolvability: filling the explanatory gap between adaptedness and the long-term mathematical conception of fitness. BIOLOGY & PHILOSOPHY 2024; 39:15. [PMID: 39021712 PMCID: PMC11249714 DOI: 10.1007/s10539-024-09951-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 06/12/2024] [Indexed: 07/20/2024]
Abstract
The new foundation for the propensity interpretation of fitness (PIF), developed by Pence and Ramsey (Br J Philos Sci 64:851-881, 2013), describes fitness as a probability distribution that encompasses all possible daughter populations to which the organism may give rise, including daughter populations in which traits might change and the possible environments that members of the daughter populations might encounter. This long-term definition of fitness is general enough to avoid counterexamples faced by previous mathematical conceptions of PIF. However, there seem to be downsides to its generality: the ecological role of fitness involves describing the degree of adaptedness between an organism and the specific environment it inhabits. When all possible changes in traits and all possible environments that a daughter population may encounter are included in the concept, it becomes difficult to see how fitness can fulfill this role. In this paper, we argue that this is a feature of Pence and Ramsey's view rather than a bug: long-term fitness accommodates evolvability considerations, which concern the role that variation plays in evolutionary processes. Building on the foundations, we show that Pence and Ramsey's fitness-F-can be partitioned into fourths: adaptedness, robustness of adaptedness, and two facets of evolvability. Conceptualizing these last three components forces us to consider the role played by grains of description of both organisms and the environment when thinking about long-term fitness. They track the possibility that there could be a change in type in a daughter population as a way of responding to environmental challenges, or that the type persists in the face of novel environments. We argue that these components are just as salient as adaptedness for long-term fitness. Together, this decomposition of F provides a more accurate picture of the factors involved in long-term evolutionary success.
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Affiliation(s)
- Pierrick Bourrat
- Department of Philosophy, Macquarie University, North Ryde, NSW 2109 Australia
- Department of Philosophy and Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006 Australia
| | - Katie Deaven
- Department of Philosophy, University of Wisconsin-Madison, 600 N. Park Street, Madison, WI 53703 USA
| | - Cristina Villegas
- Centro de Filosofia das Ciências, Departamento de História e Filosofia das Ciências, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
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2
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Toli EA, Kemppainen P, Bounas A, Sotiropoulos K. Genetic insight into a polygenic trait using a novel genome-wide association approach in a wild amphibian population. Mol Ecol 2024; 33:e17344. [PMID: 38597332 DOI: 10.1111/mec.17344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Body size variation is central in the evolution of life-history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness-related traits in small data sets from natural populations in non-model species.
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Affiliation(s)
- Elisavet-Aspasia Toli
- Molecular Ecology & Conservation Genetics Lab, Department of Biological Applications & Technology, University of Ioannina, Ioannina, Greece
| | - Petri Kemppainen
- Area of Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong City, Hong Kong SAR
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme, University of Helsinki, Helsinki, Finland
| | - Anastasios Bounas
- Molecular Ecology & Conservation Genetics Lab, Department of Biological Applications & Technology, University of Ioannina, Ioannina, Greece
| | - Konstantinos Sotiropoulos
- Molecular Ecology & Conservation Genetics Lab, Department of Biological Applications & Technology, University of Ioannina, Ioannina, Greece
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3
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Sabolić I, Mira Ó, Brandt DYC, Lisičić D, Stapley J, Novosolov M, Bakarić R, Cizelj I, Glogoški M, Hudina T, Taverne M, Allentoft ME, Nielsen R, Herrel A, Štambuk A. Plastic and genomic change of a newly established lizard population following a founder event. Mol Ecol 2024; 33:e17255. [PMID: 38133599 DOI: 10.1111/mec.17255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
Understanding how phenotypic divergence arises among natural populations remains one of the major goals in evolutionary biology. As part of competitive exclusion experiment conducted in 1971, 10 individuals of Italian wall lizard (Podarcis siculus (Rafinesque-Schmaltz, 1810)) were transplanted from Pod Kopište Island to the nearby island of Pod Mrčaru (Adriatic Sea). Merely 35 years after the introduction, the newly established population on Pod Mrčaru Island had shifted their diet from predominantly insectivorous towards omnivorous and changed significantly in a range of morphological, behavioural, physiological and ecological characteristics. Here, we combine genomic and quantitative genetic approaches to determine the relative roles of genetic adaptation and phenotypic plasticity in driving this rapid phenotypic shift. Our results show genome-wide genetic differentiation between ancestral and transplanted population, with weak genetic erosion on Pod Mrčaru Island. Adaptive processes following the founder event are indicated by highly differentiated genomic loci associating with ecologically relevant phenotypic traits, and/or having a putatively adaptive role across multiple lizard populations. Diverged traits related to head size and shape or bite force showed moderate heritability in a crossing experiment, but between-population differences in these traits did not persist in a common garden environment. Our results confirm the existence of sufficient additive genetic variance for traits to evolve under selection while also demonstrating that phenotypic plasticity and/or genotype by environment interactions are the main drivers of population differentiation at this early evolutionary stage.
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Affiliation(s)
- Iva Sabolić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Óscar Mira
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Débora Y C Brandt
- Department of Integrative Biology, University of Berkeley, Berkeley, California, USA
| | - Duje Lisičić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jessica Stapley
- Department of Environmental Sciences, ETH Zurich, Zurich, Switzerland
| | - Maria Novosolov
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert Bakarić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivan Cizelj
- Zoological Garden of Zagreb, Zagreb, Croatia
| | - Marko Glogoški
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Maxime Taverne
- C.N.R.S/M.N.H.N., Département d'Ecologie et de Gestion de la Biodiversité, Paris, France
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Rasmus Nielsen
- Department of Integrative Biology, University of Berkeley, Berkeley, California, USA
| | - Anthony Herrel
- C.N.R.S/M.N.H.N., Département d'Ecologie et de Gestion de la Biodiversité, Paris, France
- Department of Biology, Evolutionary Morphology of Vertebrates, Ghent University, Ghent, Belgium
- Department of Biology, University of Antwerp, Wilrijk, Belgium
- Naturhistorisches Museum Bern, Bern, Switzerland
| | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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4
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Yim C, Bellis ES, DeLeo VL, Gamba D, Muscarella R, Lasky JR. Climate biogeography of Arabidopsis thaliana: linking distribution models and individual variation. JOURNAL OF BIOGEOGRAPHY 2024; 51:560-574. [PMID: 38596256 PMCID: PMC11000247 DOI: 10.1111/jbi.14737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/19/2023] [Indexed: 04/11/2024]
Abstract
AIM Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range-wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. LOCATION Global. TAXON Arabidopsis thaliana ("Arabidopsis"). METHODS We fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2,194 herbarium specimens, and we asked whether predicted suitability was associated with life-history and genomic variation measured on ~900 natural accessions. RESULTS The most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate-associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late-flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the center of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well-predicted by our native-range model applied to certain regions but not others, suggesting it has colonized novel climates. MAIN CONCLUSIONS Integration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.
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Affiliation(s)
- Christina Yim
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Emily S. Bellis
- Department of Biology, Pennsylvania State University, University Park, USA
- Department of Computer Science, Arkansas State University, Jonesboro, USA
| | - Victoria L. DeLeo
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Diana Gamba
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Robert Muscarella
- Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, USA
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Fraimout A, Guillaume F, Li Z, Sillanpää MJ, Rastas P, Merilä J. Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing. Mol Ecol 2024; 33:e17299. [PMID: 38380534 DOI: 10.1111/mec.17299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most non-model wild populations. Specifically, large-sized or panmictic populations may be characterized by low variance in genetic relatedness among individuals which, in turn, can prevent accurate estimation of quantitative genetic parameters. We used estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci to estimate quantitative genetic parameters for ecologically important traits in nine-spined sticklebacks (Pungitius pungitius) from a large, outbred population. Using empirical and simulated datasets, with varying sample sizes and pedigree complexity, we assessed the performance of different crossing schemes in estimating additive genetic variance and heritability for all traits. We found that low variance in relatedness characteristic of wild outbred populations with high migration rate can impair the estimation of quantitative genetic parameters and bias heritability estimates downwards. On the other hand, the use of a half-sib/full-sib design allowed precise estimation of genetic variance components and revealed significant additive variance and heritability for all measured traits, with negligible dominance contributions. Genome-partitioning and QTL mapping analyses revealed that most traits had a polygenic basis and were controlled by genes at multiple chromosomes. Furthermore, different QTL contributed to variation in the same traits in different populations suggesting heterogeneous underpinnings of parallel evolution at the phenotypic level. Our results provide important guidelines for future studies aimed at estimating adaptive potential in the wild, particularly for those conducted in outbred large-sized populations.
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Affiliation(s)
- Antoine Fraimout
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Frédéric Guillaume
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Zitong Li
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Mikko J Sillanpää
- Research Unit of Mathematical Sciences, FI-90014 University of Oulu, Oulu, Finland
| | - Pasi Rastas
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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Jablonszky M, Canal D, Hegyi G, Herényi M, Laczi M, Markó G, Nagy G, Rosivall B, Szöllősi E, Török J, Garamszegi LZ. The estimation of additive genetic variance of body size in a wild passerine is sensitive to the method used to estimate relatedness among the individuals. Ecol Evol 2024; 14:e10981. [PMID: 38352200 PMCID: PMC10862163 DOI: 10.1002/ece3.10981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Assessing additive genetic variance is a crucial step in predicting the evolutionary response of a target trait. However, the estimated genetic variance may be sensitive to the methodology used, e.g., the way relatedness is assessed among the individuals, especially in wild populations where social pedigrees can be inaccurate. To investigate this possibility, we investigated the additive genetic variance in tarsus length, a major proxy of skeletal body size in birds. The model species was the collared flycatcher (Ficedula albicollis), a socially monogamous but genetically polygamous migratory passerine. We used two relatedness matrices to estimate the genetic variance: (1) based solely on social links and (2) a genetic similarity matrix based on a large array of single-nucleotide polymorphisms (SNPs). Depending on the relatedness matrix considered, we found moderate to high additive genetic variance and heritability estimates for tarsus length. In particular, the heritability estimates were higher when obtained with the genetic similarity matrix instead of the social pedigree. Our results confirm the potential for this crucial trait to respond to selection and highlight methodological concerns when calculating additive genetic variance and heritability in phenotypic traits. We conclude that using a social pedigree instead of a genetic similarity matrix to estimate relatedness among individuals in a genetically polygamous wild population may significantly deflate the estimates of additive genetic variation.
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Affiliation(s)
- Mónika Jablonszky
- Evolutionary Ecology Research GroupInstitute of Ecology and Botany, HUN_REN Centre for Ecological ResearchVácrátotHungary
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - David Canal
- Department of Evolutionary EcologyNational Museum of Natural Sciences (MNCN‐CSIC)MadridSpain
| | - Gergely Hegyi
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Márton Herényi
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
- Department of Zoology and EcologyHungarian University of Agriculture and Life SciencesGodolloHungary
| | - Miklós Laczi
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
- HUN‐REN‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
| | - Gábor Markó
- Department of Plant Pathology, Institute of Plant ProtectionHungarian University of Agriculture and Life SciencesBudapestHungary
| | - Gergely Nagy
- Evolutionary Ecology Research GroupInstitute of Ecology and Botany, HUN_REN Centre for Ecological ResearchVácrátotHungary
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Balázs Rosivall
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Eszter Szöllősi
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - János Török
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - László Zsolt Garamszegi
- Evolutionary Ecology Research GroupInstitute of Ecology and Botany, HUN_REN Centre for Ecological ResearchVácrátotHungary
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Westergren M, Archambeau J, Bajc M, Damjanić R, Theraroz A, Kraigher H, Oddou-Muratorio S, González-Martínez SC. Low but significant evolutionary potential for growth, phenology and reproduction traits in European beech. Mol Ecol 2023. [PMID: 37962106 DOI: 10.1111/mec.17196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/23/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1087 adult trees, seeds, 1-year-old seedlings and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.
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Affiliation(s)
| | | | - Marko Bajc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Rok Damjanić
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | | | | | - Sylvie Oddou-Muratorio
- INRAE, URFM, Avignon, France
- INRAE, Univ. de Pau et des Pays de l'Adour, E2S UPPA, ECOBIOP, Saint-Pée-sur-Nivelle, France
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8
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Pantel JH, Becks L. Statistical methods to identify mechanisms in studies of eco-evolutionary dynamics. Trends Ecol Evol 2023; 38:760-772. [PMID: 37437547 DOI: 10.1016/j.tree.2023.03.011] [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: 08/18/2022] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 07/14/2023]
Abstract
While the reciprocal effects of ecological and evolutionary dynamics are increasingly recognized as an important driver for biodiversity, detection of such eco-evolutionary feedbacks, their underlying mechanisms, and their consequences remains challenging. Eco-evolutionary dynamics occur at different spatial and temporal scales and can leave signatures at different levels of organization (e.g., gene, protein, trait, community) that are often difficult to detect. Recent advances in statistical methods combined with alternative hypothesis testing provides a promising approach to identify potential eco-evolutionary drivers for observed data even in non-model systems that are not amenable to experimental manipulation. We discuss recent advances in eco-evolutionary modeling and statistical methods and discuss challenges for fitting mechanistic models to eco-evolutionary data.
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Affiliation(s)
- Jelena H Pantel
- Ecological Modelling, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 2, 45117 Essen, Germany.
| | - Lutz Becks
- University of Konstanz, Aquatic Ecology and Evolution, Limnological Institute University of Konstanz Mainaustraße 252 78464, Konstanz/Egg, Germany
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9
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Richards TJ, McGuigan K, Aguirre JD, Humanes A, Bozec YM, Mumby PJ, Riginos C. Moving beyond heritability in the search for coral adaptive potential. GLOBAL CHANGE BIOLOGY 2023; 29:3869-3882. [PMID: 37310164 DOI: 10.1111/gcb.16719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 06/14/2023]
Abstract
Global environmental change is happening at unprecedented rates. Coral reefs are among the ecosystems most threatened by global change. For wild populations to persist, they must adapt. Knowledge shortfalls about corals' complex ecological and evolutionary dynamics, however, stymie predictions about potential adaptation to future conditions. Here, we review adaptation through the lens of quantitative genetics. We argue that coral adaptation studies can benefit greatly from "wild" quantitative genetic methods, where traits are studied in wild populations undergoing natural selection, genomic relationship matrices can replace breeding experiments, and analyses can be extended to examine genetic constraints among traits. In addition, individuals with advantageous genotypes for anticipated future conditions can be identified. Finally, genomic genotyping supports simultaneous consideration of how genetic diversity is arrayed across geographic and environmental distances, providing greater context for predictions of phenotypic evolution at a metapopulation scale.
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Affiliation(s)
- Thomas J Richards
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
| | - Katrina McGuigan
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
| | - J David Aguirre
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Adriana Humanes
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Yves-Marie Bozec
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
| | - Peter J Mumby
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Queensland, St Lucia, Australia
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10
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Metcalfe NB, Bellman J, Bize P, Blier PU, Crespel A, Dawson NJ, Dunn RE, Halsey LG, Hood WR, Hopkins M, Killen SS, McLennan D, Nadler LE, Nati JJH, Noakes MJ, Norin T, Ozanne SE, Peaker M, Pettersen AK, Przybylska-Piech A, Rathery A, Récapet C, Rodríguez E, Salin K, Stier A, Thoral E, Westerterp KR, Westerterp-Plantenga MS, Wojciechowski MS, Monaghan P. Solving the conundrum of intra-specific variation in metabolic rate: A multidisciplinary conceptual and methodological toolkit: New technical developments are opening the door to an understanding of why metabolic rate varies among individual animals of a species: New technical developments are opening the door to an understanding of why metabolic rate varies among individual animals of a species. Bioessays 2023; 45:e2300026. [PMID: 37042115 DOI: 10.1002/bies.202300026] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Abstract
Researchers from diverse disciplines, including organismal and cellular physiology, sports science, human nutrition, evolution and ecology, have sought to understand the causes and consequences of the surprising variation in metabolic rate found among and within individual animals of the same species. Research in this area has been hampered by differences in approach, terminology and methodology, and the context in which measurements are made. Recent advances provide important opportunities to identify and address the key questions in the field. By bringing together researchers from different areas of biology and biomedicine, we describe and evaluate these developments and the insights they could yield, highlighting the need for more standardisation across disciplines. We conclude with a list of important questions that can now be addressed by developing a common conceptual and methodological toolkit for studies on metabolic variation in animals.
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Affiliation(s)
- Neil B Metcalfe
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Jakob Bellman
- Department of Physiology, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Pierre Bize
- Swiss Ornithological Institute, Sempach, Switzerland
| | - Pierre U Blier
- Département de Biologie, Université de Québec à Rimouski, Rimouski, Canada
| | - Amélie Crespel
- Department of Biology, University of Turku, Turku, Finland
| | - Neal J Dawson
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Ruth E Dunn
- Lancaster Environment Centre, University of Lancaster, Lancaster, UK
| | - Lewis G Halsey
- School of Life and Health Sciences, University of Roehampton, London, UK
| | - Wendy R Hood
- Department of Biological Sciences, Auburn University, Auburn, USA
| | - Mark Hopkins
- School of Food Science and Nutrition, Leeds University, Leeds, UK
| | - Shaun S Killen
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Darryl McLennan
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Lauren E Nadler
- Ocean and Earth Science, NOC, University of Southampton, Southampton, UK
| | - Julie J H Nati
- Ocean Sciences Center, Memorial University of Newfoundland, St John's, Canada
| | - Matthew J Noakes
- School of Animal, Plant, and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tommy Norin
- DTU Aqua: National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Susan E Ozanne
- Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | - Amanda K Pettersen
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
- School of Life & Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Anna Przybylska-Piech
- Department of Vertebrate Zoology & Ecology, Nicolaus Copernicus University, Toruń, Poland
| | - Alann Rathery
- School of Life and Health Sciences, University of Roehampton, London, UK
| | - Charlotte Récapet
- Universite de Pau et des Pays de l'Adour, E2S UPPA, INRAE, ECOBIOP, Saint-Pée-sur-, Nivelle, France
| | - Enrique Rodríguez
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Karine Salin
- IFREMER, Univ Brest, CNRS, IRD, Laboratory of Environmental Marine Sciences, Plouzané, France
| | - Antoine Stier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Elisa Thoral
- Department of Biology, Lund University, Lund, Sweden
| | - Klaas R Westerterp
- Department of Nutrition & Movement Sciences, Maastricht University, Maastricht, The Netherlands
| | | | - Michał S Wojciechowski
- Department of Vertebrate Zoology & Ecology, Nicolaus Copernicus University, Toruń, Poland
| | - Pat Monaghan
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
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11
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Castellanos MC, Montero-Pau J, Ziarsolo P, Blanca JM, Cañizares J, Pausas JG. Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild. Proc Biol Sci 2023; 290:20230141. [PMID: 37122252 PMCID: PMC10130720 DOI: 10.1098/rspb.2023.0141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/22/2023] [Indexed: 05/02/2023] Open
Abstract
The vast variation in floral traits across angiosperms is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection or by low trait ability to respond even if selection is present. We studied a plant predominantly pollinated by one bee species across its range. We measured heritability and evolvability of traits, using genome-wide relatedness in a large wild population, and combined this with estimates of selection on the same individuals. We found evidence for both stabilizing selection and low trait heritability as potential explanations for stasis in flowers. The area of the standard petal is under stabilizing selection, but the variability is not heritable. A separate trait, floral weight, presents high heritability, but is not currently under selection. We show how a simple pollination environment coincides with the absence of current prerequisites for adaptive evolutionary change, while heritable variation remains to respond to future selection pressures.
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Affiliation(s)
- Maria Clara Castellanos
- School of Life Sciences, Universityof Sussex, Brighton BN1 9QG, UK
- CIDE-CSIC, Montcada, Valencia, Spain
| | - Javier Montero-Pau
- COMAV, Universitat Politècnica de València, Valencia, Spain
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València, Valencia, Spain
| | - Peio Ziarsolo
- COMAV, Universitat Politècnica de València, Valencia, Spain
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12
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Gauzere J, Pemberton JM, Slate J, Morris A, Morris S, Walling CA, Johnston SE. A polygenic basis for birth weight in a wild population of red deer (Cervus elaphus). G3 (BETHESDA, MD.) 2023; 13:jkad018. [PMID: 36652410 PMCID: PMC10085764 DOI: 10.1093/g3journal/jkad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
The genetic architecture of traits under selection has important consequences for the response to selection and potentially for population viability. Early QTL mapping studies in wild populations have reported loci with large effect on trait variation. However, these results are contradicted by more recent genome-wide association analyses, which strongly support the idea that most quantitative traits have a polygenic basis. This study aims to re-evaluate the genetic architecture of a key morphological trait, birth weight, in a wild population of red deer (Cervus elaphus), using genomic approaches. A previous study using 93 microsatellite and allozyme markers and linkage mapping on a kindred of 364 deer detected a pronounced QTL on chromosome 21 explaining 29% of the variance in birth weight, suggesting that this trait is partly controlled by genes with large effects. Here, we used data for more than 2,300 calves genotyped at >39,000 SNP markers and two approaches to characterise the genetic architecture of birth weight. First, we performed a genome-wide association (GWA) analysis, using a genomic relatedness matrix to account for population structure. We found no SNPs significantly associated with birth weight. Second, we used genomic prediction to estimate the proportion of variance explained by each SNP and chromosome. This analysis confirmed that most genetic variance in birth weight was explained by loci with very small effect sizes. Third, we found that the proportion of variance explained by each chromosome was slightly positively correlated with its size. These three findings highlight a highly polygenic architecture for birth weight, which contradicts the previous QTL study. These results are probably explained by the differences in how associations are modelled between QTL mapping and GWA. Our study suggests that models of polygenic adaptation are the most appropriate to study the evolutionary trajectory of this trait.
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Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- AGAP, Université Montpellier, CIRAD, INRAE, Institut Agro, 34090 Montpellier, France
| | | | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alison Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Craig A Walling
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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13
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Lasky JR, Josephs EB, Morris GP. Genotype-environment associations to reveal the molecular basis of environmental adaptation. THE PLANT CELL 2023; 35:125-138. [PMID: 36005926 PMCID: PMC9806588 DOI: 10.1093/plcell/koac267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/23/2022] [Indexed: 06/14/2023]
Abstract
A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation to their environment. Climate change has given new urgency to this goal, as society aims to accelerate adaptation of ecologically important plant species, endangered plant species, and crops to hotter, less predictable climates. In the pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, and ecology. Now, the rise of genomics and new computational approaches may facilitate this research. Genotype-environment associations (GEAs) use statistical associations between allele frequency and environment of origin to test the hypothesis that allelic variation at a given gene is adapted to local environments. Researchers may scan the genome for GEAs to generate hypotheses on adaptive genetic variants (environmental genome-wide association studies). Despite the rapid adoption of these methods, many important questions remain about the interpretation of GEA findings, which arise from fundamental unanswered questions on the genetic architecture of adaptation and limitations inherent to association-based analyses. We outline strategies to ground GEAs in the underlying hypotheses of genetic architecture and better test GEA-generated hypotheses using genetics and ecophysiology. We provide recommendations for new users who seek to learn about the molecular basis of adaptation. When combined with a rigorous hypothesis testing framework, GEAs may facilitate our understanding of the molecular basis of climate adaptation for plant improvement.
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Affiliation(s)
- Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily B Josephs
- Department of Plant Biology; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Geoffrey P Morris
- Department of Soil and Crop Sciences; Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80526, USA
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14
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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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15
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Johnston SE, Chen N, Josephs EB. Taking quantitative genomics into the wild. Proc Biol Sci 2022; 289:20221930. [PMID: 36541172 PMCID: PMC9768650 DOI: 10.1098/rspb.2022.1930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.
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Affiliation(s)
- Susan E. Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Edinburgh EH9 3FL, UK
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, 14627, NY, USA
| | - Emily B. Josephs
- Department of Plant Biology and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, 48824, MI, USA
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16
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Pemberton JM, Kruuk LE, Clutton-Brock T. The Unusual Value of Long-Term Studies of Individuals: The Example of the Isle of Rum Red Deer Project. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022. [DOI: 10.1146/annurev-ecolsys-012722-024041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Long-term studies of individuals enable incisive investigations of questions across ecology and evolution. Here, we illustrate this claim by reference to our long-term study of red deer on the Isle of Rum, Scotland. This project has established many of the characteristics of social organization, selection, and population ecology typical of large, polygynous, seasonally breeding mammals, with wider implications for our understanding of sexual selection and the evolution of sex differences, as well as for their population dynamics and population management. As molecular genetic techniques have developed, the project has pivoted to investigate evolutionary genetic questions, also breaking new ground in this field. With ongoing advances in genomics and statistical approaches and the development of increasingly sophisticated ways to assay new phenotypic traits, the questions that long-term studies such as the red deer study can answer become both broader and ever more sophisticated. They also offer powerful means of understanding the effects of ongoing climate change on wild populations.
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Affiliation(s)
- Josephine M. Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Loeske E.B. Kruuk
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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17
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Cristescu RH, Strickland K, Schultz AJ, Kruuk LEB, de Villiers D, Frère CH. Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression. Mol Ecol 2022; 31:5455-5467. [PMID: 36043238 PMCID: PMC9826501 DOI: 10.1111/mec.16676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 01/11/2023]
Abstract
The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and, to date, we know little about the determinants of individual susceptibility to disease. Here, we investigated the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combined data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of 342 wild koalas, 60 were found to have chlamydia. Using genotype information on 5007 SNPs to investigate the role of genetic variation in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.11 (95% CI: 0.06-0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management, as it suggests adaptive potential for the population.
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Affiliation(s)
- Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Kasha Strickland
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Anthony J. Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia,Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Loeske E. B. Kruuk
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK,Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | | | - Céline H. Frère
- School of Biological SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
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18
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Jackson N, Littleford-Colquhoun BL, Strickland K, Class B, Frere CH. Selection in the city: Rapid and fine-scale evolution of urban eastern water dragons. Evolution 2022; 76:2302-2314. [PMID: 35971751 DOI: 10.1111/evo.14596] [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: 12/06/2021] [Revised: 06/27/2022] [Accepted: 07/18/2022] [Indexed: 01/22/2023]
Abstract
Oceanic archipelagos have long been treated as a Petri dish for studies of evolutionary and ecological processes. Like archipelagos, cities exhibit similar patterns and processes, such as the rapid phenotypic divergence of a species between urban and nonurban environments. However, on a local scale, cities can be highly heterogenous, where geographically close populations can experience dramatically different environmental conditions. Nevertheless, we are yet to understand the evolutionary and ecological implications for populations spread across a heterogenous cityscape. To address this, we compared neutral genetic divergence to quantitative trait divergence within three native riparian and four city park populations of an iconic urban adapter, the eastern water dragon. We demonstrated that selection is likely acting to drive divergence of snout-vent length and jaw width across native riparian populations that are geographically isolated and across city park populations that are geographically close yet isolated by urbanization. City park populations as close as 0.9 km exhibited signs of selection-driven divergence to the same extent as native riparian populations isolated by up to 114.5 km. These findings suggest that local adaptation may be occurring over exceptionally small geographic and temporal scales within a single metropolis, demonstrating that city parks can act as archipelagos for the study of rapid evolution.
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Affiliation(s)
- Nicola Jackson
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Bethan L Littleford-Colquhoun
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, 02912, US.,Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, 02912, US
| | - Kasha Strickland
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,Department of Aquaculture and Fish Biology, Hólar University, Sauðarkrókur, 550, Iceland
| | - Barbara Class
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Celine H Frere
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Biological Sciences, University of Queensland, St. Lucia, QLD, 4072, Australia
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19
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Bosse M, van Loon S. Challenges in quantifying genome erosion for conservation. Front Genet 2022; 13:960958. [PMID: 36226192 PMCID: PMC9549127 DOI: 10.3389/fgene.2022.960958] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.
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Affiliation(s)
- Mirte Bosse
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Sam van Loon
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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20
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Kimmitt AA, Becker DJ, Diller SN, Gerlach NM, Rosvall KA, Ketterson ED. Plasticity in female timing may explain earlier breeding in a North American songbird. J Anim Ecol 2022; 91:1988-1998. [PMID: 35819093 DOI: 10.1111/1365-2656.13772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/21/2022] [Indexed: 11/27/2022]
Abstract
Many species have shifted their breeding phenology in response to climate change. Identifying the magnitude of phenological shifts and whether climate-mediated selection drives these shifts is key for determining species' resilience to climate change. Birds are a strong model for studying phenological shifts due to numerous long-term research studies; however, generalities pertaining to drivers of phenological shifts will emerge only as we add study species that differ in life history and geography. We investigated 32 years of reproductive timing in a non-migratory population of dark-eyed juncos (Junco hyemalis). We predicted that plasticity in reproductive timing would allow females to breed earlier in warmer springs. We also predicted that selection would favour earlier breeding and asked whether the temperatures throughout the breeding season would predict the strength of selection. To test these predictions, we examined temporal changes in the annual median date for reproductive onset (i.e., first egg date) and we used a sliding window analysis to identify spring temperatures driving these patterns. Next, we explored plasticity in reproductive timing and asked whether selection favoured earlier breeding. Lastly, we used a sliding window analysis to identify the time during the breeding season that temperature was most associated with selection favouring earlier breeding. First egg dates occurred earlier over time and strongly covaried with April temperatures. Further, individual females that bred in more than one year, typically bred earlier in warmer Aprils, exhibiting plastic responses to April temperature. We also found significant overall selection favouring earlier breeding (i.e., higher relative fitness with earlier first egg dates) and variation in selection for earlier breeding over time. However, temperature across diverse climatic windows did not predict the strength of selection. Our findings provide further evidence for the role of phenotypic plasticity in shifting phenology in response to earlier springs. We also provide evidence for the role of selection favouring earlier breeding, regardless of temperature, thus setting the stage for adaptive changes in female breeding phenology. We suggest for multi-brooded birds that advancing first egg dates likely increases the length of the breeding season, and therefore, reproductive success.
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Affiliation(s)
- Abigail A Kimmitt
- Department of Biology, Indiana University, 1001 E. Third St., Bloomington, Indiana.,Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK
| | - Sara N Diller
- Department of Biology, Indiana University, 1001 E. Third St., Bloomington, Indiana
| | - Nicole M Gerlach
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL
| | - Kimberly A Rosvall
- Department of Biology, Indiana University, 1001 E. Third St., Bloomington, Indiana
| | - Ellen D Ketterson
- Department of Biology, Indiana University, 1001 E. Third St., Bloomington, Indiana.,Environmental Resilience Institute, Indiana University, 717 E. Eighth St., Bloomington, Indiana
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21
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Thripob P, Fortunel C, Réjou‐Méchain M, Nathalang A, Chanthorn W. Size‐dependent intraspecific variation in wood traits has little impact on aboveground carbon estimates in a tropical forest landscape. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patcharapan Thripob
- Department of Environmental Technology and Management, Faculty of Environment Kasetsart University 50 Ngamwongwan Road, Jatujak, Bangkok 10900 Thailand
| | - Claire Fortunel
- AMAP Université de Montpellier CIRAD, CNRS, INRAE, IRD Montpellier France
| | | | - Anuttara Nathalang
- National Biobank of Thailand, National Science and Technology Development Agency Pathum Thani 12120 Thailand
| | - Wirong Chanthorn
- Department of Environmental Technology and Management, Faculty of Environment Kasetsart University 50 Ngamwongwan Road, Jatujak, Bangkok 10900 Thailand
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research UFZ, 04318 Leipzig Germany
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22
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Hunter DC, Ashraf B, Bérénos C, Ellis PA, Johnston SE, Wilson AJ, Pilkington JG, Pemberton JM, Slate J. Using genomic prediction to detect microevolutionary change of a quantitative trait. Proc Biol Sci 2022; 289:20220330. [PMID: 35538786 PMCID: PMC9091855 DOI: 10.1098/rspb.2022.0330] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/12/2022] [Indexed: 12/31/2022] Open
Abstract
Detecting microevolutionary responses to natural selection by observing temporal changes in individual breeding values is challenging. The collection of suitable datasets can take many years and disentangling the contributions of the environment and genetics to phenotypic change is not trivial. Furthermore, pedigree-based methods of obtaining individual breeding values have known biases. Here, we apply a genomic prediction approach to estimate breeding values of adult weight in a 35-year dataset of Soay sheep (Ovis aries). Comparisons are made with a traditional pedigree-based approach. During the study period, adult body weight decreased, but the underlying genetic component of body weight increased, at a rate that is unlikely to be attributable to genetic drift. Thus cryptic microevolution of greater adult body weight has probably occurred. Genomic and pedigree-based approaches gave largely consistent results. Thus, using genomic prediction to study microevolution in wild populations can remove the requirement for pedigree data, potentially opening up new study systems for similar research.
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Affiliation(s)
- D. C. Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - B. Ashraf
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Anthropology, Durham University, Durham DH1 3LE, UK
| | - C. Bérénos
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - P. A. Ellis
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - S. E. Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - A. J. Wilson
- Centre of Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn TR10 9FE, UK
| | - J. G. Pilkington
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - J. M. Pemberton
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - J. Slate
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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23
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Aase K, Jensen H, Muff S. Genomic estimation of quantitative genetic parameters in wild admixed populations. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Kenneth Aase
- Centre for Biodiversity Dynamics, Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Stefanie Muff
- Centre for Biodiversity Dynamics, Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Department of Mathematical Sciences, Norwegian University of Science and Technology Trondheim Norway
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24
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Genetic approaches for increasing fitness in endangered species. Trends Ecol Evol 2022; 37:332-345. [PMID: 35027225 DOI: 10.1016/j.tree.2021.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
The global rate of wildlife extinctions is accelerating, and the persistence of many species requires conservation breeding programs. A central paradigm of these programs is to preserve the genetic diversity of the founder populations. However, this may preserve original characteristics that make them vulnerable to extinction. We introduce targeted genetic intervention (TGI) as an alternative approach that promotes traits that enable species to persist in the face of threats by changing the incidence of alleles that impact on fitness. The TGI toolkit includes methods with established efficacy in model organisms and agriculture but are largely untried for conservation, such as synthetic biology and artificial selection. We explore TGI approaches as a species-restoration tool for intractable threats including infectious disease and climate change.
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Christmas MJ, Jones JC, Olsson A, Wallerman O, Bunikis I, Kierczak M, Whitley KM, Sullivan I, Geib JC, Miller-Struttmann NE, Webster MT. A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component. Mol Ecol 2021; 31:1111-1127. [PMID: 34837435 DOI: 10.1111/mec.16291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We generated a genome assembly of B. balteatus. We then analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species ("incognitus"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We found a significant decrease in tongue length between bees collected between 2012-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.
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Affiliation(s)
- Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Julia C Jones
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kaitlyn M Whitley
- Department of Biology, Appalachian State University, Boone, North Carolina, USA.,U.S. Department of Agriculture, Agriculture Research Service, Charleston, South Carolina, USA
| | - Isabel Sullivan
- Department of Biology, Appalachian State University, Boone, North Carolina, USA.,Marine Estuarine Environmental Sciences, University of Maryland, College Park, Maryland, USA
| | - Jennifer C Geib
- Department of Biology, Appalachian State University, Boone, North Carolina, USA
| | | | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Ahmar S, Ballesta P, Ali M, Mora-Poblete F. Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing. Int J Mol Sci 2021; 22:10583. [PMID: 34638922 PMCID: PMC8508745 DOI: 10.3390/ijms221910583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
| | - Paulina Ballesta
- The National Fund for Scientific and Technological Development, Av. del Agua 3895, Talca 3460000, Chile
| | - Mohsin Ali
- Department of Forestry and Range Management, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
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Pennington LK, Slatyer RA, Ruiz-Ramos DV, Veloz SD, Sexton JP. How is adaptive potential distributed within species ranges? Evolution 2021; 75:2152-2166. [PMID: 34164814 DOI: 10.1111/evo.14292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
Quantitative genetic variation (QGV) represents a major component of adaptive potential and, if reduced toward range-edge populations, could prevent a species' expansion or adaptive response to rapid ecological change. It has been hypothesized that QGV will be lower at the range edge due to small populations-often the result of poor habitat quality-and potentially decreased gene flow. However, whether central populations are higher in QGV is unknown. We used a meta-analytic approach to test for a general QGV-range position relationship, including geographic and climatic distance from range centers. We identified 35 studies meeting our criteria, yielding nearly 1000 estimates of QGV (including broad-sense heritability, narrow-sense heritability, and evolvability) from 34 species. The relationship between QGV and distance from the geographic range or climatic niche center depended on the focal trait and how QGV was estimated. We found some evidence that QGV declines from geographic centers but that it increases toward niche edges; niche and geographic distances were uncorrelated. Nevertheless, few studies have compared QGV in both central and marginal regions or environments within the same species. We call for more research in this area and discuss potential research avenues related to adaptive potential in the context of global change.
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Affiliation(s)
- Lillie K Pennington
- Environmental Systems Graduate Group, University of California, Merced, California, 95343
| | - Rachel A Slatyer
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, 53703.,Current Address: Research School of Biology, Australian National University, Acton, ACT, 2600, Australia
| | - Dannise V Ruiz-Ramos
- Life and Environmental Sciences Department, University of California, Merced, California, 95343.,Current Address: U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, 65201
| | - Samuel D Veloz
- Point Blue Conservation Science, Petaluma, California, 94954
| | - Jason P Sexton
- Life and Environmental Sciences Department, University of California, Merced, California, 95343
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Pfenninger M, Reuss F, Kiebler A, Schönnenbeck P, Caliendo C, Gerber S, Cocchiararo B, Reuter S, Blüthgen N, Mody K, Mishra B, Bálint M, Thines M, Feldmeyer B. Genomic basis for drought resistance in European beech forests threatened by climate change. eLife 2021; 10:e65532. [PMID: 34132196 PMCID: PMC8266386 DOI: 10.7554/elife.65532] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/07/2021] [Indexed: 12/30/2022] Open
Abstract
In the course of global climate change, Central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought-damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated single-nucleotide polymorphisms (SNPs) throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. An SNP assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding.
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Affiliation(s)
- Markus Pfenninger
- Molecular Ecology, Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute for Organismic and Molecular Evolution, Johannes Gutenberg UniversityMainzGermany
- LOEWE Centre for Translational Biodiversity GenomicsFrankfurt am MainGermany
| | - Friederike Reuss
- Molecular Ecology, Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Angelika Kiebler
- Molecular Ecology, Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Philipp Schönnenbeck
- Molecular Ecology, Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg UniversityMainzGermany
| | - Cosima Caliendo
- Molecular Ecology, Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg UniversityMainzGermany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg UniversityMainzGermany
| | - Berardino Cocchiararo
- LOEWE Centre for Translational Biodiversity GenomicsFrankfurt am MainGermany
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
| | - Sabrina Reuter
- Ecological Networks lab, Department of Biology, Technische Universität DarmstadtDarmstadtGermany
| | - Nico Blüthgen
- Ecological Networks lab, Department of Biology, Technische Universität DarmstadtDarmstadtGermany
| | - Karsten Mody
- Ecological Networks lab, Department of Biology, Technische Universität DarmstadtDarmstadtGermany
- Department of Applied Ecology, Hochschule Geisenheim UniversityGeisenheimGermany
| | - Bagdevi Mishra
- Biological Archives, Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity GenomicsFrankfurt am MainGermany
- Functional Environmental Genomics, Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Agricultural Sciences, Nutritional Sciences, and Environmental Management, Universität GiessenGiessenGermany
| | - Marco Thines
- LOEWE Centre for Translational Biodiversity GenomicsFrankfurt am MainGermany
- Biological Archives, Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-UniversityFrankfurt am MainGermany
| | - Barbara Feldmeyer
- Molecular Ecology, Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
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Correlational selection in the age of genomics. Nat Ecol Evol 2021; 5:562-573. [PMID: 33859374 DOI: 10.1038/s41559-021-01413-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/11/2021] [Indexed: 02/01/2023]
Abstract
Ecologists and evolutionary biologists are well aware that natural and sexual selection do not operate on traits in isolation, but instead act on combinations of traits. This long-recognized and pervasive phenomenon is known as multivariate selection, or-in the particular case where it favours correlations between interacting traits-correlational selection. Despite broad acknowledgement of correlational selection, the relevant theory has often been overlooked in genomic research. Here, we discuss theory and empirical findings from ecological, quantitative genetic and genomic research, linking key insights from different fields. Correlational selection can operate on both discrete trait combinations and quantitative characters, with profound implications for genomic architecture, linkage, pleiotropy, evolvability, modularity, phenotypic integration and phenotypic plasticity. We synthesize current knowledge and discuss promising research approaches that will enable us to understand how correlational selection shapes genomic architecture, thereby linking quantitative genetic approaches with emerging genomic methods. We suggest that research on correlational selection has great potential to integrate multiple fields in evolutionary biology, including developmental and functional biology, ecology, quantitative genetics, phenotypic polymorphisms, hybrid zones and speciation processes.
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31
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Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species. FORESTS 2021. [DOI: 10.3390/f12050569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications such as DNA methylation are a potential mechanism for trees to respond to changing environments. However, it remains controversial the extent to which DNA methylation impacts ecologically important traits that influence fitness. In this study, we used reduced-representation bisulfite sequencing to associate genomic and epigenomic variation with seven phenotypic traits related to growth, leaf function, and disease susceptibility in 160 valley oak (Quercus lobata) saplings planted across two common gardens in California. We found that DNA methylation was associated with a significant fraction of phenotypic variance in plant height, leaf lobedness, powdery mildew infection, and trichome density. Two of the seven traits were significantly associated with DNA methylation in the CG context, three traits were significantly associated with CHG methylation, and two traits were significantly associated with CHH methylation. Notably, controlling for genomic variation in SNPs generally reduced the amount of trait variation explained by DNA methylation. Our results suggest that DNA methylation may serve as a useful biomarker to predict phenotypic variation in trees, though it remains unclear the degree to which DNA methylation is a causal mechanism driving phenotypic variation in forest tree species.
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Curlis JD, Davis Rabosky AR, Holmes IA, Renney TJ, Cox CL. Genetic mechanisms and correlational selection structure trait variation in a coral snake mimic. Proc Biol Sci 2021; 288:20210003. [PMID: 33726595 PMCID: PMC8059570 DOI: 10.1098/rspb.2021.0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Covariation among traits shapes both phenotypic evolution and ecological interactions across space and time. However, rampant geographical variation in the strength and direction of such correlations can be particularly difficult to explain through generalized mechanisms. By integrating population genomics, surveys of natural history collections and spatially explicit analyses, we tested multiple drivers of trait correlations in a coral snake mimic that exhibits remarkable polymorphism in mimetic and non-mimetic colour traits. We found that although such traits co-occur extensively across space, correlations were best explained by a mixture of genetic architecture and correlational selection, rather than by any single mechanism. Our findings suggest that spatially complex trait distributions may be driven more by the simple interaction between multiple processes than by complex variation in one mechanism alone. These interactions are particularly important in mimicry systems, which frequently generate striking geographical variation and genetic correlations among colour pattern traits.
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Affiliation(s)
- John David Curlis
- Department of Biology, Georgia Southern University, Statesboro, GA, USA,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,University of Michigan Museum of Zoology, Ann Arbor, MI, USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,University of Michigan Museum of Zoology, Ann Arbor, MI, USA
| | - Iris A. Holmes
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,University of Michigan Museum of Zoology, Ann Arbor, MI, USA,Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA
| | - Timothy J. Renney
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Christian L. Cox
- Department of Biology, Georgia Southern University, Statesboro, GA, USA,Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
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33
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Tarlinton RE, Fabijan J, Hemmatzadeh F, Meers J, Owen H, Sarker N, Seddon JM, Simmons G, Speight N, Trott DJ, Woolford L, Emes RD. Transcriptomic and genomic variants between koala populations reveals underlying genetic components to disorders in a bottlenecked population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01340-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AbstractHistorical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future.
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Lasky JR, Hooten MB, Adler PB. What processes must we understand to forecast regional-scale population dynamics? Proc Biol Sci 2020; 287:20202219. [PMID: 33290672 PMCID: PMC7739927 DOI: 10.1098/rspb.2020.2219] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022] Open
Abstract
An urgent challenge facing biologists is predicting the regional-scale population dynamics of species facing environmental change. Biologists suggest that we must move beyond predictions based on phenomenological models and instead base predictions on underlying processes. For example, population biologists, evolutionary biologists, community ecologists and ecophysiologists all argue that the respective processes they study are essential. Must our models include processes from all of these fields? We argue that answering this critical question is ultimately an empirical exercise requiring a substantial amount of data that have not been integrated for any system to date. To motivate and facilitate the necessary data collection and integration, we first review the potential importance of each mechanism for skilful prediction. We then develop a conceptual framework based on reaction norms, and propose a hierarchical Bayesian statistical framework to integrate processes affecting reaction norms at different scales. The ambitious research programme we advocate is rapidly becoming feasible due to novel collaborations, datasets and analytical tools.
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Affiliation(s)
- Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Mevin B. Hooten
- U.S. Geological Survey, Colorado Cooperative Fish and Wildlife Research Unit, Colorado State University, Fort Collins, CO, USA
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
- Department of Statistics, Colorado State University, Fort Collins, CO, USA
| | - Peter B. Adler
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, UT, USA
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Alexandre H, Truffaut L, Klein E, Ducousso A, Chancerel E, Lesur I, Dencausse B, Louvet J, Nepveu G, Torres‐Ruiz JM, Lagane F, Musch B, Delzon S, Kremer A. How does contemporary selection shape oak phenotypes? Evol Appl 2020; 13:2772-2790. [PMID: 33294022 PMCID: PMC7691464 DOI: 10.1111/eva.13082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/09/2020] [Accepted: 07/13/2020] [Indexed: 01/12/2023] Open
Abstract
Most existing forests are subjected to natural and human-mediated selection pressures, which have increased due to climate change and the increasing needs of human societies for wood, fibre and fuel resources. It remains largely unknown how these pressures trigger evolutionary changes. We address this issue here for temperate European oaks (Quercus petraea and Q. robur), which grow in mixed stands, under even-aged management regimes. We screened numerous functional traits for univariate selection gradients and for expected and observed genetic changes over two successive generations. In both species, growth, leaf morphology and physiology, and defence-related traits displayed significant selection gradients and predicted shifts, whereas phenology, water metabolism, structure and resilience-related traits did not. However, the direction of the selection response and the potential for adaptive evolution differed between the two species. Quercus petraea had a much larger phenotypic and genetic variance of fitness than Q. robur. This difference raises concerns about the adaptive response of Q. robur to contemporary selection pressures. Our investigations suggest that Q. robur will probably decline steadily, particularly in mixed stands with Q. petraea, consistent with the contrasting demographic dynamics of the two species.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - José M. Torres‐Ruiz
- INRAEUniversity of BordeauxBIOGECOCestasFrance
- INRAEUniversity of Clermont‐AuvergnePIAFClermont‐FerrandFrance
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36
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Blanco-Pastor JL, Barre P, Keep T, Ledauphin T, Escobar-Gutiérrez A, Roschanski AM, Willner E, Dehmer KJ, Hegarty M, Muylle H, Veeckman E, Vandepoele K, Ruttink T, Roldán-Ruiz I, Manel S, Sampoux JP. Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass. Mol Ecol Resour 2020; 21:849-870. [PMID: 33098268 DOI: 10.1111/1755-0998.13289] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/10/2020] [Accepted: 10/12/2020] [Indexed: 11/28/2022]
Abstract
Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by de novo gene prediction and functional annotation of 39,967 genes. GEA-GWAS revealed eight outlier loci associated with both environmental variables and phenotypic traits. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold-dry winter versus mild-wet winter and long rainy season versus long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co-association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations. The CANCOR test provides an integrated framework to analyse adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.
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Affiliation(s)
| | - Philippe Barre
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | - Thomas Keep
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | | | | | - Anna Maria Roschanski
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Malchow/Poel, Germany
| | - Evelyn Willner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Malchow/Poel, Germany
| | - Klaus J Dehmer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Malchow/Poel, Germany
| | - Matthew Hegarty
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium
| | - Elisabeth Veeckman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Klaas Vandepoele
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stéphanie Manel
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier, Montpellier, France
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37
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Hohenlohe PA, Funk WC, Rajora OP. Population genomics for wildlife conservation and management. Mol Ecol 2020; 30:62-82. [PMID: 33145846 PMCID: PMC7894518 DOI: 10.1111/mec.15720] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/02/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.
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Affiliation(s)
- Paul A Hohenlohe
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
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38
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Koch EL, Sbilordo SH, Guillaume F. Genetic variance in fitness and its cross‐sex covariance predict adaptation during experimental evolution. Evolution 2020; 74:2725-2740. [DOI: 10.1111/evo.14119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 09/29/2020] [Accepted: 10/25/2020] [Indexed: 01/05/2023]
Affiliation(s)
- Eva L. Koch
- Department of Evolutionary Biology and Environmental Studies University of Zürich Winterthurerstr. 190 Zürich 8057 Switzerland
- Department of Animal and Plant Science University of Sheffield Western Bank Sheffield S10 2TN United Kingdom
| | - Sonja H. Sbilordo
- Department of Evolutionary Biology and Environmental Studies University of Zürich Winterthurerstr. 190 Zürich 8057 Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies University of Zürich Winterthurerstr. 190 Zürich 8057 Switzerland
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39
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De Kort H, Panis B, Deforce D, Van Nieuwerburgh F, Honnay O. Ecological divergence of wild strawberry DNA methylation patterns at distinct spatial scales. Mol Ecol 2020; 29:4871-4881. [DOI: 10.1111/mec.15689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Hanne De Kort
- Plant Conservation and Population Biology University of Leuven Leuven Belgium
| | - Bart Panis
- Bioversity InternationalK.U. Leuven Leuven Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology Ghent University Ghent Belgium
| | | | - Ollivier Honnay
- Plant Conservation and Population Biology University of Leuven Leuven Belgium
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40
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Turner KG, Lorts CM, Haile AT, Lasky JR. Effects of genomic and functional diversity on stand-level productivity and performance of non-native Arabidopsis. Proc Biol Sci 2020; 287:20202041. [PMID: 33081615 PMCID: PMC7661305 DOI: 10.1098/rspb.2020.2041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/30/2020] [Indexed: 12/25/2022] Open
Abstract
Biodiversity can affect the properties of groups of organisms, such as ecosystem function and the persistence of colonizing populations. Genomic data offer a newly available window to diversity, complementary to other measures like taxonomic or phenotypic diversity. We tested whether native genetic diversity in field experimental stands of Arabidopsis thaliana affected their aboveground biomass and fecundity in their colonized range. We constructed some stands of genotypes that we a priori predicted would differ in performance or show overyielding. We found no relationship between genetic diversity and stand total biomass. However, increasing stand genetic diversity increased fecundity in high-resource conditions. Polyculture (multiple genotype) stands consistently yielded less biomass than expected based on the yields of component genotypes in monoculture. This under-yielding was strongest in stands with late-flowering and high biomass genotypes, potentially due to interference competition by these genotypes. Using a new implementation of association mapping, we identified genetic loci whose diversity was associated with stand-level yield, revealing a major flowering time locus associated with under-yielding of polycultures. Our field experiment supports community ecology studies that find a range of diversity-function relationships. Nevertheless, our results suggest diversity in colonizing propagule pools can enhance population fitness. Furthermore, interference competition among genotypes differing in flowering time might limit the advantages of polyculture.
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Affiliation(s)
- Kathryn G. Turner
- Department of Biology, Pennsylvania State University, USA
- Department of Biological Sciences, Idaho State University, USA
| | | | - Asnake T. Haile
- Department of Biology, Pennsylvania State University, USA
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Ethiopia
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, USA
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41
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Csilléry K, Buchmann N, Fady B. Adaptation to drought is coupled with slow growth, but independent from phenology in marginal silver fir ( Abies alba Mill.) populations. Evol Appl 2020; 13:2357-2376. [PMID: 33042220 PMCID: PMC7539328 DOI: 10.1111/eva.13029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/01/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022] Open
Abstract
Drought is one of the most important selection pressures for forest trees in the context of climate change. Yet, the different evolutionary mechanisms, and their environmental drivers, by which certain populations become more drought tolerant than others is still little understood. We studied adaptation to drought in 16 silver fir (Abies alba Mill.) populations from the French Mediterranean Alps by combining observations on seedlings from a greenhouse experiment (N = 8,199) and on adult tress in situ (N = 315). In the greenhouse, we followed half-sib families for four growing seasons for growth and phenology traits, and tested their water stress response in a "drought until death" experiment. Adult trees in the field were assessed for δ 13C, a proxy for water use efficiency, and genotyped at 357 SNP loci. SNP data was used to generate a null expectation for seedling trait divergence between populations in order to detect the signature of selection, and 31 environmental variables were used to identify the selective environment. We found that seedlings originating from populations with low soil water capacity grew more slowly, attained a smaller stature, and resisted water stress for a longer period of time in the greenhouse. Additionally, adult trees of these populations exhibited a higher water use efficiency as evidenced by their δ 13C. These results suggest a correlated evolution of the growth-drought tolerance trait complex. Population divergence in bud break phenology was adaptive only in the second growing season, and evolved independently from the growth-drought tolerance trait complex. Adaptive divergence in bud break phenology was principally driven by the inter- and intra-annual variation in temperature at the geographic origin of the population. Our results illustrate the different evolutionary strategies used by populations to cope with drought stress at the range limits across a highly heterogeneous landscape, and can be used to inform assisted migration programs.
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Affiliation(s)
- Katalin Csilléry
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
- Biodiversity & Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Nina Buchmann
- Institute of Agricultural SciencesETH ZürichZürichSwitzerland
| | - Bruno Fady
- INRAEcology of Mediterranean Forests (URFM)UR629AvignonFrance
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42
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Cotto O, Schmid M, Guillaume F. Nemo‐age
: Spatially explicit simulations of eco‐evolutionary dynamics in stage‐structured populations under changing environments. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13460] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Olivier Cotto
- Mathematics and Biology Queen's University Kingston ON Canada
| | - Max Schmid
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
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43
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Duntsch L, Tomotani BM, de Villemereuil P, Brekke P, Lee KD, Ewen JG, Santure AW. Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi ( Notiomystis cincta). Proc Biol Sci 2020; 287:20200948. [PMID: 32842928 PMCID: PMC7482260 DOI: 10.1098/rspb.2020.0948] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head-bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head-bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études PSL, MNHN, CNRS, Sorbonne Université, Université des Antilles, Paris, France
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Kate D. Lee
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - John G. Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Anna W. Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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44
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An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3-GENES GENOMES GENETICS 2020; 10:2787-2799. [PMID: 32540866 PMCID: PMC7407454 DOI: 10.1534/g3.120.401268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such “cryptic relatedness” within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.
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45
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Lorts CM, Lasky JR. Competition × drought interactions change phenotypic plasticity and the direction of selection on Arabidopsis traits. THE NEW PHYTOLOGIST 2020; 227:1060-1072. [PMID: 32267968 DOI: 10.1111/nph.16593] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Populations often exhibit genetic diversity in traits involved in responses to abiotic stressors, but what maintains this diversity is unclear. Arabidopsis thaliana exhibits high within-population variation in drought response. One hypothesis is that competition, varying at small scales, promotes diversity in resource use strategies. However, little is known about natural variation in competition effects on Arabidopsis physiology. We imposed drought and competition treatments on diverse genotypes. We measured resource economics traits, physiology, and fitness to characterize plasticity and selection in response to treatments. Plastic responses to competition differed depending on moisture availability. We observed genotype-drought-competition interactions for relative fitness: competition had little effect on relative fitness under well-watered conditions, whereas competition caused rank changes in fitness under drought. Early flowering was always selected. Higher δ13 C was selected only in the harshest treatment (drought and competition). Competitive context significantly changed the direction of selection on aboveground biomass and inflorescence height in well-watered environments. Our results highlight how local biotic conditions modify abiotic selection, in some cases promoting diversity in abiotic stress response. The ability of populations to adapt to environmental change may thus depend on small-scale biotic heterogeneity.
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Affiliation(s)
- Claire M Lorts
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
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46
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Jones JC, Du ZG, Bernstein R, Meyer M, Hoppe A, Schilling E, Ableitner M, Juling K, Dick R, Strauss AS, Bienefeld K. Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee. Ecol Evol 2020; 10:6246-6256. [PMID: 32724511 PMCID: PMC7381592 DOI: 10.1002/ece3.6357] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 01/03/2023] Open
Abstract
High-throughput high-density genotyping arrays continue to be a fast, accurate, and cost-effective method for genotyping thousands of polymorphisms in high numbers of individuals. Here, we have developed a new high-density SNP genotyping array (103,270 SNPs) for honey bees, one of the most ecologically and economically important pollinators worldwide. SNPs were detected by conducting whole-genome resequencing of 61 honey bee drones (haploid males) from throughout Europe. Selection of SNPs for the chip was done in multiple steps using several criteria. The majority of SNPs were selected based on their location within known candidate regions or genes underlying a range of honey bee traits, including hygienic behavior against pathogens, foraging, and subspecies. Additionally, markers from a GWAS of hygienic behavior against the major honey bee parasite Varroa destructor were brought over. The chip also includes SNPs associated with each of three major breeding objectives-honey yield, gentleness, and Varroa resistance. We validated the chip and make recommendations for its use by determining error rates in repeat genotypings, examining the genotyping performance of different tissues, and by testing how well different sample types represent the queen's genotype. The latter is a key test because it is highly beneficial to be able to determine the queen's genotype by nonlethal means. The array is now publicly available and we suggest it will be a useful tool in genomic selection and honey bee breeding, as well as for GWAS of different traits, and for population genomic, adaptation, and conservation questions.
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Affiliation(s)
- Julia C. Jones
- Institute for Bee ResearchHohen NeuendorfGermany
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
| | - Zhipei G. Du
- Institute for Bee ResearchHohen NeuendorfGermany
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47
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Gienapp P. Opinion: Is gene mapping in wild populations useful for understanding and predicting adaptation to global change? GLOBAL CHANGE BIOLOGY 2020; 26:2737-2749. [PMID: 32108978 DOI: 10.1111/gcb.15058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 05/22/2023]
Abstract
Changing environmental conditions will inevitably alter selection pressures. Over the long term, populations have to adapt to these altered conditions by evolutionary change to avoid extinction. Quantifying the 'evolutionary potential' of populations to predict whether they will be able to adapt fast enough to forecasted changes is crucial to fully assess the threat for biodiversity posed by climate change. Technological advances in sequencing and high-throughput genotyping have now made genomic studies possible in a wide range of species. Such studies, in theory, allow an unprecedented understanding of the genomics of ecologically relevant traits and thereby a detailed assessment of the population's evolutionary potential. Aimed at a wider audience than only evolutionary geneticists, this paper gives an overview of how gene-mapping studies have contributed to our understanding and prediction of evolutionary adaptations to climate change, identifies potential reasons why their contribution to understanding adaptation to climate change may remain limited, and highlights approaches to study and predict climate change adaptation that may be more promising, at least in the medium term.
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48
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 DOI: 10.1101/642306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 05/26/2023] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest Management Colorado State University Fort Collins CO USA
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Lua Lopez
- Department of Biology Binghamton University (State University of New York) Binghamton NY USA
| | - Adrian E Platts
- Simons Center for Quantitative Biology Cold Spring Harbor Laboratory Cold Spring Harbor NY USA
- Department of Biology Center for Genomics and Systems Biology New York University New York NY USA
| | - Jesse R Lasky
- Department of Biology Pennsylvania State University University Park PA USA
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49
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Waldvogel A, Feldmeyer B, Rolshausen G, Exposito‐Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M. Evolutionary genomics can improve prediction of species' responses to climate change. Evol Lett 2020; 4:4-18. [PMID: 32055407 PMCID: PMC7006467 DOI: 10.1002/evl3.154] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/31/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023] Open
Abstract
Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco-evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large-scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco-evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available resources more effectively, to implement mitigation measures before species go extinct and ecosystems lose important functions.
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Affiliation(s)
- Ann‐Marie Waldvogel
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | | | | | - Robert Kofler
- Institute of Population GeneticsVetmeduni ViennaAustria
| | - Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwichUnited Kingdom
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute of Ecology, Evolution and DiversityGoethe‐UniversityFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
| | | | | | - Alan Bergland
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia
| | - Thomas Flatt
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Frederic Guillaume
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
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50
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 PMCID: PMC7042746 DOI: 10.1002/ece3.6002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/25/2022] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest ManagementColorado State UniversityFort CollinsCOUSA
- Department of Biological SciencesUniversity of CyprusNicosiaCyprus
| | - Lua Lopez
- Department of BiologyBinghamton University (State University of New York)BinghamtonNYUSA
| | - Adrian E. Platts
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNYUSA
- Department of BiologyCenter for Genomics and Systems BiologyNew York UniversityNew YorkNYUSA
| | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
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