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Gwee CY, Metzler D, Fuchs J, Wolf JBW. Reconciling Gene Tree Discordance and Biogeography in European Crows. Mol Ecol 2025; 34:e17764. [PMID: 40208017 PMCID: PMC12051742 DOI: 10.1111/mec.17764] [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: 10/31/2024] [Revised: 03/20/2025] [Accepted: 03/31/2025] [Indexed: 04/11/2025]
Abstract
Reconstructing the evolutionary history of young lineages diverging with gene flow is challenging due to factors like incomplete lineage sorting, introgression, and selection causing gene tree discordance. The European crow hybrid zone between all-black carrion crows and grey-coated hooded crows exemplifies this challenge. Most of the genome in Western and Central European carrion crow populations is near-identical to hooded crows, but differs substantially from their Iberian congeners. A notable exception is a single major-effect colour-locus under sexual selection aligning with the 'species' tree. To understand the underlying evolutionary processes, we reconstructed the biogeographic history of the species complex. During the Pleistocene carrion and hooded crows took refuge in the Iberian Peninsula and the Middle East, respectively. Allele-sharing of all-black Western European populations with likewise black Iberian crows at the colour-locus represents the last trace of carrion crow ancestry, resisting gene flow from expanding hooded crow populations that have homogenised most of the genome. A model of colour-locus introgression from an Iberian ancestor into hooded crow populations near the Pyrenées was significantly less supported. We found no positive relationship between introgression and recombination rate consistent with the absence of genome-wide, polygenic barriers in this young species complex. Overall, this study portrays a scenario where few large-effect loci, subject to divergent sexual selection, resist rampant and asymmetric gene exchange. This study underscores the importance of integrating population demography and biogeography to accurately interpret patterns of gene tree discordance following population divergence.
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Affiliation(s)
- Chyi Yin Gwee
- Division of Evolutionary BiologyLMU MunichPlanegg‐MartinsriedGermany
- Microevolution and BiodiversityMax Planck Institute for Biological IntelligenceSeewiesenGermany
| | - Dirk Metzler
- Division of Evolutionary BiologyLMU MunichPlanegg‐MartinsriedGermany
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, SU, EPHE, UAMuséum National d'Histoire NaturelleParisFrance
| | - Jochen B. W. Wolf
- Division of Evolutionary BiologyLMU MunichPlanegg‐MartinsriedGermany
- Microevolution and BiodiversityMax Planck Institute for Biological IntelligenceSeewiesenGermany
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2
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Wait DR, Peñalba JV. Suture zones, speciation, and evolution. Evolution 2025; 79:329-341. [PMID: 39708295 DOI: 10.1093/evolut/qpae184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 12/19/2024] [Indexed: 12/23/2024]
Abstract
In the more than 50 years since the initial conceptualization of the suture zone, little work has been done to take full advantage of the comparative capability of these geographic regions. During this time, great advances have been made in hybrid zone research that have provided invaluable insight into speciation and evolution. Hybrid zones have long been recognized to be "windows to the evolutionary process." If a single hybrid zone provides a window, then multiple hybrid zones in a suture zone can provide a panoramic view of the evolutionary process. Here, we hope to redirect attention to suture zones, bring the advances from hybrid zone research to a comparative framework, and further expand our understanding of speciation and evolution. In this review, we recount the historical discussions surrounding suture zones, briefly review what we can learn from hybrid zones, and review the comparative studies done on suture zones thus far. We also highlight the opportunities and challenges of performing research in suture zones to help guide researchers hoping to start a research project in these regions. Lastly, we propose future directions and questions for comparative research that can be done in suture zones.
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Affiliation(s)
- Daniel R Wait
- Museum of Vertebrate Zoology, Department of Integrative Biology, University of California at Berkeley, 3101 Valley Life Sciences Buildings, Berkeley, CA 94720, United States
| | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin 10115, Germany
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3
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Schwarzkopf EJ, Brandt N, Smukowski Heil C. The recombination landscape of introgression in yeast. PLoS Genet 2025; 21:e1011585. [PMID: 39937775 PMCID: PMC11845044 DOI: 10.1371/journal.pgen.1011585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 02/21/2025] [Accepted: 01/21/2025] [Indexed: 02/14/2025] Open
Abstract
Meiotic recombination is an evolutionary force that acts by breaking up genomic linkage, increasing the efficacy of selection. Recombination is initiated with a double-strand break which is resolved via a crossover, which involves the reciprocal exchange of genetic material between homologous chromosomes, or a non-crossover, which results in small tracts of non-reciprocal exchange of genetic material. Crossover and non-crossover rates vary between species, populations, individuals, and across the genome. In recent years, recombination rate has been associated with the distribution of ancestry derived from past interspecific hybridization (introgression) in a variety of species. We explore this interaction of recombination and introgression by sequencing spores and detecting crossovers and non-crossovers from two crosses of the yeast Saccharomyces uvarum. One cross is between strains which each contain introgression from their sister species, S. eubayanus, while the other cross has no introgression present. We find that the recombination landscape is significantly different between S. uvarum crosses, and that some of these differences can be explained by the presence of introgression in one cross. Crossovers are significantly reduced in heterozygous introgression compared to syntenic regions in the cross without introgression. This translates to reduced allele shuffling within introgressed regions, and an overall reduction of shuffling on most chromosomes with introgression compared to the syntenic regions and chromosomes without introgression. Our results suggest that hybridization can significantly influence the recombination landscape, and that the reduction in allele shuffling contributes to the initial purging of introgression in the generations following a hybridization event.
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Affiliation(s)
- Enrique J. Schwarzkopf
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Nathan Brandt
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
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4
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Owens GL, Caseys C, Mitchell N, Hübner S, Whitney KD, Rieseberg LH. Shared Selection and Genetic Architecture Drive Strikingly Repeatable Evolution in Long-Term Experimental Hybrid Populations. Mol Biol Evol 2025; 42:msaf014. [PMID: 39835697 PMCID: PMC11783286 DOI: 10.1093/molbev/msaf014] [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: 09/16/2024] [Revised: 11/27/2024] [Accepted: 01/09/2025] [Indexed: 01/22/2025] Open
Abstract
The degree to which evolution repeats itself has implications regarding the major forces driving evolution and the potential for evolutionary biology to be a predictive (vs. solely historical) science. To understand the factors that control evolutionary repeatability, we experimentally evolved four replicate hybrid populations of sunflowers at natural sites for up to 14 years and tracked ancestry across the genome. We found that there was very strong negative selection against introgressed ancestry in several chromosomes, but positive selection for introgressed ancestry in one chromosome. Further, the strength of selection was influenced by recombination rate. High recombination regions had lower selection against introgressed ancestry due to more frequent recombination away from incompatible backgrounds. Strikingly, evolution was highly parallel across replicates, with shared selection driving 88% of variance in introgressed allele frequency change. Parallel evolution was driven by both high levels of sustained linkage in introgressed alleles and strong selection on large-effect quantitative trait loci. This work highlights the repeatability of evolution through hybridization and confirms the central roles that natural selection, genomic architecture, and recombination play in the process.
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Affiliation(s)
- Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Celine Caseys
- Department of Plant Science, University of California, Davis, CA, USA
| | - Nora Mitchell
- Department of Biology, University of Wisconsin–Eau Claire, Eau Claire, WI, USA
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Sariel Hübner
- Department of Bioinformatics and Galilee Research Institute (MIGAL), Tel Hai Academic College, Tel Hai, Israel
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Loren H Rieseberg
- Department of Botany and Beaty Biodiversity Centre, University of British Columbia, Vancouver, BC, Canada
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5
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Peñalba JV, Runemark A, Meier JI, Singh P, Wogan GOU, Sánchez-Guillén R, Mallet J, Rometsch SJ, Menon M, Seehausen O, Kulmuni J, Pereira RJ. The Role of Hybridization in Species Formation and Persistence. Cold Spring Harb Perspect Biol 2024; 16:a041445. [PMID: 38438186 PMCID: PMC11610762 DOI: 10.1101/cshperspect.a041445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Hybridization, or interbreeding between different taxa, was traditionally considered to be rare and to have a largely detrimental impact on biodiversity, sometimes leading to the breakdown of reproductive isolation and even to the reversal of speciation. However, modern genomic and analytical methods have shown that hybridization is common in some of the most diverse clades across the tree of life, sometimes leading to rapid increase of phenotypic variability, to introgression of adaptive alleles, to the formation of hybrid species, and even to entire species radiations. In this review, we identify consensus among diverse research programs to show how the field has progressed. Hybridization is a multifaceted evolutionary process that can strongly influence species formation and facilitate adaptation and persistence of species in a rapidly changing world. Progress on testing this hypothesis will require cooperation among different subdisciplines.
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Affiliation(s)
- Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, 10115 Berlin, Germany
| | - Anna Runemark
- Department of Biology, Lund University, 22632 Lund, Sweden
| | - Joana I Meier
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
- Department of Zoology, University of Cambridge, Cambridgeshire CB2 3EJ, United Kingdom
| | - Pooja Singh
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Center for Ecology, Evolution & Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), CH-8600 Kastanienbaum, Switzerland
| | - Guinevere O U Wogan
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | | | - James Mallet
- Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Sina J Rometsch
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
- Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut 06511, USA
| | - Mitra Menon
- Department of Evolution and Ecology, University of California Davis, Davis, California 95616, USA
| | - Ole Seehausen
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Center for Ecology, Evolution & Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), CH-8600 Kastanienbaum, Switzerland
| | - Jonna Kulmuni
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Biocenter 3, Helsinki, Finland
| | - Ricardo J Pereira
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart 70191, Germany
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6
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Johnston SE. Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future. Mol Biol Evol 2024; 41:msae112. [PMID: 38959451 PMCID: PMC11221659 DOI: 10.1093/molbev/msae112] [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: 04/17/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 07/05/2024] Open
Abstract
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms of recombination are remarkably conserved across eukaryotes, yet meiotic genes and proteins show substantial variation in their sequence and function, even between closely related species. Furthermore, the rate and distribution of recombination shows a huge diversity within and between chromosomes, individuals, sexes, populations, and species. This variation has implications for many molecular and evolutionary processes, yet how and why this diversity has evolved is not well understood. A key step in understanding trait evolution is to determine its genetic basis-that is, the number, effect sizes, and distribution of loci underpinning variation. In this perspective, I discuss past and current knowledge on the genetic basis of variation in recombination rate and distribution, explore its evolutionary implications, and present open questions for future research.
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Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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Feng X, Merilä J, Löytynoja A. Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks. Mol Biol Evol 2024; 41:msae031. [PMID: 38366566 PMCID: PMC10903534 DOI: 10.1093/molbev/msae031] [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: 09/19/2023] [Revised: 12/20/2023] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.
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Affiliation(s)
- Xueyun Feng
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Area of Ecology and Biodiversity, The School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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Wong ELY, Filatov DA. The role of recombination landscape in species hybridisation and speciation. FRONTIERS IN PLANT SCIENCE 2023; 14:1223148. [PMID: 37484464 PMCID: PMC10361763 DOI: 10.3389/fpls.2023.1223148] [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: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023]
Abstract
It is now well recognised that closely related species can hybridize and exchange genetic material, which may promote or oppose adaptation and speciation. In some cases, interspecific hybridisation is very common, making it surprising that species identity is preserved despite active gene exchange. The genomes of most eukaryotic species are highly heterogeneous with regard to gene density, abundance of repetitive DNA, chromatin compactisation etc, which can make certain genomic regions more prone or more resistant to introgression of genetic material from other species. Heterogeneity in local recombination rate underpins many of the observed patterns across the genome (e.g. actively recombining regions are typically gene rich and depleted for repetitive DNA) and it can strongly affect the permeability of genomic regions to interspecific introgression. The larger the region lacking recombination, the higher the chance for the presence of species incompatibility gene(s) in that region, making the entire non- or rarely recombining block impermeable to interspecific introgression. Large plant genomes tend to have highly heterogeneous recombination landscape, with recombination frequently occurring at the ends of the chromosomes and central regions lacking recombination. In this paper we review the relationship between recombination and introgression in plants and argue that large rarely recombining regions likely play a major role in preserving species identity in actively hybridising plant species.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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9
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Dagilis AJ, Matute DR. The fitness of an introgressing haplotype changes over the course of divergence and depends on its size and genomic location. PLoS Biol 2023; 21:e3002185. [PMID: 37459351 PMCID: PMC10374083 DOI: 10.1371/journal.pbio.3002185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/27/2023] [Accepted: 06/06/2023] [Indexed: 07/28/2023] Open
Abstract
The genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature of evolution. Examples of both adaptive and deleterious introgression exist in a variety of systems. What is unclear is how the fitness of an introgressing haplotype changes as species diverge or as the size of the introgressing haplotype changes. In a simple model, we show that introgression may more easily occur into parts of the genome which have not diverged heavily from a common ancestor. The key insight is that alleles from a shared genetic background are likely to have positive epistatic interactions, increasing the fitness of a larger introgressing block. In regions of the genome where few existing substitutions are disrupted, this positive epistasis can be larger than incompatibilities with the recipient genome. Further, we show that early in the process of divergence, introgression of large haplotypes can be favored more than introgression of individual alleles. This model is consistent with observations of a positive relationship between recombination rate and introgression frequency across the genome; however, it generates several novel predictions. First, the model suggests that the relationship between recombination rate and introgression may not exist, or may be negative, in recently diverged species pairs. Furthermore, the model suggests that introgression that replaces existing derived variation will be more deleterious than introgression at sites carrying ancestral variants. These predictions are tested in an example of introgression in Drosophila melanogaster, with some support for both. Finally, the model provides a potential alternative explanation to asymmetry in the direction of introgression, with expectations of higher introgression from rapidly diverged populations into slowly evolving ones.
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Affiliation(s)
- Andrius J Dagilis
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, United States of America
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10
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Nouhaud P, Martin SH, Portinha B, Sousa VC, Kulmuni J. Rapid and predictable genome evolution across three hybrid ant populations. PLoS Biol 2022; 20:e3001914. [PMID: 36538502 PMCID: PMC9767332 DOI: 10.1371/journal.pbio.3001914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Hybridization is frequent in the wild but it is unclear when admixture events lead to predictable outcomes and if so, at what timescale. We show that selection led to correlated sorting of genetic variation rapidly after admixture in 3 hybrid Formica aquilonia × F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.
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Affiliation(s)
- Pierre Nouhaud
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Simon H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Beatriz Portinha
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- cE3c, Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Vitor C. Sousa
- cE3c, Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Jonna Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
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