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      Genetic depletion does not prevent rapid evolution in island‐introduced lizards

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          Abstract

          Experimental introductions of species have provided some of the most tractable examples of rapid phenotypic changes, which may reflect plasticity, the impact of stochastic processes, or the action of natural selection. Yet to date, very few studies have investigated the neutral and potentially adaptive genetic impacts of experimental introductions. We dissect the role of these processes in shaping the population differentiation of wall lizards in three Croatian islands (Sušac, Pod Kopište, and Pod Mrčaru), including the islet of Pod Mrčaru, where experimentally introduced lizards underwent rapid (~30 generations) phenotypic changes associated with a shift from an insectivorous to a plant‐based diet. Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction and very low neutral genetic differentiation between the introduced population and its source. However, genetic depletion did not prevent rapid population growth, as the introduced lizards exhibited population genetic signals of expansion and are known to have reached a high density. Our genome‐scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large‐effect loci and/or that phenotypic plasticity plays a major role in phenotypic changes. Nonetheless, functional annotation of the outlier loci revealed some candidate genes relevant to diet‐induced adaptation, in agreement with the hypothesis of directional selection. Our study provides important insights on the evolutionary potential of bottlenecked populations in response to new selective pressures on short ecological timescales.

          Abstract

          Our study provides unprecedented information on how demographic expansion can help genetically impoverished populations successfully adapt to new environments. Such interplay between demography and selection can have a major role in the evolution of species responding to global changes, such as introduced species and species impacted by climate change.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            Welcome to the Tidyverse

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              Minimap2: pairwise alignment for nucleotide sequences

              Heng Li (2018)
              Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.
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                Author and article information

                Contributors
                francesco.ficetola@gmail.com
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                27 November 2023
                November 2023
                : 13
                : 11 ( doiID: 10.1002/ece3.v13.11 )
                : e10721
                Affiliations
                [ 1 ] Dipartimento di Scienze e Politiche Ambientali Università degli Studi di Milano Milano Italy
                [ 2 ] Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'Ambiente Università degli Studi dell'Aquila L'Aquila‐Coppito Italy
                [ 3 ] Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório Associado Universidade do Porto Vairão Portugal
                [ 4 ] BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal
                [ 5 ] Departamento de Biologia, Faculdade de Ciências Universidade do Porto Porto Portugal
                Author notes
                [*] [* ] Correspondence

                Gentile Francesco Ficetola, Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, I‐20133 Milano, Italy.

                Email: francesco.ficetola@ 123456gmail.com

                Author information
                https://orcid.org/0000-0001-9958-0073
                https://orcid.org/0000-0002-2335-7198
                https://orcid.org/0000-0003-3414-5155
                Article
                ECE310721 ECE-2023-07-01194.R1
                10.1002/ece3.10721
                10682264
                38034325
                6d2320e0-96a7-4a0f-bf71-f24d293eb3e6
                © 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 02 October 2023
                : 14 July 2023
                : 23 October 2023
                Page count
                Figures: 5, Tables: 2, Pages: 15, Words: 10820
                Funding
                Funded by: Fundação para a Ciência e a Tecnologia , doi 10.13039/501100001871;
                Award ID: 28014 02/SAICT/2017
                Award ID: SFRH/BD/95745/2013
                Funded by: PRIN
                Award ID: 2017KLZ3MA
                Award ID: 20224FFACB
                Award ID: 2022TZZT9A
                Funded by: Rita Levi Montalcini
                Categories
                Evolutionary Ecology
                Genomics
                Population Genetics
                Research Article
                Research Articles
                Custom metadata
                2.0
                November 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.3.5 mode:remove_FC converted:28.11.2023

                Evolutionary Biology
                experimental introduction,founder effect,island,podarcis siculus,population genomics,rapid adaptation

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