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      New colonisers drive the increase of the emerging loggerhead turtle nesting in Western Mediterranean

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          Abstract

          The loggerhead sea turtle ( Caretta caretta) is sensitive to climate change and is responding by colonising the Western Mediterranean. To understand the rapid nesting increase in recent years in Spain, we sampled 45 hatchlings from 8 nests between 2016 and 2019. We sequenced a mtDNA D‐loop region, genotyped 2291 SNPs using 2bRAD and collected data on clutch size, hatching success, and incubation duration. We confirmed that the colonisation has a Mediterranean and Atlantic mixed origin and we detected that these nests were laid by different females, except for two nests within the same season. Our results suggest that the recent increase in nesting is due to an increase in the number of colonising individuals rather than females born in the same area returning to breed. We hypothesize that this increase in the number of colonisers results from successful conservation efforts, feminisation of the populations of origin and earlier sexual maturation. However, the percentage of offspring females produced in Spain suggests that future returning individuals will aid to the settlement of the new population. These results allow defining the current status of this colonisation although future efforts are needed to detect remigrants to confirm the establishment of a resident population.

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          PLINK: a tool set for whole-genome association and population-based linkage analyses.

          Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.
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            The variant call format and VCFtools

            Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk
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              Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

              Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT2, for representing and searching an expanded model of the human reference genome, in which a large catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate two initial applications of HISAT2: HLA typing, a critical need in human organ transplantation, and DNA fingerprinting, widely used in forensics. These applications are part of HISAT-genotype, with performance not only surpassing earlier computational methods, but matching or exceeding the accuracy of laboratory-based assays.
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                Author and article information

                Contributors
                carreras@ub.edu
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                17 January 2024
                17 January 2024
                2024
                : 14
                : 1506
                Affiliations
                [1 ]Department of Genetics, Microbiology and Statistics and IrBio, University of Barcelona, ( https://ror.org/021018s57) Avinguda Diagonal 643, 08028 Barcelona, Spain
                [2 ]BETA Technological Center, University of Vic - Central University of Catalonia, ( https://ror.org/006zjws59) Carretera Roda 70, 08500 Vic, Spain
                [3 ]Fundació Oceanogràfic de la Comunitat Valenciana, Ciutat de les Arts i les Ciències, 46013 Valencia, Spain
                [4 ]Centro de Recuperación de Fauna Silvestre “El Valle”, Ctra. Subida a El Valle, 62, 30150 La Alberca de las Torres, Murcia Spain
                [5 ]GRID grid.484181.0, ISNI 0000 0001 0198 1945, Consorci per a la Recuperació de la Fauna de les Illes Balears (COFIB), Servei de Protecció d′Espècies. Conselleria Agricultura, Pesca i Medi Natural. Govern de les Illes Balears, ; Carretera Palma- Sineu, Km 15,400, 07142 Santa Eugènia, Balearic Islands Spain
                [6 ]Fundación para la Conservación y la Recuperación de Animales Marinos (CRAM), 08820 El Prat de Llobregat, Barcelona Spain
                [7 ]Instituto Cavanilles de Biodiversidad y Biología Evolutiva, University of Valencia, ( https://ror.org/043nxc105) Apdo, 22085, 46071 Valencia, Spain
                Author information
                http://orcid.org/0000-0002-6189-0612
                http://orcid.org/0000-0002-2478-6445
                Article
                51664
                10.1038/s41598-024-51664-w
                10794258
                38233518
                930f656a-25ce-4e03-91bd-122f76991fb0
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 4 August 2023
                : 6 January 2024
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                © Springer Nature Limited 2024

                Uncategorized
                population genetics,evolutionary genetics
                Uncategorized
                population genetics, evolutionary genetics

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