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      Large carpenter bees show high dispersal in a tropical semi‐arid region susceptible to desertification

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          Abstract

          Desertification is a major threat to biodiversity in arid areas of the world, partly because many organisms in these regions already exist at or near the limits of their movement and physiology. Here, we used molecular data to investigate patterns of persistence and dispersal in an ecologically and economically important carpenter bee ( Xylocopa grisescens Lepeletier) found throughout the semiarid Caatinga region of Brazil. We used a genome‐wide approach (double digest restriction‐site associated DNA, ddRAD) to gather genetic data from bees sampled from eight sites within a semiarid region subject to desertification in Northeastern Brazil. Across all populations, we observed a consistent heterozygosity and effective population size deficit along with low genetic differentiation. We did not find strong evidence of dispersal limitations caused by desertification in this study system despite data collection from sites up to 300 km distant. Thus, our data suggest that human‐mediated changes in the Caatinga, such as habitat loss, have impacted the population genetic patterns of X. grisescens. However, these impacts have also been softened by the species' biological characteristics, such as its relatively high capacity for movement. This study provides insights into how habitat changes might impact the long‐term survival of large solitary bees.

          Abstract

          This study examines the genetic status of native carpenter bees in a Brazilian region vulnerable to desertification. Employing a population genomic approach, we found low genetic diversity with high homogeneity across populations, even over distances exceeding 300 km. The findings suggest that these bees may counteract desertification and habitat degradation through their mobility, facilitating gene flow and maintaining a continuous population distribution.

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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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            Welcome to the Tidyverse

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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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                Author and article information

                Contributors
                sandara.brasil@gmail.com
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                19 August 2024
                August 2024
                : 14
                : 8 ( doiID: 10.1002/ece3.v14.8 )
                : e70085
                Affiliations
                [ 1 ] Graduate Course of Ecology and Natural Resources, Department of Biology Federal University of Ceará Fortaleza‐CE Brazil
                [ 2 ] Department of Evolution, Ecology, and Organismal Biology University of California, Riverside Riverside California USA
                [ 3 ] Department of Entomology University of California, Riverside Riverside California USA
                Author notes
                [*] [* ] Correspondence

                Sandara N. R. Brasil, Graduate Course of Ecology and Natural Resources, Department of Biology, Federal University of Ceará, Fortaleza – CE, Zip Code 60440‐900, Brazil.

                Email: sandara.brasil@ 123456gmail.com

                Author information
                https://orcid.org/0000-0001-5141-608X
                Article
                ECE370085 ECE-2024-04-00678.R1
                10.1002/ece3.70085
                11333300
                d6eb6f1d-addf-48dd-b042-ae70ee5c9696
                © 2024 The Author(s). 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
                : 07 July 2024
                : 05 April 2024
                : 08 July 2024
                Page count
                Figures: 5, Tables: 1, Pages: 10, Words: 7900
                Funding
                Funded by: National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution: INCT IN‐TREE
                Award ID: 465767/2014‐1
                Funded by: National Council for Scientific and Technological Development – CNPq
                Award ID: 400890‐2014‐3
                Funded by: Brazilian Federal Agency for Support and Evaluation of Graduate Education ‐ CAPES
                Funded by: Fulbright Association , doi 10.13039/100010629;
                Categories
                Research Article
                Research Article
                Custom metadata
                2.0
                August 2024
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.4.6 mode:remove_FC converted:20.08.2024

                Evolutionary Biology
                apoidea,ddradseq,landscape,population genetic,population structure
                Evolutionary Biology
                apoidea, ddradseq, landscape, population genetic, population structure

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