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      Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control

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          Abstract

          The larvae of click beetles (Coleoptera: Elateridae), known as “wireworms,” are agricultural pests that pose a substantial economic threat worldwide. We produced one of the first wireworm genome assemblies ( Limonius californicus), and investigated population structure and phylogenetic relationships of three species ( L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada using genome-wide markers (RADseq) and genome skimming. We found two species ( L. californicus and L. infuscatus) are comprised of multiple genetically distinct groups that diverged in the Pleistocene but have no known distinguishing morphological characters, and therefore could be considered cryptic species complexes. We also found within-species population structure across relatively short geographic distances. Genome scans for selection provided preliminary evidence for signatures of adaptation associated with different pesticide treatments in an agricultural field trial for L. canus. We demonstrate that genomic tools can be a strong asset in developing effective wireworm control strategies.

          Abstract

          Andrews et al. sequenced and assembled the genome of a wireworm, or click beetle ( Limonius californicus), an agricultural pest. Their data suggest the presence of multiple genetically distinct cryptic species in addition to population structure and a local adaptive response to pesticide use.

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          Most cited references 39

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          COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients.

           Jinliang Wang (2010)
          The software package COANCESTRY implements seven relatedness estimators and three inbreeding estimators to estimate relatedness and inbreeding coefficients from multilocus genotype data. Two likelihood estimators that allow for inbred individuals and account for genotyping errors are for the first time included in this user-friendly program for PCs running Windows operating system. A simulation module is built in the program to simulate multilocus genotype data of individuals with a predefined relationship, and to compare the estimators and the simulated relatedness values to facilitate the selection of the best estimator in a particular situation. Bootstrapping and permutations are used to obtain the 95% confidence intervals of each relatedness or inbreeding estimate, and to test the difference in averages between groups. © 2010 Blackwell Publishing Ltd.
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            Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration.

            Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.
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              RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping.

              Massively parallel sequencing has revolutionized many areas of biology, but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site-associated DNA (RAD) sequencing protocol and a new method called Rapture ( R: AD c APTURE: ). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.
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                Author and article information

                Contributors
                kimberlya@uidaho.edu
                Journal
                Commun Biol
                Commun Biol
                Communications Biology
                Nature Publishing Group UK (London )
                2399-3642
                7 September 2020
                7 September 2020
                2020
                : 3
                Affiliations
                [1 ]GRID grid.266456.5, ISNI 0000 0001 2284 9900, Institute for Bioinformatics and Evolutionary Studies (IBEST), , University of Idaho, ; Moscow, ID 83844 USA
                [2 ]GRID grid.419357.d, ISNI 0000 0001 2199 3636, Computational Sciences Center, , National Renewable Energy Laboratory, ; Golden, CO 80401 USA
                [3 ]GRID grid.266456.5, ISNI 0000 0001 2284 9900, Department of Entomology, Plant Pathology and Nematology, , University of Idaho, ; Moscow, ID 83844 USA
                [4 ]GRID grid.30064.31, ISNI 0000 0001 2157 6568, Department of Entomology, , Washington State University, ; Pullman, WA 99164 USA
                [5 ]GRID grid.4391.f, ISNI 0000 0001 2112 1969, Oregon State University, Hermiston Agricultural Research and Extension Center, ; Hermiston, OR 97838 USA
                [6 ]Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, British Columbia Canada V0M 1A0
                [7 ]Sentinel IPM Services, Chilliwack, British Columbia Canada V2R 3B5
                [8 ]GRID grid.41891.35, ISNI 0000 0001 2156 6108, Department of Plant Sciences and Plant Pathology, , Montana State University, ; Bozeman, MT 59717 USA
                [9 ]Idaho Wheat Commission, Boise, ID 83702 USA
                Article
                1169
                10.1038/s42003-020-01169-9
                7477237
                © Crown 2020

                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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

                Funding
                Funded by: Idaho Wheat Commission 6625
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                © The Author(s) 2020

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