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      Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

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          Abstract

          Laboratory techniques for high‐throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site‐associated DNA probes (hy RAD) is a recently developed method for population genomics with museum specimens. The hy RAD method employs fragments produced in a restriction site‐associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hy RAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hy RAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affect sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hy RAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts % GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations

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              Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

              Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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                Author and article information

                Contributors
                elinck@uw.edu
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                23 May 2017
                July 2017
                : 7
                : 13 ( doiID: 10.1002/ece3.2017.7.issue-13 )
                : 4755-4767
                Affiliations
                [ 1 ] Department of Biology Burke Museum of Natural History & CultureUniversity of Washington Seattle WAUSA
                [ 2 ] Museum of Vertebrate ZoologyUniversity of California, Berkeley Berkeley CAUSA
                [ 3 ] Department of Integrative BiologyUniversity of California, Berkeley Berkeley CAUSA
                [ 4 ] Ornithology & MammologyCalifornia Academy of Sciences San Francisco CAUSA
                [ 5 ] Center for Comparative GenomicsCalifornia Academy of Sciences San Francisco CAUSA
                Author notes
                [*] [* ] Correspondence

                Ethan B. Linck, Department of Biology, Burke Museum of Natural History & Culture, University of Washington, Seattle, WA, USA.

                Email: elinck@ 123456uw.edu

                Author information
                http://orcid.org/0000-0002-9055-6664
                Article
                ECE33065
                10.1002/ece3.3065
                5496524
                28690805
                d45860f8-8f60-460d-b10c-8bfdf99f9c61
                © 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 22 March 2017
                : 17 April 2017
                : 19 April 2017
                Page count
                Figures: 5, Tables: 3, Pages: 13, Words: 9905
                Funding
                Funded by: Army Research Office
                Funded by: NDSEG Fellowship
                Funded by: National Science Foundation
                Award ID: 1601515
                Funded by: Washington Research Foundation‐Hall Fellowships
                Funded by: Society of Systematic Biology
                Funded by: Graduate Student Research Award
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece33065
                July 2017
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.1.2 mode:remove_FC converted:04.07.2017

                Evolutionary Biology
                ancient dna,hyrad,museum genomics,radseq,sequence capture
                Evolutionary Biology
                ancient dna, hyrad, museum genomics, radseq, sequence capture

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