DOI: 10.5061/dryad.rjdfn2zdb
title: A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population

description: Background: Allegheny woodrats (Neotoma magister) are found in
 metapopulations distributed throughout the Interior Highlands and
 Appalachia. Historically these metapopulations persisted as relatively
 fluid networks, enabling gene flow between subpopulations and
 recolonization of formerly extirpated regions. However, over the past 45
 years, Allegheny woodrat populations have experienced population declines
 throughout their range due to a combination of habitat destruction,
 declining hard mast availability, and roundworm parasitism. In an effort
 to initiate genetic rescue of a small, genetically depauperate
 subpopulation in New Jersey, woodrats were translocated from a genetically
 robust population in Pennsylvania (PA) in 2015, 2016, and 2017. Herein, we
 assess the efficacy of these translocations to restore genetic diversity
 within the recipient population.  Results: We designed a novel
 134 single nucleotide polymorphism panel, which was used to genotype the
 six woodrats translocated from PA and 82 individuals from the NJ
 population captured before and after the translocation events. These data
 indicated that a minimum of two translocated individuals successfully
 produced at least 16 offspring, who reproduced as well. Further,
 population-wide observed heterozygosity rose substantially following the
 first set of translocations, reached levels comparable to that of
 populations in Indiana and Ohio, and remained elevated throughout the
 following years. Abundance also increased during the monitoring period,
 suggesting Pennsylvania translocations initiated the genetic rescue of the
 New Jersey population. Conclusions: Our results indicate, encouragingly,
 that very small numbers of translocated individuals can successfully
 restore the genetic diversity of a threatened population. Our work also
 highlights the risks of managing very small populations, such as when
 translocated individuals have greater reproductive success relative to
 residents. Finally, we note that ongoing work with Allegheny woodrats may
 broadly shape our understanding of genetic rescue within metapopulations
 and across heterogeneous landscapes.
description: We extracted deoxyribonucleic acid (DNA) from a tail clip of a
 single <em>N. magister</em> individual by pairing commercially
 available extraction (DNEasy Blood and Tissue, Qiagen, Venlo, the
 Netherlands and clean-up (DNA clean & Concentrator, Zymo Research,
 Irvine, California) kits in accord with the manufacturers’ instructions.
 We conducted three lanes of paired-end and one lane of mate-paired
 sequencing using an Illumina HiSeq2500. We used Trimmomatic to remove
 adaptors, discard short reads, and trim poor-quality bases from 5’ and 3’
 ends of raw sequence reads. We used ABySS 1.9.0 to conduct several
 assemblies with kmer lengths ranging from 40 to 85. PE reads were used to
 generate contigs. MP reads were used to infer the order, orientation, and
 distance between contigs, linking them together in scaffolds. The assembly
 with the greatest N50 value and longest scaffold was used for downstream
 analyses. We used the MAKER 2.28 pipeline to annotate
 all scaffolds greater than 10 kb. We first used Repeat-Masker to identify
 and mask stretches of repetitive DNA. Second, we downloaded 6762
 <em>Mus musculus</em> protein sequences from the UniProtKB
 database (www.uniprot.org) and used the protein2genome setting in MAKER to
 generate gene annotations. These annotations were subsequently used to
 train SNAP and generate <em>ab initio</em> predictions. Third,
 we aligned protein sequences and 93400 <em>Mus musculus</em>
 expressed sequence tag (EST) sequences to the genome using BLAST and used
 InterProScan to identify putative protein domains. Finally, all
 <em>ab initio</em> gene predictions supported by protein, EST
 or InterProScan evidence were promoted to gene annotations.
description: The Neotoma magister draft genome was generated from mate-paired
 and paired-end reads using ABySS vs. 1.9.0.  The scaffolds greater than 10
 kb in length are described in the 10000_kmer70_scaffolds_woodrats.fasta
 file. 21,151 genes were annotated in the N. magister
 genome. These genes are described in the genome.all.gff file.