DOI: 10.5061/dryad.np5hqbzz2
title: Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink

description: The application of next‐generation sequencing (NGS) to non‐invasive
 samples is one of the most promising methods in conservation genomics, but
 these types of samples present significant challenges for NGS. The
 European mink (Mustela lutreola) is critically endangered throughout its
 range. However, important aspects such as census size and inbreeding
 remain still unknown in many populations, so it is crucial to develop new
 methods to monitor this species. In this work, we placed hair tubes along
 riverbanks in a border area of the Iberian population, which allowed the
 genetic identification of 76 European mink hair samples. We then applied a
 reduced representation genomic sequencing (ddRAD) technique to a subset of
 these samples to test whether we could extract sufficient genomic
 information from them. We show that several problems with the DNA,
 including contamination, fragmentation, oxidation, and possibly sample
 mixing, affected the samples. Using various bioinformatic techniques to
 reduce these problems, we were able to unambiguously genotype 19 hair
 samples belonging to six individuals. This small number of individuals
 showed that the demographic status of the species in this peripheral
 population is worse than expected. The data obtained also allowed us to
 perform preliminary analyses of relatedness and inbreeding. Although
 further improvements in sampling and analysis are needed, the application
 of the ddRAD technique to non‐invasively obtained hairs represents a
 significant advance in the genomic study of endangered species.
description: ### Title Evaluating the use of non-invasive hair sampling and ddRAD to
 characterize populations of endangered species: Application to a
 peripheral population of the European mink ### Authors Alfonso Balmori-de
 la Puente, Lidia Escoda, Angel Fernandez-Gonzalez, Daniel Menendez-Perez,
 Jorge Gonzalez-Esteban & Jose Castresana ### Description of the
 data Two zipped files are included in this dataset. After unzipping, a
 sequence file in FASTQ format will be generated for each sample sequenced
 by ddRAD. File 1: ddRAD\_reads\_tissues.zip Description: Quality-filtered
 ddRAD reads for the tissue samples in FASTQ format Files available after
 unzipping, corresponding to 15 tissue samples: BC3179\_sample.fq.gz
 BC3384\_sample.fq.gz BC3388\_sample.fq.gz BC3399\_sample.fq.gz
 BC3407\_sample.fq.gz BC3411\_sample.fq.gz BC3429\_sample.fq.gz
 BC3458\_sample.fq.gz BC3460\_sample.fq.gz BC3709\_sample.fq.gz
 BC3717\_sample.fq.gz BC3939\_sample.fq.gz BC3973\_sample.fq.gz
 BC4012\_sample.fq.gz BC4310\_sample.fq.gz File 2: ddRAD\_reads\_hairs.zip
 Description: Quality-filtered ddRAD reads for the hair samples in FASTQ
 format Files available after unzipping, corresponding to 34 hair samples:
 BC2796\_sample.bt.fq.gz BC2910\_sample.bt.fq.gz BC3048\_sample.bt.fq.gz
 BC3058\_sample.bt.fq.gz BC3724\_sample.bt.fq.gz BC3740\_sample.bt.fq.gz
 BC3745\_sample.bt.fq.gz BC3748\_sample.bt.fq.gz BC3751\_sample.bt.fq.gz
 BC3755\_sample.bt.fq.gz BC3759\_sample.bt.fq.gz BC3764\_sample.bt.fq.gz
 BC3771\_sample.bt.fq.gz BC4547\_sample.bt.fq.gz BC4554\_sample.bt.fq.gz
 BC4571\_sample.bt.fq.gz BC4604\_sample.bt.fq.gz BC4658\_sample.bt.fq.gz
 BC4674\_sample.bt.fq.gz BC4677\_sample.bt.fq.gz BC4689\_sample.bt.fq.gz
 BC4693\_sample.bt.fq.gz BC4694\_sample.bt.fq.gz BC4729\_sample.bt.fq.gz
 BC4732\_sample.bt.fq.gz BC4745\_sample.bt.fq.gz BC4774\_sample.bt.fq.gz
 BC4808\_sample.bt.fq.gz BC4810\_sample.bt.fq.gz BC4817\_sample.bt.fq.gz
 BC4823\_sample.bt.fq.gz BC4840\_sample.bt.fq.gz BC4850\_sample.bt.fq.gz
 BC4855\_sample.bt.fq.gz