TY  - JOUR
A1  - Paijmans, Johanna L. A.
A1  - Fickel, Jörns
A1  - Courtiol, Alexandre
A1  - Hofreiter, Michael
A1  - Foerster, Daniel W.
T1  - Impact of enrichment conditions on cross-species capture of fresh and degraded DNA
JF  - Molecular ecology resources
N2  - Abstract

By combining high-throughput sequencing with target enrichment (‘hybridization capture’), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on nonmodel species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success is not yet thoroughly understood. We evaluated the impact of a key parameter – hybridization temperature – on the capture success of mitochondrial genomes across the carnivoran family Felidae. Capture was carried out for a range of sample types (fresh, archival, ancient) with varying levels of sequence divergence between bait and target (i.e. across a range of species) using pools of individually indexed libraries on Agilent SureSelect™ arrays. Our results suggest that hybridization capture protocols require specific optimization for the sample type that is being investigated. Hybridization temperature affected the proportion of on-target sequences following capture: for degraded samples, we obtained the best results with a hybridization temperature of 65 °C, while a touchdown approach (65 °C down to 50 °C) yielded the best results for fresh samples. Evaluation of capture performance at a regional scale (sliding window approach) revealed no significant improvement in the recovery of DNA fragments with high sequence divergence from the bait at any of the tested hybridization temperatures, suggesting that hybridization temperature may not be the critical parameter for the enrichment of divergent fragments.
KW  - degraded DNA
KW  - Felidae
KW  - hybridization capture
KW  - mitogenomes
KW  - next-generation sequencing
KW  - sequence enrichment
Y1  - 2016
U6  - https://doi.org/10.1111/1755-0998.12420
SN  - 1755-098X
SN  - 1755-0998
VL  - 16
SP  - 42
EP  - 55
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Cahsan, Binia De
A1  - Westbury, Michael V.
A1  - Paraskevopoulou, Sofia
A1  - Drews, Hauke
A1  - Ott, Moritz
A1  - Gollmann, Günter
A1  - Tiedemann, Ralph
T1  - Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian
JF  - Evolutionary Applications
N2  - Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany.
KW  - adaptive introgression
KW  - admixture
KW  - Bombina bombina
KW  - genetic rescue
KW  - mitogenomes
KW  - transcriptomics
Y1  - 2020
SN  - 1752-4563
VL  - 14
IS  - 6
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  -