TY - JOUR

T1 - Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland

AU - Gauthier, Jeremy

AU - Pajkovic, Mila

AU - Neuenschwander, Samuel

AU - Kaila, Lauri

AU - Schmid, Sarah

AU - Orlando, Ludovic

AU - Alvarez, Nadir

PY - 2020

Y1 - 2020

N2 - Erosion of biodiversity generated by anthropogenic activities has been studied for decades and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analysing museum collection specimens. While providing direct access to genetic variation over time, historical DNA is usually not optimally preserved, and it is necessary to apply genotyping methods based on hybridization-capture to unravel past genetic variation. In this study, we apply such a method (i.e., HyRAD), to large time series of two butterfly species in Finland, and present a new bioinformatic pipeline, namely PopHyRAD, that standardizes and optimizes the analysis of HyRAD data at the within-species level. In the localities for which the data retrieved have sufficient power to accurately examine genetic dynamics through time, we show that genetic erosion has increased across the last 100 years, as revealed by signatures of allele extinctions and heterozygosity decreases, despite local variations. In one of the two butterflies (Erebia embla), isolation by distance also increased through time, revealing the effect of greater habitat fragmentation over time.

AB - Erosion of biodiversity generated by anthropogenic activities has been studied for decades and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analysing museum collection specimens. While providing direct access to genetic variation over time, historical DNA is usually not optimally preserved, and it is necessary to apply genotyping methods based on hybridization-capture to unravel past genetic variation. In this study, we apply such a method (i.e., HyRAD), to large time series of two butterfly species in Finland, and present a new bioinformatic pipeline, namely PopHyRAD, that standardizes and optimizes the analysis of HyRAD data at the within-species level. In the localities for which the data retrieved have sufficient power to accurately examine genetic dynamics through time, we show that genetic erosion has increased across the last 100 years, as revealed by signatures of allele extinctions and heterozygosity decreases, despite local variations. In one of the two butterflies (Erebia embla), isolation by distance also increased through time, revealing the effect of greater habitat fragmentation over time.

KW - HyRAD

KW - Lepidoptera

KW - museomics

KW - past gene frequencies

KW - population dynamics

KW - SEQUENCE CAPTURE

KW - READ ALIGNMENT

KW - LYCAENA-HELLE

KW - RAD PROBES

KW - POPULATION

KW - GENOMICS

KW - DECLINE

KW - INFERENCE

KW - SPECIMENS

KW - DYNAMICS

U2 - 10.1111/1755-0998.13167

DO - 10.1111/1755-0998.13167

M3 - Journal article

C2 - 32304133

VL - 20

SP - 1191

EP - 1205

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 5

ER -