Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics

Abstract Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next‐generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus, a steppic Southwestern‐Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of O. decorus following human‐mediated land‐use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.


Table S1
Sampling locations of all O. decorus samples used in this study across the species distribution range in Europe, northern Africa and central Asia.

Table S2
Samples used for the generation of the probes in the hyRAD protocol.

Table S3
Scenarios of population decline tested for the Finges population between 1940 and 1950 as well as the associated statistic for the comparison between the simulated and observed minor allele frequency distribution.

Table S4
Number of polymorphic sites after each filtering step for both spatial and temporal dataset.         Appendix S1 Blast search against GenBank and matching sequences extraction.
Appendix S2 Removing contaminant sequences from reference catalog.

Table S4
Number of polymorphic sites after each filtering step for both spatial and temporal dataset. Initial is the number of polymorphic sites before filtering, QUAL > 30 is after removing sites with a quality below 30; indels is after removing indels; bi-allelic is after removing sites with more than two alleles; MAC > 6 is after removing sites with a minor allele count lower than 6; max-missing < 50% is after removing sites present in less than 50% of the samples; depth > 6 is after removing sites with a depth value below 6; QUAL/DP > 0.25 is after removing sites with a quality/depth ratio inferior to 0.25 and paralogs corresponds to a removal of paralogous sites.

Data preparaƟon
SNPs search

Mapping reads BowƟe2
Postmortal damages rescaling MapDamage    12 APPENDICES Appendix S1 Blast search against GenBank and matching sequences extraction.