Over the last few centuries, millions of plant specimens have accumulated within herbaria and biocultural collections. These include type specimens, used to define species, and populations that are rare, extinct or difficult to access. They therefore represent a considerable resource for a broad range of scientific uses. However, collections degrade over time, and become increasingly difficult to characterise their genetic signatures, even considering exponential advancements in sequencing technologies. Here, we tested the genotyping performance on highly degraded samples using a commonly used high-throughput sequencing (HtS) technique, genome skimming, against a recent alternative target capture kit, the universal set Angiosperm-353. We performed phylogenomic analyses of modern leaf and historical barks of Cinchona, including 23 historical barks and six fresh leaf specimens. DNA within historical barks is highly degraded, therefore a customised DNA extraction method was developed before library preparation. We show that sample degradation over time directly impacted the quantity and quality of the data produced by both methodologies (in terms of reads mapped to the references). However, we find that both approaches generate enough data to infer phylogenetic relationships, even between highly degraded specimens that are over 230 years old. Within historical barks, the target capture kit is more advantageous than genome skimming in profiling Cinchona species since it was possible to retrieve nuclear and plastid data to infer phylogenies. This study showcases the value of historical samples in genetic studies and paves the way for further experiments across different taxonomic groups with varying levels of genetic variation or hybridisation.

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species’ establishment in an introduced range. Numerous plants are thought to have been introduced to regions outside their native ranges by European voyagers and early colonists making transoceanic journeys; however, records are scare to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to test hypotheses that the plant was brought to new regions during colonial times. We further investigate how patterns in genomic diversity facilitate the success of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique ecotypes showing very little sign of admixture. Three of the most prevalent of these ecotypes present in the native range gave rise to introduced populations in the Americas, Africa, Australia and New Zealand, indicating that more than one successful ecotype colonized and spread. The distribution of ecotypes is found to have links to colonial history, and ecotypes are further found to be restricted by latitude. Dispersal of multiple successful ecotypes and prior adaptation in the native range to latitudinally dependent environmental factors (such as climate) are likely reasons for the success of this prolific, global weed. Genomic signatures can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species in an era of global change.