This method is able to produce, depending on the experimental design, thousands to tens of thousands of gene fragments that can be used to infer large numbers of single nucleotide polymorphisms (SNPs) from populations of any non-model organism’s genome 16. One HTS-based method, which has been particularly used for phylogeographic studies, is restriction site associated DNA sequencing (RADseq) 15. The advancement of molecular methods in the era of HTS helped phylogeography, once data-limited, to become a data-rich field 14. 1A), including also recent publications in highly visible journals 10, 11, 12, 13. AFLP has been employed for over 20 years, and its applicability has been proven in thousands of studies (Fig. The method has been extensively used in the field of evolutionary ecology, spanning disciplines from phylogenetics to phylogeography and species delimitation 8, 9. This tool from the pre-HTS era is able to sample several hundred to a few thousand genetic markers from an organism without any prior knowledge of its genome. The need to look for alternative ways to generate multi-locus datasets has been constantever since the dawn of molecular systematics.Īn established and widely used method to generate genetic markers from any organism’s genome is amplified fragment length polymorphism (AFLP) fingerprinting 7. Today, the phylogenetic resolution at different time scales and on different taxonomic levels that can be achieved via high-throughput sequencing (HTS) data is unprecedented 6. As a consequence, many journals important to the field decided to no longer accept such studies (e.g. As broadly discussed, studies utilizing a single or few genetic markers are affected by incongruences due to, for example, pseudogene amplification 4, or simply different gene genealogies supporting alternative species trees 5. Owing to the large effort necessary to obtain multiple, informative genetic markers from the genomes of non-model organisms, many studies had to rely on single or a few genetic markers in the past. As such, phylogeography has become an integral part of biogeographic research in general 3. Easy access to molecular-genetic data has propelled large-scale and cross-species phylogeographic studies and offered new insights on long-standing questions such as the postglacial colonization of Europe 2. Phylogeography has led to large advancements in understanding the spatio-temporal evolution of species and the underlying climatic, geological, and ecological processes 1. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. Multi-locus genetic data are pivotal in phylogenetics.
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