Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework

Abstract

Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. 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. 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). 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 show that in four of six study species, AFLP leads to results comparable with those of RADseq. 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. 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. 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.

Conservation and Phylogeography of Plants: From the Mediterranean to the Rest of the World

“…This does not mean that the use of neutral molecular markers such as AFLP, with which a reducedrepresentation-based genome-wide marker-discovery strategy is achieved and is not still good for phylogeographic studies. A comparative work between AFLP (a non-HTS based technique) and restriction site-associated DNA sequencing (RADseq; an HTS-based technique) [151] demonstrated similarities of results from the two techniques, which validate the use of these techniques in the delimitation of evolutionary entities.…”

An Assessment of the Malaysian Oil Palm Breeding Populations Using Aflp Markers

“…Despite these limitations, the AFLP markers provided useful genetic information for oil palm genetic and breeding studies. AFLP markers can be linked to specific loci under selection (Jump and Penuelas, 2007) and Kirschner et al (2021) were of the view that since the AFLP technique can analyse a large number of loci for polymorphism with a single primer pair, it is comparable to Restriction-Site Associated DNA (RAD) sequencing in its effectiveness at genetic analysis.…”

Performance comparison of gel and capillary electrophoresis-based microsatellite genotyping strategies in a population research and kinship testing framework

“…Increasing the studies that can face the ongoing biodiversity and climate crisis in countries without access to cutting-edge technologies will need that the relevance of their studies be valued for their biological significance rather than the fanciness of the technique utilized [ 15 ]. However, the analytical and methodological limitations of the allegedly old-fashioned methods and their adequateness to address the biological question asked need to be considered.…”

“…The gold standard for microsatellite genotyping is capillary electrophoresis (CE), a technology that accurately scores the alleles owing to its technology that implements automated allele-call programs [ 13 ]. However, because this method requires sophisticated instruments, it is usually impractical for many laboratories in countries having no access to cutting-edge technologies [ 14 , 15 ]. Nonetheless, more costly-effective methods such as polyacrylamide gel electrophoresis (PAGE) have been remarkably resilient in competition against sequencing techniques [ 16 ], and are still being utilized by researchers, especially in population research [ 17 – 19 ]; though the accuracy of their results compared to those obtained using high-throughput (HTP) methods is still arguable [ 12 , 20 – 22 ].…”