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.
Highlights
Multi-locus genetic data are pivotal in phylogenetics
Information content of amplified fragment length polymorphism fingerprinting (AFLP) and restriction site associated DNA sequencing (RADseq) markers was significantly correlated for Astragalus onobrychis, Euphorbia seguieriana, Plagiolepis taurica and O. petraeus, as shown by the Mantel tests of intraspecific distance matrices derived from the respective datasets (Fig. 2C)
We show that AFLP and RADseq-derived genomic data can yield similar phylogeographic patterns
Summary
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. One HTS-based method, which has been used for phylogeographic studies, is restriction site associated DNA sequencing (RADseq)[15] 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 g enome[16]. It has been demonstrated that dozens of simple sequence repeats (SSRs) lead to the same result as hundreds to thousands of SNPs17,20,25 Such comparisons need to be interpreted carefully, especially if this is done in a phylogenetic context: while models for molecular evolution have been adapted and empirically tested for RADseq derived SNP d ata[26], such models are under discussion for S SRs27, or not available in case of AFLP. While RADseq is definitely able to resolve fine-scale phylogeographic patterns via large numbers of SNPs5,28, the question of how many markers are really needed to do so, has not been answered so far
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