A recent issue of Heredity focused on the brave new world of environmental genomics. After highlighting the special issue, I started chatting to one of the contributors, Eric Pante and became interested in his work on gorgonians.
Eric and his co-authors explored the extent to which RAD tags can be used to infer phylogeny. This paper arose from a GDR, or Groupement de Recherche (I’ll be posting an interview with Eric to go along with this summary of the Heredity paper, so check back to read more about GDR’s), that facilitated the collaboration of among researchers and labs addressing similar questions.
At the time the group began to use RAD sequencing, in silico studies, such as in Drosophila, suggested that this approach could be used for taxa that have diverged up to 60 million years ago (Cariou et al. 2013).
Pante et al. (2015) not only address the usefulness of RAD tags for phylogenetic analyses, but also test which pipelines to use. Stacks (Catchen et al. 2013) and PyRAD (Eaton 2014) differ in how homologous loci are detected. For example, Stacks does not take indels into account which is a major drawback for investigating distantly related species.
Beyond the methodological angle, it was a prime opportunity to learn more about the gorgonians themselves.
Researchers have been using morphological characters coupled with a 700 bp sequence of the mitochondrial genome to infer species. Yet, how congruent would this practice be with the data generated by RAD sequencing?
It turns out that the mtDNA, morphological characters and the RAD loci were generally telling the same deep-sea story. Thus, when new species are described based on morphology and mtDNA, they’re not so far off.
Six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia.
In these corals, 0.3% divergence (or 1 mutation in the 700 bp sequence) delimits species! The number of homologous RAD loci decreased with increasing divergence. For example,
70% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny.
This is really useful information as the sole use of morphology can be misleading. Convergent evolution of morphological characters and/or morphological plasticity could mislead the description of new species.
Cariou M, Duret L, Charlat S. (2013). Is RAD-Seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol Evol 3: 846–852.
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA. (2013). Stacks: an analysis tool set for population genomics. Mol Ecol 22: 3124–3140.
Eaton D. (2014). PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics 30: 1844–1849.
Pante E, Abdelkrim J, Viricel A, Gey D, France SC, Boisselier MC and Samadi S (2015) Use of RAD sequencing for delimiting species. Heredity 114: 450–459.