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Use of RAD sequencing for delimiting species.

E Pante1, J Abdelkrim2, A Viricel1

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RAD-tag sequencing aids deep-sea octocoral species delimitation by refining mitochondrial marker interpretations. This genomic method revealed previously undetected diversity within Chrysogorgia, enhancing evolutionary studies.

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Area of Science:

  • Genomics
  • Marine Biology
  • Evolutionary Biology

Background:

  • RAD-tag sequencing is a powerful tool for genome-wide evolutionary studies.
  • Its application above the species level, particularly in marine invertebrates, remains under-explored.
  • Deep-sea octocorals in the genus Chrysogorgia present challenges for species delimitation using traditional genetic markers.

Purpose of the Study:

  • To assess the utility of RAD-tag sequencing for species delimitation in the Chrysogorgia genus.
  • To compare phylogenetic inferences from two RAD analysis pipelines (Stacks and PyRAD).
  • To refine interpretations of mitochondrial markers for octocoral species identification.

Main Methods:

  • RAD-tag sequencing was performed on samples from 12 putative Chrysogorgia species.
  • Phylogenetic relationships were inferred using two RAD analysis pipelines.
  • Species delimitation was compared with hypotheses based on the mitochondrial mtMutS gene.

Main Results:

  • The number of homologous RAD loci decreased significantly with increasing genetic divergence.
  • Six out of nine putative species were recovered as distinct clades, supporting mitochondrial data.
  • RAD data revealed genetic structure within a putative species and intraspecific variation in mtMutS haplotypes.

Conclusions:

  • RAD-tag sequencing effectively aids in refining species delimitation for deep-sea octocorals.
  • The study highlights the loss of homologous loci with divergence but confirms RAD data's value.
  • RAD data uncovered previously unrecognized diversity within Chrysogorgia, improving evolutionary insights.