From
metabarcoding to metaphylogeography: separating the wheat from the
chaff, by Turon, Antich, Palacin, Præbel and Wangensteen.
We
are pleased to announce that our seminal paper on metaphylogeography
has been published in ESA’s journal Ecological Applications, here
is the link
In
this paper we set the foundations for the use of intra-motu
variability in the assessment of phylogeography and population
genetics patterns of many species at a time using databases intended
for biodiversity studies with COI metabarcoding.
And
here is the abstract:
Metabarcoding
is by now a well‐established
method for biodiversity assessment in terrestrial, freshwater and
marine environments. Metabarcoding data sets are usually used for α‐
and β‐diversity
estimates, that is, interspecies (or inter‐MOTU)
patterns. However, the use of hypervariable metabarcoding markers may
provide an enormous amount of intraspecies (intra‐MOTU)
information ‐
mostly untapped so far. The use of cytochrome oxidase (COI) amplicons
is gaining momentum in metabarcoding studies targeting eukaryote
richness. COI has been for a long time the marker of choice in
population genetics and phylogeographic studies. Therefore, COI
metabarcoding data sets may be used to study intraspecies patterns
and phylogeographic features for hundreds of species simultaneously,
opening a new field which we suggest to name metaphylogeography. The
main challenge for the implementation of this approach is the
separation of erroneous sequences from true intra‐MOTU
variation. Here, we develop a cleaning protocol based on changes in
entropy of the different codon positions of the COI sequence,
together with co‐occurrence
patterns of sequences. Using a data set of community DNA from several
benthic littoral communities in the Mediterranean and Atlantic seas,
we first tested by simulation on a subset of sequences a two‐step
cleaning approach consisting of a denoising step followed by a
minimal abundance filtering. The procedure was then applied to the
whole data set. We obtained a total of 563 MOTUs that were usable for
phylogeographic inference. We used semiquantitative rank data instead
of read abundances to perform AMOVAs and haplotype networks. Genetic
variability was mainly concentrated within samples, but with an
important between‐seas
component as well. There were inter‐group
differences in the amount of variability between and within
communities in each sea. For two species the results could be
compared with traditional Sanger sequence data available for the same
zones, giving similar patterns. Our study shows that metabarcoding
data can be used to infer intra‐
and interpopulation genetic variability of many species at a time,
providing a new method with great potential for basic biogeography,
connectivity and dispersal studies, and for the more applied fields
of conservation genetics, invasion genetics, and design of protected
areas.
We
hope this paper will have a strong impact, we will follow this lead
to study metaphylogeographic patterns in the framework of the
PopCOmics project!
