Testing small scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

DNA metabarcoding has been increasingly used to detail distributions of
hundreds of species. Most analyses focus on creating molecular operation
taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much
less common is use of the sequence diversity within these MOTUs. Here we
use the diversity of COI haplotypes within MOTUs from a California kelp
forest to infer patterns of population abundance, dispersal and population
history from 527 species of animals and algae from 106 samples of benthic
habitats in Monterey Bay. Using haplotypes as a unit we show fine-grained
differences of abundance across locations for 15 species, and marked
aggregation from sample to sample for most of the common species of plants
and animals. Previous analyses could not distinguish these patterns from
artefacts of amplification or sequence bias. Our haplotype data also
reveal strong population genetic differentiation over small spatial scales
for 48 species of red algae, sponges, and Bryozoa. Last, phylogenetic
analysis of mismatch frequencies among haplotypes show a wide variety of
demographic histories from recent expansions to long, stable population
sizes. These analyses show that abundant, small bodied marine species that
are often overlooked in ecological surveys can have strikingly different
patterns of ecological and genetic structure leading to population,
ecological, and perhaps adaptive differences between habitats. MOTU
diversity data from the same sequencing efforts that generate
species-level analyses, and can greatly increase the scope and value of
metabarcoding studies.