10.5061/DRYAD.NM948
Choo, Le Qin
Natural History Museum
Crampton-Platt, Alex
University College London
Vogler, Alfried P.
Natural History Museum
Data from: Shotgun mitogenomics across body size classes in a local
assemblage of tropical Diptera: phylogeny, species diversity and
mitochondrial abundance spectrum
Dryad
dataset
2017
mitochondrial metagenomics
metabolic rates
Neutral Theory of biodiversity
rarity
2017-07-24T14:23:55Z
2017-07-24T14:23:55Z
en
https://doi.org/10.1111/mec.14258
8418397 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Mitochondrial genomes can be assembled readily from shotgun-sequenced DNA
mixtures of mass-trapped arthropods (“mitochondrial metagenomics”),
speeding up the taxonomic characterization. Bulk sequencing was conducted
on some 800 individuals of Diptera obtained by canopy fogging of a single
tree in Borneo dominated by small (<1.5 mm) individuals. Specimens
were split into five body size classes for DNA extraction, to equalize
read numbers across specimens and to study how body size, a key ecological
trait, interacts with species and phylogenetic diversity. Genome assembly
produced 304 orthologous mitochondrial contigs presumed to each represent
a different species. The small-bodied fraction was the by far most
species-rich (187 contigs). Identification of contigs was through
phylogenetic analysis together with 56 reference mitogenomes, which placed
most of the Bornean community into seven clades of small-bodied species,
indicating phylogenetic conservation of body size. Mapping of shotgun
reads against the mitogenomes showed wide ranges of read abundances within
each size class. Ranked read abundance plots were largely log-linear,
indicating a uniformly filled abundance spectrum, especially for
small-bodied species. Small-bodied species differed greatly from other
size classes in neutral metacommunity parameters, exhibiting greater
levels of immigration, besides greater total community size. We suggest
that the established uses of mitochondrial metagenomics for analysis of
species and phylogenetic diversity can be extended to parameterize recent
theories of community ecology and biodiversity, and by focusing on the
number mitochondria, rather than individuals, a new theoretical framework
for analysis of mitochondrial abundance spectra can be developed that
incorporates metabolic activity approximated by the count of mitochondria.
Figure 1 data matrix304 contigs, 53 complete dipteran mitochondrial
genomes and 2 mecopteran outgroups from Genbank. 13 mitochondrial protein
coding genes (PCGs) and 2 rRNAs were concatenated to form this data
matrix. All sequences contain nad6. First and second positions were
RY-coded, third position was not
included.F800.nr.min1.nad6.1RY2.phySupplementary Figure S4 data matrix304
contigs, 53 complete dipteran mitochondrial genomes from Genbank, 16
partial dipteran mitogenomes from Wiegmann et al. (2011) and 2 mecopteran
outgroups from Genbank. 13 mitochondrial protein coding genes (PCGs) and 2
rRNAs were concatenated to form this data matrix. All sequences contain
nad6. First and second positions were RY-coded, third position was not
included.F800.nr.min1.nad6.1RY2.wWiegmann.phy
Sabah
Danum Valley
Malaysia