This is a revised submission to PeerJ for review.
Multidimensional scaling of overall gene expression (A) identifies distinct clusters of male and female nematodes. Using the same technique on the subset of genes identified in generalized linear models for genes putativelydiffering for both nematode population (B) and experimental host species (C) does not generate robust clustering.
Panel A depicts the high correlation of the contribution to the discriminant
function between populations and fixation index Fst. Panel
B shows the density distributions of different measures of
differentiation separately for SNPs with different effect on the
protein sequence. Highly differentiating SNPs are enriched for
synonymous and non-coding polymorphism over of non-synonymous
differences. In Panel C dn/ds is plotted against the maximal per gene differentiation (over loci), the green and blue line s give thresholds for “high differentiation” (maximal contribution to discriminant function > 0.8x10-5) and “positive selection” (dn/ds > 0.5), respectively.
The authors declare they have no competing interests.
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
The experiment has been approved by the responsible authorities (Regierungspräsidium Karlsruhe approval no. 35-9185.81/G-120/06 and 35-9185.81/G-31/07).
The following information was supplied regarding the deposition of DNA sequences:
Raw reads are deposited in ENA under the study accession number SRP010338.
The following information was supplied regarding the deposition of related data:
The transcriptome assembly is deposited in the online afterParty resource established for A. crassus at http://anguillicola.nematod.es.