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Supplemental Information

Multidimensional scaling of gene expression

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.

DOI: 10.7287/peerj.preprints.589v1/supp-1

Relationships of genotypic differentiation measures

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.

DOI: 10.7287/peerj.preprints.589v1/supp-2

Supplementary Data File 1 – Differential expression between male and female A. crassus

DOI: 10.7287/peerj.preprints.589v1/supp-3

Supplementary Data File 2 – Differential expression between A. crassusin the two different experimental host species

DOI: 10.7287/peerj.preprints.589v1/supp-4

Supplementary Data File 3 – Differential expression between European and Asian isolates of A. crassus

DOI: 10.7287/peerj.preprints.589v1/supp-5

Additional Information

Competing Interests

The authors declare they have no competing interests.

Author Contributions

Emanuel Heitlinger conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Horst H. Taraschewski conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Urszula Weclawski performed the experiments.

Karim Gharbi conceived and designed the experiments, contributed reagents/materials/analysis tools.

Mark Blaxter conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Animal Ethics

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).

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Raw reads are deposited in ENA under the study accession number SRP010338.

Data Deposition

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.

Funding

This work was funded by Volkswagen Foundation in the “Förderinitiative Evolutionsbiologie” (grant to Emanuel Heitlinger). Edinburgh Genomics is partly supported through core grants from NERC (R8/H10/56), MRC (MR/K001744/1) and BBSRC (BB/J004243/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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