RNA-seq reads were mapped to Ensembl annotation NCBIM37/mm9 using TopHat2 (Kim et al., 2013) with the options mate-inner-dist, mate-std-dev and library-type (fr-firststrand).
To estimate the library fragment size for TopHat, we initially mapped a subset of 1 million reads with bwa (v0.6.1) to the human genome, followed by picard version 1.80 31 module CollectInsertSizeMetrics and provided these values to TopHat options "–mate-inner-dist 87 –mate-std-dev 86".
For each combination of one female and one male clonal population, two or three different male genotypes were independently offered as alternative mating options.
Results from the first experiment suggest both that males rarely initiate divorce, even when alternative mating options are available, and that the role of female-female competition is negligible.
The intensity of competition (equivalent to the availability of alternative mating options to females), was measured as the number of individuals introduced during the second infection divided by the number of individual of the same sex introduced on the first one.
Both effects improve women's outside option, mating monogamously, and decrease the marginal benefit of the economic advantages provided by polygynous unions.
All engine options are mated to an 8-speed automatic transmission with a paddle-shifted manual mode available, and, in the first car I tested, rear-wheel drive.
Moreover, we witnessed one extra-pair copulation, suggesting that extra-pair mating options influence the trade-off between mate guarding and roaming.
How humans cognitively manage an abundance of mate options.
Reads were then assembled using gsAssembler [ 25] (version 2.6, default parameters with -notrim, or default options for the mate pair assembly).
Illumina reads for each isolate/line were mapped to the B. xylophilus reference genome (ver. 1.2) using SMALT v0.7.4 (https://www.sanger.ac.uk/resources/software/smalt/), with options –x (each mate is mapped independently) and –y 0.8 (minimum 80%% of the read length matches in mapped reads).
