As far as I'm aware the third generation Yaris D4D may weigh up to 185kg more than the first generation. That and the additional emissions control equipment will have an effect on economy compared to the first generation. According to the Honest John Real MPG info on the third generation, owners get between 47mpg and 75mpg, with an average of 61.4mpg - https://www.honestjohn.co.uk/realmpg/toyota/yaris-and-yaris-hybrid-2011/14-d-4d
Ignore the official EU fuel consumption figures, as these are based on laboratory testing and don't bear much relation to real world fuel consumption.
One thing to bear in mind with the third generation is that the fuel gauge, in common with other recent Toyotas, operates in a non-linear way - the bars of the gauge extinguish more quickly as the tank empties. Also filling up with less than 15 litres may give false readings. It may help to disconnect the battery for a short while to clear any fuel consumption data, etc from the ECU.
The only realistic way to measure fuel consumption is to use the brim to brim system, record the miles travelled and manually calculate the consumption when one next fills up.