We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of scientific landscape evolution. Capitalizing on formerly introduced science mapping methods with overlapping clustering, we propose methods to reconstruct phylogenetic networks from successive science maps, and give insight into the various dynamics of scientific domains. Two indexes - the pseudo-inclusion and the empirical quality - are introduced to qualify scientific fields and are used for reconstruction validation purpose. Phylogenetic dynamics appear to be strongly correlated to these two indexes, and to a weaker extent, to a third one previously introduced (density index). These results suggest that there exist regular patterns in the "life cycle" of scientific fields. The reconstruction of science phylogeny should improve our global understanding of science evolution and pave the way toward the development of innovative tools for our daily interactions with its productions. Over the long run, these methods should lead quantitative epistemology up to the point to corroborate or falsify theoretical models of science evolution based on large-scale phylogeny reconstruction from databases of scientific literature.