21Processes of molecular innovation require tinkering and co-option of existing genes. 22How this occurs in terms of molecular evolution at long evolutionary scales remains 23 poorly understood. Here, we analyse the natural history of a vast group of 24 membrane-associated molecular systems in Bacteria and Archaea -type IV filament 25 super-family (TFF-SF) -that diversified in systems involved in flagellar or twitching 26 motility, adhesion, protein secretion, and DNA natural transformation. We identified 27 such systems in all phyla of the two domains of life, and their phylogeny suggests 28 that they may have been present in the last universal common ancestor. From there, 29 two lineages, a Bacterial and an Archaeal, diversified by multiple gene duplications of 30 the ATPases, gene fission of the integral membrane platform, and accretion of novel 31 components. Surprisingly, we find that the Tad systems originated from the inter-32 kingdom transfer from Archaea to Bacteria of a system resembling the Epd pilus. The 33 phylogeny and content of ancestral systems suggest that initial bacterial pili were 34 engaged in cell motility and/or DNA transformation. In contrast, specialized protein 35 secretion systems arose much later, and several independent times, in natural 36 history. All these processes of functional diversification were accompanied by genetic 37 rearrangements with implications for genetic regulation and horizontal gene transfer: 38 systems encoded in fewer loci were more frequently exchanged between taxa. 39Overall, the evolutionary history of the TFF-SF by itself provides an impressive 40 catalogue of the variety of molecular mechanisms involved in the origins of novel 41 functions by tinkering and co-option of cellular machineries. 42 43 illustration of these processes is provided by the type IV filament super-family (TFF-69 SF) of bacterial and archaeal systems that include the type II protein secretion 70 system (T2SS), the type IVa pilus (T4aP), the type IVb pilus (T4bP), the mannose-71 sensitive hemagglutinin pilus (MSH), the tight adherence pilus (Tad), the competence 72 pilus (Com), and the type IV-related pili in Archaea (Archaeal-T4P), that includes the 73 archaeal flagella (Archaellum). These systems have core homologous components, 74 sometimes in multiple copies, and present similarities in terms of macro-molecular 75 architecture ( Fig. 1) [15][16][17]. They include AAA+ ATPases, among which the T4aP 76PilT is the most powerful molecular motor known [18], an integral (cytoplasmic) 77 membrane (IM) platform, and a prepilin peptidase that matures a set of specific pilins 78 or pseudo-pilins (in T2SS) [19]. Bacteria with two cell membranes (diderms) also 79 encode a secretin that forms an outer membrane pore [20]. Other proteins of these 80 systems are either specific for each system or evolve too fast to allow the inference 81 of homology among all variants. 82The TFF-SF nanomachines assemble filaments composed of subunits with an N-83 terminal sequence motif named class III signal pept...