Summary Understanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely related organisms share similar ecological preferences due to phylogenetic conservation – or if they are forced apart by competition – is still debated. Here, we explored the co‐occurrence patterns of freshwater cyanobacteria at the sub‐genus level to investigate whether more closely related taxa share more similar niches and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely related Synechococcus (in the continuous range of 93%–100% nucleotide identity in 16S) had an increased tendency to co‐occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co‐occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub‐genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation.

32Understanding how ecological traits have changed over evolutionary time is a fundamental 33 question in biology. When closely-related organisms share similar environmental preferences, 34 "habitat filtering" is expected to determine how communities are assembled. Yet in practice, it is 35 challenging to assess the impact of habitat filtering, due to our inability to measure all relevant 36 abiotic variables and distinguish the impact of biotic versus abiotic factors. Here we explored the 37 co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether 38 closely-related taxa share similar niches, and to what extent these niches were defined by abiotic 39 or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several 40 environmental parameters in water samples collected over time and space in Furnas Reservoir, 41Brazil. We found that closely-related Synechococcus did not have similar preferences for abiotic 42 niche dimensions. However, closely-related Synechococcus did tend to co-occur with one 43 another, and also with similar surrounding microbial communities. These results suggest that 44 biotic factors may be stronger niche determinants than abiotic factors. Alternatively, cryptic 45 abiotic drivers may determine niche and community structure, but biotic factors provide the most 46 informative measure of niche similarity. 47 48 49 50 51