|Understanding how ecological communities are organized and
how they change through time is critical to predicting the effects
of climate change1. Recent work documenting the co-occurrence
structure of modern communities found that most significant
species pairs co-occur less frequently than would be expected
by chance2,3. However, little is known about how co-occurrence
structure changes through time. Here we evaluate changes in
plant and animal community organization over geological time
by quantifying the co-occurrence structure of 359,896 unique
taxon pairs in 80 assemblages spanning the past 300 million years.
Co-occurrences of most taxon pairs were statistically random,
but a significant fraction were spatially aggregated or segregated.
Aggregated pairs dominated from the Carboniferous period
(307 million years ago) to the early Holocene epoch (11,700 years
before present), when there was a pronounced shift to more
segregated pairs, a trend that continues in modern assemblages.
The shift began during the Holocene and coincided with increasing
human population size4,5 and the spread of agriculture in North
America6,7. Before the shift, an average of 64% of significant pairs
were aggregated; after the shift, the average dropped to 37%.
The organization of modern and late Holocene plant and animal
assemblages differs fundamentally from that of assemblages over
the past 300 million years that predate the large-scale impacts of
humans. Our results suggest that the rules governing the assembly
of communities have recently been changed by human activity.|