bioRxiv2026
Tropical rivers in Australia and New Guinea (Sahul) provide a rare natural experiment in vertebrate evolution: unlike other continental systems, their freshwater ichthyofaunas are composed almost entirely of marine-derived lineages rather than primary freshwater fishes. This unique biogeographic setting enables replicated tests of why some marine-to-freshwater transitions give rise to extensive adaptive radiations whereas others remain species-poor, and whether these outcomes reflect ecological opportunity or temporally structured paleoenvironmental constraints. Using a densely sampled, time-calibrated phylogenomic framework spanning 2,303 teleost species, we identified a likely range of 27-34 marine-to-freshwater transitions during the Cenozoic, including a pronounced Middle Miocene peak (16-11 Ma). Although ecological opportunity in Sahul rivers enabled repeated colonization in the absence of dominant primary freshwater incumbents, younger freshwater lineages nevertheless diversify faster than older ones, contradicting the expectation that early arrivers should undergo elevated diversification when accessing vacant niche space. Although some colonizations coincide with bursts of speciation consistent with adaptive radiation, many yielded few species despite long residence times. Functional trait analyses likewise revealed no consistent relationship between colonization timing, ecological breadth, or diversification rate, although expanded functional space characterizes previously proposed Sahul adaptive radiations. Comparisons with paleoenvironmental curves indicate that colonization success correlates with sea-level minima and low-oxygen conditions, suggesting that Earth history dynamics modulated when ecological opportunity was accessible. Our results show that although ecological opportunity enabled repeated freshwater invasions into the Sahul region, diversification outcomes are governed by the interaction of paleoenvironmental dynamics and possibly lineage-specific traits, generating stark asymmetries in freshwater radiations. Significance statementTropical rivers in Australia and New Guinea host one of the most unusual continental freshwater fish assemblages on Earth, composed almost entirely of marine-derived lineages. This system allows asking why some colonizing lineages diversify dramatically while others remain species-poor on a continental scale. Using large-scale phylogenomic and functional trait data, we show that early arrival alone does not predict diversification success. Instead, the lineages that radiate most successfully are those whose arrival coincides with windows of paleoenvironmental opportunity created by sea-level and oxygen fluctuations. These results reveal that the fates of colonizing lineages are shaped not only by ecological opportunity, but also by Earth-history dynamics that govern when, where, and how species can invade and diversify.