Evolution of the Yangtze River and its biodiversity

Abstract

Documenting the origins of megadiverse (sub)tropical aquatic ecosystems is an important goal for studies of evolution and ecology. Nonetheless, the geological and ecological establishment of the modern Yangtze River remains poorly understood. Here, we reconstruct the geographic and ecological history of an endemic clade of East Asian fishes based on the mitochondrial phylogenomics analysis of Cyprinidae using 15 fossil calibrations. We estimate an ancestral condition of benthic spawning with demersal or adhesive eggs in southern East Asia before ∼23 Ma and a derived condition of riverine spawning with semibuoyant eggs in the Yangtze by ∼18 Ma. These results imply the formation of Yangtze riverine ecosystems around the Oligocene-Miocene boundary in response to plateau uplift and monsoon strengthening. Some of these cyprinids reverted to benthic spawning with adhesive eggs by ∼15 Ma, a time of rising to peak net diversification rates, indicating the formation of potamo-lacustrine ecosystems by the mid-Miocene during a strong East Asian summer monsoon. Our study provides increased spatiotemporal resolution for the co-evolutionary histories of the Yangtze River and its biodiversity and highlights biological evidence concerning the geomorphological dynamics of the Yangtze River.

Figure 1

Phylogeny of Cyprinidae and diversification history of endemic East Asian cyprinids (A) Phylogeny of 118 Cyprinidae species and three Cobitidae species inferred from mitochondrial genomes based on Bayesian inference analysis. (B) Egg type evolution (a) and schematic diagram of the historical distribution and dispersal (b–d) of the endemic East Asian clade of Cyprinidae under the development of the Yangtze River system in response to uplift of the Qinghai-Tibetan Plateau. Red dots indicate fossil sites. (C) Diversification dynamics and macroevolutionary patterns of endemic East Asian cyprinids. (a) A single rate shift configuration with the maximum a posteriori probability represented as a phylorate plot of the endemic East Asian cyprinids showing variation in speciation rates. (b) The rate-through-time plot of the endemic East Asian cyprinids implemented by Bayesian Analysis of Macroevolutionary Mixtures. (c) Net diversification rate through time for the endemic East Asian cyprinids inferred from the relationship between the net diversification rate and East Asian monsoon in RPANDA. (d) The hematite/goethite proxy of ODP Site 1148 in the South China Sea as a function of time (modified from Clift et al.¹⁰).