Phylogeography of a flooded forest specialist fish from central Amazonia based on intron DNA: the cardinal tetra Paracheirodon axelrodi

1. Historic and extant landscape structures and environmental conditions are known to influence phylogeographic patterns and population histories in organisms from Amazonia. Recent work suggests that events of the Tertiary Period have played a significant role in generating biodiversity in this exceptionally rich but understudied region. However, species distributions and population structures are also affected by recent environmental and physical changes, especially within highly dynamic ecosystems. 2. The cardinal tetra is a small luminous fish native to the dynamic flooded forest ecosystems of the Rio Negro and Orinoco basins of South America. This very popular aquarium fish represents the single most important species in the ornamental fishery of the Rio Negro, an activity of high socio‐economic value for local riverine communities. Here we use a fine‐scale sampling regime and sequence data from the second intron of the Ribosomal protein S7 (S7 2) to investigate population structure, colonisation history and genealogical relationships in cardinal tetras of the Rio Negro. 3. High levels of S7 2 polymorphisms revealed phylogeographic patterns across several temporal settings that appear associated with the complex dynamics of the region. Our results suggest a long history of isolation and persistence of cardinal tetra populations in the headwaters and upper regions of the Rio Negro and recent events of colonisation within the incipient Rio Negro floodplain. These colonisation events were followed by recent population expansions likely facilitated by the establishment of the extensive Rio Negro floodplain, an anabranching ecosystem of Holocene age. 4. Our reconstruction of the phylogeographic history of cardinal tetras based on S7 2 intron sequence data reflects the complex influence of both geomorphological and climatic events through time in the Rio Negro basin. Our findings also indicate that in order to maintain the cardinal tetra fishery as a sustainable activity for rural Amazonians, the fishery should be restricted to the middle Rio Negro, the region of the basin where population replenishment is more likely to occur.