COPIA-LIKE RETROTRANSPOSABLE ELEMENT EVOLUTION IN DIPLOID AND POLYPLOID COTTON (GOSSYPIUM L)

Copia-like retrotransposable elements were identified in allotetraploi d cotton, Gossypium hirsutum, and two species representing its diploid progenitors, G. herbaceum and G. raimondii. These elements are presen t in high copy number in all three species. Because the two diploid ge nomic groups have been isolated on opposite sides of the world for 6-1 1 million years, horizontal transfer of elements between these species is highly unlikely. Elements were intensively sampled to generate a m odel of copia-like retrotransposable element evolution in systems wher e vertical transmission is the sole probable means of descent. Copia-l ike retrotransposon diversity is equally great in all three Gossypium species. Despite this high heterogeneity, analysis of 89 partial rever se transcriptase sequences resulted in the recognition of nine sharply differentiated retrotransposon lineages, each containing elements tha t share high sequence similarity. No evidence of horizontal transfer f rom other taxa was obtained. Phylogenetic analyses demonstrate that el ement topologies are incongruent with Gossypium phylogeny. Considerati on of processes that obscure phylogenetic reconstruction of multigene families (including sampling error, variable degrees of orthology and paralogy, differential lineage age and lineage loss and/or proliferati on) demonstrates that incongruence between organismal and retrotranspo son trees is expected under conditions in which vertical processes are the sole means of transmission. Identification of closely related ele ments between species allowed rates of copia-like retrotransposon sequ ence evolution to be estimated as approximately 10(-9) nucleotide subs titutions/site/year. These rates are consistent with the interpretatio n that these retrotransposons have been evolving under functional cons traints for most of the time frame bracketed by the species studied. E xtrapolation of these results to previous studies that sampled from mo re highly divergent taxa indicates that horizontal transfer need not b e invoked to explain observed phylogenetic patterns.