Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi

Abstract

Many examples of the appearance of similar traits in different lineages are known during the evolution of organisms. However, the underlying genetic mechanisms have been elucidated in very few cases. Here, we provide a clear example of evolutionary parallelism, involving changes in the same genetic pathway, providing functional adaptation of RH1 pigments to deep-water habitats during the adaptive radiation of East African cichlid fishes. We determined the RH1 sequences from 233 individual cichlids. The reconstruction of cichlid RH1 pigments with 11-cis-retinal from 28 sequences showed that the absorption spectra of the pigments of nine species were shifted toward blue, tuned by two particular amino acid replacements. These blue-shifted RH1 pigments might have evolved as adaptations to the deep-water photic environment. Phylogenetic evidence indicates that one of the replacements, A292S, has evolved several times independently, inducing similar functional change. The parallel evolution of the same mutation at the same amino acid position suggests that the number of genetic changes underlying the appearance of similar traits in cichlid diversification may be fewer than previously expected.rhodopsin ͉ adaptation

Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence

“…The Leviviridae is a family of nonenveloped, icosahedral, positive single-strand RNA bacteriophages (van Duin 1988). The family is divided into two named genera, Allolevivirus and Levivirus, and a group of unclassified phages (Murphy et al 1995).…”

“…Members of Allolevivirus and Levivirus consist primarily of coliphages-species that infect Escherichia coli. The natural host of the coliphages has not been determined (van Duin 1988), but successful infection appears to be restricted to hosts bearing the F plasmid (van Duin and Tsareva 2005); Salmonella typhimurium, artificially transformed with the F plasmid, are susceptible to successful infection by coliphages. However, the noncoliphage species PP7 and AP205, which are not dependent on the presence of the F plasmid, have been included as members of the Levivirus in the current nomenclature due to the lack of a read-through coding region (van Duin and Tsareva 2005); this taxonomic placement, however, is not supported by phylogenetic analysis (Bollback and Huelsenbeck 2001).…”

“…The replicase is an RNA-dependent RNA polymerase that replicates both the positive and the intermediate negative sense RNA strand of these phages. The replicase is known to require and interact with a number of host factors during replication (van Duin 1988;van Duin and Tsareva 2005). The read-through protein of NL95 is a minor constituent of the virion involved in the process of infection.…”

“…The read-through protein of NL95 is a minor constituent of the virion involved in the process of infection. Translation of the read-through occurs infrequently (%6%) when a ribosome misreads the coat protein gene's UGA termination The life cycle of these phages takes $35-45 min from infection to lysis (van Duin 1988). This period exceeds the generation time of E. coli and it is unclear whether the phages suppress cell division or segregate into the daughter cells.…”

“…Similarly, it is of great interest to know whether the genetic changes underlying parallel traits are also parallel. With few exceptions (Andreev et al 1999;Wichman et al 1999;ffrench-Constant et al 2000;Sucena et al 2003;Wood et al 2005;Colosimo et al 2005;Sugawara et al 2005), little is understood about the underlying genetic nature of parallel phenotypes.…”