Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons

5S RNA genes and their nontranscribed spacers are tandemly repeated in plant genomes at one or more chromosomal loci. To facilitate an understanding of the forces that govern 5S rDNA evolution, copy-number estimation and DNA sequencing were conducted for a phylogenetically well-characterized set of 16 diploid species of cotton ( Gossypium ) and 4 species representing allopolyploid derivatives of the diploids. Copy number varies over twentyfold in the genus, from approximately 1,000 to 20,000 copies/2C genome. When superimposed on the organismal phylogeny, these data reveal examples of both array expansion and contraction. Across species, a mean of 12% of nucleotide positions are polymorphic within individual arrays, for both gene and spacer sequences. This shows, in conjunction with phylogenetic evidence for ancestral polymorphisms that survive speciation events, that intralocus concerted evolutionary forces are relatively weak and that the rate of interrepeat homogenization is approximately equal to the rate of speciation. Evidence presented also shows that duplicated 5S rDNA arrays in allopolyploids have retained their subgenomic identity since polyploid formation, thereby indicating that interlocus concerted evolution has not been an important factor in the evolution of these arrays. A descriptive model, one which incorporates the opposing forces of mutation and homogenization within a selective framework, is outlined to account for the empirical data presented. Weak homogenizing forces allow equivalent levels of sequence polymorphism to accumulate in the 5S gene and spacer sequences, but fixation of mutations is nearly prohibited in the 5S gene. As a consequence, fixed interspecific differences are statistically underrepresented for 5S genes. This result explains the apparent paradox that despite similar levels of gene and spacer diversity, phylogenetic analysis of spacer sequences yields highly resolved trees, whereas analyses based on 5S gene sequences do not.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/48052/1/239_2006_Article_BF02338802.pd

Placing the Origin of Two Species-Rich Genera in the Late Cretaceous with Later Species Divergence in the Tertiary: A Phylogenetic, Biogeographic and Molecular Dating Analysis of \u3cem\u3ePiper\u3c/em\u3e and \u3cem\u3ePeperomia\u3c/em\u3e (Piperaceae)

Nearly all of the species diversity in Piperaceae is encompassed within Piper and Peperomia. Both genera are pan-tropical with areas of diversification in the Neotropics and Southeast Asia. Piperaceae are less diverse in Africa with only two native species of Piper. This study examines the distribution of both Piper and Peperomia with representative samples from the Neotropics, Asia, Pacific Islands, and Africa. Molecular dating is used to place an age for the crown clades of Piper and Peperomia as well as ages for diversification within the clades. Both genera have origins in the late Cretaceous, but species level diversification occurred much later in the Tertiary. Biogeography of both genera are correlated with paleoclimate evidence to better explain the distribution and diversification of these large genera