Variation and Evolution in Plants and Microorganisms: Toward a New Synthesis 50 Years after Stebbins

The repetitive amino acid sequences encoded within the CR are remarkably conserved (only two amino acid motifs are known in P. falciparum, NANP and NVDP; Table 4), but there is a fair deal of synonymous nucleotide polymorphism among the repeats (Table 5). We have introduced the concept of the repeat allotype (RAT) to refer to variant nucleotide sequences that encode a single amino acid motif (Rich et al., 1997). Among the known Csp gene sequences of P. falciparum, there are 10 RATs that encode the NANP motif and four RATs that encode the NVDP motif, with an average of about 10 RATs per gene sequence (range 9–11; see Table 6). Table 4 displays the arrangement of the two amino acid motifs in 25 gene sequences of P. falciparum and one of P. reichenowi. The alignment of the RATs can be found in Rich et al. (1997; see also Ayala et al., 1999). The only known sequence of Csp in P. reichenowi is somewhat shorter than those of falciparum (35 rather than about 45 repeats per sequence, on average), but has a similar number of distinct RATs (10, the

TABLE 4. Composition of the CR of the Csp gene

		Number of repeats
Sequence	Repeat motifs	1	2	3
M15505	1212111111111111111211111111111111111111111111	43	3	0
M83173	1212111111111111111211111111111111111111111111	43	3	0
M83149	12121211111111111111111111111111111111111111	41	3	0
M83150	12121111111111111112111111111111111111111111111	44	3	0
M83156	121211111111111111111111111111111111111111111111111	49	2	0
M83158	1212121211111111111111111111111111111111111111	42	4	0
M83161	1212121111111111111111111211111111111111111.	39	4	0
M83163	12121111111111111112111111111111111111111111111	43	3	0
M83164	12121111111111111112111111111111111111111111111	46	3	0
M83165	1212121111111111111111111111111111111111111ili	43	3	0
M83166	1212121211111111111111111111111111111111111111	42	4	0
M83167	12121211111111111111111111111111111111111111111	46	3	0
M83168	1212121211111111111111111111111111111111111111	42	4	0
M83169	12121211111111111111111111111111111111111111	41	3	0
M83170	1212121211111111111111111111111111111111111111	42	4	0
M83174	1212121111111111211111111111111111111111111	39	4	0
M19752	12121211111111111111111111111111111111111111	41	3	0
M83172	121212111111111111111121111111111111111111	38	4	0
K02194	12121211111111111111121111111111111111111	37	4	0
M57499	12121212111111111111111111111111111111111111	40	4	0
U20969	1212121111111111111112111111111111111111	36	4	0
M83886	121212111111111111111112111111111111111111	38	4	0
M22982	12121211111111111111111112111111111111111111	40	4	0
X15363	12121211111111111111111112111111111111111111	40	4	0
M57498	12121211111111111111121111111111111111111	37	4	0
P. reichenowi	12121212131213131311111111111111111	26	5	4
The repeat motifs NANP, NVDP, and NVNP are represented by 1, 2, and3, respectively. Adapted from Ayala et al., (1999).

Table of Contents

Front Matter R1-R12

Part I: Early Evolution and the Origin of Cells 1-2

1 G. Ledyard Stebbins (1906-2000) -- An Appreciation 3-5

2 Solution to Darwin's Dilemma: Discovery of the Missing Precambrian Record of Life 6-20

3 The Chimeric Eukaryote: Origin of the Nucleus from the Karyomastigont in Amitochondriate Protists 21-34

4 Dynamic Evolution of Plant Mitochondrial Genomes: Mobile Genes and Introns and Highly Variable Mutation Rates 35-58

Part II: Viral and Bacterial Models 59-60

5 The Evolution of RNA Viruses: A Population Genetics View 61-82

6 Effects of Passage History and Sampling Bias on Phylogenetic Reconstruction of Human Influenza A Evolution 83-98

7 Bacteria are Different: Observations, Interpretations, Speculations, and Opinions About the Mechanisms of Adaptive Evolution in Prokaryotes 99-114

Part III: Protoctist Models 115-116

8 Evolution of RNA Editing in Trypanosome Mitochondria 117-142

9 Population Structure and Recent Evolution of Plasmodium falciparum 143-164

Part IV: Population Variation 165-166

10 Transposons and Genome Evolution in Plants 167-186

11 Maize as a Model for the Evolution of Plant Nuclear Genomes 187-210

12 Flower Color Variation: A Model for the Experimental Study of Evolution 211-234

13 Gene Genealogies and Population Variation in Plants 235-252

Part V: Trends and Patterns in Plant Evolution 253-254

14 Toward a New Synthesis: Major Evolutionary Trends in the Angiosperm Fossil Record 255-270

15 Reproductive Systems and Evolution in Vascular Plants 271-288

16 Hybridization as a Stimulus for the Evolution of Invasiveness in Plants? 289-309

17 The Role of Genetic and Genomic Attributes in the Success of Polyploids 310-330

Index 331-340