Barbara A. Schaal

Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene

Phylogeographical studies are emerging as a powerful tool for understanding the population structure and evolution of wild relatives of crop species. Because of their value as genetic resources, there is great interest in exploring the distribution of variation in wild relatives of cultivated plants. In this study, we use sequence variation from the nuclear gene, fruit vacuolar invertase (Vac), to investigate the population history of Solanum pimpinellifolium. Solanum pimpinellifolium is a close relative of the cultivated tomato and has repeatedly served as a source of valuable traits for crop improvement. We sequenced the second intron of the Vac gene in 129 individuals, representing 16 populations from the northern half of Peru. Patterns of haplotype sharing among populations indicate that there is isolation by distance. However, there is no congruence between the geographical distribution of haplotypes and their genealogical relationships. Levels of outcrossing decrease towards the southernmost populations, as previously observed in an allozyme study. The geographical pattern of Vac variation supports a centre of origin in northern Peru for S. pimpinellifolium and a gradual colonization along the Pacific coast. This implies that inbreeding populations are derived from outcrossing ones and that variation present at the Vac locus predates the spread of S. pimpinellifolium. The expansion of cities and human agricultural activity in the habitat of S. pimpinellifolium currently pose a threat to the species.

Natural selection in gene dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice

Levels of nucleotide variability are frequently positively correlated with recombination rate and negatively associated with gene density due to the effects of selection on linked variation. These relationships are determined by properties that frequently differ among species, including the mating system, and aspects of genome organization such as how genes are distributed along chromosomes. In rice, genes are found at highest density in regions with frequent crossing-over. This association between gene density and recombination rate provides an opportunity to evaluate the effects of selection in a genomic context that differs from other model organisms. Using single-nucleotide polymorphism data from Asian domesticated rice Oryza sativa ssp. japonica and ssp. indica and their progenitor species O. rufipogon, we observe a significant negative association between levels of polymorphism and both gene and coding site density, but either no association, or a negative correlation, between nucleotide variability and recombination rate. We establish that these patterns are unlikely to be explained by neutral mutation rate biases and demonstrate that a model of background selection with variable rates of deleterious mutation is sufficient to account for the gene density effect in O. rufipogon. In O. sativa ssp. japonica, we report a strong negative correlation between polymorphism and recombination rate and greater losses of variation during domestication in the euchromatic chromosome arms than heterochromatin. This is consistent with Hill-Robertson interference in low-recombination regions, which may limit the efficacy of selection for domestication traits. Our results suggest that the physical distribution of selected mutations is a primary factor that determines the genomic pattern of polymorphism in wild and domesticated rice species.

Low genetic diversity and significant population structuring in the relict Amentotaxus argotaenia complex (Taxaceae) based on ISSR fingerprinting

Amentotaxus, a genus of the Taxaceae, represents an ancient lineage that has long existed in Eurasia. All Amentotaxus species experienced frequent population expansion and contraction over periodical glaciations in Tertiary and Quaternary. Among them, Amentotaxus argotaenia complex consists of three morphologically alike species, A. argotaenia, Amentotaxus yunnanensis, and Amentotaxus formosana. This complex is distributed in the subtropical region of mainland China and Taiwan where many Pleistocene refugia have been documented. In this study, genetic diversity and population structuring within and between species were investigated based on the inter-simple sequence repeats (ISSR) fingerprinting. Mean genetic diversity within populations was estimated in three ways: (1) the percentage of polymorphic loci out of all loci (P) (2) Nei’s unbiased expected heterozygosity (He), and (3) Shannon’s index of phenotypic diversity. For a total of 310 individuals of 15 populations sampled from the three species, low levels of ISSR genetic variation within populations were detected, with P=4.66–16.58%, He=0.0176–0.0645 and Hpop=0.0263–0.0939, agreeing with their seriously threatened status. AMOVA analyses revealed that the differences between species only accounted for 27.38% of the total variation, whereas differences among populations and within populations were 57.70 and 14.92%, respectively, indicating substantial isolation between the patch-like populations. A neighbor-joining tree identified a close affinity between A. yunnanensis and A. formosana. Genetic drift due to small population size, plus limited current gene flow, resulted in significant genetic structuring. Low levels of intrapopulational genetic variation and considerable interpopulational divergence were also attributable to demographic bottlenecks during and/or after the Pleistocene glaciations.

Leavenworthia (Brassicaceae) Revisited: Testing Classic Systematic and Mating System Hypotheses

Abstract The genus Leavenworthia (Brassicaceae) has long been a focus of research on mating system evolution, due to the presence of both self-incompatible and self-compatible species within the genus. A phylogenetic hypothesis invoking multiple transitions between mating systems has been proposed for Leavenworthia, but this hypothesis has not been subject to molecular phylogenetic analysis. DNA sequence variation from four non-coding chloroplast regions (the trnL intron; and the trnT-trnL, trnL-trnF, and psbA-trnH intergenic spacers) was used to reconstruct the generic phylogeny, to test the validity of several proposed species, and to assess the number of mating system transitions within the genus. The strict consensus tree largely reflected the long-standing phylogenetic hypothesis for Leavenworthia, although additional data are needed to fully validate the recognition of L. crassa and L. alabamica. Unexpected results included the placement of L. uniflora as sister to the rest of the genus, and the apparent hybridization between L. exigua and L. torulosa. Finally, our data strongly supported a minimum of three mating system transitions within Leavenworthia.

Association between the geographic distribution during the last glacial maximum of Asian wild rice, Oryza rufipogon (Poaceae), and its current genetic variation

PREMISE OF THE STUDY The combination of traditional population genetic studies and species distribution modeling (SDM) provides many new insights in detecting phylogeographic signals. In Asian wild rice (Oryza rufipogon), the progenitor of cultivated Asian rice, geographical subdivision has been documented in many genetic studies although the root cause of this subdivision remains unknown. Surprisingly, environmental factors associated with the spatial and temporal distribution of O. rufipogon have rarely been examined. The aim of this study is to understand the historical distribution of O. rufipogon and its relationship to the current geographical pattern of genetic variation. METHODS We used SDM to examine the present, past, and future distribution of O. rufipogon. The estimated distribution during the Last Glacial Maximum was then compared with genetic data from our previous work. KEY RESULTS The predicted paleodistribution of O. rufipogon at the Last Glacial Maximum was separated into disconnected east and west ranges. This past distribution is consistent with the current geographic pattern of genetic variation, with two genetic groups that intergrade. Annual precipitation is the single factor that contributes most to SDM estimates. SDM predictions for 2080 indicate a general trend of increasing probability of presence and range expansion. CONCLUSIONS (1) The historically disjunct distribution potentially contributes to the current genetic subdivision of O. rufipogon. (2) Water availability is an important factor that limits the distribution of O. rufipogon. (3) Global warming is a lesser threat than other human-mediated factors to the conservation of this endangered species.

Apportionment of Isozyme Variability in Polygonum pensylvanicum (Polygonaceae)

The apportionment of genetic variability at ten isozyme loci was studied in six populations of Polygonum pensylvanicum L. Thirty percent of the isozymes are polymorphic and the average individual heterozygosity per plant is low, 4 percent. Populations are genetically similar; the mean standardized genetic variance among populations is 0.12. Most of the total genetic diversity, 87.3 percent, is due to dif- ferences between individuals within populations; 12.7 percent of the diversity results from differences between populations. None of the populations is in Hardy-Wein- berg equilibrium; deviation from equilibrium expectations is due to a deficiency of heterozygotes. The levels and apportionment of genetic variability within and among populations of plant species have been of major interest to plant evolu- tionists and systematists. A substantial body of theory predicts that levels of genetic variability will be related to numerous species characteristics such as karyotype, habitat, population structure, and generation length. The empirical evidence for these associations is still incomplete; the level and apportionment of genetic variability in many types of plant species is unknown. This study examines isozyme variability in a widespread weedy annual species, Polygonum pensylvanicum. Baker (1965) and others have predicted that annual weeds will have little genetic variation, both within and be- tween populations. Our purpose is to test these predictions by answering the following questions: 1) What is the level of genetic variability for the species? 2) How is the variability distributed within populations? 3) How genetically similar are populations? 4) How is the genetic diversity of the species apportioned? Polygonum pensylvanicum is a weedy herbaceous annual found in dis- turbed habitats, often near ponds or streams. The species is common from Minnesota east to New England, and Ohio north to Ontario. Plants may grow to a maximum of four feet in height, but are often much smaller in restricted environments. There may be from one to many flowering heads on a single plant and each infloresence is spikelike, hav- ing twenty to thirty perfect, self-fertile flowers. The flowers are insect pollinated, and in some populations, pollination by ants has been ob- served. One seed is produced per flower; seeds require a six month after- ripening period in a moist, 6?C environment before germination (Ran- son, 1935).

Genetic Diversity in Liatris cylindracea

A genetically substructured population of the perennial, outbreeding herb, Liatris cylindracea was marked off into a grid with quadrat size that approximates the neighborhood size of Liatris. The plants were genotyped at 27 allozyme loci, 15 of which were polymorphic. The apportionment of genetic diversity within the population was determined by the Shannon information measure. Ninety-three percent of the total diversity is represented within each neighborhood. Five percent of the diversity is due to between neighborhoods, and about 2% is due to differences between sample rozs and columns. It is concluded that the subdivision of a population does not result in a loss of genetic diversity within neighborhoods. The properties of genetically subdivided populations have received considerable attention by theoreticians (e.g., Wright, 1943a; Kimura & Weiss, 1954; Maruyama, 1970). Because of the difficulty in the past of finding suitable single locus genetic markers, few experimental studies on genetic substructuring have been available. Now, with the advent of allozyme electrophoresis as a tool for the genetic analysis of natural populations, an increased number of studies on both animals (Selander 8c Yang, 1969; Workman gc Niswander, 1970; Neel gc Ward, 1972) and plants (Schaal, 1975) have indicated that populations of some organisms are genetically