Microsatellite primers for the North American bluets (Houstonia section Amphiotis, Rubiaceae).

PREMISE OF THE STUDY: Microsatellites were developed for the native, perennial herbs Houstonia longifolia and H. purpurea to establish rates and patterns of hybridization among these and other closely related lineages within the genus. METHODS AND RESULTS: Seven primer sets were developed and tested using populations across eastern North America and into parts of the Midwest. Primers amplified di- and tri-nucleotide repeats with 1-16 alleles per locus among diploids. These primers also amplified microsatellites for H. purpurea var. montana, H. purpurea var. calycosa, H. ouachitana, and H. canadensis, and for other Houstonia species outside section Amphiotis. CONCLUSIONS: These results demonstrate the value of microsatellite loci in studies focusing on hybridization and population genetics across Houstonia section Amphiotis and could be useful in studies within other sections of Houstonia as well as in studies of related genera, such as Hedyotis.

Gene expression in a wild autopolyploid sunflower series.

Polyploidy, or genome doubling, is a common mechanism in the evolution of plants. This genome duplication can rapidly lead to genomic changes between ploidy levels. In particular, allopolyploids that result from interspecific hybridization can show a large number of changes in gene expression immediately after the polyploidy event. These are likely due to epigenetic changes that do not alter the underlying DNA sequence. This may be due in part to the hybrid origin of these allopolyploids. In autopolyploids, a small number of studies have shown that there may also be some gene expression changes between ploidy levels, albeit to a much smaller degree. However, these studies have focused on inbred lines of single populations. This study examines silencing and/or novel gene expression in diploid, autotetraploid, and autohexaploid lineages of Helianthus decapetalus. Using cDNA-amplified fragment length polymorphism, we examined gene expression in 5 populations of these lineages. The results show no ploidy level-specific differences in gene silencing or novel gene expression. All gene expression differences are among populations and may be due to independent evolutionary origins. These results support the conclusions of previous studies that gene expression differences among allopolyploids are likely due in large part to the hybrid nature of these lineages.

Using variable rate models to identify genes under selection in sequence pairs: their validity and limitations for EST sequences.

Using likelihood-based variable selection models, we determined if positive selection was acting on 523 EST sequence pairs from two lineages of sunflower and lettuce. Variable rate models are generally not used for comparisons of sequence pairs due to the limited information and the inaccuracy of estimates of specific substitution rates. However, previous studies have shown that the likelihood ratio test (LRT) is reliable for detecting positive selection, even with low numbers of sequences. These analyses identified 56 genes that show a signature of selection, of which 75% were not identified by simpler models that average selection across codons. Subsequent mapping studies in sunflower show four of five of the positively selected genes identified by these methods mapped to domestication QTLs. We discuss the validity and limitations of using variable rate models for comparisons of sequence pairs, as well as the limitations of using ESTs for identification of positively selected genes.

Speciation and hybridization among Houstonia (Rubiaceae) species: the influence of polyploidy on reticulate evolution.

Chloroplast and nuclear DNA sequence variation among populations and species was used to examine the phylogenetic history and hybridization of the North American Houstonia lineage. The ancestral species in the lineage do not show evidence of hybridization; however, the more recently derived species in eastern North America contain a wide degree of morphological and genetic variation both within and among species. Furthermore, there is a clear association between hybridization and polyploidy in the Houstonia lineage, with all potential hybrids occurring among species that contain polyploid populations. This suggests that polyploidy may break down species barriers and allow hybridization among lineages. These results indirectly support speciation models that involve genetic incompatibilities among species arising from gene silencing or genomic reorganization.

Integration of populations and differentiation of species.

The framework for modern studies of speciation was established as part of the Neo-Darwinian synthesis of the early twentieth century. Here we evaluate this framework in the light of recent empirical and theoretical studies. Evidence from experimental studies of selection, quantitative genetic studies of species' differences, and the molecular evolution of 'isolation' genes, all agree that directional selection is the primary cause of speciation, as initially proposed by Darwin. Likewise, as suggested by Dobzhansky and Mayr, gene flow does hold species together, but probably more by facilitating the spread of beneficial mutants and associated hitchhiking events than by homogenizing neutral loci. Reproductive barriers are important as well in that they preserve adaptations, but as has been stressed by botanists for close to a century, they rarely protect the entire genome from gene flow in recently diverged species. Contrary to early views, it is now clear that speciation can occur in the presence of gene flow. However, recent theory does support the long-held view that population structure and small population size may increase speciation rates, but only under special conditions and not because of the increased efficacy of drift as suggested by earlier authors. Rather, low levels of migration among small populations facilitates the rapid accumulation of beneficial mutations that indirectly cause hybrid incompatibilities.

Evidence for multiple Pleistocene refugia in the postglacial expansion of the eastern tiger salamander, Ambystoma tigrinum tigrinum.

Pleistocene glaciations were important determinants of historical migration and, hence, current levels of genetic diversity within and among populations. In many cases, these historical migrations led to the existence of disjunct populations of plants and animals. However, the origin and timing of arrival of these disjunct populations is often debated. In the current study, we identify potential refugia and estimate the timing of vicariance events of the eastern tiger salamander, Ambystoma tigrinum tigrinum, using mitochondrial sequence data. The results suggest a vicariant event 0.75-2 million years ago, separating the tiger salamanders to the east and west of the Apalachicola River Basin. East of the Appalachians, there appear to be multiple independent refugia with little migration among the remaining populations. In particular, populations along the Atlantic Coastal Plain were likely isolated in a coastal plain refugium in the Carolinas. Migrants from this refugium were the likely source of colonists for populations occupying previously glaciated areas along the northeastern Atlantic Coast. A second potential refugium occurs in the Blue Ridge Mountains of western Virginia. This refugium contains a disjunct population of the eastern tiger salamander, as well as a community of nearly 70 other disjunct plant and animal species. The tiger salamanders here have been isolated from other populations for 200,000-500,000 years. These results suggest that disjunct mountain populations of Coastal Plain species may have existed in situ throughout the Pleistocene in Appalachian refugia. Therefore, these disjunct populations are not of recent origin, but rather exist as relicts of a warmer, more widespread fauna and flora that is now restricted to the Coastal Plain.

Molecular phylogenetics of Houstonia (Rubiaceae): descending aneuploidy and breeding system evolution in the radiation of the lineage across North America.

Nuclear and chloroplast DNA sequence variation was used to infer evolutionary relationships within and among members of Houstonia (Rubiaceae) and other closely related genera in North America. Sequences from the internal transcribed spacer (ITS) of the nrDNA and a cpDNA intron in the trnL gene were used to reconstruct phylogenetic relationships of 30 species of Houstonia and closely related genera. The data suggest that the North American species of Houstonia are not monophyletic, but belong to the same lineage as Stenaria. The radiation of this lineage has been accompanied by changes in the basic chromosome number of the major clades through descending aneuploidy. This loss of chromosomes was also associated with northward colonization of North America. However, other characters, such as an annual versus perennial habit, heterostylous and homostylous breeding systems, and the evolution of self fertilization, seem to be labile throughout the lineage, originating multiple times throughout the evolutionary history of the lineage.

The evolution of reproductive isolation in spatially structured populations.

Recent models of speciation have incorporated population structure and migration into the classic model of speciation in which reproductive isolation arises as a by-product of divergence. In this paper, we expanded these models to explore the joint effects of migration and population subdivision on speciation in a spatially explicit context. The results of our simulation support previous results concerning the influence of population subdivision on the accumulation of reproductive isolation. The simulation also shows that speciation in subdivided populations occurs most rapidly when subpopulations are not strictly allopatric. These results counter the widespread notion that speciation is most likely to occur in allopatric populations and suggest that there are useful insights to be gained by incorporating increasingly realistic types of population structure into models of speciation.