Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus).

All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of 'turnover' of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6-7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.

A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.

Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.

Chloroplast microsatellite primers for cacao (Theobroma cacao) and other Malvaceae.

PREMISE OF THE STUDY: Chloroplast microsatellites were developed in Theobroma cacao to examine the genetic diversity of cacao cultivars in Trinidad and Tobago. METHODS AND RESULTS: Nine polymorphic microsatellites were designed from the chloroplast genomes of two T. cacao accessions. These microsatellites were tested in 95 hybrid accessions from Trinidad and Tobago. An average of 2.9 alleles per locus was found. CONCLUSIONS: These chloroplast microsatellites, particularly the highly polymorphic pentameric repeat, were useful in assessing genetic variation in T. cacao. In addition, these markers should also prove to be useful for population genetic studies in other species of Malvaceae.

Evolution in reverse gear: the molecular basis of loss and reversal.

Three types of regressive evolution are reviewed: loss, reversal, and regain after loss. Loss refers to the loss of a physical entity, either a structure or an organ, whereas reversals apply to character states returning to plesiomorphic from apomorphic conditions. The regain of characters after their loss represents a third type of evolutionary character change. The reconstruction of multiple losses and gains of characters by mapping on phylogenies is often problematic because of a lack of information about the relative likelihood of losses and gains. A developmental genetic approach using morphological, developmental, and molecular analysis is therefore an extremely important adjunct to phylogenetic approaches in interpreting losses, reversals, and regains. The molecular developmental basis of character loss and reversal is gradually becoming better understood. Loss of organs can occur by gain-of-function mutations (suppression) and loss-of-function mutations (that often leave a vestigial structure). The regain of characters after loss may occur by regulatory capture (a gain-of-function mutation) or by loss of function in suppressor genes. Reversals may occur by cryptic innovation (the formation of a new structure that mimics the old structure by gain-of-function mutations) or by loss of gene function associated with the apomorphic state (although this may have pleitropic or neomorphic effects). The genetic landscape of reversal is illustrated by the reversal to polysymmetry from monosymmetry in flowers. The range of observed phenotypes, loss with vestige, cryptic innovation, and loss with neomorphism matches the range of changes predicted."In plants with separated sexes, the male flowers often have a rudiment of a pistil; and Kolreuter found that by crossing such male plants with an hermaphrodite species, the rudiment of the pistil in the hybrid offspring was much increased in size; and this shows that the rudiment and the perfect pistil are essentially alike in nature" (Darwin 1859).

Plant eco-devo: the potential of poplar as a model organism.

Ecological developmental genetics is the study of how ecologically significant traits originate in the genome and how the allelic combinations responsible are maintained in populations and species. Plant development involves a continuous feedback between growth and environment and the success of individual genotype x environment interactions determines the passage of alleles to the next generation: the adaptive recursion. Outbreeding plants contain a large amount of genetic variation, mostly in the form of single nucleotide polymorphisms (SNPs). One of the challenges of eco-devo is to distinguish neutral SNPs from those with ecological consequences. The complete genome sequence of Populus trichocarpa Torr. & A. Gray will be a significant aid in this endeavour. Occurring from California to Alaska, this is the first ecologically 'keystone' species to be sequenced. It has a rich natural history and is an obligate outbreeder. The individual sequenced, Nisqually-1, appears to be heterozygous on average about every 100 bp over the c. 500 million bp of the genome. Overlaid on this within-individual variation is some ecologically based between-individual genotypic variation evident across the distribution of the species. The synthesis of information from genomics and ecology is now in prospect. This 'ecomolecular synthesis' is likely to provide a rich insight into the genomic basis of plant adaptation.

The history of the endemic flora of St Helena: late Miocene:'Trochetiopsis-like' pollen from St Helena and the origin of Trochetiopsis.

Re-examination of a fossiliferous sediment from St Helena has revealed the presence in the late Miocene of pollen grains very similar to modern Trochetiopsis pollen. Trochetiopsis is found only in St Helena and is assumed to be a palaeoendemic genus. The late Miocene material provides striking confirmation of this view. The two extant Trochetiopsis species are compared with other species in the Sterculiaceae: Dombeyeae, using multivariate methods. It is suggested that the two extant Trochetiopsis species diverged on St Helena comparatively recently, probably as a result of disruptive selection followed by ecological isolation caused by environmental change at the beginning of the Quaternary. It is also suggested that the ancestor of the extant Trochetiopsis species arrived in St Helena by long distance dispersal from African or Madagascar Dombeyeae stock at least 9 million years ago. However, since this time the pollen morphology of the Trochetiopsis lineage has changed little. The taxonomic isolation of Trochetiopsis can thus be explained partly by evolution on St Helena, but mainly by evolution and extinction in the Dombeyeae elsewhere (reliction).

THE HISTORY OF ENDEMIC FLORA OF ST HELENA: A RELICTUAL SERIES.

When the endemic plant species of St Helena are ordered according to their increasing taxonomic isolation, their corresponding 'sister groups' show a 'relictual series' of increasing geographical disjunction. This is best explained by progressive extinction and evolution in continental areas rather than by particularly high rates of evolutionary change on the island (i.e. the taxonomically isolated endemics are ancient relicts). Few of the supposed trends of oceanic island evolution are convincingly evident in the flora of St Helena. St Helena was formed in the Miocene, and it is likely that the relict genera colonized St Helena from Southern Africa before the wet forest flora in this area largely disappeared as the climate deteriorated from the late Miocene onwards.