Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications-one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.

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The spatial distribution of genetic diversity is a product of recent and historical ecological processes, as well as anthropogenic activities. A current challenge in population and conservation genetics is to disentangle the relative effects of these processes, as a first step in predicting population response to future environmental change. In this investigation, we compare the influence of contemporary population decline, contemporary ecological marginality and postglacial range shifts. Using classical model comparison procedures and Bayesian methods, we have identified postglacial range shift as the clear determinant of genetic diversity, differentiation and bottlenecks in 29 populations of butternut, Juglans cinerea L., a North American outcrossing forest tree. Although butternut has experienced dramatic 20th century decline because of an introduced fungal pathogen, our analysis indicates that recent population decline has had less genetic impact than postglacial recolonization history. Location within the range edge vs. the range core also failed to account for the observed patterns of diversity and differentiation. Our results suggest that the genetic impact of large-scale recent population losses in forest trees should be considered in the light of Pleistocene-era large-scale range shifts that may have had long-term genetic consequences. The data also suggest that the population dynamics and life history of wind-pollinated forest trees may provide a buffer against steep population declines of short duration, a result having important implications for habitat management efforts, ex situ conservation sampling and population viability analysis.

We investigate the question of naturally occurring interspecific hybrids between two forest trees: the native North American butternut ( Juglans cinerea L.) and the introduced Japanese walnut ( Juglans ailantifolia Carriè re). Using nuclear and chloroplast DNA markers, we provide evidence for 29 F 1 and 22 advanced generation hybrids in seven locations across the eastern and southern range of the native species. Two locations show extensive admixture (95% J. ailantifolia and hybrids) while other locations show limited admixture. Hybridization appears to be asymmetrical with 90.9 per cent of hybrids having J. ailantifolia as the maternal parent. This is, to our knowledge, the first genetic data supporting natural hybridization between these species. The long-term outcome of introgression could include loss of native diversity, but could also include transfer of useful traits from the introduced species.

Spatial and temporal dynamics of hybridization, in particular the influence of local environmental conditions, are well studied for sympatric species but less is known for native-introduced systems, especially for long-lived species. We used microsatellite and chloroplast DNA markers to characterize the influence of anthropogenic landscapes on the extent, direction, and spatial distribution of hybridization between a native North American tree Juglans cinerea (butternut) and an introduced tree Juglans ailantifolia (Japanese walnut) for 1363 trees at 48 locations across the native range of butternut. Remarkably, admixture in anthropogenic sites reached nearly 70%, while fragmented and continuous forests showed minimal admixture (<8%). Furthermore, more hybrids in anthropogenic sites had J. ailantifolia seed parents (95%) than hybrids in fragmented and continuous forests (69% and 59%, respectively). Our results show a strong influence of landscape type on rate and direction of realized gene flow. While hybrids are common in anthropogenic landscapes, our results suggest that even small forested landscapes serve as substantial barriers to hybrid establishment, a key consideration for butternut conservation planning, a species already exhibiting severe decline, and for other North American forest trees that hybridize with introduced congeners.