Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica.

We present the first phylogenomic analysis of relationships among all ten families of Liliales, based on 75 plastid genes from 35 species in 29 genera, and 97 additional plastomes stratified across angiosperm lineages. We used a supermatrix approach to extend our analysis to 58 of 64 genera of Liliales, and calibrated the resulting phylogeny against 17 fossil dates to produce a new timeline for monocot evolution. Liliales diverged from other monocots 124 Mya and began splitting into separate families 113 Mya. Our data support an Australian origin for Liliales, with close relationships between three pairs of lineages (Corsiaceae/Campynemataceae, Philesiaceae/Ripogonaceae, tribes Alstroemerieae/Luzuriageae) in South America and Australia or New Zealand reflecting teleconnections of these areas via Antarctica. Long-distance dispersal (LDD) across the Pacific and Tasman Sea led to re-invasion of New Zealand by two lineages (Luzuriaga, Ripogonum); LDD allowed Campynemanthe to colonize New Caledonia after its submergence until 37 Mya. LDD permitted Colchicaceae to invade East Asia and Africa from Australia, and re-invade Africa from Australia. Periodic desert greening permitted Gloriosa and Iphigenia to colonize Southeast Asia overland from Africa, and Androcymbium-Colchicum to invade the Mediterranean from South Africa. Melanthiaceae and Liliaceae crossed the Bering land-bridge several times from the Miocene to the Pleistocene.

Orchid phylogenomics and multiple drivers of their extraordinary diversification.

Orchids are the most diverse family of angiosperms, with over 25 000 species,more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here,we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. Asupermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras),and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp(-1) My(-1)) is 6.8 times that at the Asparagales crown.

A survey of the Sli gene in wild and cultivated potato.

Inbred-hybrid breeding of diploid potatoes necessitates breeding lines that are self-compatible. One way of incorporating self-compatibility into incompatible cultivated potato (Solanum tuberosum) germplasm is to introduce the S-locus inhibitor gene (Sli), which functions as a dominant inhibitor of gametophytic self-incompatibility. To learn more about Sli diversity and function in wild species relatives of cultivated potato, we obtained Sli gene sequences that extended from the 5'UTR to the 3'UTR from 133 individuals from 22 wild species relatives of potato and eight diverse cultivated potato clones. DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. DNA sequences in one group contain the 533 bp insertion upstream of the start codon identified previously in self-compatible potato. The second group lacks the insertion. Three diploid and four polyploid individuals of wild species collected from geographically disjointed localities contained Sli with the 533 bp insertion. For most of the wild species clones examined, however, Sli did not have the insertion. Phylogenetic analysis indicated that Sli sequences with the insertion, in wild species and in cultivated clones, trace back to a single origin. Some diploid wild potatoes that have Sli with the insertion were self-incompatible and some wild potatoes that lack the insertion were self-compatible. Although there is evidence of positive selection for some codon positions in Sli, there is no evidence of diversifying selection at the gene level. In silico analysis of Sli protein structure did not support the hypothesis that amino acid changes from wild-type (no insertion) to insertion-type account for changes in protein function. Our study demonstrated that genetic factors besides the Sli gene must be important for conditioning a switch in the mating system from self-incompatible to self-compatible in wild potatoes.

Phylogeny, floral evolution, and inter-island dispersal in Hawaiian Clermontia (Campanulaceae) based on ISSR variation and plastid spacer sequences.

Previous studies based on DNA restriction-site and sequence variation have shown that the Hawaiian lobeliads are monophyletic and that the two largest genera, Cyanea and Clermontia, diverged from each other ca. 9.7 Mya. Sequence divergence among species of Clermontia is quite limited, however, and extensive hybridization is suspected, which has interfered with production of a well-resolved molecular phylogeny for the genus. Clermontia is of considerable interest because several species posses petal-like sepals, raising the question of whether such a homeotic mutation has arisen once or several times. In addition, morphological and molecular studies have implied different patterns of inter-island dispersal within the genus. Here we use nuclear ISSRs (inter-simple sequence repeat polymorphisms) and five plastid non-coding sequences to derive biparental and maternal phylogenies for Clermontia. Our findings imply that (1) Clermontia is not monophyletic, with Cl. pyrularia nested within Cyanea and apparently an intergeneric hybrid; (2) the earliest divergent clades within Clermontia are native to Kauài, then Òahu, then Maui, supporting the progression rule of dispersal down the chain toward progressively younger islands, although that rule is violated in later-evolving taxa in the ISSR tree; (3) almost no sequence divergence among several Clermontia species in 4.5 kb of rapidly evolving plastid DNA; (4) several apparent cases of hybridization/introgression or incomplete lineage sorting (i.e., Cl. oblongifolia, peleana, persicifolia, pyrularia, samuelii, tuberculata), based on extensive conflict between the ISSR and plastid phylogenies; and (5) two origins and two losses of petaloid sepals, or--perhaps more plausibly--a single origin and two losses of this homeotic mutation, with its introgression into Cl. persicifolia. Our phylogenies are better resolved and geographically more informative than others based on ITS and 5S-NTS sequences and nuclear SNPs, but agree with them in supporting Clermontia's origin on Kauài or some older island and dispersal down the chain subsequently.

DNA from herbarium specimens settles a controversy about origins of the European potato.

Landrace potato cultivars are native to two areas in South America: the high Andes from eastern Venezuela to northern Argentina and the lowlands of south-central Chile. Potato first appeared outside of South America in Europe in 1567 and rapidly diffused worldwide. Two competing hypotheses suggested the origin of the "European" potato from the Andes or from lowland Chile, but the Andean origin has been widely accepted over the last 60 years. All modern potato cultivars predominantly have Chilean germplasm, explained as originating from breeding with Chilean landraces subsequent to the late blight epidemics beginning in 1845 in the UK. The Andean origin has been questioned recently through examination of landraces in India and the Canary Islands, but this evidence is inferential. Through a plastid DNA deletion marker from historical herbarium specimens, we report that the Andean potato predominated in the 1700s, but the Chilean potato was introduced into Europe as early as 1811 and became predominant long before the late blight epidemics in the UK. Our results provide the first direct evidence of these events and change the history of introduction of the European potato. They shed new light on the value of past breeding efforts to recreate the European potato from Andean forms and highlight the value of herbarium specimens in investigating origins of crop plants.