Phylogenetic utility of nuclear nitrate reductase: A multi-locus comparison of nuclear and chloroplast sequence data for inference of relationships among American Lycieae (Solanaceae)

A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago

The STORR gene fusion event is considered essential for the evolution of the promorphinan/morphinan subclass of benzylisoquinoline alkaloids (BIAs) in opium poppy as the resulting bi-modular protein performs the isomerization of (S)- to (R)-reticuline essential for their biosynthesis. Here, we show that of the 12 Papaver species analysed those containing the STORR gene fusion also contain promorphinans/morphinans with one important exception. P. californicum encodes a functionally conserved STORR but does not produce promorphinans/morphinans. We also show that the gene fusion event occurred only once, between 16.8-24.1 million years ago before the separation of P. californicum from other Clade 2 Papaver species. The most abundant BIA in P. californicum is (R)-glaucine, a member of the aporphine subclass of BIAs, raising the possibility that STORR, once evolved, contributes to the biosynthesis of more than just the promorphinan/morphinan subclass of BIAs in the Papaveraceae.

Molecular signatures of long-distance oceanic dispersal and the colonization of Pacific islands in Lycium carolinianum

PREMISE

Long-distance dispersal has been important in explaining the present distributions of many plant species. Despite being infrequent, such dispersal events have considerable evolutionary consequences, because bottlenecks during colonization can result in reduced genetic diversity. We examined the phylogeographic history of Lycium carolinianum, a widespread taxon that ranges from southeastern North America to several Pacific islands, with intraspecific diversity in sexual and mating systems.

METHODS

We used Bayesian, likelihood, and coalescent approaches with nuclear and plastid sequence data and genome-wide single nucleotide polymorphisms to reconstruct the dispersal history of this species. We also compared patterns of genetic variation in mainland and island populations using single nucleotide polymorphisms and allelic diversity at the S-RNase mating system gene.

RESULTS

Lycium carolinianum is monophyletic and dispersed once from the North American mainland, colonizing the Pacific islands ca. 40,100 years ago. This dispersal was accompanied by a loss of genetic diversity in SNPs and the S-RNase locus due to a colonization bottleneck and the loss of self-incompatibility. Additionally, we documented at least two independent transitions to gynodioecy: once following the colonization of the Hawaiian Islands and loss of self-incompatibility, and a second time associated with polyploidy in the Yucatán region of Mexico.

CONCLUSIONS

Long-distance dispersal via fleshy, bird dispersed fruits best explains the unusually widespread distribution of L. carolinianum. The collapse of diversity at the S-RNase locus in island populations suggests that self-fertilization may have facilitated the subsequent colonization of Pacific islands following a single dispersal from mainland North America.

The genus Lycium as food and medicine: A botanical, ethnobotanical and historical review

ETHNOPHARMACOLOGICAL RELEVANCE

Lycium is widely distributed in the arid to semi-arid environments of North and South America, Africa, and Eurasia. In recent years, Lycium barbarum and L. chinense have been advertised as "superfood" with healthy properties. Despite of its popularity, there is a lack of an integrated and critical appraisal of the existing evidence for the use of Lycium.

AIM OF THE STUDY

There is a need to understand: 1) Which species were used and how the uses of Lycium developed spatially and over time, 2) how uses differ among regions with different culture backgrounds, and 3) how traditional and current therapeutic and preventive health claims correlate with pharmacological findings.

METHODS

Information was retrieved from floras, taxonomic, botanical, and ethnobotanical databases, research articles, recent editions of historical Chinese herbals over the last 2000 years, and pharmacopoeias.

RESULTS

Of totally 97 species, 31 have recorded uses as food and/or medicine worldwide. Usually the fruits are used. While 85% of the Lycium species occur in the Americas and Africa, 26% of them are used, but 9 out of 14 species in Eurasia. In China, seven species and two varieties of the genus Lycium occur, of which four species have been used by different ethnic groups. Only L. barbarum and L. chinense have been transformed into globally traded commodities. In China, based on the name "", their use can be traced back over the last two millennia. Lycium fruits for anti-aging, improving eyesight and nourishment were documented already in 500C.E. (Mingyi Bielu). Recent findings explain the pharmacological foundations of the traditional uses. Especially polysaccharides, zeaxanthin dipalmitate, vitamins, betaine, and mixed extracts were reported to be responsible for anti-aging, improving eyesight, and anti-fatigue effects.

CONCLUSIONS

The integration of historical, ethnobotanical, botanical, phytochemical and pharmacological data has enabled a detailed understanding of Lycium and its wider potential. It highlights that the focus so far has only been on two species and that the genus can potentially yield a wide range of other products with different properties.

Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae)

The phenomenon of polyploidy and hybridization usually results in novel genetic combinations, leading to complex, reticulate evolution and incongruence among gene trees, which in turn may show different phylogenetic histories than the inherent species tree. The largest tribe within the subfamily Lamioideae (Lamiaceae), Stachydeae, which includes the globally distributed Stachys, and one of the largest Hawaiian angiosperm radiations, the endemic mints, is a widespread and taxonomically challenging lineage displaying a wide spectrum of morphological and chromosomal diversity. Previous molecular phylogenetic studies have showed that while the Hawaiian mints group with Mexican-South American Stachys based on chloroplast DNA sequence data, nuclear ribosomal DNA (nrDNA) sequences suggest that they are most closely related to temperate North American Stachys. Here, we have utilized five independently inherited, low-copy nuclear loci, and a variety of phylogenetic methods, including multi-locus coalescence-based tree reconstructions, to provide insight into the complex origins and evolutionary relationships between the New World Stachys and the Hawaiian mints. Our results demonstrate incongruence between individual gene trees, grouping the Hawaiian mints with both temperate North American and Meso-South American Stachys clades. However, our multi-locus coalescence tree is concurrent with previous nrDNA results placing them within the temperate North American Stachys clade. Our results point toward a possible allopolyploid hybrid origin of the Hawaiian mints arising from temperate North American and Meso-South American ancestors, as well as a reticulate origin for South American Stachys. As such, our study is another significant step toward further understanding the putative parentage and the potential influence of hybridization and incomplete lineage sorting in giving rise to this insular plant lineage, which following colonization underwent rapid morphological and ecological diversification.

Intricate patterns of phylogenetic relationships in the olive family as inferred from multi-locus plastid and nuclear DNA sequence analyses: a close-up on Chionanthus and Noronhia (Oleaceae)

Noronhia represents the most successful radiation of the olive family (Oleaceae) in Madagascar with more than 40 named endemic species distributed in all ecoregions from sea level to high mountains. Its position within the subtribe Oleinae has, however, been largely unresolved and its evolutionary history has remained unexplored. In this study, we generated a dataset of plastid (trnL-F, trnT-L, trnS-G, trnK-matK) and nuclear (internal transcribed spacer [ITS]) DNA sequences to infer phylogenetic relationships within Oleinae and to examine evolutionary patterns within Noronhia. Our sample included most species of Noronhia and representatives of the ten other extant genera within the subtribe with an emphasis on Chionanthus. Bayesian inferences and maximum likelihood analyses of plastid and nuclear data indicated several instances of paraphyly and polyphyly within Oleinae, with some geographic signal. Both plastid and ITS data showed a polyphyletic Noronhia that included Indian Ocean species of Chionanthus. They also found close relationships between Noronhia and African Chionanthus. However, the plastid data showed little clear differentiation between Noronhia and the African Chionanthus whereas relationships suggested by the nuclear ITS data were more consistent with taxonomy and geography. We used molecular dating to discriminate between hybridization and lineage sorting/gene duplication as alternative explanations for these topological discordances and to infer the biogeographic history of Noronhia. Hybridization between African Chionanthus and Noronhia could not be ruled out. However, Noronhia has long been established in Madagascar after a likely Cenozoic dispersal from Africa, suggesting any hybridization between representatives of African and Malagasy taxa was ancient. In any case, the African and Indian Ocean Chionanthus and Noronhia together formed a strongly supported monophyletic clade distinct and distant from other Chionanthus, which calls for a revised and more conservative taxonomy for this group.

Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus)

The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.

The utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference in Lycium (Solanaceae)

The identification of genomic regions with sufficient variation to elucidate fine-scale relationships among closely related species is a major goal of phylogenetic systematics. However, the accumulation of such multi-locus data sets brings its own challenges, given that gene trees do not necessarily represent the true species tree. Using genomic tools developed for Solanum (Solanaceae), we have evaluated the utility of nuclear conserved ortholog set II (COSII) regions for phylogenetic inference in tribe Lycieae (Solanaceae). Five COSII regions, with intronic contents ranging from 68% to 91%, were sequenced in 10 species. Their phylogenetic utility was assessed and compared with data from more commonly used nuclear (GBSSI, nrITS) and cpDNA spacer data. We compared the effectiveness of a traditional total evidence concatenation approach versus the recently developed Bayesian estimation of species trees (BEST) method to infer species trees given multiple independent gene trees. All of the sampled COSII regions had high numbers of parsimony-informative (PI) characters, and two of the COSII regions had more PI characters than the GBSSI, ITS, and cpDNA spacer data sets combined. COSII markers are a promising new tool for phylogenetic inference in Solanaceae, and should be explored in related groups. Both the concatenation and BEST approaches yielded similar topologies; however, when multiple individuals with polyphyletic alleles were included, BEST was clearly the more robust approach for inferring species trees in the presence of gene tree incongruence.