Jill S. Miller

Relationships within tribe Lycieae (Solanaceae): paraphyly of Lycium and multiple origins of gender dimorphism.

We infer phylogenetic relationships among Lycium, Grabowskia, and the monotypic Phrodus microphyllus, using DNA sequence data from the nuclear granule-bound starch synthase gene (GBSSI, waxy) and the chloroplast region trnT-trnF. This is the first comprehensive molecular phylogenetic study of tribe Lycieae (Solanaceae). In addition to providing an understanding of evolutionary relationships, we use the phylogenetic hypotheses to frame our studies of breeding system transitions, floral and fruit evolution, and biogeographical patterns within Lycieae. Whereas Lycium is distributed worldwide, Phrodus and the majority of Grabowskia species are restricted to South America. Tribe Lycieae is strongly supported as monophyletic, but Lycium likely includes both Grabowskia and Phrodus. Results also suggest a single dispersal event from the Americas to the Old World, and frequent dispersal between North and South America. The diversity of fruit types in Lycieae is discussed in light of dispersal patterns and recent work on fruit evolution across Solanaceae. Dimorphic gender expression has been studied previously within Lycium, and results indicate that transitions in sexual expression are convergent, occurring multiple times in North America (a revised estimate from previous studies) and southern Africa.

Evolution of sexual dimorphism in bill size and shape of hermit hummingbirds (Phaethornithinae): a role for ecological causation

Unambiguous examples of ecological causation of sexual dimorphism are rare, and the best evidence involves sexual differences in trophic morphology. We show that moderate female-biased sexual dimorphism in bill curvature is the ancestral condition in hermit hummingbirds (Phaethornithinae), and that it is greatly amplified in species such as Glaucis hirsutus and Phaethornis guy, where bills of females are 60 per cent more curved than bills of males. In contrast, bill curvature dimorphism is lost or reduced in a lineage of short-billed hermit species and in specialist Eutoxeres sicklebill hermits. In the hermits, males tend to be larger than females in the majority of species, although size dimorphism is typically small. Consistent with earlier studies of hummingbird feeding performance, both raw regressions of traits and phylogenetic independent contrasts supported the prediction that dimorphism in bill curvature of hermits is associated with longer bills. Some evidence indicates that differences between sexes of hermit hummingbirds are associated with differences in the use of food plants. We suggest that some hermit hummingbirds provide model organisms for studies of ecological causation of sexual dimorphism because their sexual dimorphism in bill curvature provides a diagnostic clue for the food plants that need to be monitored for studies of sexual differences in resource use.

A TALE OF TWO CONTINENTS: BAKER'S RULE AND THE MAINTENANCE OF SELF-INCOMPATIBILITY IN LYCIUM (SOLANACEAE)

Abstract Over 50 years ago, Baker (1955, 1967) suggested that self-compatible species were more likely than self-incompatible species to establish new populations on oceanic islands. His logic was straightforward and rested on the assumption that colonization was infrequent; thus, mate limitation favored the establishment of self-fertilizing individuals. In support of Bakers rule, many authors have documented high frequencies of self-compatibility on islands, and recent work has solidified the generality of Bakers ideas. The genus Lycium (Solanaceae) has ca. 80 species distributed worldwide, and phylogenetic studies suggest that Lycium originated in South America and dispersed to the Old World a single time. Previous analyses of the S-RNase gene, which controls the stylar component of self-incompatibility, have shown that gametophytically controlled self-incompatibility is ancestral within the genus, making Lycium a good model for investigating Bakers assertions concerning reproductive assurance following oceanic dispersal. Lycium is also useful for investigations of reproductive evolution, given that species vary both in sexual expression and the presence of self-incompatibility. A model for the evolution of gender dimorphism suggests that polyploidy breaks down self-incompatibility, leading to the evolution of gender dimorphism, which arises as an alternative outcrossing mechanism. There is a perfect association of dimorphic gender expression, polyploidy, and self-compatibility (vs. cosexuality, diploidy, and self-incompatibility) among North American Lycium. Although the association between ploidy level and gender expression also holds for African Lycium, to date no studies of mating systems have been initiated in Old World species. Here, using controlled pollinations, we document strong self-incompatibility in two cosexual, diploid species of African Lycium. Further, we sequence the S-RNase gene in 15 individuals from five cosexual, diploid species of African Lycium and recover 24 putative alleles. Genealogical analyses indicate reduced trans-generic diversity of S-RNases in the Old World compared to the New World. We suggest that genetic diversity at this locus was reduced as a result of a founder event, but, despite the bottleneck, self-incompatibility was maintained in the Old World. Maximum-likelihood analyses of codon substitution patterns indicate that positive Darwinian selection has been relatively strong in the Old World, suggesting the rediversification of S-RNases following a bottleneck. The present data thus provide a dramatic exception to Bakers rule, in addition to supporting a key assumption of the Miller and Venable (2000) model, namely that self-incompatibility is associated with diploidy and cosexuality.

FLORAL MORPHOMETRICS AND THE EVOLUTION OF SEXUAL DIMORPHISM IN LYCIUM (SOLANACEAE)

Abstract.— Plants of Lycium californicum, L. exsertum, and L. fremontii produce flowers that are either male‐sterile (female) or hermaphroditic, and populations are morphologically gynodioecious. As is commonly found in gynodioecious species, flowers on female plants are smaller than those on hermaphrodites for a number of floral traits. Floral size dimorphism has often been hypothesized to be the result of either a reduction in female flower size that allows reallocation to greater fruit and seed production, or an increase in hermaphroditic flower size due to the increased importance of pollinator attraction and pollen export for hermaphroditic flowers. We provide a test of these two alternatives by measuring 11 floral characters in eight species of Lycium and using a phylogeny to reconstruct the floral size shifts associated with the evolution of gender dimorphism. Our analyses suggest that female flowers are reduced in size relative to the ancestral condition, whereas flowers on hermaphrodites have changed only slightly in size. Female and hermaphroditic flowers have also diverged both from one another and from ancestral cosexual species in several shape characteristics. We expected sexual dimorphism to be similar among the three dimorphic taxa, as gender dimorphism evolved only a single time in the ancestor of the American dimorphic lineage. While the floral sexual dimorphism is broadly similar among the three dimorphic species, there are some species‐specific differences. For example, L. exsertum has the greatest floral size dimorphism, whereas L. fremontii had the greatest size‐independent dimorphism in pistil characters. To determine the degree to which phylogenetic uncertainty affected reconstruction of ancestral character states, we performed a sensitivity analysis by reconstructing ancestral character states on alternative topologies. We argue that investigations such as this one, that examine floral evolution from an explicitly phylogenetic perspective, provide new insights into the study of the evolution of floral sexual dimorphism.

Association of ploidy and sexual system in Lycium californicum (Solanaceae).

Abstract In North American Lycium (Solanaceae), the evolution of gender dimorphism has been proposed as a means of restoring outcrossing after polyploidization causes the loss of self‐incompatibility. Previous studies of this process in Lycium focused on comparisons between species that differ in ploidy. We examined intraspecific variation in floral morphology and DNA content in populations of L. californicum to determine correlations between sexual system and cytotype. We also used nuclear ITS and GBSSI sequence data to determine whether diploid and polyploid forms represent the same phylogenetic species, and the phylogeographic relationships among populations and ploidy levels. Within populations, no variation in ploidy was found, although among populations there was a perfect correspondence between sexual system and cytotype. Diploid populations were all hermaphroditic, whereas tetraploid populations were all gender dimorphic. There was no clear geographic pattern to the occurrence of diploid and tetraploid forms. Phylogenetic analysis confirms that L. californicum, regardless of ploidy, forms a monophyletic group within the genus Lycium. Sequences from diploid and polyploid individuals did not form reciprocally monophyletic clades, indicating either multiple gains of polyploidy, ongoing gene flow between cytotypes, or lack of lineage sorting since the evolution of polyploidy. The correspondence between ploidy and sex expression is consistent with the hypothesis that polyploidization triggers the evolution of gender dimorphism in this and other Lycium species.

Architectural effects mimic floral sexual dimorphism in Solanum (Solanaceae)

Factors underlying apparent floral sexual dimorphism were examined in six species of andromonoecious Solanum section Lasiocarpa (Solanaceae). Both multivariate and univariate analyses show that hermaphroditic flowers are significantly larger than staminate flowers for all features measured. Thus, flowers could be characterized as sexually size dimorphic. However, when size variation due to flower position (architecture) is controlled experimentally, differences between the floral genders for the nongynoecial characters disappear; there is no difference in corolla or androecium size. Staminate flowers appear to be generally smaller than hermaphroditic flowers, not because of any difference related to primary sexual function, but because they tend to occur in the distal regions of each inflorescence. In contrast, significant differences between hermaphroditic and staminate flowers for primary female traits (ovary, style, and stigma) remain after controlling for position: the two floral types are truly dimorphic for these characters. We show that consideration of architectural effects can direct and refine hypotheses concerning the evolution of andromonoecy. More generally, if architectural effects on flower size are common among taxa with unisexual flowers, then these effects may contribute to the common perception of size dimorphism in taxa with unisexual flowers.

Correlated evolution of fruit size and sexual expression in andromonoecious Solanum sections Acanthophora and Lasiocarpa (Solanaceae).

Andromonoecy is hypothesized to evolve as a mechanism enabling plants to independently allocate resources to female and male function. If staminate flower production is a mechanism to regulate allocation to female function (i.e., fruit production), then large-fruited species should be more strongly andromonoecious than smaller-fruited taxa because more resources are required to mature large fruit. We combined phylogenetically independent contrast analyses with extensive phenotypic characterization under common greenhouse conditions to examine the predicted relationship between fruit mass and the strength of andromonoecy among 13 species in Solanum sections Acanthophora and Lasiocarpa. The strength of andromonoecy, defined as the proportion of staminate flowers produced within inflorescences, was significantly and positively associated with fruit mass in both naïve and phylogenetically independent analyses. Our results are consistent with the hypothesis that andromonoecy functions as a mechanism to regulate allocation to female function and suggest that the strength of andromonoecy is also associated with resource limitation. In general, we find that strong andromonoecy appears to arise via reductions in hermaphroditic flower number. However, increases in staminate flowers have also contributed to transitions to strong andromonoecy in certain species. Finally, our analyses identified a suite of correlated characters (flower size, ovary width, fruit mass) that are associated with changes in the sexual expression of andromonoecy.

Out of America to Africa or Asia: Inference of dispersal histories using nuclear and plastid DNA and the S-RNase self-incompatibility locus

The plant genus Lycium (Solanaceae) originated in the Americas and includes approximately 85 species that are distributed worldwide. The vast majority of Old World species occur in southern Africa and eastern Asia. In this study, we examine biogeographic relationships among Old World species using a phylogenetic approach coupled with molecular evolutionary analyses of the S-RNase self-incompatibility gene. The phylogeny inferred from nuclear granule-bound starch synthase I (GBSSI), nuclear conserved ortholog set II (COSII) marker C2_At1g24360, and plastid spacer data (trnH-pbsA, trnD(GUC)-trnT(GGU), rpl32-trnL(UAG), and ndhF-rpl32) includes a clade of eastern Asian Lycium nested within the African species, suggesting initial dispersal from the Americas to Africa, with subsequent dispersal to eastern Asia. Molecular dating estimates suggest that these dispersal events occurred relatively recently, with dispersal from the Americas to Africa approximately 3.64 Ma (95% highest posterior density [HPD]: 1.58-6.27), followed by subsequent dispersal to eastern Asia approximately 1.21 Ma (95% HPD: 0.32-2.42). In accordance, the S-RNase genealogy shows that S-RNases isolated from Old World species are restricted to four lineages, a subset of the 14 lineages including S-RNases isolated from New World Lycium species, supporting a bottleneck of S-RNase alleles concomitant with a single dispersal event from the Americas to the Old World. Furthermore, the S-RNase genealogy is also consistent with dispersal of Lycium from Africa to Asia, as eastern Asian alleles are restricted to a subset of the lineages that also include African alleles. Such a multilocus approach, including complementary data from GBSSI, COSII, plastid spacer regions, and S-RNase, is powerful for understanding dispersal histories of closely related species.

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.

Do Multiple Tortoises Equal a Hare? The Utility of Nine Noncoding Plastid Regions for Species-Level Phylogenetics in Tribe Lycieae (Solanaceae)

Abstract The identification of plastid DNA markers that provide sufficient phylogenetic resolution at the species and population levels is an important challenge for plant systematics. This is mainly due to the relatively slow rate of evolution of the plastid genome. In this study, we examine the utility of several plastid DNA regions for phylogenetic inference at low taxonomic levels in tribe Lycieae (Solanaceae). The regions employed here previously provided considerable numbers of potentially informative characters in investigations of sequence variation across the plastid genome, and one region (trnH-psbA) has been advocated for use in DNA barcoding. We sequenced nine noncoding plastid DNA regions (∼8,400 bp) for a diverse sample of Lycium species and Phrodus microphyllus (tribe Lycieae), as well as the outgroup Nolana, and included published sequences from the distant outgroup Atropa. The nine regions varied with regard to their phylogenetic utility, as measured by the numbers of variable and parsimony informative characters and informative insertions/deletions. We advocate a combination of three regions, including trnDGUC—trnTGGU, rpl32—trnLUAG, and ndhF—rpl32, for phylogenetic studies at the infrageneric or tribal level in Solanaceae. Collectively, these three plastid DNA regions had >100 variable characters across 24 taxa, with 72 parsimony informative characters, and 10 phylogenetically informative indels. Future studies should explore these three noncoding markers for low level phylogenetic questions in other taxonomic groups.