Phylogenetic position of Mediterranean Astereae and character evolution of daisies (Bellis,Asteraceae) inferred from nrDNA ITS sequences

Phylogenetic analyses of nrITS sequences of Asteraceae revealed that the Bellis group is a natural assemblage comprising all the species of Bellis and Bellium, but not Rhynchospermum. In contrast, we propose to include the genera Bellis, Bellium, and Bellidastrum in the subtribe Bellidinae in the interest of circumscribing natural groups. Our results also suggest an early diversification in the western Mediterranean Basin of two monophyletic lineages, Bellis and Bellium. Three major groups can be distinguished within BELLIS: (1) the B. perennis group, containing five annual and perennial species with three ploidy levels (diploid, octoploid, and decaploid), which are distributed throughout the Mediterranean Basin despite lack of pappus; (2) the Bellis sylvestris group, with five annual and perennial species primarily from the western Mediterranean, in which there are five ploidy levels (diploid, tetraploid, hexaploid, octoploid, and decaploid); and (3) a basal grade consisting of three diploid, perennial species which displays remarkable diversification of morphologies. Striking characteristics, such as an annual life form, polyploidy, and loss of pappus, seem to have occurred in parallel several times and in different geographical areas during the early diversification of Bellis species in the western Mediterranean. Character evolution reconstructions allow us to describe a putative ancestor of the genus Bellis (proto-Bellis).     

The evolutionary origin of a second radiation of annual Castilleja (Orobanchaceae) species in South America: The role of long distance dispersal and allopolyploidy

Considerable attention has been directed toward understanding the wide gaps in range that are common among many groups of closely related organisms. By placing their biology and geography in a phylogenetic context, we may gain a broader knowledge of the series of historical events that have led to present species distributions. In addition to the North American annuals, a second radiation of annual Castilleja species is in Andean Peru and central Chile. Phylogenetic analyses of chloroplast and nuclear DNA regions revealed a complex history for the origin and diversification of annual Castilleja species in South America. In addition to at least three independent long-distance dispersal events from North America, allopolyploidy has played a significant role in this disjunct radiation. Only C. attenuata occurs in both California and South America, and these results support its recent arrival to central Chile. Two Peruvian species are inferred to be allopolyploids; hybridization between annual lineages derived from independent long-distance dispersal events from North America gave rise to C. profunda, and hybridization between South American annual and perennial species gave rise to C. cerroana. The relative importance these events are discussed with reference to the observed morphological, ecological, and distributional patterns.     

Chromosome numbers of Orthocarpus and related monotypic genera (Scrophulariaceae: Subtribe castillejinae)

A chromosome number ofn=12 is reported for the three monotypic genera of subtribe Castillejinae:Clevelandia beldingii, Gentrya racemosa, andOpicopephalus angustifolius. Chromosome numbers ofOrthocarpus correspond mostly with current infrageneric classification. SubgenusTriphysaria hasn=11.Orthocarpus sectionsCastillejoides andCordylanthoides, which are closely related toCastilleja (x=12) and the three monotypic genera above, haven=12 with aneuploid reductions ton=10 inO. linearilobus andn=11 inO. lacerus (a species also withn=12). Tetraploids are found in two species.O. brevistylus (n=24) andO. hispidus (n=12, 24). The polyploid.O. laciniatus (n=36, 48) of Peru is postulated to be of hybrid origin between a species ofCastilleja andOrthocarpus attenuatus. SubgenusOrthocarpus sectionOrthocarpus, which hasn=14 in all species except.O. bracteosus (n=15), stands apart both morphologically and in chromosome number from the remainder of the genus.     

Molecular phylogenetics of the clover genus (Trifolium--Leguminosae)

Trifolium, the clover genus, is one of the largest genera of the legume family. We conducted parsimony and Bayesian phylogenetic analyses based on nuclear ribosomal DNA internal transcribed spacer and chloroplast trnL intron sequences obtained from 218 of the ca. 255 species of Trifolium, representatives from 11 genera of the vicioid clade, and an outgroup Lotus. We confirm the monophyly of Trifolium, and propose a new infrageneric classification of the genus based on the phylogenetic results. Incongruence between the nrDNA and cpDNA results suggests five to six cases of apparent hybrid speciation, and identifies the putative progenitors of the allopolyploids T. dubium, a widespread weed, and T. repens, the most commonly cultivated clover species. Character state reconstructions confirm 2n=16 as the ancestral chromosome number in Trifolium, and infer a minimum of 19 instances of aneuploidy and 22 of polyploidy in the genus. The ancestral life history is hypothesized to be annual in subgenus Chronosemium and equivocal in subgenus Trifolium. Transitions between the annual and perennial habit are common. Our results are consistent with a Mediterranean origin of the genus, probably in the Early Miocene. A single origin of all North and South American species is hypothesized, while the species of sub-Saharan Africa may originate from three separate dispersal events.     

Correlated evolution of self-incompatibility and clonal reproduction in Solanum (Solanaceae)

It has been suggested that clonality provides reproductive assurance in cross-fertilizing species subject to pollen limitation, relieving one of the main selective pressures favoring the evolution of self-fertilization. According to this hypothesis, cross-fertilizing species subject to pollen limitation should often be clonal. Here, we investigated the association between clonality and a genetic mechanism enforcing outcrossing, self-incompatibility, in Solanum (Solanaceae). We collected self-incompatibility and clonality information on 87 species, and looked for an association between these two traits. To account for the contribution of shared evolutionary history to this association, we incorporated phylogenetic information from chloroplast (NADH dehydrogenase subunit F) sequence data. We found that self-incompatibility is strongly associated with clonal reproduction: all self-incompatible species reproduce clonally, while the absence of clonality is widespread among self-compatible taxa. The observed correlation persists after taking into account shared phylogenetic history, assumptions about the evolutionary history of self-incompatibility, uncertainty associated with phylogeny estimation, and associations with life history (annual/perennial). Our results are consistent with the hypothesis that clonality provides reproductive assurance, and suggest that the consequences of clonal growth in the evolution of plant reproductive strategies may be more significant than previously thought.     

Climate and life-history evolution in evening primroses (Oenothera, Onagraceae): a phylogenetic comparative analysis

Evolutionary ecologists have long sought to understand the conditions under which perennial (iteroparous) versus annual (semelparous) plant life histories are favored. We evaluated the idea that aridity and variation in the length of droughts should favor the evolution of an annual life history, both by decreasing adult survival and by increasing the potential for high seedling survival via reduced plant cover. We calculated phylogenetically independent contrasts of climate with respect to life history in a clade of winter-establishing evening primroses (sections Anogra and Kleinia; Oenothera; Onagraceae), which includes seven annuals, 12 perennials, and two variable taxa. Climate variables were quantified from long-term records at weather stations near collection localities. To explicitly account for phylogenetic uncertainty, contrasts were calculated on a random sample of phylogenetic trees from the posterior distribution of a Bayesian analysis of DNA sequence data. Statements of association are based on comparing the per-tree mean contrast, which has a null expectation of zero, to a set of per-tree mean contrasts calculated on the same trees, after randomizing the climate data. As predicted, increased annual aridity, increased annual potential evapotranspiration, and decreased annual precipitation were associated with transitions to the annual habit, but these trends were not significantly different from the null pattern. Transitions to the annual habit were not significantly associated with increases in one measure of aridity in summer nor with increased summer drought, but they were associated with significantly increased maximum summer temperatures. In winter, increased aridity and decreased precipitation were significantly associated with transitions to the annual habit. Changes in life history were not significantly associated with changes in the coefficient of variation of precipitation, either on an annual or seasonal (summer vs. winter) basis. Though we cannot attribute causality on the basis of a correlational, historical study, our results are consistent with the idea that increased heat and drought at certain times of the year favor the evolution of the annual habit. Increased heat in summer may cause adult survival to decline, while increased aridity and decreased precipitation in the season of seedling recruitment (winter) may favor a drought-avoiding, short-lived annual strategy. Not all of the predicted patterns were observed: the capability for drought-induced dormancy may preclude change in habit in response to summer drought in our study group.     

Phylogenetic analysis of Helianthus (Asteraceae) based on chloroplast DNA restriction site data

 Chloroplast DNA (cpDNA) restriction site data were used to analyze phylogenetic relationships within Helianthus. Data from new samples were consistent with previous results and showed the genus to be a well-defined (11 site changes) lineage within subtribe Helianthinae. The affinities of 2 species, Viguiera similis and V. phenax (V. ludens) that have sometimes been included in Helianthus were shown to lie outside the genus. The two species of Phoebanthus, however, formed a phylogenetic ingroup to the perennial Helianthus. Within the genus, cpDNA data indicated that there are four distinct phylogenetic lineages. Two of the lineages each contained a single, annual species (H. agrestis and H. porteri, respectively). The remaining annual species collectively formed a third lineage (sect. Helianthus). The fourth lineage contained all of the perennial species, including those of Phoebanthus. Within the perennial lineage, there was little variation in restriction site characters. The 3 species of series Pumili formed a paraphyletic group at the base of the perennial lineage, and the 3 species of series Ciliares formed a group that was supported by a single restriction site character. Received: 2 September 1996 / Accepted: 25 October 1996     

Diversification of Lupinus (Leguminosae) in the western New World: derived evolution of perennial life history and colonization of montane habitats

Previous phylogenetic studies of Lupinus (Leguminosae) based on nuclear DNA have shown that the western New World taxa form a monophyletic group representing the majority of species in the genus, with evidence for high rates of recent diversification in South America following final uplift of the Andes 2–4 million years ago (Mya). For this study, three regions of rapidly evolving non-coding chloroplast DNA (trnL intron, trnS–trnG, and trnT–trnL) were examined to estimate the timing and rates of diversification in the western New World, and to infer ancestral states for geographic range, life history, and maximum elevation. The western New World species (5.0–9.3 Mya, 0.6–1.1 spp./My) comprise a basally branching assemblage of annual plants endemic to the lower elevations of western North America, from which two species-rich clades are recently derived: (i) the western North American perennials from the Rocky Mountains, Great Basin, and Pacific Slope (0.7–2.1 Mya, 2.0–5.9 spp./My) and (ii) the predominantly perennial species from the Andes Mountains of South America and highlands of Mexico (0.8–3.4 Mya, 1.4–5.7 spp./My). Bayesian posterior predictive tests for association between life history and maximum elevation demonstrate that perennials are positively correlated with higher elevations. These results are consistent with a series of one or more recent radiations in the western New World, and indicate that rapid diversification of Lupinus coincides with the derived evolution of perennial life history, colonization of montane habitats, and range expansion from North America to South America.     

Chromosomal evolution in Pleurothallidinae (Orchidaceae: Epidendroideae) with an emphasis on the genus Acianthera: chromosome numbers and heterochromatin

In this study, we analysed chromosome number variation and chromomycin A₃/4′,6‐diamidino‐2‐phenylindole (CMA/DAPI) banding patterns in 48 species belonging to 12 genera of subtribe Pleurothallidinae (Orchidaceae) in order to understand the chromosome evolution based on recent phylogenetic hypotheses and taxonomic treatments. All species had small chromosomes, with numbers ranging from 2n = 20 in two Specklinia spp. to 2n = 80 in an unidentified Octomeria sp. In Acianthera, the most highly represented genus in this study, a great diversity of chromosome number and pattern of fluorescent bands was observed, showing heterochromatin accumulation in Acianthera section Sicariae subsection Pectinatae. Interspecific ascending and, mainly, descending dysploidy were the main mechanisms of chromosome number evolution in subtribe Pleurothallidinae. For Pleurothallidinae, x = 20 is suggested as the basic chromosome number, the same suggested for the related subtribe Laeliinae and for the whole tribe Epidendreae. The Brazilian species of the mega‐genus Stelis had chromosomes with small amounts of heterochromatin and chromosome numbers based on x₂ = 16. These are generally divergent from those reported for Andean and Meso‐American species, but in agreement with the monophyletic hypothesis proposed for Stelis spp. with a Brazilian Atlantic distribution. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 102–120.     

Dating and functional characterization of duplicated genes in the apple (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.) by analyzing EST data

Background  

Gene duplication is central to genome evolution. In plants, genes can be duplicated through small-scale events and large-scale duplications often involving polyploidy. The apple belongs to the subtribe Pyrinae (Rosaceae), a diverse lineage that originated via allopolyploidization. Both small-scale duplications and polyploidy may have been important mechanisms shaping the genome of this species.     

Phylogenetic reconstruction of the genus Triptilion (Asteraceae,Nassauvieae) based on nuclear and chloroplast DNA sequences

The genus Triptilion is endemic to central Chile, the Mendoza Province and western Patagonia in Argentina. It is currently composed of seven species: T. achilleae, T. benaventii, T. berteroi, T. capillatum, T. cordifolium, T. gibbosum, and T. spinosum. The main objectives of this paper were to determine the phylogenetic relationships of species of Triptilion. We also traced the evolution of annual and perennial life-forms. Historically a close relationship has been described between genera Triptilion and Nassauvia. Phylogenetic analysis of the genus Triptilion and more closely related genera was undertaken using two nuclear (ITS, ETS) and two chloroplast (trnL-F, rpl32-trnL) markers. The topology of the Bayesian inference tree shows that the genus Triptilion is paraphyletic, because Nassauvia lagascae, the only representative of Nassauvia section Caloptilium grouped with T. achilleae, Clade I. The other species of Triptilion form two clades: Clade II composed of T. cordifolium and T. gibbosum and Clade III that includes T. benaventii, T. berteroi, T. capillatum, and T. spinosum. The genus Triptilion originated and diverged during the Miocene. The results of the life history reconstructions indicate that the common ancestor of Triptilion and Nassauvia was perennial. The annual habit appears to be derived in Triptilion. The life-form of the common ancestor of Triptilion was ambiguous; it may have been annual or perennial.     

Origin and relationships of the tarweed-silversword lineage (Compositae-Madiinae)

Based on results from phylogenetic analyses of nuclear 18S-26S rDNA internal transcribed spacer (ITS) region sequences, we suggest that the monophyletic tarweed and silversword subtribe (Madiinae) is phylogenetically nested among epaleate, x = 19 species of helenioid Heliantheae. Strong bootstrap support (100%) was obtained for a sister-group relationship between Madiinae and Arnica (including Mallotopus and Whitneya) in an analysis including representatives of recognized genera in a principally Californian clade (Madieae sensu Baldwin) identified from a phylogenetic investigation of Heliantheae s.l. (sensu lato) and Eupatorieae. In all minimum-length trees, the robust lineage comprising Madiinae and Arnica (x = 19) is part of a larger clade that also comprises Eatonella s.s. (sensu stricto), Hulsea, and Venegasia, all with x = 19. The phylogenetic position of Madiinae within a group of genera based uniformly on x = 19 leads us to conclude that the modal numbers of n = 7 and n = 8 (and other numbers, as low as n = 4) in Madiinae are the results of extreme dysploidy. Among the x = 19 "arnicoid" taxa, the near-universal characteristics of perenniality (except in the monotypic Eatonella s.s. and a minority of hulseas) and montane or high-latitudinal occurrence (except in the monotypic Venegasia) lead us to suggest that the most recent common ancestor of the tarweeds (a principally annual group of seasonally dry, low-elevation habitats) was probably a montane, herbaceous perennial resembling the unusual subalpine and alpine tarweeds constituting Raillardella s.s. (x = 17), an arnica-like genus. In Madiinae, Raillardella s.s. may be plesiomorphic in habit, capitular and ecological characteristics, and high base chromosome number. Shifts to an annual habit and to low chromosome numbers in Madiinae have been followed by subsequent episodes of polyploidy and descending dysploidy. We conclude that genome evolution in Madiinae has been marked by wide swings in chromosome number that confuse identification of diploids and polyploids.     

Evolutionary history of the arid climate‐adapted Helichrysum (Asteraceae: Gnaphalieae): Cape origin and association between annual life‐history and low chromosome numbers

The basal grade of the large, widely‐distributed Helichrysum‐Anaphalis‐Pseudognaphalium (HAP) clade (Asteraceae, Gnaphalieae) comprises exclusively southern African taxa. These species possess unusual trait combinations relative to the remaining species (a high proportion of annuals, unusual capitulum arrangement, and low base chromosome numbers). A time‐proportional Bayesian phylogenetic hypothesis is generated from nuclear ribosomal sequences from 110 accessions. Ancestral area, life history, and base chromosome number are reconstructed using maximum likelihood, and correlations between life‐history and chromosome number are tested in a phylogenetic framework. The results show that the HAP clade probably originated and experienced initial diversification in the Greater Cape Floristic Region in the Early to Middle Miocene. The ancestor of the HAP clade is inferred to have been perennial with x = 7 base chromosome number. Several independent acquisitions of the annual life‐history are inferred, accompanied by reductions to x = 4 and 5. A single reversal to perennial life history is associated with a subsequent change back to the state of x = 7. Origin and early diversification within the HAP clade follows the pattern of multi‐area seeded radiations within southern Africa, with subsequent migrations to the rest of Africa and the Northern Hemisphere. Occupation of drier habitats with shorter growing seasons may select for the acquisition of a shorter life‐cycle, and our results indicate a strong association between short life‐cycle and reduced chromosome number.     

Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion

Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ～40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large‐scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow.     

Genome-wide investigation reveals high evolutionary rates in annual model plants

Background  

Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials.     

Physical leaf defenses – altered by Zea life‐history evolution,domestication, and breeding – mediate oviposition preference of a specialist leafhopper

Plant anti‐herbivore defenses are known to be affected by life‐history evolution, as well as by domestication and breeding in the case of crop species. A suite of plants from the maize genus Zea (Poaceae) and the specialist herbivore Dalbulus maidis (DeLong & Wolcott) (Hemiptera: Cicadellidae) were used to test the hypothesis that anti‐herbivore defenses are affected by plant life‐history evolution and human intervention through domestication and breeding for high yield. The suite of plants included a maize (Zea mays ssp. mays L.) commercial hybrid, a maize landrace, two populations of the annual Balsas teosinte (Z. mays ssp. parviglumis Iltis & Doebley), and perennial teosinte (Z. diploperennis Iltis, Doebley & Guzman). Leaf toughness, pubescence, and oviposition preference were compared among the suite of host plants looking for effects of transitions in life history (i.e., from perennial to annual life cycle), domestication (i.e., from wild annual to domesticated annual), and breeding (i.e., from landrace to hybrid maize) on defense against D. maidis. Results on leaf toughness suggested that the life‐history and domestication transitions weakened the plant's resistance to penetration by the mouthparts and ovipositor of D. maidis, whereas results on pubescence suggested that this putative defense was strengthened with the breeding transition, contrary to expectations. Results on oviposition preference of D. maidis coincided with the expectation that life‐history and domestication transitions would lead to preference for Balsas teosinte over perennial teosinte, and of landrace maize over Balsas teosinte. Also, a negative correlation suggested that oviposition preference is significantly influenced by leaf toughness. Overall, the results suggested that Zea defenses against the specialist herbivore D. maidis were variably affected by plant life‐history evolution, domestication, and breeding, and that chemical defense may play a role in Zea defense against D. maidis because leaf toughness and pubescence only partially explained its host preferences.     

Correlated evolution of life history and host range in the nonphotosynthetic parasitic flowering plants Orobanche and Phelipanche (Orobanchaceae)

Most members of the nonphotosynthetic parasitic genera Orobanche and Phelipanche (Orobanchaceae) have narrow host ranges, and, as they grow on perennial hosts, are (at least potentially) perennial themselves. A few species, however, have wide host ranges and grow on annual hosts, and are thus (at least facultatively) annuals themselves. Among the latter are the weedy species, which include economically important pest taxa such as Orobanche crenata or Phelipanche aegyptiaca. Using a phylogenetically based maximum likelihood approach, which takes phylogenetic and branch length uncertainty into account, we can show that the life trait host range and life history evolve in a correlated fashion. This supports the hypothesis that parasite specialization is associated with predictable resources (i.e. long-lived hosts) and generalism with unpredictable ones (i.e. short-lived hosts), a pattern often found in animal parasites. The mechanisms and temporal sequence of the life trait changes and their interrelations remain speculative.     

Life history affects the evolution of reproductive isolation among species of Coreopsis (Asteraceae)

The evolution of reproductive isolation within Coreopsis is investigated by integrating phylogenetic data with estimates of pollen viability of plants from inter- and intraspecific crosses. Three different models that predict F1 fitness are compared. The first uses ITS pairwise distances, the second is based on phylogenetic branch lengths derived from DNA sequences, and the third elaborates on the second model by dividing branch length according to reconstructions of the evolution of life history. This is the first study to use phylogenetic branch-length estimates for predicting levels of reproductive isolation. Estimated branch lengths (model 2) predict hybrid fitness more accurately than simply genetic distance (model 1) but only very slightly. This is probably because the two variables are strongly correlated in Coreopsis. Prediction is substantially improved by allowing evolutionary rates to differ between annual and perennial branches (model 3). A bootstrapping procedure indicates that the life-history effect is statistically significant. The more rapid evolution of reproductive isolation within annual species of Coreopsis may be due to differing mechanisms of reproductive isolation, that is, chromosomal rearrangements rather than genetic incompatibilities.     

Life‐history trade‐offs promote the evolution of dioecy

Most dioecious plants are perennial and subject to trade‐offs between sexual reproduction and vegetative performance. However, these broader life‐history trade‐offs have not usually been incorporated into theoretical analyses of the evolution of separate sexes. One such analysis has indicated that hermaphroditism is favoured over unisexuality when female and male sex functions involve the allocation of nonoverlapping types of resources to each sex function (e.g. allocations of carbon to female function vs. allocations of nitrogen to male function). However, some dioecious plants appear to conform to this pattern of resource allocation, with different resource types allocated to female vs. male sex functions. Using an evolutionarily stable strategy approach, we show that life‐history trade‐offs between sexual reproduction and vegetative performance enable the evolution of unisexual phenotypes even when there are no direct resource‐based trade‐offs between female and male sex functions. This result might help explain the preponderance of perennial life histories among dioecious plants and why many dioecious plants with annual life histories have indeterminate growth with ongoing trade‐offs between sexual reproduction and vegetative growth.