Time-calibrated phylogeny of the woody Australian genus Hakea (Proteaceae) supports multiple origins of insect-pollination among bird-pollinated ancestors

Fossil pollen resolves origin of the South African Proteaceae as transcontinental not transoceanic

BACKGROUND AND AIMS

The prevailing view from the areocladogenesis of molecular phylogenies is that the iconic South African Cape Proteaceae (subfamily Proteoideae) arrived from Australia across the Indian Ocean during the Late Cretaceous (100-65 million years ago, Ma). Since fossil pollen indicates that the family probably arose in North-West Africa during the Early Cretaceous, an alternative view is that it migrated to the Cape from North-West-Central Africa. The plan therefore was to collate fossil pollen records throughout Africa to determine if they are consistent with an African (para-autochthonous) origin for the Cape Proteaceae, and to seek further support from other palaeo-disciplines.

METHODS

We used palynology (identity, date and location of records), molecular phylogeny and chronogram preparation, biogeography of plate tectonics, and palaeo-atmospheric and ocean circulation models.

KEY RESULTS

Our collation of the rich assemblage of Proteaceae palynomorphs stretching back to 107 Ma (Triorites africaensis) in North-West Africa showed its progressive overland migration to the Cape by 75-65 Ma. No key palynomorphs recorded in Australia-Antarctica have morphological affinities with African fossils but specific clade assignment of the pre-Miocene records is not currently possible. The Cape Proteaceae encompass three molecular-based clades (tribes) whose most recent apparent ancestors are sisters to those in Australia. However, our chronogram shows that the major Adenanthos/Leucadendron-related clade, originating 54-34 Ma, would have 'arrived' too late as species with Proteaceae affinities were already present ~20 million years earlier. The Franklandia/Protea-related clade arose 118-81 Ma so its distinctive pollen should have been the foundation for the scores of palynomorphs recorded at 100-80 Ma, but it was not. Also, the prevailing winds and ocean currents trended away from South Africa rather than towards, as the 'out-of-Australia' hypothesis requires. Based on the evidence assembled here, we list three points favouring an Australian origin and nine against; four points favouring an Antarctic origin and seven against; and nine points favouring a North-West-Central African origin and three against.

CONCLUSIONS

We conclude that a gradual migration of the Proteaceae from North-West-Central Africa southeast→south→southwest to the Cape and its surroundings occurred via adaptation and speciation during the period 95-70 Ma. We caution that incorrect conclusions may be drawn from literal interpretations of molecular phylogenies that neglect the fossil record and do not recognize the possible confounding effects of selection under matched environments leading to parallel evolution and extinction of bona fide sister clades.

Distinctive Arbutin-Containing Markers: Chemotaxonomic Significance and Insights into the Evolution of Proteaceae Phytochemistry

Natural products isolation studies of eight endemic Tasmanian Proteaceae species - Agastachys odorata, Persoonia juniperina, Hakea megadenia, Hakea epiglottis, Orites diversifolius, Orites acicularis, Orites revolutus, and Telopea truncata - and three endemic Australian Proteaceae species Banksia serrata, Banksia praemorsa, and Banksia marginata were undertaken. Two previously unreported glycoside-derived natural products were identified, in addition to four other tremendously rare arbutin esters. The results of this study provide further evidence consistent with the proposal that these distinctive arbutin esters represent markers that can provide valuable insights into the chemical evolution of plant species within the family Proteaceae.

Ecological interactions shape the evolution of flower color in communities across a temperate biodiversity hotspot

Processes driving the divergence of floral traits may be integral to the extraordinary richness of flowering plants and the assembly of diverse plant communities. Several models of pollinator-mediated floral evolution have been proposed; floral divergence may (i) be directly involved in driving speciation or may occur after speciation driven by (ii) drift or local adaptation in allopatry or (iii) negative interactions between species in sympatry. Here, we generate predictions for patterns of trait divergence and community assembly expected under these three models, and test these predictions in Hakea (Proteaceae), a diverse genus in the Southwest Australian biodiversity hotspot. We quantified functional richness for two key floral traits (pistil length and flower color), as well as phylogenetic distances between species, across ecological communities, and compared these to patterns generated from null models of community assembly. We also estimated the statistical relationship between rates of trait evolution and lineage diversification across the phylogeny. Patterns of community assembly suggest that flower color, but not floral phenology or morphology, or phylogenetic relatedness, is more divergent in communities than expected. Rates of lineage diversification and flower color evolution were negatively correlated across the phylogeny and rates of flower colour evolution were positively related to branching times. These results support a role for diversity-dependent species interactions driving floral divergence during the Hakea radiation, contributing to the development of the extraordinary species richness of southwest Australia.

Complex interactions underlie the correlated evolution of floral traits and their association with pollinators in a clade with diverse pollination systems

Natural selection by pollinators is an important factor in the morphological diversity and adaptive radiation of flowering plants. Selection by similar pollinators in unrelated plants leads to convergence in floral morphology, or "floral syndromes." Previous investigations into floral syndromes have mostly studied relatively small and/or simple systems, emphasizing vertebrate pollination. Despite the importance of multiple floral traits in plant-pollinator interactions, these studies have examined few quantitative traits, so their co-variation and phenotypic integration have been underexplored. To gain better insights into pollinator-trait dynamics, we investigate the model system of the phlox family (Polemoniaceae), a clade of ∼400 species pollinated by a diversity of vectors. Using a comprehensive phylogeny and large dataset of traits and observations of pollinators, we reconstruct ancestral pollination system, accounting for the temporal history of pollinators. We conduct phylogenetically controlled analyses of trait co-variation and association with pollinators, integrating many analyses over phylogenetic uncertainty. Pollinator shifts are more heterogeneous than previously hypothesized. The evolution of floral traits is partially constrained by phylogenetic history and trait co-variation, but traits are convergent and differences are associated with different pollinators. Trait shifts are usually gradual, rather than rapid, suggesting complex genetic and ecological interactions of flowers at macroevolutionary scales.

Evolution of Bird and Insect Flower Traits in Fritillaria L. (Liliaceae)

Pollinators are often perceived as a primary selective agent influencing flower traits such as colour, size, and nectar properties. The genus Fritillaria L. (Liliaceae), comprising approximately 150 species, is described as generally insect pollinated. However, there are at least three exceptions: two hummingbird-pollinated North American species and one passerine-pollinated Asian species. Despite this variation in pollination, little is known about flower traits that may accompany this shift in fritillaries. In this study, we aimed to assess the attractiveness of the floral traits for (new) pollinators and track the evolution of flowers traits in the context of a shift in the principal pollinator. Therefore, we studied 14 flower traits related to the pollination in 60 Fritillaria species and traced the evolutionary trajectory of these traits. We used a phylogenetic tree of the genus, based on five DNA markers (matK, rpl16, and rbcL, 18S, and ITS) to reconstruct the ancestral state of studied flower traits. The results show that in bird-pollinated species several new traits evolved. For example, flower colouration, nectar sugar, and amino acid concentration and composition fulfil the criteria of ornithophilous flowers, although flower traits do not exclude insect pollinators in bird-pollinated fritillaries. Interestingly, we recorded potential reversals from bird to insect pollination. Our analysis, showing a broad study of flower traits among closely related species in the context of pollinator shift, serves as a starting point for future work exploring the genetic and physiological mechanisms controlling flower traits in the genus Fritillaria.

Freezing and water availability structure the evolutionary diversity of trees across the Americas

The historical course of evolutionary diversification shapes the current distribution of biodiversity, but the main forces constraining diversification are still a subject of debate. We unveil the evolutionary structure of tree species assemblages across the Americas to assess whether an inability to move or an inability to evolve is the predominant constraint in plant diversification and biogeography. We find a fundamental divide in tree lineage composition between tropical and extratropical environments, defined by the absence versus presence of freezing temperatures. Within the Neotropics, we uncover a further evolutionary split between moist and dry forests. Our results demonstrate that American tree lineages tend to retain their ancestral environmental relationships and that phylogenetic niche conservatism is the primary force structuring the distribution of tree biodiversity. Our study establishes the pervasive importance of niche conservatism to community assembly even at intercontinental scales.

Phylogeny, evolution, and biogeographic history of Calandrinia (Montiaceae)

PREMISE OF THE STUDY

Calandrinia are small, succulent herbs that vary broadly in habitat, morphology, life history, and photosynthetic metabolism. The lineage is placed within the Montiaceae, which in turn is sister to the rest of the Portulacineae (Caryophyllales). Calandrinia occupy two distinct biogeographic regions, one in the Americas (~14 species), and one in Australia (~74 species). Past analyses of the Montiaceae present conflicting hypotheses for the phylogenetic placement and monophyly of Calandrinia, and to date, there has been no molecular phylogenetic analysis of the Australian species.

METHODS

Using a targeted gene enrichment approach, we sequenced 297 loci from multiple gene families across the Montiaceae, including all named and 16 putative new species of Australian Calandrinia, and the enigmatic monotypic genus Rumicastrum.

KEY RESULTS

All data sets and analyses reject the monophyly of Calandrinia, with Australian and New World Calandrinia each comprising distinct and well-supported clades, and Rumicastrum nested within Australian Calandrinia. We provide the first well-supported phylogeny for Australian Calandrinia, which includes all named species and several phrase-named taxa.

CONCLUSIONS

This study brings much needed clarity to relationships within Montiaceae and confirms that New World and Australian Calandrinia do not form a clade. Australian Calandrinia is a longtime resident of the continent, having diverged from its sister lineage ~30 Ma, concurrent with separation of Australia from Antarctica. Most diversification occurred during the middle Miocene, with lowered speciation and/or higher extinction rates coincident with the establishment of severe aridity by the late Miocene.

Characterization of CYCLOIDEA-like genes in Proteaceae, a basal eudicot family with multiple shifts in floral symmetry

BACKGROUND AND AIMS

The basal eudicot family Proteaceae (approx. 1700 species) shows considerable variation in floral symmetry but has received little attention in studies of evolutionary development at the genetic level. A framework for understanding the shifts in floral symmetry in Proteaceae is provided by reconstructing ancestral states on an upated phylogeny of the family, and homologues of CYCLOIDEA (CYC), a key gene for the control of floral symmetry in both monocots and eudicots, are characterized.

METHODS

Perianth symmetry transitions were reconstructed on a new species-level tree using parsimony and maximum likelihood. CYC-like genes in 35 species (31 genera) of Proteaceae were sequenced and their phylogeny was reconstructed. Shifts in selection pressure following gene duplication were investigated using nested branch-site models of sequence evolution. Expression patterns of CYC homologues were characterized in three species of Grevillea with different types of floral symmetry.

KEY RESULTS

Zygomorphy has evolved 10-18 times independently in Proteaceae from actinomorphic ancestors, with at least four reversals to actinomorphy. A single duplication of CYC-like genes occurred prior to the diversification of Proteaceae, with putative loss or divergence of the ProtCYC1 paralogue in more than half of the species sampled. No shifts in selection pressure were detected in the branches subtending the two ProtCYC paralogues. However, the amino acid sequence preceding the TCP domain is strongly divergent in Grevillea ProtCYC1 compared with other species. ProtCYC genes were expressed in developing flowers of both actinomorphic and zygomorphic Grevillea species, with late asymmetric expression in the perianth of the latter.

CONCLUSION

Proteaceae is a remarkable family in terms of the number of transitions in floral symmetry. Furthermore, although CYC-like genes in Grevillea have unusual sequence characteristics, they display patterns of expression that make them good candidates for playing a role in the establishment of floral symmetry.

Paraphyly changes understanding of timing and tempo of diversification in subtribe Hakeinae (Proteaceae), a giant Australian plant radiation

PREMISE OF THE STUDY

Subtribe Hakeinae (526 spp.) represents a large Australian plant radiation central to our understanding of that flora's evolution and ecology. It contains Grevillea-the third largest plant genus in Australia and a group inferred to have among the highest diversification rates in the angiosperms. However, we lack a robust phylogenetic framework for understanding subtribe Hakeinae and recognize that Grevillea lacks an unambiguous synapomorphy supporting its monophyly.

METHODS

We used four plastid and one nuclear DNA region from a taxonomically even sampling of a third of the species to infer a time-calibrated phylogeny of Hakeinae and absolute diversification rates of major clades. We developed the R package addTaxa to add unsampled taxa to the tree for diversification rate inference.

KEY RESULTS

Grevillea is paraphyletic with respect to Hakea and Finschia. Under most parameter combinations, Hakea contains the major clade with the highest diversification rate in Hakeinae, rather than Grevillea. The crown age of the Grevillea+Hakea+Finschia crown group is about double that of prior estimates.

CONCLUSIONS

We demonstrate that the paraphyly of Grevillea considerably enlarges the number of Australian descendants from its most recent common ancestor but has also misled investigators who considered a single operational taxonomic unit as adequate to represent the genus for inferences of diversification rate and timing. Our time-calibrated phylogeny can form the basis of future evolutionary, comparative ecology, and biogeography studies involving this large Australian plant radiation, as well as nomenclatural changes.

Seed size, fecundity and postfire regeneration strategy are interdependent in Hakea

Seed size is a key functional trait that affects plant fitness at the seedling stage and may vary greatly with species fruit size, growth form and fecundity. Using structural equation modelling (SEM) and correlated trait evolution analysis, we investigated the interaction network between seed size and fecundity, postfire regeneration strategy, fruit size, plant height and serotiny (on-plant seed storage) among 82 species of the woody shrub genus, Hakea, with a wide spectrum of seed sizes (2–500 mg). Seed size is negatively correlated with fecundity, while fire-killed species (nonsprouters) produce more seeds than resprouters though they are of similar size. Seed size is unrelated to plant height and level of serotiny while it scales allometrically with fruit size. A strong phylogenetic signal in seed size revealed phylogenetic constraints on seed size variation in Hakea. Our analyses suggest a causal relationship between seed size, fecundity and postfire regeneration strategy in Hakea. These results demonstrate that fruit size, fecundity and evolutionary history have had most control over seed size variation among Hakea species.

Environmental adaptation in stomatal size independent of the effects of genome size

Cell sizes are linked across multiple tissues, including stomata, and this variation is closely correlated with genome size. These associations raise the question of whether generic changes in cell size cause suboptimal changes in stomata, requiring subsequent evolution under selection for stomatal size. We tested the relationships among guard cell length, genome size and vegetation type using phylogenetically independent analyses on 67 species of the ecologically and structurally diverse family, Proteaceae. We also compared how genome and stomatal sizes varied at ancient (among genera) and more recent (within genus) levels. The observed 60-fold range in genome size in Proteaceae largely reflected the mean chromosome size. Compared with variation among genera, genome size varied much less within genera (< 6% of total variance) than stomatal size, implying evolution in stomatal size subsequent to changes in genome size. Open vegetation and closed forest had significantly different relationships between stomatal and genome sizes. Ancient changes in genome size clearly influenced stomatal size in Proteaceae, but adaptation to habitat strongly modified the genome-stomatal size relationship. Direct adaptation to the environment in stomatal size argues that new proxies for past concentrations of atmospheric CO2 that incorporate stomatal size are superior to older models based solely on stomatal frequency.

What has molecular systematics contributed to our knowledge of the plant family Proteaceae?

Molecular systematics has revolutionized our understanding of the evolution of the Proteaceae. Phylogenetic relationships have been reconstructed down to generic level and below from alignments of chloroplast and nuclear DNA sequences. These trees have enabled the monophyly of all subfamilies, tribes, and subtribes to be rigorously tested and the construction of a new classification of the family at these ranks. Molecular data have also played a major part in testing the monophyly of genera and infrageneric taxa, some of which have been recircumscribed as a result. Molecular trees and chronograms have been used to test numerous previously postulated biogeographic and evolutionary hypotheses, some of which have been modified or abandoned as a result. Hypotheses that have been supported by molecular phylogenetic trees and chronograms include the following: that the proteaceous pattern of repeated disjunct distributions across the southern hemisphere is partly the result of long-distance dispersal; that high proteaceous diversity in south-western Australia and the Cape Floristic Region of South Africa is due to high diversification rates in some clades but is not an evolutionary response to Mediterranean climates; that the sclerophyllous leaves of many shrubby members of the family are not adaptations to dry environments but for protecting mesophyll in brightly illuminated habitats; that deeply encrypted foliar stomata are adaptations for minimizing water loss in dry environments; and that Protea originated in the Cape Floristic Region of South Africa and that one of its subclades has greatly expanded its distribution into tropical savannas. Reconstructing phylogeny down to species level is now the main goal of molecular systematists of the Proteaceae. The biggest challenge in achieving this task will be resolving species trees from numerous gene trees in complexes of closely related species.

Climate drives vein anatomy in Proteaceae

PREMISE OF STUDY

The mechanisms by which plants tolerate water deficit are only just becoming clear. One key factor in drought tolerance is the ability to maintain the capacity to conduct water through the leaves in conditions of water stress. Recent work has shown that a simple feature of the leaf xylem cells, the cube of the thickness of cell walls divided by the lumen width (t/b)(3), is strongly correlated with this ability.

METHODS

Using ecologically, phylogenetically, and anatomically diverse members of Proteaceae, we tested the relationships between (t/b)(3) and climate, leaf mass per unit area, leaf area, and vein density. To test relationships at high phylogenetic levels (mostly genus), we used phylogenetic and nonphylogenetic single and multiple regressions based on data from 50 species. We also used 14 within-genus species pairs to test for relationships at lower phylogenetic levels.

KEY RESULTS

All analyses revealed that climate, especially mean annual precipitation, was the best predictor of (t/b)(3). The variation in (t/b)(3) was driven by variation in both lumen diameter and wall thickness, implying active control of these dimensions. Total vein density was weakly related to (t/b)(3) but unrelated to either leaf area or climate.

CONCLUSIONS

We conclude that xylem reinforcement is a fundamental adaptation for water stress tolerance and, among evergreen woody plants, drives a strong association between rainfall and xylem anatomy. The strong association between (t/b)(3) and climate cannot be explained by autocorrelation with other aspects of leaf form and anatomy that vary along precipitation gradients.