Marie-Stéphanie Samain

Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages.

Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the “strangest plants in the world”, Hydnora visseri (Hydnoraceae). A ∼15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ∼91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the “temporal specialization hypothesis” (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.

Fossil evidence for low gas exchange capacities for Early Cretaceous angiosperm leaves

Abstract The photosynthetic gas exchange capacities of early angiosperms remain enigmatic. Nevertheless, many hypotheses about the causes of early angiosperm success and how angiosperms influenced Mesozoic ecosystem function hinge on understanding the maximum capacity for early angiosperm metabolism. We applied structure-functional analyses of leaf veins and stomatal pore geometry to determine the hydraulic and diffusive gas exchange capacities of Early Cretaceous fossil leaves. All of the late Aptian–early Albian angiosperms measured possessed low vein density and low maximal stomatal pore area, indicating low leaf gas exchange capacities in comparison to modern ecologically dominant angiosperms. Gas exchange capacities for Early Cretaceous angiosperms were equivalent or lower than ferns and gymnosperms. Fossil leaf taxa from Aptian to Paleocene sediments previously identified as putative stem-lineages to Austrobaileyales and Chloranthales had the same gas exchange capacities and possibly leaf water relations of their living relatives. Our results provide fossil evidence for the hypothesis that high leaf gas exchange capacity is a derived feature of later angiosperm evolution. In addition, the leaf gas exchange functions of austrobaileyoid and chloranthoid fossils support the hypothesis that comparative research on the biology of living basal angiosperm lineages reveals genuine signals of Early Cretaceous angiosperm ecophysiology.

Escaping the lianoid habit: evolution of shrub-like growth forms in Aristolochia subgenus Isotrema (Aristolochiaceae)

UNLABELLED PREMISE OF THE STUDY A large range of growth forms is a notable aspect of angiosperm diversity and arguably a key element of their success. However, few studies within a phylogenetic context have explored how anatomical, developmental, and biomechanical traits are linked with growth form evolution. Aristolochia (∼500 species) consists predominantly of climbers, but a handful of shrub-like species are known from Aristolochia subgenus Isotrema (hereafter, shortened to Isotrema). We test hypotheses proposing that the establishment of functional traits linked to lianescence might limit the ability to evolve structurally diverse growth forms, particularly self-supporting forms. • METHODS We focus on the origin of the shrub habit in Isotrema, from which we sampled representatives from climbing to self-supporting forms. Morphological, anatomical, and biomechanical characters are optimized on a chloroplast- and nuclear-derived phylogeny. • KEY RESULTS Character-state reconstructions revealed that the climbing habit is plesiomorphic in Isotrema and shrub-like forms are derived from climbers. However, shrubs do not constitute a monophyletic group. Both shrubs and climbers show large multiseriate rays, but differ in terms of vessel size and proportion of fibers and soft tissues. • CONCLUSION We suggest that while shrub-like species might have partly escaped from the constraints of life as lianas; their height size and stability are not typical of self-supporting shrubs and trees. Shrubs retained lianoid stem characters that are known to promote flexibility such as ray parenchyma. The transitions to a shrub-like form likely involved relatively simple, developmental changes that may be attributed to heterochronic processes.

Growth Form Evolution in Piperales and Its Relevance for Understanding Angiosperm Diversification: An Integrative Approach Combining Plant Architecture, Anatomy, and Biomechanics

A striking feature of early angiosperm lineages is the variety of life forms and growth forms, which ranges from herbs, aquatic herbs, climbers, and epiphytes to woody shrubs and trees. This morphological and anatomical diversity is arguably one of the factors explaining how angiosperms dominate many ecosystems worldwide. However, just how such a wide spectrum of growth forms has evolved in angiosperms remains unclear. In this review, we investigate patterns of growth form diversification in Piperales, an early-diverging lineage (with stem age estimated at 201–128 Myr ago) and the most morphologically diverse clade among magnoliids. We outline patterns of growth form diversity and architecture as well as the biomechanical significance of developmental characters, such the organization, loss, and gain of woodiness. Asaroideae and Saururaceae are terrestrial as well as semiaquatic to aquatic herbaceous perennials bearing rhizomes. The Aristolochioideae and Piperaceae show higher levels of growth form diversity and biomechanical organization, with complex patterns of increasing or decreasing woodiness and architectural organization. The climbing habit has probably evolved independently in the Aristolochiaceae and Piperaceae, while mechanically unstable shrubs and, less frequently, treelets have evolved several times within these two most species-rich clades. A key developmental character underlying diversity in most Piperales—with the exception of the herbaceous Saruma (Asaroideae)—is the conserved development of the wood cylinder, in which fusiform initials are limited to fascicular cambial initials. The resulting large fraction of raylike tissue in the stem—a highly characteristic feature of woody species in the Piperales—potentially introduced mechanical constraints on the diversification of self-supporting architectures. This was possibly circumvented by the architectural development of repeated, large-diameter meristems in some shrublike habits via sympodial growth. Patterns of growth form evolution within Piperales potentially mirror some of the overall trends observed among early-diverging angiosperms as a whole as well as angiosperms in general. These include profound changes in life form and growth form linked to large-scale transitions in woodiness, diversity of mechanical organization, and shifts in architectural development.

A comparison of leaf crystal macropatterns in the two sister genera Piper and Peperomia (Piperaceae)

PREMISE OF THE STUDY This is the first large-scale study comparing leaf crystal macropatterns of the species-rich sister genera Piper and Peperomia. It focuses on identifying types of calcium oxalate crystals and their macropatterns in leaves of both genera. The Piper results are placed in a phylogenetic context to show evolutionary patterns. This information will expand knowledge about crystals and provide specific examples to help study their form and function. One example is the first-time observation of Piper crystal sand tumbling in chlorenchyma vacuoles. METHODS Herbarium and fresh leaves were cleared of cytoplasmic content and examined with polarizing microscopy to identify types of crystals and their macropatterns. Selected hydrated herbarium and fresh leaf punches were processed for scanning electron microscopy and x-ray elemental analysis. Vibratome sections of living Piper and Peperomia leaves were observed for anatomical features and crystal movement. KEY RESULTS Both genera have different leaf anatomies. Piper displays four crystal types in chlorenchyma-crystal sand, raphides, styloids, and druses, whereas Peperomia displays three types-druses, raphides, and prisms. Because of different leaf anatomies and crystal types between the genera, macropatterns are completely different. Crystal macropattern evolution in both is characterized by increasing complexity, and both may use their crystals for light gathering and reflection for efficient photosynthesis under low-intensity light environments. CONCLUSIONS Both genera have different leaf anatomies, types of crystals and crystal macropatterns. Based on Piper crystals associated with photosynthetic tissues and low-intensity light, further study of their function and association with surrounding chloroplasts is warranted, especially active crystal movement.

Evolution and Systematic Value of Leaf Crystal Macropatterns in the Genus Peperomia (Piperaceae)

Leaves of Peperomia species vary in texture, shape, succulence, lamina size, thickness, coloration, and venation. Each leaf contains only calcium oxalate druses in palisade cells, druses in palisade and raphides in spongy parenchyma, or druses in palisade and prisms in spongy parenchyma. Collectively, these variations create distinct crystal macropatterns. Leaves from 45 species were studied to identify their macropatterns and to compare the macropatterns with molecular data. Microscopic data showed two major crystal macropatterns and five variations of them. All but one species displayed either a single druse in most palisade cells forming one or more uniform crystal layers (81.8%, uniform) or a single druse per cell in palisade cells only above veins forming a reticulate pattern (18.2%, reticulate). Most species (77.3%) did not display any crystals in spongy parenchyma; however, some clades showed spongy parenchyma raphide bundles while others had prisms. Several clades displayed more than one macropattern. Based only on crystal macropatterns, data did not demonstrate a specific phylogenetic trend and failed as synapomorphies for most of the clades. However, crystal macropattern evolution in Peperomia is generally characterized by an increasing complexity of the distribution of druses, raphides, and prisms, with few reversals.

Chasing the hare - Evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae)

BackgroundThe rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and identified a set of nuclear genes that occur in single copy in multiple sequenced angiosperms. The present study is the first to apply genomic sequence of one of these low copy genes, agt1, as a phylogenetic marker for species-level phylogenetics. Its utility is compared to the performance of several coding and non-coding chloroplast loci that have been suggested as most applicable for this taxonomic level. As a model group, we chose Tildenia, a subgenus of Peperomia (Piperaceae), one of the largest plant genera. Relationships are particularly difficult to resolve within these species rich groups due to low levels of polymorphisms and fast or recent radiation. Therefore, Tildenia is a perfect test case for applying new phylogenetic tools.ResultsWe show that the nuclear marker agt1, and in particular the agt1 introns, provide a significantly increased phylogenetic signal compared to chloroplast markers commonly used for low level phylogenetics. 25% of aligned characters from agt1 intron sequence are parsimony informative. In comparison, the introns and spacer of several common chloroplast markers (trnK intron, trnK-psbA spacer, ndhF-rpl32 spacer, rpl32-trnL spacer, psbA-trnH spacer) provide less than 10% parsimony informative characters. The agt1 dataset provides a deeper resolution than the chloroplast markers in Tildenia.ConclusionsSingle (or very low) copy nuclear genes are of immense value in plant phylogenetics. Compared to other nuclear genes that are members of gene families of all sizes, lab effort, such as cloning, can be kept to a minimum. They also provide regions with different phylogenetic content deriving from coding and non-coding parts of different length. Thus, they can be applied to a wide range of taxonomic levels from family down to population level. As more plant genomes are sequenced, we will obtain increasingly precise information about which genes return to single copy most rapidly following gene duplication and may be most useful across a wide range of plant groups.

Is morphology telling the truth about the evolution of the species rich genus Peperomia (Piperaceae)

Peperomia is with approximately 1,600 species one of the species rich angiosperm genera. Several characters on which current infrageneric classifications are based are influenced by parallel evolution. A well-resolved molecular backbone phylogeny of the genus is needed to address evolutionary questions about morphological traits. Based on separate and combined analyses of a morphological data set and three molecular data sets, phylogenetic relationships within Peperomia are investigated with respect to character evolution. The resulting trees from different datasets are highly congruent. Morphological characters are mapped on a combined molecular tree, visualizing the contrast between previously used homoplastic characters and some newly observed characters, that can be used to delimit monophyletic groups. Length mutational events of the chloroplast dataset are coded and plotted on the respective tree, to test if indels support alternative hypothesis of relationships found in the nuclear datasets as well as the overall performance of indels compared with substitutional mutations. Our findings indicate that length distribution of indels is highest among five and six bp events. Autapomorphic and synapomorphic length mutations are most frequent in both insertions and deletions and are also more frequent independent of the length of the mutation. Concluding, independent of the length, mutations are of phylogenetic importance and should not be disregarded. None of the homoplastic indels turn into synapomorphic indels, supporting the different topology of the nrDNA tree but indicate areas of molecular evolution in favour of length mutations resulting in independent events.

Major trends in stem anatomy and growth forms in the perianth-bearing Piperales, with special focus on Aristolochia

BACKGROUND AND AIMS The order Piperales has the highest diversity of growth forms among the earliest angiosperm lineages, including trees, shrubs, climbers and herbs. However, within the perianth-bearing Piperales (Asarum, Saruma, Lactoris, Hydnora, Prosopanche, Thottea and Aristolochia), climbing species only occur in the most species-rich genus Aristolochia. This study traces anatomical and morphological traits among these lineages, to detect trends in growth form evolution and developmental processes. METHODS Transverse stem sections of different developmental stages of representatives of Asarum, Saruma, Lactoris, Hydnora, Thottea and Aristolochia were compared and anatomical traits were linked to growth form evolution. Biomechanical properties of representative climbers were determined in three-point bending tests and are discussed based on the anatomical observations. Growth form evolution of the perianth-bearing Piperales was reconstructed by ancestral character state reconstruction using Mesquite. KEY RESULTS While species of Asarum and Saruma are exclusively herbaceous, species of the remaining genera show a higher diversity of growth habit and anatomy. This growth form diversity is accompanied by a more complex stem anatomy and appropriate biomechanical properties. The ancestral growth form of the perianth-bearing Piperales is reconstructed with either a shrub-like or herbaceous character state, while the following three backbone nodes in the reconstruction show a shrub-like character state. Accordingly, the climbing habit most probably evolved in the ancestor of Aristolochia. CONCLUSIONS Since the ancestor of the perianth-bearing Piperales has been reconstructed with a herb- or shrub-like habit, it is proposed that the climbing habit is a derived growth form, which evolved with the diversification of Aristolochia, and might have been a key feature for its diversification. Observed anatomical synapomorphies, such as the perivascular fibres in Lactoris, Thottea and Aristolochia, support the phylogenetic relationship of several lineages within the perianth-bearing Piperales. In addition, the hypothesis that the vegetative organs of the holoparasitic Hydnoraceae are most probably rhizomes is confirmed.

Application of the phylogenetic informativeness method to chloroplast markers: a test case of closely related species in tribe Hydrangeeae (Hydrangeaceae).

In evolutionary biology appropriate marker selection for the reconstruction of solid phylogenetic hypotheses is fundamental. One of the most challenging tasks addresses the appropriate choice of genomic regions in studies of closely related species. Robust phylogenetic frameworks are central to studies dealing with questions ranging from evolutionary and conservation biology, biogeography to plant breeding. Phylogenetic informativeness profiles provide a quantitative measure of the phylogenetic signal in markers and therefore a method for locus prioritization. The present work profiles phylogenetic informativeness of mostly non-coding chloroplast regions in an angiosperm lineage of closely related species: the popular ornamental tribe Hydrangeeae (Hydrangeaceae, Cornales, Asterids). A recent phylogenetic study denoted a case of resolution contrast between the two strongly supported clades within tribe Hydrangeeae. We evaluate the phylogenetic signal of 13 highly variable plastid markers for estimating relationships within and among the currently recognized monophyletic groups of this tribe. A selection of combined loci based on their phylogenetic informativeness retrieved more robust phylogenetic hypotheses than simply combining individual markers performing best with respect to resolution, nodal support and accuracy or those presenting the highest number of parsimony informative characters. We propose the rpl32-ndhF intergenic spacer (IGS), trnV-ndhC IGS, trnL-rpl32 IGS, psbT-petB region and ndhA intron as the best candidates for future phylogenetic studies in Hydrangeeae and potentially in other Asterids. We also contrasted the phylogenetic informativeness of coded indels against substitutions concluding that, despite their low phylogenetic informativeness, coded indels provide additional phylogenetic signal that is nearly free of noise. Phylogenetic relationships obtained from our total combined analyses showed improved resolution and nodal support with respect to recently published results.