Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach

ObjectivesThis study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity.Materials and methodsLineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification.ResultsRate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages.ConclusionsRecent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.

Biodiversity results from origination and extinction, justifying interest in identifying traits that influence this balance. Traits implicated in the success or failure of lineages include dispersal, colonization ability, and geographic range size. We investigated the impact of dispersal and range size on contemporary diversity in the Rosales. We used the multiple-state speciation and extinction (MuSSE) method to explore the effects on genus-level diversification of two genus-level traits (geographic range size and within-genus proclivity to speciate) and two species traits (seed dispersal and growth habit) and the multiple hidden-state speciation and extinction (MuHiSSE) method for species-level associations. Finally, we conducted a PGLS (phylogenetic least-squares) analysis to distinguish between speciation within genera versus origination of new genera. At the species level, animal dispersal enhances diversification rate in both woody and herbaceous lineages, while woody lineages without animal dispersal have higher extinction rates than speciation rates. At the genus level, herbaceous taxa have positive diversification rates regardless of other character states. Diversification rate variation is also explained by two interactions: (1) a three-way interaction between large geographic range, animal-mediated dispersal, and high within-genus species richness, whereby genera possessing all three traits have high diversification rates, and (2) a four-way interaction by which the three-way interaction is stronger in woody genera than in herbaceous genera. Colonization ability may underlie the relationship between dispersal type and range size and may influence past diversification rates by decreasing extinction rates during late Cenozoic climate volatility. Thus, colonization ability could be used to predict future extinction risk to aid conservation.

Flower and fruit characters were measured in ten female, five male and five fruiting male selections of A. deliciosa var deliciosa (A. Chev) Liang and Ferguson. Flowers from female vines had functional pistils, which contained many ovules. Stamens appeared to be fully developed but produced only empty pollen grains. Flowers from male vines had functional stamens that produced high percentages of pollen grains with stainable cytoplasmic contents. Pistils did not contain ovules and were generally small with vestigial styles. Fruiting male vines had both staminate and bisexual flowers. Staminate flowers were similar to those found on strictly male vines. Bisexual flowers produced ovules and stainable pollen. Pistils were smaller than in pistillate flowers. Although the three flower sexes differed in style length, ovary dimensions and ovules per carpel, staminate and bisexual flowers were similar in number of flowers per inflorescence, stamen filament length, pollen stainability, inflorescence rachis length and carpel number, and differed from pistillate flowers in these characters. The three flower sexes had similar sepal and petal numbers. The fruit of fruiting males were considerably smaller than those of females. Low ovule number appears to be the major factor limiting fruit size in the fruiting males studied. Prospects for developing hermaphroditic kiwifruit cultivars through breeding are discussed.

This study investigated the association between floral and fruiting traits in oil tree peony to inform elite breeding and hybrid programmes. Floral and fruiting metrics of Paeonia ostii ‘Fengdanbai’ and Paeonia rockii ‘Zibanbai’ were recorded under natural conditions; data were analysed using independent-samples t-tests, Pearson correlations, stepwise multiple linear regression and membership functions. Paeonia ostii ‘Fengdanbai’ produced more pollen number per flower, but fewer ovules and seeds per fruit than Paeonia rockii ‘Zibanbai’ (p < 0.05). Pollen viability and stigma receptivity followed similar unimodal temporal curves in both taxa. Peak pollen viability occurred on day 3 after anthesis in P. ostii ‘Fengdanbai’ (86.95 ± 1.41%) and on day 2 in P. rockii ‘Zibanbai’ (85.91 ± 2.99%). Optimal stigma receptivity spanned days 3–5 and 2–5 post-anthesis, respectively, yielding a 3-day overlap favourable for synchronous pollination. Seed number per fruit correlated positively with petal number per flower (r = 0.49), ovule number per fruit (r = 0.68) and seed setting rate (r = 0.70, p < 0.01); carpel number also contributed (r = 0.31, p < 0.05). Stepwise multiple regression identified ovule number per fruit and seed setting rate as the most significant predictors of seed number per fruit (p < 0.001), together explaining over 99% of the variation in the model (adjusted R2 = 0.992). Membership function analysis, based on pollen viability, ovule number per fruit, and seed setting rate, suggested that ‘Fengdanbai’ exhibits superior comprehensive performance, though selection indices should be validated across broader germplasm. We propose ovule number per fruit and seed setting rate as primary selection indices, with pollen viability as a supplementary indicator, for consideration in breeding high-yield cultivars.

The role of temperature and its relationship with gibberellic acid in the development of floral organs of tomato (<i>Lycopersicon esculentum</i>)

From forgotten taxon to a missing link? The position of the genus Verhuellia (piperaceae) revealed by molecules.

We present a comparative study of the floral structure and development of Nartheciaceae, a small dioscorealean family consisting of five genera (Aletris, Lophiola, Metanarthecium, Narthecium, and Nietneria). A noticeable diversity existed in nine floral characters. Analyses of their respective character states in the light of a phylogenetic context revealed that the flowers of Nartheciaceae, whose plesiomorphies occur in Aletris and Metanarthecium, have evolved toward in all or part of Lophiola, Narthecium, and Nietneria: (1) loss of a perianth tube; (2) stamen insertion at the perianth base; (3) congenital carpel fusion; (4) loss of the septal nectaries; (5) unilocular style; (6) unfused lateral carpellary margins in the style; (7) flower with the median outer tepal on the abaxial side; (8) flower with moniliform hairs; and (9) flower with weak monosymmetry. We further found that, as the flowers developed, the ovary shifted its position from inferior to superior. As a whole, their structure changes suggest that the Nartheciaceae flowers have evolved in close association with pollination and seed dispersal. By considering inferior ovaries and the presence of septal nectaries as plesiomorphies of Nartheciaceae, we discussed evolution of the ovary position and septal nectaries in all the monocots.

Across angiosperms, variable rates of molecular substitution are linked with life-history attributes associated with woody and herbaceous growth forms. As the number of generations per unit time is correlated with molecular substitution rates, it is expected that rates of phenotypic evolution would also be influenced by differences in generation times. Here, we make the first broad-scale comparison of growth-form-dependent rates of niche evolution. We examined the climatic niches of species on large time-calibrated phylogenies of five angiosperm clades and found that woody lineages have accumulated fewer changes per million years in climatic niche space than related herbaceous lineages. Also, climate space explored by woody lineages is consistently smaller than sister lineages composed mainly of herbaceous taxa. This pattern is probably linked to differences in the rate of climatic niche evolution. These results have implications for niche conservatism; in particular, the role of niche conservatism in the distribution of plant biodiversity. The consistent differences in the rate of climatic niche evolution also emphasize the need to incorporate models of phenotypic evolution that allow for rate heterogeneity when examining large datasets.

How did evolution generate the extraordinary diversity of vertebrates on land? Zero species are known prior to ~380 million years ago, and more than 30,000 are present today. An expansionist model suggests this was achieved by large and unbounded increases, leading to substantially greater diversity in the present than at any time in the geological past. This model contrasts starkly with empirical support for constrained diversification in marine animals, suggesting different macroevolutionary processes on land and in the sea. We quantify patterns of vertebrate standing diversity on land during the Mesozoic–early Paleogene interval, applying sample-standardization to a global fossil dataset containing 27,260 occurrences of 4,898 non-marine tetrapod species. Our results show a highly stable pattern of Mesozoic tetrapod diversity at regional and local levels, underpinned by a weakly positive, but near-zero, long-term net diversification rate over 190 million years. Species diversity of non-flying terrestrial tetrapods less than doubled over this interval, despite the origins of exceptionally diverse extant groups within mammals, squamates, amphibians, and dinosaurs. Therefore, although speciose groups of modern tetrapods have Mesozoic origins, rates of Mesozoic diversification inferred from the fossil record are slow compared to those inferred from molecular phylogenies. If high speciation rates did occur in the Mesozoic, then they seem to have been balanced by extinctions among older clades. An apparent 4-fold expansion of species richness after the Cretaceous/Paleogene (K/Pg) boundary deserves further examination in light of potential taxonomic biases, but is consistent with the hypothesis that global environmental disturbances such as mass extinction events can rapidly adjust limits to diversity by restructuring ecosystems, and suggests that the gradualistic evolutionary diversification of tetrapods was punctuated by brief but dramatic episodes of radiation.

Evolutionary origin of the latitudinal diversity gradient in liverworts

The goal of this PhD project was to study the evolution, systematics and biogeography of two African genera from the pan-tropical Annonaceae family: Isolona and Monodora. Both genera are unique within the family in that the female reproductive parts (or carpels) are fused into a single unit. All other Annonaceae have freely arranged carpels. We investigated the phylogenetic relationships of Isolona and Monodora at the intra-familial and intra-generic levels. In Chapter 2, we explore the influence of priors when using the novel Bayesian based posterior mapping to study the evolution of morphological characters. Up to now, it was unclear if these priors had any influence on the results. Using a family level molecular phylogeny of the Annonaceae, we study the evolution of two morphological characters under different prior values. We show that different prior values will return different results. Thus, inadequate prior values can lead to erroneous conclusions over the evolution of the studied morphological characters. We also indicate a practical way to choose the prior values when using the posterior mapping approach to study morphological character evolution. In Chapter 3, using the posterior mapping approach, we study the evolutionary origins of syncarpy in Annonaceae. The closest relatives of Isolona and Monodora are elucidated. We generate a well resolved phylogeny which included for the first time the majority of African Annonaceae genera. We also study additional morphological and palynological characters relevant to Annonaceae classification in general. Our phylogenetic analyses recover a fully resolved clade comprising twelve endemic African genera, including Isolona and Monodora, which was nested within the so-called long-branch clade. This is the largest and most species-rich clade of African genera identified to date within Annonaceae. Our results indicate that syncarpy arose by fusion of a moderate number of carpels. The alternative hypothesis that syncarpy arose by multiplication of an initial single carpel receives no support. In Chapter 4 we use African Annonaceae as a model family to study the biogeographical aspects of the evolutionary origins of African rain forests. It is generally thought that the large West-Central rain forest blocks was continuous during the Eocene with the now fragmented and smaller forests of East Africa, explaining the strong floristic affinities between both areas. Using dated molecular phylogenies we provide evidence of the recurring break-up and reconnection of this pan-African rain forest during the Oligocene and Miocene. The reconnections allowed for biotic exchange while the break-ups induced speciation enhancing the levels of endemicity, thus providing an explanation for present-day patterns in the distribution and diversity of plants in African rain forests. In Chapter 5, we perform a detailed analysis of pollen morphology within a strongly supported monophyletic group of five African genera, including Isolona and Monodora. We specifically assess if pollen characters are useful for classification purposes within Isolona and Monodora using a species-level molecular phylogeny. The results show a wide pollen morphological diversity. The pollen types defined within Isolona and Monodora provide little taxonomic information for major clades within both genera. However, pollen variation proves useful as a support of phylogenetic relatedness between groups of closely related species. Finally in Chapter 6, a monographic revision of both Isolona and Monodora is presented. Isolona consists of 20 species with five endemic to Madagascar and one newly described species. Monodora has a total of 14 species, three of which were described during this PhD project from Tanzania. Detailed descriptions as well as keys are provided. The conservation status of each species is assessed following the IUCN recommendations. Just under half of the total number of species from both genera is assigned to some level of threat (12 species or 60% in Isolona and four species or 28% in Monodora).

Abstract—Tovomita is a Neotropical clade of Clusiaceae that includes 52 species widely distributed throughout the Amazon, Atlantic, Antilles, and Chocoan/southern Mesoamerican rainforests. Species-level relationships within Tovomita remain largely unexplored, thus hindering our understanding of their biogeography and the evolution of key morphological characters in the genus. Here, we inferred a plastid genome phylogeny containing 18 Tovomita species using maximum likelihood and Bayesian inference approaches. Our results indicate that current infrageneric classification of Tovomita, which relies largely on leaf venation, does not reflect phylogenetic relationships. Instead, we identify carpel number as a more reliable morphological trait for infrageneric classification: clades within Tovomita tend to include species that possess either four or five (or more) carpels. Moreover, groups of species within Tovomita tend to exhibit a high degree of geographic endemicity corresponding to their clade affiliation: species within these clades are restricted to either Amazon or Atlantic forests. The well supported clade of Atlantic forest inhabitants we identify is sister to a clade of mostly Amazonian species that also includes Amazon and Atlantic forest disjunct species, which are more closely related to Amazonian than to other Atlantic forest species. These findings represent a first important step in elucidating morphological evolution and biogeography in this widespread genus of neotropical rainforest trees and shrubs.

Molecular phylogenetic analyses have revealed a superclade of mesangiosperms with five extant lineages: monocots, eudicots, magnoliids, Ceratophyllum and Chloranthaceae. Both Ceratophyllum and Chloranthaceae are ancient lineages with a long fossil record; their precise placement within mesangiosperms is uncertain. Morphological studies have suggested that they form a clade together with some Cretaceous fossils, including Canrightia, Montsechia and Pseudoasterophyllites. Apart from Canrightia, members of this clade share unilocular gynoecia commonly interpreted as monomerous with ascidiate carpels. Alternatively, the gynoecium of Ceratophyllum has also been interpreted as syncarpous with a single fertile carpel (pseudomonomerous). We investigate patterns of morphological, anatomical and developmental variation in gynoecia of three Ceratophyllum species to explore the controversial interpretation of its gynoecium as either monomerous or pseudomonomerous. We use an angiosperm-wide morphological data set and contrasting tree topologies to estimate the ancestral gynoecium type in both Ceratophyllum and mesangiosperms. Gynoecia of all three Ceratophyllum species possess a small (sometimes vestigial) glandular appendage on the abaxial side and an occasionally bifurcating apex. The ovary is usually unilocular with two procambium strands, but sometimes bilocular and/or with three strands in C. demersum. None of the possible phylogenetic placements strongly suggest apocarpy in the stem lineage of Ceratophyllum. Rescoring Ceratophyllum as having two united carpels affects broader-scale reconstructions of the ancestral gynoecium in mesangiosperms. Our interpretation of the glandular appendage as a tepal or staminode homologue makes the Ceratophyllum ovary inferior, thus resembling (semi)inferior ovaries of most Chloranthaceae and potentially related fossils Canrightia and Zlatkocarpus. The entire structure of the flower of Ceratophyllum suggests strong reduction following a long and complex evolutionary history. The widely accepted notion that apocarpy is ancestral in mesangiosperms (and angiosperms) lacks robust support, regardless of which modes of carpel fusion are considered. Our study highlights the crucial importance of incorporating fossils into large-scale analyses to understand character evolution.