Phylogenetic evidence for the herbaceous origin of angiosperms

The ancestral angiosperm is commonly interpreted as an arborescent to shrubby magnolialean with large, multiparted, complex flowers. We examined this hypothesis using a phylogenetic analysis of new and reevaluated characters polarizabled with outgroup comparison. Our cladistic analysis of basal angiosperms placed the nonmagnolialeanChloranthaceae andPiperaceae at the bottom of the tree. We further inferred the probable ancestral states of characters not polarizable with outgroup comparison by examining their distribution among taxa at the base of our cladogram. The sum of ancestral character states suggests that the protoangiosperm was a diminutive, rhizomatous to scrambling perennial herb, with small, simple flowers.     

Fossil evidence for a herbaceous diversification of early eudicot angiosperms during the Early Cretaceous

Eudicot flowering plants comprise roughly 70% of land plant species diversity today, but their early evolution is not well understood. Fossil evidence has been largely restricted to their distinctive tricolpate pollen grains and this has limited our understanding of the ecological strategies that characterized their primary radiation. I describe megafossils of an Early Cretaceous eudicot from the Potomac Group in Maryland and Virginia, USA that are complete enough to allow reconstruction of important life-history traits. I draw on quantitative and qualitative analysis of functional traits, phylogenetic analysis and sedimentological evidence to reconstruct the biology of this extinct species. These plants were small and locally rare but widespread, fast-growing herbs. They had complex leaves and they were colonizers of bright, wet, disturbance-prone habitats. Other early eudicot megafossils appear to be herbaceous rather than woody, suggesting that this habit was characteristic of their primary radiation. A mostly herbaceous initial diversification of eudicots could simultaneously explain the heretofore sparse megafossil record as well as their rapid diversification during the Early Cretaceous because the angiosperm capacity for fast reproduction and fast evolution is best expressed in herbs.     

Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail

Parallel speciation can occur when traits determining reproductive isolation evolve independently in different populations that experience a similar range of environments. However, a common problem in studies of parallel evolution is to distinguish this hypothesis from an alternative one in which different ecotypes arose only once in allopatry and now share a sympatric scenario with substantial gene flow between them. Here we show that the combination of a phylogenetic approach with life-history data is able to disentangle both hypotheses in the case of the intertidal marine snail Littorina saxatilis on the rocky shores of Galicia in northwestern Spain. In this system, numerous phenotypic and genetic differences have evolved between two sympatric ecotypes spanning a sharp ecological gradient, and as aside effect of the former have produced partial reproductive isolation. A mitochondrial phylogeny of these populations strongly suggests that the two sympatric ecotypes have originated independently several times. Building upon earlier work demonstrating size-based assortative mating as the main contributor to reproductive isolation among ecotypes, our analysis provides strong evidence that divergent selection across a sharp ecological gradient promoted the parallel divergence of body size and shape between two sympatric ecotypes. Thus, divergent selection occurring independently in different populations has produced the marine equivalent of host races, which may represent the first step in speciation.     

The origin and diversification of angiosperms

The angiosperms, one of five groups of extant seed plants, are the largest group of land plants. Despite their relatively recent origin, this clade is extremely diverse morphologically and ecologically. However, angiosperms are clearly united by several synapomorphies. During the past 10 years, higher-level relationships of the angiosperms have been resolved. For example, most analyses are consistent in identifying Amborella, Nymphaeaceae, and Austrobaileyales as the basalmost branches of the angiosperm tree. Other basal lineages include Chloranthaceae, magnoliids, and monocots. Approximately three quarters of all angiosperm species belong to the eudicot clade, which is strongly supported by molecular data but united morphologically by a single synapomorphy-triaperturate pollen. Major clades of eudicots include Ranunculales, which are sister to all other eudicots, and a clade of core eudicots, the largest members of which are Saxifragales, Caryophyllales, rosids, and asterids. Despite rapid progress in resolving angiosperm relationships, several significant problems remain: (1) relationships among the monocots, Chloranthaceae, magnoliids, and eudicots, (2) branching order among basal eudicots, (3) relationships among the major clades of core eudicots, (4) relationships within rosids, (5) relationships of the many lineages of parasitic plants, and (6) integration of fossils with extant taxa into a comprehensive tree of angiosperm phylogeny.     

Phylogenetic approaches for studying diversification

Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever‐accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non‐equilibrium theories recognising the crucial role of history.     

Evolutionary diversification of the flowers in angiosperms

Angiosperms and their flowers have greatly diversified into an overwhelming array of forms in the past 135 million years. Diversification was shaped by changes in climate and the biological environment (vegetation, interaction with other organisms) and by internal structural constraints and potentials. This review focuses on the development and structural diversity of flowers and structural constraints. It traces floral diversification in the different organs and organ complexes (perianth, androecium, gynoecium) through the major clades of extant angiosperms. The continuously improved results of molecular phylogenetics provide the framework for this endeavor, which is necessary for the understanding of the biology of the angiosperms and their flowers. Diversification appears to work with innovations and modifications of form. Many structural innovations originated in several clades and in special cases could become key innovations, which likely were hot spots of diversification. Synorganization between organs was an important process to reach new structural levels, from which new diversifications originated. Complexity of synorganization reached peaks in Orchidaceae and Apocynaceae with the independent evolution of pollinaria. Such a review throughout the major clades of angiosperms also shows how superficial and fragmentary our knowledge on floral structure in many clades is. Fresh studies and a multidisciplinary approach are needed.     

Nonstochastic variation of species-level diversification rates within angiosperms

Variations in the origination and extinction rates of species over geological time often are linked with a range of factors, including the evolution of key innovations, changes in ecosystem structure, and environmental factors such as shifts in climate and physical geography. Before hypothesizing causality of a single factor, it is critical to demonstrate that the observed variation in diversification is significantly greater than one would expect due to natural stochasticity in the evolutionary branching process. Here, we use a likelihood-ratio test to compare taxonomic rate heterogeneity to a neutral birth-death model, using data on well-supported sister pairs of taxa and their species richness. We test the likelihood that the distribution of extant species among angiosperm genera and families could be the result of constant diversification rates. Results strongly support the conclusion that there is significantly more heterogeneity in diversity at the species level within angiosperms than would be expected due to stochastic processes. This result is consistent in datasets of genus pairs and family pairs and is not affected significantly by degrading pairs to simulate inaccuracy in the assumption of simultaneous origin of sister taxa. When we parse taxon pairs among higher groups of angiosperms, results indicate that a constant rates model is not rejected by rosid and basal eudicot pairs but is rejected by asterid and eumagnoliid pairs. These results provide strong support for the hypothesis that species-level rates of origination and/or extinction have varied nonrandomly within angiosperms and that the magnitude of heterogeneity varies among major groups within angiosperms.     

The age and diversification of the angiosperms re-revisited

? Premise of the study: It has been 8 years since the last comprehensive analysis of divergence times across the angiosperms. Given recent methodological improvements in estimating divergence times, refined understanding of relationships among major angiosperm lineages, and the immense interest in using large angiosperm phylogenies to investigate questions in ecology and comparative biology, new estimates of the ages of the major clades are badly needed. Improved estimations of divergence times will concomitantly improve our understanding of both the evolutionary history of the angiosperms and the patterns and processes that have led to this highly diverse clade. ? Methods: We simultaneously estimated the age of the angiosperms and the divergence times of key angiosperm lineages, using 36 calibration points for 567 taxa and a "relaxed clock" methodology that does not assume any correlation between rates, thus allowing for lineage-specific rate heterogeneity. ? Key results: Based on the analysis for which we set fossils to fit lognormal priors, we obtained an estimated age of the angiosperms of 167-199 Ma and the following age estimates for major angiosperm clades: Mesangiospermae (139-156 Ma); Gunneridae (109-139 Ma); Rosidae (108-121 Ma); Asteridae (101-119 Ma). ? Conclusions: With the exception of the age of the angiosperms themselves, these age estimates are generally younger than other recent molecular estimates and very close to dates inferred from the fossil record. We also provide dates for all major angiosperm clades (including 45 orders and 335 families [208 stem group age only, 127 both stem and crown group ages], sensu APG III). Our analyses provide a new comprehensive source of reference dates for major angiosperm clades that we hope will be of broad utility.     

Age at maturity and diversification in woody angiosperms

Angiosperm diversification has been associated with plant-animal interactions such as seed dispersal and pollination and life-history characters such as rapid growth and fast reproduction. This paper relates a life-history character (age at maturity) to woody angiosperm diversification. Here I present a comparative analysis of data drawn from the literature, indicating that time to first reproduction is shorter in woody angiosperms than in gymnosperms. In addition, age at maturity is negatively correlated with the rate of diversification (measured as the number of species per genus) at all the taxonomic levels analyzed and also when phylogenetically independent contrasts were conducted. This correlation suggests that early reproduction promotes diversification in woody angiosperms. Furthermore, this correlation is not a confounding effect of the association between age at maturity and other ecological factors that promote angiosperm diversification, such as pollination and seed dispersal systems.     

Phylogenetic variation in the shoot mineral concentration of angiosperms

The calcium (Ca) concentration of plant shoot tissues varies systematically between angiosperm orders. The phylogenetic variation in the shoot concentration of other mineral nutrients has not yet been described at an ordinal level. The aims of this study were (1) to quantify the shoot mineral concentration of different angiosperm orders, (2) to partition the phylogenetic variation in shoot mineral concentration between and within orders, (3) to determine if the shoot concentration of different minerals are correlated across angiosperm species, and (4) to compare experimental data with published ecological survey data on 81 species sampled from their natural habitats. Species, selected pro rata from different angiosperm orders, were grown in a hydroponic system under a constant external nutrient regime. Shoots of 117 species were sampled during vegetative growth. Significant variation in shoot carbon (C), calcium (Ca), potassium (K), and magnesium (Mg) concentration occurred between angiosperm orders. There was no evidence for systematic differences in shoot phosphorus (P) or organic-nitrogen (N) concentration between orders. At a species level, there were strong positive correlations between shoot Ca and Mg concentration, between shoot P and organic-N concentration, and between shoot K concentration and shoot fresh weight:dry weight ratio. Shoot C and cation concentration correlated negatively at a species level. Species within the Poales and the Caryophyllales had distinct shoot mineralogies in both the designed experiment and in the ecological survey.     

Phylogenetic analysis of the ecological correlates of dioecy in angiosperms

We report on a phylogenetic analysis of correlations between the occurrence of dioecy and several ecological and life-history attributes: tropical distribution, woody growth form, abiotic pollination, small inconspicuous flowers and inflorescences, many-flowered inflorescences and fleshy fruits. Various hypotheses have been proposed to explain why associations occur between dioecy and several of these attributes, yet most assume that dioecy originates more often in clades with these traits than in clades with alternative character states. To investigate correlations between dioecy and these attributes, and to provide insights into the potential evolutionary pathways that have led to these associations, we assigned states of these traits to genera on a large-scale molecular phylogeny of the angiosperms; we then used maximum-likelihood analysis to analyse the presence of correlations and the sequence of acquisition of traits. Phylogenetic analysis revealed correlations between dioecy and six of the seven attributes; only many-flowered inflorescences exhibiting no association with the dioecious condition. The particular correlations that were revealed and the strength of the association differed among the three main monophyletic groups of angiosperms (Rosids, Asterids, and Eumagnoliids). Our analysis provided no general support for the hypothesis that dioecy is more likely to evolve in lineages already possessing the seven attributes we considered. Further analysis of the intercorrelations of the seven attributes provided evidence for non-independence between some of the traits, implying that functional associations among these traits have influenced the ecology and evolution of dioecious species.     

Cretaceous diversification of angiosperms in the western part of the Iberian Peninsula

The classic leaf fossil floras from the Cretaceous of the Lusitanian Basin, Portugal, which were first described more than one hundred years ago, have played an important role in the development of ideas on the early evolution of angiosperms. Insights into the nature of vegetational change in the Lusitanian Basin through the Cretaceous have also come from studies of fossil pollen and spores, but the discovery of a series of mesofossil floras containing well-preserved angiosperm reproductive structures has provided a new basis for understanding the systematic relationships and biology of angiosperms at several stratigraphic levels through the Cretaceous. In the earliest mesofossil floras from the Torres Vedras locality, which are of probable Late Barremian-Early Aptian age, angiosperms are surprisingly diverse with about 50 different taxa. In slightly later mesofossil floras, which are of probable Late Aptian-Early Albian age, the diversity of angiosperms is still more substantial with more than hundred different kinds of angiosperm reproductive structures recognized from the Famalicão locality alone. However, this early diversity is largely among angiosperm lineages that produced monoaperturate pollen (e.g., Chloranthaceae, Nymphaeales) and early diverging monocots (Alismatales). Eudicots are rare in these Early Cretaceous mesofossil floras, but already by the Late Cenomanian the vegetation of the western Iberian Peninsula is dominated by angiosperms belonging to various groups of core eudicots. The Normapolles complex is a particularly conspicuous element in both mesofossil floras and in palynological assemblages. In the Late Cretaceous mesofossil floras from Esgueira and Mira, which are of Campanian-Maastrichtian age, core eudicots are also floristically dominant and flowers show great organisational similarity to fossil flowers from other Late Cretaceous floras described from other localities in Asia, Europe and North America.     

Phylogenetic tree of vascular plants reveals the origins of aquatic angiosperms

Although aquatic plants are discussed as a unified biological group, they are phylogenetically well dispersed across the angiosperms. In this study, we annotated the aquatic taxa on the tree of vascular plants, and extracted the topology of these aquatic lineages to construct the tree of aquatic angiosperms. We also reconstructed the ancestral areas of aquatic families. We found that aquatic angiosperms could be divided into two different categories: the four aquatic orders and the aquatic taxa in terrestrial orders. Aquatic lineages evolved early in the radiation of angiosperms, both in the orders Nymphaeales and Ceratophyllales and among basal monocots (Acorales and Alismatales). These aquatic orders do not have any extant terrestrial relatives. They originated from aquatic habitats during the Early Cretaceous. Asia would have been one of the centers for early diversification of aquatic angiosperms. The aquatic families within terrestrial orders may originate from other areas besides Asia, such as America or Australia. The lineages leading to extant angiosperms diversified early in underexploited freshwater habitats. The four extant aquatic orders were relicts of an early radiation of angiosperm in aquatic environments. Their extinct ancestors might be aquatic early angiosperms.     

Phylogenetic status and timescale for the diversification of Steno and Sotalia dolphins

Molecular data have provided many insights into cetacean evolution but some unsettled issues still remain. We estimated the topology and timing of cetacean evolutionary relationships using bayesian and maximum likelihood analyses of complete mitochondrial genomes. In order to clarify the phylogenetic placement of Sotalia and Steno within the Delphinidae, we sequenced three new delphinid mitogenomes. Our analyses support three delphinid clades: one joining Steno and Sotalia (supporting the revised subfamily Stenoninae); another placing Sousa within the Delphininae; and a third, the Globicephalinae, which includes Globicephala, Feresa, Pseudorca, Peponocephala and Grampus. We also conclude that Orcinus does not belong in the Globicephalinae, but Orcaella may be part of that subfamily. Divergence dates were estimated using the relaxed molecular clock calibrated with fossil data. We hypothesise that the timing of separation of the marine and Amazonian Sotalia species (2.3 Ma) coincided with the establishment of the modern Amazon River basin.     

Phylogenetic diversification of immunoglobulin genes and the antibody repertoire

Immunoglobulins are encoded by a large multigene system that undergoes somatic rearrangement and additional genetic change during the development of immunoglobulin-producing cells. Inducible antibody and antibody-like responses are found in all vertebrates. However, immunoglobulin possessing disulfide-bonded heavy and light chains and domain-type organization has been described only in representatives of the jawed vertebrates. High degrees of nucleotide and predicted amino acid sequence identity are evident when the segmental elements that constitute the immunoglobulin gene loci in phylogenetically divergent vertebrates are compared. However, the organization of gene loci and the manner in which the independent elements recombine (and diversify) vary markedly among different taxa. One striking pattern of gene organization is the "cluster type" that appears to be restricted to the chondrichthyes (cartilaginous fishes) and limits segmental rearrangement to closely linked elements. This type of gene organization is associated with both heavy- and light-chain gene loci. In some cases, the clusters are "joined" or "partially joined" in the germ line, in effect predetermining or partially predetermining, respectively, the encoded specificities (the assumption being that these are expressed) of the individual loci. By relating the sequences of transcribed gene products to their respective germ-line genes, it is evident that, in some cases, joined-type genes are expressed. This raises a question about the existence and/or nature of allelic exclusion in these species. The extensive variation in gene organization found throughout the vertebrate species may relate directly to the role of intersegmental (V<==>D<==>J) distances in the commitment of the individual antibody-producing cell to a particular genetic specificity. Thus, the evolution of this locus, perhaps more so than that of others, may reflect the interrelationships between genetic organization and function.      

Phylogenetic diversification of the globin gene superfamily in chordates

Phylogenetic reconstructions provide a means of inferring the branching relationships among members of multigene families that have diversified via successive rounds of gene duplication and divergence. Such reconstructions can illuminate the pathways by which particular expression patterns and protein functions evolved. For example, phylogenetic analyses can reveal cases in which similar expression patterns or functional properties evolved independently in different lineages, either through convergence, parallelism, or evolutionary reversals. The purpose of this article is to provide a robust phylogenetic framework for interpreting experimental data and for generating hypotheses about the functional evolution of globin proteins in chordate animals. To do this, we present a consensus phylogeny of the chordate globin gene superfamily. We document the relative roles of gene duplication and whole-genome duplication in fueling the functional diversification of vertebrate globins, and we unravel patterns of shared ancestry among globin genes from representatives of the three chordate subphyla (Craniata, Urochordata, and Cephalochordata). Our results demonstrate the value of integrating phylogenetic analyses with genomic analyses of conserved synteny to infer the duplicative origins and evolutionary histories of globin genes. We also discuss a number of case studies that illustrate the importance of phylogenetic information when making inferences about the evolution of globin gene expression and protein function. Finally, we discuss why the globin gene superfamily presents special challenges for phylogenetic analysis, and we describe methodological approaches that can be used to meet those challenges.