Cabomba as a model for studies of early angiosperm evolution

BACKGROUND: The angiosperms, or flowering plants, diversified in the Cretaceous to dominate almost all terrestrial environments. Molecular phylogenetic studies indicate that the orders Amborellales, Nymphaeales and Austrobaileyales, collectively termed the ANA grade, diverged as separate lineages from a remaining angiosperm clade at a very early stage in flowering plant evolution. By comparing these early diverging lineages, it is possible to infer the possible morphology and ecology of the last common ancestor of the extant angiosperms, and this analysis can now be extended to try to deduce the developmental mechanisms that were present in early flowering plants. However, not all species in the ANA grade form convenient molecular-genetic models. SCOPE: The present study reviews the genus Cabomba (Nymphaeales), which shows a range of features that make it potentially useful as a genetic model. We focus on characters that have probably been conserved since the last common ancestor of the extant flowering plants. To facilitate the use of Cabomba as a molecular model, we describe methods for its cultivation to flowering in the laboratory, a novel Cabomba flower expressed sequence tag database, a well-adapted in situ hybridization protocol and a measurement of the nuclear genome size of C. caroliniana. We discuss the features required for species to become tractable models, and discuss the relative merits of Cabomba and other ANA-grade angiosperms in molecular-genetic studies aimed at understanding the origin of the flowering plants.     

The phylogenetics of Desmognathine salamander populations across the southern Appalachians

Salamanders in the genus Desmognathus (Caudata: Plethodontidae) are distributed along an aquatic to terrestrial habitat gradient in the southern Appalachian Mountains. The spatial distribution of species is believed to have formed as aquatic ancestors displaced lineages by competition and predatory interactions into less optimal terrestrial habitats. Aquatic and terrestrial species may also display different patterns of genetic diversity due to the differing likelihood of gene flow via aquatic corridors. To determine whether phylogenetic patterns were consistent with these hypotheses, we sequenced portions of the cytochrome oxidase I and 12S rRNA genes of the mitochondrial genome from 96 individuals belonging to 10 species in the genus Desmognathus. In addition, we combined our dataset with an earlier published dataset for the 12S rRNA genes. The order of species divergence is consistent with aquatic ancestors having displaced taxa into more terrestrial habitats, but the major lineages within the genus Desmognathus arose suddenly, and therefore, the specific sequence of events is not well resolved. The phylogenetic analyses among species suggest that direct-development and a terrestrial lifestyle are ancestral in the genus Desmognathus, but the degree of adult terrestriallity is labile, with some species having re-invaded terrestrial habitats. We present evidence of a clade of Desmognathus quadramaculatus from North Carolina that is distinct from the D. quadramaculatus/Desmognathus marmoratus clade. Within species, estimates of Tajima's D and Fu and Li's statistics suggest the species experienced population expansions at different times in the past. Current levels of sequence diversity in northern populations, therefore, reflect different arrival times, and hence, differences in the opportunity for among population divergence. The recent arrival of most species over large portions of their geographic ranges suggests that most extant communities have been assembled, a posteriori, by the recent assortment of species along the aquatic to terrestrial gradient according to their ecologies.     

When Earth started blooming: insights from the fossil record

Recent palaeobotanical studies have greatly increased the quantity and quality of information available about the structure and relationships of Cretaceous angiosperms. Discoveries of extremely well preserved Cretaceous flowers have been especially informative and, combined with results from phylogenetic analyses of extant angiosperms (based mainly on molecular sequence data), have greatly clarified important aspects of early angiosperm diversification. Nevertheless, many questions still persist. The phylogenetic origin of the group itself remains as enigmatic as ever and, in some cases, newly introduced techniques from molecular biology have given confusing results. In particular, relationships between the five groups of extant seed plants remain uncertain, and it has sometimes proved difficult to reconcile estimates of the time of divergence between extant lineages made using a 'molecular clock' with the fossil record. One result, however, is becoming increasingly clear: a great deal of angiosperm diversity is extinct. Some groups of angiosperms were evidently more diverse in the past than they are today. In other cases, fossils defy assignment to extant groups at the family level or below. This raises the possibility that evolutionary conclusions based solely upon extant taxa that are merely relics of groups that were once much more diverse might be misled by the effects of extinction. It also introduces the possibility that some early enigmatic fossils might represent lineages that diverged from the main line of angiosperm evolution below the most recent common ancestor of all extant taxa. These, and other questions, are among those that need to be addressed by future palaeobotanical research.     

Differences in dispersal- and colonization-related traits between taxa from the freshwater and the terrestrial realm

The aquatic and terrestrial realms differ in many physical properties that not only require specific physiological adaptations but also cause differences in dispersal options. We thus expect that life-history traits related to dispersal and colonization are under selection pressure because freshwater habitats are more isolated and thus more difficult to reach. We compared traits from European databases of three taxonomic groups along the passive–active dispersal gradient: plants (Plantes), snails (Mollusca: Gastropoda: Prosobranchia et Pulmonata) and hoverflies (Diptera: Syrphidae), all of which have both terrestrial and freshwater species (plants and snails) or early life stages (hoverflies). Aquatic taxa seem to be more successful long-distance dispersers than are terrestrial taxa. Our analysis also revealed lower numbers of seeds or eggs produced in the aquatic habitats. However, aquatic taxa often allocate resources to offspring guarding (vegetative propagules in plants, egg capsules in snails) and breeding-site selection (syrphids). Colonization of the aquatic realm is reinforced by increases in life span (plants), clonal spread (plants), shorter generation times (snails), selfing ability (marginal effect in pulmonate snails) or paedogenesis (two incidences in hoverflies, needs further studies). Probably, the variety of strategies reflects the different evolutionary backgrounds that elicit different combinations of trade-offs, but all traits also might increase invasibility of species.     

Timing and Patterns in the Taxonomic Diversification of Lepidoptera (Butterflies and Moths)

The macroevolutionary history of the megadiverse insect order Lepidoptera remains little-known, yet coevolutionary dynamics with their angiospermous host plants are thought to have influenced their diversification significantly. We estimate the divergence times of all higher-level lineages of Lepidoptera, including most extant families. We find that the diversification of major lineages in Lepidoptera are approximately equal in age to the crown group of angiosperms and that there appear to have been three significant increases in diversification rates among Lepidoptera over evolutionary time: 1) at the origin of the crown group of Ditrysia about 150 million years ago (mya), 2) at the origin of the stem group of Apoditrysia about 120 mya and finally 3) a spectacular increase at the origin of the stem group of the quadrifid noctuoids about 70 mya. In addition, there appears to be a significant increase in diversification rate in multiple lineages around 90 mya, which is concordant with the radiation of angiosperms. Almost all extant families appear to have begun diversifying soon after the Cretaceous/Paleogene event 65.51 mya.     

睡莲科系统位置评述

形态学研究显示睡莲科Nymphaeaceae具有许多原始性状。睡莲科又被称为“古草本”。最新的分子系统发育研究显示,睡莲科是现存被子植物系统树根部附近最早分异谱系的演化支之一,对研究被子植物(有花植物)的起源与早期进化具有重要价值,但有关睡莲科的范围和系统位置存在争议。被子植物的起源与辐射一直是植物学家关注的热点。本文对该科系统位置的研究历史与现状进行了评述。     

Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

The root of the angiosperm tree has not yet been established. Major morphological and molecular differences between angiosperms and other seed plants have introduced ambiguities and possibly spurious results. Because it is unlikely that extant species more closely related to angiosperms will be discovered, and because relevant fossils will almost certainly not yield molecular data, the use of duplicate genes for rooting purposes may provide the best hope of a solution. Simultaneous analysis of the genes resulting from a gene duplication event along the branch subtending angiosperms would yield an unrooted network, wherein two congruent gene trees should be connected by a single branch. In these circumstances the best rooted species tree is the one that corresponds to the two gene trees when the network is rooted along the connecting branch. In general, this approach can be viewed as choosing among rooted species trees by minimizing hypothesized events such as gene duplication, gene loss, lineage sorting, and lateral transfer. Of those gene families that are potentially relevant to the angiosperm problem, phytochrome genes warrant special attention. Phylogenetic analysis of a sample of complete phytochrome (PHY) sequences implies that an initial duplication event preceded (or occurred early within) the radiation of seed plants and that each of the two resulting copies duplicated again. In one of these cases, leading to thePHYAandPHYClineages, duplication appears to have occurred before the diversification of angiosperms. Duplicate gene trees are congruent in these broad analyses, but the sample of sequences is too limited to provide much insight into the rooting question. Preliminary analyses of partialPHYAandPHYCsequences from several presumably basal angiosperm lineages are promising, but more data are needed to critically evaluate the power of these genes to resolve the angiosperm radiation.     

Phylogenetic Composition of Angiosperm Diversity in the Cloud Forests of Mexico

Several members of the most ancient living lineages of flowering plants (angiosperms) inhabit humid, woody, mostly tropical habitats. Here we assess whether one of these forest types, the cloud forests of Mexico (CFM), contain a relatively higher proportion of phylogenetically early-diverging angiosperm lineages. The CFM houses an extraordinary plant species diversity, including members of earliest-diverging angiosperm lineages. The phylogenetic composition of CFM angiosperm diversity was evaluated through the relative representation of orders and families with respect to the global flora, and the predominance of phylogenetically early- or late-diverging lineages. Goodness-of-fit tests indicated significant differences in the proportional local and global representation of angiosperm clades. The net difference between the percentage represented by each order and family in the CFM and the global flora allowed identification of clades that are overrepresented and underrepresented in the CFM. Early-diverging angiosperm orders and families were found to be neither over- nor underrepresented in the CFM. A slight predominance of late-diverging phylogenetic levels among overrepresented clades, however, was encountered in the CFM. The resulting pattern suggests that cloud forests provide habitats where the most ancient angiosperm lineages have survived in the face of accumulating species diversity belonging to phylogenetically late-diverging lineages.     

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.     

The evolution of scarab beetles tracks the sequential rise of angiosperms and mammals

Extant terrestrial biodiversity arguably is driven by the evolutionary success of angiosperm plants, but the evolutionary mechanisms and timescales of angiosperm-dependent radiations remain poorly understood. The Scarabaeoidea is a diverse lineage of predominantly plant- and dung-feeding beetles. Here, we present a phylogenetic analysis of Scarabaeoidea based on four DNA markers for a taxonomically comprehensive set of specimens and link it to recently described fossil evidence. The phylogeny strongly supports multiple origins of coprophagy, phytophagy and anthophagy. The ingroup-based fossil calibration of the tree widely confirmed a Jurassic origin of the Scarabaeoidea crown group. The crown groups of phytophagous lineages began to radiate first (Pleurostict scarabs: 108 Ma; Glaphyridae between 101 Ma), followed by the later diversification of coprophagous lineages (crown-group age Scarabaeinae: 76 Ma; Aphodiinae: 50 Ma). Pollen feeding arose even later, at maximally 62 Ma in the oldest anthophagous lineage. The clear time lag between the origins of herbivores and coprophages suggests an evolutionary path driven by the angiosperms that first favoured the herbivore fauna (mammals and insects) followed by the secondary radiation of the dung feeders. This finding makes it less likely that extant dung beetle lineages initially fed on dinosaur excrements, as often hypothesized.     

Cretaceous floras containing angiosperm flowers and fruits from eastern North America

A recent innovation in paleobotanical studies of the Cretaceous has been the use of bulk sediment disaggregation and sieving techniques. This approach has identified numerous Cretaceous floras that contain well-preserved plant fossil debris (“mesofloras”), and many of these have yielded abundant fossil angiosperm flowers, as well as angiosperm fruits, seeds and dispersed stamens. On the Atlantic Coastal Plain of eastern North America recent research has identified a new series of fossil floras of Campanian age from central Georgia. These form part of a rich sequence of mesofloras that range in age from early Aptian (or perhaps late Barremian) to Campanian. Detailed studies of fossil flowers from these floras have clarified the systematic relationships of Cretaceous angiosperms and identified source plants of several characteristic dispersed angiosperm pollen grains. Taxa referable to extant angiosperm families appear suddenly in the Albian and Cenomanian, and the number of extant angiosperm families that can be recognized increases rapidly through the Late Cretaceous. Based on the record of Cretaceous fossil flowers, “modernization” of angiosperm lineages occurred much earlier than had been inferred previously from studies of dispersed fossil pollen. Major extinct monophyletic “higher” taxa of Cretaceous angiosperms have not yet been recognized.     

木兰藤科系统位置评述

木兰藤科(Austrobaileyaceae)含1属2种,是系统学上最孤立的科之一。其花粉类似于最古老的被子植物化石之一:晚白垩世的棒纹粉。最新的分子系统发育研究结果表明,木兰藤科是现存被子植物的基部类群之一,其对于被子植物的起源与早期进化的研究具有重要价值。被子植物(有花植物)的起源和辐射一直是植物学家关注的热点。有关木兰藤科的系统位置一直存在争议。本文对该科系统位置的研究历史与现状进行评述。     

Correlations of Life Form,Pollination Mode and Sexual System in Aquatic Angiosperms

Aquatic plants are phylogenetically well dispersed across the angiosperms. Reproductive and other life-history traits of aquatic angiosperms are closely associated with specific growth forms. Hydrophilous pollination exhibits notable examples of convergent evolution in angiosperm reproductive structures, and hydrophiles exhibit great diversity in sexual system. In this study, we reconstructed ancestral characters of aquatic lineages based on the phylogeny of aquatic angiosperms. Our aim is to find the correlations of life form, pollination mode and sexual system in aquatic angiosperms. Hydrophily is the adaptive evolution of completely submersed angiosperms to aquatic habitats. Hydroautogamy and maleflower-ephydrophily are the transitional stages from anemophily and entomophily to hydrophily. True hydrophily occurs in 18 submersed angiosperm genera, which is associated with an unusually high incidence of unisexual flowers. All marine angiosperms are submersed, hydrophilous species. This study would help us understand the evolution of hydrophilous pollination and its correlations with life form and sexual system.     

Widespread desert affiliation of trebouxiophycean algae (Trebouxiophyceae,Chlorophyta) including discovery of three new desert genera

Unlike most other green algae, trebouxiophyceans are predominantly aerophytic and contain many symbiotic representatives. In recent years, a number of new terrestrial trebouxiophycean taxa were described from soils, tree bark, and lichens. The present phylogenetic study reveals three new lineages of free‐living trebouxiophyceans found in North American desert soil crusts and proposes new generic names to accommodate them: Desertella, Eremochloris, and Xerochlorella. This survey of desert isolates also led to discovery of representatives of seven existing genera of trebouxiophyceans. Two of these genera have never been reported to contain desert representatives and one was known previously only from aquatic habitats. Furthermore, we expand the known geographic range of the recently described genus Chloropyrula, heretofore only known from the Ural Mountains. We demonstrate that the diversity of trebouxiophyceans is still underestimated and poorly understood, and that most major trebouxiophycean lineages contain desert‐dwelling taxa.     

Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)

Early diverging brachyceran fly lineages underwent a rapid radiation approximately 180 Ma, coincident in part with the origin of flowering plants. This region of the fly tree includes 25 000 described extant species with diverse ecological roles such as blood‐feeding (haematophagy), parasitoidism, predation, pollination and wood‐feeding (xylophagy). Early diverging brachyceran lineages were once considered a monophyletic group of families called Orthorrhapha, based on the shared character of a longitudinal break in the pupal skin made during the emergence of the adult. Yet other morphological and molecular evidence generally supports a paraphyletic arrangement of ‘Orthorrhapha’, with strong support for one orthorrhaphan lineage – dance flies and relatives – as the closest relative to all higher flies (Cyclorrhapha), together called Eremoneura. In order to establish a comprehensive estimate of the relationships among orthorrhaphan lineages using a thorough sample of publicly available data, we compiled and analysed a dataset including 1217 taxa representing major lineages and 20 molecular markers. Our analyses suggest that ‘Orthorrhapha’ excluding Eremoneura is not monophyletic; instead, we recover two main lineages of early brachyceran flies: Homeodactyla and Heterodactyla. Homeodactyla includes Nemestrinoidea (uniting two parasitic families Acroceridae + Nemestrinidae) as the closest relatives to the large SXT clade, comprising Stratiomyomorpha, Xylophagidae and Tabanomorpha. Heterodactyla includes Bombyliidae with a monophyletic Asiloidea (exclusive of Bombyliidae) as the closest relatives to Eremoneura. Reducing missing data, modifying the distribution of genes across taxa, and, in particular, removing rogue taxa significantly improved tree resolution and statistical support. Although our analyses rely on dense taxonomic sampling and substantial gene coverage, our results pinpoint the limited resolving power of Sanger sequencing‐era molecular phylogenetic datasets with respect to ancient, hyperdiverse radiations.     

Extinction, ecological opportunity, and the origins of global snake diversity

Snake diversity varies by at least two orders of magnitude among extant lineages, with numerous groups containing only one or two species, and several young clades exhibiting exceptional richness (>700 taxa). With a phylogeny containing all known families and subfamilies, we find that these patterns cannot be explained by background rates of speciation and extinction. The majority of diversity appears to derive from a radiation within the superfamily Colubroidea, potentially stemming from the colonization of new areas and the evolution of advanced venom-delivery systems. In contrast, negative relationships between clade age, clade size, and diversification rate suggest the potential for possible bias in estimated diversification rates, interpreted by some recent authors as support for ecologically mediated limits on diversity. However, evidence from the fossil record indicates that numerous lineages were far more diverse in the past, and that extinction has had an important impact on extant diversity patterns. Thus, failure to adequately account for extinction appears to prevent both rate- and diversity-limited models from fully characterizing richness dynamics in snakes. We suggest that clade-level extinction may provide a key mechanism for explaining negative or hump-shaped relationships between clade age and diversity, and the prevalence of ancient, species-poor lineages in numerous groups.     

腺齿木科系统位置评述

腺齿木科(Trimeniaceae)含2属5种。形态学研究显示腺齿木科具有许多原始性状。最新的分子系统发育研究显示,腺齿木科是现存被子植物的重要基部类群之一。但有关腺齿木科的系统位置存在争议。被子植物(有花植物)的起源与辐射一直是植物系统学家关注的热点。对该科系统位置的研究历史与现状进行评述。     

Phyletic hot spots for B chromosomes in angiosperms

We determined whether supernumerary B chromosomes were nonrandomly distributed among major angiosperm lineages and among lineages within families, as well as the identity of lineages with unusually high B-chromosome frequencies (hot spots). The incidence of B chromosomes for each taxon was gathered from databases showing species with and without these chromosomes (among species with known chromosome numbers). Heterogeneity was found at all ranks above the species level. About 8% of monocots had B chromosomes versus 3% for eudicots; they were rare in nonmonocot basal angiosperms. Significant heterogeneity in B-chromosome frequency occurred among related orders, families within orders, and major taxa within families. There were many B-chromosome hot spots, including Liliales and Commelinales at the order level. At the family level, there was a trend suggesting that B-chromosome frequencies are positively correlated with genome size.     

Floral color change: a widespread functional convergence

Ontogenetic color changes in fully turgid flowers are widespread throughout the angiosperms, and in many cases are known to provide signals for pollinators. A broad survey of flowering plants demonstrates that such color changes appear in at least 77 diverse families. Color-changing taxa occur commonly within what are considered derived lineages, and only rarely in early or primitive groups. The pattern of distribution of floral color change across orders, families, genera, and species demonstrates that the occurrence of the phenomenon within a group is not simply a result of phylogenetic history. Color changes can affect the whole flower or they can be localized, affecting at least nine floral parts or regions. The scale of color change (localized or whole-flower) is broadly correlated with the type of pollinator that characteristically visits the plant. Color changes can come about through seven distinct physiological mechanisms, involving anthocyanins, carotenoids, and betalains. Color changes due to appearance of anthocyanin are the most common, occurring in 68 families. Floral color change has clearly evolved independently many times, most likely in response to selection by visually oriented pollinators, and reflects a widespread functional convergence within the angiosperms.