Phylogenetics of early branching eudicots:Comparing phylogenetic signal across plastid introns,spacers,and genes

<正>Recent phylogenetic analyses revealed a grade with Ranunculales,Sabiales,Proteales,Trochodendrales, and Buxales as first branching eudicots,with the respective positions of Proteales and Sabiales still lacking statistical confidence.As previous analyses of conserved plastid genes remain inconclusive,we aimed to use and evaluate a representative set of plastid introns(group I:trnL;group II:petD,rpll6,trnK) and intergenic spacers(trnL-F,petB-petD, atpB-rbcL,rps3-rpl16) in comparison to the rapidly evolving matK and slowly evolving atpB and rbcL genes. Overall patterns of micro structural mutations converged across genomic regions,underscoring the existence of a general mutational pattern throughout the plastid genome.Phylogenetic signal differed strongly between functionally and structurally different genomic regions and was highest in matK,followed by spacers,then group II and group I introns.The more conserved atpB and rbcL coding regions showed distinctly lower phylogenetic information content.Parsimony,maximum likelihood,and Bayesian phylogenetic analyses based on the combined dataset of non-coding and rapidly evolving regions(14 000 aligned characters) converged to a backbone topology of eudicots with Ranunculales branching first,a Proteales-Sabiales clade second,followed by Trochodendrales and Buxales. Gunnerales generally appeared as sister to all remaining core eudicots with maximum support.Our results show that a small number of intron and spacer sequences allow similar insights into phylogenetic relationships of eudicots compared to datasets of many combined genes.The non-coding proportion of the plastid genome thus can be considered an important information source for plastid phylogenomics.     

Phylogeny of basal eudicots: Insights from non-coding and rapidly evolving DNA

Sequence data of the trnL group I intron, the petD group II intron, the trnL-F and petB-D spacers, and the rapidly evolving matK gene were analysed from all families of the basal eudicot grade and from representatives of 19 core eudicot orders. The dataset comprised 5654 positions of aligned sequence plus a matrix of 1087 binary indel characters. Mutational hotspots correspond in number and extension to hotspots already known from basal angiosperms and, with respect to secondary structure, are generally located in terminal parts of stem-loop regions. Parsimony, Bayesian, and likelihood analyses depict Ranunculales as sister to all remaining eudicots with maximum support. The branching order in the basal eudicot grade is further resolved as Sabiales, Proteales, Trochodendrales, and Buxales. Nearly all of the backbone nodes gain high confidence, except for the node showing Proteales diverging before Trochodendrales, which is only moderately supported (83% JK). In Ranunculales, the woody Eupteleaceae are first-branching, with Papaveraceae plus Fumariaceae coming next. Within Proteales, Nelumbo is clearly resolved as sister to a Platanaceae–Proteaceae clade. Gunnerales are found as the first branch in core eudicots, with maximum support in the combined analysis. This node is also resolved with matK alone, but unsupported. It appears that the combined analysis of sequence data from rapidly evolving and non-coding genomic regions leads to significantly improved statistical support values in comparison to earlier studies of basal eudicots using multiple conserved genes.See also Electronic Supplement at doi:10.1016/j.ode.2006.08.001     

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atpl, matR, had5, and rps3, from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK, and rbcL, and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum, magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum, relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales-Oxalidales-Malpighiales) clade is sister to malvids (or rosid Ⅱ), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade. This study shows that the mitochondrial genes are informative markers for resolving relationships among genera, families, or higher rank taxa across angiosperms. The low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes, as found in this study, make them particularly useful for reconstructing ancient phylogenetic relationships. A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes, nuclear genes, and non-molecular data to reconstruct the underlying organismal phylogeny.     

Phylogenetic relationships among early-diverging eudicots based on four genes: were the eudicots ancestrally woody?

Based on analyses of combined data sets of three genes (18S rDNA, rbcL, and atpB), phylogenetic relationships among the early-diverging eudicot lineages (Ranunculales, Proteales, Trochodendraceae, Sabiaceae, and Buxaceae) remain unclear, as are relationships within Ranunculales, especially the placement of Eupteleaceae. To clarify relationships among these early-diverging eudicot lineages, we added entire sequences of 26S rDNA to the existing three-gene data set. In the combined analyses of four genes based on parsimony, ML, and Bayesian analysis, Ranunculales are strongly supported as a clade and are sister to other eudicots. Proteales appear as sister to the remaining eudicots, which are weakly (59%) supported as a clade. Relationships among Trochodendraceae, Buxaceae (including Didymeles), Sabiaceae, and Proteales remain unclear. Within Ranunculales, Eupteleaceae are sister to all other Ranunculales, with bootstrap support of 70% in parsimony analysis and with posterior probability of 1.00 in Bayesian analysis. Our character reconstructions indicate that the woody habit is ancestral, not only for the basal angiosperms, but also for the eudicots. Furthermore, Ranunculales may not be ancestrally herbaceous, as long maintained. The woody habit appears to have been ancestral for several major clades of eudicots, including Caryophyllales, and asterids.     

Gynoecium diversity and systematics of the basal eudicots

Gynoecium and ovule structure was compared in representatives of the basal eudicots, including Ranunculales (Berberidaceae, Circaeasteraceae, Eupteleaceae, Lardizabalaceae, Menispermaceae, Papaveraceae, Ranunculaceae), Proteales (Nelumbonaceae, Platanaceae, Proteaceae), some families of the former ‘lower’ hamamelids that have been moved to Saxifragales (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, Hamamelidaceae), and some families of uncertain position (Gunneraceae, Myrothamnaceae, Buxaceae, Sabiaceae, Trochodendraceae). In all representatives studied, the carpels (or syncarpous gynoecia) are closed at anthesis. This closure is attained in different ways: (1) by secretion without postgenital fusion (Berberidaceae, Papaveraceae, Nelumbonaceae, probably Circaeaster); (2) by a combination of postgenital fusion and secretion; (2a) with a complete secretory canal and partly postgenitally fused periphery (Lardizabalaceae, Menispermaceae, some Ranunculaceae, Sabiaceae); (2b) with an incomplete secretory canal and completely fused periphery (Tro-chodendron); (3) by complete postgenital fusion without a secretory canal (most Ranunculaceae, Eupteleaceae, Platanaceae, Proteaceae, all families of Saxifragales and incertae sedis studied here). Stigmas are double-crested and decurrent in most of the non-ranunculalian taxa; unicellular-papillate in most taxa, but with multicellular protuberances in Daphniphyllaceae and Hamamelidaceae. Carpels predominantly have three vascular bundles, but five in Proteales (without Nelumbonaceae), Myrothamnaceae and Trochodendraceae. The latter two also share ‘oil’ cells in the carpels. Stomata on the outer carpel surface are present in the majority of Ranunculales and Proteales, but tend to be lacking in the saxifragalian families. In basal eudicots, especially in the non-ranunculalian families there is a trend to form more than one ovule per carpel but to develop only one seed, likewise there is a trend to have immature ovules at anthesis. Ovule number per carpel is predominantly one or two. Proteales (without Nelumbonales) mainly have orthotropous ovules, the other groups have anatropous (or hemitropous or campylotropous) ovules. The outer integument is annular in the groups with orthotropous or hemitropous ovules, and also in a number of saxifragalian families with anatropous ovules. In Proteales the integuments are predominantly lobed but there is no distinct pattern in this feature among the other groups. Among Ranunculales two pairs of families (Lardizabalaceae/Menispermaceae and Bcrberidaceae/Papaveraceae) due to similarities in gynoecium structure can be recognized, which are not apparent in molecular analyses. The close relationship of Platanaceae and Proteaceae is supported by gynoecium structure but gynoecial features do not support their affinity to Nelumbonaceae. The alliance of Daphniphyllaceae with Hamamelidaceae s.l. is also supported.     

Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species

The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core eudicots), but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ∼4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8) that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern.     

Phylogenetic signal in matK vs. trnK: a case study in early diverging eudicots (angiosperms)

The matK gene has been among the most useful loci for resolving plant phylogenetic relationships at different evolutionary time-scales, but much less is known about the phylogenetic utility of the flanking trnK intron, especially for deep level phylogenetics. We compared the relative performance of matK and trnK intron regions for resolving the relationships of the early diverging eudicots (angiosperms). The two regions display similar nucleotide compositions and distributions of rate variation among sites. The trnK intron sequences also provide similar levels of phylogenetic information per-site as matK. Combining the trnK intron sequences with matK increases overall bootstrap support for the early diverging eudicots compared to analyses of matK alone. MP, ML and Bayesian analyses provide strong support for eudicots, the sister group relationship of Ranunculales to remaining eudicots, and a Buxales+Trochodendraceae+core eudicots clade. matK and the trnK intron support conflicting positions for Buxales and Trochodendrales in relation to the core eudicots.     

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.     

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.     

Integrating Early Cretaceous fossils into the phylogeny of living angiosperms:Magnoliidae and eudicots

Over the past 25 years, discoveries of Early Cretaceous fossil flowers, often associated with pollen and sometimes with vegetative parts, have revolutionized our understanding of the morphology and diversity of early angiosperms. However, few of these fossils have been integrated into the increasingly robust phylogeny of living angiosperms based primarily on molecular data. To remedy this situation, we have used a morphological dataset for living basal angiosperms (including basal eudicots and monocots) to assess the most parsimonious positions of early angiosperm fossils on cladograms of Recent plants, using constraint trees that represent the current range of hypotheses on higher-level relationships, and concentrating on Magnoliidae (the clade including Magnoliales, Laurales, Canellales, and Piperales) and eudicots. In magnoliids, our results confirm proposed relationships of Archaeanthus (latest Albian?) to Magnoliaceae, Endressinia (late Aptian) to Magnoliales (the clade comprising Degeneria, Galbulimima, Eupomatia, and Annonaceae), and Walkeripollis pollen tetrads (late Barremian?) to Win-teraceae, but they indicate that Mauldinia (early Cenomanian) was sister to both Lauraceae and Hernandiaceae rather than to Lauraceae alone. Among middle Albian to early Cenomanian eudicots, we confirm relationships of Nelumbites to Nelumbo, platanoid inflorescences and Sapindopsis to Platanaceae, and Spanomera to Buxaceae. With the possible exception of Archaeanthus, these fossils are apparently not crown group members of living families but rather stem relatives of one or more families.     

Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification

We present a phylogenetic dating of asterids, based on a 111-taxon tree representing all major groups and orders and 83 of the 102 families of asterids, with an underlying data set comprising six chloroplast DNA markers totaling 9914 positions. Phylogenetic dating was done with semiparametric rate smoothing by penalized likelihood. Confidence intervals were calculated by bootstrapping. Six reference fossils were used for calibration. To explore the effects of various sources of error, we repeated the analyses with alternative dating methods (nonparametric rate smoothing and the Langley-Fitch clock-based method), alternative tree topologies, reduced taxon sampling (22 of the 111 taxa deleted), partitioning the data into three genes and three noncoding regions, and calibrating with single reference fossils. The analyses with alternative topologies, reduced taxon sampling, and coding versus noncoding sequences all yielded small or in some cases no deviations. The choice of method influenced the age estimates of a few nodes considerably. Calibration with reference fossils is a critical issue, and use of single reference fossils yielded different results depending on the fossil. The bootstrap confidence intervals were generally small. Our results show that asterids and their major subgroups euasterids, campanulids, and lamiids diversified during the Early Cretaceous. Cornales, Ericales, and Aquifoliales also have crown node ages from the Early Cretaceous. Dipsacales and Solanales are from the Mid-Cretaceous, the other orders of core campanulids and core lamiids from the Late Cretaceous. The considerable diversity exhibited by asterids almost from their first appearance in the fossil record also supports an origin and first phase of diversification in the Early Cretaceous.     

Mesofossils with platanaceous affinity from the Dakota Formation (Cretaceous) in Kansas, USA

The Platanaceae holds a basal position in the phylogeny of eudicots and therefore is of great interest to angiosperm systematists. The fossil record of the family is found in strata ranging from the Cretaceous to Recent in America, Europe and Asia. The research on the Platanaceae in the Dakota Formation can be traced back to 19th century; however, mesofossils of reproductive organs of the Platanaceae were never reported in the Midwest of North America before. This paper reports several specimens of Friisicarpus (Platanaceae) from the Dakota Formation in Kansas, USA. It complements the existing fossil records, and provides more information on reproductive biology of the family. The comparison with similar fossils from eastern North America and Europe provides some hints on biostratigraphy of the Cretaceous.     

Integrating Early Cretaceous fossils into the phylogeny of living angiosperms: Magnoliidae and eudicots

Over the past 25 years, discoveries of Early Cretaceous fossil flowers, often associated with pollen and sometimes with vegetative parts, have revolutionized our understanding of the morphology and diversity of early angiosperms. However, few of these fossils have been integrated into the increasingly robust phylogeny of living angiosperms based primarily on molecular data. To remedy this situation, we have used a morphological data set for living basal angiosperms (including basal eudicots and monocots) to assess the most parsimonious positions of early angiosperm fossils on cladograms of Recent plants, using constraint trees that represent the current range of hypotheses on higher-level relationships, and concentrating on Magnoliidae (the clade including Magnoliales, Laurales, Canellales, and Piperales) and eudicots. In magnoliids, our results confirm proposed relationships of Archaeanthus (latest Albian?) to Magnoliaceae, Endressinia (late Aptian) to Magnoliales (the clade comprising Degeneria, Galbulimima, Eupomatia, and Annonaceae), and Walkeripollis pollen tetrads (late Barremian?) to Winteraceae, but they indicate that Mauldinia (early Cenomanian) was sister to both Lauraceae and Hernandiaceae rather than to Lauraceae alone. Among middle Albian to early Cenomanian eudicots, we confirm relationships of Nelumbites to Nelumbo, platanoid inflorescences and Sapindopsis to Platanaceae, and Spanomera to Buxaceae. With the possible exception of Archaeanthus, these fossils are apparently not crown group members of living families but rather stem relatives of one or more families.     

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.     

Accelerated evolution of early angiosperms: Evidence from ranunculalean phylogeny by integrating living and fossil data

The new discovery of angiosperm remains in the Jehol Biota of northeastern China contributes to our understanding of the origin and early evolution of flowering plants. The earliest eudicot genus with reproductive organs, Leefructus, was recently documented from the Lower Cretaceous Yixian Formation at 125.8–123.0 Ma, and was reconsidered to be close to the extant family Ranunculaceae based on gross morphology. However, this hypothesis has not been tested using a cladistic approach. To determine the possible allies of Leefructus within extant eudicots, we constructed a 66 morphological data matrix. Molecular and morphological analyses of extant Ranunculales combined with the fossil suggest that it has an affinity with the Ranunculaceae. The earliest fossil record of the eudicots is 127–125 Ma based on tricolpate pollen grains. Thus, we suggest a hypothesis that the basal eudicots might have experienced an accelerated evolution and diversification during the latest Barremian and earliest Aptian, leading to the stem groups of at least six extant families or lineages, 10–15 Myr earlier than currently documented. Angiosperms have undergone multiple uneven pulses of radiation since their origin. Many key character innovations occurred in different stages that could have triggered those radiations in concert with various biotic and abiotic factors.     

On the systematic position of the Early Cretaceous fern genus “Athyrium”

The oldest fossils assigned to Athyrium (mostly based on the sorus morphology) comprise fronds and spores from the Lower Cretaceous of Northeast Asia. However, most molecular dating suggests that extant Athyrium diverged from its sister genus during the Eocene or later, implying that the Cretaceous fossils probably belong to another polypodiaceous taxon. By examining the sorus morphology of extant genera related to the family Athyriaceae, we found that the primary diagnostic feature for assigning the Cretaceous fossils to Athyrium, i.e., the sorus shape, is common to the entire extant family, or plesiomorphic for the genus. As the fronds are more commonly preserved than the reproductive parts, we compared the fossil frond morphology with those of living taxa of the family that is divided into two types. The Cretaceous fossil we examined here bears the frond’s costal groove characters on adaxial side, which is more closely related to that of the Deparia-clade instead of the clade including Athyrium and other genera of the family. The observation is further confirmed by the cladistic analysis using morphological characters. The systematic position of the Early Cretaceous “Athyrium” was resolved as a stem member of the total Athyriaceae using a tip-dating approach with the Fossilized Birth-Death model in a Bayesian framework. Our study suggests that Early Cretaceous fossils previously assigned to Athyrium require taxonomic revision.     

Effects of taxon sampling on molecular dating for within-genus divergence events, when deep fossils are used for calibration

A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable. A possible method for eudicots is to use a large phylogeny calibrated using deep fossils including tricolpate pollen as a fixed （124 mya） calibration point. This method was used to calculate node ages within three species-poor disjunct basal eudicot genera, Caulophyllum, Podophyllum and Pachysandra, and sensitivity of these ages to effects such as taxon sampling were then quantified. By deleting from one to three accessions related to each genus in 112 different combinations, a confidence range describing variation due only to taxon sampling was generated. Ranges for Caulophyllum, Podophyllum and Pachysandra were 8.4-10.6, 7.6-20.0, and 17.6-25.0 mya, respectively. However, the confidence ranges calculated using bootstrapping were much wider, at 3-19, 0-32 and 11-32 mya, respectively. Furthermore, deleting 10 adjacent taxa had a large effect in Pachysandra only, indicating that undersampling effects are significant among Buxales. Changes to sampling density in neighboring clades, or to the position of the fixed fossil calibration point had small to negligible effects. Non-parametric rate smoothing was more sensitive to taxon sampling effects than was penalized likelihood. The wide range for Podophyllum, compared to the other two genera, was probably due to a high degree of rate heterogeneity within this genus. Confidence ranges calculated by this method could be narrowed by sampling more individuals within the genus of interest, and by sequencing multiple DNA regions from all species in the phylogeny.     

Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data

Molecular estimates of the age of angiosperms have varied widely, and many greatly predate the Early Cretaceous appearance of angiosperms in the fossil record, but there have been few attempts to assess confidence limits on ages. Experiments with rbcL and 18S data using maximum likelihood suggest that previous angiosperm age estimates were too old because they assumed equal rates across sites-use of a gamma distribution of rates to correct for site-to-site variation gives 10-30 my (million years) younger ages-and relied on herbaceous angiosperm taxa with high rates of molecular evolution. Ages based on first and second codon positions of rbcL are markedly older than those based on third positions, which conflict with the fossil record in being too young, but all examined data partitions of rbcL and 18S depart substantially from a molecular clock. Age estimates are surprisingly insensitive to different views on seed-plant relationships. Randomization schemes were used to quantify confidence intervals due to phylogenetic uncertainty, substitutional noise, and lineage effects (deviations from a molecular clock). Estimates of the age of crown-group angiosperms range from 68 to 281 mya (million years ago), depending on data, tree, and assumptions, with most ～140-190 mya (Early Jurassic-earliest Cretaceous). Approximate 95% confidence intervals on ages are wider for rbcL than 18S, ranging up to 160 my for phylogenetic uncertainty, 90 my for substitutional noise, and 70 my for lineage effects. These intervals overlap the oldest occurrences of angiosperms in the fossil record, as well as some estimates from previous molecular studies.     

Comparative pollen morphology and ultrastructure of Platanus: Implications for phylogeny and evaluation of the fossil record

Pollen of Platanus was studied using light (LM) and electron microscopy (SEM and TEM). Overall, pollen is uniform in modern Platanus (small, tricolpate, prolate to spheroidal, reticulate, semitectate). A number of characters, however, display remarkable variability within a taxon and even a single anther (size; foveo‐reticulate, fine to coarse reticulate ornamentation). Platanus kerrii (subgenus Castaneophyllum) differs from the remaining species by its high and “folded” reticulum and possibly the smooth colpus membrane. Moreover, to our knowledge, pollen of the P. kerrii – type is not known from the fossil record. The exine in modern and fossil Platanaceae shows great structural similarity, but the thickness of the foot layer within the ectexine is less variable and normally smaller in modern taxa. Furthermore, in Early Cretaceous to Early Cainozoic Platanaceae a number of distinct pollen types occurred that are not known within the modern Platanus. Considering pollen of Platanaceae from the Early Cretaceous to today, a dynamic picture of the evolution of the family emerges. In the first phase (Early Cretaceous) pollen of extinct genera such as Aquia differed considerably from modern Platanus and shows strong similarity to basal eudicot taxa such as Ranunculales (e.g. Lardizabalaceae). The Late Cretaceous Platananthus hueberi displays a distinct coarse reticulum that is unknown from modern Platanus but similar to some taxa of Hamamelidaceae (e.g. Exbucklandia). After the first phase of eudicot radiation that appears to have been characterized by strongly reticulate evolution, platanaceous diversity decreased in the course of the Cainozoic. Despite this, the pollen type of the modern subgenus Castaneophyllum (P. kerrii type) seems to be an innovation that originated after the initial radiation of the family.     

吉林延边早白垩世大拉子组植物化石新类型--星学异麻黄

报道产自吉林省延边早白垩世大拉子组植物化石新类型——星学异麻黄(Alloephedra xingxuei gen.et sp.nov.)。大拉子组的时代处于早白垩世的阿普特期-阿尔必期(Aptian-Albian)。化石标本保存了植物的茎枝、雌球花及种子;该种的茎枝分节,节间具细纵槽纹,叶退化,雌球花单个着生于小枝顶部,种子成对且种子顶部宿存珠孔管等特征与现存麻黄科植物最为相近,因此可能属于麻黄科。