Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary

Tertiary macrofossils of the flowering plant family Leguminosae (legumes) were used as time constraints to estimate ages of the earliest branching clades identified in separate plastid matK and rbcL gene phylogenies. Penalized likelihood rate smoothing was performed on sets of Bayesian likelihood trees generated with the AIC-selected GTR+ Gamma +I substitution model. Unequivocal legume fossils dating from the Recent continuously back to about 56 million years ago were used to fix the family stem clade at 60 million years (Ma), and at 1-Ma intervals back to 70 Ma. Specific fossils that showed distinctive combinations of apomorphic traits were used to constrain the minimum age of 12 specific internal nodes. These constraints were placed on stem rather than respective crown clades in order to bias for younger age estimates. Regardless, the mean age of the legume crown clade differs by only 1.0 to 2.5 Ma from the fixed age of the legume stem clade. Additionally, the oldest caesalpinioid, mimosoid, and papilionoid crown clades show approximately the same age range of 39 to 59 Ma. These findings all point to a rapid family-wide diversification, and predict few if any legume fossils prior to the Cenozoic. The range of the matK substitution rate, 2.1-24.6 x 10(-10) substitutions per site per year, is higher than that of rbcL, 1.6- 8.6 x 10(-10), and is accompanied by more uniform rate variation among codon positions. The matK and rbcL substitution rates are highly correlated across the legume family. For example, both loci have the slowest substitution rates among the mimosoids and the fastest rates among the millettioid legumes. This explains why groups such as the millettioids are amenable to species-level phylogenetic analysis with these loci, whereas other legume groups are not.     

A new time-scale for ray-finned fish evolution

The Actinopterygii (ray-finned fishes) is the largest and most diverse vertebrate group, but little is agreed about the timing of its early evolution. Estimates using mitochondrial genomic data suggest that the major actinopterygian clades are much older than divergence dates implied by fossils. Here, the timing of the evolutionary origins of these clades is reinvestigated using morphological, and nuclear and mitochondrial genetic data. Results indicate that existing fossil-based estimates of the age of the crown-group Neopterygii, including the teleosts, Lepisosteus (gar) and Amia (bowfin), are at least 40 Myr too young. We present new palaeontological evidence that the neopterygian crown radiation is a Palaeozoic event, and demonstrate that conflicts between molecular and morphological data for the age of the Neopterygii result, in part, from missing fossil data. Although our molecular data also provide an older age estimate for the teleost crown, this range extension remains unsupported by the fossil evidence. Nuclear data from all relevant clades are used to demonstrate that the actinopterygian whole-genome duplication event is teleost-specific. While the date estimate of this event overlaps the probable range of the teleost stem group, a correlation between the genome duplication and the large-scale pattern of actinopterygian phylogeny remains elusive.     

The Impact of Ecology and Biogeography on Legume Diversity,Endemism, and Phylogeny in the Caribbean Region: A New Direction in Historical Biogeography

The legume family is so well represented in the Caribbean that if a preserve was needed somewhere on earth to harbor all of the primary lineages in this family, the flora of just Cuba would suffice. Molecular phylogenetic, biogeographic, and evolutionary rates analysis all suggest that legume diversity and endemism in the Caribbean are mostly of recent origin and are likely a function of the abundance of seasonally dry tropical forests (SDTFs) throughout the neotropics. Legumes have a strong ecological affinity for SDTFs, and the Caribbean basin is well covered by this forest type. Rate-variable molecular clock analysis suggests that the majority of worldwide island lineages of legumes have ages of much less than 30 Ma. Singular historical events invoking land bridges or mobile continental plates are thus not needed to explain Caribbean legume diversity and endemism. The Greater Antilles are large islands located close to the American continent. They are therefore expected to fairly represent the diverse continental lineages of legumes. Yet, they are distant enough to be dispersal limited. As such, island lineages can speciate and diversify over evolutionary time unimpeded by high rates of immigration from the mainland. Vicariance and other standard phylogenetic methods of historical biogeography are likely to be replaced by those of ecological and island biogeography. This is because model selection approaches derived from the neutral concept of isolation by distance will be able to quantify patterns of alpha and beta diversity and detect niche assembly and phylogenetic niche conservatism within and among metacommunities that are hypothesized to constrain phylogeny.     

Age Estimates for the Buckwheat Family Polygonaceae Based on Sequence Data Calibrated by Fossils and with a Focus on the Amphi-Pacific Muehlenbeckia

The buckwheat family Polygonaceae is a diverse group of plants and is a good model for investigating biogeography, breeding systems, coevolution with symbionts such as ants and fungi, functional trait evolution, hybridization, invasiveness, morphological plasticity, pollen morphology and wood anatomy. The main goal of this study was to obtain age estimates for Polygonaceae by calibrating a Bayesian phylogenetic analysis, using a relaxed molecular clock with fossil data. Based on the age estimates, we also develop hypotheses about the historical biogeography of the Southern Hemisphere group Muehlenbeckia. We are interested in addressing whether vicariance or dispersal could account for the diversification of Muehlenbeckia, which has a “Gondwanan” distribution.Eighty-one species of Polygonaceae were analysed with MrBayes to infer species relationships. One nuclear (nrITS) and three chloroplast markers (the trnL-trnF spacer region, matK and ndhF genes) were used. The molecular data were also analysed with Beast to estimate divergence times. Seven calibration points including fossil pollen and a leaf fossil of Muehlenbeckia were used to infer node ages.Results of the Beast analyses indicate an age of 110.9 (exponential/lognormal priors)/118.7 (uniform priors) million years (Myr) with an uncertainty interval of (90.7–125.0) Myr for the stem age of Polygonaceae. This age is older than previously thought (Maastrichtian, approximately 65.5–70.6 Myr). The estimated divergence time for Muehlenbeckia is 41.0/41.6 (39.6–47.8) Myr and its crown clade is 20.5/22.3 (14.2–33.5) Myr old. Because the breakup of Gondwana occurred from 95–30 Myr ago, diversification of Muehlenbeckia is best explained by oceanic long-distance and maybe stepping-stone dispersal rather than vicariance. This study is the first to give age estimates for clades of Polygonaceae and functions as a jumping-off point for future studies on the historical biogeography of the family.     

Ecological opportunity alters the timing and shape of adaptive radiation

The uneven distribution of diversity is a conspicuous phenomenon across the tree of life. Ecological opportunity is a prominent catalyst of adaptive radiation and therefore may alter patterns of diversification. We evaluated the distribution of shifts in diversification rates across the cichlid phylogeny and the distribution of major clades across phylogenetic space. We also tested if ecological opportunity influenced these patterns. Colonization‐associated ecological opportunity altered the tempo and mode of diversification during the adaptive radiation of cichlid fishes. Clades that arose following colonization events diversified faster than other clades. Speciation rate shifts were nonrandomly distributed across the phylogeny such that they were disproportionally concentrated around nodes that corresponded with colonization events (i.e., of continents, river basins, or lakes). Young clades tend to expand faster than older clades; however, colonization‐associated ecological opportunity accentuated this pattern. There was an interaction between clade age and ecological opportunity that explained the trajectory of clades through phylogenetic space over time. Our results indicate that ecological opportunities afforded by continental and ecosystem‐scale colonization events explain the dramatic speciation rate heterogeneity and phylogenetic imbalance that arose during the evolutionary history of cichlid fishes.     

Exploring the tempo of species diversification in legumes

Whatever criteria are used to measure evolutionary success – species numbers, geographic range, ecological abundance, ecological and life history diversity, background diversification rates, or the presence of rapidly evolving clades – the legume family is one of the most successful lineages of flowering plants. Despite this, we still know rather little about the dynamics of lineage and species diversification across the family through the Cenozoic, or about the underlying drivers of diversification. There have been few attempts to estimate net species diversification rates or underlying speciation and extinction rates for legume clades, to test whether among-lineage variation in diversification rates deviates from null expectations, or to locate species diversification rate shifts on specific branches of the legume phylogenetic tree. In this study, time-calibrated phylogenetic trees for a set of species-rich legume clades – Calliandra, Indigofereae, Lupinus, Mimosa and Robinieae – and for the legume family as a whole, are used to explore how we might approach these questions. These clades are analysed using recently developed maximum likelihood and Bayesian methods to detect species diversification rate shifts and test for among-lineage variation in speciation, extinction and net diversification rates. Possible explanations for rate shifts in terms of extrinsic factors and/or intrinsic trait evolution are discussed. In addition, several methodological issues and limitations associated with these analyses are highlighted emphasizing the potential to improve our understanding of the evolutionary dynamics of legume diversification by using much more densely sampled phylogenetic trees that integrate information across broad taxonomic, geographical and temporal levels.     

Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds

To test the hypothesis put forward by Feduccia of the origin of modern birds from transitional birds, we sequenced the first two complete mitochondrial genomes of shorebirds (ruddy turnstone and blackish oystercatcher) and compared their sequences with those of already published avian genomes. When corrected for rate heterogeneity across sites and non-homogeneous nucleotide compositions among lineages in maximum likelihood (ML), the optimal tree places palaeognath birds as sister to the neognaths including shorebirds. This optimal topology is a re-rooting of recently published ordinal-level avian trees derived from mitochondrial sequences. Using a penalized likelihood (PL) rate-smoothing process in conjunction with dates estimated from fossils, we show that the basal splits in the bird tree are much older than the Cretaceous-Tertiary (K-T) boundary, reinforcing previous molecular studies that rejected the derivation of modern birds from transitional shorebirds. Our mean estimate for the origin of modern birds at about 123 million years ago (Myr ago) is quite close to recent estimates using both nuclear and mitochondrial genes, and supports theories of continental break-up as a driving force in avian diversification. Not only did many modern orders of birds originate well before the K-T boundary, but the radiation of major clades occurred over an extended period of at least 40 Myr ago, thus also falsifying Feduccia's rapid radiation scenario following a K-T bottleneck.     

Phylogeny of the tribe Indigofereae (Leguminosae-Papilionoideae): Geographically structured more in succulent-rich and temperate settings than in grass-rich environments

This analysis goes beyond many phylogenies in exploring how phylogenetic structure imposed by morphology, ecology, and geography reveals useful evolutionary data. A comprehensive range of such diversity is evaluated within tribe Indigofereae and outgroups from sister tribes. A combined data set of 321 taxa (over one-third of the tribe) by 80 morphological characters, 833 aligned nuclear ribosomal ITS/5.8S sites, and an indel data set of 33 characters was subjected to parsimony analysis. Notable results include the Madagascan dry forest Disynstemon resolved as sister to tribe Indigofereae, and all species of the large genus Indigofera comprise just four main clades, each diagnosable by morphological synapomorphies and ecological and geographical predilections. These results suggest niche conservation (ecology) and dispersal limitation (geography) are important processes rendering signature shapes to the Indigofereae phylogeny in different biomes. Clades confined to temperate and succulent-rich biomes are more dispersal limited and have more geographical phylogenetic structure than those inhabiting tropical grass-rich vegetation. The African arid corridor, particularly the Namib center of endemism, harbors many of the oldest Indigofera lineages. A rates analysis of nucleotide substitutions confirms that the ages of the oldest crown clades are mostly younger than 16 Ma, implicating dispersal in explaining the worldwide distribution of the tribe.     

Phylogeny and historical biogeography of Agabinae diving beetles (Coleoptera) inferred from mitochondrial DNA sequences

The Agabinae, with more than 350 species, is one of the most diverse lineages of diving beetles (Dytiscidae). Using the mitochondrial genes 16S rRNA and cytochrome oxidase I we present a phylogenetic analysis based on 107 species drawn mostly from the four main Holarctic genera. Two of these genera (Ilybius and Ilybiosoma) are consistently recovered as monophyletic with strong support, Platambus is never recovered as monophyletic, and Agabus is found paraphyletic with respect to several of the species groups of Platambus. Basal relationships among the main lineages are poorly defined, although within each of them relationships are in general robust and very consistent across the parameter space, and in agreement with previous morphological analyses. In each of the two most diverse lineages (Ilybius and Agabus including part of Platambus) there is a basal split between Palearctic and Nearctic clades, estimated to have occurred in the late Eocene. The Palearctic clade in turn splits into a Western Palearctic clade and a clade containing mostly Eastern Palearctic species, and assumed to be ancestrally Eastern Palearctic but with numerous transitions to a Holarctic or Nearctic distribution. These results suggest an asymmetry in the colonization routes, as there are very few cases of transcontinental range expansions originating from the Nearctic or the Western Palearctic. According to standard clock estimates, we do not find any transcontinental shift during the Pliocene, but numerous speciation events within each of the continental or subcontinental regions.     

Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

Major disparities are recognized between molecular divergence dates and fossil ages for critical nodes in the Tree of Life, but broad patterns and underlying drivers remain elusive. We harvested 458 molecular age estimates for the stem and crown divergences of 67 avian clades to explore empirical patterns between these alternate sources of temporal information. These divergence estimates were, on average, over twice the age of the oldest fossil in these clades. Mitochondrial studies yielded older ages than nuclear studies for the vast majority of clades. Unexpectedly, disparity between molecular estimates and the fossil record was higher for divergences within major clades (crown divergences) than divergences between major clades (stem divergences). Comparisons of dates from studies classed by analytical methods revealed few significant differences. Because true divergence ages can never be known with certainty, our study does not answer the question of whether fossil gaps or molecular dating error account for a greater proportion of observed disparity. However, empirical patterns observed here suggest systemic overestimates for shallow nodes in existing molecular divergence dates for birds. We discuss underlying biases that may drive these patterns.     

Early Tertiary mammals from North Africa reinforce the molecular Afrotheria clade

The phylogenetic pattern and timing of the radiation of mammals, especially the geographical origins of major crown clades, are areas of controversy among molecular biologists, morphologists and palaeontologists. Molecular phylogeneticists have identified an Afrotheria clade, which includes several taxa as different as tenrecs (Tenrecidae), golden moles (Chrysochloridae), elephant-shrews (Macroscelididae), aardvarks (Tubulidentata) and paenungulates (elephants, sea cows and hyracoids). Molecular data also suggest a Cretaceous African origin for Afrotheria within Placentalia followed by a long period of endemic evolution on the Afro-Arabian continent after the mid-Cretaceous Gondwanan breakup (approx. 105-25 Myr ago). However, there was no morphological support for such a natural grouping so far. Here, we report new dental and postcranial evidence of Eocene stem hyrax and macroscelidid from North Africa that, for the first time, provides a congruent phylogenetic view with the molecular Afrotheria clade. These new fossils imply, however, substantial changes regarding the historical biogeography of afrotheres. Their long period of isolation in Africa, as assumed by molecular inferences, is now to be reconsidered inasmuch as Eocene paenungulates and elephant-shrews are here found to be related to some Early Tertiary Euramerican 'hyopsodontid condylarths' (archaic hoofed mammals). As a result, stem members of afrotherian clades are not strictly African but also include some Early Paleogene Holarctic mammals.     

Evolution of the species-rich Cape flora

The Cape Floristic Region ('fynbos biome') has very high levels of plant species diversity and endemism. Much of this diversity is concentrated in a relatively small number of clades centered in the region (Cape clades), and these form a vegetation called 'fynbos'. The general explanation for the origin of this diversity is that much of it evolved in the Pliocene and Late Miocene in response to progressive aridification. We present a phylogenetic analysis of an almost complete species sample of the largest clade of Restionaceae, the third largest Cape clade. This indicates that the radiation of the Restionaceae started between 20 and 42 Myr ago, and since then there were no, or at most gradual, changes in the speciation rate in this clade. For seven other clades, the estimated starting dates for their radiation ranges from 7 to 20 Myr ago. Combining the radiation patterns for these clades shows that ca. 15% of the modern species evolved during the Pleistocene, and almost 40% since the beginning of the Pliocene. We suggest that these clades might have radiated in response to the fynbos vegetation increasing its extent in the Cape as a result of climatic change.     

Angiosperm divergence times: the effect of genes, codon positions, and time constraints

An understanding of the evolution of modern terrestrial ecosystems requires an understanding of the dynamics associated with angiosperm evolution, including the timing of their origin and diversification into their extraordinary present-day diversity. Molecular estimates of angiosperm age have varied widely, and many substantially predate the Early Cretaceous fossil appearance of the group. In this study, the effect of different genes, codon positions, and chronological constraints on node ages are examined on divergence time estimates across seed plants, with a special focus on angiosperms. Penalized likelihood was used to estimate divergence times on a phylogenetic hypothesis for seed plants derived from Bayesian analysis, with branch lengths estimated with maximum likelihood. The plastid genes atpB, psaA, psbB, and rbcL were used individually and in combination, using first and second, third, and the three codon positions, including and excluding age constraints on 20 nodes derived from a critical examination of the land-plant fossil record. The optimal level of rate smoothing according to each unconstrained and constrained dataset was obtained with penalized likelihood. Tests for a molecular clock revealed significantly unclocklike rates in all datasets. Addition of fossil constraints resulted in even greater departures from constancy. Consistently with significant deviations from a clock, estimated optimal smoothing values were low, but a strict correlation between rate heterogeneity and optimal smoothing value was not found. Age estimates for nodes across the phylogeny varied, sometimes substantially, with gene and codon position. Nevertheless, estimates based on the four concatenated genes are very similar to the mean of the four individual gene estimates. For any given node, unconstrained age estimates are more variable than constrained estimates and are frequently younger than well-substantiated fossil members of the clade. Constrained estimates of ages of clades are older than unconstrained estimates and oldest fossil representatives, sometimes substantially so. Angiosperm age estimates decreased as rate smoothing increased. Whereas the range of unconstrained angiosperm age estimates spans the fossil age of the clade, the range of constrained estimates is narrower (and older) than the earliest angiosperm fossils. Results unambiguously indicate the relevance of constraints in reducing the variability of ages derived from different partitions of the data and diminishing the effect of the smoothing parameter. Constrained optimizations of divergence times and substitution rates across the phylogeny suggest appreciably different evolutionary dynamics for angiosperms and for gymnosperms. Whereas the gymnosperm crown group originated shortly after the origin of seed plants, a long time elapsed before the origin of crown group angiosperms. Although absolute age estimates of angiosperms and angiosperm clades are older than their earliest fossils, the estimated pace of phylogenetic diversification largely agrees with the rapid appearance of angiosperm lineages in stratigraphic sequences.     

Bees diversified in the age of eudicots

Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages. To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record. We explore the effect of placing a hard upper age bound near the root of the tree and the effect of different topologies on our divergence time estimates. We estimate that crown bees originated approximately 123 Ma (million years ago) (113–132 Ma), concurrently with the origin or diversification of the eudicots, a group comprising 75 per cent of angiosperm species. All of the major bee clades are estimated to have originated during the Middle to Late Cretaceous, which is when angiosperms became the dominant group of land plants.     

Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from analyses of nuclear and chloroplast DNA regions

From a phylogenetic perspective, the genus Manihot can be considered as an orphan group of plants, and the scientific knowledge acquired has been mainly related to cassava, one of the most important crops in poor tropical countries. The goal of the majority of evolutionary studies in the genus has been to decipher the domestication process and identify the closest relatives of cassava. Few investigations have focused on wild Manihot species, and the phylogeny of the genus is still unclear. In this study the DNA sequence variation from two chloroplast regions, the nuclear DNA gene G3pdh and two nuclear sequences derived from the 3'-end of two cassava ESTs, were used in order to infer the phylogenetic relationships among a subset of wild Manihot species, including two species from Cnidoscolus as out-groups. Maximum parsimony and Bayesian analyses were conducted for each data set and for a combined matrix due to the low variation of each region when analyzed independently. A penalized likelihood analysis of the chloroplast region trnL-trnF, calibrated with various age estimates for genera in the Euphorbiaceae extracted from the literature was used to determine the ages of origin and diversification of the genus. The two Mesoamerican species sampled form a well-defined clade. The South American species can be grouped into clades of varying size, but the relationships amongst them cannot be established with the data available. The age of the crown node of Manihot was estimated at 6.6 million years ago. Manihot esculenta varieties do not form a monophyletic group that is consistent with the possibility of multiple introgressions of genes from other wild species. The low levels of variation observed in the DNA regions sampled suggest a recent and explosive diversification of the genus, which is confirmed by our age estimates.     

Origin of the endemic fern genus Diellia coincides with the renewal of Hawaiian terrestrial life in the Miocene

The enigmatic fern genus Diellia, endemic to the Hawaiian archipelago, consists of five extant and one recently extinct species. Diellia is morphologically highly variable, and a unique combination of characters has led to several contrasting hypotheses regarding the relationship of Diellia to other ferns. A phylogenetic analysis of four chloroplast loci places Diellia within 'black-stemmed' rock spleenworts of the species-rich genus Asplenium, as previously suggested by W. H. Wagner. Using an external calibration point, we estimate the divergence of the Diellia lineage from its nearest relatives to have occurred at ca. 24.3 Myr ago matching an independent estimate for the renewal of Hawaiian terrestrial life (ca. 23 Myr ago). We therefore suggest that the ancestor of the Diellia lineage may have been among the first successful colonists of the newly emerging islands in the archipelago. Disparity between morphological and nucleotide sequence variation within Diellia is consistent with a recent rapid radiation. Our estimated time of the Diellia radiation (ca. 2 Myr ago) is younger than the oldest island of Kaua'i (ca. 5.1 Myr ago) but older than the younger major islands of Maui (ca. 1.3 Myr ago), Lana'i (ca. 1.3 Myr ago) and Hawaii (ca. 0.43 Myr ago).     

Phylogenetic relationships based on two mitochondrial genes and hybridization patterns in Anatidae

We produced DNA sequence data from two mitochondrial genes (cytochrome b and the NADH dehydrogenase subunit 2) to reconstruct the phylogenetic relationships among 121 species of the Anseriformes (waterfowls including ducks, geese, swans, the magpie goose and screamers). Phylogenetic analyses converged into a congruent topology and defined several well-supported clades. We calibrated a molecular clock and reconstructed ancestral biogeographical areas using Bayesian inference supporting an austral continental (Gondwanaland) origin of the waterfowls. Ducks, swans and geese might have diversified during the Miocene (23–5 Myr ago) reaching northern distributions in Holarctic and Afrotropical regions. The evolution of hybridization patterns in Anseriformes has been investigated using a cladistic analysis (morphology), which may underestimate or overestimate the phylogenetic divergence among species, or restricted only to ducks. Using a phylogenetic framework, genetic-based distances and a Bayesian time calibration, our data support the hypothesis based on immunological distances of slow rate of appearance of reproductive incompatibilities in waterfowls compared with other vertebrates and the view that these birds may be like frogs in having lost their interspecific hybridization potential more slowly than mammals.     

Ecological controls of mammalian diversification vary with phylogenetic scale

Aim

Diversity dynamics remain controversial. Here, we examine these dynamics, together with the ecological factors governing them, across mammalian clades of different ages and sizes, representing different phylogenetic scales. Specifically, we investigate whether the dynamics are bounded or unbounded, biotically or abiotically regulated, stochastic or ecologically deterministic.

Location

Worldwide.

Time period

150 Myr.

Major taxa studied

Mammals.

Methods

Integrating the newest phylogenetic and distributional data by means of several distinct methods, we study the ecology of mammalian diversification within a predictive framework, inspired by classic theory. Specifically, we evaluate the effects of several classes of factors, including climate, topography, geographical area, rates of climatic‐niche evolution, and regional coexistence between related and unrelated species. Next, we determine whether the relative effects of these factors change systematically across clades representing different phylogenetic scales.

Results

We find that young clades diversify at approximately constant rates, medium‐sized clades show diversification slowdowns, and large clades are mostly saturated, suggesting that diversification dynamics change as clades grow and accumulate species. We further find that diversification slowdowns intensify with the degree of regional coexistence between related species, presumably because increased competition for regional resources suppresses the diversification process. The richness at which clades eventually saturate depends on climate; clades residing in tropical climates saturate at low richness, implying that niches become progressively densely packed towards the tropics.

Main conclusions

The diversification process is influenced by a variety of ecological factors, whose relative effects change across phylogenetic scales, producing scale‐dependent dynamics. Different segments of the same phylogeny might therefore support seemingly conflicting results (bounded or unbounded, biotically or abiotically regulated, stochastic or ecologically deterministic diversification), which might have contributed to several outstanding controversies in the field. These conflicts can be reconciled, however, when accounting for phylogenetic scale, which might, in turn, produce a more integrated understanding of global diversity dynamics.     

The cambrian evolutionary ‘explosion’ recalibrated

The sudden appearance in the fossil record of the major animal phyla apparently records a phase of unparalleled, rapid evolution at the base of the Cambrian period, 545 Myr ago. This has become known as the Cambrian evolutionary ‘explosion’, and has fuelled speculation about unique evolutionary processes operating at that time. The acceptance of the palaeontological evidence as a true reflection of the evolutionary narrative has been criticised in two ways: from a reappraisal of the phylogenetic relationships of the early fossils, and from predicitions of molecular divergence times, based on six appropriate metazoan genes. Phylogenetic analysis of the arthropods implies an earlier, Precambrian history for most clades, and hence an extensive period of cladogenesis unrecorded by fossils. A similar argument can be applied to molluscs, lophophorates and deuterostomes. Molecular evidence implies divergence between clades to at least 1000 Myr ago. The apparent paradox between the sudden appearance of recognisable metazoans and their extended evolutionary history might be explained by a sudden Cambrian increase in body size, which was accompanied by skeletisation. A new paradigm suggests that the ‘explosion’ in the record may have been decoupled from the evolutionary innovation.     

Phylogeny of taxaceae and cephalotaxaceae genera inferred from chloroplast matK gene and nuclear rDNA ITS region

Phylogeny of the Taxaceae genera and the monotypic family Cephalotaxaceae has been extraordinarily controversial. In this paper chloroplast matK genes and nuclear ITS sequences were determined for all six genera of the two families and representatives of other conifer families. Analysis using either the nonsynonymous sites or the deduced amino acid sequences of matK genes strongly indicates that taxad genera and Cephalotaxaceae are monophyletic, with the Taxodiaceae/Cupressaceae clade as their sister group. Cephalotaxus is basal to the taxad genera, among which two clades, Torreya/Amentotaxus and Taxus/Pseudotaxus/Austrotaxus, are resolved. They correspond to Janchen's two tribes, Torreyeae and Taxeae. In Taxeae, Austrotaxus is the first to branch off. Analyses of the nuclear ITS sequence data corroborated the topology of the matK gene tree. These results refute the views that Cephalotaxaceae has no alliance with Taxaceae and that Austrotaxus and Amentotaxus should be excluded from the Taxaceae. We estimated the divergence time between the Taxodiaceae/Cupressaceae and the Cephalotaxaceae/Taxaceae clades to be 192-230 Myr ago and the divergence time between taxads and Cephalotaxus to be 149-179 Myr ago. Soon after the latter divergence event, within 6-8 Myr, the two taxad tribes originated. In conclusion, our data do not support Florin's claim that taxads could be traced to Devonian psilophytes (359-395 Myr ago).