Nothofagus: Evolution from a southern perspective

Nothofagus holds a premier position in the study of Southern Hemisphere plant evolution and biogeography, and many have attempted to reconstruct its history. A recent surge of research on both living and fossil species has added valuable data to the debate, but has also introduced complications, including the now less certain familial relationships of the genus. The vast quantity of fossil evidence provides an extremely firm base for reconstruction of the past distribution of Nothofagus, and allows informed speculation on the time and places of origin and major speciation events.     

Not so divided: the common basis of plant and animal cell division

Plant cells do not have centrioles and their mitosis is frequently likened to the chromosome-based mechanism seen in acentriolar animal cells. However, this is a false analogy. Although plants can use this mechanism, they generally divide by a method that uses bipolar mitotic caps, which is more similar to the canonical centrosome-based method of animals.     

Disentangling ancient interactions: a new extinct passerine provides insights on character displacement among extinct and extant island finches

Background

Evolutionary studies of insular biotas are based mainly on extant taxa, although such biotas represent artificial subsets of original faunas because of human-caused extinctions of indigenous species augmented by introduced exotic taxa. This makes it difficult to obtain a full understanding of the history of ecological interactions between extant sympatric species. Morphological bill variation of Fringilla coelebs and F. teydea (common and blue chaffinches) has been previously studied in the North Atlantic Macaronesian archipelagos. Character displacement between both species has been argued to explain bill sizes in sympatry. However, this explanation is incomplete, as similar patterns of bill size have been recorded in F. coelebs populations from islands with and without F. teydea.

Methodology/Principal Findings

The discovery of a new extinct species in Tenerife (Canary Islands), here named Carduelis aurelioi n. sp. (slender-billed greenfinch), provides the opportunity to study ancient ecological interactions among Macaronesian finches. To help understand the evolutionary histories of forest granivores in space and time, we have performed a multidisciplinary study combining: (1) morphological analyses and radiocarbon dating (11,460±60 yr BP) of the new taxon and, (2) molecular divergence among the extant finch species and populations in order to infer colonization times (1.99 and 1.09 My for F. teydea and F. coelebs respectively).

Conclusion/Significance

C. aurelioi, F. coelebs and F. teydea co-habited in Tenerife for at least one million years. The unique anatomical trends of the new species, namely chaffinch-like beak and modified hind and forelimbs, reveal that there was a process of divergence of resource competition traits among the three sympatric finches. The results of our study, combined with the presence of more extinct greenfinches in other Macaronesian islands with significant variation in their beak sizes, suggests that the character displacement has influenced patterns of divergence in bill size and shape on other Macaronesian islands as well.     

Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)

Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.     

Not so simple after all: searching for ecological advantages of compound leaves

Leaves come in many sizes and shapes, and the relationships between leaf traits and the environments they occur in are better understood every day. However we still know very little about the ecological consequences of plants having either compound or simple leaves. We attempted to address this knowledge gap by comparing chemical and physical characteristics (leaf area, length:width ratio, water content, leaf mass per area, ‘toughness’ and C:N ratio), as well as rates of herbivory between compound and simple leaves across 34 species in adjacent rainforest, open woodland and wet sclerophyll (tall open forest) vegetation in northeastern Australia. We found C:N ratio to be lower in simple leaves, but this was the only leaf trait that differed significantly between leaf types and did not stand up under phylogenetic analysis. Overall, we found no differences in herbivory between simple and compound leaves. While it remains unclear what the advantages of having one leaf type over another might be, the differences do not seem to lie in construction, or in vulnerability to herbivores, at least in the Australian Wet Tropics.     

Not so different after all: a comparison of methods for detecting amino acid sites under selection

We consider three approaches for estimating the rates of nonsynonymous and synonymous changes at each site in a sequence alignment in order to identify sites under positive or negative selection: (1) a suite of fast likelihood-based counting methods that employ either a single most likely ancestral reconstruction, weighting across all possible ancestral reconstructions, or sampling from ancestral reconstructions; (2) a random effects likelihood (REL) approach, which models variation in nonsynonymous and synonymous rates across sites according to a predefined distribution, with the selection pressure at an individual site inferred using an empirical Bayes approach; and (3) a fixed effects likelihood (FEL) method that directly estimates nonsynonymous and synonymous substitution rates at each site. All three methods incorporate flexible models of nucleotide substitution bias and variation in both nonsynonymous and synonymous substitution rates across sites, facilitating the comparison between the methods. We demonstrate that the results obtained using these approaches show broad agreement in levels of Type I and Type II error and in estimates of substitution rates. Counting methods are well suited for large alignments, for which there is high power to detect positive and negative selection, but appear to underestimate the substitution rate. A REL approach, which is more computationally intensive than counting methods, has higher power than counting methods to detect selection in data sets of intermediate size but may suffer from higher rates of false positives for small data sets. A FEL approach appears to capture the pattern of rate variation better than counting methods or random effects models, does not suffer from as many false positives as random effects models for data sets comprising few sequences, and can be efficiently parallelized. Our results suggest that previously reported differences between results obtained by counting methods and random effects models arise due to a combination of the conservative nature of counting-based methods, the failure of current random effects models to allow for variation in synonymous substitution rates, and the naive application of random effects models to extremely sparse data sets. We demonstrate our methods on sequence data from the human immunodeficiency virus type 1 env and pol genes and simulated alignments.     

Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers

Evolutionary theory has gained tremendous insight from studies of adaptive radiations. High rates of speciation, morphological divergence, and hybridization, combined with low sequence variability, however, have prevented phylogenetic reconstruction for many radiations. The Hawaiian honeycreepers are an exceptional adaptive radiation, with high phenotypic diversity and speciation that occurred within the geologically constrained setting of the Hawaiian Islands. Here we analyze a new data set of 13 nuclear loci and pyrosequencing of mitochondrial genomes that resolves the Hawaiian honeycreeper phylogeny. We show that they are a sister taxon to Eurasian rosefinches (Carpodacus) and probably came to Hawaii from Asia. We use island ages to calibrate DNA substitution rates, which vary substantially among gene regions, and calculate divergence times, showing that the radiation began roughly when the oldest of the current large Hawaiian Islands (Kauai and Niihau) formed, ~5.7 million years ago (mya). We show that most of the lineages that gave rise to distinctive morphologies diverged after Oahu emerged (4.0-3.7 mya) but before the formation of Maui and adjacent islands (2.4-1.9 mya). Thus, the formation of Oahu, and subsequent cycles of colonization and speciation between Kauai and Oahu, played key roles in generating the morphological diversity of the extant honeycreepers.     

Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal

The structure of human telomere DNA is of intense interest because of its role in the biology of both cancer and aging. The sequence [5′-AGGG(TTAGGG)₃] has been used as a model for telomere DNA in both NMR and X-ray crystallographic studies, the results of which show dramatically different structures. In Na⁺ solution, NMR revealed an antiparallel G-quadruplex structure that featured both diagonal and lateral TTA loops. Crystallographic studies in the presence of K⁺ revealed a flattened, propeller-shaped structure featuring a parallel-stranded G-quadruplex with symmetrical external TTA loops. We report the results of biophysical experiments in solution and computational studies that are inconsistent with the reported crystal structure, indicating that a different structure exists in K⁺ solutions. Sedimentation coefficients were determined experimentally in both Na⁺ and K⁺ solutions and were compared with values calculated using bead models for the reported NMR and crystal structures. Although the solution NMR structure accurately predicted the observed S-value in Na⁺ solution, the crystal structure predicted an S-value that differed dramatically from that experimentally observed in K⁺ solution. The environments of loop adenines were probed by quantitative fluorescence studies using strategic and systematic single-substitutions of 2-aminopurine for adenine bases. Both fluorescence intensity and quenching experiments in K⁺ yielded results at odds with quantitative predictions from the reported crystal structure. Circular dichroism and fluorescence quenching studies in the presence of the crowding agent polyethylene glycol showed dramatic changes in the quadruplex structure in K⁺ solutions, but not in Na⁺ solutions, suggesting that the crystal environment may have selected for a particular conformational form. Molecular dynamics simulations were performed to yield model structures for the K⁺ quadruplex form that are consistent with our biophysical results and with previously reported chemical modification studies. These models suggest that the biologically relevant structure of the human telomere quadruplex in K⁺ solution is not the one determined in the published crystalline state.     

Phylogeny of Saxifragales (angiosperms,eudicots): analysis of a rapid,ancient radiation

Rapid, ancient radiations pose one of the most difficult challenges for phylogenetic estimation. We used DNA sequence data of 9,006 aligned base pairs from five genes (chloroplast atpB, matK, rbcL, and 18S and 26S nrDNA) to elucidate relationships among major lineages of Saxifragales (angiosperms, eudicots). These relationships were poorly supported in previous studies, apparently because the lineages originated in rapid succession. Using an array of methods that explicitly incorporate assumptions about evolutionary process (weighted maximum parsimony, maximum likelihood, LogDet/paralinear transformed distances), we show that the initial diversification of Saxifragales was indeed rapid. We suggest that the poor resolution of our best phylogenetic estimate is not due to violations of assumptions or to combining data partitions having conflicting histories or processes. We show that estimated branch lengths during the initial diversification are exceedingly short, and we estimate that acquiring sufficient sequence data to resolve these relationships would require an extraordinary effort (approximately 10(7) bp), assuming a linear increase in branch support with branch length. However, our simulation of much larger data sets containing a distribution of phylogenetic signal similar to that of the five sampled gene sequences suggests a limit to achievable branch support. Using statistical tests of differences in the likelihoods of topologies, we evaluated whether the initial radiation of Saxifragales involved the simultaneous origin of major lineages. Our results are consistent with predictions that resolving the branching order of rapid, ancient radiations requires sampling characters that evolved rapidly at the time of the radiation but have since experienced a slower evolutionary rate.     

Genetic elucidation of cryptic and ancient diversity in a group of Australian diplodactyline geckos: the Diplodactylus vittatus complex

We examine species boundaries and phylogenetic relationships within the Australian diplodactyline geckos currently assigned to Diplodactylus granariensis and Diplodactylus vittatus using data from multiple allozyme loci, the mitochondrial ND2 gene and published karyotypic studies. These analyses uncover at least six morphologically cryptic but genetically distinctive species. The taxa identified correspond poorly with the existing taxonomy and represent a paraphyletic assemblage with respect to a number of other Diplodactylus species included in analyses. Molecular dating indicates that the species identified evolved considerably before the Pleistocene, and that the basal node of the D. vittatus species group (as redefined here) is of comparable age to entire radiations of other Australian squamate families. The antiquity of this one small group within the diplodactyline geckos suggests that further study of patterns of diversification in the diplodactylines will provide both a valuable insight into long-term patterns of environmental change in the Australian continent and a useful contrast for analysis of patterns of radiation in other Australian lizard groups.     

Ecological innovations in the Cambrian and the origins of the crown group phyla

Simulation studies of the early origins of the modern phyla in the fossil record, and the rapid diversification that led to them, show that these are inevitable outcomes of rapid and long-lasting radiations. Recent advances in Cambrian stratigraphy have revealed a more precise picture of the early bilaterian radiation taking place during the earliest Terreneuvian Series, although several ambiguities remain. The early period is dominated by various tubes and a moderately diverse trace fossil record, with the classical ‘Tommotian’ small shelly biota beginning to appear some millions of years after the base of the Cambrian at ca 541 Ma. The body fossil record of the earliest period contains a few representatives of known groups, but most of the record is of uncertain affinity. Early trace fossils can be assigned to ecdysozoans, but deuterostome and even spiralian trace and body fossils are less clearly represented. One way of explaining the relative lack of clear spiralian fossils until about 536 Ma is to assign the various lowest Cambrian tubes to various stem-group lophotrochozoans, with the implication that the groundplan of the lophotrochozoans included a U-shaped gut and a sessile habit. The implication of this view would be that the vagrant lifestyle of annelids, nemerteans and molluscs would be independently derived from such a sessile ancestor, with potentially important implications for the homology of their sensory and nervous systems.     

Taxonomy and phylogeny of the Hister servus group (Coleoptera: Histeridae): a Neotropical radiation

The Hister servus group contains ten species and two species complexes. Although the group’s diversity is centred in Mexico and Central America, one lineage, comprising H. indistinctus Say, H. defectus LeConte and H. fungicola Schaeffer, has probably diversified entirely in the south-eastern U.S. The servus group also contains the following species: H. servus Erichson , H. nodatus lewis , H. doyeni sp.n., H. lagoi sp.n., H. bullatus lewis , H. coronatus Marseul and H. diadema Marseul and two diverse species complexes, dubbed the comes complex and the montivagus complex. These two complexes require additional sampling and study before species within them can be recognized. They are, however, closely related to each other and appear to be paraphyletic with respect to a clade comprising H. bullatus, H. coronatus and H. diadema. A prior hypothesis that the servus group includes H. sallei, H. matador sp.n. and the species of Hister (Spilodiscus) is not well supported. Several sister groups within the servus group show geographical disjunction between seasonal tropical habitats of western North America and wetter montane habitats of the eastern parts of the continent along the Gulf and Caribbean coasts.     

Batesian insect-insect mimicry-related explosive radiation of ancient alienopterid cockroaches

Batesian mimicry is a relationship in which a harmful organism (the model) is mimicked by a harmless organism (the mimic), which gains protection because predators mistake it for the model. It is the most widely studied of mimicry complexes and has undoubtedly played an important role in the speciation of various animals especially insects. However, little is known about the early evolution of this important behavior and its evolutionary significance owing to a dearth of paleontological records. Here we report several specialized representatives of the family Alienopteridae from the Early Cretaceous of Brazil, mid-Cretaceous Burmite, and the Eocene of the USA. They exhibit unique morphological adaptations for wasp and ant mimicry and represent one of the oldest evidence of Batesian mimicry in the insect fossil record. Our findings reveal at least 65-million-year coevolution between extinct alienopterids and aculeates. Phylogenetic Bayesian network analysis houses Alienopteridae within Umenocoleidae explosively radiating ~127 Ma. Alienopteridae is the only Mesozoic-type cockroach family which passed K/Pg.     

Transition within the exine of Nothofagus Blume

Pollen grains with bulged areas on their proximal and distal faces were observed in some species of Nothofagus Blume in the light and electron microscopes. Pollen grains sectioned meridionally are distinctly transitionary in character in the individual strata within the exine of one pollen grain. The tectum in the apocolpia is considerably thinner than in the mesocolpia, The thickness and the character of the bacular layer in the mesocolpia differ greatly from those of the apocolpia. The foot layer, thick and always present in the mesocolpia, is entirely lacking in the apocolpia. The significant difference in the structure and thickness of the bacular layer, as well as the partial absence of the foot layer in one pollen grain, influence the cohesion between the individual strata of the exine in the apocolpia. The cohesion between the tectum and underlying, globular stratum in the central part of the apocolpia is poor, which facilitates the separation of the tectum and its bulging at that area.