Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1

This is an electronic version of an article published in Systematic Biology, 2007; 56 (4):543-563. Systematic Biology is available online at informaworld: http://www.informaworld.com/smpp/content~db=all?content=10.1080/10635150701477825A phylogeny of tetrapods is inferred from nearly complete sequences of the nuclear RAG-1 gene sampled across 88 taxa encompassing all major clades, analyzed via parsimony and Bayesian methods. The phylogeny provides support for Lissamphibia, Theria, Lepidosauria, a turtle-archosaur clade, as well as most traditionally accepted groupings. This tree allows simultaneous molecular clock dating for all tetrapod groups using a set of well-corroborated calibrations. Relaxed clock (PLRS) methods, using the amniote = 315 Mya (million years ago) calibration or a set of consistent calibrations, recovers reasonable divergence dates for most groups. However, the analysis systematically underestimates divergence dates within archosaurs. The bird-crocodile split, robustly documented in the fossil record as being around ∼ 245 Mya, is estimated at only ∼ 190 Mya, and dates for other divergences within archosaurs are similarly underestimated. Archosaurs, and particulary turtles have slow apparent rates possibly confounding rate modeling, and inclusion of calibrations within archosaurs (despite their high deviances) not only improves divergence estimates within archosaurs, but also across other groups. Notably, the monotreme-therian split (∼ 210 Mya) matches the fossil record; the squamate radiation (∼ 190 Mya) is younger than suggested by some recent molecular studies and inconsistent with identification of ∼ 220 and ∼ 165 Myo (million-year-old) fossils as acrodont iguanians and ∼ 95 Myo fossils colubroid snakes; the bird-lizard (reptile) split is considerably older than fossil estimates (≤ 285 Mya); and Sphenodon is a remarkable phylogenetic relic, being the sole survivor of a lineage more than a quarter of a billion years old. Comparison with other molecular clock studies of tetrapod divergences suggests that the common practice of enforcing most calibrations as minima, with a single liberal maximal constraint, will systematically overestimate divergence dates. Similarly, saturation of mitochondrial DNA sequences, and the resultant greater compression of basal branches means that using only external deep calibrations will also lead to inflated age estimates within the focal ingroup.Andrew F. Hugall; Ralph Foster; Michael S. Y. Le

Nucleotide polymorphisms and an improved PCR-based mtDNA diagnostic for parthenogenetic root-knot nematodes (Meloidogyne spp.)

L'analyse de séquences de 2212 paires de bases provenant de six ADN mitochondriaux haplotypes très voisins de #Meloidogyne (Hugall et al., 1994) a permis de mettre en évidence douze sites nucléotidiens polymorphiques et une délétion. En dépit de cette faible diversité, il existe assez de sites différents d'enzymes de restriction parmi ces séquences pour fournir des tests de diagnostic. En utilisant un choix de ces sites, il a été mis au point un test diagnostique multiplex fondé sur l'amplification en chaîne par polymérase (PCR), test amplifiant simultanément deux étroites régions du génome mitochondrial, et digérant ensuite le produit par HinfI ou MnlI. Ce test diagnostique permet d'identifier les haplotypes - même en mélange - présents chez #M. arenaria, #M. incognita, #M. javanica et #M. hispanica, ainsi que chez #M. hapla et #M. chitwoodi. Ce nouveau test représente une amélioration par rapport aux tests PCR sur DNA mitochondrial appliqués aux #Meloidogyne en ce sens qu'il permet la discrimination entre un plus grand nombre d'espèces et de races (par ex. : races de #M. arenaria vis-à-vis de #M. javanica) ; de plus, des produits plus réduits étant amplifiés, ce test est de ce fait plus robuste. Ont été également mis au point des amorces amplifiant une région de 63 paires de bases en nombre variable de répétitions en tandem. Les schémas de zonation qui en résultent permettent de différencier les isolats à l'intérieur des haplotypes d'enzymes de restriction et peuvent être utilisés pour vérifier l'identité des isolats de nématodes maintenus en élevage. (Résumé d'auteur

Two distinct forms of Chlamydia psittaci associated with disease and infertility in Phascolarctos cinereus (Koala)

While several diseases associated with Chlamydia psittaci infection have been reported in Phascolarctos cinereus (koala), it is still unclear whether one or more chlamydial strains are responsible. In this study, we provide evidence, obtained by restriction enzyme and gene probe analysis, that two quite distinct strains of C. psittaci infect koalas; one strain was isolated from the conjunctivae, and the other was isolated from the urogenital tract and the rectum. A gene probe, pFEN207, containing the coding sequence for an enzyme involved in the biosynthesis of the chlamydial genus-specific lipopolysaccharide antigen, and a separate probe, pCPML-4N, prepared from a DNA fragment of a koala-infecting strain of C. psittaci, were used to determine the patterns of hybridization in the koala-infecting strains; these patterns were found to be quite distinct from those observed with C. psittaci isolates from other animals. We also demonstrated by hybridization analysis with an avian strain plasmid that all three koala urogenital isolates contain a plasmid and that there is no evidence for the presence of a homologous plasmid in any of the ocular isolates

Monitoring Early-Stage Nanoparticle Assembly in Microdroplets by Optical Spectroscopy and SERS.

Microfluidic microdroplets have increasingly found application in biomolecular sensing as well as nanomaterials growth. More recently the synthesis of plasmonic nanostructures in microdroplets has led to surface-enhanced Raman spectroscopy (SERS)-based sensing applications. However, the study of nanoassembly in microdroplets has previously been hindered by the lack of on-chip characterization tools, particularly at early timescales. Enabled by a refractive index matching microdroplet formulation, dark-field spectroscopy is exploited to directly track the formation of nanometer-spaced gold nanoparticle assemblies in microdroplets. Measurements in flow provide millisecond time resolution through the assembly process, allowing identification of a regime where dimer formation dominates the dark-field scattering and SERS. Furthermore, it is shown that small numbers of nanoparticles can be isolated in microdroplets, paving the way for simple high-yield assembly, isolation, and sorting of few nanoparticle structures.J. J. Baumberg and A. Salmon acknowledge the support of the European Research Council (LINASS 320503), the UK Engineering and Physical Sciences Research Council EP/K028510/1, EP/G037221/1, EP/G060649/1, EP/L027151/1, and the Nano Science and Technology Doctoral Training Centre (NanoDTC) of the University of Cambridge. J. Aizpurua and R. Esteban acknowledge the Spanish Ministry of Economy and Competitiveness (FIS2013-41184-P). R. Esteban acknowledges the Fellow Gipuzkoa Program of the Gipuzkoako Foru Aldundia through FEDER “Una Manera de hacer Europa”.This is the final version of the article. It first appeared from Wiley via https://doi.org/10.1002/smll.20150351

msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation

<p>Abstract</p> <p>Background</p> <p>Although testing for simultaneous divergence (vicariance) across different population-pairs that span the same barrier to gene flow is of central importance to evolutionary biology, researchers often equate the gene tree and population/species tree thereby ignoring stochastic coalescent variance in their conclusions of temporal incongruence. In contrast to other available phylogeographic software packages, msBayes is the only one that analyses data from multiple species/population pairs under a hierarchical model.</p> <p>Results</p> <p>msBayes employs approximate Bayesian computation (ABC) under a hierarchical coalescent model to test for simultaneous divergence (TSD) in multiple co-distributed population-pairs. Simultaneous isolation is tested by estimating three hyper-parameters that characterize the degree of variability in divergence times across co-distributed population pairs while allowing for variation in various within population-pair demographic parameters (sub-parameters) that can affect the coalescent. msBayes is a software package consisting of several C and R programs that are run with a Perl "front-end".</p> <p>Conclusion</p> <p>The method reasonably distinguishes simultaneous isolation from temporal incongruence in the divergence of co-distributed population pairs, even with sparse sampling of individuals. Because the estimate step is decoupled from the simulation step, one can rapidly evaluate different ABC acceptance/rejection conditions and the choice of summary statistics. Given the complex and idiosyncratic nature of testing multi-species biogeographic hypotheses, we envision msBayes as a powerful and flexible tool for tackling a wide array of difficult research questions that use population genetic data from multiple co-distributed species. The msBayes pipeline is available for download at <url>http://msbayes.sourceforge.net/</url> under an open source license (GNU Public License). The msBayes pipeline is comprised of several C and R programs that are run with a Perl "front-end" and runs on Linux, Mac OS-X, and most POSIX systems. Although the current implementation is for a single locus per species-pair, future implementations will allow analysis of multi-loci data per species pair.</p

Increase of SERS Signal Upon Heating or Exposure to a High-Intensity Laser Field: Benzenethiol on an AgFON Substrate

The surface-enhanced Raman scattering (SERS) signal from an AgFON plasmonic substrate, recoated with benzenethiol, was observed to increase by about 100% upon heating for 3.5 min at 100C and 1.5 min at 125C. The signal intensity was found to increase further by about 80% upon a 10 sec exposure to a high-intensity (3.2 kW/cm^2) 785-nm cw laser, corresponding to 40 mW in a 40+/-5-um diameter spot. The observed increase in the SERS signal may be understood by considering the presence of benzenethiol molecules in an intermediate or 'precursor' state in addition to conventionally ordered molecules forming a self-assembled monolayer. The increase in the SERS signal arises from the conversion of the molecules in the precursor state to the chemisorbed state due to thermal and photo-thermal effects.Comment: 9 pages, 4 figures; J. Phys. Chem. C, accepte

Rapid progress on the vertebrate tree of life

<p>Abstract</p> <p>Background</p> <p>Among the greatest challenges for biology in the 21st century is inference of the tree of life. Interest in, and progress toward, this goal has increased dramatically with the growing availability of molecular sequence data. However, we have very little sense, for any major clade, of how much progress has been made in resolving a full tree of life and the scope of work that remains. A series of challenges stand in the way of completing this task but, at the most basic level, progress is limited by data: a limited fraction of the world's biodiversity has been incorporated into a phylogenetic analysis. More troubling is our poor understanding of what fraction of the tree of life is understood and how quickly research is adding to this knowledge. Here we measure the rate of progress on the tree of life for one clade of particular research interest, the vertebrates.</p> <p>Results</p> <p>Using an automated phylogenetic approach, we analyse all available molecular data for a large sample of vertebrate diversity, comprising nearly 12,000 species and 210,000 sequences. Our results indicate that progress has been rapid, increasing polynomially during the age of molecular systematics. It is also skewed, with birds and mammals receiving the most attention and marine organisms accumulating far fewer data and a slower rate of increase in phylogenetic resolution than terrestrial taxa. We analyse the contributors to this phylogenetic progress and make recommendations for future work.</p> <p>Conclusions</p> <p>Our analyses suggest that a large majority of the vertebrate tree of life will: (1) be resolved within the next few decades; (2) identify specific data collection strategies that may help to spur future progress; and (3) identify branches of the vertebrate tree of life in need of increased research effort.</p

Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood Bayesian and parsimony analyses

Copyright © 2007 The Natural history MuseumThe phylogeny of living and fossil snakes is assessed using likelihood and parsimony approaches and a dataset combining 263 morphological characters with mitochondrial (2693 bp) and nuclear (1092 bp) gene sequences. The ‘no common mechanism’ (NCMr) and ‘Markovian’ (Mkv) models were employed for the morphological partition in likelihood analyses; likelihood scores in the NCMr model were more closely correlated with parsimony tree lengths. Both models accorded relatively less weight to the molecular data than did parsimony, with the effect being milder in the NCMr model. Partitioned branch and likelihood support values indicate that the mtDNA and nuclear gene partitions agree more closely with each other than with morphology. Despite differences between data partitions in phylogenetic signal, analytic models, and relative weighting, the parsimony and likelihood analyses all retrieved the following widely accepted groups: scolecophidians, alethinophidians, cylindrophiines, macrostomatans (sensu lato) and caenophidians. Anilius alone emerged as the most basal alethinophidian; the combined analyses resulted in a novel and stable position of uropeltines and cylindrophiines as the second-most basal clade of alethinophidians. The limbed marine pachyophiids, along with Dinilysia and Wonambi, were always basal to all living snakes. Other results stable in all combined analyses include: Xenopeltis and Loxocemus were sister taxa (fide morphology) but clustered with pythonines (fide molecules), and Ungaliophis clustered with a boine-erycine clade (fide molecules). Tropidophis remains enigmatic; it emerges as a basal alethinophidian in the parsimony analyses (fide molecules) but a derived form in the likelihood analyses (fide morphology), largely due to the different relative weighting accorded to data partitions.Michael S. Y. Lee, Andrew F. Hugall, Robin Lawson & John D. Scanlo

A general scenario of Hox gene inventory variation among major sarcopterygian lineages

<p>Abstract</p> <p>Background</p> <p><it>H</it>ox genes are known to play a key role in shaping the body plan of metazoans. Evolutionary dynamics of these genes is therefore essential in explaining patterns of evolutionary diversity. Among extant sarcopterygians comprising both lobe-finned fishes and tetrapods, our knowledge of the <it>Hox </it>genes and clusters has largely been restricted in several model organisms such as frogs, birds and mammals. Some evolutionary gaps still exist, especially for those groups with derived body morphology or occupying key positions on the tree of life, hindering our understanding of how <it>Hox </it>gene inventory varied along the sarcopterygian lineage.</p> <p>Results</p> <p>We determined the <it>Hox </it>gene inventory for six sarcopterygian groups: lungfishes, caecilians, salamanders, snakes, turtles and crocodiles by comprehensive PCR survey and genome walking. Variable <it>Hox </it>genes in each of the six sarcopterygian group representatives, compared to the human <it>Hox </it>gene inventory, were further validated for their presence/absence by PCR survey in a number of related species representing a broad evolutionary coverage of the group. Turtles, crocodiles, birds and placental mammals possess the same 39 <it>Hox </it>genes. <it>HoxD12 </it>is absent in snakes, amphibians and probably lungfishes. <it>HoxB13 </it>is lost in frogs and caecilians. Lobe-finned fishes, amphibians and squamate reptiles possess <it>HoxC3</it>. <it>HoxC1 </it>is only present in caecilians and lobe-finned fishes. Similar to coelacanths, lungfishes also possess <it>HoxA14</it>, which is only found in lobe-finned fishes to date. Our <it>Hox </it>gene variation data favor the lungfish-tetrapod, turtle-archosaur and frog-salamander relationships and imply that the loss of <it>HoxD12 </it>is not directly related to digit reduction.</p> <p>Conclusions</p> <p>Our newly determined <it>Hox </it>inventory data provide a more complete scenario for evolutionary dynamics of <it>Hox </it>genes along the sarcopterygian lineage. Limbless, worm-like caecilians and snakes possess similar <it>Hox </it>gene inventories to animals with less derived body morphology, suggesting changes to their body morphology are likely due to other modifications rather than changes to <it>Hox </it>gene numbers. Furthermore, our results provide basis for future sequencing of the entire <it>Hox </it>clusters of these animals.</p

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

As top predators, falcons possess unique morphological, physiological and behavioral adaptations that allow them to be successful hunters: for example, the peregrine is renowned as the world's fastest animal. To examine the evolutionary basis of predatory adaptations, we sequenced the genomes of both the peregrine (Falco peregrinus) and saker falcon (Falco cherrug), and we present parallel, genome-wide evidence for evolutionary innovation and selection for a predatory lifestyle. The genomes, assembled using Illumina deep sequencing with greater than 100-fold coverage, are both approximately 1.2 Gb in length, with transcriptome-assisted prediction of approximately 16,200 genes for both species. Analysis of 8,424 orthologs in both falcons, chicken, zebra finch and turkey identified consistent evidence for genome-wide rapid evolution in these raptors. SNP-based inference showed contrasting recent demographic trajectories for the two falcons, and gene-based analysis highlighted falcon-specific evolutionary novelties for beak development and olfaction and specifically for homeostasis-related genes in the arid environment–adapted saker