1 99311 nterestingy, the effect of betaine may have been just the opposte, that is, to enhance the difference between the forces requ~red to Induce the trans~t~on in AT-arid CG-r~ch regions 24 The f~tted Kuhn segment length of 15 A rnpes a persstence length of 7.5 A for ssDNA Ths vdue s about half that estrnated by E K Achter end G. Fesenfed iB~ooolyt-ies 10. 1625 (1 971)] for apurineted ssDNA by us~ng g h t scattering ancl sedilnentat~on I: was assumed n that study that 1 M NaCl s a theta solvent for ssDNA. In the present study, the contrectie force on e ssDNA molecule n 1 M NaCl. extrepoated to zero extenson, was about 5 pN (see Fig. 6, nset blue). Ths force offset probably Indicates secondat? st1 ucture forlnation or condensailon with~n the --~olecule If such structure forlned n the sednentation studes, then an erroneously large value for the r~gidty of ssDNA end for RNA could hzve been obtzned 25 In the presence of adenosne trphosphate (ATP) or ATPiylS. RecA ~lndergoes an aloster~c change n t o a high-affnty form that bnds dsDNA cooperatvey n a stocholnetrc rato of 1 RecN3 bp of dsDNA to form a r~ght-handed h e c a falnent [S C \!Vest, An!iii Rev B I O C~J~~ 61. 603 (1 992)] There are six RecA molec~~les and 18 6 bp;turn of the DNA molecule that s overstretched by a factor of 1 5 t~mes its B-form contour length 26. A Klug and F H C Cr~ck [h'atatlii -e 255. 530 (1975)l have suqgtisted that formaton of a few highly bent regons or "knks" n DNA mght be energetcaly fawarable relative to srnooth bendng o. er a longer DNA length. The argument requres that after the ensung of a o c a z e d knk n the DNA molec~lle, the energy re3,u red to bend ;he DNA further by an angle 8 at that locat~on, be smaller than the energy needed to bend the DNA by the same angle before the ensuing of the knk Ths s ndeed obsetved n macroscopic eastc medawhen the deformaton goes beyond the eastc nto the "plastc" regme (a plastc straw s a good example) 27 Carboxyate-polystyrene beads (3 56 ILm n dameter. CV = 2.7'0, Spherotech) were covelently coated vlith streptav~d~n uslng l-ethyl-3-(3-d1methylam1nopropy) carbodmde (EDAC) Each molecule was puled both r~ght and left from the p~pette to determ n e the pont of attachment of the molecule on the ppette bead. Because the o p t c a y trapped bead can rotate freely, but the ppette-trapped bead cannot. Ex can be deterlnned n abso ute un~ts jmlcrometers), In each F-Ex cuwe, data representng the folowng four processes s ~~~p e r i m p o s e d : extendng the molecule to right of the ppette, then relaxing t froln the right, extendng t leftward, then relaxng t from the left. Each data point was taken after a -0.5 ILm change n extension and a 2-s waitn g perod. The force sgna was then averaged for an add~t~ona 2 s and recorded A complete r~ghr-left stretch cycle took about 10 m n . 28 A video showing actual bead-DNA-bead assembly IFlg. 1 B) can be viewed on the Word W!de Web at 29. D W! . Ussey. R \VJ Hoepfner, R R Sinden Met!i-0dS E~z J /~o / 21 2. 262 (1 992) 30.The nat...

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Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized equipment, is highly flexible and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.

The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to the cichlid fishes. Despite the importance of labrids to coastal reef ecology, we lack evolutionary analysis of feeding biomechanics among labrids. Here, we combine a molecular phylogeny of the Labridae with the biomechanics of skull function to reveal a broad pattern of repeated convergence in labrid feeding systems. Mechanically fast jaw systems have evolved independently at least 14 times from ancestors with forceful jaws. A repeated phylogenetic pattern of functional divergence in local regions of the labrid tree produces an emergent family-wide pattern of global convergence in jaw function. Divergence of close relatives, convergence among higher clades and several unusual 'breakthroughs' in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes.

The locations of Li+ and Na+ cations in dehydrated chabazite were studied by neutron powder diffraction, 7Li and 23Na magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, and 23Na multiple quantum MAS (MQMAS) NMR spectroscopy. Neutron powder diffraction data were collected on lithium chabazite (space group:  R3̄m, a = 9.3357(5) Å, α = 93.482(4)°, R wp = 5.83%, R p = 4.65%, χ2 = 1.24) and on a mixed lithium sodium chabazite (space group:  R3̄m, a = 9.3385(5) Å, α = 93.382(4)°, R wp = 5.94%, R p = 4.83%, χ2 = 1.27). Both neutron diffraction and 7Li MAS reveal lithium chabazite to have two cationic sites:  one at the six-ring window of the hexagonal prism (SII) and one in the supercage at the four-ring window of the hexagonal prism (SIII). Mixed lithium−sodium chabazites reveal strong evidence of selective occupancy accompanied by concomitant rearrangement effects. While the introduction of sodium into lithium chabazite reduces occupation primarily at the SIII site, a decrease of the SII site lithium cation population is also observed at sodium levels above 24%. At low sodium content, sodium cations occupy a site in the eight-ring window of the channel (SIII‘). At sodium content around 70% and higher, sodium cations also reside at the SII sites vacated by the lithium cations. The increased population of SII sites by Na+ is associated with a marked increase in the lattice constant. The implications of the observed site preferences for noncryogenic air separation are discussed.

Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers in nonmodel organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, typically using a reference genome to identify intron-exon boundaries to exclude shorter exons (<200 bp). Here, we test directly using transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Using 1260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic scales for frogs, including outgroups~100 Myr divergent from the ingroup. We recovered a large phylogenomic data set consisting of sequence alignments for 1047 of the 1260 transcriptome-based loci (~561 000 bp) and a large quantity of highly variable regions flanking the exons in transcripts (~70 000 bp), the latter improving substantially by only including ingroup species (~797 000 bp). We recovered both shorter (<100 bp) and longer exons (>200 bp), with no major reduction in coverage towards the ends of exons. We observed significant differences in the performance of blocking oligos for target enrichment and nontarget depletion during captures, and differences in PCR duplication rates resulting from the number of individuals pooled for capture reactions. We explicitly tested the effects of phylogenetic distance on capture sensitivity, specificity, and missing data, and provide a baseline estimate of expectations for these metrics based on a priori knowledge of nuclear pairwise differences among samples. We provide recommendations for transcriptome-based exon capture design based on our results, cost estimates and offer multiple pipelines for data assembly and analysis.

Regulatory genes control the expression of other genes and are key components of developmental processes such as segmentation and embryonic construction of the skull in vertebrates. Here we examine the variability and evolution of three vertebrate regulatory genes, addressing issues of their utility for phylogenetics and comparing the rates of genetic change seen in regulatory loci to the rates seen in other genes in the parrotfishes. The parrotfishes are a diverse group of colorful fishes from coral reefs and seagrasses worldwide and have been placed phylogenetically within the family Labridae. We tested phylogenetic hypotheses among the parrotfishes, with a focus on the genera Chlorurus and Scarus, by analyzing eight gene fragments for 42 parrotfishes and eight outgroup species. We sequenced mitochondrial 12s rRNA (967 bp), 16s rRNA (577 bp), and cytochrome b (477 bp). From the nuclear genome, we sequenced part of the protein-coding genes rag2 (715 bp), tmo4c4 (485 bp), and the developmental regulatory genes otx1 (672 bp), bmp4 (488 bp), and dlx2 (522 bp). Bayesian, likelihood, and parsimony analyses on the resulting 4903 bp of DNA sequence produced similar topologies that confirm the monophyly of the scarines and provide a phylogeny at the species level for portions of the genera Scarus and Chlorurus. Four major clades of Scarus were recovered, with three distributed in the Indo-Pacific and one containing Caribbean/Atlantic taxa. Molecular rates suggest a Miocene origin of the parrotfishes (22 mya) and a recent divergence of species within Scarus and Chlorurus, within the past 5 million years. Developmentally important genes made a significant contribution to phylogenetic structure, and rates of genetic evolution were high in bmp4, similar to other coding nuclear genes, but low in otx1 and the dlx2 exons. Synonymous and nonsynonymous substitution patterns in developmental regulatory genes support the hypothesis of stabilizing selection during the history of these genes, with several phylogenetic regions of accelerated nonsynonymous change detected in the phylogeny.