Cheryl Y Hayashi

University of California, Riverside, Riverside, California, United States

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Publications (66)506.64 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Previous studies have reported inactivated copies of six enamel-related genes (AMBN, AMEL, AMTN, ENAM, KLK4, MMP20) and one dentin-related gene (DSPP) in one or more toothless vertebrates and/or vertebrates with enamelless teeth, thereby providing evidence that these genes are enamel or tooth-specific with respect to their critical functions that are maintained by natural selection. Here, we employ available genome sequences for edentulous and enamelless mammals to evaluate the enamel specificity of four genes (WDR72, SLC24A4, FAM83H, C4orf26) that have been implicated in amelogenesis imperfecta, a condition in which proper enamel formation is abrogated during tooth development. Coding sequences for WDR72, SCL24A4, and FAM83H are intact in four edentulous taxa (Chinese pangolin, three baleen whales) and three taxa (aardvark, nine-banded armadillo, Hoffmann's two-toed sloth) with enamelless teeth, suggesting that these genes have critical functions beyond their involvement in tooth development. By contrast, genomic data for C4orf26 reveal inactivating mutations in pangolin and bowhead whale as well as evidence for deletion of this gene in two minke whale species. Hybridization capture of exonic regions and PCR screens provide evidence for inactivation of C4orf26 in eight additional baleen whale species. However, C4orf26 is intact in all three species with enamelless teeth that were surveyed, as well as in 95 additional mammalian species with enamel-capped teeth. Estimates of selection intensity suggest that dN/dS ratios on branches leading to taxa with enamelless teeth are similar to the dN/dS ratio on branches leading to taxa with enamel-capped teeth. Based on these results, we conclude that C4orf26 is tooth-specific, but not enamel-specific, with respect to its essential functions that are maintained by natural selection. A caveat is that an alternative splice site variant, which translates exon 3 in a different reading frame, is putatively functional in Catarrhini and may have evolved an additional role in this primate clade.
    Molecular Phylogenetics and Evolution 11/2015; DOI:10.1016/j.ympev.2015.11.002 · 3.92 Impact Factor
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    ABSTRACT: Spider silk research has largely focused on spidroins, proteins that are the primary components of spider silk fibers. Although a number of spidroins have been characterized, other types of proteins associated with silk synthesis are virtually unknown. Previous analyses of tissue-specific RNAseq libraries identified 647 predicted genes that were differentially expressed in silk glands of the Western black widow, Latrodectus hesperus. Only ~5% of these transcripts encode spidroins, and though the remaining predicted genes presumably encode other proteins associated with silk production, this is mostly unverified. Here, we used proteomic analysis of multiple silk glands and dragline silk fiber to investigate the translation of the differentially expressed genes. We find 48 proteins encoded by the differentially expressed transcripts in L. hesperus major ampullate, minor ampullate, and tubuliform silk glands, and detect 17 SST encoded proteins in major ampullate silk fibers. The observed proteins include known silk-related proteins, but most are uncharacterized, with no annotation. These unannotated proteins likely include novel silk associated proteins. Major ampullate and minor ampullate glands have the highest overlap of identified proteins, consistent with their shared, distinctive ampullate shape and the overlapping functions of major ampullate and minor ampullate silks. Our study substantiates and prioritizes predictions from differential expression analysis of spider silk gland transcriptomes.
    Journal of Proteome Research 08/2015; 14(10). DOI:10.1021/acs.jproteome.5b00353 · 4.25 Impact Factor
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    ABSTRACT: The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (Order Scorpionida) and spiders (Order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared to other transcripts. Thus an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Genome Biology and Evolution 06/2015; 7(7). DOI:10.1093/gbe/evv110 · 4.23 Impact Factor
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    ABSTRACT: Background Spiders (Order Araneae) are essential predators in every terrestrial ecosystem largely because they have evolved potent arsenals of silk and venom. Spider silks are high performance materials made almost entirely of proteins, and thus represent an ideal system for investigating genome level evolution of novel protein functions. However, genomic level resources remain limited for spiders. Results We de novo assembled a transcriptome for the Western black widow (Latrodectus hesperus) from deeply sequenced cDNAs of three tissue types. Our multi-tissue assembly contained ~100,000 unique transcripts, of which > 27,000 were annotated by homology. Comparing transcript abundance among the different tissues, we identified 647 silk gland-specific transcripts, including the few known silk fiber components (e.g. six spider fibroins, spidroins). Silk gland specific transcripts are enriched compared to the entire transcriptome in several functions, including protein degradation, inhibition of protein degradation, and oxidation-reduction. Phylogenetic analyses of 37 gene families containing silk gland specific transcripts demonstrated novel gene expansions within silk glands, and multiple co-options of silk specific expression from paralogs expressed in other tissues. Conclusions We propose a transcriptional program for the silk glands that involves regulating gland specific synthesis of silk fiber and glue components followed by protecting and processing these components into functional fibers and glues. Our black widow silk gland gene repertoire provides extensive expansion of resources for biomimetic applications of silk in industry and medicine. Furthermore, our multi-tissue transcriptome facilitates evolutionary analysis of arachnid genomes and adaptive protein systems. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-365) contains supplementary material, which is available to authorized users.
    BMC Genomics 06/2014; 15(1):365. DOI:10.1186/1471-2164-15-365 · 3.99 Impact Factor
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    ABSTRACT: Animal venoms attract enormous interest given their potential for pharmacological discovery and understanding the evolution of natural chemistries. Next-generation transcriptomics and proteomics provide unparalleled, but underexploited, capabilities for venom characterization. We combined multi-tissue RNA-Seq with mass spectrometry and bioinformatic analyses to determine venom gland specific transcripts and venom proteins from the Western black widow spider (Latrodectus hesperus) and investigated their evolution. We estimated expression of 97,217 L. hesperus transcripts in venom glands relative to silk and cephalothorax tissues. We identified 695 venom gland specific transcripts (VSTs), many of which BLAST and GO term analyses indicate may function as toxins or their delivery agents. ~38% of VSTs had BLAST hits, including latrotoxins, inhibitor cystine knot toxins, CRISPs, hyaluronidases, chitinase, and proteases, and 59% of VSTs had predicted protein domains. Latrotoxins are venom toxins that cause massive neurotransmitter release from vertebrate or invertebrate neurons. We discovered ≥ 20 divergent latrotoxin paralogs expressed in L. hesperus venom glands, significantly increasing this biomedically important family. Mass spectrometry of L. hesperus venom identified 49 proteins from VSTs, 24 of which BLAST to toxins. Phylogenetic analyses showed venom gland specific gene family expansions and shifts in tissue expression. Quantitative expression analyses comparing multiple tissues are necessary to identify venom gland specific transcripts. We present a black widow venom specific exome that uncovers a trove of diverse toxins and associated proteins, suggesting a dynamic evolutionary history. This justifies a reevaluation of the functional activities of black widow venom in light of its emerging complexity.
    BMC Genomics 06/2014; 15(1):366. DOI:10.1186/1471-2164-15-366 · 3.99 Impact Factor
  • Shen Xu · Zaoli Xu · James Starrett · Cheryl Hayashi · Xinwei Wang ·
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    ABSTRACT: This work reports on the first study of thermal transport capacity in the thickness direction (similar to mu m scale) for spider silk films. Fresh (minimally processed) and hexafluoroisopropanol (HFIP) films of Nephila clavipes and Latrodectus hesperus major ampullate silk are studied. Detailed Raman spectroscopy reveals that the fresh films have more crystalline secondary protein structures such as antiparallel beta-sheets than the HFIP films for N. clavipes. For N. clavipes, the randomly distributed antiparallel beta-sheets in fresh films have nearly no effect in improving thermal conductivity in comparison with HFIP films. For L. hesperus, the films mainly consist of alpha-helices and random coils while the fresh film has a higher concentration of alpha-helices. The higher concentration of alpha-helices in fresh films gives rise to a higher heat capacity than HFIP films, while the thermal conductivity shows little effect from the alpha-helices concentration. Thickened HFIP films are heated at different temperatures to study the effect of heat treatment on structure and thermal transport capacity. These experiments demonstrate that alpha-helices are formed by thermal treatment and that thermal effusivity increases with the appearance of alpha-helices in films.
    Polymer 04/2014; 55(7). DOI:10.1016/j.polymer.2014.02.020 · 3.56 Impact Factor
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    ABSTRACT: Spider silks are spectacular examples of phenotypic diversity arising from adaptive molecular evolution. An individual spider can produce an array of specialized silks, with the majority of constituent silk proteins encoded by members of the spidroin gene family. Spidroins are dominated by tandem repeats flanked by short, non-repetitive N- and C-terminal coding regions. The remarkable mechanical properties of spider silks have been largely attributed to the repeat sequences. However, the molecular evolutionary processes acting on spidroin terminal and repetitive regions remain unclear due to a paucity of complete gene sequences and sampling of genetic variation among individuals. To better understand spider silk evolution, we characterize a complete aciniform spidroin gene from an Argiope orb-weaving spider and survey aciniform gene fragments from congeneric individuals. We present the complete aciniform spidroin (AcSp1) gene from the silver garden spider Argiope argentata (Aar_AcSp1), and document multiple AcSp1 loci in individual genomes of A. argentata and the congeneric A. trifasciata and A. aurantia. We find that Aar_AcSp1 repeats have >98% pairwise nucleotide identity. By comparing AcSp1 repeat amino acid sequences between Argiope species and with other genera, we identify regions of conservation over vast amounts of evolutionary time. Through a PCR survey of individual A. argentata, A. trifasciata, and A. aurantia genomes, we ascertain that AcSp1 repeats show limited variation between species whereas terminal regions are more divergent. We also find that average dN/dS across codons in the N-terminal, repetitive, and C-terminal encoding regions indicate purifying selection that is strongest in the N-terminal region. Using the complete A. argentata AcSp1 gene and spidroin genetic variation between individuals, this study clarifies some of the molecular evolutionary processes underlying the spectacular mechanical attributes of aciniform silk. It is likely that intragenic concerted evolution and functional constraints on A. argentata AcSp1 repeats result in extreme repeat homogeneity. The maintenance of multiple AcSp1 encoding loci in Argiope genomes supports the hypothesis that Argiope spiders require rapid and efficient protein production to support their prolific use of aciniform silk for prey-wrapping and web-decorating. In addition, multiple gene copies may represent the early stages of spidroin diversification.
    BMC Evolutionary Biology 02/2014; 14(1):31. DOI:10.1186/1471-2148-14-31 · 3.37 Impact Factor
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    Amanda Kelly Lane · Cheryl Y Hayashi · Gregg B Whitworth · Nadia A Ayoub ·
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    ABSTRACT: Orb-web and cob-web weaving spiders spin dragline silk fibers that are among the strongest materials known. Draglines are primarily composed of MaSp1 and MaSp2, two spidroins (spider fibrous proteins) expressed in the major ampullate (MA) silk glands. Prior genetic studies of dragline silk have focused mostly on determining the sequence of these spidroins, leaving other genetic aspects of silk synthesis largely uncharacterized. Here, we used deep sequencing to profile gene expression patterns in the Western black widow, Latrodectus hesperus. We sequenced millions of 3[prime]-anchored "tags" of cDNAs derived either from MA glands or control tissue (cephalothorax) mRNAs, then associated the tags with genes by compiling a reference database from our newly constructed normalized L. hesperus cDNA library and published L. hesperus sequences. We were able to determine transcript abundance and alternative polyadenylation of each of three loci encoding MaSp1. The ratio of MaSp1:MaSp2 transcripts varied between individuals, but on average was similar to the estimated ratio of MaSp1:MaSp2 in dragline fibers. We also identified transcription of TuSp1 in MA glands, another spidroin family member that encodes the primary component of egg-sac silk, synthesized in tubuliform glands. In addition to the spidroin paralogs, we identified 30 genes that are more abundantly represented in MA glands than cephalothoraxes and represent new candidates for involvement in spider silk synthesis. Modulating expression rates of MaSp1 variants as well as MaSp2 and TuSp1 could lead to differences in mechanical properties of dragline fibers. Many of the newly identified candidate genes likely encode secreted proteins, suggesting they could be incorporated into dragline fibers or assist in protein processing and fiber assembly. Our results demonstrate previously unrecognized transcript complexity in spider silk glands.
    BMC Genomics 12/2013; 14(1):846. DOI:10.1186/1471-2164-14-846 · 3.99 Impact Factor
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    ABSTRACT: Spider silks combine a significant number of desirable characteristics in one material, including large tensile strength and strain at breaking, biocompatibility, and the possibility of tailoring their properties. Major ampullate gland silk (MAS) is the most studied silk and their properties are explained by a double lattice of hydrogen bonds and elastomeric protein chains linked to polyalanine β-nanocrystals. However, many basic details regarding the relationship between composition, microstructure and properties in silks are still lacking. Here we show that this relationship can be traced in flagelliform silk (Flag) spun by Argiope trifasciata spiders after identifying a phase consisting of polyglycine II nanocrystals. The presence of this phase is consistent with the dominant presence of the -GGX- and -GPG- motifs in its sequence. In contrast to the passive role assigned to polyalanine nanocrystals in MAS, polyglycine II nanocrystals can undergo growing/collapse processes that contribute to increase toughness and justify the ability of Flag to supercontract.
    Scientific Reports 10/2013; 3:3061. DOI:10.1038/srep03061 · 5.58 Impact Factor
  • James Starrett · Marshal Hedin · Nadia Ayoub · Cheryl Y Hayashi ·
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    ABSTRACT: Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a-g), which combine to form a 24-mer (4 X 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order to infer the evolution of the hemocyanin gene family and estimate spider relationships using these conserved loci. Our hemocyanin gene tree is largely consistent with previous hypotheses of paralog relationships based on immunological studies, but reveals some discrepancies in which paralog types have been lost or duplicated in specific spider lineages. Analyses of concatenated hemocyanin sequences resolved deep nodes in the spider phylogeny and recovered a number of clades that are supported by other molecular studies, particularly for mygalomorph taxa. The concatenated data set is also used to estimate dates of higher-level spider divergences and suggests that the diversification of extant mygalomorphs preceded that of extant araneomorphs. Spiders are diverse in behavior and respiratory morphology, and our results are beneficial for comparative analyses of spider respiration. Lastly, the conserved hemocyanin sequences allow for inference of spider relationships and ancient divergence dates.
    Gene 04/2013; 524(2). DOI:10.1016/j.gene.2013.04.037 · 2.14 Impact Factor
  • James Starrett · Cheryl Y Hayashi ·
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    ABSTRACT: Spider silk genes are composed mostly of repetitive sequence that is flanked by non-repetitive terminal regions. Inferences about the evolutionary processes that influenced silk genes have largely been made from analyses using distantly related taxa and ancient silk gene duplicates. These studies have relied on comparisons across the conserved non-repetitive terminal regions to determine orthologous and paralogous relationships, as well as the influence of selection on silk genes. While the repetitive region heavily influences silk fiber mechanical properties, few molecular evolutionary analyses have been conducted on this region due to difficulty in determining homology. Here, we sample internal repetitive and carboxy terminal regions from all extant species of the trapdoor spider genus, Aliatypus. Aliatypus spiders are highly dispersal limited and rely on their silk lined burrow for protection. We determine positional homology across species for the carboxy terminal regions and relative positional homology for the internal repetitive regions. Gene trees based on each of these regions are in good agreement with the Aliatypus species tree, which indicates we sampled single spidroin orthologs in each species. In addition, we find that purifying selection and concerted evolution have acted to conserve Aliatypus spidroin internal repetitive regions. In contrast, selection testing identifies evidence of sites that evolved under positive selection and amino acid replacements that result in radical physicochemical changes in the carboxy terminal region. These findings indicate that comparison of spidroin orthologs across a comprehensive sample of congenerics reveal molecular evolutionary patterns obscured from studies using higher-level sampling of silk encoding genes.
    Journal of Molecular Evolution 03/2013; 76(4). DOI:10.1007/s00239-013-9550-7 · 1.68 Impact Factor
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    Jessica E Garb · Cheryl Y Hayashi ·
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    ABSTRACT: Black widow spiders (members of the genus Latrodectus) are widely feared because of their potent neurotoxic venom. α-Latrotoxin is the vertebrate-specific toxin responsible for the dramatic effects of black widow envenomation. The evolution of this toxin is enigmatic because only two α-latrotoxin sequences are known. In this study, ∼4 kb α-latrotoxin sequences and their homologs were characterized from a diversity of Latrodectus species, and representatives of Steatoda and Parasteatoda, establishing the wide distribution of latrotoxins across the mega-diverse spider family Theridiidae. Across black widow species, α-latrotoxin shows ≥94% nucleotide identity and variability consistent with purifying selection. Multiple codon and branch-specific estimates of the nonsynonymous/synonymous substitution rate ratio also suggest a long history of purifying selection has acted on α-latrotoxin across Latrodectus and Steatoda. However, α-latrotoxin is highly divergent in amino acid sequence between these genera, with 68.7% of protein differences involving non-conservative substitutions, evidence for positive selection on its physiochemical properties and particular codons, and an elevated rate of nonsynonymous substitutions along α-latrotoxin’s Latrodectus branch. Such variation likely explains the efficacy of red-back spider, L. hasselti, antivenom in treating bites from other Latrodectus species, and the weaker neurotoxic symptoms associated with Steatoda and Parasteatoda bites. Long-term purifying selection on α-latrotoxin indicates its functional importance in black widow venom, even though vertebrates are a small fraction of their diet. The greater differences between Latrodectus and Steatoda α-latrotoxin, and their relationships to invertebrate-specific latrotoxins, suggest a shift in α-latrotoxin toward increased vertebrate toxicity coincident with the evolution of widow spiders.
    Molecular Biology and Evolution 01/2013; 30(5). DOI:10.1093/molbev/mst011 · 9.11 Impact Factor
  • Marshal Hedin · James Starrett · Cheryl Hayashi ·
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    ABSTRACT: Antrodiaetus riversi is a dispersal-limited, habitat-specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. Here, we build upon prior phylogeographic research using a much larger geographic sample and include additional nuclear genes, providing more detailed biogeographic insights throughout the range of this complex. Of particular interest is the uncovering of unexpected and replicated trans-valley biogeographic patterns, where in two separate genetic clades western haplotypes in the California south Coast Ranges are phylogenetically closely related to eastern haplotypes from central and northern Sierran foothills. In both instances, these trans-valley phylogenetic patterns are strongly supported by multiple genes. These western and eastern populations are currently separated by the Central Valley, a well-recognized modern-day and historical biogeographic barrier in California. For one clade, the directionality is clearly northeast to southwest, and all available evidence is consistent with a jump dispersal event estimated at 1.2-1.3 Ma. During this time period, paleogeographic data indicate that northern Sierran rivers emptied to the ocean in the south Coast Ranges, rather than at the San Francisco Bay. For the other trans-valley clade genetic evidence is less conclusive regarding the mechanism and directionality of biogeographic exchange, although the estimated timeframe is similar (approximately 1.8 Ma). Despite the large number of biogeographic studies previously conducted in central California, to the best of our knowledge no prior studies have discussed or revealed a northern Sierran to south Coast Range biogeographic connection. This uniqueness may reflect the low-dispersal biology of mygalomorph spiders, where 'post-event' gene exchange rarely erases historical biogeographic signal.
    Molecular Ecology 12/2012; 22(2). DOI:10.1111/mec.12130 · 6.49 Impact Factor
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    Nadia A Ayoub · Jessica E Garb · Amanda Kuelbs · Cheryl Y Hayashi ·
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    ABSTRACT: Spider silk fibers have impressive mechanical properties and are primarily composed of highly repetitive structural proteins (termed spidroins) encoded by a single gene family. Most characterized spidroin genes are incompletely known because of their extreme size (typically >9 kb) and repetitiveness, limiting understanding of the evolutionary processes that gave rise to their unusual gene architectures. The only complete spidroin genes characterized thus far form the dragline in the Western black widow, Latrodectus hesperus. Here we describe the first complete gene sequence encoding the aciniform spidroin AcSp1, the primary component of spider prey-wrapping fibers. L. hesperus AcSp1 contains a single enormous (∼19 kb) exon. The AcSp1 repeat sequence is exceptionally conserved between two widow species (∼94% identity) and between widows and distantly related orb-weavers (∼30% identity), consistent with a history of strong purifying selection on its amino acid sequence. Furthermore, the 16 repeats (each 371-375 amino acids long) found in black widow AcSp1 are, on average, >99% identical at the nucleotide level. A combination of stabilizing selection on amino acid sequence, selection on silent sites, and intragenic recombination likely explains the extreme homogenization of AcSp1 repeats. In addition, phylogenetic analyses of spidroin paralogs support a gene duplication event occurring concomitant with specialization of the aciniform glands and the tubuliform glands, which synthesize egg-case silk. With repeats that are dramatically different in length and amino acid composition from dragline spidroins, our L. hesperus AcSp1 expands the knowledge-base for developing silk-based biomimetic technologies.
    Molecular Biology and Evolution 11/2012; 30(3). DOI:10.1093/molbev/mss254 · 9.11 Impact Factor
  • Cheryl Hayashi ·

    Entomological Society of America Annual Meeting 2012; 11/2012
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    ABSTRACT: A phylogenetic analysis of the order Embioptera is presented with a revised classification based on results of the analysis. Eighty-two species of Embioptera are included from all families except Paedembiidae Ross and Embonychidae Navás. Monophyly of each of the eight remaining currently recognized families is tested except Andesembiidae Ross, for which only a single species was included. Nine outgroup taxa are included from Blattaria, Grylloblattaria, Mantodea, Mantophasmatodea, Orthoptera, Phasmida and Plecoptera. Ninety-six morphological characters were analysed along with DNA sequence data from the five genes 16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase I and histone III. Data were analysed in combined analyses of all data using parsimony and Bayesian optimality criteria, and combined molecular data were analysed using maximum likelihood. Several major conclusions about Embioptera relationships and classification are based on interpretation of these analyses. Of eight families for which monophyly was tested, four were found to be monophyletic under each optimality criterion: Clothodidae Davis, Anisembiidae Davis, Oligotomidae Enderlein and Teratembiidae Krauss. Australembiidae Ross was not recovered as monophyletic in the likelihood analysis in which one Australembia Ross species was recovered in a position distant from other australembiids. This analysis included only molecular data and the topology was not strongly supported. Given this, and because parsimony and the Bayesian analyses recovered a strongly supported clade including all Australembiidae, we regard this family also as monophyletic. Three other families – Notoligotomidae Davis, Archembiidae Ross and Embiidae Burmeister, as historically delimited – were not found to be monophyletic under any optimality criterion. Notoligotomidae is restricted here to include only the genus Notoligotoma Davis with a new family, Ptilocerembiidae Miller and Edgerly, new family, erected to include the genus Ptilocerembia Friederichs. Archembiidae is restricted here to include only the genera Archembia Ross and Calamoclostes Enderlein. The family group name Scelembiidae Ross is resurrected from synonymy with Archembiidae (new status) to include all other genera recently placed in Archembiidae. Embiidae is not demonstrably monophyletic with species currently placed in the family resolved in three separate clades under each optimality criterion. Because taxon sampling is not extensive within this family in this analysis, no changes are made to Embiidae classification. Relationships between families delimited herein are not strongly supported under any optimality criterion with a few exceptions. Either Clothodidae Davis (parsimony) or Australembiidae Ross (Bayesian) is the sister to the remaining Embioptera taxa. The Bayesian analysis includes Australembiidae as the sister to all other Embioptera except Clothididae, suggesting that each of these taxa is a relatively plesiomorphic representatative of the order. Oligotomidae and Teratembiidae are sister groups, and Archembiidae (sensu novum), Ptilocerembiidae, Andesembiidae and Anisembiidae form a monophyletic group under each optimality criterion. Each family is discussed in reference to this analysis, diagnostic combinations and taxon compositions are provided, and a key to families of Embioptera is included.
    Systematic Entomology 07/2012; 37(3). DOI:10.1111/j.1365-3113.2012.00628.x · 2.78 Impact Factor
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    ABSTRACT: Silk spinning is essential to spider ecology and has had a key role in the expansive diversification of spiders. Silk is composed primarily of proteins called spidroins, which are encoded by a multi-gene family. Spidroins have been studied extensively in the derived clade, Orbiculariae (orb-weavers), from the suborder Araneomorphae ('true spiders'). Orbicularians produce a suite of different silks, and underlying this repertoire is a history of duplication and spidroin gene divergence. A second class of silk proteins, Egg Case Proteins (ECPs), is known only from the orbicularian species, Lactrodectus hesperus (Western black widow). In L. hesperus, ECPs bond with tubuliform spidroins to form egg case silk fibers. Because most of the phylogenetic diversity of spiders has not been sampled for their silk genes, there is limited understanding of spidroin gene family history and the prevalence of ECPs. Silk genes have not been reported from the suborder Mesothelae (segmented spiders), which diverged from all other spiders >380 million years ago, and sampling from Mygalomorphae (tarantulas, trapdoor spiders) and basal araneomorph lineages is sparse. In comparison to orbicularians, mesotheles and mygalomorphs have a simpler silk biology and thus are hypothesized to have less diversity of silk genes. Here, we present cDNAs synthesized from the silk glands of six mygalomorph species, a mesothele, and a non-orbicularian araneomorph, and uncover a surprisingly rich silk gene diversity. In particular, we find ECP homologs in the mesothele, suggesting that ECPs were present in the common ancestor of extant spiders, and originally were not specialized to complex with tubuliform spidroins. Furthermore, gene-tree/species-tree reconciliation analysis reveals that numerous spidroin gene duplications occurred after the split between Mesothelae and Opisthothelae (Mygalomorphae plus Araneomorphae). We use the spidroin gene tree to reconstruct the evolution of amino acid compositions of spidroins that perform different ecological functions.
    PLoS ONE 06/2012; 7(6):e38084. DOI:10.1371/journal.pone.0038084 · 3.23 Impact Factor
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    ABSTRACT: The mechanical behavior and microstructure of minor ampullate gland silk (miS) of two orb-web spinning species, Argiope trifasciata and Nephila inaurata, were extensively characterized, enabling detailed comparison with other silks. The similarities and differences exhibited by miS when compared with the intensively studied major ampullate gland silk (MAS) and silkworm (Bombyx mori) silk offer a genuine opportunity for testing some of the hypotheses proposed to correlate microstructure and tensile properties in silk. In this work, we show that miSs of different species show similar properties, even when fibers spun by spiders that diverged over 100 million years are compared. The tensile properties of miS are comparable to those of MAS when tested in air, significantly in terms of work to fracture, but differ considerably when tested in water. In particular, miS does not show a supercontraction effect and an associated ground state. In this regard, the behavior of miS in water is similar to that of B. mori silk, and it is shown that the initial elastic modulus of both fibers can be explained using a common model. Intriguingly, the microstructural parameters measured in miS are comparable to those of MAS and considerably different from those found in B. mori. This fact suggests that some critical microstructural information is still missing in our description of silks, and our results suggest that the hydrophilicity of the lateral groups or the large scale organization of the sequences might be routes worth exploring.
    Biomacromolecules 06/2012; 13(7):2087-98. DOI:10.1021/bm3004644 · 5.75 Impact Factor
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    Jordan D Satler · James Starrett · Cheryl Y Hayashi · Marshal Hedin ·
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    ABSTRACT: The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin) in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley), and the genus as a whole occupies an impressive variety of habitats. We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches) recovered a general "3 clade" structure for the genus (A. gulosus, californicus group, erebus group), with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations). Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism. This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages are discovered, with more geographic sampling likely to lead to additional species diversity. These dispersal-limited taxa provide novel insight into the biogeography and Earth history processes of California.
    PLoS ONE 09/2011; 6(9):e25355. DOI:10.1371/journal.pone.0025355 · 3.23 Impact Factor
  • Matthew A Collin · Janice S Edgerly · Cheryl Y Hayashi ·
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    ABSTRACT: Embiopterans (webspinning insects) are renowned for their prolific use of silk. These organisms spin silk to construct elaborate networks of tubes in which they live, forage, and reproduce. The silken galleries are essential for protecting these soft-bodied insects from predators and other environmental hazards. Despite the ecological importance of embiopteran silk, very little is known about its constituent proteins. Here, we characterize the silk protein cDNAs from four embiopteran species to better understand the function and evolution of these adaptive molecules. We show that webspinner fibroins (silk proteins) are highly repetitive in sequence and possess several conserved characteristics, despite differences in habitat preferences across species. The most striking similarities are in the codon usage biases of the fibroin genes, particularly in the repetitive regions, as well as sequence conservation of the carboxyl-terminal regions of the fibroins. Based on analyses of the silk genes, we propose hypotheses regarding codon bias and its effect on the translation and replication of these unusual genes. Furthermore, we discuss the significance of specific fibroin motifs to the mechanical and structural characteristics of silk fibers. Lastly, we report that the conservation of webspinner fibroin carboxyl-terminal regions suggests that fiber formation may occur through a mechanism analogous to that found in Lepidoptera. From these results, insight is gained into the tempo and mode of evolution that has shaped embiopteran fibroins.
    Zoology 09/2011; 114(4):239-46. DOI:10.1016/j.zool.2011.01.004 · 1.67 Impact Factor

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3k Citations
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  • 2001-2015
    • University of California, Riverside
      • Department of Biology
      Riverside, California, United States
  • 2006
    • Biomedical Research Institute, Rockville
      Maryland, United States
  • 1998-2002
    • University of Wyoming
      • Department of Molecular Biology
      Laramie, WY, United States
  • 1994
    • Yale University
      New Haven, Connecticut, United States