1
|
Torosin NS, Argibay H, Webster TH, Corneli PS, Knapp LA. Comparing the selective landscape of TLR7 and TLR8 across primates reveals unique sites under positive selection in Alouatta. Mol Phylogenet Evol 2020; 152:106920. [PMID: 32768453 DOI: 10.1016/j.ympev.2020.106920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 03/06/2020] [Accepted: 07/31/2020] [Indexed: 11/24/2022]
Abstract
Among primates, susceptibility to yellow fever (YFV), a single-stranded (ss) RNA virus, ranges from complete resistance to high susceptibility. Howler monkeys (genus Alouatta) are the most susceptible to YFV. In order to identify Alouatta-specific genetic factors that may be responsible for their susceptibility, we collected skin samples from howler monkey museum specimens of the species A. caraya and A. guariba clamitans. We compared the rate of nonsynonymous to synonymous (dN/dS) changes of Toll-like receptor (TLR) 7 and TLR8, the two genes responsible for detecting all ssRNA viruses, across the Primate order. Overall, we found that the TLR7 gene is under stronger purifying selection in howler monkeys compared to other New World and Old World primates, but TLR8 is under the same selective pressure. When we evaluated dN/dS at each codon, we found six codons under positive selection in Alouatta TLR8 and two codons under positive selection in TLR7. The changes in TLR7 are unique to A. guariba clamitans and are found in functionally important regions likely to affect detection of ssRNA viruses by TLR7/TLR8, as well as downstream signaling. These amino acid differences in A. guariba clamitans may play a role in YFV susceptibility. These results have implications for identifying genetic factors affecting YFV susceptibility in primates.
Collapse
Affiliation(s)
- Nicole S Torosin
- Department of Anthropology, University of Utah, 260 S. Central Campus Dr., Salt Lake City, UT 84112, United States.
| | - Hernan Argibay
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Intendente Güiraldes 2160 - Ciudad Universitaria (C1428EGA) Ciudad Autónoma de Buenos Aires, Argentina
| | - Timothy H Webster
- Department of Anthropology, University of Utah, 260 S. Central Campus Dr., Salt Lake City, UT 84112, United States
| | - Patrice Showers Corneli
- Department of Biology, University of Utah, 257 S. 1400 E., Salt Lake City, UT 84112, United States
| | - Leslie A Knapp
- Department of Anthropology, University of Utah, 260 S. Central Campus Dr., Salt Lake City, UT 84112, United States
| |
Collapse
|
2
|
Safavi-Hemami H, Lu A, Li Q, Fedosov AE, Biggs J, Showers Corneli P, Seger J, Yandell M, Olivera BM. Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa. Mol Biol Evol 2016; 33:2924-2934. [PMID: 27524826 PMCID: PMC5062327 DOI: 10.1093/molbev/msw174] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A specialized insulin was recently found in the venom of a fish-hunting cone snail, Conus geographus Here we show that many worm-hunting and snail-hunting cones also express venom insulins, and that this novel gene family has diversified explosively. Cone snails express a highly conserved insulin in their nerve ring; presumably this conventional signaling insulin is finely tuned to the Conus insulin receptor, which also evolves very slowly. By contrast, the venom insulins diverge rapidly, apparently in response to biotic interactions with prey and also possibly the cones' own predators and competitors. Thus, the inwardly directed signaling insulins appear to experience predominantly purifying sele\ction to target an internal receptor that seldom changes, while the outwardly directed venom insulins frequently experience directional selection to target heterospecific insulin receptors in a changing mix of prey, predators and competitors. Prey insulin receptors may often be constrained in ways that prevent their evolutionary escape from targeted venom insulins, if amino-acid substitutions that result in escape also degrade the receptor's signaling functions.
Collapse
Affiliation(s)
- Helena Safavi-Hemami
- Department of Biology, University of Utah, Salt Lake City, UT Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Aiping Lu
- School of Life Sciences and Technology, Institute of Protein Research, Tongji University, Shanghai, China
| | - Qing Li
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT
| | - Alexander E Fedosov
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Science, Leninsky Prospect, Moscow, Russia
| | - Jason Biggs
- University of Guam Marine Laboratory, Agana, Guam
| | | | - Jon Seger
- Department of Biology, University of Utah, Salt Lake City, UT
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT
| | | |
Collapse
|
3
|
Olivera BM, Showers Corneli P, Watkins M, Fedosov A. Biodiversity of cone snails and other venomous marine gastropods: evolutionary success through neuropharmacology. Annu Rev Anim Biosci 2013; 2:487-513. [PMID: 25384153 DOI: 10.1146/annurev-animal-022513-114124] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Venomous marine snails (superfamily Conoidea) are a remarkably biodiverse marine invertebrate lineage (featuring more than 10,000 species). Conoideans use complex venoms (up to 100 different components for each species) to capture prey and for other biotic interactions. Molecular phylogeny and venom peptide characterization provide an unusual multidisciplinary view of conoidean biodiversity at several taxonomic levels. Venom peptides diverge between species at an unprecedented rate through hypermutation within gene families. Clade divergence within a genus occurs without recruiting new gene families when a saltatory event, such as colonization of new prey types (e.g., fish), leads to a new radiation. Divergence between genera in the same family involves substantial divergence in gene families. In the superfamily Conoidea, the family groups recruited distinct sets of different venom gene superfamilies. The associated morphological, behavioral, and prey-preference changes that accompany these molecular changes are unknown for most conoidean lineages, except for one genus, Conus, for which many associated phenotypic changes have been documented.
Collapse
|
4
|
Kraus NJ, Watkins M, Bandyopadhyay PK, Seger J, Olivera BM, Corneli PS. A very short, functionally constrained sequence diagnoses cone snails in several Conasprella clades. Mol Phylogenet Evol 2012; 65:335-8. [PMID: 22750110 DOI: 10.1016/j.ympev.2012.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 06/15/2012] [Accepted: 06/16/2012] [Indexed: 11/27/2022]
Abstract
The traditional taxonomy of ca. 700 cone snails assigns all species to a single genus, Conus Linnaeus 1758. However, an increasing body of evidence suggests that some belong to a phylogenetically distinct clade that is sometimes referred to as Conasprella. Previous work (Kraus et al., 2011) showed that a short (259 bp) conserved intronic sequence (CIS) of the γ-glutamyl carboxylase gene (intron 9) can be used to delineate deep phylogenetic relationships among some groups of Conus. The work described here uses intron 9 (338 bp) to resolve problematic relationships among the conasprellans and to distinguish them from Conus proper. Synapomorphic mutations at just 39 sites can resolve several groups within Conasprella because the informative region of intron 9 is so well conserved that the phylogenetic signal is not obscured by homoplasies at conflicting sites. Intron 9 also unambiguously distinguishes Conasprella as a whole from Conus because the conserved regions that are so well conserved within each group are not alignable and clearly not homologous between them. This pattern suggests that expression of the γ-glutamyl carboxylase gene may have undergone a functionally significant change in Conus or Conasprella shortly after they diverged.
Collapse
Affiliation(s)
- Nicole J Kraus
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | | | | | | | | | | |
Collapse
|
5
|
Kaltenpoth M, Showers Corneli P, Dunn DM, Weiss RB, Strohm E, Seger J. Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps. PLoS One 2012; 7:e32826. [PMID: 22412929 PMCID: PMC3295772 DOI: 10.1371/journal.pone.0032826] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/06/2012] [Indexed: 12/03/2022] Open
Abstract
Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae), and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera) based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase). The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes). Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes.
Collapse
Affiliation(s)
- Martin Kaltenpoth
- Research Group Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | | | | | | | | | | |
Collapse
|
6
|
Cabang AB, Imperial JS, Gajewiak J, Watkins M, Corneli PS, Olivera BM, Concepcion GP. Characterization of a venom peptide from a crassispirid gastropod. Toxicon 2011; 58:672-80. [PMID: 21939682 DOI: 10.1016/j.toxicon.2011.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/02/2011] [Accepted: 09/06/2011] [Indexed: 11/18/2022]
Abstract
The crassispirids are a large branch of venomous marine gastropods whose venoms have not been investigated previously. We demonstrate that crassispirids comprise a major group of toxoglossate snails in a clade distinct from all turrids whose venoms have been analyzed. The isolation and biochemical definition of the first venom component from any crassispirid is described. Crassipeptide cce9a from Crassispira cerithina (Anton, 1838) was purified from crude venom by following biological activity elicited in young mice, lethargy and a lack of responsiveness to external stimuli. Using Edman sequencing and mass spectrometry, the purified peptide was shown to be 29 amino acid residues long, with the sequence: GSCGLPCHENRRCGWACYCDDGICKPLRV. The sequence assignment was verified through the analysis of a cDNA clone encoding the peptide. The peptide was chemically synthesized and folded; the synthetic peptide was biologically active and coelution with the native venom peptide was demonstrated. When injected into mice of various ages, the peptide elicited a striking shift in behavioral phenotype between 14 and 16 days, from lethargy to hyperactivity.
Collapse
Affiliation(s)
- April B Cabang
- Marine Science Institute, University of the Philippines, Diliman, Quezon City
| | | | | | | | | | | | | |
Collapse
|
7
|
Kraus NJ, Corneli PS, Watkins M, Bandyopadhyay PK, Seger J, Olivera BM. Corrigendum to “Against expectation: A short sequence with high signal elucidates cone snail phylogeny” [Mol. Phylogenet. Evol. 58 (2011) 149–414]. Mol Phylogenet Evol 2011. [DOI: 10.1016/j.ympev.2011.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
8
|
Kraus NJ, Corneli PS, Watkins M, Bandyopadhyay PK, Seger J, Olivera BM. Against expectation: a short sequence with high signal elucidates cone snail phylogeny. Mol Phylogenet Evol 2010; 58:383-9. [PMID: 21147238 DOI: 10.1016/j.ympev.2010.11.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 10/11/2010] [Accepted: 11/23/2010] [Indexed: 11/30/2022]
Abstract
A short (259 nucleotide) conserved intronic sequence (CIS) is surprisingly informative for delineating deep phylogenetic relationships in cone snails. Conus species previously have been assigned to clades based on the evidence from mitochondrial 12S and 16S rRNA gene sequences (1129 bp). Despite their length, these genes lack the phylogenetic information necessary to resolve the relationships among the clades. Here we show that the relationships can be inferred from just 46 sites in the very short CIS sequence (a portion of "intron 9" of the γ-glutamyl carboxylase gene). This is counterintuitive because in short sequences sampling error (noise) often drowns out phylogenetic signal. The intron 9 CIS is rich in synapomorphies that define the divergence patterns among eight clades of worm- and fish-hunting Conus, and it contains almost no homoplasy. Parsimony, maximum likelihood and Bayesian analyses of the combined sequences (mt rRNA+CIS) confirm most of the relationships among 23 Conus sequences. This phylogeny implies that fish-hunting behavior evolved at least twice during the history of Conus-once among New World species and independently in the Indo-Pacific clades.
Collapse
Affiliation(s)
- Nicole J Kraus
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, United States
| | | | | | | | | | | |
Collapse
|
9
|
Aldenhoven JT, Miller MA, Corneli PS, Shapiro MD. Phylogeography of ninespine sticklebacks (Pungitius pungitius) in North America: glacial refugia and the origins of adaptive traits. Mol Ecol 2010; 19:4061-76. [PMID: 20854276 DOI: 10.1111/j.1365-294x.2010.04801.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The current geographical distribution of the ninespine stickleback (Pungitius pungitius) was shaped in large part by the glaciation events of the Pleistocene epoch (2.6 Mya-1 Kya). Previous efforts to elucidate the phylogeographical history of the ninespine stickleback in North America have focused on a limited set of morphological traits, some of which are likely subject to widespread convergent evolution, thereby potentially obscuring relationships among populations. In this study, we used genetic information from both mitochondrial DNA (mtDNA) sequences and nuclear microsatellite markers to determine the phylogenetic relationships among ninespine stickleback populations. We found that ninespine sticklebacks in North America probably dispersed from at least three glacial refugia-the Mississippi, Bering, and Atlantic refugia-not two as previously thought. However, by applying a molecular clock to our mtDNA data, we found that these three groups diverged long before the most recent glacial period. Our new phylogeny serves as a critical framework for examining the evolution of derived traits in this species, including adaptive phenotypes that evolved multiple times in different lineages. In particular, we inferred that loss of the pelvic (hind fin) skeleton probably evolved independently in populations descended from each of the three putative North American refugia.
Collapse
|
10
|
Biggs JS, Watkins M, Corneli PS, Olivera BM. Defining a Clade by Morphological, Molecular and Toxinological Criteria: Distinctive Forms related to Conus praecellens A. Adams, 1854. Nautilus (Philadelphia) 2010; 124:1-19. [PMID: 20835370 PMCID: PMC2936482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We carried out a definition of the species group to which Conus praecellens A. Adams 1854 belongs using a combination of comparative morphological data, molecular phylogeny based on standard genetic markers and toxinological markers. Prior to this work, Conus praecellens was generally postulated to belong to a clade of similarly high-spired, smaller Conusspecies such as Conus pagodus Kiener, 1845, Conus memiae (Habe & Kosuge, 1970) and Conus arcuatus Broderip & Sowerby, 1829. The molecular phylogeny and toxinological data demonstrate that these prior hypotheses are incorrect, and that instead, Conus praecellens is in a branch of Conus that includes Conus stupa (Kuroda, 1956), Conus stupella (Kuroda, 1956), Conus acutangulus Lamark, 1810 and surprisingly, some species that are morphologically strikingly different, Conus mitratus Sowerby, 1870 and Conus cylindraceus Broderip & Sowerby, 1830. A more careful analysis of the morphologically diverse forms assigned to Conus praecellens suggests that from the Philippine material alone, there are at least three additional undescribed species, Conus andremenezi, Conus miniexcelsus and Conus rizali. A reevaluation of protoconch/early teleoconch morphology also strongly suggests that Conus excelsus Sowerby III, 1908 is related to these species. Together, the different data suggest a clade including the 10 species above that we designate, the Turriconus (Shikama and Habe, 1968) (clade; there are additional distinctive forms within the clade that may be separable at the species level. The phylogenetic definition using the multidisciplinary approach described herein provides a framework for comprehensively investigating biodiverse lineages of animals, such as the cone snails.
Collapse
Affiliation(s)
- Jason S. Biggs
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU, USA, 96923
- Department of Biology, University of Utah, Salt Lake City, UT 84112
| | - Maren Watkins
- Department of Biology, University of Utah, Salt Lake City, UT 84112
| | | | | |
Collapse
|
11
|
Heralde FM, Kantor YI, Astilla MAQ, Lluisma AO, Geronimo R, Aliño PM, Watkins M, Corneli PS, Olivera BM, Santos AD, Concepcion GP. THE INDO-PACIFIC GEMMULA SPECIES IN THE SUBFAMILY TURRINAE: ASPECTS OF FIELD DISTRIBUTION, MOLECULAR PHYLOGENY, RADULAR ANATOMY AND FEEDING ECOLOGY. Philipp Sci Lett 2010; 3:20105. [PMID: 22039575 PMCID: PMC3203214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The biology, feeding ecology and phylogenetic relationships of marine snails in the family Turridae remain poorly understood. Here we report our study on four deep-water species in the genus Gemmula, a major group in this family. The four species G. speciosa (Reeve 1843), G. sogodensis (Olivera 2005), G. kieneri (Doumet 1940) and G. diomedea (Powell 1964) were collected at five different sites in the Philippines, and their pattern of distribution in the sites, their feeding behaviour as well as their phylogenetic relationships with each other and with other members of the subfamily Turrinae were investigated. The radular morphology (of two Gemmula species) and potential prey (for one Gemmula species) were also examined. Actual feeding observations were also conducted for Gemmula speciosa and compared with two turrids from other genera.All four Gemmula species showed strikingly different patterns of distribution; each species was found to be relatively much more abundant at one site but not at the other sites. Molecular phylogenetic analysis based on 16S sequences correlated with previously reported 12S sequences and revealed that the four species all belong to a well-supported Gemmula clade within the subfamily Turrinae; and that this clade appeared more closely related to the clades Xenuroturris, Turris and Lophiotoma than to the other clades in the subfamily (i.e., Turridrupa, Unedogemmula and Polystira). Morphological analysis of the radula of both G. speciosa and G. sogodensis revealed that the radulae of the two species were similar but differed from the other turrids, Lophiotoma acuta and Unedogemmula bisaya, by the absence of central teeth, consistent with the separation of the Gemmula clade from the Lophiotoma and Unedogemmula clade.To identify the polychaete group that is targeted as prey by species of Gemmula, analysis of regurgitated food fragments was made; phylogenetic analysis of an mtCOI gene fragment that was PCR-amplified from the regurgitated tissue of one specimen (G. diomedea) indicated close affinity of the prey to the terebellid polychaete Amphitritides. Specimens of Gemmula speciosa, when challenged with the terebellid polychaete Loimia sp., were observed to attack the worm suggesting that Gemmula species feed on terebellid polychaetes. Lophiotoma acuta were also observed to feed on the same species of terebellid but were usually group-feeding in contrast to the solitary feeding of G. speciosa. Unedogemmula bisaya did not feed on the terebellid which also supports the separation of the Gemmula and Unedogemmula clade.Two lines of proof (i.e. the molecular phylogenetic analysis and the feeding challenge) supporting the toxin homology findings previously reported, provide consistent evidence that Gemmula is a distinct clade of worm-hunting Turrinae that feeds on Terebellidae.
Collapse
Affiliation(s)
- Francisco M Heralde
- National Institute of Molecular Biology and Biotechnology, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Nam HH, Corneli PS, Watkins M, Olivera B, Bandyopadhyay P. Multiple genes elucidate the evolution of venomous snail-hunting Conus species. Mol Phylogenet Evol 2009; 53:645-52. [PMID: 19616106 DOI: 10.1016/j.ympev.2009.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 07/07/2009] [Accepted: 07/10/2009] [Indexed: 11/17/2022]
Abstract
The species-rich Cone snails (Conus sp.) are predatory, marine gastropods known for small venom peptides that are valuable for pharmacological research applications. Phylogenetic analyses with mitochondrial rRNA sequences have facilitated peptide discovery. However, these relatively conserved genes leave unresolved the closer relationships among many species. We sequenced 26 internal transcribed spacer 2 (ITS2) sequences from genomic ribosomal DNA to elucidate the evolutionary relationships among molluscivorous species and to piscivorous and vermivorous species. We show that ITS2 sequences are well conserved within species but are sufficiently variable among species to resolve recent divergences. Using Bayesian, maximum likelihood and log-determinant methods, we use the ITS sequences to resolve portions of the tree that could not be resolved using the more conventional mt rRNA sequences. When the ITS2 sequences are added to existing COI and to the more conserved rRNA sequences and then properly modeled, support throughout the tree is increased. This enables us to show finer relationships among the molluscivorous species that reveal three well-supported clades (Conus, Cylinder, and Darioconus) and renders the ITS2 sequences an essential component in advancing the discovery and pharmacological characterization of novel peptides from the venoms of these molluscs.
Collapse
Affiliation(s)
- Hannah H Nam
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
| | | | | | | | | |
Collapse
|
13
|
|
14
|
Abstract
Since branch lengths provide important information about the timing and the extent of evolutionary divergence among taxa, accurate resolution of evolutionary history depends as much on branch length estimates as on recovery of the correct topology. However, the empirical relationship between the choice of genes to sequence and the quality of branch length estimation remains ill defined. To address this issue, we evaluated the accuracy of branch lengths estimated from subsets of the mitochondrial genome for a mammalian phylogeny with known subordinal relationships. Using maximum-likelihood methods, we estimated branch lengths from an 11-kb sequence of all 13 protein-coding genes and compared them with estimates from single genes (0.2-1.8 kb) and from 7 different combinations of genes (2-3.5 kb). For each sequence, we separated the component of the log-likelihood deviation due to branch length differences associated with alternative topologies from that due to those that are independent of the topology. Even among the sequences that recovered the same tree topology, some produced significantly better branch length estimates than others did. The combination of correct topology and significantly better branch length estimation suggests that these gene combinations may prove useful in estimating phylogenetic relationships for mammalian divergences below the ordinal level. Thus, the proper choice of genes to sequence is a critical factor for reliable estimation of evolutionary history from molecular data.
Collapse
Affiliation(s)
- P S Corneli
- Department of Biology, University of Utah, Salt Lake City 84112, USA.
| | | |
Collapse
|
15
|
Abstract
OBJECTIVE To determine the risk of cesarean delivery for women who themselves were born via operative delivery. METHODS A linked data base was constructed between the birth certificates of individuals born in Utah during 1947-1957 (parental cohort) and who subsequently became a parent of offspring born in Utah between 1970-1991 (offspring cohort). Parental cohort women (cases) who had been delivered operatively (cesarean delivery, mid- or high forceps) as well as women who had a sibling delivered by an operative procedure were matched (1:2) with parental-cohort women born by spontaneous vaginal delivery (controls). Both cases and controls were selected based on having a record of at least one delivery in Utah during 1970-1991. RESULTS Women who were delivered by cesarean were at increased risk of subsequently delivering their children by cesarean (odds ratio [OR] 1.41, 95% confidence interval [CI] 1.18-1.70; P < .001). Progressive risk was associated with parental delivery by mid- or high forceps (OR 1.72, 95% CI 1.20-2.47; P = .004), parental cesarean because of cephalopelvic disproportion alone (OR 1.83, 95% CI 1.16-2.88; P = .01), or parental cesarean for dysfunctional labor (OR 5.97, 95% CI 1.5-23.6; P < .001). The attributable risk for cesarean delivery to the contemporary population is 3.5%. CONCLUSION An intergenerational predisposition to cesarean delivery exists.
Collapse
Affiliation(s)
- M W Varner
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, USA
| | | | | | | | | |
Collapse
|
16
|
Ludwig E, Corneli PS, Anderson JL, Marshall HW, Lalouel JM, Ward RH. Angiotensin-converting enzyme gene polymorphism is associated with myocardial infarction but not with development of coronary stenosis. Circulation 1995; 91:2120-4. [PMID: 7697839 DOI: 10.1161/01.cir.91.8.2120] [Citation(s) in RCA: 113] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Although both genetic and nongenetic factors contribute to the pathogenesis of coronary artery disease, the identification of specific genetic lesions has lagged behind the identification of critical environmental risk factors. A reported association between myocardial infarction (MI) and the insertion/deletion (I/D) polymorphism of the angiotensin-converting enzyme (ACE) gene in European men suggests a critical role for this genomic region. However, the generality of this association remains to be determined. It also is not clear at what stage in disease progression the association with the ACE I/D polymorphism becomes important. METHODS AND RESULTS We evaluated the ACE I/D polymorphism in patients who had undergone coronary angiography (402 men and 295 women) and in 203 representative control subjects. After polymerase chain reaction amplification, genotypes were determined by agarose gel sizing and by hybridization with allele-specific oligonucleotides. After patients were categorized by the degree of coronary artery stenosis and the occurrence of an MI, the distribution of ACE I/D genotypes was evaluated by log linear analysis. Patients were genetically representative of the regional population, and patients with > 60% stenosis of their coronary arteries had the same distribution of ACE I/D genotypes as did patients with < 10% stenosis. However, among patients with stenosis, the occurrence of an MI was significantly associated with the D allele in all patients (odds ratio [OR], 1.59; P = .002) and in men alone (OR, 1.63; P = .006). The lack of significance in women (OR, 1.40; P = .263) is probably due to the fact that only 36 women in the present study had experienced an MI. Furthermore, the association between MI and the ACE I/D polymorphism was independent of blood pressure, smoking habits, and body mass index. CONCLUSIONS Segregation of the ACE I/D polymorphism is a pervasive genetic risk factor for MI in whites but has no evident effect on the events leading to stenosis of the coronary arteries. This suggests that risk of MI is influenced by two independent processes--atherogenesis that leads to coronary stenosis followed by conversion to MI. The renin-angiotensin system appears to confer significant risk of infarction by influencing the conversion to MI but has no apparent effect on the development of atherostenosis.
Collapse
Affiliation(s)
- E Ludwig
- Department of Human Genetics, University of Utah, Salt Lake City 84112, USA
| | | | | | | | | | | |
Collapse
|
17
|
Carroll SP, Corneli PS. Divergence in male mating tactics between two populations of the soapberry bug: II. Genetic change and the evolution of a plastic reaction norm in a variable social environment. Behav Ecol 1995. [DOI: 10.1093/beheco/6.1.46] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
18
|
Marshall HW, Morrison LC, Wu LL, Anderson JL, Corneli PS, Stauffer DM, Allen A, Karagounis LA, Ward RH. Apolipoprotein polymorphisms fail to define risk of coronary artery disease. Results of a prospective, angiographically controlled study. Circulation 1994; 89:567-77. [PMID: 8313545 DOI: 10.1161/01.cir.89.2.567] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND Because genetic factors are believed to contribute to the etiology of coronary artery disease (CAD), it has been suggested that DNA polymorphisms at candidate loci might identify individuals at high risk for developing disease. In this regard, apolipoprotein genes represent extremely promising loci because levels of apolipoproteins and their associated lipoproteins represent a major risk factor for CAD, and rare dysfunctional mutations in these genes result in a significant risk for CAD. To date, although some reports indicate that DNA polymorphisms at these loci are associated with increased risk of CAD, other reports have failed to find such associations. METHODS AND RESULTS To resolve the question of whether genetic polymorphisms at apolipoprotein loci can be used to identify individuals at increased risk for CAD, we evaluated the distribution of apolipoprotein genetic polymorphisms in a large series of subjects (n = 848) undergoing coronary angiography. Blinded assessment of angiograms was used to discriminate between patients with CAD (> or = 60% stenosis of any major branch, n = 444) and control subjects without disease (< or = 10% stenosis, n = 404). A total of 12 polymorphisms were evaluated at the following loci: apolipoprotein (apo) A-I/C-III/A-IV (five restriction site polymorphisms--Msp I, Pst I, Sst I, Pvu IIa, Pvu IIb), apo B (three restriction site polymorphisms--Xba I, EcoRI, Msp I, plus an insertion/deletion polymorphism), apo A-II (Msp I polymorphism), apo C-II (Taq I polymorphism), and apo E (protein isoforms revealed by DNA analysis). All subjects were of Northern European (primarily Angloscandinavian) descent, and, within each sex, patients and control subjects were of comparable age. All 12 loci were in Hardy-Weinberg equilibrium, with no indication of population heterogeneity. As expected, patients were distinguished from control subjects by their lipid profiles and a higher frequency of known risk factors for CAD. However, analysis by log-linear models indicated that there were no significant associations between apolipoprotein polymorphisms and the risk of CAD (P = .10 to .90). The lack of association was maintained irrespective of whether the analysis was carried out for the entire sample or the contrast was made more stringent by comparing patients most likely to have a genetic component to their disease (ie, young patients with early-onset CAD) with the control subjects least likely to have genetic susceptibility (ie, older control subjects who had ample time to develop CAD). CONCLUSIONS Despite the fundamental role of apolipoprotein genes in lipid metabolism, we find no evidence that common genetic polymorphisms of the major apolipoprotein loci have a significant influence on the risk of developing angiographically defined CAD in this representative population. Therefore, at this time we find no support for the hypothesis that mass screening for genetic polymorphisms at candidate loci can reduce the burden of CAD by identifying a substantial proportion of high-risk individuals. Instead, it appears more appropriate to direct attention toward modifying high-risk behaviors to alleviate the consequences of traditional environmental risk factors.
Collapse
Affiliation(s)
- H W Marshall
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City
| | | | | | | | | | | | | | | | | |
Collapse
|