Abstract：
:Species identification is one of the most important issues in biological studies. Due to recent increases in the amount of genomic information available and the development of DNA sequencing technologies, the applicability of using DNA sequences to identify species (commonly referred to as "DNA barcoding") is being tested in many areas. Several methods have been suggested to identify species using DNA sequences, including similarity scores, analysis of phylogenetic and population genetic information, and detection of species-specific sequence patterns. Although these methods have demonstrated good performance under a range of circumstances, they also have limitations, as they are subject to loss of information, require intensive computation and are sensitive to model mis-specification, and can be difficult to evaluate in terms of the significance of identification. Here, we suggest a new DNA barcoding method in which support vector machine (SVM) procedures are adopted. Our new method is nonparametric and thus is expected to be robust for a wide range of evolutionary scenarios as well as multilocus analyses. Furthermore, we describe bootstrap procedures that can be used to test the significances of species identifications. We implemented a novel conversion technique for transforming sequence data to real-valued vectors, and therefore, bootstrap procedures can be easily combined with our SVM approach. In this study, we present the results of simulation studies and empirical data analyses to demonstrate the performance of our method and discuss its properties.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Seo TKdoi
10.1007/s00239-010-9380-9subject
Has Abstractpub_date
2010-10-01 00:00:00pages
250-67issue
4eissn
0022-2844issn
1432-1432journal_volume
71pub_type
杂志文章abstract：:The slow-evolving mitochondrial DNAs of plants have potentially conserved information on the phylogenetic branching of the earliest land plants. We present the nad2 gene structures in hornworts and liverworts and in the presumptive earliest-branching vascular land plant clade, the Lycopodiopsida. Taken together with t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2324-2
更新日期：2002-09-01 00:00:00
abstract：:We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene arose recently by horizontal transfer from a fungal donor species. A 1,716-bp fragment of the mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the polymerase chain reaction and sequenced. Compar...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00175814
更新日期：1995-11-01 00:00:00
abstract：:The complete or partial sequences of 47 E. coli ribosomal proteins described in the literature have been examined by computerized search and matching programs. In contrast to results previously reported by other investigators, sequence homologies were uncovered among some of these ribosomal proteins that are well beyo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01732666
更新日期：1980-05-01 00:00:00
abstract：:The internal transcribed spacer region (ITS) of the nuclear rDNA cistron represents the barcoding locus for Fungi. Intragenomic variation of this multicopy gene can interfere with accurate phylogenetic reconstruction of biological entities. We investigated the amount and nature of this variation for the lichenized fun...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-013-9603-y
更新日期：2014-02-01 00:00:00
abstract：:We characterized the organization of mitochondrial genes from a diverse range of hymenopterans. Of the 21 taxa characterized, 12 had distinct, derived organizations. Some rearrangements were consistent with the duplication-random loss mechanism, while others were not. Local inversions were relatively common, i.e., rea...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2420-3
更新日期：2003-05-01 00:00:00
abstract：:Transfer RNA (tRNA) is the central intellectual property in the evolution of life on Earth. tRNA evolved from repeats and inverted repeats of known sequence. The anticodon and the T stem-loop-stems are homologs with significant conserved sequence identity. A number of models have been advanced to explain tRNA evolutio...
journal_title：Journal of molecular evolution
pub_type： 信件
doi：10.1007/s00239-020-09928-2
更新日期：2020-04-01 00:00:00
abstract：:Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Pr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006160
更新日期：1997-04-01 00:00:00
abstract：:Sequence data from regions of five vertebrate vitellogenin genes were used to examine the frequency, distribution, and mutability of the dinucleotide CpG, the preferred modification site for eukaryotic DNA methyltransferases. The observed level of the CpG dinucleotide in all five genes was markedly lower than that exp...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101752
更新日期：1987-01-01 00:00:00
abstract：:Natural populations of the Midas cichlid species in several different crater lakes in Nicaragua exhibit a conspicuous color polymorphism. Most individuals are dark and the remaining have a gold coloration. The color morphs mate assortatively and sympatric population differentiation has been shown based on neutral mole...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9340-4
更新日期：2010-05-01 00:00:00
abstract：:In Trypanoplasma borelli, a representative of the Bodonina within the Kinetoplastida, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activity was detected in both the cytosol and glycosomes. This situation is similar to that previously found in Trypanosomatidae, belonging to a different Kinetoplastida suborder. In T...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00164030
更新日期：1995-04-01 00:00:00
abstract：:Fish protamines are highly specialized molecules which are responsible for chromatin condensation during the last stages of spermatogenesis (spermiogenesis). However, not all fish contain protamines in their sperm nuclei; rather, there seems to be a random distribution of protamines within this group. The origin of th...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160152
更新日期：1994-09-01 00:00:00
abstract：:Hypoxia at deep-sea hydrothermal vents represents one of the most basic challenges for metazoans, which then requires specific adaptations to acquire oxygen to meet their metabolic needs. Hydrothermal vent scale-worms (Polychaeta; Polynoidae) express large amounts of extracellular single- and multi-domain hemoglobins,...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-017-9815-7
更新日期：2017-12-01 00:00:00
abstract：:51 polypeptides of known 3-dimensional structures have been submitted to a search for internal similarities. It is shown that the frequency of proteins displaying significant amounts of internal similarities is higher than predicted by chance. A non-negligible part of those similarities probably occurs in connection w...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101639
更新日期：1983-01-01 00:00:00
abstract：:One of the key problems in the study of ancient DNA is that of authenticating sequences obtained from PCR amplifications of highly degraded samples. Contamination of ancient samples and postmortem damage to endogenous DNA templates are the major obstacles facing researchers in this task. In particular, the authenticat...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-006-0259-8
更新日期：2007-07-01 00:00:00
abstract：:This study examines the diverse maximum wavelength absorption (lambdamax) found in crayfishes (Decapoda: Cambaridae and Parastacidae) and the associated genetic variation in their opsin locus. We measured the wavelength absorption in the photoreceptors of six species that inhabit environments of different light intens...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006257
更新日期：1997-11-01 00:00:00
abstract：:In mammals, chicken-type (c-type) lysozymes are part of the innate immune system, killing bacteria by degrading peptidoglycan in their cell walls. Many of the studies on the evolution of c-type lysozymes have focused on its new digestive function, including the duplicated stomach lysozymes in ruminants. Similarly, in ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-019-09910-7
更新日期：2019-12-01 00:00:00
abstract：:We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus--Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color visio...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-009-9283-9
更新日期：2009-10-01 00:00:00
abstract：:The NF-κB family of transcription factors is activated in response to many environmental and biological stresses, and plays a key role in innate immunity across a broad evolutionary expanse of animals. A simple NF-κB pathway is present in the sea anemone Nematostella vectensis, an important model organism in the phylu...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9479-7
更新日期：2011-12-01 00:00:00
abstract：:The amino acid sequences of 22 alpha-amylases from family 13 of glycosyl hydrolases were analyzed with the aim of revealing the evolutionary relationships between the archaeal alpha-amylases and their eubacterial and eukaryotic counterparts. Two evolutionary distance trees were constructed: (i) the first one based on ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006486
更新日期：1999-04-01 00:00:00
abstract：:We provide here evidence for a conserved regulatory element for transcription of the β-family globin genes based on a comparative study of 32 genes from 16 mammals. The element is characterized by the appearance of AA or TT dinucleotides in the A + T-rich region located 200-400 bp upstream of the cap sites. G-tracts 3...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9459-y
更新日期：2011-10-01 00:00:00
abstract：:Alu elements are not distributed homogeneously throughout the human genome: old elements are preferentially found in the GC-rich parts of the genome, while young Alus are more often found in the GC-poor parts of the genome. The process giving rise to this differential distribution remains poorly understood. Here we in...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0020-0
更新日期：2005-03-01 00:00:00
abstract：:Low oxygen and fluctuant ambient temperature pose serious challenges to mammalian survival. Physiological adaptations in mammals to hypoxia and low temperatures have been intensively investigated, yet their underlying molecular mechanisms need further exploration. Independent invasions of high-altitude plateaus, subte...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9870-8
更新日期：2018-12-01 00:00:00
abstract：:Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked seque...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0239-9
更新日期：2005-05-01 00:00:00
abstract：:The beta-globin gene cluster of Wistar rat was extensively cloned and the embryonic genes were mapped and sequenced. Four overlapping lambda Dash recombinant clones cover about 31 kb and contain four nonadult beta-globin genes, 5'-epsilon1-gamma1-gamma2-psigamma3-3'. The epsilon1 and gamma2 are active genes, since the...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006525
更新日期：1999-07-01 00:00:00
abstract：:Antibody binding site are formed by six hypervariable regions or complementarity determining regions (CDRs). The CDRs, three from the heavy chain and three from the light chain, are known as hypervariable segments and provide a surface complementary to that of the epitope. In recent work it was found that the amino ac...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00175497
更新日期：1994-01-01 00:00:00
abstract：:Previous studies have revealed a major difference in the phylogenetic structure, extent of genetic diversity, and selection pressure between the surface glycoproteins and internal gene segments of avian influenza viruses (AIV) sampled from wild birds. However, what evolutionary processes are responsible for these stri...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-009-9312-8
更新日期：2010-01-01 00:00:00
abstract：:Life as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We obs...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9876-2
更新日期：2018-12-01 00:00:00
abstract：:The evolutionary relationships among arthropod hemocyanins and insect hexamerins were investigated. A multiple sequence alignment of 12 hemocyanin and 31 hexamerin subunits was constructed and used for studying sequence conservation and protein phylogeny. Although hexamerins and hemocyanins belong to a highly divergen...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006366
更新日期：1998-07-01 00:00:00
abstract：:The periodic protein collagen is of special interest for the study of the relationship which exists between the structure of a protein and that of its mRNA, because oligopeptides containing glycine, proline (hydroxyproline) and alanine occur with great frequency in it. Collagen is particularly rich in these amino acid...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01739101
更新日期：1976-08-03 00:00:00
abstract：:Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. N...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-012-9504-5
更新日期：2012-06-01 00:00:00
