Molecular phylogenetics is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominately in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved; the result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that includes the use of molecular data in taxonomy and biogeography. Molecular phylogenetics and molecular evolution correlate. Molecular evolution is the process of selective changes at a molecular level throughout various branches in the tree of life. Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and results in the construction of a phylogenetic tree; the figure displayed on the right depicts the phylogenetic tree of life as one of the first detailed trees, according to information known in the 1870s by Haeckel.
The theoretical frameworks for molecular systematics were laid in the 1960s in the works of Emile Zuckerkandl, Emanuel Margoliash, Linus Pauling, Walter M. Fitch. Applications of molecular systematics were pioneered by Charles G. Sibley, Herbert C. Dessauer, Morris Goodman, followed by Allan C. Wilson, Robert K. Selander, John C. Avise. Work with protein electrophoresis began around 1956. Although the results were not quantitative and did not improve on morphological classification, they provided tantalizing hints that long-held notions of the classifications of birds, for example, needed substantial revision. In the period of 1974–1986, DNA-DNA hybridization was the dominant technique used to measure genetic difference. Early attempts at molecular systematics were termed as chemotaxonomy and made use of proteins, enzymes and other molecules that were separated and characterized using techniques such as chromatography; these have been replaced in recent times by DNA sequencing, which produces the exact sequences of nucleotides or bases in either DNA or RNA segments extracted using different techniques.
In general, these are considered superior for evolutionary studies, since the actions of evolution are reflected in the genetic sequences. At present, it is still a expensive process to sequence the entire DNA of an organism. However, it is quite feasible to determine the sequence of a defined area of a particular chromosome. Typical molecular systematic analyses require the sequencing of around 1000 base pairs. At any location within such a sequence, the bases found in a given position may vary between organisms; the particular sequence found in a given organism is referred to as its haplotype. In principle, since there are four base types, with 1000 base pairs, we could have 41000 distinct haplotypes. However, for organisms within a particular species or in a group of related species, it has been found empirically that only a minority of sites show any variation at all, most of the variations that are found are correlated, so that the number of distinct haplotypes that are found is small. In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material.
Haplotypes of individuals of related, yet different, taxa are determined. Haplotypes from a smaller number of individuals from a different taxon are determined: these are referred to as an outgroup; the base sequences for the haplotypes are compared. In the simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: this is referred to as the number of substitutions; the difference between organisms is re-expressed as a percentage divergence, by dividing the number of substitutions by the number of base pairs analysed: the hope is that this measure will be independent of the location and length of the section of DNA, sequenced. An older and superseded approach was to determine the divergences between the genotypes of individuals by DNA-DNA hybridization; the advantage claimed for using hybridization rather than gene sequencing was that it was based on the entire genotype, rather than on particular sections of DNA. Modern sequence comparison techniques overcome this objection by the use of multiple sequences.
Once the divergences between all pairs of samples have been determined, the resulting triangular matrix of differences is submitted to some form of statistical cluster analysis, the resulting dendrogram is examined in order to see whether the samples cluster in the way that would be expected from current ideas about the taxonomy of the group. Any group of haplotypes that are all more similar to one another than any of them is to any other haplotype may be said to constitute a clade, which may be visually represented as the figure displayed on the right demonstrates. Statistical techniques such as bootstrapping and jackknifing help in providing reliability estimates for the positions of haplotypes within the evolutionary trees; every living organism contains deoxyribonucleic acid, ribonucleic acid, proteins. In general related organisms have a high degree of similarity in the molecular structure of these substances, while the molecules of organisms distantly related s
Nucleic acid sequence
A nucleic acid sequence is a succession of letters that indicate the order of nucleotides forming alleles within a DNA or RNA molecule. By convention, sequences are presented from the 5' end to the 3' end. For DNA, the sense strand is used; because nucleic acids are linear polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is termed the primary structure; the sequence has capacity to represent information. Biological deoxyribonucleic acid represents the information which directs the functions of a living thing. Nucleic acids have a secondary structure and tertiary structure. Primary structure is sometimes mistakenly referred to as primary sequence. Conversely, there is no parallel concept of tertiary sequence. Nucleic acids consist of a chain of linked units called nucleotides; each nucleotide consists of three subunits: a phosphate group and a sugar make up the backbone of the nucleic acid strand, attached to the sugar is one of a set of nucleobases.
The nucleobases are important in base pairing of strands to form higher-level secondary and tertiary structure such as the famed double helix. The possible letters are A, C, G, T, representing the four nucleotide bases of a DNA strand — adenine, guanine, thymine — covalently linked to a phosphodiester backbone. In the typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, read left to right in the 5' to 3' direction. With regards to transcription, a sequence is on the coding strand if it has the same order as the transcribed RNA. One sequence can be complementary to another sequence, meaning that they have the base on each position in the complementary and in the reverse order. For example, the complementary sequence to TTAC is GTAA. If one strand of the double-stranded DNA is considered the sense strand the other strand, considered the antisense strand, will have the complementary sequence to the sense strand. Comparing and determining % difference between two nucleotide sequences.
AATCCGCTAG AAACCCTTAG Given the two 10-nucleotide sequences, line them up and compare the differences between them. Calculate the percent similarity by taking the number of different DNA bases divided by the total number of nucleotides. In the above case, there are three differences in the 10 nucleotide sequence. Therefore, divide 7/10 to get the 70% similarity and subtract that from 100% to get a 30% difference. While A, T, C, G represent a particular nucleotide at a position, there are letters that represent ambiguity which are used when more than one kind of nucleotide could occur at that position; the rules of the International Union of Pure and Applied Chemistry are as follows: These symbols are valid for RNA, except with U replacing T. Apart from adenine, guanine and uracil, DNA and RNA contain bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is 5-methylcytidine. In RNA, there are many modified bases, including pseudouridine, inosine, ribothymidine and 7-methylguanosine.
Hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination. Hypoxanthine is produced from adenine, xanthine is produced from guanine. Deamination of cytosine results in uracil. In biological systems, nucleic acids contain information, used by a living cell to construct specific proteins; the sequence of nucleobases on a nucleic acid strand is translated by cell machinery into a sequence of amino acids making up a protein strand. Each group of three bases, called a codon, corresponds to a single amino acid, there is a specific genetic code by which each possible combination of three bases corresponds to a specific amino acid; the central dogma of molecular biology outlines the mechanism by which proteins are constructed using information contained in nucleic acids. DNA is transcribed into mRNA molecules, which travels to the ribosome where the mRNA is used as a template for the construction of the protein strand. Since nucleic acids can bind to molecules with complementary sequences, there is a distinction between "sense" sequences which code for proteins, the complementary "antisense" sequence, by itself nonfunctional, but can bind to the sense strand.
DNA sequencing is the process of determining the nucleotide sequence of a given DNA fragment. The sequence of the DNA of a living thing encodes the necessary information for that living thing to survive and reproduce. Therefore, determining the sequence is useful in fundamental research into why and how organisms live, as well as in applied subjects; because of the importance of DNA to living things, knowledge of a DNA sequence may be useful in any biological research. For example, in medicine it can be used to identify and develop treatments for genetic diseases. Research into pathogens may lead to treatments for contagious diseases. Biotechnology is a burgeoning discipline, with the potential for services. RNA is not sequenced directly. Instead, it is copied to a DNA by reverse transcriptase, this DNA is sequenced. Current sequencing methods rely on the discriminatory ability of DNA polymerases, therefore can only distinguish four bases. An inosine is read as a G, 5-methyl-cytosine is read as a C.
A holotype is a single physical example of an organism, known to have been used when the species was formally described. It is either the single such physical example or one of several such, but explicitly designated as the holotype. Under the International Code of Zoological Nomenclature, a holotype is one of several kinds of name-bearing types. In the International Code of Nomenclature for algae and plants and ICZN the definitions of types are similar in intent but not identical in terminology or underlying concept. For example, the holotype for the butterfly Lycaeides idas longinus is a preserved specimen of that species, held by the Museum of Comparative Zoology at Harvard University. An isotype is a duplicate of the holotype and is made for plants, where holotype and isotypes are pieces from the same individual plant or samples from the same gathering. A holotype is not "typical" of that taxon, although ideally it should be. Sometimes just a fragment of an organism is the holotype in the case of a fossil.
For example, the holotype of Pelorosaurus humerocristatus, a large herbivorous dinosaur from the early Jurassic period, is a fossil leg bone stored at the Natural History Museum in London. If a better specimen is subsequently found, the holotype is not superseded. Under the ICN, an additional and clarifying type could be designated an epitype under Article 9.8, where the original material is demonstrably ambiguous or insufficient. A conserved type is sometimes used to correct a problem with a name, misapplied. In the absence of a holotype, another type may be selected, out of a range of different kinds of type, depending on the case, a lectotype or a neotype. For example, in both the ICN and the ICZN a neotype is a type, appointed in the absence of the original holotype. Additionally, under the ICZN the Commission is empowered to replace a holotype with a neotype, when the holotype turns out to lack important diagnostic features needed to distinguish the species from its close relatives. For example, the crocodile-like archosaurian reptile Parasuchus hislopi Lydekker, 1885 was described based on a premaxillary rostrum, but this is no longer sufficient to distinguish Parasuchus from its close relatives.
This made. Texan paleontologist Sankar Chatterjee proposed that a new type specimen, a complete skeleton, be designated; the International Commission on Zoological Nomenclature considered the case and agreed to replace the original type specimen with the proposed neotype. The procedures for the designation of a new type specimen when the original is lost come into play for some recent, high-profile species descriptions in which the specimen designated as the holotype was a living individual, allowed to remain in the wild. In such a case, there is no actual type specimen available for study, the possibility exists that—should there be any perceived ambiguity in the identity of the species—subsequent authors can invoke various clauses in the ICZN Code that allow for the designation of a neotype. Article 75.3.7 of the ICZN requires that the designation of a neotype must be accompanied by "a statement that the neotype is, or upon publication has become, the property of a recognized scientific or educational institution, cited by name, that maintains a research collection, with proper facilities for preserving name-bearing types, that makes them accessible for study", but there is no such requirement for a holotype.
Type Allotype Paratype Type species Genetypes- genetic sequence data from type specimens. BOA Photographs of type specimens of Neotropical Rhopalocera
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence Database Collaboration; the National Center for Biotechnology Information is a part of the National Institutes of Health in the United States. GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms; the database started in 1982 by Los Alamos National Laboratory. GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling every 18 months. Release 194, produced in February 2013, contained over 150 billion nucleotide bases in more than 162 million sequences. GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.
Only original sequences can be submitted to GenBank. Direct submissions are made to GenBank using BankIt, a Web-based form, or the stand-alone submission program, Sequin. Upon receipt of a sequence submission, the GenBank staff examines the originality of the data and assigns an accession number to the sequence and performs quality assurance checks; the submissions are released to the public database, where the entries are retrievable by Entrez or downloadable by FTP. Bulk submissions of Expressed Sequence Tag, Sequence-tagged site, Genome Survey Sequence, High-Throughput Genome Sequence data are most submitted by large-scale sequencing centers; the GenBank direct submissions group processes complete microbial genome sequences. Walter Goad of the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory and others established the Los Alamos Sequence Database in 1979, which culminated in 1982 with the creation of the public GenBank. Funding was provided by the National Institutes of Health, the National Science Foundation, the Department of Energy, the Department of Defense.
LANL collaborated on GenBank with the firm Bolt and Newman, by the end of 1983 more than 2,000 sequences were stored in it. In the mid 1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL; as one of the earliest bioinformatics community projects on the Internet, the GenBank project started BIOSCI/Bionet news groups for promoting open access communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly created National Center for Biotechnology Information; the GenBank release notes for release 162.0 state that "from 1982 to the present, the number of bases in GenBank has doubled every 18 months". As of 15 June 2018, GenBank release 226.0 has 209,775,348 loci, 263,957,884,539 bases, from 209,775,348 reported sequences. The GenBank database includes additional data sets that are constructed mechanically from the main sequence data collection, therefore are excluded from this count.
Public databases which may be searched using the National Center for Biotechnology Information Basic Local Alignment Search Tool, lack peer-reviewed sequences of type strains and sequences of non-type strains. On the other hand, while commercial databases contain high-quality filtered sequence data, there are a limited number of reference sequences. A paper released in the Journal of Clinical Microbiology evaluated the 16S rRNA gene sequencing results analyzed with GenBank in conjunction with other available, quality-controlled, web-based public databases, such as the EzTaxon-e and the BIBI databases; the results showed that analyses performed using GenBank combined with EzTaxon-e were more discriminative than using GenBank or other databases alone. Ensembl Human Protein Reference Database Sequence analysis UniProt List of sequenced eukaryotic genomes List of sequenced archaeal genomes RefSeq — the Reference Sequence Database Geneious — includes a GenBank Submission Tool Open science data This article incorporates public domain material from the National Center for Biotechnology Information document "NCBI Handbook".
GenBank Example sequence record, for hemoglobin beta BankIt Sequin — a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database. EMBOSS — free, open source software for molecular biology GenBank, RefSeq, TPA and UniProt: What's in a Name
In biology, a type is a particular specimen of an organism to which the scientific name of that organism is formally attached. In other words, a type is an example that serves to anchor or centralize the defining features of that particular taxon. In older usage, a type was a taxon rather than a specimen. A taxon is a scientifically named grouping of organisms with other like organisms, a set that includes some organisms and excludes others, based on a detailed published description and on the provision of type material, available to scientists for examination in a major museum research collection, or similar institution. According to a precise set of rules laid down in the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae and plants, the scientific name of every taxon is always based on one particular specimen, or in some cases specimens. Types are of great significance to biologists to taxonomists. Types are physical specimens that are kept in a museum or herbarium research collection, but failing that, an image of an individual of that taxon has sometimes been designated as a type.
Describing species and appointing type specimens is part of scientific nomenclature and alpha taxonomy. When identifying material, a scientist attempts to apply a taxon name to a specimen or group of specimens based on his or her understanding of the relevant taxa, based on having read the type description, preferably based on an examination of all the type material of all of the relevant taxa. If there is more than one named type that all appear to be the same taxon the oldest name takes precedence, is considered to be the correct name of the material in hand. If on the other hand the taxon appears never to have been named at all the scientist or another qualified expert picks a type specimen and publishes a new name and an official description; this process is crucial to the science of biological taxonomy. People's ideas of how living things should be grouped shift over time. How do we know that what we call "Canis lupus" is the same thing, or the same thing, as what they will be calling "Canis lupus" in 200 years' time?
It is possible to check this because there is a particular wolf specimen preserved in Sweden and everyone who uses that name – no matter what else they may mean by it – will include that particular specimen. Depending on the nomenclature code applied to the organism in question, a type can be a specimen, a culture, an illustration, or a description; some codes consider a subordinate taxon to be the type, but under the botanical code the type is always a specimen or illustration. For example, in the research collection of the Natural History Museum in London, there is a bird specimen numbered 18126.96.36.199. This is a specimen of a kind of bird known as the spotted harrier, which bears the scientific name Circus assimilis; this particular specimen is the holotype for that species. That species was named and described by Jardine and Selby in 1828, the holotype was placed in the museum collection so that other scientists might refer to it as necessary. Note that at least for type specimens there is no requirement for a "typical" individual to be used.
Genera and families those established by early taxonomists, tend to be named after species that are more "typical" for them, but here too this is not always the case and due to changes in systematics cannot be. Hence, the term name-bearing type or onomatophore is sometimes used, to denote the fact that biological types do not define "typical" individuals or taxa, but rather fix a scientific name to a specific operational taxonomic unit. Type specimens are theoretically allowed to be aberrant or deformed individuals or color variations, though this is chosen to be the case, as it makes it hard to determine to which population the individual belonged; the usage of the term type is somewhat complicated by different uses in botany and zoology. In the PhyloCode, type-based definitions are replaced by phylogenetic definitions. In some older taxonomic works the word "type" has sometimes been used differently; the meaning was similar in the first Laws of Botanical Nomenclature, but has a meaning closer to the term taxon in some other works: Ce seul caractère permet de distinguer ce type de toutes les autres espèces de la section.
… Après avoir étudié ces diverses formes, j'en arrivai à les considérer comme appartenant à un seul et même type spécifique. Translation: This single character permits distinguish this type from all other species of the section... After studying the diverse forms, I came to consider them as belonging to the one and the same specific type. In botanical nomenclature, a type, "is that element to which the name of a taxon is permanently attached." In botany a type is either an illustration. A specimen is a real plant and kept safe, "curated", in a herbarium. Examples of where an illustration may serve as a type include: A detailed drawing, etc. depicting the plant, from the early days of plant taxonomy. A dried plant was difficult to transport and hard to keep safe for the future. Skilled botanical artists were sometimes employed by a botanist to make a faithful and detailed illustration; some such illustrations have become the best record a
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change, or a long one, like minisatellites. For many years, gene mapping was limited to identifying organisms by traditional phenotype markers; this included genes that encoded observable characteristics such as blood types or seed shapes. The insufficient number of these types of characteristics in several organisms limited the mapping efforts that could be done; this prompted the development of gene markers which could identify genetic characteristics that are not observable in organisms. Some used types of genetic markers are: RFLP SSLP AFLP RAPD VNTR SSR Microsatellite polymorphism, SNP STR SFP DArT RAD markers Molecular genetic markers can be divided into two classes a) biochemical markers which detect variation at the gene product level such as changes in proteins and amino acids and b) molecular markers which detect variation at the DNA level such as nucleotide changes: deletion, inversion and/or insertion.
Markers can exhibit two modes of i.e. dominant/recessive or co-dominant. If the genetic pattern of homozygotes can be distinguished from that of heterozygotes a marker is said to be co-dominant. Co-dominant markers are more informative than the dominant markers. Genetic markers can be used to study the relationship between an inherited disease and its genetic cause, it is known that pieces of DNA that lie near each other on a chromosome tend to be inherited together. This property enables the use of a marker, which can be used to determine the precise inheritance pattern of the gene that has not yet been localized. Genetic markers are employed in genealogical DNA testing for genetic genealogy to determine genetic distance between individuals or populations. Uniparental markers are studied for assessing paternal lineages. Autosomal markers are used for all ancestry. Genetic markers have to be identifiable, associated with a specific locus, polymorphic, because homozygotes do not provide any information.
Detection of the marker can be direct by indirect using allozymes. Some of the methods used to study the genome or phylogenetics are RFLP, Amplified fragment length polymorphism, RAPD, SSR, they can be used to create genetic maps. There was a debate over. Many researchers hypothesized that virus like particles were responsible for transforming the cell, while others thought that the cell itself was able to infect other canines as an allograft. With the aid of genetic markers, researchers were able to provide conclusive evidence that the cancerous tumor cell evolved into a transmissible parasite. Furthermore, molecular genetic markers were used to resolve the issue of natural transmission, the breed of origin, the age of the canine tumor. Genetic markers have been used to measure the genomic response to selection in livestock. Natural and artificial selection leads to a change in the genetic makeup of the cell; the presence of different alleles due to a distorted segregation at the genetic markers is indicative of the difference between selected and non-selected livestock.
Molecular marker DNA marking de Vicente C, Fulton T. Molecular Marker Learning Modules – Vol. 1. IPGRI, Rome and Institute for Genetic Diversity, New York, USA. de Vicente C, Fulton T. Molecular Marker Learning Modules – Vol. 2. IPGRI, Rome and Institute for Genetic Diversity, New York, USA. de Vicente C, Glaszmann JC. Molecular Markers for Allele Mining. AMS, CIRAD, GCP, IPGRI, M. S. Swaminathan Research Foundation. P. 85. Spooner D, van Treuren R, de Vicente MC. Molecular markers for genebank management. CGN, IPGRI, USDA. P. 126. Media related to Genetic markers at Wikimedia Commons
Leptoderma is a genus of slickheads found in the deep waters of the oceans. There are 6 recognized species in this genus: Leptoderma affinis Alcock, 1899 Leptoderma lubricum T. Abe, Marumo & Kawaguchi, 1965 Leptoderma macrophthalmum Byrkjedal, J. Y. Poulsen & J. K. Galbraith, 2011 Leptoderma macrops Vaillant, 1886 Leptoderma ospesca Angulo, C. C. Baldwin & D. R. Robertson, 2016 Leptoderma retropinna Fowler, 1943