Journal of Molecular Evolution

The Journal of Molecular Evolution is a monthly peer-reviewed scientific journal that covers molecular evolution. It is published by Springer Science+Business Media and was established in 1971. The founding editor was Emile Zuckerkandl, who remained editor-in-chief until the late 1990s. In 1994, the journal became associated with the then existent International Society of Molecular Evolution.[1][2]

Journal of Molecular Evolution
Journal of Molecular Evolution
DisciplineMolecular evolution
LanguageEnglish
Edited byDavid Liberles
Publication details
Publication history
1971-present
Publisher
FrequencyMonthly
1.957
Standard abbreviations
J. Mol. Evol.
Indexing
CODENJMEVAU
ISSN0022-2844 (print)
1432-1432 (web)
LCCN72626641
OCLC no.01784021
Links

Scope

In a 1998 editorial, Zuckerkandl stated that he wanted the journal to "insure that this field be covered in its broadest sense" by publishing research that is of broad interest to the field of molecular evolution that it helped define, as well as to biology in general. To this end, Zuckerkandl stated that the journal does not cover research either on practical applications of molecular evolution, or articles "whose focus is very restricted and that do not lead to valuable insights beyond their narrow topic". However, he looked forward to coverage of new, rapidly developing areas of molecular evolution such as molecular developmental biology and work connecting molecular evolution to higher levels of biological organization.[3]

In 1999, under the new joint editorship of Martin Kreitman, Takashi Gojobori, and Giorgio Bernardi, the journal made explicit its focus on "the fundamental issues in molecular evolution", to the exclusion of molecular phylogenetics (the purview of several other molecular evolution journals, most significantly Molecular Phylogenetics and Evolution), except in cases that have "a special significance and impact".[4]

An editorial by Niles Lehman, editor-in-chief at the time, in 2013 stated a refocus of the journal’s aims towards its original scope with the inclusion of an emphasis on the mechanisms of evolution. “Studies performed using computational, chemical, in vitro, and experimental evolutionary methods, and those that target species-independent phenomena such as ribosomal function, genetic code evolution, and regulatory processes will occupy more of the journal space than before, with the consequence that work that is organism-, lineage-, or gene-specific will require a broader impact to be considered for publication."[5]

Zuckerkandl Prize

In 2001, the publisher established the yearly Zuckerkandl Prize for the best paper from the journal, in honor of Emile Zuckerkandl.[6]

References

  1. ^ Zuckerkandl, Emile; Bernardi, Giorgio (January 1995). "Editorial". Journal of Molecular Evolution. 40 (1): 1–2. doi:10.1007/BF00166589.
  2. ^ Zuckerkandl, Emile (1993-07-26). "Molecular Evolution Journals". The Scientist. 1993 (7): 15.
  3. ^ Zuckerkandl E (September 1998). "The journal and its field: a case of co-evolution". Journal of Molecular Evolution. 47 (3): 236–237. PMID 9732449.
  4. ^ Giorgio Bernardi; Takashi and Martin Kreitman, Editorial, Journal of Molecular Evolution, vol. 48 (1999), p. 1
  5. ^ Lehman, Niles (2013). "Editorial Changes at the Journal of Molecular Evolution". Journal of Molecular Evolution. 76 (1–2): 1–3. Bibcode:2013JMolE..76....1L. doi:10.1007/s00239-013-9546-3. PMID 23392526.
  6. ^ Giorgio Bernardi; Takashi Gojobori; and Martin Kreitman, Editorial, Journal of Molecular Evolution, vol. 52 (2001), p. 1

External links

Adiponectin receptor

The adiponectin receptors (AdipoRs) include the following two receptors, which are bound and activated by adiponectin:

Adiponectin receptor 1 (AdipoR1, PAQR1)

Adiponectin receptor 2 (AdipoR2, PAQR2)They are members of the progestin and adipoQ receptor (PAQR) family.In 2016, the University of Tokyo announced it was launching an investigation into anonymously made claims of fabricated and falsified data on the identification of AdipoR1 and AdipoR2.

Conservative replacement

A conservative replacement (also called a conservative mutation or a conservative substitution) is an amino acid replacement in a protein that changes a given amino acid to a different amino acid with similar biochemical properties (e.g. charge, hydrophobicity and size).Conversely, a radical replacement, or radical substitution, is an amino acid replacement that exchanges an initial amino acid by a final amino acid with different physicochemical properties.

Dinokaryota

Dinokaryota is a main grouping of dinoflagellates. They include all species where the nucleus remains a dinokaryon throughout the entire cell cycle, which is typically dominated by the haploid stage. All the "typical" dinoflagellates, such as Peridinium and Gymnodinium, belong here. Others are more unusual, including some that are colonial, amoeboid, or parasitic. Symbiodinium contains the symbiotic zooxanthellae.

The non-photosynthetic members are believed to derive from photosynthetic ancestors.

Drosophilinae

The Drosophilinae are the largest subfamily in the Drosophilidae. The other subfamily is the Steganinae.

Genetic code

The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences) into proteins. Translation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.The code defines how sequences of nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes (such as in human mitochondria) exist.

While the "genetic code" determines a protein's amino acid sequence, other genomic regions determine when and where these proteins are produced according to various "gene regulatory codes".

Isochore (genetics)

In genetics, an isochore is a large region of DNA (greater than 300 kb) with a high degree uniformity in guanine (G) and cytosine (C): G-C and C-G (collectively GC content).

Bernardi and colleagues first uncovered the compositional non-uniformity within vertebrate genomes using thermal melting and density gradient centrifugation. The DNA fragments extracted by the gradient centrifugation were later termed "isochores", which was subsequently defined as "very long (much greater than 200 KB) DNA segments" that "are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content". Subsequently, the isochores "grew" and were claimed to be ">300 kb in size." The theory proposed that isochore’s composition varied markedly between "warm-blooded" (homeotherm) vertebrates and "cold-blooded" (poikilotherm) vertebrates and later became known as the isochore theory.

Jack Lester King

Jack Lester King (March 9, 1934 – June 29, 1983) was an American evolutionary biologist best known for co-authoring (with Thomas H. Jukes) a seminal paper on the neutral theory of molecular evolution, "Non-Darwinian Evolution".King was born in Oakland, California and received both undergraduate and doctoral training at the University of California, Berkeley, earning a Ph.D. in Zoology in 1963. From 1963 to 1969, he remained at UC Berkeley as a postdoctoral fellow in population genetics, then independent researcher in biophysics, at the Donner Laboratory. In 1969, King became a professor at University of California, Santa Barbara.King and Jukes' "Non-Darwinian Evolution", published in Science in 1969 shortly after Motoo Kimura first mooted the neutral theory, brought together a variety of experimental evidence and theoretical arguments in support of the idea that the vast majority of mutations, at the molecular level, are neither beneficial nor harmful. As the intentionally provocative title implies, King and Jukes suggested that for most molecular evolution, genetic drift rather than natural selection is the main factor. King himself was "a staunch but progressive Darwinian", but he enjoyed the strong reactions the paper provoked. This marked the beginning of the controversy over neutral evolution and the "neutralist-selectionist debate", primarily between organismal and molecular biologists, which would continue throughout King's career. His later work in this area focused on neutral substitutions, isoalleles, and the measurement of variation through electrophoresis.King became an associate editor of the Journal of Molecular Evolution in 1971, shortly after the journal's founding. He co-authored a 1981 textbook, Biology, The Science of Life. King died unexpectedly in 1983 from a brain hemorrhage caused by acute myelomonocytic leukemia. King was survived by his second wife Ethel and their two children as well as six children from his first marriage.

Leviviridae

Leviviridae is a family of viruses. Bacteria, including Enterobacteria, Caulobacter, Pseudomonas, and Acinetobacter serve as natural hosts for these bacteriophages. There are currently four species in this family, divided among 2 genera. They are small RNA viruses with linear, positive-sense, single-stranded RNA genomes that encode only four proteins. All phages of this family require bacterial pili to attach to and infect cells.

Models of DNA evolution

A number of different Markov models of DNA sequence evolution have been proposed. These substitution models differ in terms of the parameters used to describe the rates at which one nucleotide replaces another during evolution. These models are frequently used in molecular phylogenetic analyses. In particular, they are used during the calculation of likelihood of a tree (in Bayesian and maximum likelihood approaches to tree estimation) and they are used to estimate the evolutionary distance between sequences from the observed differences between the sequences.

Ochrophyta

Ochrophyta is a group of mostly photosynthetic heterokonts.The classification of the group is still being worked out. Some authors (e.g., Cavalier-Smith) divide it into two subphyla, Phaeista Cavalier-Smith 1995 (comprising Hypogyristea and Chrysista in some classifications, or Limnista and Marista in others) and Khakista Cavalier-Smith, 2000 (comprising Bolidomonas and diatoms). Others prefer not to use the subphyla, listing only lower taxa (e.g., Reviers, 2002, Guiry & Guiry, 2014).

Ornithine

Ornithine is a non-proteinogenic amino acid that plays a role in the urea cycle. Ornithine is abnormally accumulated in the body in ornithine transcarbamylase deficiency. The radical is ornithyl.

Ostariophysi

Ostariophysi is the second-largest superorder of fish. Members of this superorder are called ostariophysians. This diverse group contains 10,758 species, about 28% of known fish species in the world and 68% of freshwater species, and are present on all continents except Antarctica. They have a number of common characteristics such as an alarm substance and a Weberian apparatus. Members of this group include fish important to people for food, sport, the aquarium industry, and research.

Proteromonadidae

Proteromonadidae is a paraphyletic family of heterokonts, that resemble Opalinidae.

Small nucleolar RNA SNORA73

In molecular biology, the small nucleolar RNA SNORA73 (also called U17/E1 RNA) belongs to the H/ACA class of small nucleolar RNAs (snoRNAs). Vertebrate U17 is intron-encoded and ranges in length from 200-230 nucleotides, longer than most snoRNAs. It is one of the most abundant snoRNAs in human cells and is essential for the cleavage of pre-rRNA within the 5' external transcribed spacer (ETS). This cleavage leads to the formation of 18S rRNA. Regions of the U17 RNA are complementary to rRNA and act as guides for RNA/RNA interactions, although these regions do not seem to be well conserved between organisms.

Sudan golden sparrow

The Sudan golden sparrow (Passer luteus) is a small bird in the sparrow family found in sub-Saharan Africa. It is a popular cage bird, and in aviculture it is known as the golden song sparrow. The Arabian golden sparrow and this species are sometimes considered one species, as the "golden sparrow".

Systematic evolution of ligands by exponential enrichment

Systematic evolution of ligands by exponential enrichment (SELEX), also referred to as in vitro selection or in vitro evolution, is a combinatorial chemistry technique in molecular biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands, which are commonly referred to as aptamers.

Although SELEX has emerged as the most commonly used name for the procedure, some researchers have referred to it as SAAB (selected and amplified binding site) and CASTing (cyclic amplification and selection of targets) SELEX was first introduced in 1990. In 2015 a special issue was published in the Journal of Molecular Evolution in the honor of quarter century of the SELEX discovery .

The process begins with the synthesis of a very large oligonucleotide library consisting of randomly generated sequences of fixed length flanked by constant 5' and 3' ends that serve as primers. For a randomly generated region of length n, the number of possible sequences in the library is 4n (n positions with four possibilities (A,T,C,G) at each position). The sequences in the library are exposed to the target ligand - which may be a protein or a small organic compound - and those that do not bind the target are removed, usually by affinity chromatography or target capture on paramagnetic beads. The bound sequences are eluted and amplified by PCR to prepare for subsequent rounds of selection in which the stringency of the elution conditions can be increased to identify the tightest-binding sequences. A caution to consider in this method is that the selection of extremely high, sub-nanomolar binding affinity entities may not in fact improve specificity for the target molecule. Off-target binding to related molecules could have significant clinical effects.

SELEX has been used to develop a number of aptamers that bind targets interesting for both clinical and research purposes. Also towards these ends, a number of nucleotides with chemically modified sugars and bases have been incorporated into SELEX reactions. These modified nucleotides allow for the selection of aptamers with novel binding properties and potentially improved stability.

Thomas H. Jukes

Thomas Hughes Jukes (August 26, 1906 – November 1, 1999) was a British-American biologist known for his work in nutrition, molecular evolution, and for his public engagement with controversial scientific issues, including DDT, vitamin C and creationism. He was the co-author, with Jack Lester King, of the 1969 Science article "Non-Darwinian Evolution" which, along with Motoo Kimura's earlier publication, was the origin of the neutral theory of molecular evolution.

Jukes was born in Hastings, England, but moved to Toronto in 1924. In 1933, he earned a Ph.D. in biochemistry from the University of Toronto. He spent the next decade in the University of California system, first as a postdoctoral fellow at UC Berkeley, then as Instructor and Assistant Professor at UC Davis. At Davis, he helped determine the relationships among the B complex vitamins through experiments on chickens. He then left academia to work for American Cyanamid's Lederle Laboratories, where he helped established that folic acid is a vitamin and discovered that feeding livestock a continual supply of antibiotics significantly enhances growth (a practice that has become widespread in the meat industry).Following the rise of molecular biology, Jukes returned to UC Berkeley, where he spent the rest of his career. Independently of Motoo Kimura, Jukes (with Jack King) proposed in 1969 that the evolution of proteins is primarily driven by genetic drift acting on mutations that are neither beneficial nor deleterious—the neutral theory of molecular evolution. Despite the provocative paper ("Non-Darwinian Evolution"), he was not a prominent participant in the ensuing "neutralist-selectionist debate"; defense of the neutral theory was primarily left to others, especially Kimura. In 1971, Jukes was one of the founders of the Journal of Molecular Evolution; his subsequent work with molecular evolution focused especially on the origin and evolution of the genetic code.After returning to Berkeley, he also became heavily involved in a number of public scientific controversies, and was a gifted polemicist. In the 1960s, he fought against the introduction of creationism into the California public schools. Following the rise of the environmental movement, he fought against DDT bans, citing lack of evidence for detrimental effects to ecosystems. Between 1975 and 1980 he was one of the only scientists ever to have a regular column in the journal Nature, which he used to denounce a variety of what he considered pseudoscience, expressing "his deep suspicion that categorical statements of scientific 'fact' are usually exaggerations." He was one of the most prominent critics of Linus Pauling's claims about the benefits of vitamin C megadosage, and a frequent critic of other nutrition-based health and treatment claims, such as for homeopathy and the supposed cancer cure Laetrile.Thomas Jukes died of pneumonia, leaving his wife Marguerite, two daughters, one daughter-in-law, and seven grandchildren.

Toxicofera

Toxicofera (Greek for "those who bear toxins") is a proposed clade of scaled reptiles (squamates) that includes the Serpentes (snakes), Anguimorpha (monitor lizards, gila monster, and alligator lizards) and Iguania (iguanas, agamas, and chameleons). Toxicofera contains about 4,600 species, (nearly 60%) of extant squamata. It encompasses all venomous reptile species, as well as numerous related non-venomous species. There is little morphological evidence to support this grouping, however it has been recovered by all molecular analyses as of 2012.

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