Molecular phylogenetics is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly 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 also includes the use of molecular data in taxonomy and biogeography.
The Curculionidae are a family of weevils, commonly called snout beetles or true weevils. They are one of the largest animal families with 6,800 genera and 83,000 species described worldwide. They are the sister group to the family Brentidae.
The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin. The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly removed by natural selection, they do not make significant contributions to variation within and between species at the molecular level. A neutral mutation is one that does not affect an organism's ability to survive and reproduce. The neutral theory assumes that most mutations that are not deleterious are neutral rather than beneficial. Because only a fraction of gametes are sampled in each generation of a species, the neutral theory suggests that a mutant allele can arise within a population and reach fixation by chance, rather than by selective advantage.
Ecdysozoa is a group of protostome animals, including Arthropoda, Nematoda, and several smaller phyla. The grouping of these animal phyla into a single clade was first proposed by Eernisse et al. (1992) based on a phylogenetic analysis of 141 morphological characters of ultrastructural and embryological phenotypes. This clade, that is, a group consisting of a common ancestor and all its descendants, was formally named by Aguinaldo et al. in 1997, based mainly on phylogenetic trees constructed using 18S ribosomal RNA genes.
The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins. The benchmarks for determining the mutation rate are often fossil or archaeological dates. The molecular clock was first tested in 1962 on the hemoglobin protein variants of various animals, and is commonly used in molecular evolution to estimate times of speciation or radiation. It is sometimes called a gene clock or an evolutionary clock.
Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution holds that all species are related and gradually change over generations. In a population, the genetic variations affect the phenotypes of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed onto their offspring. Some examples of evolution in species over many generations are the peppered moth and flightless birds. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology.
Émile Zuckerkandl was an Austrian-born French biologist considered one of the founders of the field of molecular evolution. He introduced, with Linus Pauling, the concept of the "molecular clock", which enabled the neutral theory of molecular evolution.
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids or proteins across species, or within a genome, or between donor and receptor taxa. Conservation indicates that a sequence has been maintained by natural selection.
Semantides are biological macromolecules that carry genetic information or a transcript thereof. Three different categories or semantides are distinguished: primary, secondary and tertiary. Primary Semantides are genes, which consist of DNA. Secondary semantides are chains of messenger RNA, which are transcribed from DNA. Tertiary semantides are polypeptides, which are translated from messenger RNA. In eukaryotic organisms, primary semantides may consist of nuclear, mitochondrial or plastid DNA. Not all primary semantides ultimately form tertiary semantides. Some primary semantides are not transcribed into mRNA and some secondary semantides are not translated into polypeptides. The complexity of semantides varies greatly. For tertiary semantides, large globular polypeptide chains are most complex while structural proteins, consisting of repeating simple sequences, are least complex. The term semantide and related terms were coined by Linus Pauling and Emile Zuckerkandl. Although semantides are the major type of data used in modern phylogenetics, the term itself is not commonly used.
Neutral mutations are changes in DNA sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce. In population genetics, mutations in which natural selection does not affect the spread of the mutation in a species are termed neutral mutations. Neutral mutations that are inheritable and not linked to any genes under selection will be lost or will replace all other alleles of the gene. That loss or fixation of the gene proceeds based on random sampling known as genetic drift. A neutral mutation that is in linkage disequilibrium with other alleles that are under selection may proceed to loss or fixation via genetic hitchhiking and/or background selection.
Masatoshi Nei was a Japanese-born American evolutionary biologist who was affiliated with the Department of Biology at Temple University as an adjunct Laura H. Carnell Professor. He was previously an Evan Pugh Professor of Biology at Pennsylvania State University and Director of the Institute of Molecular Evolutionary Genetics; working there from 1990 to 2015.
Wen-Hsiung Li is a Taiwanese-American scientist working in the fields of molecular evolution, population genetics, and genomics. He is currently the James Watson Professor of Ecology and Evolution at the University of Chicago and a Principal Investigator at the Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan.
In genetics, an isochore is a large region of genomic DNA with a high degree of uniformity in GC content; that is, guanine (G) and cytosine (C) bases. The distribution of bases within a genome is non-random: different regions of the genome have different amounts of G-C base pairs, such that regions can be classified and identified by the proportion of G-C base pairs they contain.
The history of molecular evolution starts in the early 20th century with "comparative biochemistry", but the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. The advent of protein sequencing allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock to estimate the time since the last common ancestor. In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a reconceptualization of the early history of life.
Morris Goodman was an American scientist known for his work in molecular evolution and molecular systematics. Goodman was a distinguished professor at the Center for Molecular Medicine and Genetics at Wayne State University School of Medicine, editor-in-chief of the journal Molecular Phylogenetics and Evolution, and a member of the anthropology section of the United States National Academy of Sciences.
Takashi Gojobori is a Japanese molecular biologist, Vice-Director of the National Institute of Genetics (NIG) and the DNA Data Bank of Japan (DDBJ) at NIG, in Mishima, Japan. Gojobori is a Distinguished Professor at King Abdullah University of Science and Technology (KAUST) in Thuwal, Saudi Arabia. He is a Professor of Bioscience and Acting Director at the Computational Bioscience Research Center at KAUST.
Martin Edward Kreitman is an American geneticist at the University of Chicago, most well known for the McDonald–Kreitman test that is used to infer the amount of adaptive evolution in population genetic studies.
A compositional domain in genetics is a region of DNA with a distinct guanine (G) and cytosine (C) G-C and C-G content. The homogeneity of compositional domains is compared to that of the chromosome on which they reside. As such, compositional domains can be homogeneous or nonhomogeneous domains. Compositionally homogeneous domains that are sufficiently long are termed isochores or isochoric domains.
The rate of evolution is quantified as the speed of genetic or morphological change in a lineage over a period of time. The speed at which a molecular entity evolves is of considerable interest in evolutionary biology since determining the evolutionary rate is the first step in characterizing its evolution. Calculating rates of evolutionary change is also useful when studying phenotypic changes in phylogenetic comparative biology. In either case, it can be beneficial to consider and compare both genomic data and paleontological data, especially in regards to estimating the timing of divergence events and establishing geological time scales.
Montserrat Aguadé Porres is a professor emeritus of genetics at University of Barcelona and member of the Institut d'Estudis Catalans.
