Molecular phylogenetics ( / m ə ˈ l ɛ k j ʊ l ər ˌ f aɪ l oʊ dʒ ə ˈ n ɛ t ɪ k s , m ɒ -, m oʊ -/ ) 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 .
31-499: In the APG IV system (2016) for the classification of flowering plants , the name asterids denotes a clade (a monophyletic group). Asterids is the largest group of flowering plants , with more than 80,000 species, about a third of the total flowering plant species. Well-known plants in this clade include the common daisy , forget-me-nots , nightshades (including potatoes , eggplants , tomatoes , chili peppers and tobacco ),
62-431: 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 that is 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 An older and superseded approach was to determine the divergences between the genotypes of individuals by DNA–DNA hybridization .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
93-524: A constant rate of mutation, provide a molecular clock for dating divergence. Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms. With the invention of Sanger sequencing in 1977, it became possible to isolate and identify these molecular structures. High-throughput sequencing may also be used to obtain the transcriptome of an organism, allowing inference of phylogenetic relationships using transcriptomic data . The most common approach
124-427: 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, and most of the variations that are found are correlated, so that the number of distinct haplotypes that are found is relatively small. In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material ; a substantial sample of individuals of
155-547: A phylogenetic tree. The third stage includes different models of DNA and amino acid substitution. Several models of substitution exist. A few examples include Hamming distance , the Jukes and Cantor one-parameter model, and the Kimura two-parameter model (see Models of DNA evolution ). The fourth stage consists of various methods of tree building, including distance-based and character-based methods. The normalized Hamming distance and
186-641: A significant complication to molecular systematics, indicating that different genes within the same organism can have different phylogenies. HGTs can be detected and excluded using a number of phylogenetic methods (see Inferring horizontal gene transfer § Explicit phylogenetic methods ). In addition, molecular phylogenies are sensitive to the assumptions and models that go into making them. Firstly, sequences must be aligned; then, issues such as long-branch attraction , saturation , and taxon sampling problems must be addressed. This means that strikingly different results can be obtained by applying different models to
217-417: A total of 64 angiosperm orders and 416 families. In general, the authors describe their philosophy as "conservative", based on making changes from APG III only where "a well-supported need" has been demonstrated. This has sometimes resulted in placements that are not compatible with published studies, but where further research is needed before the classification can be changed. Key to symbols used: Like
248-575: Is a simple method; however, it is less accurate than the neighbor-joining approach. Finally, the last step comprises evaluating the trees. This assessment of accuracy is composed of consistency, efficiency, and robustness. MEGA (molecular evolutionary genetics analysis) is an analysis software that is user-friendly and free to download and use. This software is capable of analyzing both distance-based and character-based tree methodologies. MEGA also contains several options one may choose to utilize, such as heuristic approaches and bootstrapping. Bootstrapping
279-442: Is an approach that is commonly used to measure the robustness of topology in a phylogenetic tree, which demonstrates the percentage each clade is supported after numerous replicates. In general, a value greater than 70% is considered significant. The flow chart displayed on the right visually demonstrates the order of the five stages of Pevsner's molecular phylogenetic analysis technique that have been described. Molecular systematics
310-404: Is an essentially cladistic approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be monophyletic . This is a limitation when attempting to determine the optimal tree(s), which often involves bisecting and reconnecting portions of the phylogenetic tree(s). The recent discovery of extensive horizontal gene transfer among organisms provides
341-415: Is available at Nature Protocol. Another molecular phylogenetic analysis technique has been described by Pevsner and shall be summarized in the sentences to follow (Pevsner, 2015). A phylogenetic analysis typically consists of five major steps. The first stage comprises sequence acquisition. The following step consists of performing a multiple sequence alignment, which is the fundamental basis of constructing
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#1732797736295372-482: 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
403-482: Is the comparison of homologous sequences for genes using sequence alignment techniques to identify similarity. Another application of molecular phylogeny is in DNA barcoding , wherein the species of an individual organism is identified using small sections of mitochondrial DNA or chloroplast DNA . Another application of the techniques that make this possible can be seen in the very limited field of human genetics, such as
434-406: Is the process of selective changes (mutations) at a molecular level (genes, proteins, etc.) throughout various branches in the tree of life (evolution). Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and results in the construction of a phylogenetic tree. The theoretical frameworks for molecular systematics were laid in the 1960s in
465-798: The Angiosperm Phylogeny Group (APG). It was published in 2016, seven years after its predecessor the APG III system was published in 2009, and 18 years after the first APG system was published in 1998. In 2009, a linear arrangement of the system was published separately; the APG IV paper includes such an arrangement, cross-referenced to the 2009 one. Compared to the APG III system, the APG IV system recognizes five new orders ( Boraginales , Dilleniales , Icacinales , Metteniusales and Vahliales ), along with some new families, making
496-568: The Cronquist system (1981) and as Sympetalae in earlier systems. The name asterids (not necessarily capitalised) resembles the earlier botanical name but is intended to be the name of a clade rather than a formal ranked name, in the sense of the ICBN . Genetic analysis carried out after APG II maintains that the sister to all other asterids are the Cornales . A second order that split from
527-418: The common sunflower , petunias , yacon , morning glory , lettuce , sweet potato , coffee , lavender , lilac , olive , jasmine , honeysuckle , ash tree , teak , snapdragon , sesame , psyllium , garden sage , blueberries , table herbs such as mint , basil , and rosemary , and rainforest trees such as Brazil nut . Most of the taxa belonging to this clade had been referred to as Asteridae in
558-529: The Jukes-Cantor correction formulas provide the degree of divergence and the probability that a nucleotide changes to another, respectively. Common tree-building methods include unweighted pair group method using arithmetic mean ( UPGMA ) and Neighbor joining , which are distance-based methods, Maximum parsimony , which is a character-based method, and Maximum likelihood estimation and Bayesian inference , which are character-based/model-based methods. UPGMA
589-843: The base of the asterids are the Ericales . The remaining orders cluster into two clades, the lamiids and the campanulids. The structure of both of these clades has changed in APG III . In the APG III system, the following clades were renamed: The phylogenetic tree presented hereinafter has been proposed by the APG IV project. Cornales Ericales Aquifoliales Asterales Escalloniales Bruniales Apiales Dipsacales Paracryphiales Icacinales Metteniusales Garryales Boraginales Gentianales Vahliales Lamiales Solanales The lamiid subclade consists of about 40,000 species and account for about 15% of angiosperm diversity, characterized in general by superior ovaries and corollas with any fusion of
620-434: The core lamiids. It has been suggested that the core lamiids radiated from an ancestral line of tropical trees in which the flowers were inconspicuous and the fruit large, drupaceous and often single-seeded. APG IV system The APG IV system of flowering plant classification is the fourth version of a modern, mostly molecular -based, system of plant taxonomy for flowering plants (angiosperms) being developed by
651-904: The earlier APG systems, the APG IV revision is based on a phylogenetic tree for the angiosperms, as shown below. Amborellales Nymphaeales Austrobaileyales Chloranthales Magnoliales Laurales Piperales Canellales Acorales Alismatales Petrosaviales Pandanales Dioscoreales Liliales Asparagales Arecales Poales Commelinales Zingiberales Ceratophyllales Ranunculales Proteales Trochodendrales Buxales ( continued ) Gunnerales Dilleniales Saxifragales Vitales Zygophyllales Fabales Rosales Fagales Cucurbitales Celastrales Malpighiales Oxalidales Geraniales Myrtales Crossosomatales Picramniales Sapindales Huerteales Molecular phylogenetics Molecular phylogenetics and molecular evolution correlate. Molecular evolution
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#1732797736295682-606: The ever-more-popular use of genetic testing to determine a child's paternity , as well as the emergence of a new branch of criminal forensics focused on evidence known as genetic fingerprinting . There are several methods available for performing a molecular phylogenetic analysis. One method, including a comprehensive step-by-step protocol on constructing a phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment , model-test (testing best-fitting substitution models), and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference,
713-419: 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 ultimately reflected in the genetic sequences. At present, it is still a long and expensive process to sequence the entire DNA of an organism (its genome ). However, it is quite feasible to determine
744-415: The petals (sympetaly) occurring late in the process of development. The major part of lamiid diversity occurs in the group of five orders from Boraginales to Solanales, referred to informally as "core lamiids" (sometimes called Laminae), although Vahliales consists of the single small genus Vahlia . The remainder of the lamiids are referred to as "basal lamiids", in which Garryales is the sister group to
775-486: The positions of haplotypes within the evolutionary trees. Every living organism contains deoxyribonucleic acid ( DNA ), ribonucleic acid ( RNA ), and proteins . In general, closely related organisms have a high degree of similarity in the molecular structure of these substances, while the molecules of organisms distantly related often show a pattern of dissimilarity. Conserved sequences, such as mitochondrial DNA, are expected to accumulate mutations over time, and assuming
806-659: The results were not quantitative and did not initially 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 also termed chemotaxonomy and made use of proteins, enzymes , carbohydrates , and other molecules that were separated and characterized using techniques such as chromatography . These have been replaced in recent times largely by DNA sequencing , which produces
837-476: 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 4 distinct haplotypes. However, for organisms within
868-423: 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 (other kinds of differences between haplotypes can also occur, for example, the insertion of a section of nucleic acid in one haplotype that is not present in another). The difference between organisms is usually re-expressed as
899-403: The target species or other taxon is used; however, many current studies are based on single individuals. Haplotypes of individuals of closely related, yet different, taxa are also determined. Finally, haplotypes from a smaller number of individuals from a definitely different taxon are determined: these are referred to as an outgroup . The base sequences for the haplotypes are then compared. In
930-424: The works of Emile Zuckerkandl , Emanuel Margoliash , Linus Pauling , and Walter M. Fitch . Applications of molecular systematics were pioneered by Charles G. Sibley ( birds ), Herbert C. Dessauer ( herpetology ), and Morris Goodman ( primates ), followed by Allan C. Wilson , Robert K. Selander , and John C. Avise (who studied various groups). Work with protein electrophoresis began around 1956. Although
961-398: 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 , and the resulting dendrogram