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38-598: See text Alcedo cristata Pallas, 1764 The malachite kingfisher ( Corythornis cristatus ) is a river kingfisher which is widely distributed in Africa south of the Sahara . It is largely resident except for seasonal climate-related movements. The malachite kingfisher was described by the German naturalist Peter Simon Pallas in 1764 and given the binomial name Alcedo cristata . The specific epithet cristata

76-431: 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 An older and superseded approach was to determine the divergences between the genotypes of individuals by DNA–DNA hybridization .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

114-531: A black bill and greenish crest, and is not quite as dependent on water as the African species. It is otherwise similar in plumage and behaviour to the more widespread malachite kingfisher. The São Tomé kingfisher and the Príncipe kingfisher were sometimes considered as distinct species but a study published in 2008 showed that they are both subspecies of the malachite kingfisher. There are five subspecies: It

152-563: A burrow in an earth bank and lays two or more white eggs onto the bare surface. Both parents incubate the eggs and feed the chicks. Egg laying is staggered at one-day intervals so that if food is short only the older larger nestlings get fed. The chicks are naked, blind and helpless when they hatch, and stand on their heels, unlike any adult bird. The small Ceyx and Ispidina species feed mainly on insects and spiders, but also take tadpoles, frogs and mayfly nymphs from puddles. They will flycatch, and their red bills are flattened to assist in

190-524: 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

228-401: A different bill colour as with common kingfisher to a completely different appearance. The male blue-banded kingfisher has white underparts with a blue breast band, whereas the female has orange underparts. The small kingfishers that make up the rest of the family have blue or orange upperparts and white or buff underparts, and show little sexual variation. Across the family, the bill colour

266-427: 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

304-547: 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

342-581: A self-excavated burrow . Both adults incubate the eggs and feed the chicks. A molecular phylogenetic study of the river kingfishers published in 2007 found that the genera as then defined did not form monophyletic groups. The species were subsequently rearranged into four monophyletic genera. A clade containing four species were placed in the resurrected genus Corythornis and five species ( little kingfisher , azure kingfisher , Bismarck kingfisher , silvery kingfisher and indigo-banded kingfisher ) were moved from Alcedo to Ceyx . All except one of

380-641: 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

418-575: 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

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456-462: Is a small kingfisher, around 13 cm (5.1 in) in length. In Southern Africa, the reference size is 14cm and in East Africa and Ethiopia, 12cm. The general color of the upper parts of the adult bird is bright metallic blue. The head has a short crest of black and blue feathers, which gives rise to the scientific name. The face, cheeks, and underparts are rufous and there are white patches on

494-442: 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

532-404: 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

570-415: 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

608-482: 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

646-759: Is found across most of Europe and temperate Asia. No members of this family are found in the Americas, although the American green kingfishers are believed to have derived from alcedinid stock. The origin of the family is thought to have been in southern Asia, which still has the most species. The Ceyx and Ispidina species are mainly birds of wet rainforest or other woodland, and are not necessarily associated with water. The Alcedo kingfishers are usually closely associated with fresh water, often in open habitats although some are primarily forest birds. River kingfishers are monogamous and territorial. The pair excavates

684-586: Is from the Latin cristatus meaning "crested" or "plumed". The adjective " malachite " in the vernacular name normally refers to the dark green colour of the copper containing mineral. This kingfisher has blue upperparts but has black banding with pale blue or greenish-blue on its forehead. A molecular phylogenetic study published in 2007 confirmed that the most closely related species is the Malagasy kingfisher , ( Corythornis vintsioides ). The Malagasy kingfisher has

722-412: Is linked to diet. The insectivorous species have red bills, and the fish-eaters have black bills. When perched, kingfishers sit quite upright, and the flight is fast and direct. The call is typically a simple high-pitched squeak, often given in flight. Most alcedinids are found in the warm climates of Africa and southern and southeast Asia. Three species reach Australia, but only the common kingfisher

760-482: 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

798-406: 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

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836-509: The Madagascar pygmy kingfisher is most closely related to the malachite kingfisher . All kingfishers are short-tailed large-headed compact birds with long pointed bills. Like other Coraciiformes , they are brightly coloured. Alcedo species typically have metallic blue upperparts and head, and orange or white underparts. The sexes may be identical, as with Bismarck kingfisher , but most species show some sexual dimorphism , ranging from

874-529: 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

912-440: The capture of insects. The Alcedo kingfishers are typically fish-eaters with black bills, but will also take aquatic invertebrates, spiders and lizards. A few species are mainly insectivorous and have red bills. Typically fish are caught by diving into the water from a perch, although the kingfisher might hover briefly. Molecular phylogenetic Molecular phylogenetics and molecular evolution correlate. Molecular evolution

950-606: 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,

988-419: 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

1026-526: The kingfishers in the reconstituted Ceyx have three rather than the usual four toes. The exception is the Sulawesi dwarf kingfisher which retains a vestigial fourth toe. The subfamily includes 35 species divided into four genera. The African dwarf kingfisher is sometimes placed in the monotypic genus Myioceyx , and sometimes with the pygmy kingfishers in Ispidina . Molecular analysis suggests that

1064-492: The malachite kingfisher is rapid, with the short, rounded wings whirring until they appear a mere blur. It usually flies low over water. The nest is a tunnel in a sandy bank, usually over water. Both birds excavate. Most burrows incline upward before the nesting chamber is reached. Three or four clutches of three to six round, white eggs are placed on a litter of fish bones and disgorged pellets. The bird has regular perches or stands from which it fishes. These are usually low over

1102-486: 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

1140-659: 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

1178-476: 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

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1216-423: 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

1254-403: 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

1292-621: The three subfamilies of kingfishers . The river kingfishers are widespread through Africa and east and south Asia as far as Australia, with one species, the common kingfisher ( Alcedo atthis ) also appearing in Europe and northern Asia. This group includes many kingfishers that actually dive for fish. The origin of the subfamily is thought to have been in Asia. These are brightly plumaged, compact birds with short tails, large heads, and long bills . They feed on insects or fish, and lay white eggs in

1330-407: The throat and rear neck sides. The bill is black in young birds and reddish-orange in adults; the legs are bright red. Sexes are similar, but juveniles are a duller version of the adult. This species is common to reeds and aquatic vegetation near slow-moving water or ponds. It occurs throughout Sub-Saharan Africa except for the very arid parts of Somalia, Kenya, Namibia and Botswana. The flight of

1368-623: The water. It sits upright, its tail pointed downwards. It drops suddenly with a splash and usually returns at once with a struggling captive. Large food items are beaten on a bough or rail; small fish and insects are promptly swallowed. A fish is usually lifted and carried by its middle, but its position is changed, sometimes by tossing it into the air, before it is swallowed head downwards. Fish , aquatic insects , and crustaceans are eaten. River kingfisher Ispidina Corythornis Alcedo Ceyx The river kingfishers or pygmy kingfishers , subfamily Alcedininae , are one of

1406-424: 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

1444-398: 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

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