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Mitochondrial DNA is the DNA located in the mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate (ATP). Mitochondrial DNA is a small portion of the DNA contained in a eukaryotic cell; most of the DNA is in the cell nucleus, and, in plants and algae, the DNA also is found in plastids, such as chloroplasts.
A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.
Agamidae is a family of over 550 species of iguanian lizards indigenous to Africa, Asia, Australia, and a few in Southern Europe. Many species are commonly called dragons or dragon lizards.
The Indian spot-billed duck is a species of large dabbling duck that is a non-migratory breeding duck throughout freshwater wetlands in the Indian subcontinent. The name is derived from the red spot at the base of the bill that is found in the mainland Indian population. When in water it can be recognized from a long distance by the white tertials that form a stripe on the side, and in flight it is distinguished by the green speculum with a broad white band at the base. This species and the eastern spot-billed duck were formerly considered conspecific, together called the spot-billed duck.
The Euarchonta are a proposed grandorder of mammals: the order Scandentia (treeshrews), and its sister Primatomorpha mirorder, containing the Dermoptera or colugos and the primates.
Internal transcribed spacer (ITS) is the spacer DNA situated between the small-subunit ribosomal RNA (rRNA) and large-subunit rRNA genes in the chromosome or the corresponding transcribed region in the polycistronic rRNA precursor transcript.
Cirrina or Cirrata is a suborder and one of the two main divisions of octopuses. Cirrate octopuses have a small, internal shell and two fins on their head, while their sister suborder Incirrina has neither. The fins of cirrate octopods are associated with a unique cartilage-like shell in a shell sac. In cross-section, the fins have distinct proximal and distal regions, both of which are covered by a thin surface sheath of muscle.
A nuclear gene is a gene that has its DNA nucleotide sequence physically situated within the cell nucleus of a eukaryotic organism. This term is employed to differentiate nuclear genes, which are located in the cell nucleus, from genes that are found in mitochondria or chloroplasts. The vast majority of genes in eukaryotes are nuclear.
Extrachromosomal DNA is any DNA that is found off the chromosomes, either inside or outside the nucleus of a cell. Most DNA in an individual genome is found in chromosomes contained in the nucleus. Multiple forms of extrachromosomal DNA exist, and, while some of these serve important biological functions, they can also play a role in diseases such as cancer.
Cytochrome b is a protein found in the membranes of aerobic cells. In eukaryotic mitochondria and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III — also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is a homologous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase, also known as the b6f complex. These complexes are involved in electron transport, the pumping of protons to create a proton-motive force (PMF). This proton gradient is used for the generation of ATP. These complexes play a vital role in cells.
The Rafflesiaceae are a family of rare parasitic plants comprising 36 species in 3 genera found in the tropical forests of east and southeast Asia, including Rafflesia arnoldii, which has the largest flowers of all plants. The plants are endoparasites of vines in the genus Tetrastigma (Vitaceae) and lack stems, leaves, roots, and any photosynthetic tissue. They rely entirely on their host plants for both water and nutrients, and only then emerge as flowers from the roots or lower stems of the host plants.
The rock-wallabies are the wallabies of the genus Petrogale.
Nuclear mitochondrial DNA (NUMT) segments or genetic loci describe a transposition of any type of cytoplasmic mitochondrial DNA into the nuclear genome of eukaryotic organisms.
The Alethinophidia are an infraorder of snakes that includes all snakes other than blind snakes and thread snakes. Snakes have long been grouped into families within Alethinophidia based on their morphology, especially that of their teeth. More modern phylogenetic hypotheses using genetic data support the recognition of 19 extant families, although the taxonomy of alethinophidian snakes has long been debated, and ultimately the decision whether to assign a particular clade to a particular Linnaean rank is arbitrary.
DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections, an individual sequence can be used to uniquely identify an organism to species, just as a supermarket scanner uses the familiar black stripes of the UPC barcode to identify an item in its stock against its reference database. These "barcodes" are sometimes used in an effort to identify unknown species or parts of an organism, simply to catalog as many taxa as possible, or to compare with traditional taxonomy in an effort to determine species boundaries.
Bovina is a subtribe of the Bovini tribe that generally includes the two living genera, Bison and Bos. However, this dichotomy has been challenged recently by molecular work that suggests that Bison should be regarded as a subgenus of Bos. Wild bovinans can be found naturally in North America and Eurasia.
The Amerophidia, also known as amerophidian snakes, are a clade of snakes that contains two families: Aniliidae and the boa-like Tropidophiidae.
The Colubroides are a clade in the suborder Serpentes (snakes). It contains over 85% of all the extant species of snakes. The largest family is Colubridae, but it also includes at least six other families, at least four of which were once classified as "Colubridae" before molecular phylogenetics helped in understanding their relationships. It has been found to be monophyletic.
Fungal DNA barcoding is the process of identifying species of the biological kingdom Fungi through the amplification and sequencing of specific DNA sequences and their comparison with sequences deposited in a DNA barcode database such as the ISHAM reference database, or the Barcode of Life Data System (BOLD). In this attempt, DNA barcoding relies on universal genes that are ideally present in all fungi with the same degree of sequence variation. The interspecific variation, i.e., the variation between species, in the chosen DNA barcode gene should exceed the intraspecific (within-species) variation.
Genome skimming is a sequencing approach that uses low-pass, shallow sequencing of a genome, to generate fragments of DNA, known as genome skims. These genome skims contain information about the high-copy fraction of the genome. The high-copy fraction of the genome consists of the ribosomal DNA, plastid genome (plastome), mitochondrial genome (mitogenome), and nuclear repeats such as microsatellites and transposable elements. It employs high-throughput, next generation sequencing technology to generate these skims. Although these skims are merely 'the tip of the genomic iceberg', phylogenomic analysis of them can still provide insights on evolutionary history and biodiversity at a lower cost and larger scale than traditional methods. Due to the small amount of DNA required for genome skimming, its methodology can be applied in other fields other than genomics. Tasks like this include determining the traceability of products in the food industry, enforcing international regulations regarding biodiversity and biological resources, and forensics.
References
- ↑ Potter, Sally; Moritz, Craig; Piggott, Maxine P; Bragg, Jason G; Afonso Silva, Ana C; Bi, Ke; McDonald-Spicer, Christiana; Turakulov, Rustamzhon; Eldridge, Mark D B (2024-04-05). "Museum skins enable identification of introgression associated with cytonuclear discordance". Systematic Biology. 73 (3): 579–593. doi: 10.1093/sysbio/syae016 . ISSN 1063-5157. PMC 11377193 .
- ↑ Hunter, Margaret E.; Johnson, Nathan A.; Smith, Brian J.; Davis, Michelle C.; Butterfield, John S. S.; Snow, Ray W.; Hart, Kristen M. (September 2018). "Cytonuclear discordance in the Florida Everglades invasive Burmese python ( Python bivittatu s) population reveals possible hybridization with the Indian python ( P. molurus )". Ecology and Evolution. 8 (17): 9034–9047. Bibcode:2018EcoEv...8.9034H. doi:10.1002/ece3.4423. ISSN 2045-7758. PMC 6157680 . PMID 30271564.
- ↑ Mochales-Riaño, Gabriel; Burriel-Carranza, Bernat; Barros, Margarida Isabel; Velo-Antón, Guillermo; Talavera, Adrián; Spilani, Loukia; Tejero-Cicuéndez, Héctor; Crochet, Pierre-André; Piris, Alberto (2023-10-04), Hidden in the sand: phylogenomics unravel an unexpected evolutionary history on the desert-adapted vipers of the genus Cerastes, doi:10.1101/2023.10.03.560686 , retrieved 2024-04-07
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