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Mitochondrial DNA is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP). Mitochondrial DNA is only a small portion of the DNA in a eukaryotic cell; most of the DNA can be found in the cell nucleus and, in plants and algae, also 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.
The parrotbills are a family, Paradoxornithidae, of passerine birds that are primarily native to East, Southeast and South Asia, with a single species in western North America, though feral populations exist elsewhere. They are generally small birds that inhabit reedbeds, forests and similar habitats. The traditional parrotbills feed mainly on seeds, e.g. of grasses, to which their robust bill, as the name implies, is well-adapted. Members of the family are usually non-migratory.
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.
Capra is a genus of mammals, the goats, comprising ten species, including the markhor and several species known as ibexes. The domestic goat is a domesticated species derived from the wild goat. Evidence of goat domestication dates back more than 8,500 years.
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.
Trimeresurus is a genus of venomous pit vipers found in Asia from the Indian Subcontinent throughout Southeast Asia, China, and the Pacific Islands. Currently 44 species are recognized. Common names include Asian palm pit vipers, Asian lanceheads, and green pit vipers.
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.
Testudo, the Mediterranean tortoises, are a genus of tortoises found in North Africa, Western Asia, and Europe. Several species are under threat in the wild, mainly from habitat destruction.
Oreochromis is a large genus of oreochromine cichlids, fishes endemic to Africa and the Middle East. A few species from this genus have been introduced far outside their native range and are important in aquaculture. Many others have very small ranges; some are seriously threatened, and O. ismailiaensis and O. lidole possibly are extinct. Although Oreochromis primarily are freshwater fish of rivers, lakes and similar habitats, several species can also thrive in brackish waters and some even survive in hypersaline conditions with a salinity that far surpasses that of seawater. In addition to overfishing and habitat loss, some of the more localized species are threatened by the introduction of other, more widespread Oreochromis species into their ranges. This is because they—in addition to competing for the local resources—often are able to hybridize.
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.
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.
The Tilapiini are a tribe within the family Cichlidae commonly known as tilapiine cichlids. Formerly this tribe contained many other genera and species, including the economically important Oreochromis and Sarotherodon, but a taxonomic review found that this grouping was paraphyletic and most were moved to Coelotilapini, Coptodonini, Heterotilapini, Oreochromini and Pelmatolapiini. Together, most species in these tribes are called "tilapias". In a more distant past, a number of other, more different genera like Steatocranus also were included in Tilapiini. With these as separate, Tilapiini now is a much more restricted tribe with only three genera and about half a dozen species from Central and Southern Africa.
Syconycteris is a genus of megabat in the family Pteropodidae. There are three described species at present, with more likely to be added. Members of this genus are found in Indonesia, New Guinea and Australia. Their diet mainly consists of nectar and fruit, making them important for pollination and seed dispersal in their environment.
Daboia is a genus of venomous vipers.
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 superfamily of snakes that contains two families: Aniliidae and the boa-like Tropidophiidae.
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. doi:10.1093/sysbio/syae016. ISSN 1063-5157.
- ↑ 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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