CP/NNLS

Last updated

CP/NNLS, standing for "ChromoPainter (CP) non-negative least squares (NNLS)" is a statistical method used in genetics. "ChromoPainter" is the name of a tool for finding haplotypes in sequence data, in which each individual is "painted" as a combination of all other sequences. It is used in Principal Components Analysis (PCA) to create data summaries, or dating admixture events. [1] [2] Non-negative least squares (NNLS) is a kind of regression analysis, which aims at finding the best possible correlation between a large set of dependent variables. It here used within the functionalities of ChromoPainter.

CP/NNLS is often used in conjunction with qpAdm. [3] [4]

Related Research Articles

<span class="mw-page-title-main">Estonians</span> Finnic ethnic group native to Estonia

Estonians or Estonian people are a Finnic ethnic group who speak the Estonian language. Their nation state is Estonia.

In historical linguistics, the homeland or Urheimat of a proto-language is the region in which it was spoken before splitting into different daughter languages. A proto-language is the reconstructed or historically-attested parent language of a group of languages that are genetically related.

<span class="mw-page-title-main">Lithuanians</span> Ethnic group native to the Baltics (north-central Europe)

Lithuanians are a Baltic ethnic group. They are native to Lithuania, where they number around 2,378,118 people. Another two millions make up the Lithuanian diaspora, largely found in countries such as the United States, United Kingdom, Brazil, Russia, and Canada. Their native language is Lithuanian, one of only two surviving members of the Baltic language family along with Latvian. According to the census conducted in 2021, 84.6% of the population of Lithuania identified themselves as Lithuanians, 6.5% as Poles, 5.0% as Russians, 1.0% as Belarusians, and 1.1% as members of other ethnic groups. Most Lithuanians belong to the Catholic Church, while the Lietuvininkai who lived in the northern part of East Prussia prior to World War II, were mostly Lutherans.

<span class="mw-page-title-main">Haplogroup Y</span> Human mitochondrial DNA grouping indicating common ancestry

In human mitochondrial genetics, Haplogroup Y is a human mitochondrial DNA (mtDNA) haplogroup.

The Kunda culture, originating from the Swiderian culture, comprised mesolithic hunter-gatherer communities of the Baltic forest zone extending eastwards through Latvia into northern Russia, dating to the period 8500–5000 BC according to calibrated radiocarbon dating. It is named after the Estonian town of Kunda, about 110 kilometres (70 mi) east of Tallinn along the Gulf of Finland, near where the first extensively studied settlement was discovered on Lammasmäe Hill and in the surrounding peat bog. The oldest known settlement of the Kunda culture in Estonia is Pulli. The Kunda culture was succeeded by the Narva culture, who used pottery and showed some traces of food production.

<span class="mw-page-title-main">BTNL2</span> Protein-coding gene in the species Homo sapiens

Butyrophilin-like protein 2 is a protein that in humans is encoded by the BTNL2 gene.

The Glazkov culture, Glazkovo culture, or Glazkovskaya culture, was an archaeological culture in the Lake Baikal area during the Early Bronze Age.

<span class="mw-page-title-main">Baltic Finnic peoples</span> Finno-Ugric peoples resident to the Baltic seashores

The Baltic Finnic or Balto-Finnic peoples, also referred to as the Baltic Sea Finns, Baltic Finns, sometimes Western Finnic and often simply as the Finnic peoples, are the peoples inhabiting the Baltic Sea region in Northern and Eastern Europe who speak Finnic languages. They include the Finns, Estonians, Karelians, Veps, Izhorians, Votes, and Livonians. In some cases the Kvens, Ingrians, Tornedalians and speakers of Meänkieli are considered separate from the Finns.

<span class="mw-page-title-main">Haplogroup R1a</span> Human Y-chromosome DNA haplogroup

Haplogroup R1a, or haplogroup R-M420, is a human Y-chromosome DNA haplogroup which is distributed in a large region in Eurasia, extending from Scandinavia and Central Europe to Central Asia, southern Siberia and South Asia.

<span class="mw-page-title-main">Seima-Turbino culture</span> Bronze Age archaeological culture of northern Eurasia

The Seima-Turbino culture, also Seima-Turbinsky culture or Seima-Turbino phenomenon, is a pattern of burial sites with similar bronze artifacts currently dated to c. 2200–1900 BCE. Previously dated to c. 2300–1700 BCE found across northern Eurasia, particularly Siberia and Central Asia, maybe from Fennoscandia to Mongolia, Northeast China, Russian Far East, Korea, and Japan. The homeland is considered to be the Altai Mountains. These findings have suggested a common point of cultural origin, possession of advanced metal working technology, and unexplained rapid migration. The buried were nomadic warriors and metal-workers, traveling on horseback or two-wheeled carts.

Haplogroup Q-Z780 is a subclade of the Y-DNA Haplogroup Q-L54. Q-Z780 is defined by the presence of the Z780 Single Nucleotide Polymorphism (SNP).

The Tasmola culture was an early Iron Age culture during the Saka period in central Kazakhstan. The Tasmola culture was replaced by the Korgantas culture. They may correspond to the Issedones of ancient Greek sources.

Haplogroup K2b (P331), also known as MPS is a human y-chromosome haplogroup that is thought to be less than 3,000 years younger than K, and less than 10,000 years younger than F, meaning it probably is around 50,000 years old, according to the age estimates of Tatiana Karafet et al. 2014.

The Mezhovskaya culture is an archaeological culture of the late Bronze Age. It was localized in the Southern Urals and named after the village of Mezhovka on the banks of the Bagaryak river in the northern part of the Chelyabinsk Oblast.

<span class="mw-page-title-main">Scytho-Siberian world</span> Iron Age Eurasian steppe cultures

The Scytho-Siberian world was an archaeological horizon which flourished across the entire Eurasian Steppe during the Iron Age from approximately the 9th century BC to the 2nd century AD. It included the Scythian, Sauromatian and Sarmatian cultures of Eastern Europe, the Saka-Massagetae and Tasmola cultures of Central Asia, and the Aldy-Bel, Pazyryk and Tagar cultures of south Siberia.

The Sauromatian culture was an Iron Age culture of horse nomads in the area of the lower Volga River to the southern Ural Mountain, in southern Russia, dated to the 6th to 4th centuries BCE.

ADMIXTOOLS is a software package that is primarily used for analyzing admixture in population genetics. The original version was developed as a set of standalone C programs by Nick Patterson and colleagues and published in 2012. A reimplemented version, ADMIXTOOLS 2, was developed as an R package by Robert Maier and colleagues and published in 2023.

The Vatya culture was an archaeological culture of the Early to Middle Bronze Age located in the central area of the Danube basin in Hungary. The culture formed from the background of the Nagyrév culture together with influences from the Kisapostag culture. It is characterized mainly by fortified settlements, cremation burial sites, and bronze production. It was succeeded by the Urnfield culture.

<span class="mw-page-title-main">Filippovka kurgans</span>

The Filippovka kurgans are Late-Sauromatian to Early-Sarmatian culture kurgans, forming "a transition site between the Sauromation and the Sarmatian epochs", just north of the Caspian Sea in the Orenburg region of Russia, dated to the second half of the 5th century and the 4th century BCE.

<span class="mw-page-title-main">Itkul culture</span>

The Itkul culture is one of these Early Saka culture, based in the eastern foothills of the Urals. The Itkul culture was part of an East to West mouvement of Asiatic Saka tribes towards the Ural regions during the Iron Age period. Other Saka groups, such as the Tasmola culture circa 600 BCE, were also involved in similar mouvements and settled in the southern Urals.

References

  1. Lawson, Daniel John; Hellenthal, Garrett; Myers, Simon; Falush, Daniel (January 2012). "Inference of population structure using dense haplotype data". PLOS Genetics. 8 (1): e1002453. doi: 10.1371/journal.pgen.1002453 . ISSN   1553-7404. PMC   3266881 . PMID   22291602.
  2. Lawson, Daniel. "ChromoPainter". people.maths.bris.ac.uk.
  3. Järve, Mari; Saag, Lehti; Scheib, Christiana Lyn; Pathak, Ajai K.; Montinaro, Francesco; Pagani, Luca; Flores, Rodrigo; Guellil, Meriam; Saag, Lauri; Tambets, Kristiina; Kushniarevich, Alena; Solnik, Anu; Varul, Liivi; Zadnikov, Stanislav; Petrauskas, Oleg; Avramenko, Maryana; Magomedov, Boris; Didenko, Serghii; Toshev, Gennadi; Bruyako, Igor; Grechko, Denys; Okatenko, Vitalii; Gorbenko, Kyrylo; Smyrnov, Oleksandr; Heiko, Anatolii; Reida, Roman; Sapiehin, Serheii; Sirotin, Sergey; Tairov, Aleksandr; Beisenov, Arman; Starodubtsev, Maksim; Vasilev, Vitali; Nechvaloda, Alexei; Atabiev, Biyaslan; Litvinov, Sergey; Ekomasova, Natalia; Dzhaubermezov, Murat; Voroniatov, Sergey; Utevska, Olga; Shramko, Irina; Khusnutdinova, Elza; Metspalu, Mait; Savelev, Nikita; Kriiska, Aivar; Kivisild, Toomas; Villems, Richard (22 July 2019). "Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance". Current Biology. 29 (14): 2430–2441.e10. doi: 10.1016/j.cub.2019.06.019 . ISSN   0960-9822. PMID   31303491.
  4. Saag, Lehti; Vasilyev, Sergey V.; Varul, Liivi; Kosorukova, Natalia V.; Gerasimov, Dmitri V.; Oshibkina, Svetlana V.; Griffith, Samuel J.; Solnik, Anu; Saag, Lauri; D’Atanasio, Eugenia; Metspalu, Ene; Reidla, Maere; Rootsi, Siiri; Kivisild, Toomas; Scheib, Christiana Lyn; Tambets, Kristiina; Kriiska, Aivar; Metspalu, Mait (3 July 2020). "Genetic ancestry changes in Stone to Bronze Age transition in the East European plain". Science Advances. 7 (4). doi:10.1101/2020.07.02.184507. PMC   7817100 .