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Monday, November 4, 2019

Genealogical DNA test

From Wikipedia, the free encyclopedia

A genealogical DNA test is a DNA-based test which looks at specific locations of a person's genome, in order to find or verify ancestral genealogical relationships or (with lower reliability) to estimate the ethnic mixture of an individual. Since different testing companies use different ethnic reference groups and different matching algorithms, ethnicity estimates for an individual will vary between tests, sometimes dramatically.

Three principal types of genealogical DNA tests are available, with each looking at a different part of the genome and useful for different types of genealogical research: autosomal, mitochondrial (mtDNA), and Y-DNA.

Autosomal tests may result in a large amount of DNA matches (other test persons that the individual may be related to), along mixed male and female lines, each match with an estimated distance in the family tree. However, due to the random nature of which and how much DNA is inherited by each tested person from their common ancestors, precise conclusions can only be made for close relations. Traditional genealogical research, and the sharing of family trees, is typically required for interpretation of the results. Autosomal tests are also used in estimating ethnic mix.

MtDNA and Y-DNA tests are much more objective. However, they give considerably fewer DNA matches, if any, since they are limited to relationships along a strict female line and a strict male line respectively. MtDNA and Y-DNA tests are utilized to identify archeological cultures and migration paths of a person's ancestors along a strict mother's line or a strict father's line. Based on MtDNA and Y-DNA, a person's haplogroup(s) can be identified. Only men can take Y-DNA tests, since women lack a Y chromosome.

DNA testing for consumers

The first company to provide direct-to-consumer genetic DNA testing was the now defunct GeneTree. However, it did not offer multi-generational genealogy tests. In fall 2001, GeneTree sold its assets to Salt Lake City-based Sorenson Molecular Genealogy Foundation (SMGF) which originated in 1999. While in operation, SMGF provided free Y-Chromosome and mitochondrial DNA tests to thousands. Later, GeneTree returned to genetic testing for genealogy in conjunction with the Sorenson parent company and eventually was part of the assets acquired in the Ancestry.com buyout of SMGF in 2012.

In 2000, Family Tree DNA, founded by Bennett Greenspan and Max Blankfeld, was the first company dedicated to direct-to-consumer testing for genealogy research. They initially offered eleven marker Y-Chromosome STR tests and HVR1 mitochondrial DNA tests. They originally tested in partnership with the University of Arizona.

In 2007, 23andMe was the first company to offer a saliva-based direct-to-consumer genetic testing. It was also the first to implement using autosomal DNA for ancestry testing, which all other major companies now use.

MyHeritage launched its genetic testing service in 2016, allowing users to use cheek swabs to collect samples. In 2019, new analysis tools were presented: autoclusters (grouping all matches visually into clusters) and family tree theories (suggesting conceivable relations between DNA matches by combining several Myheritage trees as well as the Geni global family tree).

Living DNA, founded in 2015, also provides a genetic testing service. Living DNA uses SNP chips to provide reports on autosomal ancestry, Y, and mtDNA ancestry. Living DNA provides detailed reports on ancestry from the UK as well as detailed Y chromosome and mtDNA reports.

In 2019 it was estimated that large genealogical testing companies had about 26 million DNA profiles. Many transferred their test result for free to multiple testing sites, and also to genealogical services such as Geni.com and GEDmatch. GEDMatch said half of their profiles were from the USA.
The popular consciousness of DNA testing and of DNA generally is subject to a number of misconceptions involving the reliability of testing, the nature of the connections with one's ancestors, the connection between DNA and personal traits, etc.

Procedure

A hospital corpsman uses a swab to take a DNA sample from a sailor aboard USS Iwo Jima (LHD 7)
 
A genealogical DNA test is performed on a DNA sample. This DNA sample can be obtained by a cheek-scraping (also known as a buccal swab), spit-cups, mouthwash, and chewing gum. Typically, the sample collection uses a home test kit supplied by a service provider such as 23andMe, AncestryDNA, Family Tree DNA, or MyHeritage. After following the kit instructions on how to collect the sample, it is returned to the supplier for analysis.

Types of tests

There are three major types of genealogical DNA tests: Autosomal and X-DNA, Y-DNA and mtDNA.
  • Autosomal tests look at chromosomes 1–22 and X. The autosomes (chromosomes 1–22) are inherited from both parents and all recent ancestors. The X-chromosome follows a special inheritance pattern. Ethnicity estimates are often included with this sort of testing.
  • Y-DNA looks at the Y-chromosome, which is inherited father to son, and so can only be taken by males to explore their direct paternal line.
  • mtDNA looks at the mitochondria, which is inherited from mother to child and so can be used to explore one's direct maternal line.
Y-DNA and mtDNA cannot be used for ethnicity estimates, but can be used to find one's haplogroup, which is unevenly distributed geographically. Direct-to-consumer DNA test companies have often labeled haplogroups by continent or ethnicity (e.g., an "African haplogroup" or a "Viking haplogroup"), but these labels may be speculative or misleading.

Autosomal DNA (atDNA) testing

Testing

Autosomal DNA is contained in the 22 pairs of chromosomes not involved in determining a person's sex. Autosomal DNA recombines each generation, and new offspring receive one set of chromosomes from each parent. These are inherited exactly equally from both parents and roughly equally from grandparents to about 3x great-grand parents. Therefore, the number of markers (one of two or more known variants in the genome at a particular location – known as Single-nucleotide polymorphisms or SNPs) inherited from a specific ancestor decreases by about half each generation; that is, an individual receives half of their markers from each parent, about a quarter of their markers from each grandparent; about an eighth of their markers from each great grandparent, etc. Inheritance is more random and unequal from more distant ancestors. Generally, a genealogical DNA test might test about 700,000 SNPs (specific points in the genome).

Shared DNA for different relatives

Reporting process

The preparation of a report on the DNA in the sample proceeds in multiple stages:
  • identification of the DNA base pair at specific SNP locations
  • comparison with previously stored results
  • interpretation of matches
Base pair identification
All major service providers use equipment with chips supplied by Illumina. The chip determines which SNP locations are tested. Different versions of the chip are used by different service providers. In addition, updated versions of the Illumina chip may test different sets of SNP locations. The list of SNP locations and base pairs at that location is usually available to the customer as "raw data". The raw data can sometimes be uploaded to another service provider to produce an additional interpretation and matches. For additional analysis the data can also be uploaded to GEDmatch (a third-party web based set of tools that analyzes raw data from the main service providers).
Identification of Matches
The major component of an autosomal DNA test is matching other individuals. Where the individual being tested has a number of consecutive SNPs in common with a previously tested individual in the company's database, it can be inferred that they share a segment of DNA at that part of their genomes. If the segment is longer than a threshold amount set by the testing company, then these two individuals are considered to be a match. Unlike the identification of base pairs, the data bases against which the new sample is tested, and the algorithms used to determine a match, are proprietary and specific to each company.

The unit for segments of DNA is the centimorgan (cM). For comparison, a full human genome is about 6500 cM. The shorter the length of a match, the greater are the chances that a match is spurious. An important statistic for subsequent interpretation is the length of the shared DNA (or the percentage of the genome that is shared).
Interpretation of Autosomal matches
Most companies will show the customers how many cMs they share, and across how many segments. From the number of cMs and segments, the relationship between the two individuals can be estimated, however due to the random nature of DNA inheritance, relationship estimates, especially for distant relatives, are only approximate. Some more distant cousins will not match at all. Although information about specific SNPs can be used for some purposes (eg suggesting likely eye colour), the key information is the percentage of DNA shared by 2 individuals. This can indicate the closeness of the relationship. However, it does not show the roles of the 2 individuals - eg 50% shared suggests a parent - child relationship, but does not identify which individual is the parent. 

Various advanced techniques and analysis can be done on this data. This includes features such as In-common/Shared Matches, Chromosome Browsers and Triangulation. This analysis is often required if DNA evidence is being used to prove or disprove a specific relationship.

X-chromosome DNA testing

The X-chromosome SNP results are often included in Autosomal DNA tests. Both males and females receive an X-chromosome from their mother, but only females receive a second X-chromosome from their father. The X-chromosome has a special path of inheritance patterns and can be useful in significantly narrowing down possible ancestor lines compared to Autosomal DNA – for example an X-chromosome match with a male can only have come from his maternal side. Like autosomal DNA, X-chromosome DNA undergoes random recombination at each generation (except for father to daughter X-chromosomes which are passed down unchanged). There are specialised inheritance charts which describe the possible patterns of X-chromosome DNA inheritance for males and females.

STRs

Some genealogical companies offered autosomal STRs (short tandem repeats). These are similar to Y-DNA STRs. The number of STRs offered is limited, and results have been used for personal identification, paternity cases and inter-population studies.

Law enforcement agencies in the US and Europe use autosomal STR data to identify criminals.

Mitochondrial DNA (mtDNA) testing

The mitochondrion is a component of a human cell, and contains its own DNA. Mitochondrial DNA usually has 16,569 base pairs (the number can vary slightly depending on addition or deletion mutations) and is much smaller than the human genome DNA which has 3.2 billion base pairs. Mitochondrial DNA is transmitted from mother to child, thus a direct maternal ancestor can be traced using mtDNA. The transmission occurs with relatively rare mutations compared to the genome DNA. A perfect match found to another person's mtDNA test results indicates shared ancestry of possibly between 1 and 50 generations ago. More distant matching to a specific haplogroup or subclade may be linked to a common geographic origin.

Test

mtDNA, by current conventions, is divided into three regions. They are the coding region (00577-16023) and two Hyper Variable Regions (HVR1 [16024-16569], and HVR2 [00001-00576]).

The two most common mtDNA tests are a sequence of HVR1 and HVR2 and a full sequence of the mitochondria. Generally, testing only the HVRs has limited genealogical use so it is increasingly popular and accessible to have a full sequence. The full mtDNA sequence is only offered by Family Tree DNA among the major testing companies and is somewhat controversial because the coding region DNA may reveal medical information about the test-taker.

Haplogroups

Map of human migration out of Africa, according to Mitochondrial DNA. The numbers represent thousands of years before present time. The blue line represents the area covered in ice or tundra during the last great ice age. The North Pole is at the center. Africa, the center of the start of the migration, is at the top left and South America is at the far right.
 
All humans descend in the direct female line from Mitochondrial Eve, a female who lived probably around 200,000 years ago in Africa. Different branches of her descendants are different haplogroups. Most mtDNA results include a prediction or exact assertion of one's mtDNA Haplogroup. Mitochrondial haplogroups were greatly popularized by the book The Seven Daughters of Eve, which explores mitochondrial DNA.

Understanding mtDNA test results

It is not normal for test results to give a base-by-base list of results. Instead, results are normally compared to the Cambridge Reference Sequence (CRS), which is the mitochondria of a European who was the first person to have their mtDNA published in 1981 (and revised in 1999). Differences between the CRS and testers are usually very few, thus it is more convenient than listing one's raw results for each base pair.
Examples
Note that in HVR1, instead of reporting the base pair exactly, for example 16,111, the 16 is often removed to give in this example 111. The letters refer to one of the four bases (A, T, G, C) that make up DNA.

Region HVR1 HVR2
Differences from CRS 111T,223T,259T,290T,319A,362C 073G,146C,153G

Y chromosome (Y-DNA) testing

The Y-Chromosome is one of the 23rd pair of human chromosomes. Only males have a Y-chromosome, because women have two X chromosomes in their 23rd pair. A man's patrilineal ancestry, or male-line ancestry, can be traced using the DNA on his Y chromosome (Y-DNA), because the Y-chromosome is transmitted father to son nearly unchanged. A man's test results are compared to another man's results to determine the time frame in which the two individuals shared a most recent common ancestor, or MRCA, in their direct patrilineal lines. If their test results are very close, they are related within a genealogically useful time frame. A surname project is where many individuals whose Y-chromosomes match collaborate to find their common ancestry.

Women who wish to determine their direct paternal DNA ancestry can ask their father, brother, paternal uncle, paternal grandfather, or a paternal uncle's son (their cousin) to take a test for them.
There are two types of DNA testing: STRs and SNPs.

STR markers

Most common is STRs (short tandem repeat). A certain section of DNA is examined for a pattern that repeats (e.g. ATCG). The number of times it repeats is the value of the marker. Typical tests test between 12 and 111 STR markers. STRs mutate fairly frequently. The results of two individuals are then compared to see if there is a match. DNA companies will usually provide an estimate of how closely related two people are, in terms of generations or years, based on the difference between their results.

SNP markers and Haplogroups

Strand 1 differs from strand 2 at a single base pair location (a C → T polymorphism).
 
A person's haplogroup can often be inferred from their STR results, but can be proven only with a Y-chromosome SNP test (Y-SNP test).

A single-nucleotide polymorphism (SNP) is a change to a single nucleotide in a DNA sequence. Typical Y-DNA SNP tests test about 20,000 to 35,000 SNPs. Getting a SNP test allows a much higher resolution than STRs. It can be used to provide additional information about the relationship between two individuals and to confirm haplogroups. 

The most common Y-DNA-haplogroup in different regions in Europe
 
All human men descend in the paternal line from a single man dubbed Y-chromosomal Adam, who lived probably between 200,000 and 400,000 years ago. A 'family tree' can be drawn showing how men today descend from him. Different branches of this tree are different haplogroups. Most haplogroups can be further subdivided multiple times into sub-clades. Some known sub-clades were founded in the last 1000 years, meaning their timeframe approaches the genealogical era (c.1500 onwards).

New sub-clades of haplogroups may be discovered when an individual tests, especially if they are non-European. Most significant of these new discoveries was in 2013 when the haplogroup A00 was discovered, which required theories about Y-chromosomal Adam to be significantly revised. The haplogroup was discovered when an African-American man tested STRs at FamilyTreeDNA and his results were found to be unusual. SNP testing confirmed that he does not descend patrilineally from the "old" Y-chromosomal Adam and so a much older man became Y-Chromosomal Adam.

Using DNA test results

Ethnicity estimates

Many companies offer a percentage breakdown by ethnicity or region. Generally the world is specified into about 20–25 regions, and the approximate percentage of DNA inherited from each is stated. This is usually done by comparing the frequency of each Autosomal DNA marker tested to many population groups. The reliability of this type of test is dependent on comparative population size, the number of markers tested, the ancestry informative value of the SNPs tested, and the degree of admixture in the person tested. Earlier ethnicity estimates were often wildly inaccurate, but as companies receive more samples over time, ethnicity estimates have become more accurate. Testing companies such as Ancestry.com will often regularly update their ethnicity estimates, which has caused some controversy from customers as their results update. Usually the results at the continental level are accurate, but more specific assertions of the test may turn out to be incorrect.

Audience

The interest in genealogical DNA tests has been linked to both an increase in curiosity about traditional genealogy and to more general personal origins. Those who test for traditional genealogy often utilize a combination of autosomal, mitochondrial, and Y-Chromosome tests. Those with an interest in personal ethnic origins are more likely to use an autosomal test. However, answering specific questions about the ethnic origins of a particular lineage may be best suited to an mtDNA test or a Y-DNA test.

Maternal origin tests

For recent genealogy, exact matching on the mtDNA full sequence is used to confirm a common ancestor on the direct maternal line between two suspected relatives. Because mtDNA mutations are very rare, a nearly perfect match is not usually considered relevant to the most recent 1 to 16 generations. In cultures lacking matrilineal surnames to pass down, neither relative above is likely to have as many generations of ancestors in their matrilineal information table as in the above patrilineal or Y-DNA case: for further information on this difficulty in traditional genealogy, due to lack of matrilineal surnames (or matrinames), see Matriname. However, the foundation of testing is still two suspected descendants of one person. This hypothesize and test DNA pattern is the same one used for autosomal DNA and Y-DNA.

Tests for ethnicity and membership of other groups

European genetic structure (based on Autosomal SNPs) by PCA
 
As discussed above, autosomal tests usually report the ethnic proportions of the individual. These attempt to measure an individual's mixed geographic heritage by identifying particular markers, called ancestry informative markers or AIM, that are associated with populations of specific geographical areas. Geneticist Adam Rutherford has written that these tests "don’t necessarily show your geographical origins in the past. They show with whom you have common ancestry today."

The haplogroups determined by Y-DNA and mtDNA tests are often unevenly geographically distributed. Many direct-to-consumer DNA tests described this association to infer the test-taker's ancestral homeland. Most tests describe haplogroups according to their most frequently associated continent (e.g., a "European haplogroup"). When Leslie Emery and collaborators performed a trial of mtDNA haplogroups as a predictor of continental origin on individuals in the Human Genetic Diversity Panel (HGDP) and 1000 Genomes (1KGP) datasets, they found that only 14 of 23 haplogroups had a success rate above 50% among the HGDP samples, as did "about half" of the haplogroups in the 1KGP. The authors concluded that, for most people, "mtDNA-haplogroup membership provides limited information about either continental ancestry or continental region of origin."

African ancestry

Y-DNA and mtDNA testing may be able to determine with which peoples in present-day Africa a person shares a direct line of part of his or her ancestry, but patterns of historic migration and historical events cloud the tracing of ancestral groups. Due to joint long histories in the US, approximately 30% of African American males have a European Y-Chromosome haplogroup Approximately 58% of African Americans have at least the equivalent of one great-grandparent (13%) of European ancestry. Only about 5% have the equivalent of one great-grandparent of Native American ancestry. By the early 19th century, substantial families of Free Persons of Color had been established in the Chesapeake Bay area who were descended from free people during the colonial period; most of those have been documented as descended from white men and African women (servant, slave or free). Over time various groups married more within mixed-race, black or white communities.

According to authorities like Salas, nearly three-quarters of the ancestors of African Americans taken in slavery came from regions of West Africa. The African-American movement to discover and identify with ancestral tribes has burgeoned since DNA testing became available. African Americans usually cannot easily trace their ancestry during the years of slavery through surname research, census and property records, and other traditional means. Genealogical DNA testing may provide a tie to regional African heritage.

United States – Melungeon testing

Melungeons are one of numerous multiracial groups in the United States with origins wrapped in myth. The historical research of Paul Heinegg has documented that many of the Melungeon groups in the Upper South were descended from mixed-race people who were free in colonial Virginia and the result of unions between the Europeans and Africans. They moved to the frontiers of Virginia, North Carolina, Kentucky and Tennessee to gain some freedom from the racial barriers of the plantation areas. Several efforts, including a number of ongoing studies, have examined the genetic makeup of families historically identified as Melungeon. Most results point primarily to a mixture of European and African, which is supported by historical documentation. Some may have Native American heritage as well. Though some companies provide additional Melungeon research materials with Y-DNA and mtDNA tests, any test will allow comparisons with the results of current and past Melungeon DNA studies

Native American ancestry

The pre-columbian indigenous people of the United States are called "Native Americans" in American English. Autosomal testing, Y-DNA, and mtDNA testing can be conducted to determine the ancestry of Native Americans. A mitochondrial Haplogroup determination test based on mutations in Hypervariable Region 1 and 2 may establish whether a person's direct female line belongs to one of the canonical Native American Haplogroups, A, B, C, D or X. The vast majority of Native American individuals belong to one of the five identified mtDNA Haplogroups. Thus, being in one of those groups provides evidence of potential Native American descent. However, DNA ethnicity results cannot be used as a substitute for legal documentation. Native American tribes have their own requirements for membership, often based on at least one of a person's ancestors having been included on tribal-specific Native American censuses (or final rolls) prepared during treaty-making, relocation to reservations or apportionment of land in the late 19th century and early 20th century. One example is the Dawes Rolls.

Cohanim ancestry

The Cohanim (or Kohanim) is a patrilineal priestly line of descent in Judaism. According to the Bible, the ancestor of the Cohanim is Aaron, brother of Moses. Many believe that descent from Aaron is verifiable with a Y-DNA test: the first published study in genealogical Y-Chromosome DNA testing found that a significant percentage of Cohens had distinctively similar DNA, rather more so than general Jewish or Middle Eastern populations. These Cohens tended to belong to Haplogroup J, with Y-STR values clustered unusually closely around a haplotype known as the Cohen Modal Haplotype (CMH). This could be consistent with a shared common ancestor, or with the hereditary priesthood having originally been founded from members of a single closely related clan.

Nevertheless, the original studies tested only six Y-STR markers, which is considered a low-resolution test. In response to the low resolution of the original 6-marker CMH, the testing company FTDNA released a 12-marker CMH signature that was more specific to the large closely related group of Cohens in Haplogroup J1. 

A further academic study published in 2009 examined more STR markers and identified a more sharply defined SNP haplogroup, J1e* (now J1c3, also called J-P58*) for the J1 lineage. The research found "that 46.1% of Kohanim carry Y chromosomes belonging to a single paternal lineage (J-P58*) that likely originated in the Near East well before the dispersal of Jewish groups in the Diaspora. Support for a Near Eastern origin of this lineage comes from its high frequency in our sample of Bedouins, Yemenis (67%), and Jordanians (55%) and its precipitous drop in frequency as one moves away from Saudi Arabia and the Near East (Fig. 4). Moreover, there is a striking contrast between the relatively high frequency of J-58* in Jewish populations (»20%) and Kohanim (»46%) and its vanishingly low frequency in our sample of non-Jewish populations that hosted Jewish diaspora communities outside of the Near East."

Recent phylogenetic research for haplogroup J-M267 placed the "Y-chromosomal Aaron" in a subhaplogroup of J-L862, L147.1 (age estimate 5631-6778yBP yBP): YSC235>PF4847/CTS11741>YSC234>ZS241>ZS227>Z18271 (age estimate 2731yBP).

Benefits

Genealogical DNA tests have become popular due to the ease of testing at home and their usefulness in supplementing genealogical research. Genealogical DNA tests allow for an individual to determine with high accuracy whether he or she is related to another person within a certain time frame, or with certainty that he or she is not related. DNA tests are perceived as more scientific, conclusive and expeditious than searching the civil records. However, they are limited by restrictions on lines that may be studied. The civil records are always only as accurate as the individuals having provided or written the information.

Y-DNA testing results are normally stated as probabilities: For example, with the same surname a perfect 37/37 marker test match gives a 95% likelihood of the most recent common ancestor (MRCA) being within 8 generations, while a 111 of 111 marker match gives the same 95% likelihood of the MRCA being within only 5 generations back.

As presented above in mtDNA testing, if a perfect match is found, the mtDNA test results can be helpful. In some cases, research according to traditional genealogy methods encounters difficulties due to the lack of regularly recorded matrilineal surname information in many cultures (see Matrilineal surname).

Autosomal DNA combined with genealogical research has been used by adoptees to find their biological parents, has been used to find the name and family of unidentified bodies and by law enforcement agencies to apprehend criminals (for example, the Contra Costa County District Attorney's office used the "open-source" genetic genealogy site GEDmatch to find relatives of the suspect in the Golden State Killer case.). The Atlantic magazine commented in 2018 that "Now, the floodgates are open. ..a small, volunteer-run website, GEDmatch.com, has become ... the de facto DNA and genealogy database for all of law enforcement." Family Tree DNA announced in February 2019 it was allowing the FBI to access its DNA data for cases of murder and rape. However in May 2019 GEDmatch initiated stricter rules for accessing their autosomal DNA database and Family Tree DNA shut down their Y-DNA database ysearch.org, making it more difficult for law enforcement agencies to solve cases.

Drawbacks

Common concerns about genealogical DNA testing are cost and privacy issues. Some testing companies retain samples and results for their own use without a privacy agreement with subjects.

Autosomal DNA tests can identify relationships but they can be misinterpreted. For example, transplants of stem cell or bone marrow will produce matches with the donor. In addition, identical twins (who have identical DNA) can give unexpected results.

Testing of the Y-DNA lineage from father to son may reveal complications, due to unusual mutations, secret adoptions, and non-paternity events (i.e., that the perceived father in a generation is not the father indicated by written birth records). According to the Ancestry and Ancestry Testing Task Force of the American Society of Human Genetics, autosomal tests cannot detect "large portions" of DNA from distant ancestors because it has not been inherited.

With the increasing popularity of the use of DNA tests for ethnicity tests, uncertainties and errors in ethnicity estimates are a drawback for Genetic genealogy. While ethnicity estimates at the continental level should be accurate (with the possible exception of East Asia and the Americas), sub-continental estimates, especially in Europe, are often inaccurate. Customers may be misinformed about the uncertainties and errors of the estimates.

Some have recommended government or other regulation of ancestry testing to ensure its performance to an agreed standard.

A number of law enforcement agencies took legal action to compel genetic genealogy companies to release genetic information that could match cold case crime victims or perpetrators. A number of companies fought the requests.

Medical information

Though genealogical DNA tests are not designed mainly for medical purposes, autosomal DNA tests can be used to analyze the probability of hundreds of heritable medical conditions, albeit the result is complex to understand and may confuse a non-expert. 23andMe provides medical and trait information from their genealogical DNA test and for a fee the Promethease web site analyses genealogical DNA test data from Family Tree DNA, 23andMe, or AncestryDNA for medical information. Promethease, and its research paper crawling database SNPedia, has received criticism for technical complexity and a poorly defined "magnitude" scale that causes misconceptions, confusion and panic among its users.

The testing of full MtDNA and YDNA sequences is still somewhat controversial as it may reveal even more medical information. For example, a correlation exists between a lack of Y-DNA marker DYS464 and infertility, and between mtDNA haplogroup H and protection from sepsis. Certain haplogroups have been linked to longevity in some population groups. The field of linkage disequilibrium, unequal association of genetic disorders with a certain mitochondrial lineage, is in its infancy, but those mitochondrial mutations that have been linked are searchable in the genome database Mitomap. Family Tree DNA's MtFull Sequence test analyses the full MtDNA genome and the National Human Genome Research Institute operates the Genetic And Rare Disease Information Center that can assist consumers in identifying an appropriate screening test and help locate a nearby medical center that offers such a test.

DNA in genealogy software

Some genealogy software programs — such as Family Tree Maker, Legacy Family Tree (Deluxe Edition) and the Swedish program Genney — allow recording DNA marker test results. This allows for tracking of both Y-chromosome and mtDNA tests, and recording results for relatives.

Sunday, November 3, 2019

Hale Telescope

From Wikipedia, the free encyclopedia
Hale Telescope
P200 Dome Open.jpg
Named afterGeorge Ellery Hale 
Part ofPalomar Observatory 
Location(s)Palomar Mountain, California, US
Coordinates33°21′23″N 116°51′54″WCoordinates: 33°21′23″N 116°51′54″W
Altitude1,713 m (5,620 ft)
Built1936 –1948 
First lightJanuary 26, 1949, 10:06 pm PST
DiscoveredCaliban, Sycorax, Jupiter LI
Telescope styleoptical telescope
reflecting telescope 
Diameter200 in (5.1 m)
Collecting area31,000 sq in (20 m2)
Focal length16.76 m (55 ft 0 in)
MountingEquatorial mount 
Websitewww.astro.caltech.edu/palomar/about/telescopes/hale.html
Hale Telescope is located in the United States
Hale Telescope
Location of Hale Telescope

The Hale Telescope is a 200-inch (5.1 m), f/3.3 reflecting telescope at the Palomar Observatory in California, US, named after astronomer George Ellery Hale. With funding from the Rockefeller Foundation in 1928, he orchestrated the planning, design, and construction of the observatory, but with the project ending up taking 20 years he did not live to see its commissioning. The Hale was groundbreaking for its time, with double the diameter of the second-largest telescope, and pioneered many new technologies in telescope mount design and in the design and fabrication of its large aluminum coated "honeycomb" low thermal expansion Pyrex mirror. It was completed in 1949 and is still in active use.

The Hale Telescope represented the technological limit in building large optical telescopes for over 30 years. It was the largest telescope in the world from its construction in 1949 until the Russian BTA-6 was built in 1976, and the second largest until the construction of the Keck Observatory Keck 1 in 1993.

History

Base of the tube
Crab Nebula, 1959
Hale supervised the building of the telescopes at the Mount Wilson Observatory with grants from the Carnegie Institution of Washington: the 60-inch (1.5 m) telescope in 1908 and the 100-inch (2.5 m) telescope in 1917. These telescopes were very successful, leading to the rapid advance in understanding of the scale of the Universe through the 1920s, and demonstrating to visionaries like Hale the need for even larger collectors.

The chief optical designer for Hale's previous 100-inch telescope was George Willis Ritchey, who intended the new telescope to be of Ritchey–Chrétien design. Compared to the usual parabolic primary, this design would have provided sharper images over a larger usable field of view. However, Ritchey and Hale had a falling-out. With the project already late and over budget, Hale refused to adopt the new design, with its complex curvatures, and Ritchey left the project. The Mount Palomar Hale Telescope turned out to be the last world-leading telescope to have a parabolic primary mirror.

In 1928 Hale secured a grant of $6 million from the Rockefeller Foundation for "the construction of an observatory, including a 200-inch reflecting telescope" to be administered by the California Institute of Technology (Caltech), of which Hale was a founding member. In the early 1930s, Hale selected a site at 1,700 m (5,600 ft) on Palomar Mountain in San Diego County, California, US, as the best site, and less likely to be affected by the growing light pollution problem in urban centers like Los Angeles. The Corning Glass Works was assigned the task of making a 200-inch (5.1 m) primary mirror. Construction of the observatory facilities and dome started in 1936, but because of interruptions caused by World War II, the telescope was not completed until 1948 when it was dedicated. Due to slight distortions of images, corrections were made to the telescope throughout 1949. It became available for research in 1950.

The 200-inch (510 cm) telescope saw first light on January 26, 1949, at 10:06 pm PST under the direction of American astronomer Edwin Powell Hubble, targeting NGC 2261, an object also known as Hubble's Variable Nebula. The photographs made then were published in the astronomical literature and in the May 7, 1949 issue of Collier's Magazine

The telescope continues to be used every clear night for scientific research by astronomers from Caltech and their operating partners, Cornell University, the University of California, and the Jet Propulsion Laboratory. It is equipped with modern optical and infrared array imagers, spectrographs, and an adaptive optics system. It has also used lucky cam imaging, which in combination with adaptive optics pushed the mirror close to its theoretical resolution for certain types of viewing.

One of the Corning Labs' glass test blanks for the Hale was used for the C. Donald Shane telescope's 120-inch (300 cm) primary mirror.

The collecting area of the mirror is about 31,000 square inches (20 square meters).

Components

The Hale was not just big, it was better, and not just but better but combined breakthrough technologies including a new lower expansion glass from Corning, a newly invented Serruier truss, and vapor deposited aluminum.

Mounting structures

The Hale Telescope uses a special type of equatorial mount called a "horseshoe mount", a modified yoke mount that replaces the polar bearing with an open "horseshoe" structure that gives the telescope full access to the entire sky, including Polaris and stars near it. The optical tube assembly (OTA) uses a Serrurier truss, then newly invented by Mark U. Serrurier of Caltech in Pasadena in 1935, designed to flex in such a way as to keep all of the optics in alignment. Theodore von Karman designed the lubrication system to avoid potential issues with turbulence during tracking.
Left: The 200-inch (508 cm) Hale Telescope inside on its equatorial mount.
Right: Principle of operation of a Serrurier truss similar to that of the Hale Telescope compared to a simple truss. For clarity, only the top and bottom structural elements are shown. Red and green lines denote elements under tension and compression, respectively.

200-inch mirror

The 5 meter (16 ft. 8 in.) mirror in December 1945 at the Caltech Optical Shop when grinding resumed following World War 2. The honeycomb support structure on the back of the mirror is visible through the surface.
Originally, the Hale Telescope was going to use a primary mirror of fused quartz manufactured by General Electric, but instead the primary mirror was cast in 1934 at Corning Glass Works in New York State using Corning's then new material called Pyrex (borosilicate glass). Pyrex was chosen for its low expansion qualities so the large mirror would not distort the images produced when it changed shape due to temperature variations (a problem that plagued earlier large telescopes).
Entrance door to 200 inch Hale telescope dome
The mirror was cast in a mold with 36 raised mold blocks (similar in shape to a waffle iron). This created a honeycomb mirror that cut the amount of Pyrex needed down from over 40 short tons (36 t) to just 20 short tons (18 t), making a mirror that would cool faster in use and have multiple "mounting points" on the back to evenly distribute its weight (note – see external links 1934 article for drawings). The shape of a central hole was also part of the mold so light could pass through the finished mirror when it was used in a Cassegrain configuration (a Pyrex plug for this hole was also made to be used during the grinding and polishing process). While the glass was being poured into the mold during the first attempt to cast the 200-inch mirror, the intense heat caused several of the molding blocks to break loose and float to the top, ruining the mirror. The defective mirror was used to test the annealing process. After the mold was re-engineered, a second mirror was successfully cast.
After cooling several months, the finished mirror blank was transported by rail to Pasadena, California. Once in Pasadena the mirror was transferred from the rail flat car to a specially designed semi-trailer for road transport to where it would be polished. In the optical shop in Pasadena (now the Synchrotron building at Caltech) standard telescope mirror making techniques were used to turn the flat blank into a precise concave parabolic shape, although they had to be executed on a grand scale. A special 240 in (6.1 m) 25,000 lb (11 t) mirror cell jig was constructed which could employ five different motions when the mirror was ground and polished. Over 13 years almost 10,000 lb (4.5 t) of glass was ground and polished away reducing the weight of the mirror to 14.5 short tons (13.2 t). The mirror was coated (and still is re-coated every 18–24 months) with a reflective aluminum surface using the same aluminum vacuum-deposition process invented in 1930 by Caltech physicist and astronomer John Strong.
The Hale's 200 in (510 cm) mirror was near the technological limit of a primary mirror made of a single rigid piece of glass. Using a monolithic mirror much larger than the 5-meter Hale or 6-meter BTA-6 is prohibitively expensive due to the cost of both the mirror, and the massive structure needed to support it. A mirror beyond that size would also sag slightly under its own weight as the telescope is rotated to different positions, changing the precision shape of the surface, which must be accurate to within 2 millionths of an inch (50 nm). Modern telescopes over 9 meters use a different mirror design to solve this problem, with either a single thin flexible mirror or a cluster of smaller segmented mirrors, whose shape is continuously adjusted by a computer-controlled active optics system using actuators built into the mirror support cell.

Dome

The moving weight of the upper dome is about 1000 US tons, and can rotate on wheels. The dome doors weigh 125 tons each.
The dome is made of welded steel plates about 10 mm thick.

Observations and research

Dome of the 200-inch aperture Hale telescope
The first observation of the Hale telescope was of NGC 2261 on January 26, 1949.
Halley's Comet (1P) upcoming 1986 approach to the Sun was first detected by astronomers David C. Jewitt and G. Edward Danielson on 16 October 1982 using the 200-inch Hale telescope equipped with a CCD camera.
Two moons of the planet Uranus were discovered in September 1997, in addition to the planet's 15 other known moons at that time. One was Caliban (S/1997 U 1), which was discovered on 6 September 1997 by Brett J. Gladman, Philip D. Nicholson, Joseph A. Burns, and John J. Kavelaars using the 200-inch Hale telescope. The other Uranian moon discovered then is Sycorax (initial designation S/1997 U 2) and was also discovered using the 200 inch Hale telescope.
In 1999, astronomers used a near-infrared camera and adaptive optics to take some of the best Earth-surface based images of planet Neptune up to that time. The images were sharp enough to identify clouds in the ice giant's atmosphere.
The Cornell Mid-Infrared Asteroid Spectroscopy (MIDAS) survey used the Hale Telescope with a spectrograph to study spectra from 29 asteroids. An example of a result from that study, is that the asteroid 3 Juno was determined to have average radius of 135.7±11 km using the infrared data.
In 2009, using a coronograph, the Hale telescope was used to discover the star Alcor B, which is a companion to Alcor in the famous Big Dipper constellation.
In 2010, a new satellite of planet Jupiter was discovered with the 200-inch Hale, called S/2010 J 1 and later named Jupiter LI.
In October 2017 the Hale telescope was able to record the spectrum of the first recognized interstellar object, 1I/2017 U1 ("ʻOumuamua"); while not specific mineral was identified it showed the visitor had a reddish surface color.

Direct imaging of exoplanets

Up until the year 2010, telescopes could only directly image exoplanets under exceptional circumstances. Specifically, it is easier to obtain images when the planet is especially large (considerably larger than Jupiter), widely separated from its parent star, and hot so that it emits intense infrared radiation. However, in 2010 a team from NASA's Jet Propulsion Laboratory demonstrated that a vortex coronagraph could enable small scopes to directly image planets. They did this by imaging the previously imaged HR 8799 planets using just a 1.5 m portion of the Hale Telescope.
Direct image of exoplanets around the star HR8799 using a vortex coronagraph on a 1.5m portion of the Hale Telescope

Comparison

Size comparison of the Hale Telescope (upper left, blue) to some modern and upcoming extremely large telescopes
The Hale had four times the light-collecting area of the second-largest scope when it was commissioned in 1949. Other contemporary telescopes were the Hooker Telescope at the Mount Wilson Observatory and the Otto Struve Telescope at the McDonald Observatory.
The three largest telescopes in 1949
# Name /
Observatory
Image Aperture Altitude First
Light
Special advocate(s)
1 Hale Telescope
Palomar Obs.
P200 Dome Open.jpg 200-inch
508 cm
1713 m
(5620 ft)
1949 George Ellery Hale
John D. Rockefeller
Edwin Hubble
2 Hooker Telescope
Mount Wilson Obs.
100inchHooker.jpg 100-inch
254 cm
1742 m
(5715 ft)
1917 George Ellery Hale
Andrew Carnegie
3 Otto Struve Telescope
McDonald Obs.
Otto Struve Telescope.jpg 82-inch
210 cm
2070 m
(6791 ft)
1939 Otto Struve

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