Appeal to the stone , also known as  argumentum ad lapidem , is a logical  fallacy  that dismisses an argument as untrue or absurd. The dismissal is made by stating or reiterating that the argument is absurd, without providing further argumentation. This theory is closely tied to  proof by assertion  due to the lack of evidence behind the statement and its attempt to persuade without providing any evidence.


Appeal to the stone is a  logical fallacy . Specifically, it is an  informal fallacy , which means that it relies on  inductive reasoning  in an argument to justify an  assertion . Informal fallacies contain erroneous reasoning in content of the argument and not the form or structure of it, as opposed to  formal fallacies , which contain erroneous reasoning in argument form.


An example would be a conversation about the  germ theory of disease  and  denialism of it :


Speaker B denies Speaker A's claim without providing evidence to support their denial.  This may not be unreasonable if the claim is inherently self-contradictory ("I am not speaking to you right now") or too malformed to be a sensical claim at all.


The name "appeal to the stone" originates from an argument between  Dr. Samuel Johnson  and  James Boswell  over  George Berkeley 's theory of  subjective idealism  (known previously as "immaterialism").  Subjective idealism states that reality is dependent on a person's perceptions of the world and that material objects are intertwined with one's perceptions of these material objects. [ 1 ]


After we came out of the church, we stood talking for some time together of Bishop Berkeley's ingenious sophistry to prove the non-existence of matter, and that every thing in the universe is merely ideal. I observed, that though we are satisfied his doctrine is not true, it is impossible to refute it. I never shall forget the alacrity with which Johnson answered, striking his foot with mighty force against a large stone, till he rebounded from it, "I refute it  thus ." [ 2 ]


Johnson's intent, apparently, [ 3 ]  was to imply that it was absurd of Berkeley to call such a stone "immaterial," when in fact Johnson could kick it with his foot.


Informal logical fallacies are misconceptions derived from faulty reasoning. Informal logical fallacies use  inductive reasoning  and thus can cause errors in reasoning by creating the illusion of a sound argument when it is not sound. [ 4 ]


Irrelevant conclusions , also known as  ignoratio elenchi  (Latin for ''ignoring the list" or "ignoring refutation'') or missing the point, follows a similar structure to appeal to the stone.  As an informal fallacy, it may not be valid or sound in its reasoning. [ 5 ]  Irrelevant conclusions hold similarity to appeal to the stone because it provides evidence towards a conclusion that has already been formed about the subject matter being debated, instead of the original subject that was being discussed. [ 6 ]  Dr. Samuel Johnson’s refutation of Bishop Berkeley’s theory of immaterialism by kicking a stone did not actually address the theory, but rather asserted a conclusion incompatible with the theory and then echoed his conclusion without discussing the subject matter of the theory of immaterialism directly.


Appeal to the stone utilizes inductive reasoning to derive its argument. Formal fallacies use deductive reasoning and formal properties to structure an argument and inductive arguments do not use this structure. Inductive reasoning is reasoning with uncertain conclusions because of inferences made about a specific situation, object, or event. [ 7 ]  In the context of Appeal to the stone, inductive reasoning is asserted against an initial claim without further elaboration. Inductive arguments can be affected by the acquisition of new information or evidence that can debunk an inductive assumption. [ 8 ]


Inductive reasoning asserts that the probability of a conclusion being correct is adequate evidence to support the argument. [ citation needed ]  Inductive arguments are judged on the strength or weakness of an argument and an argument's strength is subjective to each participant based on preconceptions about the subject being discussed.


The weakness of inductive reasoning (in comparison to  deductive reasoning ), lies in the inability to gauge the  validity  or  soundness  of claims within an argument. Validity of an argument is based on whether the information presented is factual. However, if evidence presented to prove a conclusion are false, this can provide a valid argument based on false information to substantiate the conclusion. Therefore, soundness of an argument is deemed when the assumptions of an argument are factual. Unlike deductive reasoning, inductive arguments cannot prove their deductive validity and therefore lead to the problem of induction.


Arguments are typically structured by a claim being defended with reasoning and evidence. It typically consists of statements that provide premises to support a conclusion. In the case of appeal to the stone, there is an explicit conclusion but it is likely not substantiated with many premises to validate the conclusion being asserted. [ 9 ]


According to the theory of argumentation, there must assumptions or premises that follow a method of reasoning or deduction to form the conclusion or point. An appeal to the stone's lack of evidence to substantiate the rejection of the initial claim puts the burden of proof on the other member of the argument and limits rebuttals.


In contrast to the  burden of proof , appeal to the stone does not allow for debate past the dismissal of the first claim. Therefore, the burden of proof is placed upon the person who made the initial statement to prove it is correct. However, when appeal to the stone is used to argue, there is a diminished ability for a person to create a rebuttal due to lack of elaboration on why there has been a disagreement. [ 10 ]  Additionally, the appeal to the stone technique is often paired with other logical fallacies that restrict the ability to further dialogue. [ 11 ]  Participants presenting an appeal to the stone argument may use ad-hominem attacks [ 12 ]  to avoid the discussion’s topic, or may pair it with a straw-man argument to discredit the other participant. [ 13 ]


The two systems theory, by Israeli psychologist  Daniel Kahneman  in his book  Thinking, Fast and Slow , explains the reasoning behind illogical fallacies. In the two systems theory,  decision-making  is categorized into system 1 and system 2. System 1 decision-making only uses quick and usually  heuristic  based interpretations to aid in low-engagement decisions. System 2 decision-making uses more deliberate and rational consideration when creating a conclusion. [ 14 ]


Many illogical fallacies employ quick judgement based on emotion to create conclusions in system 1 type decision-making. However, by having a skeptical mindset on one’s own conclusions and engaging in methodological thinking, one can avoid an illogical fallacy. [ 15 ]


As demonstrated in  Toulmin’s argumentation framework , the grounds of an assumption require warrant and backing to legitimize the claim and prove the soundness of the conclusion. The framework involves a claim, grounds, warrant,  qualifier ,  rebuttal , and backing. The initial claim of an argument is the assertion that the arguer is trying to confirm to another member in an argument. The grounds of an argument are the evidence to support the initial assertion. The warrant are the assumptions that are being used to connect the grounds to the claim. Backing is any additional supporting evidence to prove a claim and to support the warrant. Qualifiers are used to show that a claim may not always be correct (such as: sometimes, rather, somewhat) to show that the claim may not always apply to every situation. Finally, a rebuttal provides another member in a discussion to propose another valid claim for the argument. [ 16 ]


In an appeal to the stone, there is only grounds and claims without providing valid warrants or backing to substantiate their claim. Furthermore, appeals to the stone typically do not use qualifiers, limiting the scope of a rebuttal. Without providing valid evidence in an appeal to the stone, it is difficult to provide a rebuttal to the claim. [ citation needed ]


Appeal to the stone shares similarities in structure to  reductio ad absurdum  (Latin for “reduction to absurdity”) which states that an argument's assumptions or methods will lead to absurd conclusions. [ 17 ]  Although appeal to the stone does not explicitly state that an initial statement is absurd, a rejection of the initial claim often times presumes that the initial claim is incorrect or absurd.  Reductio ad absurdum  makes the assertion that if an initial claim is true, then some other absurd conclusion must also be true. [ 18 ]


Begging the question , also called  petitio principii , is a conclusion based on an assumption that requires further proof or elaboration to be validated. [ 19 ]  Begging the question, is more formally synonymous with “ignoring a question under the assumption it has already been answered.” Begging the question often creates further questioning and colloquial use of this theory has been repurposed to mean “a question that begs to be answered”. [ 20 ]


Ad nauseam  is Latin and is associated with repeating something to a sickening or excessive degree. This fallacy can be used in arguments to by asserting an opinion on a subject matter to an excessive degree. In an appeal to the stone, with a lack of evidence to support a rejection of a claim, it can likely lead to an  ad nauseam  argument. If an argument with an appeal to the stone cannot be resolved, it will likely lead to both parties arguing until they are bored of the discussion and cannot come to a satisfactory conclusion. [ 21 ]


Denialism  is a rejection of facts and reality even when there is strong evidence. [ 22 ]  Those using denialism are likely using it with ulterior motives such as self-interests or to avoid an uncomfortable truth. The most common way to rebut a denial is through debunking by dissecting the root of the belief and providing evidence to disprove their idea, point by point.


Appeal to tradition  (also known as  argumentum ad antiquitatem  or  argumentum ad antiquitam , [ 1 ]   appeal to antiquity , or  appeal to common practice ) is a claim in which a thesis is deemed correct on the basis of correlation with past or present  tradition . The appeal takes the form of "this is right because we've always done it this way", and is a logical fallacy. [ 2 ] [ 3 ]  The opposite of an appeal to tradition is an  appeal to novelty , in which one claims that an idea is superior just because it is new.


An appeal to tradition essentially makes two assumptions that may not be  necessarily  true :


Appeal to tradition imports the value of not needing to reinvent ways to do things for which effective ways have already been established. But, "is fallacious when it confuses a long tradition of careful testing with the mere tendency to hold on to ideas because they are old". [ 2 ]


An appeal to tradition can be complicated by the possibility that different people might have different views, each with their own tradition to appeal to. For example, " Augustine 's appeal to tradition against the  Donatists  is more complicated because the Donatists had appealed to tradition against the Catholics". [ 4 ]


An  argument from authority [ a ]  is a form of  argument  in which the opinion of an  authority figure  (or figures) is used as evidence to support an argument. [ 1 ]


The argument from authority is a  logical fallacy , [ 2 ]  and obtaining knowledge in this way is fallible. [ 3 ] [ 4 ]


However, in particular circumstances, it is alright to use as a practical although fallible way of obtaining information that can be considered  generally likely  to be correct if the  authority  is a real and pertinent intellectual authority and there is universal consensus about these statements in this field. [ 1 ] [ 5 ] [ 6 ] [ 7 ] [ 8 ]  This is specially the case when the revision of all the information and data "from scratch" would impede advances in an investigation or education. Further ways of validating a  source  include: evaluating the veracity of previous works by the author, their competence on the topic, their coherence, their conflicts of interest, etc.


This argument has been considered a logical fallacy since its introduction by  John Locke  and  Richard Whately . [ 9 ]  In particular, this is a form of  genetic fallacy ; in which the conclusion about the validity of a statement is justified by appealing to the characteristics of the person who is speaking, such as in the  ad hominem  fallacy. [ 10 ]  For this argument, Locke coined the term  argumentum ad verecundiam  (appeal to shamefacedness/modesty) because it appeals to the fear of humiliation by appearing disrespectful to a particular authority. [ 11 ]


This qualification as a logical fallacy implies that this argument is invalid when using the deductive method, and therefore it cannot be presented as infallible. [ 12 ]  In other words, it is logically invalid to prove a claim is true simply because an authority has said it. The explanation is: authorities can be wrong, and the only way of logically proving a claim is providing real evidence or a valid logical deduction of the claim from the evidence. [ 13 ] [ 14 ] [ 15 ]


It is also a fallacious  ad hominem  argument to argue that a person presenting statements lacks authority and thus their arguments do not need to be considered. [ 10 ]  Other related fallacious arguments assume that a person without status or authority is inherently reliable. For instance, the  appeal to poverty  is the fallacy of thinking that someone is more likely to be correct because they are poor. [ 16 ]  When an argument holds that a conclusion is likely to be true precisely because the one who holds or is presenting it lacks authority, it is an "appeal to the common man". [ 17 ]


However, when used in the inductive method, which implies the conclusions can not be proven with certainty, [ 12 ]  this argument can be considered a  inductive argument . If a person has a credible authority i.e. is an expert in the field in question, it is more likely that their assessments would be correct, especially if there is consensus about the topic between the credible sources.


The general form of this type of argument is:


Person  A  claims that  X  is true.
Person  A  is an expert in the field concerning  X .
Therefore,  X  should be believed. [ 18 ]


Nonetheless, it would also be a fallacy, even in the inductive method, when the source of the claim is a false authority, such as when the supposed authority is not a real expert, or when supporting a claim outside of their area of expertise. This is referred to as an "argument from false authority". [ 19 ]
It can also be considered a fallacy when the authority is an expert in the topic but their claims are controversial or not unanimous between other experts in the field. Some consider that it can be used in a cogent form if all sides of a discussion agree on the reliability of the cited authority in the given context. [ 20 ]  This form of argument can be considered sound if both parties to the debate agree that the authority is in fact an expert; [ 20 ] [ 21 ] [ 22 ]


Furthermore, some claim that the act of trusting authorities is unavoidable for science to progress, since it would be a lot harder if not impossible for students and researchers to always resort to the factual evidence and demonstrations for all the knowledge they need to obtain to be able to come across new scientific findings. [ 23 ]


At the same time, others claim that authority "has no place in science", [ 24 ]  meaning that the validity of claims always has to lay, ultimately, on the evidence and proofs provided, and not in the prestige of the authors. [ citation needed ]


The qualification of this type of argument as logical fallacy implies that it is not a valid way to deduce a conclusion, that is, to prove it. [ 12 ]  This does not mean that a claim from a credible respected authority does not generally have a bigger probability of being correct than that of somebody who has no expertise at all; but the strength of this argument is not absolute as is believed by some.


Scientific knowledge is best established by evidence and experiment rather than argued through authority [ 13 ] [ 14 ] [ 15 ]  as  authority  has no place in science. [ 14 ] [ 25 ] [ 26 ]   Carl Sagan  wrote of arguments from authority: "One of the great commandments of science is, 'Mistrust arguments from authority.' ... Too many such arguments have proved too painfully wrong. Authorities must prove their contentions like everybody else." [ 24 ]  Conversely, it has been argued that science is fundamentally dependent on arguments from authority to progress as "they allow science to avoid forever revisiting the same ground". [ 23 ]


One example of the use of the appeal to authority in science dates to 1923, [ 27 ]  when leading American zoologist  Theophilus Painter  declared, based on poor data and conflicting observations he had made, [ 28 ] [ 29 ]  that humans had 24 pairs of  chromosomes . From the 1920s until 1956, [ 30 ]  scientists propagated this "fact" based on Painter's authority, [ 31 ] [ 32 ] [ 29 ]  despite subsequent counts totaling the  correct number  of 23. [ 28 ] [ 33 ]  Even textbooks [ 28 ]  with photos showing 23 pairs incorrectly declared the number to be 24 [ 33 ]  based on the authority of the then-consensus of 24 pairs. [ 34 ]


This seemingly established number generated  confirmation bias  among researchers, and "most cytologists, expecting to detect Painter's number, virtually always did so". [ 34 ]  Painter's "influence was so great that many scientists preferred to believe his count over the actual evidence", [ 33 ]  and scientists who obtained the accurate number modified [ 35 ]  or discarded [ 36 ]  their data to agree with Painter's count.


Arguments from authority that are based on the idea that a person should conform to the opinion of a perceived authority or authoritative group are rooted in psychological  cognitive biases [ 37 ]  such as the  Asch effect . [ 38 ] [ 39 ] [ 40 ]  In repeated and modified instances of the  Asch conformity experiments , it was found that high-status individuals create a stronger likelihood of a subject agreeing with an obviously false conclusion, despite the subject normally being able to clearly see that the answer was incorrect. [ 41 ]


Further, humans have been shown to feel strong emotional pressure to conform to authorities and majority positions. A repeat of the experiments by another group of researchers found that "Participants reported considerable  distress  under the group pressure", with 59% conforming at least once and agreeing with the clearly incorrect answer, whereas the incorrect answer was much more rarely given when no such pressures were present. [ 42 ]


Another study shining light on the psychological basis of the fallacy as it relates to perceived authorities are the  Milgram experiments , which demonstrated that people are more likely to go along with something when it is presented by an authority. [ 43 ]  In a variation of a study where the researchers did not wear lab coats, thus reducing the perceived authority of the tasker, the obedience level dropped to 20% from the original rate, which had been higher than 50%. Obedience is encouraged by reminding the individual of what a perceived authority states and by showing them that their opinion goes against this authority. [ 43 ]


Scholars have noted that certain environments can produce an ideal situation for these processes to take hold, giving rise to  groupthink . [ 44 ]  In groupthink, individuals in a group feel inclined to minimize conflict and encourage  conformity . Through an appeal to authority, a group member might present that opinion as a consensus and encourage the other group members to engage in groupthink by not disagreeing with this perceived consensus or authority. [ 45 ] [ 46 ]  One paper about the philosophy of mathematics states that, within academia,


If...a person accepts our discipline, and goes through two or three years of graduate study in mathematics, he absorbs our way of thinking, and is no longer the critical outsider he once was...If the student is unable to absorb our way of thinking, we flunk him out, of course. If he gets through our obstacle course and then decides that our arguments are unclear or incorrect, we dismiss him as a crank, crackpot, or misfit. [ 47 ]


Corporate environments are similarly vulnerable to appeals to perceived authorities and experts leading to groupthink, [ 48 ]  as are governments and militaries. [ 49 ]


An  argumentum ad crumenam   argument , also known as  an argument to the purse , is the  informal fallacy  of drawing conclusions based on the speaker's financial status. [ 1 ]  The term generally refers to the assumption that having wealth is indicative of insight or virtue, and that poverty denotes the opposite. [ 1 ]


The opposite is the  argumentum ad lazarum .


Examples:


Argumentum ad lazarum  or  appeal to poverty  is the  informal fallacy  of thinking a conclusion is correct solely because the speaker is poor, or it is incorrect because the speaker is rich. It is named after  Lazarus , a beggar in a  New Testament   parable  who receives his reward in the afterlife.


This is popularly summarized as the statement, "Poor, but honest."


The opposite is the  argumentum ad crumenam .


Some experimental evidence supports the appeal to poverty. A 2017 study by Igor Grossmann and Justin Brienza at the University of Waterloo in Canada found that when "wisdom" is defined as the ability to consider opposing perspectives and find a compromise that defuses an interpersonal dispute, poor and working-class people are more likely to show such an ability compared to those in higher socioeconomic classes. [ 1 ] [ 2 ]  As with all fallacies though, the tendency is not absolute.


In  argumentation theory , an  argumentum ad populum  ( Latin  for 'appeal to the people') [ 1 ]  is a  fallacious argument  which is based on claiming a truth or affirming something is good or correct because many people think so. [ 2 ]


Other names for the fallacy include:


Argumentum ad populum  is a type of  informal fallacy , [ 1 ] [ 14 ]  specifically a  fallacy of relevance , [ 15 ] [ 16 ]  and is similar to an  argument from authority  ( argumentum ad verecundiam ). [ 14 ] [ 4 ] [ 9 ]  It uses an appeal to the beliefs, tastes, or values of a group of people, [ 12 ]  stating that because a certain opinion or attitude is held by a majority, or even everyone, it is therefore correct. [ 12 ] [ 17 ]


Appeals to popularity are common in commercial advertising that portrays products as desirable because they are used by many people [ 9 ]  or associated with popular sentiments [ 18 ]  instead of communicating the merits of the products themselves.


The  inverse  argument, that something that is unpopular must be flawed, is also a form of this fallacy. [ 6 ]


The fallacy is similar in structure to certain other fallacies that involve a confusion between the "justification" of a belief and its "widespread acceptance" by a given group of people. When an argument uses the appeal to the beliefs of a group of experts, it takes on the form of an appeal to authority; if the appeal relates to the beliefs of a group of respected elders or the members of one's community over a long time, then it takes on the form of an  appeal to tradition .


The philosopher  Irving Copi  defined  argumentum ad populum  differently from an appeal to popular opinion itself, [ 19 ]  as an attempt to rouse the "emotions and enthusiasms of the multitude". [ 19 ] [ 20 ]


Douglas N. Walton  argues that appeals to popular opinion can be logically valid in some cases, such as in political dialogue within a  democracy . [ 21 ]


In some circumstances, a person may argue that the fact that Y people believe X to be true implies that X is  false . This line of thought is closely related to the  appeal to spite  fallacy given that it invokes a person's contempt for the general populace or something about the general populace to persuade them that most are wrong about X. This  ad populum  reversal commits the same logical flaw as the original fallacy given that the idea "X is true" is inherently separate from the idea that "Y people believe X": "Y people believe in X as true, purely because Y people believe in it, and not because of any further considerations. Therefore X must be false." While Y people can believe X to be true for fallacious reasons, X might still be true. Their motivations for believing X do not affect whether X is true or false.


Y = most people, a given quantity of people, people of a particular demographic.


X = a statement that can be true or false.


In general, the reversal usually goes: "Most people believe A and B are both true. B is false. Thus, A is false." The similar fallacy of  chronological snobbery  is not to be confused with the  ad populum  reversal. Chronological snobbery is the claim that if belief in both X and Y was popularly held in the past and if Y was recently proved to be untrue then X must also be untrue. That line of argument is based on a belief in historical progress and not—like the  ad populum  reversal is—on whether or not X and/or Y is currently popular.


Appeals to public opinion are valid in situations where consensus is the determining factor for the validity of a statement, such as linguistic usage and definitions of words.


Linguistic descriptivists  argue that correct grammar, spelling, and expressions are defined by the language's speakers, especially in languages which do not have a central governing body. According to this viewpoint, if an incorrect expression is commonly used, it becomes correct. In contrast,  linguistic prescriptivists  believe that incorrect expressions are incorrect regardless of how many people use them.  [ 22 ]


Special functions  are  mathematical functions  that have well-established names and mathematical notations due to their significance in mathematics and other scientific fields.


There is no formal definition of what makes a function a special function; instead, the term  special function  is defined by consensus. Functions generally considered to be special functions include  logarithms ,  trigonometric functions , and the  Bessel functions .


The  association fallacy  is a  formal logical fallacy  that asserts that properties of one thing must also be properties of another thing if both things belong to the same group. For example, a fallacious arguer may claim that "bears are animals, and bears are dangerous; therefore your dog, which is also an animal, must be dangerous."


When it is an attempt to win favor by exploiting the audience's preexisting spite or disdain for something else, it is called  guilt by association  or an  appeal to spite  ( Latin :  argumentum ad odium ). [ 1 ]  Guilt by association is similar to  ad hominem  arguments which attack the speaker rather than addressing the claims, but in this case the ill feeling is not created by the argument; it already exists.


Using the language of  set theory , the formal fallacy can be written as follows:


In the notation of  first-order logic , this type of fallacy can be expressed as ( ∃ x   ∈   S  :  φ ( x )) ⇒ ( ∀ x  ∈  S  :  φ ( x )).


The fallacy in the argument can be illustrated through the use of an  Euler diagram : A satisfies the requirement that it is part of both sets S1 and S2, but representing this as an Euler diagram makes it clear that B could be in S2 but not S1.


This form of the argument is as follows:


An example of this fallacy would be "My opponent for office just received an endorsement from the Puppy Haters Association. Is that the sort of person you would want to vote for?"


Some  syllogistic  examples of guilt by association:


Guilt by association can sometimes also be a type of  ad hominem , if the argument attacks a person because of the similarity between the views of someone making an argument and other proponents of the argument. [ 2 ] [ 3 ]


A form of the association fallacy often used by those denying a well-established scientific or historical proposition is the so-called  Galileo gambit  or  Galileo fallacy . [ 4 ]  The argument runs thus:  Galileo  was ridiculed in his time for his scientific observations, but was later acknowledged to be right; the proponent argues that since their non-mainstream views are provoking ridicule and rejection from other scientists, they will later be recognized as correct, like Galileo. [ 5 ]  The gambit is flawed in that being ridiculed does not necessarily correlate with being right and that many people who have been ridiculed in history were, in fact, wrong. [ 4 ] [ 6 ]  Similarly,  Carl Sagan  opined that people laughed at such geniuses as  Christopher Columbus [ a ]  and the  Wright brothers , but "they also laughed at  Bozo the Clown ". [ 8 ] [ 9 ]  It is often committed by those whose theories reject common scientific consensus. [ 10 ]


Ergo decedo ,  Latin  for "therefore I leave" or "then I go off", a truncation of  argumentum ergo decedo , and colloquially denominated the  traitorous critic fallacy , [ 1 ]  denotes responding to the criticism of a critic by implying that the critic is motivated by undisclosed favorability or affiliation to an  out-group , rather than responding to the criticism itself. The fallacy implicitly alleges that the critic does not appreciate the  values and customs  of the criticized group or is  traitorous , and thus suggests that the critic should avoid the question or topic entirely, typically by leaving the criticized group. [ 2 ]


Argumentum ergo decedo  is generally categorized as a type of  informal fallacy  and more specifically as a species of the subclass of  ad hominem  informal fallacies.


Argumentum ergo decedo  is directly related to the  tu quoque  fallacy when responding to political criticism. As  whataboutism  is used against external criticism,  ergo decedo  is used against internal criticism.


An  etymological fallacy  is an  argument of equivocation , arguing that a word is defined by its  etymology , and that its  customary usage is therefore incorrect . [ 1 ] [ 2 ]


Ancient Greeks  believed that there was a "true meaning" of a word, distinct from common use. There is evidence that a similar belief existed among ancient  Vedic  scholars. In modern days, this fallacy can be found in some arguments of  language purists . [ 1 ]


An etymological fallacy becomes possible when a word's meaning  shifts  over time from its original meaning. Such changes can include a narrowing or widening of scope or a change of connotation (amelioration or pejoration). In some cases, modern usage can shift to the point where the new meaning has no evident connection to its  etymon . [ examples needed ] [ 1 ]


The term  antisemitism  refers to anti- Jewish  beliefs and practices. [ 3 ] [ 4 ] [ 5 ]  It replaced the earlier term  Jew-hatred . The etymological fallacy arises when a speaker asserts its meaning is the one implied by the structure of the word— racism  against any of the  Semitic peoples . [ 6 ] [ 7 ]


Godwin's law  (or  Godwin's rule ), short for  Godwin's law of Nazi analogies , [ 1 ]  is an Internet  adage  asserting: "As an  online discussion  grows longer, the probability of a  comparison involving Nazis  or Hitler  approaches 1 ." [ 2 ]


Promulgated by the American attorney and author  Mike Godwin  in 1990, [ 1 ]  Godwin's law originally referred specifically to  Usenet newsgroup  discussions. [ 3 ]  He stated that he introduced Godwin's law in 1990 as an experiment in  memetics , [ 1 ]  specifically to address the ubiquity of such comparisons which he believes regrettably  trivialize  the  Holocaust . [ 4 ] [ 5 ]  Later, it was applied to any  threaded online discussion , such as  Internet forums ,  chat rooms , and  social-media  comment threads, as well as to speeches, articles, and other  rhetoric [ 6 ] [ 7 ]  where  reductio ad Hitlerum  occurs.


In 2012,  Godwin's law  became an entry in the third edition of the  Oxford English Dictionary . [ 8 ]


Godwin's law can be applied mistakenly or abused as a distraction, a diversion, or even  censorship , when miscasting an opponent's argument as  hyperbole  even when the comparison made by the argument is appropriate. [ 9 ]  Godwin has criticized the over-application of the adage, claiming that it does not articulate a  fallacy , but rather is intended to reduce the frequency of inappropriate and hyperbolic comparisons: [ 10 ]


Although deliberately framed as if it were a  law of nature or of mathematics , its purpose has always been rhetorical and  pedagogical : I wanted folks who glibly compared someone else to Hitler to think a bit harder about  the Holocaust .


In 2021,  Harvard  researchers published an article showing that the Nazi-comparison phenomenon does not occur with  statistically meaningful  frequency in  Reddit  discussions. [ 11 ] [ 12 ]


Godwin's law has many  corollaries , some considered more canonical (by being adopted by Godwin himself) [ 2 ]  than others. For example, many newsgroups and other Internet discussion forums have a tradition that, when a Nazi or Hitler comparison is made, the thread is finished and whoever made the comparison loses whatever  debate  is in progress. [ 13 ]  This idea is itself sometimes mistakenly referred to as Godwin's law. [ 14 ]


Godwin rejects the idea that whoever invokes Godwin's law has lost the argument, and suggests that, applied appropriately, the rule "should function less as a conversation ender and more as a conversation starter." [ 15 ]  In an interview with  Time Magazine , Godwin said that making comparisons to Hitler would actually be appropriate under the right circumstances: [ 16 ]


I urge people to develop enough perspective to do it thoughtfully. If you think the comparison is valid, and you've given it some thought, do it. All I ask you to do is think about the human beings capable of acting very badly. We have to keep the magnitude of those events in mind, and not be glib. Our society needs to be more humane, more civilized and to grow up.


In August 2017, while commenting on the  Unite the Right rally  in  Charlottesville, Virginia , Godwin himself endorsed and encouraged social-media users to compare its " alt-right " participants to Nazis. [ 17 ] [ 18 ]


Godwin has denied the need to update or amend the rule. In June 2018, he wrote, in an opinion piece for the  Los Angeles Times : "It still serves us as a tool to recognize specious comparisons to Nazism – but also, by contrast, to recognize comparisons that aren't." [ 15 ]
Additionally, when a potential subject of Godwin's law seems "intent on making the Hitler comparison", [ 19 ]  the comparison with fascism may be appropriate rather than devaluing the argument; a " MAGA " corollary to the Law recognizes the pernicious embrace of Nazi-inspired tropes and phrases by the " alt-right ".


In 2023, Godwin published an opinion on  The Washington Post  stating "Yes, it's okay to compare Trump to Hitler. Don't let me stop you." In the article, Godwin says "But when people draw parallels between Donald Trump’s 2024 candidacy and Hitler’s progression from fringe figure to Great Dictator, we aren’t joking. Those of us who hope to preserve our democratic institutions need to underscore the resemblance before we enter the twilight of American democracy." [ 20 ]


Ipse dixit  ( Latin  for "he said it himself") is an assertion without proof, or a  dogmatic  expression of opinion. [ 1 ] [ 2 ]


The  fallacy  of defending a  proposition  by baldly asserting that it is "just how it is" distorts the argument by opting out of it entirely: the claimant declares an issue to be intrinsic and immutable. [ 3 ]


The Latin form of the expression comes from the Roman orator and philosopher  Marcus Tullius Cicero  (106–43 BC) in his theological studies  De Natura Deorum  ( On the Nature of the Gods ) and is his translation of the Greek expression (with the identical meaning)  autòs épha  ( αὐτὸς ἔφα ), an  argument from authority  made by the  disciples of Pythagoras  when appealing to the pronouncements of the master rather than to reason or evidence. [ 4 ]


Before the early 17th century,  scholars  applied the  ipse dixit  term to justify their subject-matter arguments if the arguments previously had been used by the  ancient Greek  philosopher  Aristotle  (384–322 BC). [ 5 ]


In the late 18th century,  Jeremy Bentham  adapted the term  ipse dixit  into the word  ipse-dixitism. [ 6 ]  Bentham coined the term to apply to all non- utilitarian  political arguments. [ 7 ]


In modern legal and administrative decisions, the term  ipse dixit  has generally been used as a criticism of arguments based solely upon the authority of an individual or organization. For example, in  National Tire Dealers & Retreaders Association, Inc. v. Brinegar,  491 F.2d 31, 40 (D.C. Cir. 1974), Circuit Judge  Wilkey  considered that the Secretary of Transportation's "statement of the reasons for his conclusion that the requirements are practicable is not so inherently plausible that the court can accept it on the agency's mere  ipse dixit. " [ 8 ]


In 1997, the  Supreme Court of the United States  recognized the problem of "opinion evidence which is connected to existing data only by the  ipse dixit  of an expert." [ 9 ]  Likewise, the  Supreme Court of Texas  has held "a claim will not stand or fall on the mere  ipse dixit  of a credentialed witness." [ 10 ]  "[W]hen you come across an argument that you recall the majority took issue with," U.S. Supreme Court Justice  Elena Kagan  advised readers of her dissent in 2023's  Andy Warhol Foundation for the Visual Arts, Inc. v. Goldsmith , "go back to its response and ask yourself about the ratio of reasoning to  ipse dixit ." [ 11 ]


In 1858,  Abraham Lincoln  said in his speech at  Freeport, Illinois , at the  second joint debate  with  Stephen A. Douglas : [ 12 ]


I pass one or two points I have because my time will very soon expire, but I must be allowed to say that Judge Douglas recurs again, as he did upon one or two other occasions, to the enormity of Lincoln,—an insignificant individual like Lincoln,— upon his  ipse dixit  charging a conspiracy upon a large number of members of Congress, the Supreme Court, and two Presidents, to nationalize slavery. I want to say that, in the first place, I have made no charge of any sort upon my  ipse dixit . I have only arrayed the evidence tending to prove it, and presented it to the understanding of others, saying what I think it proves,  but giving you the means of judging whether it proves it or not. This is precisely what I have done. I have not placed it upon my  ipse dixit  at all.


Poisoning the well  (or attempting to  poison the well ) is a type of  informal fallacy  where adverse information about a target is preemptively presented to an  audience , with the intention of discrediting or ridiculing something that the target person is about to say. Poisoning the well can be a special case of  argumentum ad hominem , and the term was first used in this sense by  John Henry Newman  in his work  Apologia Pro Vita Sua  (1864). [ 1 ]


Poisoning the well can take the form of an (explicit or implied) argument, and is considered by some philosophers an  informal fallacy . [ 1 ]


A poisoned-well "argument" has the following form:


Poisoned-well arguments are sometimes used with preemptive invocations of the  association fallacy . In this pattern, an unfavorable attribute is ascribed to any future opponents, in an attempt to discourage debate. For example, "That's my stance on funding the public education system, and anyone who disagrees with me hates children." Any person who steps forward to dispute the claim will then risk applying the tag to themselves in the process. This is a  false dilemma : not all future opponents necessarily have the unfavorable attribute. For example, not everyone who has a different opinion on funding the public education system necessarily hates children.


A poisoned-well "argument" can also be in this form: [ 3 ]


Example: Boss, you heard my side of the story, and why I think Bill should be fired and not me.  Now, I am sure Bill is going to come to you with some pathetic attempt to weasel out of this lie that he has created.


The etymology of the phrase lies in  well poisoning , an ancient wartime practice of pouring poison into sources of  fresh water  before an invading army, to diminish the invading army's strength.


Reductio ad Hitlerum  ( Latin  for "reduction to Hitler"), also known as  playing the Nazi card , [ 1 ] [ 2 ]  is an attempt to invalidate someone else's argument on the basis that the same idea was promoted or practised by  Adolf Hitler  or the  Nazi Party . [ 3 ]  Arguments can be termed  reductio ad Hitlerum  if they are fallacious (e.g., arguing that because  Hitler abstained from eating meat  or  was against smoking , anyone else who does so is a Nazi). Contrarily, straightforward arguments critiquing specifically fascist components of  Nazism  like  Führerprinzip  are not part of the  association fallacy .


Invented by  Leo Strauss  in 1953,  reductio ad Hitlerum  takes its name from the term used in logic called  reductio ad absurdum  ("reduction to the absurd"). [ 4 ]  According to Strauss,  reductio ad Hitlerum  is a type of  ad hominem ,  ad misericordiam , or a  fallacy of irrelevance . The suggested rationale is one of  guilt by association . It is a tactic often used to derail arguments because  such comparisons  tend to distract and anger the opponent. [ 5 ]


Reductio ad Hitlerum  is a type of  association fallacy . [ 5 ] [ 6 ]  The argument is that a policy leads to—or is the same as—one advocated or implemented by  Adolf Hitler  or  Nazi Germany  and so "proves" that the original policy is undesirable. Another type of  reductio ad Hitlerum  is asking a question of the form "You know who else...?" with the deliberate intent of impugning a certain idea or action by implying Hitler had that idea or performed such an action. [ 7 ]


A comparison to Hitler or  Nazism  is not a  reductio ad Hitlerum  if it illuminates an argument instead of causing distraction from it. [ 8 ]  Straightforward comparisons can be used to criticize fascist components of Nazism like  führerprinzip . However, one could argue fallaciously that because  Hitler abstained from eating meat  or was  against smoking , anyone else who does so is a Nazi. [ 9 ]


The phrase  reductio ad Hitlerum  is first known to have been used in an article written by  University of Chicago  professor  Leo Strauss  for  Measure: A Critical Journal  in spring 1951, [ 10 ]  although it was made famous in a book by Strauss published in 1953 [ 3 ]   Natural Right and History , Chapter II:


In following this movement towards its end we shall inevitably reach a point beyond which the scene is darkened by the shadow of Hitler. Unfortunately, it does not go without saying that in our examination we must avoid the fallacy that in the last decades has frequently been used as a substitute for the  reductio ad absurdum : the  reductio ad Hitlerum . A view is not refuted by the fact that it happens to have been shared by Hitler.


The phrase was derived from the  logical argument  termed  Reductio ad absurdum . The  argumentum  variant takes its form from the names of many classic fallacies such as  argumentum ad hominem . The  ad Nazium  variant may be further humorously derived from  argumentum ad nauseam .


Historian  Daniel Goldhagen , who had written about  the Holocaust , argues that not all comparisons to Hitler and Nazism are logical fallacies since if they all were, there would be nothing to learn from the events that resulted in the Holocaust. He argues in his book  Hitler's Willing Executioners  that many people who were complicit or active participants in the Holocaust and subsequently in  fascist  and  neo-Nazi  movements have manipulated the historical narrative to escape blame or to deny aspects of the Holocaust. [ 11 ] [ 12 ]  Claims that allegations of  antisemitism  are  reductio ad Hitlerum  have also been employed by  David Irving , a British  Holocaust denier . [ 13 ]


In 2000,  Thomas Fleming  claimed that  reductio ad Hitlerum  was being used by his opponents against his values:


Leo Strauss called it the  reductio ad Hitlerum . If Hitler liked neoclassical art, that means that classicism in every form is Nazi; if Hitler wanted to strengthen the German family, that makes the traditional family (and its defenders) Nazi; if Hitler spoke of the "nation" or the "folk", then any invocation of nationality, ethnicity, or even folkishness is Nazi ... [ 14 ]


Although named for Hitler, the logical fallacy existed before  World War II . Other individuals from history were used as stand-ins for evil. [ 15 ]  Author  Tom Holland  compares the use of Hitler as the standard of evil with earlier invocations of the  Devil  (such as the phrase ' Deal with the Devil '). [ 16 ]  During the 18th, 19th and early 20th centuries, the  Pharaoh of the Book of Exodus  was commonly considered the most villainous person in history. [ 15 ]  During the years prior to the  American Civil War ,  abolitionists  referred to enslavers as modern-day Pharaohs. After  VE Day , Pharaoh continued to appear in the speeches of social reformers like  Martin Luther King Jr. [ 15 ]   Judas Iscariot  and  Pontius Pilate  were also commonly held up as pure evil. However, there was no universal Hitler-like person, and different regions and times used different stand-ins. [ 15 ]  In the years after the  American Revolution ,  King George III  was often vilified in the United States. "King George" comparison was publicly used as recently as 1992 by  Pat Buchanan  when referring to president  George H. W. Bush , in the course of the  U.S. presidential campaign . [ 17 ] [ 18 ]  During the American Civil War, some  Confederates  called Lincoln a "modern Pharaoh". [ 15 ]


In 1991, Michael André Bernstein alleged  reductio ad Hitlerum  over a full-page advertisement placed in  The New York Times  by the  Lubavitch  community after the  Crown Heights riot  under the heading "This Year  Kristallnacht  Took Place on August 19th Right Here in Crown Heights".  Henry Schwarzschild , who had witnessed  Kristallnacht , wrote to  The New York Times  that "however ugly were the anti-Semitic slogans and the assaultive behavior of people in the streets [during the Crown Heights riots] ... one thing that clearly did not take place was a  Kristallnacht ". [ 19 ]


The American Conservative  accused  Jonah Goldberg 's book  Liberal Fascism  of employing the  reductio  fallacy:


That Nazism and  contemporary liberalism  both promote healthy living is as meaningless a finding as that  bloody marys  and  martinis  may both be made with  gin . Repeatedly, Goldberg fails to recognize a  reductio ad absurdum . ... In no case does Goldberg uncover anything more ominous than a coincidence. [ 20 ]


Since  Hitler was against smoking , some in the tobacco industry invoked the argument to compare those who are  against smoking  to Nazis. [ 21 ]


Sippenhaft  or  Sippenhaftung  ( German:   [ˈzɪpənˌhaft(ʊŋ)] ,  kin liability ) is a German term for the idea that a family or clan shares the responsibility for a crime or act committed by one of its members, justifying  collective punishment . [ 1 ] [ 2 ]  As a legal principle, it was derived from  Germanic law  in the  Middle Ages , usually in the form of fines and compensations. It was adopted by  Nazi Germany  to justify the punishment of kin (relatives, spouse) for the offence of a family member. Punishment often involved imprisonment and execution, and was applied to relatives of the conspirators of  the failed  1944 bomb plot to assassinate Hitler .


Prior to the adoption of  Roman law  and  Christianity ,  Sippenhaft  was a common legal principle among Germanic peoples, including  Anglo-Saxons  and  Scandinavians . [ 3 ]  Germanic laws distinguished between two forms of justice for severe crimes such as murder:  blood revenge , or  extrajudicial killing ; and  blood money , pecuniary restitution or fines in lieu of revenge, based on the  weregild  or "man price" determined by the victim's wealth and social status. [ 4 ]  The principle of  Sippenhaft  meant that the family or clan of an offender, as well as the offender, could be subject to revenge or could be liable to pay restitution. [ 5 ]  Similar principles were common to  Celts ,  Teutons , and  Slavs . [ 6 ]


In Nazi Germany, the term was revived to justify the punishment of kin (relatives, spouse) for the offence of a family member. In that form of  Sippenhaft , the relatives of persons accused of crimes against the state were held to share the responsibility for those crimes and subject to arrest and sometimes execution.


Examples of  Sippenhaft  being used as a threat exist within the  Wehrmacht  from around 1943. Soldiers accused of having "blood impurities" or soldiers conscripted from outside of Germany also began to have their families threatened and punished with  Sippenhaft . An example is the case of  Panzergrenadier  Wenzeslaus Leiss, who was accused of desertion on the  Eastern Front  in December 1942. After the  Düsseldorf   Gestapo  discovered supposed Polish links in the Leiss family, in February 1943 his wife, two-year-old daughter, two brothers, sister and brother-in-law were arrested and executed at  Sachsenhausen concentration camp . By 1944, several general and individual directives were ordered within divisions and corps, threatening troops with consequences against their families.


Many people who had committed no crimes were arrested and punished under  Sippenhaft  decrees introduced after the failed  20 July plot  to assassinate  Adolf Hitler  in July 1944. [ 7 ] : 121–166  After the failure of the 20 July plot, the  SS  chief  Heinrich Himmler  told a meeting of  Gauleiters  in  Posen  that he would "introduce absolute responsibility of kin ... a very old custom practiced among our forefathers". According to Himmler, this practice had existed among the ancient  Teutons . "When they placed a family under the ban and declared it outlawed or when there was a  blood feud  in the family, they were utterly consistent. ... This man has committed treason; his blood is bad; there is traitor's blood in him; that must be wiped out. And in the blood feud the entire clan was wiped out down to the last member. And so, too, will  Count Stauffenberg 's family be wiped out down to the last member." [ 8 ]  Accordingly, the members of the family of von Stauffenberg (the officer who had planted the bomb that failed to kill Hitler) were all under suspicion. His wife,  Nina Schenk Gräfin von Stauffenberg , was sent to  Ravensbrück concentration camp  (she survived and lived until 2006). His brother  Alexander , who knew nothing of the plot and was serving with the  Wehrmacht  in Greece , was also sent to a concentration camp. Similar punishments were meted out to the relatives of  Carl Goerdeler ,  Henning von Tresckow ,  Adam von Trott zu Solz  and many other conspirators.  Erwin Rommel  opted to commit suicide, rather than being tried for his suspected role in the plot, in part because he knew that his wife and children would suffer well before his own all-but-certain conviction and execution.


After the 20 July plot, numerous families connected to the Soviet-sponsored  League of German Officers  made up of German prisoners of war, such as those of  Walther von Seydlitz-Kurzbach  and  Friedrich Paulus , were also arrested. Unlike a number of the 20 July conspirators families, those arrested for connection to the League were not released after a few months but remained in prison until the end of the war. Younger children of arrested plotters were not jailed but sent to orphanages under new names. Stauffenberg's children were renamed "Meister". [ 9 ]


After 20 July 1944 these threats were extended to include all German troops, in particular, German commanders. A decree of February 1945 threatened death to the relatives of military commanders who showed what Hitler regarded as cowardice or defeatism in the face of the enemy. After  the surrender of Königsberg  to the Soviets in April 1945, the family of the German commander General  Otto Lasch  were arrested. These arrests were publicized in the  Völkischer Beobachter . [ 7 ] : 53–88


The principle of  Sippenhaftung  is considered incompatible with  German Basic Law , and therefore has no legal definition. [ citation needed ]


" Three men make a tiger " ( Chinese :  三人成虎 ;  pinyin :  sān rén chéng hǔ ) is a  Chinese   proverb  or  chengyu  (four-character idiom). "Three men make a tiger" refers to an individual's tendency to accept absurd information as long as it is repeated by enough people. It refers to the idea that if an unfounded premise or  urban legend  is mentioned and repeated by many individuals, the premise will be erroneously accepted as the truth.  This concept is related to  communal reinforcement  or the fallacy of  argumentum ad populum  and  argumentum ad nauseam .


The proverb came from the story of an alleged speech by Pang Cong ( 龐蔥 ), an official of  the state of Wei  in the  Warring States period  (475 BC – 221 BC) in  Chinese History .  According to the  Warring States Records , or  Zhan Guo Ce , before he left on a trip to the  state of Zhao , Pang Cong asked the King of Wei whether he would hypothetically believe in one civilian's report that a  tiger  was roaming the markets in the capital city, to which the King replied no.  Pang Cong asked what the King thought if two people reported the same thing, and the King said he would begin to wonder.  Pang Cong then asked, "what if three people all claimed to have seen a tiger?" The King replied that he would believe in it. Pang Cong reminded the King that the notion of a live tiger in a crowded market was absurd, yet when repeated by numerous people, it seemed real.


Since Pang Cong, as a high-ranking official, had more than three opponents and critics, he was in fact urging the King to pay no attention to those who would spread rumors about him (Pang Cong) while he was away.  "I understand", the King replied, and Pang Cong left for Zhao.  Yet, slanderous talk took place.  When Pang Cong returned to Wei, the King indeed stopped seeing him. [ 1 ]


The tendency to accept absurd information is caused by certain cognitive biases. The first of which is the  motivated reasoning  concept, which is an emotion-biased decision-making phenomenon. It is the idea that humans are motivated to believe whatever confirms their opinions. Motivated reasoning can lead to a false social consensus over time. The second concept is  social consensus reality , which explains that beliefs with high societal consensus are treated like facts, whereas beliefs with relatively low consensus are more susceptible to persuasion and attitude change. The latter is most likely a product of the social consensus of the specific community one lives in. [ 2 ]


One application of the cognitive biases highlighted through the anecdote is that markets are efficient. Often investors jump on a wagon that is either directed in buying or shorting a certain stock or index with the main motivation that many other investors are behaving in a unilateral way. In the short-term when many investors buy a certain stock the market experiences a self-fulfilling prophecy and the stock actually gains value although the company might be underperforming and just benefiting from current market trends. Investors who take such decisions are not basing their justification on fundamental analysis or certain limited information but mainly follow an investment trend that is demonstrated by a high number of other investors. [ 3 ]


ANNOVAR  ( ANNOtate VARiation ) is a bioinformatics software tool for the interpretation and prioritization of  single nucleotide variants  (SNVs),  insertions ,  deletions , and  copy number variants (CNVs)  of a given genome. [ 1 ]


It has the ability to annotate human genomes hg18, hg19, hg38, and model organisms genomes such as: mouse ( Mus musculus ), zebrafish ( Danio rerio ), fruit fly ( Drosophila melanogaster ) , roundworm ( Caenorhabditis elegans ), yeast ( Saccharomyces cerevisiae ) and many others. [ 2 ]  The annotations could be used to determine the functional consequences of the mutations on the genes and organisms, infer cytogenetic bands, report functional importance scores, and/or find variants in conserved regions. [ 2 ]  ANNOVAR along with SNP effect ( SnpEFF ) and  Variant Effect Predictor (VEP)  are three of the most commonly used variant annotation tools.


The cost of high throughput  DNA sequencing  has reduced drastically from around $100 million/human genome in 2001 to around $1000/human genome in 2017. [ 3 ]  Due to this increase in accessibility, high throughput DNA sequencing has become more widely used in research and clinical settings. [ 4 ] [ 5 ]  Some common areas that utilize high throughput DNA sequencing extensively are:  Whole Exome Sequencing ,  Whole Genome Sequencing (WGS) , and  genome wide association studies (GWAS) . [ 6 ] [ 7 ]


There are a growing number of tools available seeking to comprehensively manage, analyze and interpret the enormous amount of data generated from high-throughput DNA sequencing. The tools are required to be efficient and robust enough to analyze a large number of variants (more than 3 million in human genome) though sensitive enough to identify rare and clinically relevant variants that are likely harmful/deleterious. [ 8 ]  ANNOVAR was developed by Kai Wang in 2010 at the Center for Applied Genomics in Children's Hospital of Philadelphia. [ 1 ]  It is a type of variant annotation tool that compiles deleterious genetic variant prediction scores from programs such as PolyPhen, ClinVar, and CADD and annotates the SNVs, insertions, deletions, and CNVs of the provided genome. ANNOVAR is one of the first efficient, configurable, extensible and cross-platform compatible variant annotation tools created.


In terms of the larger bioinformatics workflow, ANNOVAR fits in near the end, after DNA sequencing reads having between mapped, aligned, and variants have been predicted from an alignment file (BAM), also known as variant calling. This process will produce a resultant  VCF  file, a tab-separated text file in a tabular like structure, containing genetic variants as rows. This file can then be used as input into the ANNOVAR software program for the variant annotation process, outputting interpretations of the variants identified from the upstream bioinformatics pipeline.


This approach identifies whether the input variants cause protein coding changes and the amino acids that are affected by the mutations. [ 9 ]  The input file can be composed of exons, introns, intergenic regions, splice acceptor/donor sites, and 5′/3′ untranslated regions. The focus is to explore the relationship between non-synonymous mutations (SNPs, indels, or CNVs) and their functional impact on known genes. [ 10 ]  Especially, gene-based annotation will highlight the exact amino acid change if the mutation is in the exonic region and the predicted effect on the function of the known gene. This approach is useful for identifying variants in known genes from Whole Exome Sequencing data.


This approach identifies deleterious variants in specific genomic regions based on the genomic elements around the gene. [ 11 ]  Some categories region-based annotation will take into account are:


Non-coding regions encompasses 99% of the human genome [ 13 ]  and region-based annotation is extremely useful in identifying variants in those regions. This approach can be used on WGS data.


This approach identifies variants that are documented in specific databases. [ 14 ]  The variants could be obtained from dbSNP,  1000 Genomes Project , or user-supplied list. Additional information could be obtained from the frequency of the variants from the above databases or the predicted deleterious scores created by PolyPhen, CADD, ClinVar or many others. [ 1 ]  The more infrequent a variant appears in the public database, the more deleterious it is likely to be. Results from different deleterious score prediction tools can combined together by the researcher to make a more accurate call on the variant.


Taken together, these approaches complement one another to filter through over 4 million variants in a human genome. Common, low-deleterious score variants are eliminated to reveal the rare, high-deleterious score variants which could be causal for congenital diseases.


ANNOVAR is a command-line tool written in the  Perl  programming language and can be run on any  operating system  that has a Perl interpreter installed. [ 1 ]  If used for non-commercial purposes, it is available free as an  open-source  package that is downloadable through the ANNOVAR website. ANNOVAR can process most  next-generation sequencing  data which has been run through a  variant calling  software.


The ANNOVAR software accepts text-based input files, including  VCF (Variant Call Format) , the gold standard for describing genetic loci.


The program's main annotation script,  annotate_variation.pl  requires a custom input file format, the ANNOVAR input format (.avinput). Common file types can be converted to ANNOVAR input format for annotation using a provided script (see below). It is a simple text file where each line in the file corresponds to a variant and within each line are tab-delimited columns representing the basic genomic coordinate fields (chromosome, start position, end position, reference nucleotides, and observed nucleotides), followed by optional columns [ 2 ]


The ANNOVAR file input contains the following basic fields:


For basic "out-of-the-box" usage:


A popular function of the ANNOVAR tool is the use of the  table_annovar.pl  script which simplifies the workflow into one single command-line call, given that the data sources for annotation have already been downloaded. File conversion from  VCF file  is handled within the function call, followed by annotation and output to an Excel-compatible file. The script takes a number of parameters for annotation and outputs a VCF file with the annotations as  key-value pairs  inside of the  INFO  column of the VCF file for each genetic variant, e.g. "genomic_function=exonic".


File conversion to the ANNOVAR input format is possible using the provided file format conversion script  convert2annovar.pl . The program accepts common file formats outputted by upstream  variant calling  tools. Subsequent functional annotation scripts  annotate_variation.pl  use the ANNOVAR input file. File formats that are accepted by the  convert2annovar.pl  include the following: [ 2 ]


Generating input files based on specific variants, transcripts, or genomic regions:


When investigating candidate loci that are linked to diseases, using the above variant calling file formats as input to ANNOVAR is a standard workflow for functional annotation of genetic variants outputted from an upstream bioinformatics pipeline. ANNOVAR can also be used to in other scenarios, such as interrogating a set of genetic variants of interest based on a list of  dbSNP  identifiers as well as variants within specific genomic or exomic regions. [ 2 ]


In the case of dbSNP identifiers, providing to the  convert2annovar.pl  script a list of identifiers (e.g. rs41534544, rs4308095, rs12345678) in a text file along with the  reference genome  of interest as a parameter, ANNOVAR will output an ANNOVAR input file with the genomic coordinate fields for those variants which can then be used for functional annotation. [ 2 ]


In the case of genomic regions, one can provide a genomic range of interest (e.g. chr1:2000001-2000003) along with the reference genome of interest and ANNOVAR will generate an ANNOVAR input file of all the genetic loci spanning that range. In addition, insertion and deletion size could also be specified in which the script will select all the genetic loci where a specific size of interest insertion or deletion is found. [ 2 ]


Last, if looking at variants within specific exonic regions, users can generate ANNOVAR input files for all possible variants in exons (including splicing variants) when the convert2annovar.pl  script is provided an RNA  transcript  identifier (e.g. NM_022162) based on the standard HGVS (Human Genome Variation Society) nomenclature. [ 2 ]


The possible output files are an annotated .avinput file,  CSV ,  TSV , or  VCF . Depending on the annotation strategy taken (see Figure below), the input and output files will differ. It is possible to configure the output file types given a specific input file, by providing the program the appropriate parameter.


For example, for the  table_annovar.pl  program, if the input file is VCF, then the output will also be a VCF file. If the input file is of the ANNOVAR input format type, then the output will be a TSV by default, with the option to output to CSV if the  -csvout  parameter is specified. By choosing CSV or TSV as the output file type, a user could open the files to view the annotations in  Excel  or a different spreadsheet software application. This is a popular feature among users.


The output file will contain all the data from the original input file with additional columns for the desired annotations. For example, when annotating variants with characteristics such as (1) genomic function and (2) the functional role of the coding variant, the output file will contain all the columns from the input file, followed additional columns "genomic_function" (e.g. with values "exonic" or "intronic") and "coding_variant_function" (e.g. with values "synonymous SNV" or "non-synonymous SNV").


Benchmarked on a modern desktop computer (3 GHz Intel Xeon CPU, 8GB memory), for 4.7 million variants, ANNOVAR requires ~4 minutes to perform gene-based functional annotation, or ~15 minutes to perform stepwise "variants reduction". It is said to be practical for performing variant annotation and variant prioritization on hundreds of human genomes in a day. [ 2 ]


ANNOVAR could be sped up by using the  -thread  argument which enables  multi-threading  so that input files could be processed in parallel.


To use ANNOVAR for functional annotation of variants, annotation datasets can be downloaded using the  annotate_variation.pl  script, which saves them to local disk. [ 1 ]  Different annotation data sources are used for the three major types of annotation (gene-based, region-based, and filter-based).


These are some of the data sources for each annotation type:


Given the large number of data sources for filter-based annotation, here are examples of which subsets of the datasets to use for a few of the most common use cases. [ 14 ]


ANNOVAR is one of the common annotation tools for identifying candidate and causal mutations and genes for rare genetic diseases.


Using a combination of gene-based and filter-based annotation followed by variant reduction based on the annotation values of the variants, the causal gene in a rare recessive Mendelian disease called Miller syndrome can be identified. [ 1 ]


This will involve synthesizing a genome-wide data set of ~4.2 million single nucleotide variants (SNVs )  and ~0.5 million insertions and deletions ( indels ). [ 1 ]  Two known causal mutations for  Miller syndrome  (G152R and G202A in the  DHODH  gene) are also included [ 1 ]


Steps in identifying the causal variants for the disease using ANNOVAR: [ 1 ]


Two limitations of ANNOVAR relate to detection of common diseases and larger structural variant annotations. These problems are present in all current variant annotation tools.


Most common diseases such as diabetes and Alzheimer have multiple variants throughout the genome which are common in the population. [ 15 ] [ 16 ]  These variants are expected to have low individual deleterious scores and cause disease though the accumulation of multiple variants. However ANNOVAR has default "variant-reduction" schemes that provides a small list of rare and highly predicted deleterious variants. [ 10 ]  These default settings could be optimized so the output data would display additional variants with decreasing predicted deleterious scores. [ 2 ]  ANNOVAR is primarily used for identifying variants involved rare diseases where the causal mutation is expected to be rare and highly deleterious.


Larger  structural variants (SVs)  such as chromosomal inversions, translocations, and complex SVs have been shown to cause diseases such as haemophilia A and Alzheimer's. [ 17 ] [ 18 ]  However, SVs are often difficult to annotate because it is difficult to assign specific deleterious scores to large mutated genomic regions. Currently, ANNOVAR can only annotate genes contained within deletions or duplications, or small indels of <50bp. ANNOVAR cannot infer complex SVs and translocations [ 10 ]


There are also two other types of SNP annotation tools that are similar to ANNOVAR: SNP effect ( SnpEFF ) and  Variant Effect Predictor (VEP) . Many of the features between ANNOVAR, SnpEFF, and VEP are the same including the input and output file format, regulatory region annotations, and know variant annotations. However, the main differences are that ANNOVAR cannot annotate for loss of function predictions whereas both SnpEFF and VEP can. Also, ANNOVAR cannot annotate  microRNA  structural binding locations whereas VEP can. [ 19 ]  MicroRNA structural binding location predictions can be informative in revealing  post-transcriptional  mutations’ role in disease pathogenesis. [ 20 ]   Loss of function  mutations are changes in the genome that results in the total dysfunction of the gene product. Thus, these predictions could be extremely informative in regards to disease diagnosis, especially in rare monogenic diseases. [ citation needed ]


*Table adapted from McLaren et al. (2016).


Gene Designer  is a computer  software  package for  bioinformatics . [ 1 ] [ 2 ]  It is used by  molecular biologists  from academia, government, and the pharmaceutical, chemical, agricultural, and biotechnology industries to design, [ 3 ]  clone, and validate genetic sequences. It is  proprietary software , released as  freeware  needing registration.


Gene Designer enables molecular biologists to manage the full gene design process in one application, using a range of design tools.


This free software has been incorporated into classroom and lab curricula for synthetic biology, systems biology, bioengineering, and bioinformatics. Students create and complete projects which manage the full gene design process in one application, using a range of design tools.


Examples of use in curricula:


Gene Relationships Across Implicated Loci   (GRAIL)  is a free web application developed by  Soumya Raychaudhuri   at the  Broad Institute  with the goal of determining the relationships among  genes  in different disease associated  loci  through  statistical analysis . [ 1 ]


When  single-nucleotide polymorphisms  (SNPs) are identified through a  genome-wide association study (GWAS)  as being possibly linked to a human disease, GRAIL works by comparing those with SNPs already identified in the scientific literature as being tied to the disease (using a  text-mining   algorithm  going through  PubMed   abstracts ), [ 1 ]  and determines the degree of functional connectivity among the associated genes. SNPs identified with this method have been shown to be replicated in independent sets at a much higher probability than randomly selected ones. [ 2 ]  GRAIL has also demonstrated better performance than other published algorithms. [ 3 ]


However, the software is still in its  Beta phase , and has shown varied levels of success depending on the  phenotype  in question. [ 3 ]


GenGIS [ 1 ]  merges geographic, ecological and phylogenetic biodiversity data in a single interactive visualization and analysis environment. A key feature of GenGIS is the testing of geographic axes that can correspond to routes of migration or gradients that influence community similarity. [ 2 ]  Data can also be explored using graphical summaries of data on a site-by-site basis, as 3D geophylogenies, or custom visualizations developed using a plugin framework. Standard statistical test such as linear regression and Mantel are provided, and the  R statistical language  can be accessed directly within GenGIS. Since its release, GenGIS has been used to investigate the phylogeography of viruses and bacteriophages, bacteria, and eukaryotes.


Haploview [ 1 ]  is a commonly used  bioinformatics software  which is designed to analyze and visualize patterns of  linkage disequilibrium  (LD) in  genetic  data. Haploview can also perform association studies, choosing tag SNPs [ 2 ]  and estimating  haplotype   frequencies . Haploview is developed and maintained by  Dr. Mark Daly 's lab at the  MIT / Harvard   Broad Institute .


Haploview currently supports the following functionalities:


HomoloGene , a tool of the United States  National Center for Biotechnology Information  (NCBI), is a system for automated detection of  homologs  (similarity attributable to descent from a common ancestor) among the annotated genes of several completely sequenced eukaryotic genomes. [ 1 ]


The HomoloGene processing consists of the protein analysis from the input organisms. Sequences are compared using blastp, then matched up and put into groups, using a taxonomic tree built from sequence similarity, where closer related organisms are matched up first, and then further organisms are added to the tree. The protein alignments are mapped back to their corresponding DNA sequences, and then distance metrics as molecular distances  Jukes and Cantor (1969) ,  Ka/Ks ratio  can be calculated.


The sequences are matched up by using a  heuristic algorithm  for maximizing the score globally, rather than locally, in a bipartite matching (see  complete bipartite graph ). And then it calculates the statistical significance of each match. Cutoffs are made per position and Ks values are set to prevent false  "orthologs"  from being grouped together.  “Paralogs”  are identified by finding sequences that are closer within species than other species.


This resource ceased making updates in 2014. [ 2 ]


" Homo sapiens ,  Pan troglodytes ,  Mus musculus ,  Rattus norvegicus ,  Canis lupus familiaris ,  Bos taurus ,  Gallus gallus ,  Xenopus tropicalis ,  Danio rerio "


" Drosophila melanogaster ,  Anopheles gambiae ,  Caenorhabditis elegans "


" Saccharomyces cerevisiae ,  Schizosaccharomyces pombe ,  Kluyveromyces lactis ,  Eremothecium gossypii ,  Magnaporthe grisea ,   Neurospora crassa "


" Arabidopsis thaliana "


" Oryza sativa "


" Plasmodium falciparum ".


The HomoloGene is linked to all Entrez databases and based on homology and phenotype information of these links:


As a result, HomoloGene displays information about Genes, Proteins, Phenotypes, and Conserved Domains.


NeighborNet [ 1 ]  is an algorithm for constructing  phylogenetic networks  which is loosely based on the  neighbor joining  algorithm. Like neighbor joining, the method takes a  distance matrix  as input, and works by agglomerating clusters. However, the NeighborNet algorithm can lead to collections of clusters which overlap and do not form a  hierarchy , and are represented using a type of phylogenetic network called a  splits graph . If the distance matrix satisfies the  Kalmanson combinatorial conditions  then Neighbor-net will return the corresponding circular ordering. [ 2 ] [ 3 ]  The method is implemented in the  SplitsTree  and  R /Phangorn [ 4 ] [ 5 ]  packages.


Examples of the application of Neighbor-net can be found in virology, [ 6 ]  horticulture, [ 7 ]  dinosaur genetics, [ 8 ]   comparative linguistics , [ 9 ]  and archaeology. [ 10 ]


PLINK [ 1 ]  is a free, commonly used, open-source  whole-genome association  analysis toolset designed by  Shaun Purcell . The software is designed flexibly to perform a wide range of basic, large-scale genetic analyses.


PLINK currently supports following functionalities:


PLINK has its own format of text files ( .ped ) and binary text files ( .bed ) that serve as input files for most analyses. [ 2 ]  A .map accompanies a  .ped  file and provides information about variants, while  .bim  and  .fam  files accompany  .bed  files as part of the binary dataset. Additionally, PLINK accepts inputs of  VCF , BCF, Oxford, and 23andMe files, which are typically extracted into the binary  .bed  format prior to performing desired analyses. With certain formats such as VCF, some information such as phase and dosage will be discarded.


PLINK has a variety of output files depending on the analysis. PLINK has the ability to output files for BEAGLE and can recode a  .bed  file into a VCF for analyses in other programs. Additionally, PLINK is designed to work in conjunction with  R , and can output files to be processed by certain R packages.


This  free and open-source software  article is a  stub . You can help Wikipedia by  expanding it .


SequenceVariantAnalyzer (SVA)  is a computer program for annotating and analyzing  genetic variants  called (identified) from a  whole genome  or  exome  sequencing study ( Shotgun sequencing ).


DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. [ 1 ]  Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of  linkage disequilibrium , [ 2 ]  thus, in theory, is more possible to directly identify the genetic variants contributing to biological  traits  or  medical outcomes .


The rapidly evolving high-throughput DNA sequencing technologies have now allowed the rapid generation of large amounts of sequence data for the purpose of performing such whole-genome sequencing studies, at a reasonable cost. SequenceVariantAnalyzer, or SVA, is software that analyzes genetic variants identified in such studies.


SVA is designed for two specific aims:


(1) To annotate the biological functions of the identified genetic variants and group them, conveniently;


(2) To find the genetic variants that are associated with or responsible for the biological  traits  or medical outcomes of interest.


SVA is developed on the  Java platform .


SVA is developed and maintained by Dr. Dongliang Ge and Dr. David B. Goldstein at Duke University, Center for Human Genome Variation.


SLiM  ("Selection on Linked Mutations") is software designed for conducting forward-in-time genetic simulations of eco-evolutionary scenarios. It allows researchers to simulate complex  population genetics  models, accommodating both  Wright-Fisher  and non-Wright-Fisher models.


SLiM supports various evolutionary processes, including  mutation , recombination, migration, and  genetic drift , [ 1 ]  selection on  fecundity  or survival, [ 2 ]  and is designed to enable users to explore the dynamics of  genomes  under different  selective pressures  and demographic events of one or multiple populations and species. [ 3 ]


The SLiM also offers a  scripting language , Eidos, which provides customization options for defining evolutionary parameters and interactions within and between populations. Almost all information regarding Eidos and SLiM are available in the SLiM [ 4 ]  and Eidos manuals. [ 5 ]


This  simulation software  article is a  stub . You can help Wikipedia by  expanding it .


SnpEff  is an  open source  tool that performs  annotation  on  genetic variants  and predicts their effects on genes by using an interval forest approach. This program takes pre-determined variants listed in a  data file  that contains the nucleotide change and its position and predicts if the variants are  deleterious . This program was first developed to predict effects of single nucleotide  polymorphisms  (SNPs) in  Drosophila . [ 1 ]  As of July 2024, this SnpEff paper has been cited 10076 times. SnpEff has been used for various applications [ 2 ] [ 3 ] [ 4 ]  – from  personalized medicine , [ 5 ]  to profiling  bacteria . [ 6 ]   This annotation and prediction software can be compared to  ANNOVAR  and  Variant Effect Predictor , but each use different  nomenclatures . [ 7 ] [ 8 ]


SnpEff has the capability to work on Windows, Unix or Mac systems, although the installation steps differ. For all systems, SnpEff is first downloaded as a ZIP file, decompressed  [ 9 ]  and then copy-pasted into the desired software (Windows) or requires an additional command line (Unix and Mac). Once the  software  is  installed , the user inputs a  VCF  or  TXT file  into the tool kit that contains the tab-separated columns:  Chromosome  name, Position, Variant’s ID,  Reference genome , Alternative, Quality score, Quality filter and Information.


The chromosome name and position columns describe where the variant is located – chromosome number and nucleotide position. If the variant has a previously determined name (example: rs34567), it goes in the ID column. The reference column provides the specific  nucleotide  in the reference genome – differentiations from the reference are noted in the Alternative section. How accurate the variant is will be the Quality column and its readout from Quality filters are included in the filter column. Any other genomic information is put in the INFO column, which is altered to display the output after running SnpEff.


The output in the INFO section includes: the effect of the variant (stop loss, stop gain, etc.), effect impact on gene (High, Moderate, Low or Modifier), functional class of the variant (nonsense, missense, frameshift etc.), codon change, amino acid change, amino acid length, gene name, gene biotype (protein coding, pseudogene, rRNA, etc. [ 10 ] ), coding information, transcript information, exon information and any errors or warnings detected. The Effect impact is what SnpEff uses to determine how deleterious the variant is on genes. For example, a HIGH impact output means that SnpEff predicts that the variant causes deleterious gene effects.


SnpEff is typically used for research and academic purposes at institutions and companies - and in some instances,  personalized medicine . [ citation needed ]   However, Pablo Cingolani now recommends that  ClinEff  (a combination of SnpEff and SnpSift) be used for medical purposes. [ citation needed ]


SnpEff contains many advantages and limitations. It is able to analyze all variants from the 1000 Genome Project in less than 15 minutes and can be integrated into other tools such as Galaxy, GATK and GKNO. It can be combined with other toolkits to narrow variant prediction parameters (example: whitelist  [ 11 ] ).


SnpEff Limitations:


WGAViewer [ 1 ]  is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a  genome wide association study  (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.


WGAViewer currently offers several classes of annotation of the GWAS results:


(1) Overview of WGA results allowing


(2) Genic annotation of WGA results with explicit reference to:


(3)  Annotation for SNPs :


(4) Gene/SNP finding :
locating and annotating specific genes, SNPs, or LD proxies for SNPs, and aligning the results with the latest genome build.


(5) Evidence from multiple scans.


(6) Supporting/QC databases:
displaying supporting information, for example, HWE P values, effect size, effect direction, QC scores, or other user-customized data.


WGAViewer is developed on the  Java platform .


WGAViewer is developed and maintained by Dr. Dongliang Ge and Dr. David B. Goldstein at Duke University, Institute for Genome Sciences & Policy, Center for Human Genome Variation.


A number of GWAS projects  [1]  used the WGAViewer software tool.


One of these projects leads to the identification of the genetic variant predicting the hepatitis C treatment-induced viral clearance. The finding from that project, originally reported in Nature, [ 5 ]  showed that genotype 1 hepatitis C patients carrying certain genetic variant alleles near the IL28B gene are more possibly to achieve sustained virological response after the treatment of  Pegylated interferon-alpha-2a  or  Pegylated interferon-alpha-2b  (brand names Pegasys or PEG-Intron) combined with  ribavirin .  A later report from Nature  [ 6 ]  demonstrated that the same genetic variants are also associated with the natural clearance of the genotype 1 hepatitis C virus.


I2a1b:  Bosnia and Herzegovina , [ 3 ]


Haplogroup I-M438 , also known as  I2  (ISOGG 2019), is a human  DNA   Y-chromosome   haplogroup , a subclade of  haplogroup I-M170 . Haplogroup I-M438 originated some time around 26,000–31,000 BCE. It originated in Europe and developed into several main subgroups: I2-M438*, I2a-L460, I2b-L415 and I2c-L596. [ 2 ]  The haplogroup can be found all over Europe and reaches its maximum frequency in the  Dinaric Alps  ( Balkans ) via  founder effect , related to the migrations of the  Early Slavs  to the Balkan peninsula.


The oldest example so far found is that of  Hohle Fels (49)  from  Germany , being at least 14,200 years old. [ 4 ]


Haplogroup I2a was the most frequent Y-DNA among  Mesolithic   Western European hunter-gatherers  (WHG) belonging to Villabruna Cluster. A 2015 study found haplogroup I2a in 13,500 year old remains from the  Azilian  culture (from  Grotte du Bichon , modern  Switzerland ). [ 5 ]  Subclades of I2a1 (I-P37.2), namely I-M423 and I-M26, have been found in remains of WHGs dating from 10,000 to 8,000 years  before present . [ 6 ]


In a 2015 study published in  Nature , the remains of six individuals from  Motala  ascribed to the  Kongemose culture  were successfully analyzed. With regards to  Y-DNA , two individuals were ascribed to  haplogroup I2a1b , one individual was ascribed to  haplogroup I2a1 , and one individual was ascribed to haplogroup I2c. [ 7 ]


The  I-P37.2+  (also known as  I2a1a ) (ISOGG 2019). The subclade divergence for I-P37.2 occurred 10.7±4.8 kya. The age of YSTR variation for the P37.2 subclade is 8.0±4.0 kya. [ 2 ]  It is the predominant version of I2 in Eastern Europe. [ 8 ]  The I2a is further made up by subgroups I-M26, I-M423, I-L1286, I-L880.


Haplogroup  I-M26  (or  M26 )   I2a1a1a  (ISOGG 2019).


Haplogroup I-L158 (L158, L159.1/S169.1, M26) accounts for approximately 40% of all  patrilines  among  Sardinians . [ 9 ] [ 10 ]  It is also found at low to moderate frequency among populations of the  Pyrenees  (9.5% in Bortzerriak, Navarra; 9.7% in Chazetania, Aragon; 8% in Val d'Aran, Catalunya; 2.9% in Alt Urgell, Catalunya; and 8.1% in Baixa Cerdanya, Catalunya) and  Iberia , and it has been found in 1.6% of a sample of  Albanians  living in the  Republic of North Macedonia [ 11 ]  and 1.2% (3/257) of a sample of  Czechs . [ 12 ]  The age of YSTR variation for the M26 subclade has been calculated as 8.0±4.0 kya. [ 2 ]


I-L178 is very rare, but has been found in two persons from Germany and one from Poland. The age of YSTR variation for the M423 subclade is 8.8±3.6 kya. [ 1 ]


I2a1a2b-L621 is typical of the  Slavic  populations, being highest in  Southeastern European  regions of  Bosnia-Herzegovina  and  South Croatia  (>45%), [ 3 ] [ 13 ] [ 14 ]  in  Croats  (37.7-69.8%),  Bosniaks  (43.53-52.17%), and  Serbs  (36.6-42%)—often called "Dinaric". [ 15 ]  It has the highest variance and concentration in  Eastern Europe  (i.e.,  Ukraine ,  Southeastern Poland ,  Belarus ). [ 16 ]  According to YFull YTree it formed 11,400  YBP  and had  TMRCA  6,500  YBP , while its main subclades lineage is I-CTS10936 (6,500-5,600 YBP) > I-S19848 (5,600 YBP) > I-CTS4002 (5,600-5,100 YBP) > I-CTS10228 (5,100-3,400 YBP) > I-Y3120 (3,400-2,100 YBP) > I-Y18331 (2,100 YBP)  / I-Z17855 (2,100-1650 YBP) / I-Y4460 (2,100 YBP) / I-S17250 (2,100-1,850 YBP) > I-PH908 (1,850-1,700 YBP). [ 17 ]


Older research considered that the high frequency of this subclade in the  South Slavic -speaking populations to be the result of "pre-Slavic"  paleolithic  settlement in the region. Peričić  et al.  (2005) for instance placed its expansion to have occurred "not earlier than the  YD  to  Holocene  transition and not later than the early  Neolithic ". [ 2 ] [ 3 ] [ 18 ] [ 19 ]  However, the prehistoric  autochthonous  origin of the haplogroup I2 in the Balkans is now considered as outdated, [ nb 1 ]  as already Battaglia  et al.  (2009) observed highest variance of the haplogroup in  Ukraine , and Zupan  et al.  (2013) noted that it suggests it arrived with  Slavic migration  from the homeland which was in present-day Ukraine. [ 24 ]  O.M. Utevska (2017), in her PhD thesis, despite being a part of research team who came to a different conclusion in 2015, [ 25 ]  proposed that the haplogroup STR  haplotypes  have the highest diversity in Ukraine, with ancestral STR marker result "DYS448=20" comprising " Dnieper - Carpathian " cluster, while younger derived result "DYS448=19" comprising the "Balkan cluster" which is predominant among the South Slavs. [ 16 ]  According to her, this "Balkan cluster" also has the highest variance in Ukraine, which indicates that the very high frequency in the Western Balkan is probably because of a  founder effect . [ 16 ]  Utevska calculated that the STR cluster divergence and its secondary expansion from the middle reaches of the Dnieper river or from  Eastern Carpathians  towards the Balkan peninsula happened approximately 2,860 ± 730 years ago, relating it to the times before Slavs, but much after the decline of the  Cucuteni–Trypillia culture . [ 16 ]  However, STR-based calculations give overestimated dates, [ 26 ] [ 27 ]  and more specifically, the "Balkan cluster" is represented by a single SNP, I-PH908, known as I2a1a2b1a1a1c in  ISOGG  phylogenetic tree (2019), and according to YFull YTree it formed and had TMRCA approximately 1,850-1,700 YBP (2nd-3rd century AD). [ 17 ]


It is considered that I-L621 could have been present in the Cucuteni–Trypillia culture, [ 28 ]  but until now was mainly found  G2a  and non-I2-L621 clades, [ 29 ] [ 30 ]  and another clade I2a1a1-CTS595 was present in the  Baden culture  of the  Chalcolithic  Carpathian Basin. [ 28 ] [ 31 ] [ 32 ]  Although it is dominant among the modern Slavic peoples on the territory of the former Balkan provinces of the  Roman Empire , until now it was not found among the samples from the Roman period and is almost absent in contemporary population of  Italy . [ 15 ]  According to Pamjav  et al.  (2019) and Fóthi  et al.  (2020), the distribution of ancestral subclades like of I-CTS10228 among contemporary carriers indicates a rapid expansion from Southeastern  Poland , is mainly related to the Slavs and their medieval migration, and the "largest demographic explosion occurred in the Balkans". [ 15 ] [ 33 ]  According to a 2023 archaeogenetic study, I2a-L621 is absent in the antiquity and appears only since the Early Middle Ages "always associated with Eastern European related ancestry in the autosomal genome, which supports that these lineages were introduced in the Balkans by Eastern European migrants during the Early Medieval period." [ 34 ]


Some of the earliest archeogenetic samples until now is  Sungir 6  (~900 YBP) near  Vladimir, Russia  which belonged to the I-S17250 > I-Y5596 > I-Z16971 > I-Y5595 > I-A16681 subclade, [ 35 ] [ 36 ]  as well I-CTS10228 and I-Y3120 subclades found in two  Vikings  from Sweden (VK53) and Ukraine (VK542) with predominantly Slavic ancestry of which the second belongs to  Gleb Svyatoslavich  (11th century). [ 37 ]  It was also found in the skeletal remains of  Hungarian conquerors  of the  Carpathian Basin  from the 9th century, part of Western Eurasian-Slavic component of the Hungarians. [ 15 ] [ 28 ] [ 38 ]


Haplogroup  I-M223 aka I2a1b1 (ISOGG 2019), formerly I2a2a (ISOGG 2014). The age of YSTR variation for the I-M223  subclade  has been variously estimated as 13.2±2.7 kya, [ 2 ]  12.3±3.1 kya., [ 1 ]  14.6 kya [ 39 ]  and 14.6±3.8 kya (Rootsi 2004). I-M223 has a peak in Germany and another in the northeast of Sweden, but also appears in  Romania / Moldova , Russia, Greece, Italy and around the Black Sea. [ 40 ]  Haplogroup I-M223 has been found in over 4% of the population only in  Germany , the  Netherlands ,  Belgium ,  Denmark ,  Scotland , and  England  (excluding  Cornwall ) – also the southern tips of  Sweden  and  Norway  in Northwest Europe; the provinces of  Normandy ,  Maine ,  Anjou , and  Perche  in northwestern  France ; the province of  Provence  in southeastern France; the regions of  Tuscany ,  Umbria , and  Latium  in  Italy ;  Moldavia  and the area around Russia's  Ryazan Oblast  and  Mordovia  in Eastern Europe. Of historical note, both haplogroups I-M253 and I-M223 appear at a low frequency in the historical regions of  Bithynia  and  Galatia  in  Turkey . Haplogroup I-M223 also occurs among approximately 1% of  Sardinians .


Haplogroup I2a1b1a1a (ISOGG 2019) or I-M284, has been found almost exclusively amongst the populations of the  United Kingdom  and  Ireland  suggesting that it may have arisen amongst the  Ancient Britons , with a  most recent common ancestor  (MRCA) who lived about 3,100 years  BP . [ 41 ]   The presence of this subclade "provides some tentative evidence of ancient flow with eastern areas that could support the idea that the [late Celtic]  La Tene culture  was accompanied by some migration." [ 42 ]


Where it is found in those of predominately Irish descent, with  Gaelic  surnames, it may suggest an ancestor who arrived in Ireland during prehistory, from Celtic Britain. [ 42 ]  For example, I-M284 includes many males with the surnames McGuinness and McCartan, who have a single, historically recorded male ancestor in the 6th century; thus it is unlikely to be the result of subsequent migration from Britain to Ireland. [ 42 ]  Some subclades of I-M284 that are atypical of Ireland are relatively common in continental Europe, [ 42 ]  which also supports a point of origin east of Ireland.


Continentals. Mother Haplogroup for group I-Z161 (Continental 1 and 2) and I-L701 group (Continental 3). Around 10.000 years old.


Haplogroup I2a1b1a2b (ISOGG 2019). Z161+ defines the I2 Continental clade 1 and 2. Its age is estimated around 7,000 years old. It is mainly found in North Europe, especially in Denmark, Germany, the Netherlands, and England. In Northwest Sicily it can also be found; this is believed to be due to remnants of a Norman settlement.


Called Continental 3. Continental 3 has a wide distribution. Found in Central Europe from Germany, Austria to Poland, Romania and Ukraine, but also in lower frequencies in Greece, Italy, France, Spain, England, Ireland, and Armenia. It may have been disseminated in part by the  Goths . It is nearly absent from Scandinavia and Scotland.


Up-to-date phylogenetic trees listing subclades of I can be found at  Y-Full  and  FamilyTreeDNA