Post Published » 07 Jan 2016, 20:55, recent changes » 15 Jan 2016, 03:14

Explanations and a brief glossary


Abstraction — (lat. abstractio) in its main sense is a conceptual process by which general rules and concepts are derived from the usage and classification of specific examples, literal ("real" or "concrete") signifiers, first principles, or other methods. "An abstraction" is the product of this process—a concept that acts as a super-categorical noun for all subordinate concepts, and connects any related concepts as a group, field, or category.

Affirmation — in logic, the union of the subject and predicate of a proposition.

A.D. — Anno Domini (in the year of our Lord).

AMOVA - Analysis of molecular variation [Excoffier 1992].

Analogy — (from Greek ἀναλογία, analogia, "proportion") is a cognitive process of transferring information or meaning from a particular subject (the analogue or source) to another (the target), or a linguistic expression corresponding to such a process. In a narrower sense, analogy is an inference or an argument from one particular to another particular, as opposed to deduction, induction, and abduction, where at least one of the premises or the conclusion is general. The word analogy can also refer to the relation between the source and the target themselves, which is often, though not necessarily, a similarity, as in the biological notion of analogy

Antinomy — (Greek ἀντί, antí, "against, in opposition to," and νόμος, nómos, "law") literally means the mutual incompatibility, real or apparent, of two laws. It is a term used in logic and epistemology, particularly in the philosophy of Kant and Roberto Unger.

Argument — in logic and philosophy, an argument is a series of statements typically used to persuade someone of something or to present reasons for accepting a conclusion. The general form of an argument in a natural language is that of premises (typically in the form of propositions, statements or sentences) in support of a claim: the conclusion. The structure of some arguments can also be set out in a formal language, and formally defined "arguments" can be made independently of natural language arguments, as in math, logic, and computer science.

A.H. — After Hijra. The Hijri year or era is the era used in the Islamic lunar calendar, beginning its count from 622 ce, the year of the migration of Muhammad and his followers from Mecca to Yathrib (later Medina), an event known as the Hijra.

Axiom — Aas defined in classic philosophy, is a statement (in mathematics often shown in symbolic form) that is so evident or well-established, that it is accepted without controversy or question.


Bayesian probability — is one interpretation of the concept of probability. In contrast to interpreting probability as frequency or propensity of some phenomenon, Bayesian probability is a quantity that we assign to represent a state of knowledge, or a state of belief. In the Bayesian view, a probability is assigned to a hypothesis, whereas under frequentist inference, a hypothesis is typically tested without being assigned a probability.

B.C. — Before Christ.

B.C.E. — Before the Common Era.

B.P. — Before Present.


C.E. — Common Era.

Concept — is an abstraction or generalization from experience or the result of a transformation of existing ideas.


Deductive reasoning — also deductive logic, logical deduction or, informally, "top-down" logic, is the process of reasoning from one or more statements (premises) to reach a logically certain conclusion. It differs from inductive reasoning or abductive reasoning. Deductive reasoning links premises with conclusions. If all premises are true, the terms are clear, and the rules of deductive logic are followed, then the conclusion reached is necessarily true.

Definition — is a statement of the meaning of a term (a word, phrase, or other set of symbols). Definitions can be classified into two large categories, intensional definitions (which try to give the essence of a term) and extensional definitions (which list every single object that a term describes).

DNA — deoxyribonucleic acid is a molecule that carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses. DNA is a nucleic acid; alongside proteins and carbohydrates, nucleic acids compose the three major macromolecules essential for all known forms of life. Read more.


Fact — is something that has really occurred or is actually the case. The usual test for a statement of fact is verifiability—that is, whether it can be demonstrated to correspond to experience. Standard reference works are often used to check facts. Scientific facts are verified by repeatable careful observation or measurement (by experiments or other means).


Generalization — is a concept in the inductive sense of that word, or an extension of the concept to less-specific criteria. Generalizations posit the existence of a domain or set of elements, as well as one or more common characteristics shared by those elements (thus creating a conceptual model). As such, they are the essential basis of all valid deductive inferences.


Haplotype diversity — haplotype diversity calculated by the formula:

  where 'n' - the number of copies of the gene, 'k' - the number of haplotypes
  и 'Pi' - Haplotype frequency of the type 'i' in the sample.

Haplotype variances - a dispersion of haplotypes.

Hypothesis - a hypothesis (plural hypotheses) is a proposed explanation for a phenomenon. For a hypothesis to be a scientific hypothesis, the scientific method requires that one can test it. Scientists generally base scientific hypotheses on previous observations that cannot satisfactorily be explained with the available scientific theories. Even though the words "hypothesis" and "theory" are often used synonymously, a scientific hypothesis is not the same as a scientific theory. A working hypothesis is a provisionally accepted hypothesis proposed for further research.


Law — universal principles that describe the fundamental nature of something.

LCA — Last common ancestor.

Logic — (from the Ancient Greek: λογική, logike) is the branch of philosophy concerned with the use and study of valid reasoning.


Median haplotype — an averaged haplotype. The standard deviation of the number of repeats among all the chromosomes of the sample and the founder haplotype.

Microsatellite variances - dispersion of short tandem repeats (microsatellites), calculated according to the formula by Kayser 1997.

Modal haplotype (Founder haplotype) — ancestral haplotype of groups of samples, the founder haplotype.

MRCA (TMRCA) — Most recent common ancestor (Time to a MRCA).


Objection — in informal logic an objection (also called expostulation or refutation), is a reason arguing against a premise, lemma, or main contention. An objection to an objection is known as a rebuttal.

Occam's razor — is a problem-solving principle attributed to William of Ockham (c. 1287–1347). The principle can be interpreted as: Among competing hypotheses, the one with the fewest assumptions should be selected.


Paradigm — in science and epistemology, is a distinct concept or thought pattern.

Paradox — is a statement that apparently contradicts itself and yet might be true (or wrong at the same time). Some logical paradoxes are known to be invalid arguments but are still valuable in promoting critical thinking.

Presumption — an assumption taken as a probable.

Proof — a proof is sufficient evidence or an argument for the truth of a proposition. The concept is applied in a variety of disciplines, with both the nature of the evidence or justification and the criteria for sufficiency being area-dependent. In the area of oral and written communication such as conversation, dialog, rhetoric, etc., a proof is a persuasive perlocutionary speech act, which demonstrates the truth of a proposition. In any area of mathematics defined by its assumptions or axioms, a proof is an argument establishing a theorem of that area via accepted rules of inference starting from those axioms and other previously established theorems. The subject of logic, in particular proof theory, formalizes and studies the notion of formal proof. In the areas of epistemology and theology, the notion of justification plays approximately the role of proof, while in jurisprudence the corresponding term is evidence, with burden of proof as a concept common to both philosophy and law.

Proposition — is used to refer to some or all of the following: the primary bearers of truth-value, the objects of belief and other "propositional attitudes" (i.e., what is believed, doubted, etc.), the referents of that-clauses and the meanings of declarative sentences.


Semantics — (from Ancient Greek: σημαντικόςsēmantikós, "significant") is the study of meaning. It focuses on the relation between signifiers, like words, phrases, signs, and symbols, and what they stand for; their denotation.

S.E. — Standard Error.

Sophism — is a method of teaching. In ancient Greece, sophists were a category of teachers who specialized in using the techniques of philosophy and rhetoric for the purpose of teaching arete — "excellence" or "virtue" — predominantly to young statesmen and nobility.

Syllogism — (Greek: συλλογισμόςsyllogismos, "conclusion, inference") is a kind of logical argument that applies deductive reasoning to arrive at a conclusion based on two or more propositions that are asserted or assumed to be true.


Tautology — in logic, a tautology (from the Greek word ταυτολογία) is a formula that is true in every possible interpretation.

Td (Tc) - Coalescent time.

Truth — is a concept most often used to mean in accord with fact or reality, or fidelity to an original or to a standard or ideal.

Theorem — is a statement that has been proven on the basis of previously established statements, such as other theorems—and generally accepted statements, such as axioms.

Theory — is a contemplative and rational type of abstract or generalizing thinking, or the results of such thinking.


π - Nucleotide diversity [Nei 1981, Holsinger 1996].


The general concepts of DNA genealogy

A Dictionary of Genetics, 7-th ed., King 2006