T-61.186 Special course in language technology
September 22

Lecture notes: Evolution basics

What evolution is
"A natural phenomenon where the form and behaviour of organisms have changed and continue to change so that offspring is different from the parent organisms." (Vocabulary of Biology)
"Maintenance (or improvement) of adaptedness and the origin of diversity." (Ernst Mayr)

Some basic concepts

Genotype: The active genetic heritage of an individual.
Phenotype: The final product, the result of interaction between the genotype and the environment. A single genotype can end up producing very different phenotypes in different environments.
Ontogeny: The development of an individual from embryo to adult .
Phylogeny: The development of species.
Alleles: The different forms of a single gene. E.g. the gene responsible for eye colour has two main alleles, one for blue and the other for brown eyes.

Definition of evolution

Necessary and sufficient conditions:
1) variation
2) heritability
3) natural selection

"Variation proposes and selection disposes." (Stephen Jay Gould)

Variation
Main sources of variation:
	a) recombinations
	b) mutations

Recombination is responsible for most of the genetic variation in nature. Main types:
a) Sexual recombination: Long thought to be random, but evidence of directional components has been found; for instance, meiotic drive may distort the randomness of which chromosomes prevail.
b) Crossing-over: homological (one from each parent) chromosomes exchange parts

New genes are formed only by mutation. Mutations are due to errors in DNA replication. The replacement of a base pair by a different one is called a gene mutation. Polyploidy (additional replication of a chromosome) and changes in gene arrangement are chromosomal mutations. 

Natural selection
A process of non-random elimination
Two steps:
	1) production of variation
	2) elimination of excess
Not so much the survival of the fittest as the elimination of the least fit.

"Selection of" vs. "selection for" refer to different questions: what is the object of selection (’of’), and what is the entity that benefits from this (’for’). For example, if the individual survives, the whole genotype benefits from this.

Dispute 1: The object of selection
Commonly: the individual
Other possibilities:
	The gene? (Dawkins et al.)
	The social group?
	The species?

Dawkins's formulation of the selfishness of genes has been very influential, especially among non-specialists. Ernst Mayr has criticized the view on the grounds that the genes in the genotype of an individual interact in complicated ways, making the fitness contribution of individual genes variable.  Instances of such interactions include e.g. the following:

Pleiotropy: a single gene affects simultaneously several aspects of the phenotype.
Polygenic inheritance: a single aspect of the phenotype is simultanously affected by several genes.
Regulatory genes: there are genes that regulate the impact of other genes, for example hox & pax genes (pax 6 gene has been found to contribute to the formation of eyes in all phylogenetic lineages where eyes have developed).
Directly variable fitness contributions:  The sickle cell gene protects from malaria in heterotsygotic individuals (only one instance of the gene is present in homologous chromosomes) but is sooner or later lethal in homotsygotic individuals. 

Group selection: Group selection can be considered to take place if the group's fitness is greater than the fitness average of its members. E.g. a group of ground squirrels benefits from good sentinels.

Species selection: Sometimes two species compete from the same resources and the other may eradicate the other; however, the actual competition is between individuals of both species. Species are usually not considered to count as objects of selection.

Fitness (1/2)
The relative ability of an individual or a genotype to have reproductive offspring, consisting of
	The ability to survive till reproductive age.
	Reproductive capacity.
	Fertility of offspring .
All differences in the phenotype of an individual that have an effect on fitness lead to selection, but only those with a heritable genetic origin will have an effect on the genetic frequencies of the population.

Adaptation: any feature of an individual that adds to its fitness. Not all features of an individul are adaptations; some have no effect on selection; others originated as byproducts of other adaptations.

Lamarckism: A long-abandoned theory, according to which acquired characteristics are inherited. The theory was used to explain e.g. why giraffes had long necks: it was a result of many generations of giraffes stretching their necks a little bit when trying to reach higher leaves.

Fitness (2/2)
Chance is ever present: a fine phenotype may not protect an individual if the whole planet is devoured by a black hole.

Haldane’s classical calculations (1927): a variant that produces 1% more offspring than its competitors will increase its frequency in the population from 0.1% to 99.9% in a span of 4000 generations. This observation underscores the potential of small incremental changes.

Factors that limit the effectiveness of selection

Evolution is limited by historical constraints: a single gene mutation cannot change the phenotype to something completely different. E.g. the offspring of a Homo sapiens cannot acquire fully functional wings within one generation.

Adaptations are often compromises between conflicting selection pressures: agility may come together with fragility, and strength with clumsiness.

Not all evolution is adaptive: a storm may blow a group of insects to an island, but nothing guarantees that the wind chooses the insects that are best adapted to the new environment.

Selection can only act on existing variation: variation doesn't function on-demand; if a suitable phenotype doesn't exist, natural selection cannot select it.

Dispute 2: Gradualism vs. saltationism

Gradualism: Gradual accumulation of small adaptive changes. The prevailing view among today's evolutionists.
Saltationism: Sudden emergence of major structural innovations, divided by periods when no changes occur. Also known as the theory of punctuated equilibria. Philosophically akin to essentialism, the belief that the variety of nature may be divided into a limited number of basic types that have more or less sharp distinctions. In other words, an essentialist believes that species and types "exist" in the same way as individuals. Some claim that humans have a language organ that is the result of a major (macro)mutation.

Levels of evolution

Microevolution: The change of gene frequencies in a population, the basic evolutionary step.
Macroevolution: The formation of new species. Usually takes place via isolation. The practical definition of species is that different species do not interbreed, although successfull breeding between any individuals of the same species is also stochastic.

What evolution is not

Evolution is not directed towards a goal: no designer behind everything.
Evolution is not progress towards perfection. There's no independent way of determining what is perfect.
Evolution is not development towards greater complexity: In some niches, complexity increases, in others, it decreases, in yet others, it remains more or less constant.

Other basic concepts

Exaptation: A structure that has originally developed to perform some function takes on a new one. Some think that the language ability of Homo sapiens is an exaptation of some other cognitive capabilities. Most evolutionary novelties are modified versions of older structures.

Spandrel: a byproduct of some other structure(s). A spandrel is called an exaptation if it has received an adaptive function. 

Genetic drift: A stochastic process whereby some alleles may be lost due to errors in sampling. In large populations genetic drift is quickly remedied, but in smaller founder populations it may lead to an unbalanced sampling of the parental population and, eventually, to a restructuring of the genotype of the population.

Coevolution: The parallel evolution of two or more species that are interdependent, or where at least one is dependent on the other and where a change in one will lead to an adaptive response in the other. For example, flowering plants and their pollinators (say, bees) coevolve, and so do predators and their prey. Coevolution of language and the brain is frequently used to explain certain phenomena in language evolution.

Cultural evolution
The evolution of ideas/concepts, termed "memes" by Richard Dawkins. Much more rapid than genetic evolution. Language is one of the carriers of memes. In language evolution: Language is also an object of selection (Deacon, Kirby). Language differentiation as an equivalent to speciation?

Language and evolution

Some competing paradigms regarding the evolutionary origins of language:
1) Gradualist explanations vs. exaptations vs. macromutations 
2) Genetic adaptations vs. cultural adaptations vs. combinations of both (e.g. coevolution)

Sept 28
kanto@james.hut.fi