An Online Introduction to the Biology of Animals and Plants


Key Concepts


Section 1

Chapter 6





In keeping with the concept that people of earlier ages were not stupid, it was long understood that most reproduction produced offspring that somehow were a combination of the traits of the parents.  If you bred individuals with some common trait together, you increased the chance that such a trait would be prominent in the offspring, but it didn't always work that way.  You could make plant cuttings and pretty much get a duplicate plant, traitwise, but pollination produced the same sort of mixtures that animal reproduction gave.  How did it work?  Were there hidden rules that could be discovered and applied to make results more predictable?

Gregor Mendel was fascinated with science and Nature, but in order to continue his education beyond a certain point, he had to enter a monastery in what was then Austria (now Brno of the Czech Republic).  In a classic example of using the materials at hand, Mendel took advantage of the monastery's production of peas:  for years he bred peas in special separate plots, focusing on a few one-or-the-other features (such as Tall / Short, or Wrinkly Pea / Smooth Pea) that he could isolate in a "pure" form.  After hundreds of tests, with new plots of hybrid plants and plots of hybrid-hybrid crosses, Mendel developed the first basic rules of what would come to be called genetics.

decided that traits were determined by some sort of internal codes which he called genes.  For any particular trait, there might be code variations that changed the nature, like leaf color, or degree of the trait, such as one variation in the Height gene for Tall and one for Short.  These variations he called alleles, which he determined to be carried in each individual in pairs (although there may be way more than two allele variations in a population, each individual just carries two), of which only one is passed on to offspring from each parent.  For each trait that is determined by a single gene (many traits are produced from multiple genes working together), an individual's particular version of that trait is a product of their two alleles.  Mendel thought that every single allele pair was sorted separately for reproduction, which turned out later to not be true, but many of them do sort separately.

As a
side effect of Mendel's choice of pea traits, he also discovered a genetic feature called dominance, where the presence of a dominant allele can completely hide the presence of a recessive allele.  This either-or condition was necessary to his working out genetic rules, but it has since been found (and he probably realized) that many traits don't follow such an extreme pattern.  Many allele effects are not that strong or weak, but rather blend to produce the trait.  (In human eye color, very dark alleles can be dominant over very light alleles - brown can dominate blue - but middle-strength alleles blend, such as when green and light brown produce hazel).  It also turns out that many traits, in fact most traits, are a product of at least two genes working together, two alleles per gene;  these multiple-gene traits do follow rules based upon Mendel's discoveries, but the complex mixing of many alleles makes predictions of offspring traits a matter of probabilities.  With all that we know of genetics, breeding racehorses is still a matter of mating parents with desired traits and hoping everything mixes properly in the offspring, which is what breeders were doing before Mendel was born.

Mendel wrote and published several papers on his discoveries, but no one in the scientific community seemed to notice.  When he died, as far as he knew his research and findings would make no difference to the world.  However, in the very early 1900's, three scientists investigating the same sorts of processes discovered Mendel's papers, and his rules became the foundation of a basic building block of biology today.

We know quite a bit more about genes today.  The researchers who followed up on Mendel's work through the 20th century discovered some additional details:

of genes are linked together.
  It turns out that our cells do not carry thousands of separate codes floating about;   genes are bound together along the lengths of chromosomes.  This is called linkage:  for example, genes that are found on sex chromosomes exhibit sex linkage (not because they have anything to do particularly with sex, but because they are on "sex-determining" chromosomes).  One feature of any species is its characteristic chromosome number, usually an even number in sexually-reproducing species because of the pairs  (humans have a chromosome number of 46, 23 pairs).  There are advantages and disadvantages to both low and high chromosome numbers:  with low numbers, the distribution of copies that must happen whenever new cells are made is easier - there are fewer chromosomes and chromosome copies to control;  but with higher numbers, the sorting of various allele combinations goes up, increasing potential variability in offspring, which increases evolutionary flexibility.  The numbers among species vary widely, including some protists and plants with amazingly high numbers.

One weakness
of Darwin's original theory of evolution is that it could not explain where "new" (really, old but dramatically changed) features came from - natural variations couldnt really explain how snake venom evolved from saliva, for instance.  But many years later, mutations were discovered:  spontaneous changes in genetic material, producing new alleles that usually have no altering effect on the coded trait, or a bad effect if an effect exists, but occasionally might produce a useful change.  And a particular type of mutation, called genetic redundancy (which is actually one of two types of genetic redundancy), could duplicate genes, allowing the mutational change of an existing trait (say, snake saliva to venom through changes of the "extra" saliva gene) while preserving the original action (not losing the original saliva).  This might also explain why more "advanced" organisms seemed to have more genes than more "primitive" ones.

, it was discovered what exactly a gene is:  a stretch of the molecule DNA that contains a sequence that can be used to produce particular proteins.  Cells then use those proteins to create the "traits" that Mendel connected to genes.  His Height gene, for instance, codes for a type of plant growth hormone.  Alleles produce proteins that have  molecular differences, sometimes slight, sometimes major, often changing how things work, and how the trait looks.

Since Mendel
, it has been discovered that in some circumstances having two different alleles can be better than a pair of either variant, a condition called hybrid vigor.  This often is the reason that human genetic diseases have spread through a population.  For example, the gene for the oxygen carrier hemoglobin has a allele that makes a nonround version of the protein;  if you get a pair of these alleles, it gives you sickle-cell anemia, a dangerous disease that impairs circulation.  In areas where malaria, a disease caused by a blood parasite, is common, people carrying one regular hemoglobin allele and one sickle-cell allele have more resistance to malaria than those with two regular alleles, giving them an advantage that passes sickle-cell alleles to their offspring.  Other genetic diseases may have similar effects:  cystic fibrosis alleles might make single-carriers resistant to diarrhetic diseases (which kill huge numbers across the world), Tay-Sachs seems to produce a tuberculosis resistance, and schizophrenia (which is a multiple-gene trait and harder to sort out) may in some combinations increase creativity and the willingness to take risks.




Warning:  prepare to abandon your preconceived notions about reproduction!!!

There are two basic forms of reproduction in living things, asexual reproduction and sexual reproduction.

ASEXUAL REPRODUCTION.   If you're thinking this means "reproduction without intercourse," now's a good time to lose that idea - most sexually-reproducing organisms do it without intercourse.  No, "doing it" is not any part of the definitions here.  In asexual reproduction, offspring are genetic copies of the original. They may or may not be physical copies - all of your cells, produced asexually, have the same genetic make-up, but they are not physically identical (you'd be a formless blob if they were).  This ability to exactly pass on a parent's genes to offspring is a huge evolutionary advantage - it's the only form of reproduction that really is reproduction.  But there is a problem:  evolution, adapting to changing environments, depends upon variation, and there just isn't as much with this approach.  A change in environment that hurts one individual would be damaging to all.  To survive the course of time, asexual reproducers typically produce huge numbers of offspring.  This allows variation from mutation (which rarely is good, but if you make a trillion offspring your odds get better) and often spreads offspring out so any local changes will miss some.  This need to generate on a large scale usually keeps such reproducers small, also.  Some have also survived in those rare, extremely stable ecosystems.

SEXUAL REPRODUCTION.  No, it does not require two parents;  many many sexual reproducers can accomplish it with just one that is simultaneously male and female, a condition called monoecious (species with two separate genders are dioecious, but genders are not even required for sexual reproduction - many sexually- reproducing protistans and fungi do not different forms playing different roles).  In sexual reproduction, single sets of chromosomes / alleles from two sources are combined in offspring.  The huge advantage here is the mixing aspect of the allele sets:  potentially, every individual produced is different from every other one, increasing the variation that evolutionary processes need.  This allows evolution to work while only small numbers of offspring are made, a necessity in the making of larger organisms.  The disadvantage, of course, is that copies cannot be made, even of extremely successful individuals.  You can't pass on everything that makes you what you are, or even the best aspects - it's all luck, even if the odds work in your favor as a species.

In general, asexual reproducers are small, often tiny, and capable of producing the huge amounts of offspring needed for meaningful variation.  Sexual reproducers exist across the range of organism sizes (although sexual reproduction in prokaryotes is only a "sort of" sexual reproduction - they swap genes and clusters of genes with each other in those small chromosome-like packets called plasmids), and produce offspring numbers roughly according to their chances of surviving long enough to make offspring on their own.  Some organisms are capable of reproducing either way according to circumstances - one wonders why this option isn't more common - and a few groups of organisms reproduce first asexually, then sexually, then asexually again, and so on, following a pattern called alternation of generations.

Of the three major circumstances under which alternation of generations has evolved, only one seems connected to the evolutionary advantages of being able to produce both ways:  several types of parasites, organisms that live by stealing resources from other, larger organisms, will go through an asexual stage in one host then a sexual phase in another, then back to a host of the first type, etc.  Making copies of a successful form alternates with mixing genes from successful forms, worthwhile for complex life cycles with the odds stacked against them.  The other two circumstances where alternation of generations is common involve life cycles with at least one stage stuck in one place:  in animals, such types as corals asexually produce huge colonies in place, then generate swimming jellyfish-like forms that swim off and mate sexually and help to distribute offspring away from the original site;  in the first land plants, still tied to using open water for sperm to swim during mating, larger asexual reproducers could spread by way of airborne spores, but the sexual reproducing forms stayed small and in places where water accumulated to support sperm.  

This is just a preview - alternation of generations will be discussed again when these groups come back up.




Today, relationships among organisms are often determine by comparative biochemistry, which can be done by looking at three different types of molecules:

- Metabolic molecules.  This is an older approach, originally using analogies.  Snakes might be grouped according to similarities in action of their venoms, for instance.

- Proteins.  These long sequential molecules provide lots of comparison points, a type of comparative anatomy on the molecule level.

DNA.  Also a long sequential molecule, its assumed that close relatives will share similar sequences, but once two groups lose contact, they will accumulate different mutations at a predictable rate.  Differences in DNA sequences are used like molecular clocks to decide how far back in time two organisms shared an ancestor.  Mutational changes in the sequences are considered the "ticks" of the clock.




It was soon recognized that what really changed in an evolving population was the frequencies at which certain alleles appeared, since they were what produced Darwin's trait variations.  But what might influence how allele frequencies in a whole population (all of the genes in a population are called a gene pool) might change over time?

Godfrey H. Hardy
, an English mathematician, and Wilhelm Weinberg, a German doctor, developed a set of rules under which the allele frequencies in a population would stay the same indefinitely:  this is called Hardy-Weinberg Equilibrium, sometimes the Hardy-Weinberg Law.  It kind of has had a backwards effect on evolutionary theory.  We know that allele frequencies do change as species evolve - this law tells us what factors must be involved...

NO NATURAL SELECTION.  Well, obviously natural selection has an impact on evolution.

NO MATING SELECTION.  (Also, all population  members breed and produce the same number of offspring)  This amount to No Sexual Selection.

of members in or out. 
This would remove alleles from a population or bring in others.  This led to the realization that the more isolated a population is, the more chance that the other evolutionary effects could work, without mixing with alleles from populations adapted to different conditions.  It also became obvious that connections between populations in somewhat different environments might preserve a "type" suited to both but not particularly suited to either.  Something else can happen even groups isolated in similar environments:  genetic drift is made from unique combinations and mutations that change the flow of evolution in the two groups, producing separate species when natural selection seems like it would have kept them the same.

NO MUTATION.  This process actually alters alleles.  Even though the odds for a beneficial mutation are not good, it still can have a profound effect on how a group evolves, and any new allele changes the numbers from what existed before.

In a population of only 100, any lost individual will have a strong effect on the allele make-up, the gene pool, of the group;  the more individuals in the group, the harder it is for chance occurrances to strongly affect the ratios of the gene pool.  This also means that all of the other factors will affect a small group more powerfully than a large one.  Some processes are based upon this principle:

               - The founder effect is used to describe what happens when a small group breaks off from a large population and becomes isolated.  The break-off group's gene pool frequencies probably do not duplicate the larger group's, changing the odds of possible combinations and altering the potential for evolution.

              - The bottleneck effect is made when some catastrophe reduces a population to a much smaller group, which then evolves starting with that restricted gene pool.




Basically, any situation that reproductively isolates one group from another allows them to set up their own separately-evolving gene pool.  It turns out that this can be done in more than the obvious way...

- Geographic isolation.  When groups become physically isolated from one another - one winds up on an island, or separated by a river, mountain range, desert, whatever - this will give you separate breeding populations.

- Niche isolation.  A niche is a functional "spot" or "job," a role in an ecosystem that can be performed by some type of living thing.  Niches are determined by place, time, and relationships.  Most ecosystems have a top predator, for instance, although just what species occupies that niche varies in different places, and in a single place that may change from day to night or season to season.  If a single species begins to break into a day-active group and a night-active group, you have one type of  temporal isolation (time-based);  another type of temporal isolation might be when a group varies its breeding season, but this is not a type of niche isolation.

- Behavioral isolation can arise from many different types of behavior:  groups with different courtship rituals, or which cease to recognize each other as possible partners are examples.

- Mechanical isolation.  In groups that copulate (and many do not), occasionally changes in the physical features of genitals can isolate a group.  There are species of beetle that show this isolation.

- Chemical and Immunological Isolation.  Sometimes a mutational change in chemistry will cause a rejection of sperm or zygote (the first cell of the next generation) so that one group can no longer reproduce with the other.  This may be more common with plants, where mate selection affects pollen compatibility.

These ideas have led to a biology discipline called biogeography, which is concerned with the distribution of living things.  Biogeography has been a huge source of evidence for the theory of evolution by natural selection, by how often features of organisms in an ecosystem reflect the nature of the environment.





You have inherited features that are not in your genes - a particular language and culture, a particular community and physical location, things that came to you both from parents and from others.  These can be passed down through generations, but are not passed as packets of DNA;  factors such as these were called epigenetic factors.  Today, this term is used mostly for ways that DNA may be modified without changing the actual codes (kind of reversible "clip-on" molecules) during a generation and sometimes get passed on in that modified form, affecting how easily those genes can be accessed.

An offspring can be affected by the chemicals and organelles passed in the sperm and egg cells.  Effects can also be passed along through such factors as learning, physical placement in territory, and other things that work outside-in.  Organisms that reproduce asexually by physically dividing will pass on bits and pieces of themselves directly to offspring.  This is, in a way, the inheritance that Lamarck's theories were based upon.

An entire
subdiscipline, memetics, has grown up around this idea, with memes being the external equivalent of genes.  Whether such inheritance can really be described in classic evolutionary terms is a bit controversial still.




Click on term to go to it in the text.
Terms are in the order they appear.


Gregor Mendel (mid to late 1800s)
Dominant / Recessive Alleles
Multiple-gene traits
Chromosome number
Genetic redundancy
Gene - Modern definition
Hybrid vigor
Asexual vs Sexual Reproduction

Alternation of Generations
Reproduction types and evolution
Comparative biochemistry
Molecular clocks
Hardy-Weinberg Law
Evolution & Isolation
Genetic Drift
Gene Pool
Evolution and chance
Founder Effect
Bottleneck Effect
Isolation Types
Epigenetic Factors





Online Introduction to the Biology of Animals and Plants.

Copyright 2001-2022, Michael McDarbyContact.

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