Linked Inheritance

THOMAS HUNT MORGAN and his work

T.H. Morgan studied fruit flies (muslica).  One day, in 1910, he came across male fruit flies that had white eyes.   They were mutants among the red-eyed wildtypes.

He then bred the white-eyed males with red-eyed females and all of the offspring had red eyes.

The F2 progeny though, contained males with white eyes.

From this, Morgan concluded that in some way eye colour was associated with the gender of the animal and that this association was because the gene that determined eye colour was on the same chromosome that determined the gender (or sex) of the animal.


What are sex chromosomes?

In animals, sex chromosomes define the animal's sex and are an unmatched chromosome pair.
In most animals:
XX is female
XY is male
But there are some animals among the butterflies, birds, snakes and fish in which:
WZ is female
WW is male

So, in animals with XX, XY sex chromosomes, the female carries a matched pair of chromosomes (therefore two alleles for each gene coded on the X chromosomes) and the male carries an unmatched pair (thus only one allele for each gene coded on the X chromosome - so recessive characteristics for these genes show up more often in males, since there is no pair that might be dominant)

Most sex-linked traits are coded for on the X chromosome, since it is the larger of the two chromosomes, but there are a few characteristics that are coded on the Y.  For example, in mammals, the gene that triggers testis (here) development is found on the Y chromosome (logically enough!!).

Recessive forms of sex-linked traits that are coded on the X chromosome show up more commonly in males, since they only need one allele to express the phenotype, while females require two recessive alleles to express the phenotype.

Some typical human sex-linked (or X-linked) characteristics include a form of haemophilia and red-green colour-blindness.  About 8% of males are red-green colour-blind, but only 0.7% of females are.

Going back to fruit flies.....
Morgan observed that some flies had miniature wings and that this also showed sex-linked inheritance, suggesting that the gene for wing size was on the X chromosome.  But he also noticed that having miniature wings and white eyes most often showed up together, but NOT always.  Sometimes the flies had white eyes and mini wings, sometimes they had white eyes and long wings.....
This led him to the idea of Genetic Linkage.

This is the idea that if 2 genes are found on the same chromosome, then the alleles on that chromosome usually sort together in the production of gametes.  Occasionally though, the two alleles sort separately.  Morgan was able to explain this with crossing-over which occurs during meiosis.

So linkage can be observed with the sex of the organism, but it can also be observed between traits found on the same autosomal (not sex) chromosomes.

Morgan observed that certain traits in fruit flies tended to be found together (irrelevant of the sex of the fly).  For example, grey flies tended to have long wings, while black flies tended to have vestigial (csökevényes) wings.  So he assumed that the genes for these two characteristics are on the same chromosome.  If these characteristics are inherited together, he expected the following:

In reality, a 3:1 ratio is not acheived, because total linkage is very rare since crossing over occurs.  So Morgan actually saw four different phenotypes as follows:

Note that the majority of the offspring were like one or the other parent and only a small percentage showed a recombination of the traits.

This recombination was the result of crossing over occuring on the chromosome at a point between the two genes.

Morgan suggested that the likelyhood of crossing over occuring between two genes increases as the distance between two genes increases.

And observing the number of offspring that are like the parents and the number that are not (the recomibinants), a frequency of recombination can be calculated and this can be used to predict distances between genes on a chromosome.

Since Morgan came up with this idea, some time later the English geneticist, J.B.S. Haldane, suggested name the measurement of distance on the chromosome after Morgan.  So today  a 1% frequency of recombination is also called 1 map unit or 1 centiMorgan.

A few more interesting things.....

If you remember back to last year, you may recall learning about Lynn Margulis' Endosymbiotic Theory, about how eukaryotes came to be.  When we discussed it, we said that one of the proofs for her theory was that the mitochondria had its own DNA.  It is called mitochondrial DNA.  It is a small circular DNA, similar to that of prokaryotes.  In most organisms the mitochondrial DNA is inherited solely from the mother.  So mitochondrial DNA can be used to research the maternal line of ancestry of an individual.  (Likewise, since the Y-chromosome is only inherited in males, it can be used to research the paternal line).  

A famous case that was solved using mitochondrial DNA was that of the woman who claimed she was Anastasia Romanov (daughter of Csar Nicholas, who was killed by the Bolsheviks).  In the 1920's a woman appeared in Berlin claiming to be the princess.  The royal families of Europe refused to believe her claim, but she spent her whole life claiming that is who she was.  After her death, researchers used mitochondrial DNA from her hair and compared it with that of Prince Philip (consort to Queen Elizabeth II), who would be Anastasia's closest living relative in her maternal line. It was not a match.

Barr Bodies

In the 1940's some researchers noticed dark staining spots at the edge of the nucleus in female somatic cells, but not in males.  

They concluded that the dark spot was a tightly coiled X chromosome and named it a Barr body.  So in all female cells, one X chromosome has normal appearance and is in its active state, while the other is tightly coiled up and in a resting state.  This is called X inactivation.  The determination of which X chromosome coils and which remains active occurs early in development and seems to be random from cell to cell. 

This is very obvious in calico or tortoiseshell cats.  

A female calico cat

Since one aspect of colouration is an X-linked gene, the situation where the cat is not a solid colour only shows up in heterozygous females, depending on which X became inactive (a Barr body)

Family Pedigrees

Pedigrees, or the creation of family trees, are often used in the genetic research of humans, especially in the research of genetically determined diseases.  They play a particularly important role, as humans have very long generations (approximately 17-22 years) and very few offspring.

Standard symbols are used in the creation of pedigrees so that they can be easily understood.

Pedigrees can indicate if the condition is autosomal or sex-linked and whether it is dominant or recessive.

This pedigree considers attached earlobes (or the recessive phenotype) to be the condition being studied, so the homozygous recessive individuals are the coloured symbols.

A pedigree for an unknown X-linked dominant condition

A pedigree for Y-linked inheritance

The Importance of Genetic Research

Advances in genetics have presented humans with many new possibilities in science, medicine and agriculture.  New research continues to give us new insight  and genetics is a rapidly developing and changing field of study.

The Human Genome Project was begun in October of 1990 and completed in June of 2000.  It resulted in the determination of the nucleotide sequence of the human genome (3 billion nucleotides).  Of course, this information does not mean we know what all of those nucleotides actually code for!!  Work is now being carried out to determine the actual gene sequences, the function (if there is) of sequences that don't code genes and other such work.  Many new possibilities for cures and treatments of different diseases are now on the horizon.  Knowledge of a person's genome will give doctors advanced information about sensitivities to medicines, about tendencies towards certain diseases and the ability to diagnose genetically inherited diseases.  

The work did indicate that humans have about 30-40 000 genes, which is much fewer than previously thought.  Also, it appears that the human genome has several hundred genes that are similar to bacterial genes, but aren't found in other complex species.  From this, it has been concluded that these genes are not the remains of an evolutionary process, but rather than they entered our genome directly from bacteria.  One interesting fact is that the DNA of unrelated humans is 99.9% the same!!

Biotechnology and GMO's (genetically modified organisms) are common words in news articles these days.  GMO's refer to organisms that contain genes that were inserted into their genome by researchers and give those organisms some kind of characteristic that is useful to humans.  Some of the uses of biotechnology are well-accepted and considered harmless, while others create intense public outcry.  

The use of microorganisms that have been genetically modified to produce antibiotics, insulin, vaccines, other medicines and industrial enzymes is widespread and has few opponents, as it is both economical and the modified organisms are contained within the confines of the laboratory or industry.

The use of GMO's is widespread in other areas as well.  In many industries, such as food, textile, paper, chemical and mining industries, GMO's are used to help degrade environmentally damaging wastes, such as oils, plastics, and heavy metals.  Once again, this is an area where their usefulness is mostly accepted.

The use of GMO's in agriculture has received the most criticism.  The most common GMO crops include corn and soy, although others such as rice and potatoes also exist.  

Usually the organisms are given some characteristics that make them more economical for the farmers to produce them.  Perhaps they grow more quickly, have higher nutrient values or are more drought tolerant.  One of the most criticized of the GMO's are Monsanto's Round-up resistant crops.  Round-up is a herbicide that generally kills all plants.  In GMO's that contain a Round-up resistance gene, the crops can be sprayed with Round-up, killing all the weeds that surround the crop plant, but not harming the crop and allowing it to grow without competition.  Of course, this results in better harvests for the farmers and less hassle with weeding.  In this case though, one of the biggest concerns is that people and animals who consume these crops are potentially getting high doses of herbicide in their diet and the effects of the herbicide on humans and animals is not truly known, although there are studies that suggest links with cancer.

Cloning is the production of an individual that is identical to the 'parent'.  In multicellular organisms, this is acheived by inserting the nucleus of a somatic cell from the parent into an ovum that has had its nucleus removed.  Growth of the cell then requires the use of hormones and cell division factors.  

Stem cell research is a very promising area.  Stem cells are cells that can differentiate into many different kinds of cells.  The most perfect stem cell is, of course, the zygote, since it gives rise to the whole organism.  The cells that develop specialize in response to growth factors and contact with other cells.  As they specialize, cells lose the ability to be omnipotent (turn into anything).  Some remain pluripotent (can turn into many types of cells) such as bone marrow (can become different kinds of blood cells), while others can only divide to form an identical cell.  Right now, stem cells taken from umbilical cords at birth seem to be our best and most ethical source of stem cells.

As we learn more and more about the genetics of disease and different conditions, genetic counselling has become increasingly widespread in families where the risk of inheritable conditions is high.  Genetic counsellors help the couple to make decisions about whether or not to attempt a pregnancy, or even end a pregnancy, based on the genetic information that they have available.  While some conditions may be treated in utero (during the pregnancy) through special diets or surgery, most cannot yet.

Epigenetics is a newer area of research within genetics.  It looks at how different factors affect which genes are turned on and which are turned off.  (For a quick verbal explanation, go here.) In other words, why the phenotype is different even though the genotype is the same.  Just think, your skin cells contain exactly the same DNA as your muscle cells, yet they look and behave differently.  This is the result of some genes being active in one type of cell, but not in the other.  Genes can be inactivated if they are bound to methyl groups or non-coding RNA or if the segment of DNA on which they are coded is tightly wrapped around histone proteins.  The activation or inactivation of genes is to a certain extent programmed in the cell, but it is also highly affected by external, environmental cues.  Aging is one of them, but there are many others, from what you eat, to what chemicals you are exposed to, and in some organisms, even the temperature of the air around them has epigenetic effects.  In fact, environmental factors that affected your grandmother while she was pregnant with your mom or dad, may have methylated some of the growing embryo's genes and those methyl groups are still present in your DNA and can affect your development or health!!  Cancer was the first disease to be associated with epigenetics, where changes in methylation can either activate oncogenes (cancer-causing genes) or inactivate tumor suppressor genes.  It has since been found that epigenetics plays a role in autoimmune diseases, as well as a number of neuro/psychological diseases, like autism and schizophrenia.  Just a final comment:  sugar is known to affect methylation and is thought to increase cancer risk, while the opposite is true of broccoli and tumeric....  Just a thought.

The use of genetic information, or perhaps more importantly, its misuse, is an area of much ethical debate, which is the feild of bioethics.  As research and progress continues, humans will be faced with a steady stream of ethical decisions that will need to be broached and slowly, both the law and politicians are tackling these problems.

Genetics Practice Problems

Okay, here are some sites go check out.

This one has some nice explanations and starts easy

More really easy problems

Another site that leads to other sites

And there are some good problems here too

This one has some DNA/RNA questions that deal with last year's material.  I won't ask about it on this test, but a good review

Quick quiz on sex-linked inheritance

Some more sex-linked questions

Linkage and recombination

If you are not clear on linkage and recombination, there is an explanation here

Quick quiz on linkage and recombination

Family pedigree problems

Pedigrees and probabilities

Ecology - biosphere and biomes

Ecology is the study of interrelationships of organisms with each other and the environment.  It deals with the distributions of populations and communities in space and time caused by biotic and abiotic interactions.

The Hierarchy of Life

1.  Biosphere:  it is the Earth.  It contains all the ecosystems (életközösségek)
2.  Biomes:  these are defined by geographical zones and climate
3.  Ecosystems (életközösségek):  these are communities and their physical environments, so the associations of biotic and abiotic factors, linked through the flow of energy and the cycling of materials
4.  Communities (társulások):  populations of all species that live in one area
5.  Populations:  individuals of a species that live in the same area, interbreed with one another
6.  Individuals (egyedek):  single organisms of a given species


1.  Biosphere
This is the whole planet.

Attempts have been made to create artificial biospheres, most successfully Biosphere 2 in the desert outside Tuscon, Arizona.  It now belongs to the University of Arizona, although the initial lock-in experiments were carried out by a research company.  Constructed between 1987 and 1991, it explored the web of interactions withing life systems in a structure containing 5 biome-based areas, an agricultural area and human living and working spaces.  It also explored the use of closed biospheres for space colonization and allowed the study and manipulation of a biosphere without harming the Earth's (source:  Wikipedia).  The first mission ran for 2 years (the humans were locked in), while the second only lasted 6 months (due to company management problems)

Biosphere 2 (source:  Wikipedia)

http://archive.bio.ed.ac.uk/jdeacon/biosphere/biosph.htm

http://discovermagazine.com/2010/oct/20-life-under-the-bubble

http://www.tripadvisor.com/LocationPhotoDirectLink-g31296-d108684-i77149467-Biosphere_2-Oracle_Arizona.html

A theory that is related to the biosphere is called the Gaia theory.  It was created in 1970 by James Lovelock and later co-developed with Lynn Margulis (she also came up with the endosymbiotic theory).  It remains quite criticized, but is nonetheless an interesting idea.  It states that organisms interact with their inorganic surroundings to form a self-regulating complex system that contributes to maintaining the conditions for life on the planet.  Topics of interest include how the biosphere and the evolution of life forms affect the stability of global temperature, ocean salinity, oxygen in the atmosphere and other environmental variables that affect the habitability of Earth.

2.  Biomes

 Biomes are defined by their geographic locations and climate (especially precipition and temperature, but also light, soil, nutrient availability and oxygen).  In general biodiversity (the number and variety of species) is highest in the tropical biomes and lowest in the arctic biomes.  The following map shows a general distribution of terrestrial biomes on the planet.

http://www2.brevard.edu/pfi/BiologicalDiversity1.htm

The combination of temperature and precipitation define where certain biomes will exist.

http://www.learner.org/courses/envsci/unit/text.php?unit=4&secNum=2

http://en.wikipedia.org/wiki/Biome

Some of the major biomes are the following:

a) Tropical rainforest: 2000-5000mm precipitation/yr, average temperature 25C, fast rates of decay and nutrient uptake, poor soil, plants include giant trees with shallow roots and many types of lianas and epiphytes.

http://www.blueplanetbiomes.org/rainforest.htm

http://room42.wikispaces.com/Rainforest+Geography

b) Tropical seasonal (monsoon) forest:  these forests experience a wet and a dry season, trees grow to about 40m, there are more shrubs and fewer epiphytes than in the rainforest

http://www.marietta.edu/~biol/biomes/tropdry.htm

http://mobile.ztopics.com/Monsoon%20forest/

c) Savanna:  also experience wet and dry seasons, greater daily temperature change than in the forests and soil is more fertile.  Both woody and grassy savannas exist.  Generally good agricultural land.

http://www.blueplanetbiomes.org/savanna.htm

http://bioexpedition.com/savanna-biome/

d) Desert: less than 250mm precipiation/year, large temperature variation, both sandy and rocky deserts can be found, little vegetation, primarily succulents and ephemerals

http://scienceray.com/biology/ecology/plants-and-animals-adaptations-to-the-desert-biome/

http://archive.bio.ed.ac.uk/jdeacon/desbiome/biome.htm

http://www.glogster.com/cknguyen/the-desert-biome/g-6lrs72d0n7n0f4vp288sga0

e) Temperate grasslands:  experience 4 seasons, 200-500mm precipitation/yr, lots of humus, rich soil

http://www.roebuckclasses.com/105/physical/biomes/grassland/tempgrassland.htm

http://prezi.com/pb0dy3lrxzgc/temperate-grasslands/

f) Deciduous (lombhullató) forest: more than 500mm precipitation/yr, have 4 seasons with min. 5-6 month growing season, extent of undergrowth depends on how closed the canopy is, richer animal life than in the grasslands

http://www.ducksters.com/science/ecosystems/temperate_forest_biome.php

http://www.bio.miami.edu/dana/dox/biomes.html

g) Taiga (Boreal forest):  long, cold winters and cool, short summers, low levels of precipitation which falls primarily as snow, soil is thin and acidic, slow rates of decomposition, swamps and fens are commonly found in this biome

http://claremontgeography12.blogspot.hu/2011/05/tundra-biome.html

http://www.bio.utexas.edu/faculty/sjasper/Bio301M/biomes.html

h) Tundra: cold, very low precipitation, dwarf forests and grassy tundra (sedges, mosses and lichens), much of the animal life are seasonal summer migrants

http://shawn-miller.weebly.com/

http://laurentmikhail.hubpages.com/hub/Tundra-Biome

http://www.earthonlinemedia.com/ebooks/tpe_3e/biomes/biomes_tundra.html

i) Polar ice: phototrophs are only algae, life depends on surrounding oceans, ground is permanently frozen

http://www.zo.utexas.edu/faculty/sjasper/images/f37.34b.jpg

j) Mountains (Alpine): exhibit vertical zonality in which altitude acts similarly to latitude.  Also gradient and aspect (eg. northern vs. southern exposure) affects light, precipitation (eg. rainshadow) and other abiotic factors

http://uanews.org/story/rain-gods-in-a-desert-sea-new-book-celebrates-southern-arizona-s-mountains

http://prezi.com/_luflm2zbbcb/the-alpine-biome/

k) Marine (about 71% of the Earth's surface):  exhibits both horizontal (following major geographic zones - tropical, temperate, artic) and vertical (light decreases with depth) zonality.  Light is available in the euphotic zone, but below about 400m, no light penetrates through the water column, creating an aphotic zone.  Temperature variation in the marine environment is minimal in any given location and worldwide only ranges between about 2C-30C.  Nutrient availability is a determining factor for live in this biome.  Nutrient-rich waters are found near the shores, where nutrients enter from rivers, streams and run-off.  Upwellings (feláramlások) are also areas of high nutrients.  Organisms in this biome can be classified as benthic (bottom-dwellers), nektonic (swimmers) or planktonic (floaters).  Three major zones exist:  

http://earthsciencetopics.wikispaces.com/13

littoral (tengerparti): includes the intertidal and the area found above the continental shelf (about 200m deep).  It is an area of rich life and high biodiversity with both plants (monocots) and algae supporting a wide range and number of consumers.

http://www.glogster.com/jconway429/intertidal-zone/g-6mfcd9jg6qdsahtrimu1oa0

pelagic (nyíltvízí): the top 200m of water beyond the continental shelf, lower biodiversity, colder water.  Life in this zone is based on plankton (especially phytoplankton, which is more abundant in colder waters than in the tropics)

http://tracc-borneo.org/pom-pom-island-biodiversity/pelagic-fish-schools/

abyssal (mélytengeri):  darkness prevails here, along with high pressure, low temperatures, low nutrients (most fall from above).  Most living organisms in this zone are predators, scavengers and decomposers. 

http://www.artinaid.com/2013/04/the-ocean-layers/

Thermal vents are an exception to some of the above limits.

http://www.wildmusic.org/soundmap/sounds/blacksmoker

http://www.bio.utexas.edu/faculty/sjasper/Bio301M/aquahab.html

http://www.learner.org/courses/envsci/visual/img_lrg/aquatic_biomes.jpg

l) Freshwater: degree of diversity depends upon the surrounding geographical zone.  Includes lakes, ponds, streams and rivers.  Zones in lakes include: littoral - where plants can grow on the bottom because there is sufficient light, limnetic - open water within the euphotic zone, profundal - the aphotic zone

http://www.fondriest.com/environmental-measurements/parameters/weather/photosynthetically-active-radiation/