Biological interactions

Biological interactions are the effects that the organisms in a community have on one another.
In the natural world no organism exists in absolute isolation, and thus every organism must
interact with the environment and other organisms. An organism's interactions with its
environment are fundamental to the survival of that organism and the functioning of the
ecosystem as a whole.

In ecology, biological interactions can involve individuals of the same species (intraspecific
interactions) or individuals of different species (interspecific interactions). These can be
further classified by either the mechanism of the interaction or the strength, duration and
direction of their effects. Species may interact once in a generation (e.g. pollination) or live
completely within another (e.g. endo-symbiosis). Effects range from consumption of another
individual (predation, herbivory, or cannibalism), to mutual benefit (mutualism). Interactions
need not be direct; individuals may affect each other indirectly through intermediaries such as
shared resources or common enemies.

Interactions categorized by effect

Terms (as suggested by Edward Haskell) that explicitly indicate the quality of benefit or harm in
terms of fitness experienced by participants in an interaction are listed in the chart below. The
combinations range from mutually beneficial through neutral to mutually harmful interactions.

Effect on Effect on Type of

X Y interaction Table: Some types of relationships listed by the
effect they have on each partner. '0' is no
- - Competition effect, '-' is detrimental, and '+' is beneficial.

- 0 Amensalism

- + Antagonism

0 0 Neutralism

0 + Commensalism

+ + Mutualism

- - Synnecrosis

+ - Predation or
 Parasitism

Competition can be defined as an interaction between organisms or species, in which the

fitness of one is lowered by the presence of another. It is a mutually detrimental interaction
between individuals, populations or species, but rarely between clades. Limited supply of at
least one resource (such as food, water, and territory) used by both usually facilitates this type of
interaction, although the competition may also exist over other 'amenities', such as females for
reproduction (in case of male organisms of the same species).

Neutralism is a lack of interaction. Since all species sharing an environment interact in some
way, a complete lack of interaction is rarely seen in nature. However, the term can also signify a
relationship in which each species derives neither benefit nor detriment to any measurable
degree. However, the term is often used to describe situations where interactions are negligible
or insignificant.

Mutualism is the interaction between two or more species, where species derive a mutual benefit.
Mutualism may be classified in terms of the closeness of association, the closest being
symbiosis, which is often confused with mutualism. One or both species involved in the
interaction may be obligate, meaning they cannot survive in the short or long term without the
other species. Examples include cleaner fish, pollination and seed dispersal, gut flora, and
nitrogen fixation by bacteria in the root nodules of legumes.

Synnecrosis is detrimental to both species. It is a rare and necessarily short-lived condition as

evolution selects against benefits both populations it.

Amensalism is detrimental to one species and neutral to the other. A clear case of amensalism is
where sheep or cattle trample grass. Whilst the presence of the grass causes negligible
detrimental effects to the animal's hoof, the grass suffers from being crushed

Commensalism benefits one organism and the other organism is neither benefited nor harmed. A
good example is a remora fish living with a shark.Antagonism: In antagonistic interactions, one
species benefits at the expense of another. Predation is an interaction between organisms in
which one organism captures biomass from another. It is often used as a synonym for carnivory
but in its widest definition includes all forms of one organism eating another, regardless of
trophic level (e.g., herbivory), closeness of association (e.g., parasitism and parasitoidism) and
harm done to prey (e.g., grazing). Intraguild predation occurs when an organism preys upon
another of different species but at the same trophic level (e.g., coyotes kill and ingest gray foxes
in southern California). Batesian mimicry is also an antagonistic interaction, where one species
has evolved to mimic another, to the advantage of the copying species but to the detriment of the
species being mimicked.

It is important to note that these interactions are not always static. In many cases, two species
will interact differently under different conditions. This is particularly true in, but not limited to,
cases where species have multiple, drastically different life stages.
Interactions classified by mechanism

Symbiosis is an obligatory relationship between two populations. Partners in a symbiotic

relationship are constantly in contact with each other. Often one lives inside the other. It often
implies mutualism, but most formal definitions also include other types of relationships like
parasitism and commensalism.

Competition is an association between two species in which both need some limited
environmental factor for growth.

ECOLOGICAL CONCEPT

Ecology is the scientific study of ecosystems, which are generally defined as local units of
nature, consisting of the aggregate of plants, animals, the physical environment, and their
interactions.

Ecosystems consist of both biotic (living) and abiotic (non-living) components. Biotic
components include plants, animals, and microorganisms. The abiotic components are the
physical factors of the ecosystem. The roots of ecology can be traced to the writings of early
Greek philosophers such as Aristotle and Theophrastus, who were keen observers of plants and
animals in their natural habitats.

The word “ecology” was first proposed in 1869 by the German biologist Ernst Haeckel. It soon
came to be defined as “environmental biology,” or the effect of environmental factors on living
things.

Habitat

The term habitat refers to the kind of place where an organism normally lives. It includes the
arrangement of food, water, shelter and space that is suitable to meet an organism's needs. You
can think of this as the "address" where an organism lives. For example, a habitat might be an
aquatic or terrestrial environment that can be further categorized as a montane or alpine
ecosystem. Biotope and habitat are sometimes used interchangeably, but the former applies to a
community's environment, whereas the latter applies to a species' environment.

Niche

G. Evelyn Hutchinson made conceptual advances in 1957 by introducing a widely adopted

definition: "the set of biotic and abiotic conditions in which a species is able to persist and
maintain stable population sizes. It defines the role of an organism in an ecosystem, such as a
"fish-eating wader" for a heron, or a "plant-juice-sipping summer buzzer" for a cicada. The
ecological niche is a central concept in the ecology of organisms and is sub-divided into the
fundamental and the realized niche. The fundamental niche is the set of environmental
conditions under which a species is able to persist. The realized niche is the set of environmental
plus ecological conditions under which a species persists.

Environment: Physical environment (non-living environment and biotic environment (living).

Community Ecology: The study of the animals and plants forming a community.

Ecosystem: Physical environment and organisms of a habitat form an ecological complex or

ecosystem.

Autoecology/ autecology: Study of single species or individual ecology e.g.: tiger, ecology, deer
ecology, snow leopard ecology.

Gynecology/ synecology: Study of groups of organisms – plant ecology, animal ecology, forest
ecology, cropland ecology, etc.

Biosphere or Ecosphere: The portion of the earth in which ecosystems operate.

Among the specialties that have developed from theoretical ecology are autecology (study at the
level of individuals or species), synecology (study at the community level), and the ecosystems
approach, which is largely concerned with the flow of energy and the cycling of nutrients within
ecosystems.

Cell division
Cell division is the process by which a parent cell divides into two or more daughter cells. Cell
division usually occurs as part of a larger cell cycle. In eukaryotes, there are two distinct types of
cell division: a vegetative division, whereby each daughter cell is genetically identical to the
parent cell (mitosis), and a reductive cell division, whereby the number of chromosomes in the
daughter cells is reduced by half, to produce haploid gametes (meiosis). Meiosis results in four
haploid daughter cells by undergoing one round of DNA replication followed by two divisions:
homologous chromosomes are separated in the first division, and sister chromatids are
separated in the second division. Both of these cell division cycles are in sexually reproducing
organisms at some point in their life cycle, and both are believed to be present in the last
eukaryotic common ancestor. Prokaryotes also undergo a vegetative cell division known as
binary fission, where their genetic material is segregated equally into two daughter cells. All cell
divisions, regardless of organism, are preceded by a single round of DNA replication.

For simple unicellular organisms such as the amoeba, one cell division is equivalent to
reproduction – an entire new organism is created. On a larger scale, mitotic cell division can
create progeny from multicellular organisms, such as plants that grow from cuttings. Cell
division also enables sexually reproducing organisms to develop from the one-celled zygote,
which itself was produced by cell division from gametes. And after growth, cell division allows
for continual construction and repair of the organism. A human being's body experiences
about 10 quadrillion cell divisions in a lifetime.

The primary concern of cell division is the maintenance of the original cell's genome. Before
division can occur, the genomic information that is stored in chromosomes must be replicated,
and the duplicated genome must be separated cleanly between cells. A great deal of cellular
infrastructure is involved in keeping genomic information consistent between "generations".

STAGES OF MITOSIS (See attached power point)

The mitotic phase is a relatively short period of the cell cycle. It alternates with the much longer
interphase, where the cell prepares itself for the process of cell division. The process of mitosis is
divided into stages corresponding to the completion of one set of activities and the start of the
next. These stages are prophase, prometaphase, metaphase, anaphase, and telophase.

Prophase

During prophase, which occurs after G2 interphase, the cell prepares to divide by tightly
condensing its chromosomes and initiating mitotic spindle formation. During interphase, the
genetic material in the nucleus consists of loosely packed chromatin. At the onset of prophase,
chromatin fibers condense into discrete chromosomes that are typically visible at high
magnification through a light microscope. Gene transcription ceases during prophase and does
not resume until late anaphase to early G1 phase. The nucleolus also disappears during early
prophase.

Prometaphase

At the beginning of prometaphase in animal cells, phosphorylation of nuclear lamins causes the
nuclear envelope to disintegrate into small membrane vesicles. As this happens, microtubules
invade the nuclear space. This is called open mitosis, and it occurs in some multicellular
organisms. Fungi and some protists, such as algae or trichomonads, undergo a variation called
closed mitosis where the spindle forms inside the nucleus, or the microtubules penetrate the
intact nuclear envelope.

In late prometaphase, kinetochore microtubules begin to search for and attach to chromosomal
kinetochores. A kinetochore is a proteinaceous microtubule-binding structure that forms on the
chromosomal centromere during late prophase. A number of polar microtubules find and
interact with corresponding polar microtubules from the opposite centrosome to form the mitotic
spindle. Although the kinetochore structure and function are not fully understood, it is known
that it contains some form of molecular motor.

Metaphase

After the microtubules have located and attached to the kinetochores in prometaphase, the two
centrosomes begin pulling the chromosomes towards opposite ends of the cell. The resulting
tension causes the chromosomes to align along the metaphase plate or equatorial plane, an
imaginary line that is centrally located between the two centrosomes (at approximately the
midline of the cell). To ensure equitable distribution of chromosomes at the end of mitosis, the
metaphase checkpoint guarantees that kinetochores are properly attached to the mitotic spindle
and that the chromosomes are aligned along the metaphase plate. If the cell successfully passes
through the metaphase checkpoint, it proceeds to anaphase.

Anaphase

During anaphase A, the cohesins that bind sister chromatids together are cleaved, forming two
identical daughter chromosomes. Shortening of the kinetochore microtubules pulls the newly
formed daughter chromosomes to opposite ends of the cell. During anaphase B, polar
microtubules push against each other, causing the cell to elongate. In most animal cells, anaphase
A precedes anaphase B, but some vertebrate egg cells demonstrate the opposite order of events.

Telophase

Telophase is a reversal of prophase and prometaphase events. At telophase, the polar

microtubules continue to lengthen, elongating the cell even more. If the nuclear envelope has
broken down, a new nuclear envelope forms using the membrane vesicles of the parent cell's old
nuclear envelope. The new envelope forms around each set of separated daughter chromosomes
(though the membrane does not enclose the centrosomes) and the nucleolus reappears. Both sets
of chromosomes, now surrounded by new nuclear membrane, begin to "relax" or decondense.
Mitosis is complete. Each daughter nucleus has an identical set of chromosomes. Cell division
may or may not occur at this time depending on the organism.

Cytokinesis

Cytokinesis is not a phase of mitosis but rather a separate process, necessary for completing cell
division. In animal cells, a cleavage furrow (pinch) containing a contractile ring develops where
the metaphase plate used to be, pinching off the separated nuclei. In both animal and plant cells,
cell division is also driven by vesicles derived from the Golgi apparatus, which move along
microtubules to the middle of the cell. In plants, this structure coalesces into a cell plate at the
center of the phragmoplast and develops into a cell wall, separating the two nuclei. The
phragmoplast is a microtubule structure typical for higher plants, whereas some green algae use a
phycoplast microtubule array during cytokinesis. Each daughter cell has a complete copy of the
genome of its parent cell. The end of cytokinesis marks the end of the M-phase.

There are many cells where mitosis and cytokinesis occur separately, forming single cells with
multiple nuclei. The most notable occurrence of this is among the fungi, slime molds, and
coenocytic algae, but the phenomenon is found in various other organisms. Even in animals,
cytokinesis and mitosis may occur independently, for instance during certain stages of fruit fly
embryonic development.
Significance

Mitosis is important for the maintenance of the chromosomal set; each cell formed receives
chromosomes that are alike in composition and equal in number to the chromosomes of the
parent cell.

Mitosis occurs in the following circumstances:

Development and growth

The number of cells within an organism increases by mitosis. This is the basis of the
development of a multicellular body from a single cell, i.e., zygote and also the basis of
the growth of a multicellular body.

Cell replacement

In some parts of body, e.g. skin and digestive tract, cells are constantly sloughed off and
replaced by new ones. New cells are formed by mitosis and so are exact copies of the
cells being replaced. In like manner, red blood cells have short lifespan (only about 4
months) and new RBCs are formed by mitosis.

Regeneration

Some organisms can regenerate body parts. The production of new cells in such instances
is achieved by mitosis. For example, starfish regenerate lost arms through mitosis.

Asexual reproduction

Some organisms produce genetically similar offspring through asexual reproduction. For
example, the hydra reproduces asexually by budding. The cells at the surface of hydra
undergo mitosis and form a mass called a bud. Mitosis continues in the cells of the bud
and this grows into a new individual. The same division happens during asexual
reproduction or vegetative propagation in plants.

MEIOSIS

Because meiosis is a "one-way" process, it cannot be said to engage in a cell cycle as mitosis
does. However, the preparatory steps that lead up to meiosis are identical in pattern and name to
the interphase of the mitotic cell cycle.

Interphase is followed by meiosis I and then meiosis II. Meiosis I consists of separating the pairs
of homologous chromosome, each made up of two sister chromatids, into two cells. One entire
haploid content of chromosomes is contained in each of the resulting daughter cells; the first
meiotic division therefore reduces the ploidy of the original cell by a factor of 2.
Meiosis II consists of decoupling each chromosome's sister strands (chromatids), and
segregating the individual chromatids into haploid daughter cells. The two cells resulting from
meiosis I divide during meiosis II, creating 4 haploid daughter cells. Meiosis I and II are each
divided into prophase, metaphase, anaphase, and telophase stages, similar in purpose to their
analogous subphases in the mitotic cell cycle. Therefore, meiosis includes the stages of meiosis I
(prophase I, metaphase I, anaphase I, telophase I), and meiosis II (prophase II, metaphase II,
anaphase II, telophase II).

Meiosis-phases (See attached power point)

Meiosis I

Meiosis I separates homologous chromosomes, producing two haploid cells (23 chromosomes,
N in humans), so meiosis I is referred to as a reductional division. A regular diploid human cell
contains 46 chromosomes and is considered 2N because it contains 23 pairs of homologous
chromosomes. However, after meiosis I, although the cell contains 46 chromatids it is only
considered as being N, with 23 chromosomes, because later in anaphase I the sister chromatids
will remain together as the spindle pulls the pair toward the pole of the new cell. In meiosis II, an
equational division similar to mitosis will occur whereby the sister chromatids are finally split,
creating a total of 4 haploid cells (23 chromosomes, N) per daughter cell from the first division.

Prophase I

During prophase I, DNA is exchanged between homologous chromosomes in a process called

homologous recombination. This often results in chromosomal crossover. The new
combinations of DNA created during crossover are a significant source of genetic variation, and
may result in beneficial new combinations of alleles. The paired and replicated chromosomes are
called bivalents or tetrads, which have two chromosomes and four chromatids, with one
chromosome coming from each parent. At this stage, non-sister chromatids may cross-over at
points called chiasmata (plural; singular chiasma).

Leptotene

The first stage of prophase I is the leptotene stage, also known as leptonema, from Greek words
meaning "thin threads". During this stage, individual chromosomes begin to condense into long
strands within the nucleus. However the two sister chromatids are still so tightly bound that they
are indistinguishable from one another.

Zygotene

The zygotene stage, also known as zygonema, from Greek words meaning "paired threads",
occurs as the chromosomes approximately line up with each other into homologous
chromosomes. This is called the bouquet stage because of the way the telomeres cluster at one
end of the nucleus. At this stage, the synapsis (pairing/coming together) of homologous
chromosomes takes place.
Pachytene

The pachytene stage, also known as pachynema, from Greek words meaning "thick threads",
contains the following chromosomal crossover. Non-sister chromatids of homologous
chromosomes randomly exchange segments of genetic information over regions of homology.
Sex chromosomes, however, are not wholly identical, and only exchange information over a
small region of homology. Exchange takes place at sites where recombination nodules (the
chiasmata) have formed. The exchange of information between the non-sister chromatids results
in a recombination of information; each chromosome has the complete set of information it had
before, and there are no gaps formed as a result of the process. Because the chromosomes cannot
be distinguished in the synaptonemal complex, the actual act of crossing over is not perceivable
through the microscope.

Diplotene

During the diplotene stage, also known as diplonema, from Greek words meaning "two threads",
the synaptonemal complex degrades and homologous chromosomes separate from one another a
little. The chromosomes themselves uncoil a bit, allowing some transcription of DNA.
However, the homologous chromosomes of each bivalent remain tightly bound at chiasmata, the
regions where crossing-over occurred. The chiasmata remain on the chromosomes until they are
severed in Anaphase I.

In human fetal oogenesis all developing oocytes develop to this stage and stop before birth. This
suspended state is referred to as the dictyotene stage and remains so until puberty. In males,
only spermatogonia (spermatogenesis) exist until meiosis begins at puberty.

Diakinesis

Chromosomes condense further during the diakinesis stage, from Greek words meaning "moving
through". This is the first point in meiosis where the four parts of the tetrads are actually visible.
Sites of crossing over entangle together, effectively overlapping, making chiasmata clearly
visible. Other than this observation, the rest of the stage closely resembles prometaphase of
mitosis; the nucleoli disappear, the nuclear membrane disintegrates into vesicles, and the
meiotic spindle begins to form.

Synchronous processes

During these stages, two centrosomes, containing a pair of centrioles in animal cells, migrate to
the two poles of the cell. These centrosomes, which were duplicated during S-phase, function as
microtubule organizing centers nucleating microtubules, which are essentially cellular ropes and
poles. The microtubules invade the nuclear region after the nuclear envelope disintegrates,
attaching to the chromosomes at the kinetochore. The kinetochore functions as a motor, pulling
the chromosome along the attached microtubule toward the originating centriole, like a train on
a track. There are four kinetochores on each tetrad, but the pair of kinetochores on each sister
chromatid fuses and functions as a unit during meiosis I.
Microtubules that attach to the kinetochores are known as kinetochore microtubules. Other
microtubules will interact with microtubules from the opposite centriole: these are called non-
kinetochore microtubules or polar microtubules. A third type of microtubules, the aster
microtubules, radiates from the centrosome into the cytoplasm or contacts components of the
membrane skeleton.

Metaphase I

Homologous pairs move together along the metaphase plate: As kinetochore microtubules from
both centrioles attach to their respective kinetochores, the homologous chromosomes align along
an equatorial plane that bisects the spindle, due to continuous counterbalancing forces exerted on
the bivalents by the microtubules emanating from the two kinetochores of homologous
chromosomes. The physical basis of the independent assortment of chromosomes is the random
orientation of each bivalent along the metaphase plate, with respect to the orientation of the other
bivalents along the same equatorial line.

Anaphase I

Kinetochore microtubules shorten, severing the recombination nodules and pulling homologous
chromosomes apart. Since each chromosome has only one functional unit of a pair of
kinetochores, whole chromosomes are pulled toward opposing poles, forming two haploid sets.
Each chromosome still contains a pair of sister chromatids. Non-kinetochore microtubules
lengthen, pushing the centrioles farther apart. The cell elongates in preparation for division down
the center.

Telophase I

The last meiotic division effectively ends when the chromosomes arrive at the poles. Each
daughter cell now has half the number of chromosomes but each chromosome consists of a pair
of chromatids. The microtubules that make up the spindle network disappear, and a new nuclear
membrane surrounds each haploid set. The chromosomes uncoil back into chromatin.
Cytokinesis, the pinching of the cell membrane in animal cells or the formation of the cell wall in
plant cells, occurs, completing the creation of two daughter cells. Sister chromatids remain
attached during telophase I.

Cells may enter a period of rest known as interkinesis or interphase II. No DNA replication
occurs during this stage.

Meiosis II

Meiosis II is the second part of the meiotic process. Much of the process is similar to mitosis.
The end result is production of four haploid cells (23 chromosomes, 1N in humans) from the
two haploid cells (23 chromosomes, 1N * each of the chromosomes consisting of two sister
chromatids) produced in meiosis I. The four main steps of Meiosis II are: Prophase II, Metaphase
II, Anaphase II, and Telophase II.
Prophase II takes an inversely proportional time compared to telophase I. In this prophase we
see the disappearance of the nucleoli and the nuclear envelope again as well as the shortening
and thickening of the chromatids. Centrioles move to the polar regions and arrange spindle fibers
for the second meiotic division.

In metaphase II, the centromeres contain two kinetochores that attach to spindle fibers from the
centrosomes (centrioles) at each pole. The new equatorial metaphase plate is rotated by 90
degrees when compared to meiosis I, perpendicular to the previous plate.

This is followed by anaphase II, where the centromeres are cleaved, allowing microtubules
attached to the kinetochores to pull the sister chromatids apart. The sister chromatids by
convention are now called sister chromosomes as they move toward opposing poles.

The process ends with telophase II, which is similar to telophase I, and is marked by uncoiling
and lengthening of the chromosomes and the disappearance of the spindle. Nuclear envelopes
reform and cleavage or cell wall formation eventually produces a total of four daughter cells,
each with a haploid set of chromosomes. Meiosis is now complete and ends up with four new
daughter cells.

Meiosis generates genetic diversity in two ways: (1) independent alignment and subsequent
separation of homologous chromosome pairs during the first meiotic division allows a random
and independent selection of each chromosome segregates into each gamete; and (2) physical
exchange of homologous chromosomal regions by homologous recombination during prophase I
results in new combinations of DNA within chromosomes.

Significance
Meiosis facilitates stable sexual reproduction. Without the halving of ploidy, or chromosome
count, fertilization would result in zygotes that have twice the number of chromosomes as the
zygotes from the previous generation. Successive generations would have an exponential
increase in chromosome count. In organisms that are normally diploid, polyploidy, the state of
having three or more sets of chromosomes, results in extreme developmental abnormalities or
lethality. Polyploidy is poorly tolerated in most animal species. Plants, however, regularly
produce fertile, viable polyploids. Polyploidy has been implicated as an important mechanism in
plant speciation.

Most importantly, recombination and independent assortment of homologous chromosomes

allow for a greater diversity of genotypes in the population. This produces genetic variation in
gametes that promote genetic and phenotypic variation in a population of offspring.
 VARIATION AND HEREDITY

The term Genetics was first coined by William Bateson in 1906 from Greek word ‘gen” which
means ‘to become”. According to Webster’s dictionary, Genetics is the branch of Biology which
deals with Heredity and Variation among related organisms. There are two main components of
this discipline. The first is heredity which is the study of factors responsible for the resemblance
between the parents and their offspring. Thus heredity can be defined as the ‘The transmission
of characters from parents to offspring”. The second, called variation is concerned with the
forces or influences due to which no two organisms are exactly alike. Thus the occurrence of
differences among the individuals of the same species is known as variation.

The concept of heredity is not new. Selective breeding (e.g. of horses, donkeys and date palm)
was done during the ancient civilization of Babylon and Assyria nearly 6000 years ago. The
science of heredity and variation, the scientific principle of the science of genetics originated in
1900 with the re-discovery of a scientific article published in 1886 by Gregor Johann Mendel.
Mendel’s ‘factors’, the carriers of heredity information, are known as ‘genes’, a term coined by
Johansen in 1909.

The contribution of Mendel (born in 1822) to Genetics is called Mendelism. Mendel is called the
father of Genetics.

Mendel’s work

Mendel did his work on garden pea (Pisum sativum L.) The following were the reasons for the
success of Mendel:

 It is very easy to cultivate the pea plant in open ground

 The flowers of pea plants are normally self-fertilized.
 The pea plants show a number of contrasting characters
 The hybrid of garden pea are perfectly fertile
 Cross pollination is not very difficult in pea plant
 Artificial fertilization was almost successful
 He studied the inheritance of only one character at a time in most of the experiments
 He maintained statistical records of his results. He helped Mendel to drive numerical
ratios of significance.

Mendel carried out experiments on pea plants involving seven pairs of different/contrasting
characters. Each time he obtained similar results. The seven pairs of contrasting traits are as
follow:
 Alternative
No. Characters
Dominant Recessive
1 The length of the stem Tall Dwarf
2 The position of the flower Axial Terminal
3 The colour of the pod Green Yellow
4 The shape of the pod Inflated Constricted
5 The shape of the seed Round Wrinkled
6 The colour of seed coat Coloured White
7 The colour of the cotyledon Yellow Green

Figure: The Seven Traits that Mendel Studied in Pisum Sativum

 Mendel's Laws of Inheritance
Law Definition
During gamete formation, the alleles for each gene segregate from each other
Law of Segregation
so that each gamete carries only one allele for each gene.
Law of Independent Genes for different traits can segregate independently during the formation
Assortment of gametes.
Some alleles are dominant while others are recessive; an organism with at
Law of Dominance
least one dominant allele will display the effect of the dominant allele.

In the pea plant example above, the capital "P" represents the dominant allele for purple
flowers and lowercase "p" represents the recessive allele for white flowers. Both parental
plants were true-breeding, and one parental variety had two alleles for purple flowers (PP)
while the other had two alleles for white flowers (pp). As a result of fertilization, the F1 hybrids
each inherited one allele for purple flowers and one for white. All the F1 hybrids (Pp) had
purple flowers, because the dominant P allele has its full effect in the heterozygote, while the
recessive p allele has no effect on flower color. For the F2 plants, the ratio of plants with purple
flowers to those with white flowers (3:1) is called the phenotypic ratio. The genotypic ratio, as
seen in the Punnett square, is 1 PP : 2 Pp : 1 pp. i.e. 1:2:1.

Law of Segregation (the "First Law")

Figure 1 Dominant and recessive phenotypes.

(1) Parental generation.
(2) F1 generation.
(3) F2 generation. Dominant (red) and recessive (white) phenotype look alike in the F1 (first)
generation and show a 3:1 ratio in the F2 (second) generation.

The Law of Segregation states that every individual contains a pair of alleles for each particular
trait which segregate or separate during cell division (assuming diploidy) for any particular trait
and that each parent passes a randomly selected copy (allele) to its offspring. The offspring then
receives its own pair of alleles of the gene for that trait by inheriting sets of homologous
chromosomes from the parent organisms. Interactions between alleles at a single locus are
termed dominance and these influence how the offspring expresses that trait (e.g. the color
and height of a plant, or the color of an animal's fur).

*Book definition: The Law of Segregation states that the two alleles for a heritable
character segregate (separate from each other) during gamete formation and end up in
different gametes.

More precisely, the law states that when any individual produces gametes, the copies of a
gene separate so that each gamete receives only one copy (allele). A gamete will receive one
allele or the other. The direct proof of this was later found following the observation of meiosis
by two independent scientists, the German botanist Oscar Hertwig in 1876, and the Belgian
zoologist Edouard Van Beneden in 1883. Paternal and maternal chromosomes get separated in
meiosis and the alleles with the traits of a character are segregated into two different gametes.
Law of Independent Assortment (the "Second Law")

Figure 2 Dihybrid cross. The phenotypes of two independent traits show a 9:3:3:1 ratio in the
F2 generation. In this example, coat color is indicated by B (brown, dominant) or b (white),
while tail length is indicated by S (short, dominant) or s (long). When parents are homozygous
for each trait (SSbb and ssBB), their children in the F1 generation are heterozygous at both loci
and only show the dominant phenotypes (SsbB). If the children mate with each other, in the F2
generation all combinations of coat color and tail length occur: 9 are brown/short (purple
boxes), 3 are white/short (pink boxes), 3 are brown/long (blue boxes) and 1 is white/long
(green box).

Law of Independent Assortment (the "Second Law")

In short, the 2nd law states that: In the inheritance of more than one pair of traits in a cross
simultaneously, the factor responsible for each pair of traits are distributed to the gametes.

The Law of Independent Assortment, also known as "Inheritance Law", states that separate
genes for separate traits are passed independently of one another from parents to offspring.
That is, the biological selection of a particular gene in the gene pair for one trait to be passed to
the offspring has nothing to do with the selection of the gene for any other trait. More precisely,
the law states that alleles of different genes assort independently of one another during
gamete formation. While Mendel's experiments with mixing one trait always resulted in a 3:1
ratio (Fig. 1) between dominant and recessive phenotypes, his experiments with mixing two
traits (dihybrid cross) showed 9:3:3:1 ratios (Fig. 2). But the 9:3:3:1 table shows that each of
the two genes is independently inherited with a 3:1 phenotypic ratio. Mendel concluded that
different traits are inherited independently of each other, so that there is no relation, for example,
between a cat's color and tail length. This is actually only true for genes that are not linked to
each other.

Independent assortment occurs in eukaryotic organisms during meiotic metaphase I, and

produces a gamete with a mixture of the organism's chromosomes. The physical basis of the
independent assortment of chromosomes is the random orientation of each bivalent chromosome
along the metaphase plate with respect to the other bivalent chromosomes. Along with crossing
over, independent assortment increases genetic diversity by producing novel genetic
combinations.

Law of Dominance (the "Third Law")

Mendel's Law of Dominance states that recessive alleles will always be masked by dominant
alleles. Therefore, a cross between a homozygous dominant and a homozygous recessive will
always express the dominant phenotype, while still having a heterozygous genotype. Law of
Dominance can be explained easily with the help of a monohybrid cross experiment:- In a cross
between two organisms pure for any pair (or pairs) of contrasting traits (characters), the
character that appears in the F1 generation is called "dominant" and the one which is
suppressed (not expressed) is called "recessive." Each character is controlled by a pair of
dissimilar factors. Only one of the characters expresses. The one which expresses in the F1
generation is called Dominant. It is important to note however, that the law of dominance is
significant and true but is not universally applicable.

According to the latest revisions, only two of these rules are considered to be laws. The third
one is considered as a basic principle but not a genetic law of Mendel.

Mendelian trait

A Mendelian trait is one that is controlled by a single locus in an inheritance pattern. In such
cases, a mutation in a single gene can cause a disease that is inherited according to Mendel's
laws. Examples include sickle-cell anemia, Tay-Sachs disease, cystic fibrosis and xeroderma
pigmentosa. A disease controlled by a single gene contrasts with a multi-factorial disease, like
arthritis, which is affected by several loci (and the environment) as well as those diseases
inherited in a non-Mendelian fashion.
Non-Mendelian inheritance

In four o'clock plants, (Mirabilis jalapa), the alleles for red and white flowers show incomplete
dominance. As seen in the F1 generation, heterozygous (wr) plants have "pink" flowers—a
mix of "red" (rr) and "white" (ww) coloring. The F2 generation shows a 1:2:1 ratio of
red:pink:white.

Non-Mendelian inheritance

Mendel explained inheritance in terms of discrete factors—genes—that are passed along from
generation to generation according to the rules of probability. Mendel's laws are valid for all
sexually reproducing organisms, including garden peas and human beings. However, Mendel's
laws stop short of explaining some patterns of genetic inheritance. For most sexually reproducing
organisms, cases where Mendel's laws can strictly account for the patterns of inheritance are
relatively rare. Often, the inheritance patterns are more complex.

The F1 offspring of Mendel's pea crosses always looked like one of the two parental varieties. In
this situation of "complete dominance," the dominant allele had the same phenotypic effect
whether present in one or two copies. But for some characteristics, the F 1 hybrids have an
appearance in between the phenotypes of the two parental varieties. A cross between two four
o'clock plants (Mirabilis jalapa) shows this common exception to Mendel's principles. Some
alleles are neither dominant nor recessive. The F 1 generation produced by a cross between red-
flowered (RR) and white flowered (WW) Mirabilis jalapa plants consists of pink-colored
flowers (RW). Which allele is dominant in this case? Neither one. This third phenotype results
from flowers of the heterozygote having less red pigment than the red homozygotes. Cases in
which one allele is not completely dominant over another are called incomplete dominance. In
incomplete dominance, the heterozygous phenotype lies somewhere between the two
homozygous phenotypes.
A similar situation arises from codominance, in which the phenotypes produced by both alleles
are clearly expressed. For example, in certain varieties of chicken, the allele for black feathers is
codominant with the allele for white feathers. Heterozygous chickens have a color described as
"erminette," speckled with black and white feathers. Unlike the blending of red and white colors
in heterozygous four o'clocks, black and white colors appear separately in chickens. Many
human genes, including one for a protein that controls cholesterol levels in the blood, show
codominance, too. People with the heterozygous form of this gene produce two different forms
of the protein, each with a different effect on cholesterol levels.

In Mendelian inheritance, genes have only two alleles, such as a and A. In nature, such genes
exist in several different forms and are therefore said to have multiple alleles. A gene with more
than two alleles is said to have multiple alleles. An individual, of course, usually has only two
copies of each gene, but many different alleles are often found within a population. One of the
best-known examples is coat color in rabbits. A rabbit's coat color is determined by a single gene
that has at least four different alleles. The four known alleles display a pattern of simple
dominance that can produce four coat colors. Many other genes have multiple alleles, including
the human genes for ABO blood type.

Furthermore, many traits are produced by the interaction of several genes. Traits controlled by
two or more genes are said to be polygenic traits. Polygenic means "many genes." For example,
at least three genes are involved in making the reddish-brown pigment in the eyes of fruit flies.
Polygenic traits often show a wide range of phenotypes. The variety of skin color in humans
comes about partly because more than four different genes probably control this trait.

EVOLUTION
Evolution is change in the heritable traits of biological populations over successive generations.
Evolutionary processes give rise to diversity at every level of biological organization, including
the levels of species, individual organisms, and molecules.

All life on Earth shares a common ancestor known as the last universal ancestor, which lived
approximately 3.5–3.8 billion years ago, although a study in 2015 found "remains of biotic life"
from 4.1 billion years ago in ancient rocks in Western Australia. According to one of the
researchers, "If life arose relatively quickly on Earth ... then it could be common in the universe.

Repeated formation of new species (speciation), change within species (anagenesis), and loss of
species (extinction) throughout the evolutionary history of life on Earth are demonstrated by
shared sets of morphological and biochemical traits, including shared DNA sequences. These
shared traits are more similar among species that share a more recent common ancestor, and can
be used to reconstruct a biological "tree of life" based on evolutionary relationships
(phylogenetics), using both existing species and fossils.
Darwin's Theory of Evolution

In the mid-19th century, Charles Darwin formulated the scientific theory of evolution by natural
selection, published in his book On the Origin of Species (1859). Evolution by natural selection
is a process demonstrated by the observation that more offspring are produced than can possibly
survive, along with three facts about populations: 1) traits vary among individuals with respect to
morphology, physiology, and behaviour (phenotypic variation), 2) different traits confer different
rates of survival and reproduction (differential fitness), and 3) traits can be passed from
generation to generation (heritability of fitness). Thus, in successive generations members of a
population are replaced by progeny of parents better adapted to survive and reproduce in the
biophysical environment in which natural selection takes place. This teleonomy is the quality
whereby the process of natural selection creates and preserves traits that are seemingly fitted for
the functional roles they perform. Natural selection is the only known cause of adaptation but not
the only known cause of evolution. Other, non-adaptive causes of microevolution include
mutation and genetic drift.

In the early 20th century the modern evolutionary synthesis integrated classical genetics with
Darwin's theory of evolution by natural selection through the discipline of population genetics.
The importance of natural selection as a cause of evolution was accepted into other branches of
biology.

Mechanisms

From a Neo-Darwinian perspective, evolution occurs when there are changes in the frequencies
of alleles within a population of interbreeding organisms. For example, the allele for black colour
in a population of moths becoming more common. Mechanisms that can lead to changes in allele
frequencies include natural selection, genetic drift, genetic hitchhiking, mutation and gene flow.

Evidence for Evolution

During and since Darwin's time, people have been looking for and studying evidence in nature
that teaches them more about evolution. Some types of evidence, such as fossils and similarities
between related living organisms, were used by Darwin to develop his theory of natural
selection, and are still used today. Others, such as DNA testing, were not available in Darwin's
time, but are used by scientists today to learn more about evolution.

Five types of evidence for evolution are discussed in this section: ancient organism remains,
fossil layers, similarities among organisms alive today, similarities in DNA, and similarities of
embryos. Another important type of evidence that Darwin studied and that is still studied and
used today is artificial selection, or breeding.
Ancient Organism Remains

Darwin found many types of remains of ancient organisms. In addition to fossil layers, he saw
other fossils, bones, insects in amber (hardened tree sap), and petrified wood. Another type of
preserved organism, which Darwin did not find, is animals such as mammoths frozen and
preserved in ice. Darwin and scientists today have discovered that the ancient organisms whose
remains they find look like organisms alive today because they are the living organisms'
ancestors or evolved from a common ancestor.

Fossil Layers

Fossil layers are fossils that formed in sedimentary rock. Sedimentary rock is rock that is formed
in layers by the depositing and pressing of sediments on top of each other. Sediments are any
loose material that gets broken away and carried. Because sediments sometimes include once-
living organisms, sedimentary rock often contains a lot of fossils. Once thing that Darwin noticed
on his travels, and that people continue to notice today, is that fossils in the bottom layers are
very different from the organisms alive today. From this, Darwin concluded that organisms have
not remained the same since earth's beginning, and that they have changed a lot, gradually
becoming more and more complex. He also realized that as new species arise, other ones become
extinct.

Similarities among Living Organisms

One type of evidence for evolution (evidence that organisms are related, descended from a few
common ancestors, and change to adapt to their environments) is that organisms are similar to
each other, but not exactly the same. Similar organisms have differences that help them adapt to
their environments. Many organisms have similar body plans. Horses', donkeys', and zebras'
bodies are set up in pretty much the same way, because they are descended from a common
ancestor. As organisms adapt and evolve, not everything about them changes. The differences,
such as the zebra's stripes, show that each species adapted to its own environment after branching
off from the common ancestor. All insects have heads, abdomens, and thoraxes, antennae, six
legs, and wings. However, each species is different, and while all insects have wings, some have
small, useless wings, because their environments did not force them to evolve useful wings, or
because their wings became harmful to survival.

All birds have feathers, beaks, and wings, but are different because they had to adapt to different
environments, such as the webbed feet of water birds but not of land birds. On a more distant
level, fish and zebras both have eyes, frogs and baboons both have spines. Generally, the longer
ago the last common ancestor lived, the less the organisms have in common.

Similarities of DNA

Similarities are often easy to see when one looks at two organisms that evolved from a common
ancestor, and until recently, looking at physical features and behavior was the only way to
determine how closely related two organisms are. However, now scientists can also analyze
DNA to discover how closely organisms are related. Every living creature has DNA, which has a
lot of inherited information about how the body builds itself. Scientists can compare the DNA of
two organisms; the more similar the DNA, the more closely related the organisms. This method
can also help when looks are deceptive. One example of looks being deceptive is: The bat and
the crow both have wings, and the squirrel does not. From this, one may think that bats and
crows are more closely related than bats and squirrels, while the opposite is indeed the case.

DNA testing is a tool that Darwin never had, but it has helped scientists after him to learn and
discover a lot about evolution.

Similarities of Embryos

The study of one type of evidence of evolution is called embryology, the study of embryos. An
embryo is an unborn (or unhatched) animal or human young in its earliest phases. Embryos of
many different kinds of animals: mammals, birds, reptiles, fish, etc. look very similar and it is
often difficult to tell them apart. Many traits of one type of animal appear in the embryo of
another type of animal. For example, fish embryos and human embryos both have gill slits. In
fish they develop into gills, but in humans they disappear before birth.

This shows that the animals are similar and that they develop similarly, implying that they are
related, have common ancestors and that they started out the same, gradually evolving different
traits, but that the basic plan for a creature's beginning remains the same.

Applications

Concepts and models used in evolutionary biology, such as natural selection, have many
applications.

Artificial selection is the intentional selection of traits in a population of organisms. This has
been used for thousands of years in the domestication of plants and animals. More recently, such
selection has become a vital part of genetic engineering, with selectable markers such as
antibiotic resistance genes being used to manipulate DNA. Proteins with valuable properties
have evolved by repeated rounds of mutation and selection (for example modified enzymes and
new antibodies) in a process called directed evolution.

Understanding the changes that have occurred during an organism's evolution can reveal the
genes needed to construct parts of the body, genes which may be involved in human genetic
disorders. For example, the Mexican tetra is an albino cavefish that lost its eyesight during
evolution. Breeding together different populations of this blind fish produced some offspring
with functional eyes, since different mutations had occurred in the isolated populations that had
evolved in different caves. This helped identify genes required for vision and pigmentation.

Many human diseases are not static phenomena, but capable of evolution. Viruses, bacteria,
fungi and cancers evolve to be resistant to host immune defences, as well as pharmaceutical
drugs. These same problems occur in agriculture with pesticide and herbicide resistance. It is
possible that we are facing the end of the effective life of most of available antibiotics and
predicting the evolution and evolvability of our pathogens and devising strategies to slow or
circumvent it is requiring deeper knowledge of the complex forces driving evolution at the
molecular level.

In computer science, simulations of evolution using evolutionary algorithms and artificial life
started in the 1960s and were extended with simulation of artificial selection. Artificial evolution
became a widely recognised optimisation method as a result of the work of Ingo Rechenberg in
the 1960s. He used evolution strategies to solve complex engineering problems. Genetic
algorithms in particular became popular through the writing of John Henry Holland. Practical
applications also include automatic evolution of computer programmes. Evolutionary algorithms
are now used to solve multi-dimensional problems more efficiently than software produced by
human designers and also to optimize the design of systems.

Biostatistics
Biostatistics (or biometry) is the application of statistics to a wide range of topics in biology.
The science of biostatistics encompasses the design of biological experiments, especially in
medicine, pharmacy, agriculture and fishery; the collection, summarization, and analysis of data
from those experiments; and the interpretation of, and inference from, the results. A major
branch of this is medical biostatistics, which is exclusively concerned with medicine and health.

History

Biostatistical reasoning and modeling were of critical importance to the foundation theories of
modern biology. In the early 1900s, after the rediscovery of Gregor Mendel's Mendelian
inheritance work, the gaps in understanding between genetics and evolutionary Darwinism led to
vigorous debate among biometricians, such as Walter Weldon and Karl Pearson, and Mendelian,
such as Charles Davenport, William Bateson and Wilhelm Johannsen. By the 1930s, statisticians
and models built on statistical reasoning had helped to resolve these differences and to produce
the neo-Darwinian modern evolutionary synthesis.

The leading figures in the establishment of population genetics and this synthesis all relied on
statistics and developed its use in biology.

 Ronald Fisher developed several basic statistical methods in support of his work studying
the field experiments at Rothamsted Research, including in his 1930 book The Genetical
Theory of Natural Selection
 Sewall G. Wright developed F-statistics and methods of computing them
 J. B. S. Haldane's book, The Causes of Evolution, re-established natural selection as the
premier mechanism of evolution by explaining it in terms of the mathematical
consequences of Mendelian genetics.
These individuals and the work of other biostatisticians, mathematical biologists, and statistically
inclined geneticists helped bring together evolutionary biology and genetics into a consistent,
coherent whole that could begin to be quantitatively modeled.

In parallel to this overall development, the pioneering work of D'Arcy Thompson in On Growth
and Form also helped to add quantitative discipline to biological study.

Despite the fundamental importance and frequent necessity of statistical reasoning, there may
nonetheless have been a tendency among biologists to distrust or deprecate results which are not
qualitatively apparent. One anecdote describes Thomas Hunt Morgan banning the Friden
calculator from his department at Caltech, saying "Well, I am like a guy who is prospecting for
gold along the banks of the Sacramento River in 1849. With a little intelligence, I can reach
down and pick up big nuggets of gold. And as long as I can do that, I'm not going to let any
people in my department waste scarce resources in placer mining

Recent developments in modern biostatistics

The advent of modern computer technology and relatively cheap computing resources have
enabled computer-intensive biostatistical methods like bootstrapping and resampling methods.
Furthermore, new biomedical technologies like microarrays, next generation sequencers (for
genomics) and mass spectrometry (for proteomics) generate enormous amounts of (redundant)
data that can only be analyzed with biostatistical methods. For example, a microarray can
measure all the genes of the human genome simultaneously, but only a fraction of them will be
differentially expressed in diseased vs. non-diseased states. One might encounter the problem of
multicolinearity: Due to high intercorrelation between the predictors (in this case say genes), the
information of one predictor might be contained in another one. It could be that only 5% of the
predictors are responsible for 90% of the variability of the response. In such a case, one would
apply the biostatistical technique of dimension reduction (for example via principal component
analysis). Classical statistical techniques like linear or logistic regression and linear discriminant
analysis do not work well for high dimensional data (i.e. when the number of observations n is
smaller than the number of features or predictors p: n < p). As a matter of fact, one can get quite
high R2-values despite very low predictive power of the statistical model. These classical
statistical techniques (esp. least squares linear regression) were developed for low dimensional
data (i.e. where the number of observations n is much larger than the number of predictors p: n
>> p). In cases of high dimensionality, one should always consider an independent validation test
set and the corresponding residual sum of squares (RSS) and R 2 of the validation test set, not
those of the training set.

In recent times, random forests have gained popularity. This technique, invented by the
statistician Leo Breiman, generates a lot of decision trees randomly and uses them for
classification (In classification the response is on a nominal or ordinal scale, as opposed to
regression where the response is on a ratio scale). Decision trees have of course the advantage
that you can draw them and interpret them (even with a very basic understanding of mathematics
and statistics). Random Forrests have thus been used for clinical decision support systems.
Gene Set Enrichment Analysis (GSEA) is a new method for analyzing biological high
throughput experiments. With this method, one does not consider the perturbation of single
genes but of whole (functionally related) gene sets. These gene sets might be known biochemical
pathways or otherwise functionally related genes. The advantage of this approach is that it is
more robust: It is more likely that a single gene is found to be falsely perturbed than it is that a
whole pathway is falsely perturbed. Furthermore, one can integrate the accumulated knowledge
about biochemical pathways (like the JAK-STAT signaling pathway) using this approach.

Applications of biostatistics

 Public health, including epidemiology, health services research, nutrition, environmental

health and healthcare policy & management.
 Design and analysis of clinical trials in medicine
 Assessment of severity state of a patient with prognosis of outcome of a disease.
 Population genetics, and statistical genetics in order to link variation in genotype with a
variation in phenotype. This has been used in agriculture to improve crops and farm
animals (animal breeding). In biomedical research, this work can assist in finding
candidates for gene alleles that can cause or influence predisposition to disease in human
genetics
 Analysis of genomics data, for example from microarray or proteomics experiments.
Often concerning diseases or disease stages.
 Ecology, ecological forecasting
 Biological sequence analysis
 Systems biology for gene network inference or pathways analysis.