Phylogeny and The Tree of Life

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PHYLOGENY AND THE TREE OF LIFE

 Phylogenies Show Evolutionary Relationships


1) Binomial Nomenclature
 Was instituted in the 18th century by Carolus Linnaeus.
 The first part of a binomial is the name of the genus to which the species
belongs.
 The second part, called the specific epithet, is unique for each spesies within
the genus.
 Notice that the first letter on the genus is capitalized and the entire binomial is
italicized.
 An example of a binomial is Panthera pardus, the scientific name for the large
cat commonly called the leopard.
2) Hierarchial Classification
 The first grouping is built into the binomial : Species that appear to be closely
related are grouped into the same genus. For example, the leopard (Phantera
pardus) belongs to a genus that also includes the African lion (Phantera leo),
the tiger (Phantera tigris), and the jaguar (Phantera onca).
 The Linnaean system places related genera in the same family, families into
orders, orders into classes, classes into phyla, phyla into kingdoms, and
kingdoms into domain.
 The name taxonomic unit at any level of the hierarchy is called taxon. In the
leopard example, Phantera is a taxon at the genus level, and mamalia is a
taxon at the class level.
3) Linking Classification and Phylogeny
 The evolutionary history of a group of organisms can be represented in a
Phylogenetic tree.
 Some systematists propose that classification be based entirely on
evolutionary relationships.
 In other situations, however, certain similarities among organisms may lead
taxonomists to place a species within a group organisms other than the group
to which it is most closely related.
 Organisms that share very similar morphologies are likely to be more closely.
 Homology (similarity due to shared ancestry) must be sorted from analogy
(similarity due to convergent evolution).
 Cladistics is a monophyletic grouping that includes an ancestral species and all
of its descendants.
 Among phylogenies, the most parsimonious tree is the one that requires the
fewest evolutionary changes.
 The tree of life which consists of three great domains : Bacteria, Archaea, and
Eukarya.
 Phylogenies based on rRNA genes suggest that eukaryotes are most closely
related to archaea.
 The earliest organisms may have formed a “ring of life” in which eukaryotes
are equally closely related to bacteria and archaea.

 An Organism’s Evolutionary history is documented in its genome


 Gen Duplications and Gen Families. The term orthologous genes refers to
homologous genes thst are found in different species because of speciation.
 Paralogous genes result from gene duplication, so they are found in more
than one copy in the same genome.
 Genome Evolution. Distantly related species often have orthologous genes.
 A molecular clock analysis suggests that the most common strain of HIV
jumped from primates to humans in the 1930s.

BACTERIA AND ARCHAEA


 Structural and Functional Adaptations Contribute to Prokaryotic success
 Prokaryotic populations have been and continue to be subjected to natural
selection under many different environmental conditions.
 Most prokaryotes are unicellular.
 Prokaryotic cells have a variety of shapes, the three most common of which
are spheres (cocci), rods (bacilli), and spirals.
1) Cell Surface Structures
 Cell wall in prokaryotic cell which maintains cell shape, provides physical
protection, and prevents the cell from hypotonic environment.
 In a hypertonic environment most prokaryotes lost water and shrink away
from their wall (plasmolyze)
 Moat bacterial cell walls contain peptidoglycan.
 Archaeal cell walls contain a variety of polysaccharides and proteins but lack
peptidoglycan.
 Gram-positive bacteria have simpler walls with a relatively large amount of
peptidoglycan.
 Gram-negative bacteria have less peptidoglycan with an outer membrane that
contains lipopolysaccharides.
 The cell wall is covered by a capsule to adhere to their individuals in a colony.
 Fimbriae hairlike appendages that help cells adhere to other cells.
 Sex pilus appendage that facilitates conjugation.
 Circular chromosome often accompanied by smaller rings of DNA called
plasmids
2) Reproduction and Adaptation
 Prokaryotes can reproduce quickly by binary fission.
 Prokaryotic populations can evolve in short periods of time in response to
changing environmental conditions.
 Rapid Reproduction, Mutation, and Genetic Recombination Promote Genetic
Diversity in Prokaryotes.
1) Rapid Reproduction and Mutation
 Because prokaryotes can often proliferate rapidly, mutations can quickly
increase a population’s genetic variation, enabling adaptive evolution.

2) Genetic Recombination
 Genetic diversity in prokaryotes also can arise by recombination of the DNA
from two different cells.
 Diverse Nutrional and Metabolic Adaptations Have Evolved in Prokaryotes
 Four modes of nutrition : Photoautotrophy, Chemoautotrophy,
Photoheterotrophy, and Chemoheterotrophy.
1) The Role of Oxygen in Metabolism
 Obligate aerobes use o2 for cellular respiration and cannot grow without it.
 Obligate anaerobes are poisoned by o2, some obligate anaerobes live by
fermentation; extract chemival energy by anaerobic respiration.
2) Nitrogen Metabolism
 Prokaryotes can metabolize nitrogen in a wide variety of forms. For example,
some cyanobacteria and some methanogens convert atmospheric nitrogen to
ammonia, a prosess called nitrogen fixation.
3) Metabolic Cooperation
 Metabolic cooperation between different prokaryotic species often occurs in
surface-coating colonies known as biofilms.
 Archaea
 The first prokaryotes assigned to domain Archaea live in environments so
extreme, such organisms called extremophiles.
 Extreme halophiles live in highly saline environments, such as the Great Salt
Lake, The Dead Sea, and Owens Lake.
 Extreme thermophiles thrive in very hot environments.
 Other archaea live in more moderate environments, some of these are included
among the methanogens.
 Bacteria
 Bacteria include the vast majority of prokaryotes from the pathogenic spesies
that cause strep throat and tuberculosis.
 Major groups of bacteria :
a. Proteobacteria
b. Chlamydias
c. Spirochetes
d. Cyanobacteria
e. Gram-positive bacteria
 Prokaryotes Play Curcial Roles in The Biosphere
1) Chemical Recycling
 Chemoheterotrophic prokaryotes function as decomposer.
 Prokaryotes also convert inorganic compounds to forms that can be taken up
by organisms.
 Prokaryotes can also decrease the availability of key plant nutrients.
2) Ecological Interactions
 An ecological interaction between two species in which both benefit, the
interaction takes the form of commensalism.
 Some prokaryotes engage in parasitism.
 Prokaryotes Have Both Harmful and Benefit Impacts on Human
1) Pathogenic Bacteria
 Pathogenic prokaryotes usually cause illness by producing poisons, which are
classified as exotoxins and endotoxins.
 Exotoxins are proteins secreted by certain bacteria and other organisms.
Cholera, a dangerous diarrheal disease, is caused by an exotoxins secreted by
the proteobacterium.
 Endotoxins are lipopolysaccharide components of the outer membrane of
gram-negative bacteria. Endotoxins are released only when the bacteria die
and their cell walls break down.
2) Prokaryotes in Research and Technology
 Experiments involving bacteria such E.coli and A.tumefaciens have led to
important advances in DNA technology.

PROTISTS
 Most Eukaryotes are Single-Celled Organisms
 Protists along with plants, animals, and fungi are classified as eukaryotes, they
are in domain Eukarya.
 Organisms in most eukaryotic lineages are protists, and most protists are
unicellular.
1) Structural and Functional Diversity in Protists
 Most protists are unicellular, although there are some colonial and
multicellular spesies.
 Single-celled protists are justifiably considered the simplest eukaryotes.
 In multicellular organisms, essential biological functions are carried out by
organs.
 Unicellular protists carry out the same essential function, but they do so using
subcellular organelles.
 Some protists are photoautotrophs and contain chloroplasts.
 Some are heterotrophs, absorbing organic molecules.
 Still others called mixotrophs, combine photosynthesis and heterotrophic
nutrition.
 Some protists are exclusively asexsual.
 Others can also reproduce sexually or at least employ sexual processes of
meiosis and fertilization.
2) Endosymbiosis in Eukaryotic Evolution
 Much f protists diversity has its origins in endosymbiosis, the process in which
certain unicellular organisms engulf other cells, which become endosymbionts
and ultimately organelles in the host cell.
 Red algae and green algae underwent secondary endosymbiosis.
3) Five Supergroups of Eukaryotes
 Excavata – Excavates include parasites such as Giardia.
 Chromalveolata – include some of the most important photosynthetic
organisms.
 Rhizaria – this group consists of spesies of amoebas.
 Archaeplastida – includes red algae and green algae along with land plants.
 Unikonta – includes amoebas that have lobe or tube shaped pseudopodia.
 Protists Play key Roles in Ecological Relationshipps
1) Symbiotic Protists
 Protists form a range of mutualistic and parasitic relationships that affect their
symbiotic partners and many other members of the community.
2) Photosynthetic Protists
 Among the most important producers in aquatic communities, because they
are at the base of the food web, factors that affect photosynthetic protists affect
many other species in the community.

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