Introduction to Systematics and Taxonomy Flashcards
systematic biology is a coombination of two major disciplines in biology:
taxonomy
systematics
naming, describing, and cllassifying of organisms.
branch of biology concerned with identifying, naming, and classifyying organisms
taxonomy
relationship and evolutionary development among organisms
systematics
2 things that consist systematics
cladistics
phenetics
pathways of evolution (how)
cladistics
degree of similarity (how much)
phenetics
5 components/principles of systematic biology
classification
identification
description
nomenclature
phylogeny
principle - similarities among observed organisms
classification
3 components under the principle classification
artificial based
natural based
phylogenetic
classification using gross morphological structures
artificial based
classification based on developmental and morphological structures
natural based
classification based on genetic inheritance, similarity and difference across species
phylogenetic
principle - assignment of distinct ecological niche (specific role)
identification
principle - unique (diagnostic) characteristics of the organism
statement of characters in taxonomy
description
principle - standard naming procedures of new species
nomenclature
principle - genealogy (ancestor and descendant analysis)
phylogeny
described the idea that organic compounds (C-containing) are capable of self-assembly, self-replication, auto-catalysis of chemicals under the similar conditions in the early period of Earth.
Oparin-Haldane Hypothesis
term associated with the Primordial Soup Model
abiogenesis
other name for primordial soup model
prokaryotic cell evolution
term associated with prokaryotic ingestion model
endosymbiosis
other name for prokaryotic ingestion model
eukaryotic cell evolution
it describes that certaiin prokaryotes are capable of engulfing and assimilating other prokaryotes to generate double-membrane cells that contains combined functions of both cells.
endosymbiosis hypothesis
it describes the idea that the statistical probability of successful evolution cannot occur without a guiding intellectual cause - unlike in the theory of evolution by natural selection
intelligent design theory/hypothesis
three hypotheses explaining the origin of life
Oparin-Haldane hypothesis
Endosymbiosis hypothesis
Intelligent design hypothesis
5 mechanisms of evolution that generate biodiversity
mutation
non-random mating
gene flow (migration)
genetic drift
natural selection
mechanism of evolution - changes in the DNA yields different expressions of traits
mutation
mechanism of evolution - reproduction preference and conditions can influence the general characteristic of the population
non-random mating
mechanism of evolution - movement oof organisms across different population
gene flow (migration)
mechanism of evolution - declining frequency of specific genes is an advantage to others
genetic drift
mechanism of evolution - suitability of specific traits to environment is disadvantageous
natural selection
application of a correct name to an organism or a taxonomic group
nomenclature
standard nomenclature in naming organisms
binomical nomenclature (Linnaean)
main proponent of binomial nomenclature.
developed in the mid-eighteenth centure
Carl von Lannaeus
4 characteristics of binomial nomenclature
- binomial (2 epithet)
- genus epithet - uppercase first letter
- italicized/underline (both epithets). If genus is mentioned already, use a capital letter (G.)
- 8 hierarchical classification
8 hierarchical classification
domain
king
phylum
class
order
family
genus
species
a group of organisms that fills a particular category of classification
taxon
year that the Primordial Soup Theory ws introduced
1924
taxonomy word origin
taxis - arrangement
nomia - method
science of naming, defining, (circumscribing) and classifying groups of biological organisms on the basis of shared charactristics which includes the bases, rules, and procedures of naming organisms.
taxonomy
study of the diversification of living forms, both past and present, and the relationships among living things tthrough time.
biological systematics
or
systematic biology
used to understand the evolutionary history of life on earth.
systematics
studies the pathways of evolution
cladistics
the study of relatinoship among a group of organisms on the basis of the degree of similarity between them, be it molecular, phenotypic, or anatomical.
phenetics
analytical branch of biology that relies on fossil record data, comparative anatomy and development, and molecular data to determine evolutionary relationship
systematics
5 components of systematics
classification
identification
description
nomenclature
phylogeny
arrangement of organisms into groups on the basis of similarities
classification
3 types of classification
artificial
natural
phylogenetic
based on arbitrary, easily observable characters
artificial
uses overall simmilarity in grouping
natural
based on evolutionary descent of a group of organism
relationship depicted through phylogram
phylogenetiic
recognizing unknown specimen with an already known taxon and assigning a correct rank and position in an extant classification.
identification
involves listing taxon’s features by recognizing appropriate characters or character states known as diagnostic characters.
description
determination of a correct name for a taxonusing rules and recommendations of the CODE which contains rules to obey and has recommendations which is strongly advised to follow.
nomenclature
study of the genealogy and evolutionary histoy of a taxonomic group
phylogeny
study of ancestral relationships ad lineages; relationships are depicted through a diagram known as a phylogram/cladogram
genealogy
theory stating that all life sprouted froma complex RNA world
Ribonucleic acid (RNA) Theory
the first self-replicating information-storage molecule
catalyzed the assembly of the first proteins
RNA
RNA is older than DNA?
true
the first genetic material
RNA
RNA is older, and far more sefl-eplicating, if less efficient, than DNA
true
___ from the soup model catalyst the formation of ___ in the form of ____ which started as marine photosynthetic bacteria which emerged around 2.5 billion years ago.
RNA
prokaryotes
Cyanobacteria
the ___ and __ succeeded the cyanobacteria
Archaebacteria
Eubacteria
evolution of prokaryotes (process)
inorganic molecules > RNA nucleotides > RNA macromolecules (self-replicating) > RNA molecules catalyze protein synthesis > Proteins
___ were the first eukaryotes andd evolved into ___ the first multicellular organisms around 700 million years ago.
protists
algae
the first vertebrates to evolve into amphibians
fishes
amphibians > reptiles > birds and mammals (t/f)
true
the different genetic traits, species, and ecosystem components of the earth.
biodiversity
identified the first principle of the origin o modern biodiversity, namely that all species were linked in a single great phylogeny, or tree of life, and that all could be traced back to a presumed single original species at some distant time in the geological past.
Charles Darwin
5 mechanisms of evolution that leads to biodiversity of life
mutation
non-random mating
gene flow (migration)
genetic drift
natural selection
the changing of the structure of a
gene, resulting in a variant form that may be
transmitted to subsequent generations, caused
by the alteration of single base units in DNA, or
the deletion, insertion, or rearrangement of
larger sections of genes or chromosomes.
“mutation is, ultimately, the only way in which
new variation enters the species”
mutation
organisms choose their
mate with each other, with preference for
particular genotypes. It occurs when the
probability that two individuals in a population
will mate is not the same for all possible pairs of
individuals. Nonrandom mating can take two
forms: Inbreeding - individuals are more likely to mate with close relatives (e.g. their neighbors)
than with distant relatives.
non-random mating
is any movement of
individuals, and/or the genetic material they
carry, from one population to another. Gene
flow includes lots of different kinds of events,
such as pollen being blown to a new destination
or people moving to new cities or countries. If
gene versions are carried to a population where
those gene versions previously did not exist,
gene flow can be a very important source of
genetic variation. In the graphic below, the gene
version for brown coloration moves from one
population to another.
gene flow/migration
the genes of a strong individual
will persist and may, just by chance, leave
behind a few more descendants or genes than
other individuals. The genes of the next
generation will be the genes of the “lucky”
individuals, not necessarily the healthier or
“better” individuals.
genetic drift
the process through which
populations of living organisms adapt and
change. Individuals in a population are naturally
variable, meaning that they are all different in
some ways. This variation means that some
individuals have traits better suited to the
environment than others
natural selection
says that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection. (Behe MJ and Meyer SC 2018).
intelligent design theory
scientific theory which has its roots in information theory and observations about intelligent action.
intelligent design
“global species richness”
biodiversity
employs a very slim chance of creating new
species hence it requires a very long period of time.
evolution
intelligent design theory makes no statements about the identity
of the intelligent designer(s), but merely says that
intelligent action was involved at some points with the
origins of various aspects of biological life.
true
Mutation could not produce
speciation because it violates the two natural laws.
true
application of a correct name to an organism or a taxonomic group
nomenclature
why are scientific names in Latin?
latin is a dead language because it does not change or modify
reasons for using Latin language
consistent name of species worldwide
intenational name
make use everybody is using the same Latin name for a speices
for plants, ___ is used instead of phylum
division
need for scientific name instead of vernacular or common name
a. Vernacular names are not available for all the
species known to man,
b. Vernacular names are restricted in usage and are
applicable in one or few language only or not
universal,
c. Common names usually do not provide information
indicating family or generic relationship,
d. Many common names may exist for the same
species in the same language in the same or
different localities, and
e. Often two or more unrelated species are known by
the same name.
plants
ICBN
animals
ICZN
bacteria
international code for nomenclature of bacteria
cultivated plants
international code of nomeclature for cultivated plants, based on ICBN
- Simplest plants
- No true roots
- No vascular tissues (no transport system)
- Simple stems and leaves
- Have rhizoids for anchorage
- Spores from capsules (wind-dispersals)
- Damp terrestrial land
mosses
- Roots, feathery leaves, and underground stems
- Have vascular tissues (transport and support)
- Spore-producing organ on the underside of leaves
(reproduction) - Damp and shady places
ferns
- Tall, evergreen trees
- Roots, woody stems
- Needle-shaped leaves
- Vascular tissues (transport)
- Cones with reproductive structures
- Naked seeds in female cones
- Dry places
gymnosperms
*One-seed leaf
* Leaves have parallel veins
* Herbaceous plants
* E.g. grass, maize
monocotyledon
- Two-seed leaves
- Leaves have veins in network
- E.g. trees, sunflower, rose
dicotyledons
- Prokaryotic
- (+) cell membrane
- Cell wall is made up of pseudomurein
- extremophiles
- chemoautotrophs
- some are heterotrophs
Archaea
thrive in extreme conditions
extremophiles
Ability to produce methane (methanogenesis),
utilize alternative energy sources like sulfur or
hydrogen gas, and perform photosynthesis.
archaea
derives energy from inorganic compounds
chemoautotrophs
obtains energy from organic matter
heterotrophs
ecological significance of Archaea
- Found in diverse environments worldwide
- Important roles in biogeochemical cycles
- Involved in nutrient cycling, carbon fixation,
and the degradation of complex organic
compounds.
symbiotic relationships of Archaea
- Methanogenic archaea can be found in the
digestive tracts of animals - Symbiotic associations with marine animals
- these are not typically associated with human diseases
- some species can be found in human microbiomes
Archaea
4 classifications of Archaea
euryarchaeota
crenarchaeota
nanoarchaeota
korarchaeota
methanogens
halobacteria
euryarchaeota
produce methane as a metabolic waste product
methanogens
thrive in extreme saline environments
can form reddish blooms
halobacteria
the ability of halobacteria to form reddish forms is attributed to the presence of ___
bacteriorhodopsin
- Play a crucial role in carbon fixation.
- Many members are extremophiles that are
sulphur-dependent, thermophilic, or
hyperthermophilic. - Examples include Sulfolobus
crenarchaeota
grow in volcanic springs at high temperatures and low pH
sulfolobus
- Contains a single species,
- isolated from the bottom of the Atlantic Ocean
and hydrothermal vents at Yellowstone National
Park. - Forms an obligate symbiotic relationship with
Ignococcus, another species of archaea
nanoarchaeota
the only species under nanoarchaeota
Nanoarchaeum equitans
- Considered one of the most primitive forms of
life. - Found only in the Obsidian Pool, a hot spring at
Yellowstone National Park.
korarchaeota
methanogens and other archaea play a vital role in ____
biogeochemical cycle
methane produced by methanogens affect the global climate change
true
some archaea form ____ with other organisms
symbiotic associations
methanogens aid ____ and ____ in ruminant animals
digestion
methane production
archaea provide energy through ___ in symbiotic associations in marine animals
chemosynthesis
- Archaea represent an early diverging domain of
life. - Studying archaea sheds light on cellular
processes, genetics, and metabolism. - Understanding the archaea enhances our
knowledge of the tree of life and biological
origins.
importance of the evolutionary insights of Archaea
cell wall of archaea is made up of
pseudomurein
- Prokaryote
- (+) cell membrane
- Cell wall is made up of peptidoglycan
eubacteria
cell wall of eubacteria is made up of
peptidoglycan
eubacteria are classified into
nutritional categories
some bacteria can fix __ for other organisms
nitrogen
ecological roles of eubacteria
- Participate in nutrient cycling, decomposition,
and compound recycling. - Form symbiotic relationships wit plants,
animals, and humans.
positive impacts of bacteria
beneficial bacteria aid in digestion, produce vitamins, and
support the immune system
bacteria that can cause diseases
pathogenic bacteria
industrial and biotechnological appllications of eubacteria
- Antibiotics, enzymes, biofuels, and other
bioproducts. - Wastewater treatment, bioremediation, and
agriculture.
genes are different from eukarya
bacteria
genes are more similar to eukarya
archaea
5 classifications of eubacteria
proteobacteria
chlamydiae
spirochetes
cyanobacteria
gram-positive bacteria
proteobacteria that is photoautotrophic, symbionts, or pathogens
alpha proteobacteria
proteobacteria - human gut symbionts and pathogens
beta proteobacteria
proteobacteria - generate spore-forming fruiting bodies or reduce sulfur
delta proteobacteria
proteobacteria - in animal digestive tracts and hydrothermal vents
epsilon proteobacteria
- Obligate intracellular parasites of animal cells.
- (-) peptidoglycan
- STDs and other infections
chlamydiae
- Spiral-shaped cells with flagella running
lengthwise. - May be harmless or pathogenic.
- Species causing syphilis and Lyme disease
spirochetes
- Obtain energy through photosynthesis.
- In various environments and produce oxygen.
- Eukaryotic chloroplasts
cyanobacteria
- (+) thick cell wall
- (-) outer membrane
- May decompose organic matter, others causing
disease. - Species causing anthrax, botulism, and
antibiotic-resistant infections
gram-positive bacteria
classifications of bacteria based on shape
cocci
bacilli
spirilla
coccobacilli
vibrios
- Spherical-shaped bacteria
- Staphylococcus and Streptococcus
cocci
- Rod-shaped bacteria
- Escherichia coli and Bacillus anthracis
bacilli
- Spiral-shaped bacteria
- Treponema pallidum and Spirillum volutans
spirilla
classification of bacteria on the compostion of the cell wall
gram-positive
gram-negative
- Thick peptidoglycan layer in cell wall.
- Retain crystal violet stain in Gram staining.
- Staphylococcus aureus, Streptococcus pyogenes
gram-positive
- Thinner peptidoglycan layer and outer
membrane. - Contain lipopolysaccharides.
- Do not retain crystal violet stain in Gram
staining. - Escherichia coli, Pseudomonas aeruginosa
gram-negative
classification based on the mode of nutrition (source of carbon)
autotrophs
heterotrophs
- Principal source of carbon utilization is CO2
- Purple and green sulfur bacteria
atutotrophs
- Depend on the others’ organic compounds
- Escherichia coli, Salmonella Typhi, Proteus
spp., Staphylococcus aureus, Lactobacillus
acidophilus
heterotrophs
classification of bacteria based on the mode of nutrition (source of energy)
phototrophs
chemotrophs
- Utilize light as their source of energy
- Chromatium okenii, Rhodospirillum rubrum,
etc.
phototrophs
- Energy from the oxidation of organic or
inorganic compounds. - Nitrosomonas, Pseudomonas pseudoflava
chemotrophs
classification of bacteria baed on mode of nutrition (source of electrons)
lithotrophs
organotrophs
- Use inorganic compounds as the electron
source - Nitrobacter, Thiobacillus denitrificans,
Nitrosomonas, etc.
lithotrophs
- Use organic compounds as electron source
- Pseudomonas pseudoflava
organotrophs
classification of bacteria based on the type of flagella
monotrichous
lophotrichous
amphitrichous
peritrichoous
- Flagellum is present only at one end of bacteria,
polar. - Pseudomonas aeruginosa
monotrichous
- A cluster of flagella is present only at one end of
bacteria. - Pseudomonas fluorescens
lophotrichous
- Flagella are present in both ends of the bacteria
in single or clusters. - Aquaspirillum serpens
amphitrichous
- Flagella are present all around the body.
- Salmonella Typhi
peritrichous
classification of bacteria based on the ability to form spores
non-spore formers
spore formers
- Do not form spores
- E. coli, Staphylococcus aureus
non-spore formers
- produce spores
8 exospores - endospores
spore formers
- spores roduced outside of the cell
- Methylosinus
exospores
spores produced inside but at different locations
endospores
3 types of endospores
terminal spore
central spore
subterminal spore
classification of bacteria based on the optimal growth pH
acidophiles
neutrophiles
alkalophiles
- Grow at low pH with the pH optimum of pH 0 to
5.5. - Sulfolobus, Picrophilus, Ferroplasma, Cyanidium
caldarium
acidophiles
- Grow at neutral pH with a pH optimum of 5.5.
to 8.0. - Escherichia coli, Salmonella, etc.
neutrophiles
- These bacteria grow at high pH with a pH
optimum of 8.0 to 11.5.
alkalophiles
classification of bacteria based on the required growth temperature
psychrophiles
mesophiles
thermophiles
hyperthermophiles
grows at arounf -5 to 20 C
psychrophiles
grows at 15 C to 45 C
mesophiles
grows at around 45 C to 80 C
thermophiles
grows are 65 C to 105 C
hyperthermophiles
classification based on the mode of respiration
obligate aerboes
obligate anaerobes
facultative anaerobes
facultative aerboes
aerotolerant anaerobes
microaerophiles
no oxygen level preference
aerotolerant
grow in the basence and presence of oxygen bt prefers O2 presence
facultative aerobes
require 2% of atmosphere oxygen for growth
microaerophiles
killed by normal atmospheric concentrations of oxygen
obligate anaerobes
need oxygen because they cannot ferment or respire anaerobically
obligate aerobes
ecological roles of eubacteria
- Involved in nutrient cycling, including nitrogen
fixation and organic matter decomposition.
positive impact of eubacteria to human health
digestion, vitamin production, and immune system
bacteria that can cause infectious diseases
pathogenic bacteria
importance of eubacteria to biotechnology and industry
- Economic significance in biotechnology and
industry. - Used in the production of antibiotics, enzymes,
and bioactive compounds. - Model organisms for genetic engineering.
importance of eubacteria to food production and fermentation
- Crucial in food production and fermentation
processes. - Contribute to the production of fermented food
like yogurt and cheese. - Bacteria enhance flavor, texture, and
preservation of food products
governs the scientific names for bacteria and archaea
international code of nomenclature for prokaryotes
ICSP
international committee on systematics of prokaryotes
International Code of Botanical Nomenclature
included bacteria, but references to bacteria
were removed in ___
1975
Early code for bacterial nomenclature was
approved in ___ but later discarded.
1947
2008 revision was published in the
international journal of systematics and evolutionary microbiology (IJSEM)
Until 1975, most bacteria were covered by the
bacterial code, while cyanobacteria were
covered by the ___
botanical code
Starting in ___, cyanobacteria were included in
both the botanical and bacteriological codes,
causing nomenclatural problems
1999
By 2020, three proposals were suggested to
resolve the situation
(1) excluding
cyanobacteria from the bacteriological code,
(2)
applying the bacteriological code to all
cyanobacteria, or
(3) considering valid
publication under the botanical code as valid
under the bacteriological code
in 2021, the ICSP held a frmal vote and chose the ___ as the resolution
third option
living culture to which the scientific name of the organism is attached
type strain
To validly publish a new species name, the type
strain must be deposited in a public culture
collection in at least ___ different countries
2
since ___ a type strain must be designated when describing a new bacterial or archaeal species
2001
In cases where a prokaryotic species cannot be
cultivated in the laboratory, it may be given a
________ but is not
considered validly published
provisional candidatus name
Starting in ____, prokaryotic species and
subspecies can be named and considered validly
published under the ______ using high-quality genome
sequences as type
2022
Code of Nomenclature of
Prokaryotes Described from Sequence Data
(SeqCode)
spore found near the end of the cell
subterminal spore
crystal violet serves as the ___ in gram staining
primary stain
the mordant used in gram staining
iodine
spore found at the end of the cell
terminal spore
classification of bacteria with grape-like clustered spherical cells
staphylococci
95% of ethanol or acetone serves as ____ in gram staining
decolorizer
