BIS 2C Lab Practical

phylogenetic tree

a diagram that represents the pattern of **ancestor-descendent relationships** among a group of organisms

phylogenies

these are routinely used in many areas of biology, including biogeography, conservation biology, epidemiology, forensics, pharmaceutical chemistry and medicine.

speciation

in the simplest model, this is shown through the rise of new species when an ancestral lineage splits into two descendents

taxon

we use the term ____________ forever to a group group of organisms at an unspecified taxonomic rank. A ____________ can be a family, phylum, genus, or any other rank of in the Linnaean hierarchy.

node

the intersection of each split in a phylogenetic tree is referred to as a ____________ and it represents the MCRA of two or more descendent lineages, each one represents a speciation event

root node

what represents the MCRA of **ALL** taxa on the phylogeny

internal node

all nodes that are not the root node are referred to as a what?

sister taxa

the pair of taxa resulting from a lineage split are referred to as ___________ _____________. By definition the arise at the same time.

rotate

When deciphering the pattern of lineage splitting it is important to note that each node is free to ____________ without changing our interpretation of relationships.

cladogram

only shows the pattern of lineage splitting; the lengths of the branches have no meaning

phylogram

shows the pattern of lineage splitting and the proportion of genetic change on each branch, the length of the branches on these vary and they are typically accompanied by a scale bar proportional to the amount of genetic change. The amount of change is expressed as the as the average number of changes per site in DNA sequence. Therefore, the longer a branch is on a ____________, the more divergent taxa are from each other.

chronogram

shows the pattern of lineage splitting associated with specific (absolute) geologic times, often presented in millions of years ago (MYA)

characters

heritable traits or features are often referred to as ____________, the most common ones that are used by phylogeneticists are morphology, genetics and behavior

ancestral

a character state present in the MRCA of a group (node) is often referred to as ____________.

derived

any states that evolved after the ancestral character are referred to as ____________.

homology

a key concept that refers to the similarity in characteristics among organisms that is due to a **shared ancestry**. A classic example of this bones within the limbs of humans, birds and bats.

homoplasies

characters that appear similar, but are a result of convergent evolution, are called ____________. A good example is wings.

parsimony

when using ____________, we seek a phylogeny that minimizes the number of evolutionary changes; so the tree with the fewest number of character changes is our preferred hypothesis.

ingroup

organisms which are the specific focus of a study are referred to as what?

outgrip

An ____________ is one or more taxa that are as closely related to the in-group as possible without actually being part of it, ideally they would be the sister taxon of the ingroup.

taxonomy

the naming and description of species is a science onto itself and it is known as ____________

binomial nomenclature

In this system, each species gets a two part name where the first part is the genus (homo) and the second part is the specific epithet (sapiens). Note that genus is capitalized and specific epithet is lowercase, both are underlined or italicized.

monophyletic group

a group that contains all descendants of the MRCA, another name for it is a clade

polytomy

these are used to reflect uncertainty, whether it be missing or incomplete data (soft) or just rapid divergence (hard).

congruence

common branching pattern

Bacteria, Archaea, and Eukarya

Carl Woese was the first to propose a system where all living organisms are separated into three domains, what are the three domains?

prokaryotes

Bacteria and Archaea are often collectively referred to as _______________ because they lack a nucleus (it’s important to note that they are not each other’s closest relatives though

microbe

this term is used to refer to microscopic organisms in **any** of the domains and **viruses**

two domain

current studies have shown some support for the alternative “___________ ___________” tree of life

Asgard

In the two domain hypothesis, the sister group of eukaryotes are a subset of archaea called what? (hint, think Marvel)

coccus

this morphology of bacteria and archaea is sphere shaped

bacillus

this morphology of bacteria and archaea is rod-shaped

helical or spiral

this morphology of bacteria and archaea is an elongate spiral, goes by two names

biofilm

a group of microbes that is bound to a surface

binary fission

most bacteria and archaea reproduce through ___________ ____________ , where the chromosome is copied so that each daughter cell is genetically identical

energy, electron, and carbon

what three components (sources) drive metabolism

photography

energy is captured from light

chemotrophy

energy is taken from chemical reactions

lithotrophs

organisms that use inorganic electron donors, like hydrogen sulfide

organotrophs

organisms that use organic electron donors, like methane

autotrophs

organisms that utilize inorganic compounds as a carbon source, like CO2

heterotrophs

organisms that utilize organic, more complex compounds as a carbon source that include C, H and O, such as sugars

extremophiles

habitats for _______________ included the most acidic or basic conditions, temperatures fall to -12° C or rise to 113° C; the water is too salty to support any other life and the radiation irreparably damages the DNA of most other organisms

mesophiles

organisms that live in more ‘normal’ temperatures are called _____________.

acidophile

lives in pH less than 2

alkaliphile

lives in pH greater than 8

psychrophile

lives in temperatures less than 15°C

halophile

lives in salty conditions

thermophile

lives in temperatures about 40°C

xerophile

lives in extremely dry temperatures

lateral gene transfer

In ____________ ____________ ____________, DNA moves from one organism to another via specialized processes

transformation

this is a process of LBT whereby DNA found in the environment (e.g., DNA that came from a cell that is dead and lysed) are moved into an intact cell. The DNA can replace a portion of the recipient’s chromosome or it can add new DNA to the recipient cell’s chromosome. It can also stay as a separate replicating entity.

conjugation

this is a process of LGT that looks similar to mating, but it can occur between distantly related cells and does not result in offspring. It generally involves the transfer from one cell to another of a small piece of DNA known as a plasmid. In ______________ a tube called a sex pilus forms between two cells and a plasmid in the donor cell replicates and one copy passes through the pilus. The plasmid duplicates inside the daughter cell and the pilus breaks.

transduction

_____________ is the incorporation of new genetic material into a host throughout the action of viral particles. Virus particles carry DNA from one host to another and once in the new host, the DNA can be incorporated into the cell’s chromosome or replicate as a separate entity.

great plate count anomaly

the discrepancy between observed microbes in the field and those that can be grown in pure lab cultures in know as the what?

false

True or false, scientists have been able to study most bacteria and archaea directly in a lab

last universal common ancestor

what does LUCA stand for?

mutualism

both organisms benefit from this interaction

parasitism

the parasite benefits while the host is harmed

commensalism

an interaction where one organism benefits but the effect on the other is unknown or negligible

microbial eukaryotes

As with all eukaryotes, _________ ______________ have a nucleus, mitochondria and a cytoskeleton. Some lineages also have chloroplasts that are used for photosynthesis. They can be unicellular, multicellular and colonial. This group also shows great diversity in morphology.

protists

historically, microbial eukaryotes were referred to as what?

locomotion

there are many different body forms of microbial eukaryotes but, unlike Bacteria and Archaea, their body morphologies tend to be associated with forms of ______________.

Ciliate

The _______________ form has numerous short hair like structures in rows across the cell surface, some _______________s are capable of very rapid movement and often use their hair like structures to feed. (the hair like structures are a shortened version of the name of this form)

Amoeboid

The _______________ form has an irregular shape and moves by cytoplasmic streaming using pseudopodia, this type of movement is typically slow.

Flagellate

This body form has one to many whip like structures and are capable of very fast movement. It is important to note that this structure is **not** homologous among bacterial and eukaryotes

microtubules, microfilaments

______________ are part of a cilium or a flagellum, whereas _________________ are active in amoeboid movement.

phagocytosis

the lack of a cell wall the use of a cytoskeleton allows many eukaryotes to perform _____________ where soil food particles are taken directly into the cell

symbiosis

Eukaryotic cells are most likely the product of a _______________ between bacteria and a eukaryotic cell.

Lynn Margulis

who was the the first person to synthesize all of the evidence and eventually many of her arguments formed the foundation of endosymbiotic theory?

asexual reproduction

the genotype is copied into a new body and the all organisms are gentically identical, aside from mutations. However in many taxa, these genetically identical organisms do not have the same body morphology.

1\.778

When calculating the size of an organism in a microscope, the field diameter depends on the lens. What is the field diameter of a microscope at 10x magnification (in mm)?

0\.55

When calculating the size of an organism in a microscope, the field diameter depends on the lens. What is the field diameter of a microscope at 40x magnification (in mm)?

euglena

these use ciliate movement, size approximately 0.05 mm

blepharisma

these use ciliate movement, size approximately 1 mm

chlamydomonas

they use flagellate movement, size approximately 0.01 mm

paramecium

they use ciliate movement, size approximately .05 to 0.32 mm

stentor

large and green with irregular trumpet shape, they use ciliate movement, size approximately 2mm

distance matrix

a way of summarizing the percent difference between taxa

eukaryote

what type of organism is being consumed during secondary endosymbiosis? Is it a bacterium or a eukaryote?

primary endosymbiosis

secondary endosymbiosis

tertiary endosymbiosis

apicomplexa

a phylum of diverse obligate intracellular parasites including Plasmodium spp., the cause of malaria;

plasmodial slime mold

A ___________ ________ _________ is enclosed within a single membrane without walls and is one large cell. This "supercell" (a syncytium) is essentially a bag of cytoplasm containing thousands of individual nuclei.

cellular slime mold

___________ ________ _________(dictyostelids) are groups of unicellular amoebae that collaborate to form fruiting structures to disperse spores

Naeglaria

a microbial eukaryote that has the unusual ability to change its body form from amoeboid to flagellate and back again. We performed an experiment with this microbial eukaryote where we removed food and observed them given different time intervals. This helped show us how body morphology changed in response to time without food.

eukaryotes

_______________ are characterized by the presence of a mitochondrion, a nucleus and membrane bound organelles

Plantae, embryophytes, algae

___________ is a lineage that includes the familiar land plants (___________)__ but also includes a variety of unicellular and multicellular photosynthetic eukaryotes often referred to as _____________. (put a common between three answers)

synapomorphy

a characteristic present in an __ancestral__ species and shared exclusively (in more or less modified form) by its __evolutionary__ __descendants__.

embryophytes

these are synapomorphies of what group?

* waxy cuticle
* alternation of generations
* multicellular gametangia with sterile jacket
* multicellular embryo
* apical cell with 2 or more cutting faces

lycopodium and selaginella

what two groups of plants have microphylls?

selaginella

where did heterospory **first** evolve?

tracheophytes

these are synapomorphies of which group?

* vascular tissue (xylem and phloem)
* traceids
* apical meristem
* reduced gametophyte
* dominate branched sporophyte

euphyllophytes

these are synapomorphies of which group

* chloroplast DNA inversion
* megaphylls

monilophytes

these plants are all part of which group?

* equisetum
* psilotum
* ferns

seed plants

these are all synapomorphies of which group?

* integument (the outer layer(s) of the ovule and develop into a seed coat as the ovule matures following fertilization)
* ovule
* seeds
* pollen
* pollen with pollen tube
* bifacial vasular cambium
* heterospory

gymnosperms

these are all plants in which group

* cycad
* ginko
* gnetophytes
* conifers

gnetophytes

which plant evolved to have vessel elements on the plant phylogeny **before** they appeared as a synapomorphy of a plant group?

angiosperms

these are all synapomorphies of which group?

* endosperm
* double fertilization
* carpel
* fruit
* vessel elements