BIS 2C Midterm 1

Conservation via phylogeny

"preserve the greatest diversity of lineages"--the set of species that best capture the evolutionary history of the group. Ex: African Cichlids--want to preserve/target the Madagascar and east Africa groups.

Monophyletic groups (clades) can be characterized by specific features or characters called what? Why?

(synapomorphies). Because monophyletic groups inherit them from a common ancestor that is not shared with other clades.

Stramenopiles (DOB)

*two flagella*, all cell types (uni, multi, col), plastids from secd. endosym. (DOB) *Diatoms* major primary producers, primarily marine, silica in cell walls--industrial uses, vacuoles hold oil as energy reserve and floatation mechanism--> form natural gas and petroleum deposits. *Oomycetes* water molds, thought to be a fungi, non-photosynthetic--important plants (potato blight) *Brown algae* multicellular (kelp) photosynthetic, carotenoids give color

Prokaryote summary

-Prokaryotes are not a monophyletic group. -All are unicellular -Lack a cell nucleus and cytoskeleton (do not divide by mitosis) -DNA is in a single circular chromosome (usually) -No membrane organelles

Hints that mitochondria and chloroplasts were once bacteria

-surrounded by membrane components found only in bacterial membranes -Morphological similarity -new mito. and chloroplasts form by binary fission -contain own genome and encode some proteins and RNA

How does genetic variation occur in prokaryotes?

1) vertically (asexual reproduction) through mutations that are then selected upon. 2) Plasmids--where small circular genes or sections of a chromosome are passed to clone cells through vertical transmission (can be easily lost) 3) Lateral Gene Transfer (horizontal transmission)

Virus life cycle

1. Enter a susceptible host 2. Replicate and make more virus 3. Move to the newly made virus to susceptible host. Replication: Entering: attach to host cell membrane and go through endocytosis (animal) or penetrate host cell membrane (fungal and plant) through a wound or trauma

Procedure for finding the most parsimonious tree

1. Ignore parsimony-uninformative characters (initially). These are invariant characters that are the same for all taxa or that only one taxa differs in the character state. 2. Draw all possible trees--meaning changing the relationship between taxa via branching patterns 3. For each informative character, count the minimum number of steps required for each tree 4. Sum all the characters--the number of steps in the tree.. including the parsimony uninformative characters. 5. the most parsimonious tree(s) is/are the ones with the least amount of steps overall 6. Root the tree along the branch leading to the outgroup (if known)

How much of the tree of life is microbial? Why have microbes been difficult to place on the tree of life historically?

A large portion of it (Bacteria, protists, prokaryotic archaea). Microbes have been hard to place on the tree of life for many reason, unculturable in a lab, LGT confuses relationships, many convergent evolution traits...

Amoebozoans and example

Amoeboid body form, feed by phagocytosis, unicellular, colonial, multicellular?, i) Plasmodial Slime molds are individual motile cells followed by the formation a single multinucleate cell (plasmodium), forms spores on stalks called fruiting bodies, ii) Cellular Slime molds are individual motile cells that aggregate into a multicellular fruiting body. Each cell retains plasma membrane and individuality, quorum sensing used.

What are the most important sources of human diseases(in terms of evolution)?

Animals because a lot of human associated viruses have jumped from an animal host to humans. (HIV, Influenza, smallpox) Zoonotic disease is an infectious disease that can be transmitted from animals to humans. (Anthrax, plague-yersinia pestis-proteobacterium)

How is antibiotic reproduction (?) related to prokaryote reproduction? How is LGT important for human health?

Antibiotic resistance is an increasingly growing issue, because quickly after an antibiotic is discovered it quickly develops antibiotic resistance. This occurs because of LGT--transferring antibiotic resistance genes and through the quick reproduction as well as clone aspect of reproduction.

Great Chain of Being

Aristotle's idea that each species was designed for a particular "purpose" and species were thought to be fixed and unchanging.

Eukaryotic Reproduction (Sexual and Asexual)

Asexual reproduction often occurs in ideal conditions. Equal splitting-mitosis followed by cytokinesis Budding- outgrowth of a new cell from the surface of an old cell Multiple fission- splitting into more than two cells Spores- specialized cells that are capable of growing a new individual. Sexual reproduction-- all eukaryotic life cycles have at least two steps: 1) fusion of haploid cells to produce a diploid cell. 2) meiosis to reduce diploid cells to haploid. Diplontic life cycle expands only the diploid phase and only the haploid cells are gametes (humans and elephants) Haplontic life cycle expands only the haploid phase and only diploid cells are the zygote generated through fertilization. (fungi and algae) Alternation of generations expansion of haploid and diploid phase through mitosis--both multicellular stages undergo mitosis. (land plants)--Isomorphic alternations of generations means that haploid and diploid phases are morphologically identical.

Cholera in Haiti

Assistance after earthquake in Haiti resulted in a large outbreak of cholera in the area along the river. AID workers who were present in Bangladesh during the last cholera outbreak set up facilities along the river--fecal oral transmission. Proteobacterium--Vibrio cholerae

Differences between Archaea, Bacteria, and Eukarya

Bacteria are the only organisms that have peptidoglycan. Pathogens, photosynthesis via chlorophyll a. Bacteria and Eukarya have unbranched ester membrane lipids. Whereas Archaea have branched and ether linked membranes. Archaea have only known methanogens. Eukarya are unicellular and multicellular whereas prokaryotes are only unicellular. Eukarya also are the only ones with membrane bound organelles Bacteria and archaea can transfer and receive plasmids.

Firmicutes (BCFP)

Bacteria: most are Gram +, low C+G/A+T ratio, some produce endospores that are resistant seeds that germinate when conditions are good, many agents of disease (anthrax, staphylococcus, botulinum, tetanus), many agricultural and industrial use (lactic acid bacteria), some (mycoplasmas) have no cell wall and are extremely small-mycroplasms-smallest cellular organisms known.

Ernst Haeckel

Based his tree of life on morphology and had the plantae, Protista, and animalia groups

What is a biofilm? What are the steps in producing a biofilm? (Positives and negatives?)

Biofilm is a collection of unicellular prokaryotes behaving as a group (Plaque and pond scum) 1) Free-living prokaryote(s) attachment to surface 2) Irreversible attachment, aggregation of prokaryotes, creation of extracellular polysaccharide matrix 3) Growth and division of matrix--signal production attracts same species 4) Structural heterogeneity, mature biofilm, is when other organisms are attracted to the signals and are incorporated into the biofilm. Positives-- protect against pathogenic bacteria, bioremediation (sewage treatment and oil spills), nutrient cycling, component of food chain Negatives-- associated with infectious diseases, dental plaque, corrosion in pipes, boat hulls.

Phylogram

Branch length is proportional to the amount of character change, branching pattern is still relevant.

Chronogram

Branch length is proportional to time.

Nipah virus

Came from bats, infected agricultural animals via infected fruit that was then able to jump host from pigs to humans. Malaysian singapore outbreak--million pigs culled. Overlap of Nipah and Hendra regions leads to possible recombination of viruses through an animal host (bat overlap = pigs eating fruit infected by both viruses)

Single Tree of life

Darwin set the stage for "tree thinking"

Disease, infectious vs. non-infectious

Disease is injurious physiological activity caused by the continuous irritation by a primary causal factor expressed in symptoms Infectious disease caused by a pathogen that can be spread from an infected host to a healthy host. Non-infectious disease is usually caused by environmental or host factors and is unable to spread from infected to healthy host.

What is the difference between prokaryote and eukaryote metabolism

Eukaryotes can only perform limited types of metabolism (photolithoautotroph and chemoorganoheterotroph) whereas prokaryotes dominate in metabolic diversity. For this reason, eukaryotes establish symbiotic relationships with many prokaryotic organisms to benefit from their diverse metabolic abilities

Excavates and example

Eukaryotes: Ancient and diverse lineage, most commonly flagellate, includes many parasites, some groups have lost mitochondria. *Includes medically significant parasites such as Giardia*

How is LGT important for biotechnology?

Example: Agrobacterium tumefaciens (causes crown gall) the TI plasmid can have its TI DNA removed and replaced with foreign DNA that can than be put back into the bacterium cell, the bacterium can then infect plant cells, a plant can be grown from those infected cells w/new DNA and see how those introduced genes affected the plant.

What are Extremophiles? Are more Archaea or bacteria extremophiles?

Extremophiles are microorganisms that can live in very "extreme" conditions--meaning that the environment is skewed towards one end of a spectrum with regards to a condition. A large portion of extremophiles are archaea but occur in both. Thermophiles/psychrophile (temp), halophile (salt), radiophile, pressure (barophile), xerophile (desiccation), alkaliphile/acidophile (pH), anaerobe (oxygen), chemical extremes and gases.

Whittaker

Five kingdoms—based on morphology, philology, and ecology.

Microbes for human use

Food: yogurt, xanthan gum--xanthamonas capestris, pickles, chocolate. Industry: enzymes, bioproducts Health: medicine, probiotics, pathogens Environment: global cycles, biodiversity, bioremediation

Carl Woese and why rRNA?

Found the third domain of life--archaea through rRNA sequencing because DNA sequencing at the time was not good enough. rRNA is present in all free living organisms and can be compared throughout the tree of life, it has evolved slowly enough to still be able to align sequences in distantly related species, it was found in the common ancestor of life, they are phylogenetically informative.

human microbiome and current research

Human microbiome is the community of microbes that live in or on the human body. ----FINSIH

Eocyte Tree

Is the alternate hypothesis that has *two domains of life* archaea and bacteria where eukarya splits off from archaea later in the lineage. This is controversial. In the eocyte tree prokaryotic archaea is paraphyletic but archaea is monophyletic.

What is the purpose of a phylogenetic tree?

It allows us to trace the history of changes in morphology, behavior, geographical distribution, and other features of interest in an organism. Allow us to predict similarities and differences among organisms. They also can reveal surprising relationships--such as birds are a highly modified dinosaur that evolved from an avian dinosaur..

What do changes actually mean in character states?

It is more specifically the substitution of a nucleotide at a specific site in the organisms DNA sequence. This substitution CAN lead to change in population genetics.

What is Lateral Gene Transfer? What are the different ways it happens?

It is the transfer of a small set of genes from one host to another--can be between species, different species, and even different domains. 1) Bacterial Conjugation--sex pilus forms between two cells and plasmids are transferred unidirectionally. 2) Transformation--the ability of a cell to take up genetic material from its environment 3) Transduction-- a bacteriophage injects its viral DNA into a host cell, it hijacks the cellular machinery (it is a parasite of the cell) and uses it to replicate its DNA and then it picks up both viral and host DNA, the cell lyses and the phages are released to further infect other cells.

Limitations of LGT How is LGT different than convergent evolution?

LGT can only transfer small sets of genes that encode for metabolic processes, antibiotic resistance, or virulence attributes but it CANNOT make changes throughout an entire genome-- --> Some adaptations require major changes to be made in the genome to most/all genes (thermophily), which is not possible to occur from LGT so it was most likely convergent evolution

What is the Impact of lateral gene transfer to phylogeny reconstruction?

LGT complicates the reconstruction of a phylogeny because it can make two distantly related taxa appear to be more closely related than they actually are--conflict. So, it is important to use genes likely not inherited from LGT to establish accurate relationships between taxa.

How is the lysogenic cycle relevant to our genome? How are viruses and virus recombination important for human health?

Lysogenic cycle results in the recombination of genes into a genome. The human genome has about 9% of genes derived from viruses. Virus recombination affects our ability to effectively prevent and treat viruses as they are constantly changing--example of the flu vaccine.

Eukaryotic metabolism, morphology, and locomotion

Metabolism--limited. Photolithoautotroph and chemoorganohetertroph Morphology: unicellular, multicellular, and colonial Locomotion: flagella, amoeboid (cytoplasmic streaming), and ciliate

Rhizaria

Mostly unicellular and amoeboid, produce elaborate shells from calcium carbonate, thin pseudopods extend through holes in their shell, they make up a lot of sand on beaches (Foraminiferans)

Cladogram

Only the relative branching order is depicted. No meaning to branch length.

Parasite vs. Pathogen

Parasite is an organism that lives in or on a host organism that obtains its nutrients and energy at the cost of its host--doesn't have to be a pathogen Pathogen is a biological agent that causes disease in a host

Primary and Secondary Endosymbiosis

Primary endosymbiosis is when a eukaryote engulfs a bacterium. Secondary endosymbiosis is when a eukaryote engulfs another eukaryote. Mitochondria was a primary endosymbiosis between a eukaryotic cell (had nucleus) and a proteobacterium. Happened once. Chloroplasts was primary event that occurred in the Plantae lineage when a eukaryote engulfed a cyanobaceterium. Secondary and tertiary endosyms. explain chloroplasts in other lineages

Prokaryotes in the ecosystem

Primary productivity--photosynthesis Organic matter degradation Mineral weathering Nitrogen fixation, rhizobium (proteobacterium) Global cycles

What is quorum sensing? What are the main steps in quorum sensing? Why is it important?

Quorum sensing is the way that bacteria communicate with the same and different species in their environment. Bacterium has a signal producing protein that pumps out chemical signal molecules into the extracellular environment. In larger numbers of the same species, the concentration of these molecules grows, when the concentration of signal molecules is high enough the signal is able to bind to a receptor protein on the cell which signals group behavior genes (Vibrio Fischer produces light in groups but not alone) All bacterium also have a universally understood signal that allows them to better understand the composition of their environment

Compare and contrast LGT and Sexual Reproduction

Similarities: can result in recombination and new genetic combinations Differences: Sexual reproduction can only occur between closely related species, LGT involves only a part of a genome, LGT isn't linked to reproduction, LGT has multiple mechanisms

The microbe problem(s)

Some traits not clear if homologous (morphology, nutritional requirements, motility)

Parts of a tree diagram

Terminal (or tip) taxa represent the organism, species, or group of species most recent in the history of evolution. Internal node it the point at which a lineage splits--it is the hypothetical ancestral taxa. Internal branch-space between internal nodes, evolution can occur here for derived traits of an ingroup. Root node is the oldest point of the tree, it is the common ancestor of all the taxa on the tree. Trees can be oriented left(old) to right or bottom (old) to top (recent). Branches can be rotated about nodes and the meaning of the tree does not change.

How do we research microbes that are not culturable?

The Great Plate Anonmaly states that the number of microbes seen under a microscope or sequenced is always much greater than those that are cultured. Because many microbes have very specific environmental conditions that they need to grow in, they have to find alternative ways to identify them without culturing. Barcoding: Sample, extract DNA, amplify 18s rRNA genes Metagenomics: extract all DNA in sample communnity and determine what the genes are or what the genes do. compare sequences to databases.

Diversification rates via phylogenies

The diversification rate of a clade may be effected by a key innovation--making the clade more diverse in comparison to its sister lineage. Ex. Many plants have canals for holing latex of toxic resins which are released upon herbivore damage, acting as a defense system. In a study of 16 pairs of sister taxa, 13/16 clades with canals were more diverse than the clade without canals.--> plant clades with canals have higher diversification rates than those without.

What is the lytic versus the lysogenic cycle?

The lytic cycle results in the destruction of the infected cell and its membrane. A key difference between the lytic and lysogenic phage cycles is that in the lytic phage, the viral DNA exists as a separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA. The location of viral DNA in the lysogenic phage cycle is within the host DNA, therefore in both cases the virus/phage replicates using the host DNA machinery.

Unrooted tree

The root has been removed and the relationship among taxa are more ambiguous. They show branch splitting patterns but say nothing about the *temporal sequence* of these events--it is a tree without a sense of direction. Change is depicted as bidirectional.

Human uses of extremophiles?

Thermophiles--stable enzymes Halophiles--indisutrial enzymes and soy sauce production Alkaliphiles-detergents Acidophiles/Radiophiles-bioremediation

Where do viruses fit on the tree of life?

They don't have rRNA.. There are three main hypotheses about where they sit on the tree of life. 1) they are relics from a pre-cellular world 2)Viruses are escaped portions of cellular organisms 3) viruses are extremely derived and reduced cellular organisms. *Viruses as a group are polyphyletic*

What does "Tree of Life" vs. the "Web of Life" refer to?

Tree of life is based on the evolutionary history between taxa and is based on a core set of genes that don't transfer--like rRNA Web-LGT in prokaryotes messes up the tree of life making it look more like a web because of the transfer of genes between distantly related species.

What is a virus? What are the main components of a virus?

Virus is the active stage that causes the synthesis of virions. Virions are the dormant stage of the virus which can exist outside the cell and replicate once within the cell. Virions constist of nucleic acid genome, a protectice coat (capsid) and some have a lipid membrane Virion shapes: helical, isochohedral. complex (phage) Size: varies (mimivirus so large ~1000 genes to Tobacco Mosaic virus ~4 genes) Genomes: circular, linear, segmented. DNA, RNA, or both. double or single strand or both. RNA viruses + or - sense, how its read.

Why are viruses important for ecosystem function?

Viruses are the most abundant biological entities on the planet. There are many plant viruses that impact the food system. Microbes run global cycles (Carbon, nitrogen, phosphorous, etc(

Paraphyletic group

a group of organisms consisting of their MRCA but not all of its descendants. Example of this is the reptile group which did not originally include birds.

Monophyletic. How does this relate to number of nodes?

a group of organisms that consisting of their MRCA and all its descendants. If a tree has 'n' internal nodes, then there are 'n; monophyletic groups in that tree. Protist group is not monophyletic group because is excludes some descendants.

Polyphyletic group

a group of organisms where the MRCA is not included

Clade

a monophyletic group

Outgroup method

a way of reconstructing the most parsimonious tree by using one or more outgroups to estimate the ancestral character states of the MRCA in the ingroup.

Taxon (plural:taxa)

any organism, species, or group of species that is designated a name.

Cyanobacteria (BCFP)

are Gram -, photoautotrophic (use chlorophyll a, and contain internal membrane system for photosynthesis), chloroplasts are derived from endosymbiotic cyanobacteria, colonies can differentiate into vegetative cells, spores, and *heterocysts*--specialized for nitrogen fixation (circular part of cell), some make powerful toxins.

Universal homologies

are characters found in all organisms like *DNA, Three letter codons, and the central dogma* so they are *phylogenetically uninformative*

Homologous traits

are those that are inherited from a common ancestor

Transitions and Transversions

are two types of nucleotide substitutions. *Transitions* are changes from one purine to another (A <-> G) or from one pyrimidine to another (C<-> T) *Transversions* are changes from a purine to a pyrimidine or vice versa. *Transitions are more likely to occur than transversions* This means that a tree with two transitions is not that much better than a tree with one because transitions are common. However, a tree with less transversions may have a higher likelihood because transversions are more rare-- so it is less likely to have many transversions in a tree.

Difference between multicellular and colony

colony-incomplete cytokinesis, cells remain attached but have individual reproduction. Multicellular--division of labor, only specific cells reproduce. Has evolved multiple times in euk groups.

Anaerobe types

do not require the presence of oxygen Facultative anaerobes--shift between aerobic and anaerobic Obligate--oxygen is toxic Aerotolerant anaerobes--do not use oxygen but are not damaged by it

Ancestral traits

features that were present in the common ancestor.

Non-monophyletic groups & relation to classification (naming)

groups that include some but not all descendants of the MRCA of that group. In a historical sense, non-monophyletic groups are artificial groups. non-monophyletic groups cannot be delimited by features that arose in a unique common ancestor these reasons are by when naming groups of species it is important to ensure that they are monophyletic groups.

Alveolates (DAC)

have sac like structures, alveoli below their membrane, ALL are UNIcellular, most have plastids from secd. endosym. *Dinoflagellates* (Zoocanthellae-coral & red tide): mostly marine and freshwater, primary producers, two flagella, *Apicomplexans* (Malaria-plasmodium falc. /toxoplasma): all are *internal parasites* that use the apical complex organelle to enter hosts. Apicoplast is a non-photosynthetic plastid that is a possible target for control. *Ciliates* (Blepharisma, paramecium, Stentor)--have hair like organelles called cilia

Molecular Clocks

how phylogenies can show timing of events . 1. build a tree with DNA 2. use the number of mutations along a branch as an indicator of elapsed time (molecular clock) 3. Calibrate the clock with another data set. *Rates of molecular evolution are constant enough that we can calculate rates of molecular divergence to estimate times of divergence in a species* Rates of DNA change must be relatively constant in the branches of interest, generation times must be similar, and sites should be neutral. Ex. Snapping shrimp species actually didn't diverge due to the Isthmus of Panama formation-- they diverged at a wide range of times 3-18mya (not all at same time) and they diverged before the formation which was ~4.5 mya.

Trait evolution via phylogeny

identifying where/when an event occurred on a phylogenetic tree. 1. Use characters (traits) to build a tree--often using DNA 2. Investigate how other traits evolved (morphology, ecology, behavior) Ex. Leptosiphon species that outcross versus selfing. They named 3 species L. "bicolor" not knowing they were different species but assumed so because they were all selfing species-- it is a convergent trait that has evolved independently 3 times--and using model-based approach we know that it is more likely to evolve the selfing characters instead of the outcrossing. Ex: Gigantism in tortoises is a homopalsious trait that evolved twice on islands where there was strong selection for it.

ingroup and outgroup

ingroup is the set of taxa under study outgroup is one or more taxa that fall phylogenetically outside the group under study

Maximum likelihood--inferring trees

is a model-based approach to estimating phylogenies. 1. develop a probabilistic *model of evolution* of the characters. 2. Search for the most likely tree--the maximum likelihood tree is the tree which makes the observed data most likely to have evolved, under the model. advantages: often more accurate than parsimony, gives branch estimates disadvantage: computationally intensive.

Binary Fission how is it different from mitosis?

is asexual reproduction in prokaryotes and gives rise to clones. It does not require a partner organism, it can happen rapidly, and is influenced by environmental conditions. Different because it does not require a partner- mitosis is for growth while binary fission is for reproduction and the lack of cytoskeleton in prokaryotes makes the division process different.

Polymorphism

is the existence of both character states in a population after a nucleotide substitution...Changes in character states is actually a population level process that takes multiple generations.

Proteobacteria (BCFP)

is the largest group of bacteria that has high diversity of metabolic phenotypes, Gram -, mitochondria derived from endosymbiotic proteobacteria. E.coli is a proteobacteria which is important for genetic engineering and is a human pathogen. Rhizobium is included in the nitrogen fixing genera. Includes many human and animal pathogens: Yersinia pestis (plague), Vibrio cholerae, Salmonella typhimurium, agrobacterium tumefaciens (crown gall).

Classification

is the naming of taxa and their placement in a hierarchical arrangement. 1) species are given a binomial name consisting of the genus name and the species name 2) groups of species are put into more inclusive or higher taxa with a single name and are placed in a ranked hierarchy of increasingly more inclusive groups: genus, family, order, class, and phylum.

Convergent evolution

is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches.

Symbiosis and types of

living in close association with two or more organisms. Parasitism -/+ commensalism 0/+ Mutualism +/+

Creanarchaeota (ACEMH)

most are both thermophilic and acidophilic. *Sulfolobus* lives in hot sulfur springs. *Ferroplasma* lives at a pH near 0.

Synonymous substitution & Non-synonymous subsitution

no change in the encoded amino acid is synonymous, if the change in nucleotide changes the encoded amino acid it is not synonymous. In nucleotides that occur in sets of three (codons) changing the third position of the codon does not always change the amino acid--meaning that third codon position changes are more likely to occur than 1st and 2nd.

Origin of the nucleus

not an endosymbiosis. Loss of cell wall, folding of cell membrane, cytoskeleton complexity increased, ...

Euryarchaeota (ACEMH)

only known *Methanogens*- produce CH4 (methane) by reducing CO2 via *chemoautotrophy,* release 2 billion tons of methane/year. Many live in guts of grazing animals or deep ocean hydrothermal vents. *Halophiles*-pink carotenoid pigments, found in pH up to 11.5, live in salty (most alkaline environment), many have Bacteriorhodopsin which uses light energy to synthesize ATP

Microbial eukaryotes

paraphyletic group (Amoebozoans, Alveolates, Excavates, Rhizaria, Stamenopiles)

Tree of life

refers to the concept that all living organisms are related to one another through common ancestry.

Aerobes

require oxygen

Synapomorphies

specific features or characters that are unique or especially characteristic of a clade/monophyletic group.

Polytomy/Polytomies

the case whereby some nodes in a tree have three or more descendant branches, such nodes are called polytomies and they usually reflect uncertainty about phylogenetic relationships. The possible ways to resolve polytomy in a bifurcating trees grows like a factorial (fast) as the number of taxa involved increases. 3 taxa=3 ways, 8 taxa ~135,135 ways.

Phylogeny

the history of evolutionary relationships among organisms. Phylogeny can be depicted by a branching diagram called a tree. A tree shows the divergence of lineages that have become permanently separated--hence the branches do not fuse back together after splitting.

Principle of Parsimony

the most likely path of evolution is the tree that explains all the available evidence but requires the least amount of change in character states (i.e. the fewest number of steps in the tree--most parsimonious tree)

Speciation

the process whereby one species gives rise to two descendant species (simplified definition)

Biogeography

the study of the geographical distribution of organisms. Historical biogeographers are interested in the roles of dispersal and geological events in determining the distribution of taxa. Ex. Snapping shrimp across the isthmus of Panama and exchange of terrestrial species.

Characters

traits or features of organisms. They must exhibit some variation as character states, in order to be able to use them to infer phylogenies

Derived traits

traits that arise or were modified in the ingroup

Bifurcating trees

trees in which each internal node gives rise to two descendant branches

Sister group

two species or two clades that are each other's closest relatives (the two descendant taxa of a single node). Sister species are the same age because they originate as lineages at the same time.