Exam 2 Picture review file

Phylogeny

The evolutionary history of a species or group of related species

systematics

classifies organisms and determines their evolutionary relationships

Binomial Nomenclature

Classification system in which each species is assigned a two-part scientific name

In the 18th century, Carolus Linnaeus published a

system of taxonomy based on resemblances

Two key features of his system remain useful today: two-part names for

species and hierarchical classification

Linnaean classification

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

The evolutionary history of a group of organisms can be represented in a

branching phylogenetic tree

The "tips" of the tree branches represent the

the taxa in the study

Phylogenetic trees can be drawn

horizontally, vertically, or diagonally without changing the relationships between groups

Tree branches can be rotated around a branch point without

changing the evolutionary relationships

Phylogenetic trees show patterns of descent, not

phenotypic similarity

Phylogenetic trees do not indicate _______ species evolved or how much ________ occurred in a lineage

When, How much

It should not be assumed that a taxon evolved from

the taxon next to it

To infer phylogenies, systematists gather information about the

morphologies, genes, and biochemistry of living organisms

Phenotypic and genetic similarities due to shared ancestry are called

homologies

Organisms with similar morphologies or DNA sequences are likely to be more

closely related than organisms with different structures or sequences

Systematists need to determine if a similarity is the result of

homology or analogy when creating trees

Homology is similarity due to

shared ancestry

Analogy is similarity due to

convergent evolution

A valid clade is monophyletic

signifying that it consists of the ancestor species and all its descendants

A polyphyletic grouping includes distantly related species but does not include their most

most recent common ancestor

In some trees, the length of a branch can

reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage

A paraphyletic grouping consists of

an ancestral species and some, but not all, of the descendants

MONOPLYLETIC

pertaining to a group of taxa that consists of a common ancestor and all its descendants, equivalent to a clade

Polyphlyletic

set of organisms that includes members derived from two or more distinct ancestral lineages, rather than a single common ancestor

the longer the branch lengths connecting two organisms

more genetic changes have taken place

PARAPLYLETIC

a taxonomic grouping that includes a common ancestor and some, but not all, of its descendants

Examples of a paraphyletic and a polyphyletic group

the tree different types of phyletic groupings

When inferring evolutionary relationships, it is useful to know _

in which clade a shared derived character first appeared

Occam's razor

The simplest explanation is usually the right one.

Which would have more genetic changes: comparing chicken vs. human -OR- human vs. mouse?

more genetic changes than a comparison between a human and a mouse.

In other trees, branch length can be

proportional to time, and branching points can be determined from the fossil record

Which organism is the most ancient here

Drosophila

How many EXTANT species?

7

Repeated gene duplications result

in gene families

You should know how parsimony can be used to estimate which tree would be the "best" or the "most accurate" one from a given data set.

So which two species would be more closely related using this approach?

Species I and II

Gene duplication increases the number

of genes in the genome, providing more opportunities for evolutionary changes

Duplicated genes can be

traced to a common ancestor

Orthologous vs. Paralogous genes example

-Orthologous genes are found in different organisms, but are derived from a single common ancestral gene present in the common ancestor of those organisms

-Paralogous genes are genes present in a particular organism that are related to each other through a gene duplication event

Individual genes vary

in how clocklike they are

Orthologous genes are found in

a single copy in the genome and are homologous between species

Primate proteins appear to

Have evolved more slowly than other mammals

Paralogous genes result from

gene duplication so are found in more than one copy in the genome

They can diverge only after

speciation occurs

HISTONE gene

Example of paralogous and orthologous genes in organisms.

Molecular clocks are

calibrated against branches whose dates are known from the fossil record

They can diverge within the species

that carries them and often evolve new functions

why HIV is so interesting from a biological perspective for viruses.

HIV is a retrovirus, meaning it carries its genetic info as RNA. Once it enters a cell, it uses an enzyme called reverse transcriptase to turn its RNA into DNA.

HIV is estimated to have first appeared in the human population in

HIV first appeared in the human population in the early 20th century, specifically around 1920.

Gram-positive bacteria are

particularly susceptible to this type of antibiotics

Scales at which Organisms "Mutate" or "Evolve"

organisms "mutate" or "evolve" vary dramatically from months (viruses) to millions of years (animals). The figure above plots the average genome size in base-pairs (x-axis) versus the average mutation-rate(y-axis) for various organisms. In addition, a second y-axis ("minimum time to 1% mutation") illustrate approximate timescales corresponding to each rate.

horizontal gene transfer

The transfer of genes from one genome to another through mechanisms such as transposable elements, plasmid exchange, viral activity, and perhaps fusions of different organisms.

how horizontal gene transfer contributed to our understanding of the tree of life.

HGT proved that genes can also move horizontally between unrelated organisms, even across different species.

Cocci

spherical bacteria (ball shaped) (1 nano meter)

Bacilli (bacillus)

rod-shaped bacteria (cause of tuberculosis) (1 nano meter)

Spirilli

spiral shaped bacteria (3 nano meters)

Gram-positive bacteria

Bacteria that have a thick peptido glycan cell wall, and no outer membrane. They stain very darkly (purple) in Gram stain.

Gram-negative bacteria

Bacteria that have complex cell walls with less peptidoglycan but with lipopolysaccharides. Very toxic and hard to treat.

A sticky outer layer of polysaccharide or protein called a

capsule is present in some prokaryotes

Antibiotics used for gram-negative

Ciprofloxcin, gentamicin

Many antibiotics target

peptidoglycan and damage bacterial cell walls

The capsule allows

adherence to the substrate, or other individuals, and can shield pathogenic bacteria from the host immune system

Antibiotics used for gram-positive

Erythromycin, penicillin

fimbriae

finger or fringe like projections at the end of the fallopian tubes

Many prokaryotes form metabolically inactive endospores

which can remain viable in harsh conditions for centuries (spores in tombs of Egyptian pharaohs)

Some prokaryotes have hair-like appendages called

fimbriae

Pili (or sex pili) are longer than

fimbriae and allow prokaryotes to exchange DNA

compartmentalization in bacteria

Bacteria use compartmentalization to organize their internal chemistry, much like a factory uses different rooms for different hazards.

Prokaryotic cells usually

lack complex compartmentalization

Some prokaryotes do have specialized

membranes that perform metabolic functions

These are usually infoldings of the

plasma membrane

The prokaryotic genome has

less DNA than the eukaryotic genome

Most of the genome consists

of a circular chromosome

A piece of DNA called the F factor

is required for the production of pili

The chromosome is not contained in a nucleus; it is located in the

nucleoid region with no surrounding membrane

Typical prokaryotes also have smaller rings of independently replicating DNA called

plasmids

Conjugation is the process where genetic material is transferred

between prokaryotic cells

In bacteria, the DNA transfer is

always one way

A donor cell attaches to a recipient by a

pilus and transfers DNA through a structure called the "conjugation or mating bridge"

Metabolic cooperation

occurs between different prokaryotic species in surface-coating colonies called biofilms

Cooperation between prokaryotes allows them to use

environmental resources they could not use as individual cells

These gram-negative bacteria include

photoautotrophs, chemoautotrophs, heterotrophs

how metabolic cooperation plays a role in bacteria.

It occurs when different bacterial cells or species work together to survive and grow in environments where they couldn't succeed alone.

In the cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixing cells called

heterocysts (or heterocytes) exchange metabolic products

Some are

anaerobic and others aerobic

Sulfate-consuming bacteria and methane-consuming bacteria on the ocean floor use

each other's waste products

Scientists hypothesize that mitochondria evolved from

aerobic alpha proteobacteria through endosymbiosis

There are currently five subgroups of proteobacteria recognized by molecular systematists

Alpha,Beta, gamma ,Delta ,epsilon

Alpha Proteobacteria

closely associated with eukaryotic hosts

Rhizobium, which forms

root nodules in legumes and fixes atmospheric N2

Agrobacterium

which produces tumors in plants and is used in genetic engineering

Nitrosomonas, a soil bacterium

converts NH4+ to NO2-

Beta Proteobacteria

the soil bacterium Nitrosomonas, which converts NH4+ to NO2- ,subgroup is nutritionally diverse

Other members include

aquatic species and pathogens

Some heterotrophs are pathogenic, such as

Legionella, Salmonella, and Vibrio cholerae

Gamma Proteobacteria

Autotrophic members include sulfur bacteria such as Thiomargarita namibiensis

Campylobacter (epsilon $

a bacterium that sometimes causes abortion in animals and food poisoning in humans.

Helicobacter pylori (H. pylori) (epsilon)

a bacterium residing in the GI tract that causes peptic ulcers

Delta Proteobacteria

The slime-secreting myxobacteria, which produces drought-resistant "myxospores"