BIS 2C Final Locked in Core

Ancestral State

the character state of the most recent common ancestor.

Character

a trait that can be quantified and put on a data matrix (ability to fly, presence of a post anal tail etc. )

Character state

the actual state of the character (post anal tail is absent, animal is not able to fly etc.)

Chronogram

branch lengths reflect temporal information

cladogram

branch lengths arbitrary, only topographic info

data matrix

a chart of characters and character states that is quantified with numbers

derived state

a state that is different from the ancestral state as it has been derived along the branch leading to the taxa

extinction

the taxon no longer exists.

extant

the taxa(on) still exists

homology

similarity in a trait among different organisms that is due to inheritance from a common ancestor, similarity of states reflects common ancestor, evolutionary history, trait evolution that mirrors phylogeny

homoplasy

similarity in a trait among different organisms that has evolved independently, similarity of states contradicts phylogeny

ingroup

a set of species that is helpful in estimating evolutionary relationships

monophyly

natural groupings, includes all descendant species of a common ancestor. A monophyletic group can be defined for each internal node

MRCA

most recent common ancestor

outgroup

group that is used in comparison to the ingroup, used to root unrooted trees

paraphyly

includes some but not all descendants of a given common ancestor, unnatural

parsimony

Occam's razor, prefer the competing hypothesis that minimizes the number of ad hoc/just so assumptions. We prefer evolutionary history that minimizes the number of required changes

phylogeny

a graphical description of the evolutionary relationships between taxa(on) and phyla

phylogram

branch lengths reflect amount of character change

Polyphyly

excludes MRCA of included species, unnatural

polytomy

uncertainty in the estimated phylogeny. We generally assume the underlying tree is dichotomous (each speciation event involves 2 immediate descendant species)

sister group

2 groups that are each other's closest relatives - share common ancestor

speciation

one species diverging into separate species

synapomorphy

shared derived traits

systematics

used formal methods to estimate evolutionary relationships

trait

observable features of an organism can be discrete (e.g. wings present or not present) or continuous (e.g. plant height). All traits novelties when first arise (by mutation in a single individual). For phylogeny estimation, we are concerned w/ traits that are heritable, discrete, fixed within species, potentially variable between species. Trait evolution occurs over branches of tree.

unrooted tree

constrains but doesn't completely specify the possible set of ancestor-descendant relationships. Not a phylogeny. No root node. Used to estimate phylogeny (most phylogeny estimation programs perform evaluations on unrooted trees). Evolutionary relationships change depending on where the optimal unrooted tree is rooted. For a given number of species, N, there are many more rooted than unrooted trees (2N-3). For internal nodes, all possible state assignments=#states^(#internal nodes)

natural evolutionary groups

are completely consistent with the phylogeny Natural groups are monophyletic groups, which includes all of the descendants of a given common ancestor

unnatural evolutionary groups

conflict with the phylogeny (evolutionary relationships) There are two kinds of unnatural groups:

Paraphyletic groups exclude some of the descendants of a given common ancestor (e.g., the original definition of Reptilia)

Polyphyletic groups exclude the most recent common ancestor of the included species (e.g., the proposed grouping of mammals and birds in the group "Homeothermia" based on their of possession of convergent traits)

phylogeny

is a history of branching (speciation) events.

sister species

The two descendants of a speciation event are called ______ (or sister groups), and are each other's closest relatives.

N-1

A phylogeny with N species has ________ speciation events (internal nodes)

dichotomous

We typically assume that the underlying phylogeny is ________: i.e., that every speciation event gives rise to only two descendant species

polytomies

However, phylogenies may contain ______, an internal with 3 or more descendant branches, which may reflect:

hard

An episode of simultaneous speciation, where 3 or more descent species are produced from a single speciation event (in which case we call it a _______ polytomy')

soft

Uncertainty in the phylogeny (in which case we call it a ________ 'polytomy')

additional

We cannot distinguish between these two types of polytomies from the tree alone: the interpretation of a polytomy as soft or hard requires _______ information

true

outgroups are not primitive/less derived than species within the ingroup. (T/F)

independent

Character evolution and species are two processes are largely _________, but the characters of living species provide evidence that we use to estimate phylogeny.

Occam's razor

prefer the hypothesis that minimizes the number of ad hoc assumptions.

principle of parsimony,

One approach for inferring phylogeny from character data based on the _________ that uses Occam's razor.

invariant characters

characters that all share the same character state

unique chacters

characters where all but one species have the same character state

parsimony informative

minimum number of steps for character change will differ

problems with parsimony

we assume the cost is the same for all steps, not actually the case ie character developed costs more than character lost

Universal common traits/homologies

What evidence would be needed to determine if life on another planet was related to life on earth?

evidence all life on earth shares common descent

Use of ACTG in DNA, ACUG in RNA, 3 letter genetic code, central dogma, 20 core amino acids, ribosome for translation, RNA polymerase proteins

different nucleotide bases in DNA

If life on Earth had multiple origins, what might one see if one compared features of organisms from the separate origins to each other?

rRNA

What did Carl Woese use to infer the Three Domain Tree of Life

peptidoglycan

What are some features found in most/all bacteria but not in archaea or eukaryotes?

ether linkage

What are some features found in most/all archaea but not in bacteria or eukaryotes?

No operons

Plasmids rare

3 DNA polymerases

80S polymerase

What are some features found in most/all eukaryotes but not in bacteria or archaea?

great plate count anomaly

More organisms observed than can be cultured. rRNA sequencing from environmental samples. Metagenomics: study of genetic material recovered directly from environmental samples improves phylogenetic resolution

endosymbiosis levels

Endosymbiosis: when an organism (the host) brings in another organism (the symbiont) inside of its cell, only really works w/ eukaryotic cells as hosts. Primary--symbiont has not experienced a prior symbiosis, secondary--symbiont has undergone primary endosymbiosis

Chloroplasts: cyanobacterium

Mitocondria: proteobacterium

From what lineage on the Tree of Life did chloroplasts and mitochondria evolve?

once

How many times did the symbioses for chloroplasts and mitochondria evolve?

distribution of chloroplasts

Scattered distribution. Primary endosymbiosis in the common ancestor plantae, secondary symbiosis in other lineages.

culturingq

Growth of microorganisms in controlled/defined conditions. General approach to collect sample, make environment w/ specific growth conditions (energy, electrons, carbon, etc), dilution/passing until one obtains a pure sample w/ just a single clone.

pure cultures

Allows one to connect processes and properties to single type of organism, enhances ability to do experiments, provides possibility of large volumes of uniform material for study, can supplement appearance based classification with other types of data.

halophily vs. thermophily

Extreme halophiles in 1 monophyletic group in 1 phylum of archea

Hundreds of thermophiles scattered, can't make into monophyletic group

extremophile adaptations

Make proteins more stable, slow down enzyme rates, decrease fluidity of membranes, increase osmolality inside cell

phototrophy

energy source= light

chemotrophy

energy source= chemicals

heterotrophy

carbon source= organic

autotrophy

carbon source= inorganic

lithotrophy

e- source= inorganic

organotrophy

e- source= organic

LGT, sexual recombination, interactions w/ other organisms

How can organisms acquire functions from external sources?

archaea

What kinds of organisms are not known to be pathogens and parasites?

4th domain, separate origin, from within other groups

Explain how DNA analysis could be used in microbial forensic studies. What are different models for the origin of viruses?

Desiccation

water transport

Gravity

intense UV radiation

dispersal of gametes

challenges of life on land

aquatic

plants arose in what type of environment?

haplontic

expansion of haploid phase (fungi and some algae).

The diploid stage is unicellular, spores produced by meiosis.

Only the haploid stage is multicellular, gametes produced by mitosis.

sporic

alternation of multicellular haploid and diploid generations (land plants)

Gametophyte: multicellular haploid organism that makes gametes

Gametangia: the multicellular sex organs of the gametophyte that produce the gametes via mitosis

Archegonia: produce female gametes (eggs)

Antheridia: produce male gametes (sperm)

Gametes fuse at fertilization to produce single cell diploid zygote that gives rise to multicellular diploid sporophyte

Homosporous

male and female gametangia occur on each individual

Heterosporous

male and female gametangia occur on separate individuals

Cuticle (waxy layer to reduce desiccation)

Pigments for UV protection

Mutualistic fungal associations

Sporic life cycle

diagnostic features of land plants

stomata

Mosses & Hornworts have _______ to regulate gas exchange

early vascular plants

Small

Relatively simple organisms (lacked leaves, roots, tracheids)

Dichotomously branching sporophyte with apical sporangia

*Increased spore production relative to branched counterparts

*Facilitated evolution of novel organ types

xylem

conducts water and minerals from soil to aerial parts of the plant. Secondary thickening of cell walls (lignin) provides structural support. Tracheid cells are the principal water conducting element of the xylem and are dead at functional maturity. Transpiration-cohesion-tension system. Passive transport. Tracheids occur in the xylem of all vascular plants.

phloem

conducts products of photosynthesis throughout the plant. Comprised of sieve tube cells that are alive at functional maturity. Many cell components lost at functional maturity (incl. nucleus). Nurtured by companion cells. Nutrients transported actively via the pressure flow model, moved from sites of production to sites of storage.

overtopping growth

Apical meristem divides asymmetrically, such as there is a main stem and side branches

Allows taller growth and enhanced competition for sunlight

Allows elaboration of novel organs

adaptive value of vascular system

*Efficient transport of water & nutrients allows plants to colonize more fully terrestrial environments

*Rigid structural support allows plants to grow taller and to compete more effectively for sunlight and to enhance spore dispersal

leaves

compressed photosynthetic structure emerging laterally from a stem or branch that possesses vascular tissue

microphyllous leaves

small, simple leaf with a single vascular strand. Lycophytes. Originated from sterile lateral sporangia.

megaphyll

larger, more complex leaf with ramified vascular tissue. Monilophytes and seed plants

stigmarian roots

of lycophytes: simple dichotomously branching root system derived from rhizomes. Spirally arranged rootlets derived from microphyllous leaves

complex roots

f Euphyllophytes: complex branching root system derived from stems, root hairs developed form dermis

adaptive value of heterospory

Genetic diversity. Separate, unisexual male and female gametophytes reduces the probability of self fertilization, which maintains genetic diversity in the population via outcrossing

Parental investment. Provisioning the megaspore & thus female gametophyte with nutrients

secondary growth

Produced by lateral meristems

Meristematic cells give rise to many tissues

Vascular cambium: ring of cells between primary xylem and phloem, allows shoot and root to increase in girth.Produces secondary xylem to interior (gives rise to wood), secondary phloem to exterior (gives rise to bark)

Secondary vascular tissues maintain efficient transport as plant ages

Rigid structural support allows plants to grow taller, compete more effectively for light & enhance dispersal

Formation of bark prevents water loss and infection

pollen

Microgametophyte consists of 4-8 haploid cells. 2 are male gametes/sperm, rest form protective coating/sporopollenin (protect pollen from desiccation, can be elaborated to enhance dispersal)

Efficient transfer of sperm to megagametophyte--fertilization can occur w/o water, sperm can travel further by wind or animal pollinator

gymnosperms

Fleshy megasporangium (2n) protected by integument

Megaspore grows into multicellular haploid female gametophyte (n)

A pollen grain (n) enters through the micropyle and develops a pollen tube (germinates)

The germinated pollen grain releases a sperm nucleus, fertilizing the egg nucleus and initiating seed formation

Mature diploid embryo (baby plant)

Nutritive haploid tissue (to help support establishing plant)

Protective seed coat (from previous sporophyte)

angiosperms

Mature diploid embryo

Nutritive triploid tissue (endosperm to nourish embryo)

Protective seed coat

Angiosperm seed is enclosed by the ovary wall of the carpel that gives rise to fruit

advantages of seeds

Efficient dispersal of next sporophyte generation

Protection of developing sporophyte plant

Dormancy

Embryo can rest for long time

Development resume when conditions favorable

Seed is provisioned w/ nutrients to help establish plant

Integument often modified to facilitate seed dispersal

fruit

expanded ovary

carpel

female sex organ of flower plants

perfect flowers

flowers that have stamens and carpels

imperfect flowers

flowers that have stamens or carpels

monoecious

imperfect male and female flowers on the same individual plant

dioecious

imperfect flowers on different plants