Prelim 1 Flashcards

3 Eras of the Phanerozoic Eon [Macroevo. 1]

1) Paleozoic

2) Mesozoic

3) Cenozoic

7 Periods of the Paleozoic Era (Oldest to Youngest) (Hint: COSDCP) [Macroevo. 1]

1) Cambrian

2) Ordovician

3) Silurian

4) Devonian

5) Carboniferous

6) Permian

3 Periods of the Mesozoic Era (Oldest to Youngest) (Hint: TJC) [Macroevo. 1]

1) Triassic

2) Jurassic

3) Cretaceous

3 Periods of the Cenozoic Era (Oldest to Youngest) (Hint: PNQ) [Macroevo. 1]

1) Paleogene

2) Neogene

3) Quaternary

What age is the oldest evidence of life? [Macroevo. 1]

3.7 bya

When was the end of the Paleozoic Era & Start of Mesozoic Era? [Macroevo. 1]

250 mya

When was the end of the Mesozoic era & Start of Cenozoic Era? [Macroevo. 1]

65 mya

Hypothesis of how Paleozoic Era ended? [Macroevo. 1]

Extinction Event via volcanic eruptions

Hypothesis of how Mesozoic Era ended? [Macroevo. 1]

Massive Meteorite strike that killed the dinosaurs

About when was the birth of Earth? [Macroevo. 1]

4.6 bya

When was the Cambrian Explosion / Start of Paleozoic Era? [Macroevo. 1]

540 mya

About when was the start of the agricultural era / Anthropocene? [Macroevo. 1]

10,000 years ago (10 kya)

Steno's Principles of Stratigraphy (4) [Macroevo. 1]

1) Superposition - earlier rock layers are above later ones

2) Original Horizontality - rock layer were originally deposited horizontally, but eventually became deformed throughout time

3) Cross-Cutting Relationship - geological cuts across layers are more recent than layers it cuts across

4) Lateral Continuity - layers are spread across wide area

Radiometric Dating Method [Macroevo. 1]

determining absolute age of fossils via measuring percentage of parent isotope and the daughter isotope it decayed into in an object (Usually 14 C -> 14 N) ; starting at 100% of parent isotope when an igneous rock, used alongside known half-life of isotope in order to determine length of time that's passed

Index Fossil & Properties of Good Index Fossils [Macroevo. 1]

fossils of widely distributed organisms that lived during only one short period; used to relatively date layers

1) Geographically Widespread

2) Organism Lived for Relatively Short Time

3) Only Appears within 1-2 rock layers

Lagerstätten & Examples (2) [Macroevo. 1]

a site with an abundant supply of unusually well-preserved fossils from the same period of time, often including soft tissues; provides sufficient notions of make-up of certain environment/time period

1) Green River Formation (Wyoming)

2) Burgess Shale (British Columbia - provides evidence for Cambrian Explosion species)

What typically act as impediments for fossilization of organisms? [Macroevo. 1]

1) Predators & Scavengers - eat/crush remains of species

2) Bacterial Decay - breakdown of organic matter

3) Dissolution in Water/Liquid

4) Physical Disturbance - ex: wind & waves

Importance of Rapid Burial for Fossilization [Macroevo. 1]

Facilitates Fossilization of organisms due to protection from physical disturbances & maintenance of anaerobic environments (mitigates bacterial decay)

What parts of animals are commonly fossilized? (3) [Macroevo. 1]

Hard Parts - Bones, Teeth, Shells

What parts of tree are fossilized? (5)[Macroevo. 1]

1) Petrified Wood (wood that undergoes mineralization)

2) Seeds

3) Pollen

4) Leaves

5) Flowers (Rarely)

How are bacteria/microbes fossilized? [Macroevo. 1]

Within Organisms or Biofilms from Stromatolites

Types of Preservation [Macroevo. 1]

1) Original Remains - unaltered body parts of organisms (usually skeleton); used in phylogenic construction

2) Permineralization/Petrification - filling of minerals in pores of bones/plants to form stone

3) Trace Fossils - evidence of organism movement (ex: footprints, trials, etc...)

4) Impression Fossils - carbonaceous film left behind by organic material of organism, suggesting fossil structure

Types of Phylogenetic Groups [Phylogeny 1-2]

1) Monophyletic - consists of common ancestor and ALL of its descendants; defining trait amongst group is called a synapomorphy

2) Polyphyletic - consists of numerous taxa that DON'T share a common ancestor; defining trait amongst group is called an ancestral/primitive trait

3) Paraphyletic - consists of common ancestor and only SOME of its descendants; defining trait amongst group is called a symplesiomorphy (derived trait shared with other descendants)

What do internal nodes on phylogenetic tree represent? [Phylogeny 1-2]

Ancestral Species that no longer exist

Parsimony for Phylogeny [Phylogeny 1-2]

Since phylogenetic trees are ultimately just hypotheses, phylogenetic tree with least number of steps/assumptions (fewer number of character changes) is considered the most compelling one

Homoplasy & Explanations (2) [Phylogeny 1-2]

A similar (analogous) structure or molecular sequence that has evolved independently in two species.

1) Convergent Evolution - independently originated in species, usually due to similar selective pressures

2) Evolutionary Reversal / Atavism - reverting back to ancestral trait

Polytomy [Phylogeny 1-2]

a branch point from which more than two descendant groups emerge, indicative of lack of sufficient information in differentiating species

How to determine if a taxon is more closely/less related to one taxon over another [Phylogeny 1-2]

The earlier the Most Recent Common Ancestor (MRCA) of the taxa are, the more closely related they are; taxa would be considered equally related to another if they all share the same MRCA

Homology vs Homoplasy [Phylogeny 1-2]

Homology - organisms sharing similar structures due to having common ancestry

Homoplasy - organisms sharing similar structures due to independent evolution of same trait

Types of Phylogenies [Phylogeny 2]

1) Cladogram - phylogeny that just depicts ancestry relationships

2) Phylogram - type of cladogram where branch length is indicative of magnitude of evolutionary change a species has underwent

3) Chronogram - type of cladogram where branch is indicative of magnitude of time having elapsed

Synonymous Substitution (silent substitution) [Phylogeny 3]

A change of one nucleotide in a sequence to another when that change does not affect the amino acid specified

Neutral Evolution [Phylogeny 3]

Nonadaptive evolutionary changes due to random genetic drift

Molecular Clock Hypothesis [Phylogeny 3]

Rates of molecular change (random DNA mutations) are constant enough to predict timing of evolutionary divergence

Applications of Phylogenies in Disease Ecology (3) [Phylogeny 3]

1) Date Disease Origin (molecular clock)

2) Determine Disease Origin (based on dating of related variants of disease)

3) Explore Biogeography of Disease Spread

Ecomorphs [Phylogeny 3]

species with the same structural habitat/niche, similar in morphology and behavior, but not necessarily close phyletically (convergent evolution); usually undergo niche differentiation in order to co-exist

Transcription Factor [Evo. Devo. 1]

A regulatory protein that binds to DNA (promoters/enchancers) and affects transcription of specific genes

Hox Genes [Evo. Devo. 1]

genes which encode transcription factor for the expression / suppression of specific body parts at specific parts of an animal

Novel Traits [Evo. Devo. 1]

traits that arise de novo (not inherited from an ancestor) within a lineage and have no obvious counterparts (homologs) in related lineages

Genetic Toolkit [Evo. Devo. 1]

An ancient group of genes found throughout the animal kingdom that directs the development of embryos; usually involves encoding of transcription factors

Differential Gene Expression [Evo. Devo. 1]

cells with the same genome are differentiated into specific functions via differential regulations of gene; explanation for humans having relatively low gene count (can just use same genes in different ways via regulation

What is most of genome made up of? [Evo. Devo. 2]

Non-coding DNA, can contain regulatory sequences which can receive "inputs" from genes that encode for certain transcription factors

Gene Regulatory Network [Evo. Devo. 2]

a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins;

Inputs come in form of the binding of transcription factors to regulatory sequences to promote/inhibit gene expression;

Outputs come in form of transcription factors that certain genes encode for synthesizing

Genetic Mechanisms of Phenotype Evolution [Evo. Devo. 2]

1) Protein Evolution - mutations of DNA causing differences in amino acid sequences of proteins, thus leading to different protein functions

2) Genetic Duplication - duplication of the genes, in which duplicate gene undergoes mutations in order to yield new function, whilst having the function of original gene

3) Regulatory Evolution - change of the timing & local of gene expression; often is the cause when slight morphological changes occur with an animal

Chitinase [Evo. Devo. 2]

Digestive Enzyme within carnivorous plants, which can either be used for fungal defense or dissolving of exoskeletons; example of evolution being driven by gene duplication (same gene -> same/similar protein synthesized for different function

What clade are hox genes a synapomorphy for? [Evo. Devo. 2] [Evo. Devo. 2]

Clade containing...

1) Cnidarians - mostly aquatic organisms with stinging tentacles (ex: Jellyfish, Coral, Hydras)

2) Bilaterians - organisms with bilateral symmetry (ex: vertabrates)

(Not all Eumetazoans - ex: Sponges & Ctenophores)

General Trends of Hox Genes (3) [Evo. Devo. 2]

1) Number of Hox Genes is proportion to phenotypical Complexity

2) Not all animals possess these genes

3) Essential for bodily development

Evolutionary Modularity [Evo. Devo. 2]

idea of individual segments of body being susceptible to having unique identities due to hox genes; leads to organisms with these unique traits undergoing independent evolution

Ubx [Evo. Devo. 2]

type of hox gene; represses wing development, promotes haltere (pair of organs for flight rotations) development

When ubx is "turned off," fly can gain 2nd pair of wings

Mullerian vs Batesian Mimicry [Evo. Devo. 2]

Mullerian - unrelated toxic/distasteful species look like each other; meant to reinforce message to predators via positive frequency dependent selection

Batesian - unrelated non-harmful species has appearance of more harmful one in order to ward off predators

Genome Wide Association Studies (GWAS) [Evo. Devo. 2]

genetic method in which researchers scan the entire genome and develop Manhattan Plot compares those of SAME species that do and don't have particular trait and finds if/where there is a significant genetic difference to locate gene responsible

CRISPR [Evo. Devo. 2]

group of molecules that can specifically locate, cut out, and replace genes and DNA sequences (gene editing); can be used to confirm if gene is responsible for particular function

Gene Recruitment [Evo. Devo. 2]

the co-option of a particular gene or network for a totally different function as a result of mutation

Cis-Regulatory Elements [Evo. Devo. 2]

A non-coding DNA sequence in or near a gene required for proper expression of that gene, often containing binding sites for transcription factors binded to RNA polymerase

Slight genotypic/phenotypic changes are often due to mutations of... [Evo. Devo. 2]

Regulatory Elements (mutations of actually coding regions can induce too drastic of changes & woukd likely kill embroyo )

What group of individuals are usually compared using GWAS? [Evo. Devo. 2]

Individuals with and without mutant phenotype WITHIN species (genetic differences are too large across different species)

Sonic hedgehog (Shh) Gene [Evo. Devo. 2]

a toolkit gene used for human development (nervous system, digestive system, embryonic patterns, limb development etc...); expressed in polarizing zone of limb bud (for posterior growth)

Standing Diversity [Marcoevo. 2]

the number of species (or other taxonomic unit) present in a particular area at a given time

Calculating Standing Diversity using Stratigraphic Range Graphs [Marcoevo. 2]

Standing Diversity = D₁ + Originations - Extinctions

D₁ - Standing Diversity at start of previous stage

Origination - when new species arises (new lines forms)

Extinction - when species goes extinct (line ends)

Sepkoski's Curve + Three Major Faunas [Marcoevo. 2]

Diversity curve that shows changes in marine invertebrates through the Phanerozoic eon, classic diversity curve, showed patterns of extinction and origination

1) Cambrian

2) Paleozoic

3) Modern

Anagenesis vs. Cladogenesis [Marcoevo. 2]

Anagenesis - gradual genetic change with no branches (Phyletic Gradualism); acknowledges gaps in fossil record of intermediate organisms

Cladogenesis - rapid genetic change after periods of stasis (Punctuated Equilibria); most commonly accepted mode of evolution

Population Speciation + Types (4) [Marcoevo. 2]

evolution of individuals of a population into different species due to barrier of gene flow (doesn't allow breeding)

1) Allopatric Speciation - population is divided via geographic boundary, caused them to separate genetically

2) Sympatric Speciation - members of population in same geographic area undergo divergent evolution, likely due to differentiation in niche

3) Parapatric Speciation - species are spread out over large region geographically, with members of species of different areas speciating, only breeding with those of close geographic proximity & still exchanging genetic material with one another

4) Peripatric Speciation - small subset of population are separated from ancestor population and found new population different in genetic content due to propagation of likely rarer genotypes/phenotypes (due to it being small part of population)

Background vs Mass Extinction [Marcoevo. 2]

Background: Ongoing extinction of species due to environmental or ecological factors (climate change, predation, etc...)

Mass: significant rise in extinction rates above the background level, global/extreme event where large groups of species are wiped out

Permian Extinction [Marcoevo. 2]

extinction at the end of the Paleozoic Period (250 Mya); wiped out nearly all species (~96%) via largest volcanic eruption, releasing CO₂ & CH₄, leading to high temperatures & ocean acidification

Cretaceous-Tertiary Extinction (KPG) [Marcoevo. 2]

extinction at end of Mesozoic Period (65 Mya); wiped out large portion of species (~75%), having non-avian dinosaurs go extinct, via large meteorite strike

Adaptive Radiation [Marcoevo. 2]

the rapid diversification and speciation from a single common ancestor through character displacement & novel traits via expanded number/size of niches; usually caused by extinctions & new habitat (ex: migration to islands)

Anthropocene [Marcoevo. 2]

the modern geological epoch during which humans have dramatically affected the environment; proposed to becoming 6th Mass Extinction Event

Still learning (9)

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Major Clades of Opisthokonts (2)

1) Fungi

2) Choanoflagellates + Animalia (Synapomorphy is presence of cadherins - proteins that help with cell-cell adhesion)

Synapomorphy for Opisthokonts

single posterior flagellum (often either manifests sperm cells or as been lost [most Fungi] )

Synapomorphies for Fungi (2)

1) Chitin (Polysaccharide) in Cell Wall (strengthens walls of hyphae)

2) Absorptive Heterotrophy - absorbs nutrients from environment via secrete enzyme with digest organic materials from environment

Major Groups of Fungi (4)

1) Microsporidia (Sister to Chytrids)

2) Chytrids (Sister to Arbuscular Mychorrhizae + Dikarya Clade)

3) Arbuscular Mycorrhiza (sister to Dikarya)

4) Dikarya

Microsporidia (2 Synapomorphies)

intracellular obligate parasites due to reduced mitochondria (1), infecting hosts with a polar tube (2) that releases spores into host; acts as a dangerous human pathogen

Chytrids (1 Synapomorphy + Ecological Impact)

fungi species that have retained flagella on gametes, thus being mostly aquatic; Amphibian Killer Fungus

Arbuscular Mycorrhizae

fungi that have microscopic fungal hyphae extend into the root of a plant; has mutualism with plant, increasing surface area of absorption to allow certain plants to live in distinct environments while obtaining photosynthates from plant

Structure of Fungi (3)

1) Hyphae - filaments that made up body of fungi; site of nutrient absorption

2) Mycelium - network of hyphae that form body

3) Septa (only in Dikarya) - cross walls that separate hyphae into cells

Synapomorphies of Dikarya (2)

1) Dikaryon Stage of Life cycle - two nuclei coexist within each cell

2) Septate Hyphae - hyphae are separated by septa (cross walls)

Major Groups of Dikarya (2)

1) Ascomycota (sac/cup fungi) - spores burst out of ascus under pressure

2) Basidiomycota (club fungi) - produces spores on basidium (prototypical mushroom top), from which spores fall

Examples of Ascomycota (5)

1) Yeast - unicellular with asexual reproduction

2) Truffles

3) Morels

4) (Most) Lichen

5) (Most) Molds

What type of fungi is a model organism?

Baker's/Brewer's Yeast [Diakarya -> Ascomycota]:

Saccharomyces cerevisiae

Mating Types

analogous of "sex" for fungi; set of two groups, where fungi of same mating type can't sexually reproduce with one another

Fungal Lifestyles (4)

1) Saprobic - decomposers: take up nutrients from dead organic matter

2) Predators - secretes sticky substances to trap organisms & grow within them

3) Parasitic

4) Mutualism (Ex: Lichens & Arbuscular Mycorrhizae)

Examples of Basidiomycota (4)

1) Mushroom

2) Rusts - plant pathogen

3) Smuts - plant pathogen

4) Brackets

Synapomorphy for Plants

Primary Chloroplasts: Chloroplasts were derived from ancestral cyanobacteria

Glaucophytes

unicellular algae species that undergoes asexual reproduction; retained peptidoglycan in cell wall; sister to Red Algae & Green Plants

Major Groups of Plants (3)

1) Glaucophytes (Sister to Red Algae + Green Plants)

2) Red Algae (Sister to Green Plants)

3) Green Plants

Red Algae

almost all multicellular algae that's red; sister to Green Plants, both having synapomorphy of the loss of peptidoglycan in the cell wall

Major Groups of Green Plants (2)

1) Green Algae

2) Land Plants

Synapomorphies for Green Plants (2)

1) Chlorophyll b - photosynthetic pigment which broadened light absorption range

2) Starch Storage

Synapomorphies for Land Plants (2) & Importance

1) Cuticle - waxy, hydrophobic coating of epidermis in order to mitigate water loss

2) Retention of Embryo - young plant has embryo within protective structure of maternal tissues

Important Evolutions for plants to be able to live on land (cuticle mitigates water loss & protective structure of embryo prevents desiccation)

Alternation of Generations Life Cycle Steps (5)

1) Diploid Sporophytes produces & releases spores (Meiosis)

2) Spores germinate and divide, developing into haploid gametophyte (Mitosis)

3) Gametophyte produces and releases haploid gametes (Mitosis)

4) Gametes fuses into Zygote (Fertilization)

5) Zygote develops into diploid sporophyte (Mitosis)

Difference in Alternation of Generation between Non-vascular & Vascular Land Plants

Non-Vascular Plants: Gametophyte is Dominant Generation (Sporophyte is smaller & dependent on gametophyte)

Vascular Plants: Sporophyte is Dominant Generation (Gametophyte is smaller & dependent on sporophyte)

Major Nonvascular Plant Groups (3)

1) Liverworts - leaf-like gametophytes; doesn't have stomata, lie close to ground to avoid water loss

2) Mosses - appears a thick mats of gametophytes with small sporophytes protruding up; despite not having vascular system, transports water via hydroid cell (small channel)

3) Hornworts - sporophytes lack stalk, allowing for indefinite cell division

All are sister to each other & Vascular Plants

Vascular System

collection of specialized tissues in some plants that transports mineral nutrients up from the roots (xylem) and brings sugars down from the leaves (phloem)

Haploid vs Diploid

one set of chromosomes vs two sets of chromosomes

Main Groups of Vascular Plants (3)

1) Lycophytes - bear microphylls (synapomorphy: simple leave structures with single vein); Sister to Ferns & Seed Plants

2) Ferns - alongside Seed Plants, bear megaphylls (leaves with branching veins)

3) Seed Plants

Main Groups of Seed Plants (2)

1) Gymnosperms - don't grow flowers & fruits, having naked seeds that aren't protected by ovaries (ovaries include fruits)

2) Angiosperms - flowering plants; flower acts as sexual structure, leading to enclosed seed

Structure of Angiosperms (4)

1) Stamen - tube structure that bears anther at top

2) Anther - site of production of pollen grain (found also in gymnosperms), which either form pollen tubes or male gametophytes (sperm)

3) Ovary - site of production of megaspores, which develop into female gametophyte (egg)

4) Pollen Tubes - deliver sperm into ovary to fertilize egg

Double Fertilization

2 sperms engage in fertilization within angiosperms:

One fertilizes egg to produce diploid zygote;

Another fuses with two nuclei to form triploid endosperm - which provides nutrients to zygote

Both are part of seed structure

Examples of Gymnosperms (4)

1) Cycads - palmlike plants

2) Ginkgos

3) Gnetophytes

4) Conifers - cones act as reproductive structure

All Subgroups of Plants

Plants -> Green Plants -> Land Plants -> Vascular Plants -> Seed Plants