Bio152 Midterm 1

Biogeography

the geographic distribution of living organism- does not appear random

similar species tend to be found geograpically close together

Common Ancestry

the concept that if you trace back the lineages of living species far enough in time, those species will converge to a shared ancestor

Supported by:

1. Similar species clustered in geographical areas even when there are other parts of the world that they would likely thrive in. Ex. Pengius only in the Southern Hemisphere

2. Homoogies are structures that have deep, underlying similarities between species

3. Studies of Fossils- transitional fossils

4. Nested Structure 

Evolution

the change in frequency of genetic variants in a population

3 core ideas:

1. Common Ancestry unites all life

2. Populations will change

3. Change in populations over time is not random but is adaptive b/c of natural selection

Fixation

the loss of all variants except one from a population

probability of ____ is entirely dependent upon the starting allele frequency

small populations—> quicker ___

biggere populations —> slower ___

Homology

Traits whose similarities are explained by common ancestry

traits that are truly the same because they trace back to an evolutionary origin in a common ancestor

Ex. land vertebrates have similar forelimb bone structure, regardless of the function of that forelimb

Natural Selection

the tendency for genetic variants that enhance fitness to go to fixation and variants that reduce fitness to be lost from populations

whichever genetic variants make an organism better equipped for the pressures of their environemt will tend to inc. in frequency in populations over time. 

Nested Hierarchy

a pattern of groups nested within groups (w/o overlaps) as seen in taxonomies

if taxonomic groups shared common ancestry at different times in the past, it is expected that taxonomies would be structured with groups within groups

Polymorphism

The existence of multiple variants within a population

Ex. one flower produces a single offspring with purple flowers due to a genetic mutation—> population with genetic variation

Transitional fossil

fossil taxa that have some, but not all, of the derived traits of living group

fossils tend to carry subsets of the traits found in living groups

Ex. some fossils shared similar characteristics to birds, like feathers and hllow bones, but lacked additional traits, such as wings

Branch

The lines that make up a tree diagram, which represent population lineages

Clade

All the descendants of an ancestral lineage

grouping of branches and tips

identify a chuck of the tree that can be removed from the root with a single cut

Lineage Splitting

A splitting of a pop. into genetically separate populations that no longer have gene flow

depicted at the nodes of a tree- separates two sister lineages

allow them to accumulate different traits

sometimes called speciation

1. Continous population that gets fragmented into two subpopulations by a geological or climate change process

2. large population on one land mass and a rare event resulting in a dispersal of some propagules to another land mass

Node

Branching points of tree diagrams, which represent lineage splitting

Phylogenetic Tree

A branching diagram used to represent evolutionary relationships and relatedness between different organisms based on their common ancestry

Pruning

Remove tips or clades from a tree w/o changing the topology

Root

The base of a tree, representing the common ancestral lineage of all taxa in the tree

Speciation

Lineage splitting that ultimately leads to taxa that are classified as separate species

can occur without geographic isolation with disruptive selection and assortative mating 

Taxon (Taxa)

a named groups of biological organisms, often shown at the tips of a tree

Tree Thinking

the ability to use the metaphor of a phylogenetic tree to convey accurate evolutionary information

Tree topology

A list of all the clades that a tree contains

representation of relationships between the clades

Convergent evolution

the phenomenon observed in phylogenetic trees where the same trait evolves separately in more than one lineage; although they appear similar, these traits are not homologous

Homologus

A descriptor of a character shared in separate species that was inherited from the common ancestor of those species

Principle of Parsimony

the idea that given multiple alternative hypotheses, the most likely hypothesis is the one that makes the fewest assumptions; in relation to phylogenies, parsimony favors the scenario that invokes the min, number of evolutionary changes (charater loss/ gain)

Reversal

The phenomenon in which an ancestral trait was lost and then re-evolved along a lineage

Separate ancestry

the alternative hypothesis to common ancestry, which proposes that each living taxon has an independent origin

Allele Frequency

In a pop. the proportion of all alleles at a locus that are of a particular type

Allele

A particular variant of a gene

Diploid

The trait of having two sets of chromosomes, as in humans

Evolution

change in the genetic composition of a pop. over time

Fixed

an allele that has a frequency of 1.0 in a pop.

all other variants become extinct.

Purple variant became fixed

After fixation, evolution does not stop b/c new variants can arise (mutation)

Genotype

genetic makeup of an organism

all the allels that organism has

Haploid

the trait of having one set of chromosomes in an organism

Hardy Weinberg Law

the law that, when a few key assumptions hold, makes it is possible to predict the genotype frequencies in a pop. for the next generation, based on the allele frequencies in the current generation.

1. No new allels emerge

2. mating happens randomly 

3. all alleles have equal fitness

4. population is infinitely large

Locus

a place in the genome where alleles reside; in diploids, each individual has two alleles per locus

Phenotype

the physical and behavioral characteristics of an organism that result from the interaction of the organism’s genotype and its environment. 

Polymorphic

when more than one allele is found at a given locus in a pop.

Populations

a groups of interbreeding organisms

Selfing

when an organism reproduces with itself, providing both the egg and sperm components. 

Beneficial mutation

a new allele that enhances the fitness of organisms

rare

selection coefficients greater than zero

Deleterious mutation

a new allele that decreases organimsal fitness

phenotype is altered in some way that negatively impacts the organism’s fitness

selection coefficient (s) less than zero

Directional selection

selection that arises when one allele consistently raises fitness; eventually, the beneficial allele is expected to become fixed in the population

causes a directional trend favoring an increase in the freq. of a favored allele relative to all other allels

when a beneficial allele is rare in the pop., directional selection works more slowly than when the beneficial allele is dominant

tends to remove genetic variation from populations

Ex. Peppered Moth

Mutation

a change in a gene sequence; arises independent of the needs of the organism

rate will never be zero

occur frequently in a large population

constantly being added into populations

random- does not change when the environment changes

larger genes provide a bigger target to “hit” by a ____

Natural Selection

the process of allele frequency change due to fitness variation among genotypes at that locus

Neutral Mutation

a new allele with neither a beneficial nor a deleterious effect

common especially in organisms like humans, which have a large amount of non-coding sequences in their genomes

selection coefficient (s) of zero

Relative Fitness (W)

the fitness of a given genotype divided by the fitness of a reference genotype, which relative fitness is assigned to be 1.0

their proportional success or lack of success at surviving and producing offspring

Genetic Bottleneck

the phenomenon in which a population lineage shrinks to a small size for period, causing that pop. to lose genetic variation

often occur during migration, when a few founder individuals move from one populations to establish a new population

Genetic Drift

random change in allele frequencies in a pop. over time

allele frequencies are always changing

two alleles with equal fitness and each with a frequency of 0.5—> 50% chance of going to fixation

can overcome directional selection when allele starts at a lower frequency and pop. is small

Genetic Load

the frequency of deleterious alleles that have accumulated in a pop. 

Carrier

an individual who is heterozygous for a disease

rare disease alleles occur much more often as heterozygotes than as homozygotes

Overdominant selection

selection in which heterozygote genotypes have the highest fitness

single gene with two alleles (AA,Aa, aa)

reaches stable equilibrium: balanced polymorphism 

prevents changes in allele frequency

Trans-specific polymorphisms

A set of alleles that are shared between closely related species; they arose before speciation and were maintained as polymorphisms

Underdominant selection

Selection in which heterozygote genotypes have the lowest fitness

tends to favor whichever allele has the highest frequency

unstable equilibrium

Continuous trait

A trait that is characterized by values on a continous scale, rather than being controlled by a single locus.

a range of variation

most populations have a trait value around the mean value and there are fewer indiviudals with trait values

Ex. height, weight, length and hair density

Disruptive selection

selection that favors trait values at both extremes of the trait value distribution

trait values at either extreme have a higher fitness than trait values nearer the mean

variance and SD increases over time

will still trait values near mean as long as there is random mating

Hertiability (h^2)

the fraction of the variation in a population that can be explained by genetics

Response to selection (r )

the amount the mean trait value in a population changes after one generation

subtract the mean of the parental generation from the mean of the offspring/selected generation

r= h²s

Stabilizing selection

selection that disfavors extreme trait values and favors trait values towards the center of the trait distribution

reduces the trait variation in the population

Ex. babies with either very high or very low birth weights have lower rates of survival than babies w/ moderate weight 

Standard Deviation

square root of the variance

variance

A measure of the spread of the distribution of a trait values in a population (technically, the sum of the squared deviations from the mean value)

Altruistic behavior

actions (or tendencies to act) that result in the organism exhibiting the behavior lowering its own fitness while inc. the fitness of other organisms within its pop

Ex of altriusm in humans: charity, adoption, and service in the military 

Exaggerated secondary sexual characteristics

dramatic traits in an organism that lower the organism’s viability but evolve because they are favored by sexual selection

all found in male

Ex. Male Peacock’s tail large and colorful

exaptation

phenomenon in which a trait that evolved for one function is currently used for a different function

fused collarbones is an _______ for flight 

polygamy

the phenomenon in which one male can mate with many females

males tend to have a higher variance in reproductive success

runaway sexual selection

the phenomenon in which secondary sexual characteristics become exaggerated due to feedback between male traits and female preferences (or, more rarely, female traits and male preferences)

allopatric speciation

speciation driven by geographic isolation

assortative mating

the phenomenon in which individual organisms tend to mate with other organisms with trait values like theirs

Ex. spiders long-legged individuals would preferentially mate w/ one another.

biological species concept

the view that species are defined by the ability of their members to reproduce with one another and to be unable to reproduce with the members of other species

clinal variation

gradual changes in traits as a function of geographical separation

discrete variation

genetic variation among geographically separated populations, where each population contains genetically similar individuals

results when there are barriers to gene flow between the distinct areas, but realtively free gene flow within an area

recognize genetically differentiated local populations within a species as distinct subspecies, varieties, or biological races

extrinsic reproductive isolation

the phenomenon in which two organisms are unable to reproduce due to geographic separation

intrinsic reproductive isolation

the phenomenon in which two organisms are no longer able to reproduce, even when they encounter one another 

phylogenetic species concept

the view that species are clades (monophyletic groups), like other in the taxonomic hierarchy (genera, subspecies, etc.), that biologists have chose to assign to the species rank for practical reasons

speciation

the splitting of an ancestral species into descendant species

sympatric speciaiton

speciation w/o geographical separation, driven by assortative mating within a population

population becomes internally by assortative mating so that there exisst two separate breed subgroups that can diverge and become separate species

Anoxygenic photosynthesis

reduction of carbon dioxide to organic molecules using light energy in which something other than water is the electron donor and oxygen gas is not released

use usually Sulfur

autogenous hypothesis for eukaryotes

theory that mitochondria and nucleus both evolved within the same eukaryotic lineage

the genomic material never evolved into linear chromosomes

phylogenetic tree should show that the mitochondrial genome is more closely related to eukaryotic nucleus than to bactera

cyanobacteria

clade of bacteria characterized by its ability to perform oxygenic photosynthesis

can be single-celled or form filaments of many cells

endosymbiosis

the phenomenon in which a prokaryotic cell comes to live and divide within a host cell

endosymbiotic hypothesis for eukaryotes

theory that mitochondria are derived from endosymbiotic bacteria taken up by the host cell whose genome is found in the eukaryotic nucleus

also explains the origin of chloroplasts

eukaryotic cells

a category of cells characterized by an outer membrane and many internal membrane-bound compartments including the mitochondria and nucleus

inside-out model

a theory for development of eukaryotic internal compartments that suggests that the outer plasma membrane of a prokaryotic ancestor was pushed outward and ultimately fused to create the cytoplasm and plasma membrane of eukaryotes

Last Universal Common Ancestor (LUCA)

most recent ancestor of all known life

last living thing that was ancestral to all known life

had features that are shared by bacteria, archaea, and eukaryotes

organelle

membrane-bound compartment of a eukaryotic cell that perform many various functions

Ex. nucleus

outside-in model

a theory for development of eukaryotes that starts with the production of vesicles within the cytoplasm by internalization

oxygenic photosynthesis

reduction of carbon dioxide to organic molecules using light energy in which water is the electron donor and oxygen gas is released

cyanobacteria is the only lineage that has evolved from this

originated ~2.3 billion years old

Prokaryotic cells

a category of cells characterized by an outer membrane containing no internal membrane structure

adaptive landscapes

visualizations of how selection acts on lineages over time

selection tends to push lineages onto the nearest fitness peak and that lineage will remain there until something changes

may be another peak that the lineage could occupy if it had the right set of phenotypes- would have to first experience a dec. in fitness

adaptive radiations

rapids expansions of clades to give rise to many diverse species adapted to different ecological niches

occur when a lineage undergoes a major transition that allows it to access some ecological space that was previously inaccessible

this lineage can now radiate into many species, each adapted to different eco

rare b/c stabilizing selection will mainatin adaptaions to the current adaptive zone

amniotes

a clade of tetrapods characterized by an egg that can persist on dry land, complex lungs, and protective skin

arthropods

a clade characterized by exoskeletons

wel adapted to life on land b/c their exoskeletons make them naturally resistant to desiccation

baleen

specialized filter-feeding structures found in whales

bilateral symmtery

trait of having a single plane of symmetry

aslo have three tissue layers, muscles, nerves

most modern animals are ______

key innovations is ability for organisms to search out food by moving around the environment efficiently

Cambrian Period

the first period of the Paleozoic Era; a time characterized by rapid radiation of bilaterians

began 542 million years ago

all bilaterian phyla appeared

Evolutionary Arms Race

a cycle of measures and countermeasures between interacting lineages

traits in females and traits in males keep evolving back and forth in reaction to one another resulting in extreme trait values

Exaptation

The re-purposing of the pre-existing trait for a novel function

Key Innovation

a trait that allows a lineage to occupy a new niche

Opisthokont clade

a clade of eukaryotes characterized by a flagellum

greek for “rear” 

“whip” referring to the flagellum

Pre-adaptations

traits in a lineage that existed had prior to a transition that give that lineage some advantage in a new ecological niche

Radiations

Rapid expansions of clades to give rise to many species

Red Queen Principle

idea that populations must keep adapting via directional selection b/c other species with which they interact are also constantly evolving

Ex. thicker armor, optimal tooth size inc. and so on