Bio 114 final

WTF

Pattern

the general observations of repetition one sees within a system

Process

the mechanism/way in which the pattern occurs

proximate

what occurs in a short time frame (fraction of a life time)

ultimate

what occurs in longer timeframe

cell theory

all organisms are made of cells and all cells from pre-existing cells

1) limitations that exist among cells exist among all cells

2) life continous

Evolution

heritable change in a population over time:

1) if certain heritable traits help individuals produce more offspring, then those traits become more common in the population over time

2) evolutionary success can only be seen over a time longer than their lifespan and by comparing their success with that of other members of the population

Evolutionary Theory

all life, as we know it, is the product of evolutionary processes:

1) evolution explains variation, how that variation came about, and what can happen if environmental conditions change

2) all species are related to each other through common ancestry. Natural selection acts on individuals, but evolutionary change affects only population

Biological Hierarchy Level

framework of organization regarding all life around us - consists of atoms, molecules, organelles, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, and biosphere

Organisms

individuals that are collection of organ systems and is single-celled. Individuals are acted on by natural selection

Population

collections of individuals of the same species (interbreeding) and is affected by evolutionary change

Communities

collection of populations of different species living together in the same area. boundaries may be set up by natural structure or determined by people

Ecosystems (biomes)

communities and their abiotic factors (water, temperature, geology, sunlight, and etc.)

Biosphere

all of the ecosystems put together (all that gets in is sunlight and leaves that is heat energy, everything else stays - good or bad)

Emergent property

collection of units at one level takes on a trait that is greater than the sum of the parts (next higher level in the hierarchy)

Jean - Baptiste de Lamarack

1) first to state that species have changed through time

2) based on Aristotle’s thinking and simple organisms spontaneously generated

3) species change through time via acquired characteristics (individuals change as a result of environmental pressures and then pass those changed traits to offsprings)

Darwin concluded

1) variation in conjunction with environmental pressure is the key to understanding diversity and how snd why species change

2) all species have a common ancestor

3) all species show changes in characteristics through time

4) all species show change in characteristics in different environment

Modern Theory of Natural Selection

1) evolution is the change in genetic (allele) frequency w/in a population over time

2) natural selection is a process by which evolution can occur

Natural selection requirement

1) trait variation in a population - variation is the fuel of natural selection

2) heritability - trait that is passed from parent to offspring by genes

3) differential survival - needs to be a difference in survival to reproductive age based on the condition of the trait, which then leads to differential reproduction

4) differential reproduction result of a condition of the trait, individuals will have more breeding offspring than others and passing the genes for that condition into the next generation

Fitness

as a result of the greater survivorship and reproductive success of individuals possessing a particular trait, considered to be “naturally selected”

Adaptation

1) a heritable trait that increases the relative fitness of individuals having the trait

2) process by which individuals within a population acquire traits that increase their relative fitness

Artificial Selection

similar to natural selection but the selecting agent are humans, organism have been selected because they possess a desirable trait and the resulting offspring would continue that trait as well

Evidence for Evolution

1) species are related

2) species and species diversity change over time

3) evolution should be able to be seen in short-term

1 and 2 are referred as macroevolution - the change of one major taxonomic group into another or the creation/extinction of species

3 referred as microevolution - the change in a population over generations that helps to separate populations from each other genetically. accumulation over a long period may result in creation of new species

Macroevolution - evidence that some species are related

1) geographic proximity of similar, non-interbreeding species (Galapagos islands)

2) homology - similar traits in separate species due to a shared common ancestor

• genetic homology - similar gene sequences between individuals of different species

• developmental homology - similarities in the morphology of embryos of different species

• structural homology - similarities in the structure of body parts of different species

Macroevolution - evidence that species/species diversity change over time

1) fossil record

• not all species were together at one time'

• extinction has taken place

• transitional forms exist

• major increase in species complexity takes billions of years

• life began in the sea

2) vestigial traits structures in organisms commonly found in the species that serve little to or no function

Misconceptions about evolution

1) if evolution is true, then there is no God

2) humans evolved from apes

3) individuals evolve

4) adaptation occurs because a species needs/wants it

5) evolution always results in a more complex or better organism

6) animals do things for the good of the species

7) all traits are adaptive

8) functional traits have unlimited adaptive potential

Evolutionary trends

some long-term trends that resulted from macroevolutionary processes over billions of years

1) increase in multicellularity

2) increase in complexity

3) increase in ways to capture energy for use

4) increase in ways to deal w/ the environment - biotic and abiotic

5) increase in diversity

Adaptation compromises

compromises produced by competing selection pressures, often adaptation exist in direct conflict with each other, one providing success in a situation while another acting as a detriment

Environment changes over time

Natural selection favors traits suited to the environment of the previous generation, causing a lag in adaptation when conditions change. If the environment shifts frequently, adaptations may never fully match current conditions. As a result, species may evolve generalist traits that work moderately well across various environments, even if they seem suboptimal in any one situation.

Adaptations limited by historical constraints

Natural selection is not an engineer that designs new organisms from scratch. acts on new mutations and existing genetic variation. Because new mutations are fairly rare, natural selection works primarily with alleles that have been present for many generations. Thus, adaptive changes in the morphology of a species are often based on small modifications of existing structures. (bipedal posture of humans)

How to determine if its adaptation or modification

1) adaptation - a phenotype that is selected for within a population. Heritable trait that increases the fitness of the individual with that trait.

2) Contrivance - an adaptation in an organism, where the adaptation exists as a result of the modification of the original (or previous) adaptation in an ancestor.

3) Exaptation (pre-adaptation) - A trait that was adaptive under a prior set of conditions and later provides the initial stage for evolution of a new adaptation (contrivance) under a new set of conditions (in descendants).

Atavism

a trait possessed by only a few members of the population that is no longer used or has no use in the present environment, but was likely an adaptation for an ancestor

Homology

the similarity in traits between individuals as a result of the inheritance of those traits from a common ancestor

Homoplasy

when organisms have a trait in common but do not have a common ancestor that provided them with those traits

Convergent evolution

the independent natural selection of similar traits by unrelated individuals

phenotype/genotypes

phenotypes (measurable traits) are caused by genotypes (genes that code or traits). However, don’t always get a predictable phenotype from a specific genotype. And not everything is so hardwired. And it is that genetic variation that encodes for phenotypic variation. If genes did not cause phenotypes, there would be no variation among individuals within a population. Variation is important for species survival in the face of selection. But genes are selfish and don’t work for the good of the species

Genes

1) Genome – all of the hereditary information within an individual (includes non- gene stretches of DNA)

2) Gene pool – all the alleles of all the genes within a population. Each individual has only a small set of the genes in the population, unless the population is made of
clones.

3) Genotype – all of the alleles of all the genes within an individual or may refer to a specific set of alleles of a set of genes under study (compare Phenotype).

4) Genes – section of DNA found on chromosomes that encodes for a polypeptide, which, in turn, causes (directly or indirectly) a trait (phenotype), may also regulate
the activity of other genes.

5) Locus – (plural loci) the location of a gene on a chromosome. In a population the locus for a specific gene is considered to be the same throughout.

6) Alleles – particular versions of a gene that occur at the same locus on homologous
chromosomes.

Does Genotype equal to phenotype

1) Similar genotypes can result in different phenotypes. Environmental pressures can have a dramatic effect on how phenotypes are expressed.

• Two otherwise identical plants can be raised in two settings- one with plenty of light and the other with less light. The result is that one plant will
  look different than the other.

• identical twins do not encounter the exact same developmental environments, which affect “regulator” genes, which result in slight differences in appearance, esp. as they age

2) Similar phenotypes can result from different genotypes (gray timber wolf and Tasmanian wolf)

3) all traits of individuals in similar environments, but possessing different genotypes, will not be the same. Nor will those with identical genotypes necessarily have the same phenotypes, due to differing environmental pressures.

Variation in Eukaryotes

1) Genes are located on chromosomes, which are made of DNA and proteins; each species has a specific number and variety of chromosomes per set (e.g., humans have 23 per set).

2) Cells can have multiple sets of chromosomes; ploidy refers to both the number of chromosomes per set and the number of sets in a cell.

3) Diploid cells (2n) have homologous chromosome pairs—one from each parent—that contain the same genes but possibly different alleles.

4) Organisms may be haploid (1n, one set) or diploid (2n, two sets); some species like ants and bees have haploid males and diploid females.

5) In diploids, dominance occurs when one allele masks the expression of another at the same gene locus.

Meiosis

Gametes (egg and sperm) are produced through meiosis, a process that halves the chromosome number so that when two haploid gametes unite, they form a diploid zygote. Meiosis involves two divisions—Meiosis I and II—that generate genetic diversity.

1) In Meiosis I, homologous chromosomes pair up to form tetrads. Each tetrad has non-sister chromatids (from each parent) that align closely.

2) First source of variation: crossing over occurs at chiasmata, where non-sister chromatids exchange genetic segments, mixing maternal and paternal genes.

3) Second source of variation: during metaphase I, tetrads line up randomly, so each resulting cell gets a unique combination of maternal and paternal chromosomes.

4) Third source of variation: in Meiosis II, sister chromatids separate randomly into gametes, further shuffling genetic combinations.

How much variation

1) w/o cross-over - 2 homologous pairs yields 4 gametes (2ⁿ where n = haploid number of chromosomes)

2) with cross-over - the number of different gametes is almost infinite b/c cross-over occurs randomly, and can occur anywhere along the chromosome

Other sources of variation

mutations from a change in nucleotide sequence caused by environmental mutagens like radiation, chemicals, and physical irritation

• Most mutations are not deleterious – occur in junk DNA, are small, and not expressed. (These are used to measure genetic relationship of taxa. These mutations build up over time and are not selected for or against (since they are not expressed). The greater the differences between individuals, the longer their lineages have been apart.)

• Most expressed mutations are harmful and are removed from the population by natural selection

2) Mutations from replication errors occur and are expressed much more frequently

3) Nondisjunction – during cell divisions in meiosis I and II, one cell ends up with both pairs of homologs of one chromosome (or both sister chromatids if occurring in meiosis II). The rest of meiosis occurs normally and 2 gametes
are left with an extra chromosome (n+1) and 2 are left with one chromosome too few (n-1)

• Example Down Syndrome is trisomy (3 copies of the
  chromosome after fertilization) at chromosome 21 (trisomy 21). n-1 is monosomy

• Too many or too few chromosomes are referred to as
  aneuploidy Happens in 10% of meiotic divisions, but most are not expressed, since many end as fetal death.

4. Unequal crossing over – where one arm of a chromatid ends up longer than its sister (Huntington’s Disease)

Asexually reproducing organisms

1) Bacteria reproduce asexually through binary fission, producing identical haploid daughter cells. Without additional variation mechanisms, all offspring would be genetically identical.

2) Transformation: Bacteria absorb DNA fragments from the environment, which may integrate into their genome or exist as independent plasmids.

3) Transduction: Viruses infect bacteria and may transfer bacterial DNA from one cell to another, incorporating it into the genome of the new host.

4) Conjugation: A plasmid is transferred through a cytoplasmic bridge (pilus) from one bacterium to another, potentially introducing new genetic variants.

Before Mendel

1) Practical genetics - farmers knew that you could select certain livestock/plants that provided some benefit and breed them. The resulting offspring would frequently provide the same benefits their parents did.

2) Blending - For over a century prior to Mendel’s work scientists believed that offspring traits should be a blend of their parents.

• A black cow mated with a white bull should result in a gray calf (or at least one with black and white patches in its fur)

3) Acquired characteristics - Lamarck

Mendel’s Experiment

Mendel’s 2 guiding questions:

• Why do offspring resemble parents?

• Why are most offspring not ‘blends’ of parents

Mendel worked with pea plants (Pisum spp.). Pea plants are self-fertilizing if undisturbed. Petals on pea flowers enclose the pistil and stamens, but can be pulled apart to cross pollinate plants using an artist’s brush to transfer pollen from the anther of one plant to the pistil of the other. Cutting off the anthers from the recipient plant prevents self-pollination. Pea plants readily produce pure lines (homozygous condition at each locus) as a result of self-pollination. This was known and exploited by Mendel to produce pure lines of various traits, such as wrinkled and round peas.

Are offspring spring of parents?

1) Prediction: If blending occurs, then a cross of pure-breeding wrinkled and round peas (P generation) would produce all mildly wrinkled F1 offspring. And self- fertilizing of the F1 offspring would produce all mildly wrinkled offspring in the F2 generation.

2) Results: All F1 peas were round and indistinguishable from those of the round parent, discounting blending. F2 offspring had a ratio of 3:1 round to wrinkled, further evidence that there was no blending.

3) Interpretation 1: No blending. Mendel proposed that both the round and wrinkled traits were present in the F1 generation and that the wrinkled trait was not expressed in the F1 generation because the round trait dominated it. Hence dominant and recessive traits.

4) Interpretation 2: Particles occur in pairs, and in order to occur in the 3:1 ratio in F2, the particles must segregate into the gametes (egg and sperm) before they leave the reproductive structures.

Mendel’s Law of Segregation

alleles separate w/o dilution into gametes where each gamete contains one allele of each trait (gene)

Are different traits inherited together or separately

1) Prediction: If the 2 traits sorted dependently, would get one set of results in F2 (round yellow OR wrinkled green). If they assorted independently, would get an entirely different result in the F2.

2) Results: Round, yellow 315 (9/16), wrinkled, yellow 101 (3/16), Round, green 108 (3/16), and wrinkled, green 32 (1/16).

3) Interpretation: Particles (alleles) of one particular trait (gene) are passed on to offspring independently of each other (Mendel’s Law of Independent Assortment )

Mendel’s Law of Independent Assortment

1) Only works for genes occurring on different chromosomes.

2) Mendel still didn’t know about chromosomes, thought about his “particles (allele)” as independent little bodies floating around in the cells. Almost as if each gene had its own chromosome, not many, many genes on a few chromosomes.

3) Those genes on the same chromosome

T.H Morgan worked with fruitflies

1) Morgan discovered a white-eyed male fruit fly in a population of wild type,red-eyed individuals.

2) Mated male with a red-eyed female. Resulting F1 offspring had red eyes. He concluded that white eyes is recessive to red eyes.

3) performed a Reciprocal Cross: crossing the opposite way (in this case, switching the traits of male and female parents). mated females with white eyes with males with red eyes. The resulting F1 females had red eyes, BUT males had white eyes! Doesn’t seem to agree with Mendel.

4) There seemed to be some linkage between gender and eye color

Morgan’s conclusion

1) some traits are transmitted by X-linked inheritance patterns because the gene is located on the X chromosome. The Y
chromosome does not carry alleles for most genes occurring on the X chromosome, so the trait coded for by the allele on the X chromosome is observed in the phenotype.

2) Inheritance of genes located on non-sex chromosomes is called autosomal inheritance. Inheritance of genes located on the sex chromosomes is called sex- linked inheritance.

Multiple allelism

1) The occurrence of more than two alleles for a locus in a
population, even though only one occurs on each chromosome (2 on homologs in diploid cells). In Mendel’s world two alleles creates 3 genotypes and two phenotypes
only.

2) In most populations, dozens of alleles can be identified for each gene.

Human Blood Types

Has 3 alleles at one locus

Issues with Mendel’s results

1) Incomplete dominance: Where a heterozygous genotype expresses an intermediate phenotype ( like blending)

2) Codominance: Both genotypes are expressed, not as a dilution of one (like incomplete) but as a combination of the two.

3) Polygenic effects: a single trait is affected by many genes with the effects being additive. Leads to continuous variation rather than an either/or situation.

4) Pleiotropic effects: A single allele affects many traits.

5) Environmental effects: It’s important to distinguish how much of a trait ,is due to environmental pressures vs. how much is strictly genetic.

6) Epigenetic effects: Environmental cues can cause certain genes to be turned on and off. These traits may last for generations, and then be switched back for generations.

Probability

p = # of defined (or desired) events / # of total events

Mutually exclusive events (or)

events that cannot happen at the same time. This can
be described in more general terms: p(tail and head) = 0
The joint probability of mutually exclusive events occurring is their individual probabilities added together. Therefore, the probably of getting heads or tails, is equal to 1. This can also be described in more general terms: p(head or tail) = p(head) + p(tail)

Independent

events are those that are not affected by previous events, nor do the events affect each other. The probability of two independent events occurring at the same time is their two independent probabilities multiplied together P(A and B) = P(A) * P(B)

Punnett Square

a chart that predicts all possible numeric (genetic) combinations in a cross of events (coin tosses, parents creating offspring, etc.) whose possible outcomes (coin side, allelic combinations, etc.) are known. They are often used by genetic counselors, in order to find the likelihood that a particular trait will be passed to an offspring and in the construction of Pedigree Trees, are performed by utilizing Mendel’s Laws

Variation

Differences that exist between individual organisms in their structures, functions, and behaviorsmeasurements are obtained to describe and give information about a
particular trait within a group of subjects. If an entire population is available for measurement, then very accurate data may be obtained. Therefore, data are collected on a smaller sample of the larger population. This “sampling”,
and the resulting conclusions drawn about the population as a whole, can lead to problems if the sample does not accurately reflect the source population. It is easy to see how population estimates can be significantly affected by things like sample size and how the population looks in terms of its predictability

Hyptheses

1) Working Hypothesis - to make conclusions and further learn about our world, scientists reject one idea after another to narrow down the possibilities of correct ideas that answer their guiding research question

2) Null hypothesis - based on the concept of randomness, or “no difference”, or “chance prevails”

3) Alternative Hypothesis - needed in the event you reject your null and is typically the opposite of the null hypothesis. the alternative hypothesis reflects the working hypothesis, but it doesn’t have to

Chi-square

1) used in a variety of circumstances where data are recorded as events occurring in categories. That is, data that are continuous in nature may not be used, but data that are recorded as the number of times certain categories are achieved can be use:

X² = ∑ (obs-exp)²/exp

2) Goodness of fit - used for analyses involving two or more outcomes within a single variable

3) rejecting our null hypothesis - α < 0.05

4) fail to reject null hypothesis - α > 0.05

Monohybrid Cross

1) The mating of two purebred individuals having a trait that is caused by 2 alleles within a population yields an F1 generation of heterozygous individuals

2) The crossing of these hybrids yields an F2 generation of individuals that have one of two phenotypes, but three distinct genotypes.

3) If the alleles in question (R and r) did not come from a single organism, but were randomly selected in pairs from a pool of independently occurring alleles within the population, the resulting genotypes, and their probabilities, would be represented by: (R x R) + (r x R) + (R x r) + (r x r) = 1 combined: R² + 2Rr +r² = 1 (p² + 2pq + q² = 1)

Before Hardy-Weinberg

1) Dominant traits would eventually go to fixation in a population and recessive traits (unless they were selected for) would go away.

2) alleles would get distributed equally (50/50 in a 2 allele set),

3) And/or the only way alleles change frequency was through sexual reproduction

Hardy-Weinberg says

1) p is always the same generation after generation.

2) q is always the same generation after generation

Assumptions of the Hardy-Weinberg model

1) Random mating

2) No mutation

3) No migration

4) Infinite population size

5) No natural selection

Bottlenecks

where a gene pool is significantly reduced for some reason and a relatively small allele diversity remains (cheetahs)

Genetic Drift

constant changing of allele frequencies (that percentage of all
alleles any one, or more, allele occupies in a population) in a population over time, due to random mating( has the effect of changing how frequently an allele is found in a population)

1. Genetic drift is Random

2. Any change in allele frequency is due to chance.

3. Allele frequencies are constantly drifting up and down over time.

4. Allele changes are not adaptive

5. Drift is most influential in small populations

6. Drift can lead to the fixation or loss of alleles

7. Genetic drift does not increase allele frequency distribution in a population

8. Drift from generation to generation is not a violation of H-W, because the allele changes are within what randomness would predict is ok, and one of the assumptions of the H-W equilibrium is that randomness is occurring.

Gene flow

1) The movement of individuals and their alleles from one population to another

2) Gene flow typically results in equilibrating allele frequencies between populations (makes the populations look more alike genetically)
3) Gene flow into a population is one of two ways in which allele frequency distribution increases. Although it may cause a decline in allele diversity in the population that the individuals are emigrating from. The other way to increase allele diversity is mutation

Non-random mating

H-W model is based on mates being selected at random. However, random mate selection is not the norm in insects, vertebrates and many other animals. Even in organisms that broadcast gametes, population mixing is not entirely homogeneous. This is not random with respect to the entire interbreeding population. There are three different ways in which non-random mating occurs: Assortative Mating, Inbreeding, and Sexual Selection

Assortative mating

An individual is more likely to mate with another that is similar in phenotype to itself (Assortative Mating), or mate with another that has a different phenotype from itself (Disassortative Mating) - ex: plants

Inbreeding

1) mating of individuals that share a recent common ancestor.
“Recent” is relative to the organism in question and the intent to introduce novel alleles into the offspring, or maintain allele frequency distributions the way they are.

2) individuals are likely to share alleles they inherited from their
common ancestor, causing Inbreeding Depression.

3) Inbreeding depression is the loss of fitness as homozygosity in resulting offspring, future generations, and the population increases and heterozygosity decreases.

4) Evolution does not occur here since allele
frequency does not change. Only the genotypes do

Sexual Selection

1) Special case of natural selection that favors individuals with traits that increase their ability to obtain mates.

2) Acts on males more so than females because females are typically the higher investment sex. Since females invest so much in their offspring, they should be choosy about what males they mate with. They should choose males that
appear the most healthy, wealthy, and/or wise. Males invest little. Therefore, they should be willing to mate with any female. Therefore, females of many species look less showy/large

Sexual Dimorphism

the tendency of the two sexes of a species to look different - not all species that exhibit sexual dimorphism are that way due to sexual selection

Taxonomic Hierarchy

1) a system of classifying and naming species for the
purpose of understanding and establishing relatedness between species or larger groupings.

2) 7 basic levels: Kingdom, Phylum, Class, Order,
Family, Genus, and Species. The last two (Genus and Species) are the words used to name an individual type of organism.

3) In some systems of classification, you may find the prefixes super- and sub- (e.g., Superorder, or Subfamily) to describe further refinement of groupings above and below a certain level, respectively

How many kingdoms are there

1) Linnaeus divided all life into two kingdoms: Plantae and Animalia.

2) Some have used a 3-kingdom hierarchy: Plantae, Animalia, and Fungi.

3) Until recently, the most commonly used hierarchy included 5 kingdoms: Monera, Protista, Plantae, Fungi, and Animalia. Many now use the Domains (level above Kingdom) Bacteria and Archaea instead of Monera and then use the other four groups to describe all the rest (included in the domain
Eukarya)

Domain Eukarya

1. Kingdom: Animalia - animal

2. Phylum: Chordata – has a spinal cord

3. Class: Mammalia – has hair, mammary glands

4. Order: Artriodactyla – quadruped with even number of digits

5. Family: Cervidae – bony antlers

6. Genus: Odocoileus – small groups, white hair under tail

7. Species: virginianus – Odocoileus virginianus - antler points extend from single main beam

Species

1) an evolutionarily independent group, meaning that mutation, selection, and drift act on the group independently of what’s happening in other groups. gene flow between groups causes allele frequencies to be the same. If gene flow stops, then mutation, selection, and drift begin to work independently between groups. Although these things are working all the time at some level. If new alleles arise in one group, there is no way for it to get to the other group. If allele frequencies change sufficiently over time, populations become distinct species.

2) There are 3 different criteria for designating species. They involve the Biological, Morphological, and Phylogenetic species concepts

Separate Species

1) If two populations do not interbreed in nature, or do so but fail to produce viable offspring

2) problematic for distinguishing species in the fossil record and for organisms whose populations do not overlap (they cannot interbreed)

Prezygotic isolation

prevention of individuals from mating and creating
a zygote – fertilized egg (lightning bugs).

1) temporal- breeding at different times

2) habitat- breed in different habitats

3) behavioral – courtship displays differ

4) gametic barrier – eggs and sperm are incompatible

5) mechanical – genitalia incompatible

Postzygotic isolation

(zygote) offspring of individuals do not survive or
reproduce (Example: horse, donkey, and mule)

1) hybrid viability – offspring die as embryo

2) hybrid sterility – offspring mature, but are sterile

Morphospecies concept

1) Differences between groups in size, shape, or other morphological features (and sometimes in behaviors), indicate the two groups are different species.

2) Logic is that in order to be this different, the populations must have been apart and separated long enough to become distinct species.

3) works with sexual, asexual, and fossilized/extinct species.

4) Problems arise because traits are often subjective. Differences seen between groups of organisms may represent variation within the species, the effects of genetic drift, mutations, and/or natural selection

Phylogenetic Species Concept

1) Phylogenetics is the reconstruction of the evolutionary history of populations.

2) This concept takes into account a variety of traits specific to the population in order to establish relatedness between groups, and, therefore, distinction between them. Species are determined by populations having distinctions from other populations, whether these distinctions are morphological,
behavioral, or genetic

Phylogenetic Tree

1)a branching diagram that depicts relatedness/distinction among groups.

2) Branches within the tree represent a population through time.

3) Nodes (where branches come together) are points in time when an ancestral group split into 2 or more descendant groups, each group represented by each branch.

4) Terminal nodes at the ends of branches represent a group (species, or larger) - living or extinct.

Phylogenetic analyses

1) Phenetics – Grouping of species by similarity of traits, whether those traits are ancestral or more recently derived.

2) Cladistics – Grouping of species by shared, recently derived
characters only.

3) Monophyletic group – Most recent common ancestor and all its descendants

4) Paraphyletic group – Most recent common ancestor and not all of its descendants. This is not a really useful tool to studying
phylogenies, but is often used when trying to clarify the loss of
evolved traits and convergence

Phylogenetic terms

1) Homology – traits are similar due to a shared ancestry

2) Homoplasy – traits are similar due to other reasons than common ancestry.

3) Convergent Evolution – the independent evolution (by natural selection) of similar traits in distantly related organisms, where the common ancestor does not have the trait. (most common cause of homoplasy)

4) Parsimony – the most likely explanation or pattern is the one that implies the least amount of change (i.e., the simplest)

how to get new species

1) based on isolation of one or more groups from an ancestral group, and the genetic divergence between the new and ancestral groups. Speciation is not one group separating into two new species then those separating into two new species, etc. Speciation occurs when subgroups are isolated (reproductively) and divergence occurs during this separation. The ancestral population may continue to look roughly the same for a very long time while the new group diverges dramatically, or the two groups may diverge more or less equally.

2) Speciation can occur in Allopatric and Sympatric populations

Allopatric speciation

when subpopulations are separated by some physical barrier. The two subpopulations remain reproductively
isolated (no gene flow) and, over time, diverge from each other. After enough genetic divergence has taken place, the two populations may be classified as distinct species.

1) Dispersal – When a group emigrates from an area, and they are isolated long enough to have allele changes that eventually lead to a new species.

2) Vicariance – When a population is divided by a change in the geologic landscape. If the sub populations remain separated long enough, allele frequencies will change enough to call them separate species

Sympatric speciation

occurs when new species are created in areas where there is no physical barrier between subpopulations (can interbreed) .
Gene flow between groups would overwhelm differences that occur. However, if parts of a population prefer certain foods or habitats, they may eventually become separate species. (Golden-winged and Blue- winged Warblers)

What happens if formed species come back into contact

1) Reinforcement of species – if pops. can interbreed, and produce young, and hybrids have suppressed fitness (sterile or lowered fitness), then selection would favor those that do not interbreed, then further separation will occur.

2) Hybrid zones – Areas where 2 populations overlap and hybrids exist. May be small or large, short-lived or long-lived

3) New species through hybridization – hybrids contain a unique blend of alleles from parents and therefore different characteristics. If these traits can be selected for, then the genes are passed on to the next generation. A new
species may be created as a result.

major characteristics of Kingdom Plantae

1) Chloroplasts with chlorophyll a, b and β-carotene for wider spectral sensitivity – in green algae and all land plants – evolved for early competition for sunlight.

2) Multiple membrane layers in chloroplasts [thylacoid condition = stacked and flattened vesicles without connection to the inner of two membranes enclosing the chloroplast), for more efficient extraction of radiant energy

3) Cellulose cell wall outside of flexible cell membrane (for greater protection – and structural support)

4. Starch as an energy storage product

evolution of plante

1) Wavelength resource limitation - Photosynthesis evolved in early unicellular bacteria (Prokaryote: Cyanobacteria) with the
appearance of a pigment molecule able to absorb radiant energy and transform it into high-energy chemical bonds that could be used as an energy source by the cell for many metabolic purposes. Different pigments eventually evolved as the competition for different wavelengths of light penetrating the sea surface intensified with the increased diversity of aquatic autotrophs.

2. CO2 was also becoming less available, and oxygen more available, in the shallow marine waters congested with marine autotrophs. Here again, the air above the water had much more readily available CO2 than was dissolved in sea water.

early competition for energy sources

1) Elongated cells in multicellular algae evolved to reach light and CO₂ near the water surface, improving internal transport efficiency compared to intercellular exchange.

2) Larger, elongated cells developed enhanced contractile fibers and cytoplasmic streaming to distribute resources and reduce predation, while helping parts of the organism access more sunlight

3) Photosynthetic protists evolved structural reinforcements—cellulose, silicon, or calcium carbonate—for protection against predators and harsh shoreline environments, with cellulose later becoming central to land plant cell walls.

New niches

Untapped possibilities (resources) were just centimeters away in the air above very shallow water or on land: Land invasion and the evolution of land plants

Resources out of the water

1) Sunlight unfiltered and unabsorbed by water, and hence energy is more available

2) CO2 is more available in air than in water, and photosynthetic organisms were being driven to the most surface waters and even momentarily out of the water and onto land to get enough CO2 [diffusion of CO2 occurs about 10,000 times faster in air than water]

3) Freedom from heterotrophs, at least early in the evolution of land plants

challenges of life on land

1) Dehydration and getting enough water for photosynthesis

2) Support of plant structure above ground (overcoming gravity)

3) Transport of water within the plant from buried or submerged cells to air-exposed cells

4) Transport of photosynthate sugars to non-photosynthesizing cells, such as “root” cells

5) Sexual reproduction in dry environments where flagellated sperm can’t swim.

6) Exposure to harmful ultraviolet radiation (blue end of the wavelength spectrum); fortunately some pigments evolved to absorb blue wavelengths and offer protection

Non-vascular plants wlo cuticle

urely aquatic, simple plants with no major adaptations for
existence on land (e.g. green algae)

1. Mainly immersed in nearshore and freshwater habitats

2. Division (Phylum) Chlorophyta (Green algae)

Non-vascular plants w/ cuticle

Parts of plants out of water have a cuticle that gives dehydration resistance, but lack of support structure (and vascular tissue) results in low, sprawling growth (e.g. true
mosses). Extending out of the water just a little greatly increases wavelength and CO2 availability.
1. Mosses have specialized conducting tubular cells,

2. First to have stoma,

3. Water/nutrient intake and intercellular transport mainly by diffusion.

4. The gametophyte (haploid) is the dominant life cycle stage

Diversity

3 Divisions (Phyla): mosses, liverworts and hornworts

1) Largest Phylum: Bryophyta (Mosses)

2) First land plants (mosses); but not the ancestors of higher plants.

3) Sphagnum moss during drought becomes dormant until water returns

Vasular, seedless plants

The first plants with true vascular tissue enabling them to grow to greater heights, reaching above the non-vascular plants to compete for sunlight, but still limited sexually to moist environments because of depending on flagellated sperm for reproduction (e.g. ferns).

1. Vascular system

2. The sporophyte (diploid) is the dominant life cycle stage, as in all higher (land) plants.

3. Diversity: 4 major Divisions: Club mosses, Horsetails, Whisk ferns, Ferns.

4)Largest Phylum: Pteridophyta (Ferns): largest leaves, many epiphytes, and oldest vascular plants

Vascular, naked-seed plants (gymnosperms):

the innovation of pollen and dehydration-resistant seeds enable greater freedom (and dispersal) of sexual reproduction on land, but absence of fruit compromises even greater seed dispersal.
1) Seed is 1st major innovation: protects embryo against water loss, protects the embryo against herbivores, permits dormancy, and promotes dispersal.

2) Pollen is 2nd major innovation.

3) Cones of males (small) and females (large) usually in separate trees; scales partially protect female megaspore (eggs).

4) Needles of conifers reduce the photosynthetic surface, but this feature in combination with pollen allow conifers to thrive in more arid habitats.

5. Diversity: 4 major Divisions: Cycads, Ginkgos, Gnetophytes, Conifers (pines, spruces, firs)
a. Largest Division: Coniferophyta (Pines/spruces/firs)
b. Includes the largest (redwoods, sequoias) and oldest (Bristle cone pine ~ 4,900 yr) plant

Vascular plants with fruit-covered seeds (angiosperms, the flowering plants)

The fruit increases the protection and dispersal of seeds; the largest number of species of all plants.

1) Flower: a major innovation over gymnosperms: they facilitate pollination by attracting animal Pollinators (but many are wind- or water-pollinated).

2) Fruit = a mature, ripened ovary enclosing seed(s);

3) Diversity: One large Division: Anthophyta: the most widely distributed group of all land plants.

• Traditionally separated into monocotyledonous and dicotyledonous plants. Monocots have one leaf at germination, scattered vascular bundles, parallel leaf veins, and flower petals in multiples of 3; dicots have 2 leaves at germination, a circular arrangement of vascular bundles, branching leaf veins, and petals in multiples of 4 or 5.

• Most angiosperm plants are annuals (die off at the end of the year leaving only seeds for the
  next growing season) and herbaceous (are short-lived and non-woody [little or no lignin]).