04 PPT NOTES Speciation_and_Phylogeny
Lecture Notes
How do we get new species?
Isolation → genetic divergence → speciation. The mechanisms of evolution (flow, drift, mutation, N.S) will operate on these isolated groups in different ways
Species = no gene flow between two groups → reproductively isolated groups.
Ex: You can’t mate with a chimpanzee successfully, pre-zygotic and post-zygotic mechanisms can happen, for example, the fetus dies, or the offspring is infertile. This is because chimps and humans are different species and therefore, reproductively isolated.
Pre-zygotic and post-zygotic barriers are the mechanisms by which species remain reproductively isolated from each other
Pre-zygotic: Zygote isn’t formed. Ex: Females don’t mate with males from other species. Egg cells don’t fertilize by sperm cells form other species.
Post-zygotic: Zygote is formed, but cannot pass on their genes. Ex: Mules (Horses + Donkeys) are infertile. Zygote forms, but is inviable and dies.
How do we get reproductive isolation → new species?
Allopatric Speciation: Physical separation → New species (vicariance)
Ex: Oceans, continents, glaciers
Ex: Small humans in Indonesia (Homo Floresiensis)
Ex: Shrimp in Panama being geographically separated into 10 species.
Sympatric Speciation: Same geographical area → new species
Ex: Anemone Flowers that diverge due to a polyploidy. (2n→3n) 3n individuals are reproductively isolated from 2n individuals.
Speciation. How do we define species? How to we draw those lines?
EX: The butterflies can be defined morphologically, but one species of butterfly have evolutionary adapted to look like the poisonous butterflies to avoid being hunted.
4 species concepts
4 Species Concepts
Morphology; same look → same species.
Pros: Easy to determine, usually right.
Cons: Mimicry, and convergent evolution (ex: Butterflies that adapted to look like poisonous butterflies, but are not the same species). Polymorphic species could be confused as different species when they are actually one species. (ex: Male and female cardinals that look different, male and female angler fish that look different, grasshoppers and locusts look different due to different serotonin levels, but they are the same species)
Biological; natural interbreeding that produces viable young → same species
Pros: Provides a solid answer about whether or not two animals are the same species.
Cons: Does not apply to asexual species. Can be contradicted by other species concepts.
Ex: Ligers (Lion + Tiger) are sterile.
Ex: Lions and tigers do not live in the same areas and would never interbreed normally, therefore they are not the same species.
Ex: Pizzly bears (Grizzly + Polar bears), not the same species even though the offspring is viable, the other biological species concepts such as the morphological one would contradict this because polars and grizzlys do not look the same.
Ex: Chihuahuas and great danes are the same species, but they can’t interbreed.
Ecological; same ecological niche → same species
Pros: This approach accounts for the adaptations and resource utilization of species within their environments. It can also help identify the boundaries by which competition between species can arise.
Cons: Males and females of the same species can occupy different ecological niches. Ex: Mosquitos, females suck blood, males don’t.
ex: Caterpillars that occupy different host plants are different species.
Phylogenetic; genetic clustering similarities in the mitochondria → same species
Used as a confirmatory species concept used in tandem with other species concepts.
Pros: Useful for distinguishing between species that are similar in appearance but genetically distinct.
Cons: Some parts of the genome could be similar or different based on selection. That’s why we compare mitochondrial DNA.
Ex: You having more genetic overlap with your family, compared to another family.
Hybrid Zones
Primary (away): Speciation with trace amounts of mixing. Ex: Polar bears and grizzly bears drifting apart.
Secondary (towards): Different species coming back together.
Hybrid zones can also vary depending on the fitness of the hybrid, which gives way to 3 different types of hybrid zones.
Reinforcement: Hybrid is not favorable → Interbreeding discouraged → species drift apart. The reproductive barrier between the species is reinforced. Result: 2 reproductively isolated species
Fusion: Hybrid has equal fitness to o.g → Interbreeding encouraged → gene pools blend. Result: Populations merge into one.
Stability: Hybrid has higher fitness in it’s own niche → hybrids continue to form, the o.g populations remain distinct over time because of selective pressures. Result: Populations remain distinct, with hybrids persisting in a specific zone.
Rate of Speciation/Evolution
Opportunity and Innovation determine the ROS
Opportunity: new ecological niches being constructed in the environment
Innovation; favorable mutations causes evolution.
Innovation and Opportunity must match each other to cause change
ROS can be quantified by 2 different models
Gradualism: Species from a common ancestor gradually diverge in morphology as they acquire unique adaptations.
Punctuated equilibrium; A new species changes most as it buds from a parent species and then changes little for the rest of it’s existence.
Adaptive radiation → spontaneous burst of new evolutionary characteristics due to opportunity/innovation. Ex: The ability to walk on land, to lay eggs on land.
Phylogeny (trees based on mitochondrial genetics)
Evolutionary history of group of organisms
Initially proposed by Darwin with the divergent finches when he observed varying levels of difference between groups of finches.
This became the notion of drawing phylogenic trees.
They are based on genetic similarity/homology
Based on the phylogenetic species concept.
Groups that can exist within phylogenic trees are monophyletic, paraphyletic, and polyphyletic groups.
Monophyletic:
Definition: A group that contains an ancestor and all its descendants.
Represents a complete branch on the tree of life.
Example: Birds and reptiles as part of the clade Archosauria.
Paraphyletic:
Definition: A group that contains a common ancestor and some, but not all, of its descendants.
Represents a fragment of a branch on the tree of life.
Example: The group "Reptiles" which excludes birds, even though birds descended from reptiles.
Polyphyletic:
Definition: A group that is defined based on similarities, often convergent traits, rather than from a common ancestor.
Does not include the last common ancestor of all members of the group.
Example: Bats and birds as a group based on the trait of flight, despite not sharing an immediate common ancestor.
Rules to build phylogenic traits:
Maximum parsimony; The simplest explanation, or the tree that requires the fewest evolutionary changes, is preferred. It focuses on minimizing the number of changes or steps needed to explain observed characteristics among species. Essentially, the best tree is the one that limits the appearance of derived traits to a single occurrence.
Maximum likelihood; % difference between species dictates how recently species split from each other. More homologies between two species means they split more recently. Based on the mitochondrial DNA to account for species evolving at different rates. Ex; If two species are 10% percent different from each other, we say they split x amount of years ago. If another species is 20% different, we assume they split 2x amount of years ago.
when considering multiple phylogenetic hypotheses, one should take into account the hypothesis that reflects the most likely sequence of evolutionary events, given certain rules about how DNA changes over time.
Cladistics (trees based on morphology)
Phylogenic trees based on morphological species concept, common species are organized into clades.
The morphological species concept is not very accurate in explaining relationships between species and defining species so they were replaced by phylogenic trees.
Defined by specific traits that were added to the gene pool at certain points in time.
Shared ancestral traits; not exclusive owners of that trait evolutionarily. Ex: backbones
Shared derived traits from that group/ecological niche; exclusive owners of that trait Ex: Hair, feathers.
Phylogenic trees are better based off of shared derived traits because they can actually divide species into specific groups because they are not shared by everyone. Ex: You wouldn’t use backbones to define a phylogenic tree because all species have backbones so it wouldn’t help you to differentiate between species.
Molecular Clock
Associating evolutionary change with a timeline
estimates evolutionary divergence times between species based on the rate of genetic mutations, which accumulate at a relatively constant rate
Volcanic islands assist in calibrating the molecular clock by providing dating for geological events, allowing researchers to compare genetic variations in island species to known island ages for accurate divergence time estimates.
Use fossil records to estimate a timeline for divergence
%change/time = ROC of species/evolutionary rate
End of chapter questions + Jeopardy questions:
Which species is most closely related to species W?
V because they share the most recent common ancestor.
What evolutionary group (monophyletic, paraphyletic, or polyphyletic) is species X, Y, Z, and their most recent common ancestor?
Polyphyletic. X Y and Z are grouped based on similarities rather than ancestry.
Which of these five species is the extant (i.e., not extinct) species that is most closely related to species X, and why is this so?
V because they share the most recent common ancestor, and because W is extinct.
What are shared ancestral traits and shared derived traits of mammals?
Ancestral traits of mammals (5)
Vertebral column
Jaws
Lungs
4 limbs. Tetrapods.
Amniotic egg
Shared derived traits (3)
Hair/fur
Mammary glands
3 Middle Ear Bones
What is the difference between a monophyletic and paraphyletic group? Use reptiles and birds to make your point.
Comparison of Monophyletic, Paraphyletic, and Polyphyletic Groups:
Monophyletic:
A group that contains an ancestor and all its descendants.
Represents a complete branch on the tree of life.
Example: Birds and reptiles form a monophyletic group when both are considered part of the clade Archosauria, which includes the common ancestor and all descendants.
Paraphyletic:
A group that contains a common ancestor and some, but not all, of its descendants.
Represents a fragment of a branch on the tree of life.
Example: The group "Reptiles" is paraphyletic because it excludes birds, which descended from reptiles.
Polyphyletic:
A group that is defined based on similarities, often convergent traits, rather than a common ancestor.
Does not include the last common ancestor of all members of the group.
Example: The group that includes bats and birds is polyphyletic because they do not share an immediate common ancestor but share the trait of flight.
What is parsimony?
Parsimony in phylogenetics refers to the preference for the simplest explanation or pathway when constructing phylogenetic trees. In other words, it suggests that the best tree is the one that requires the least number of evolutionary changes or transformations to explain the observed characteristics among species.
What are the two principles used when building phylogenetic trees using molecular systematics?
The two principles used when building phylogenetic trees using molecular systematics are:
1. Maximum parsimony: The simplest explanation with the least amount of branches.
2. Maximum likelihood: Considers the probabilities of a specific monoevolution.
In phylogeny, why is it crucial to compare genetic sequences not under selection? What principle to building phylogenetic trees would using traits under selection violate? What technique can we use to test whether a particular sequence is not under selection?
Comparing genetic sequences that are not under selection is crucial because these sequences evolve primarily through neutral mutations, which accumulate at a roughly constant rate over time. This makes them reliable molecular clocks for estimating evolutionary relationships and divergence times. Sequences under selection may experience adaptive changes or purifying selection, leading to uneven rates of change and skewed relationships that do not reflect true evolutionary history.
Maximum likelihood assumes that mutations occur at a consistent rate (or a defined rate matrix) across different lineages. Traits under selection may experience adaptive radiation (rapid bursts of change during adaptive selection or conservation during purifying selection), which biases the likelihood calculations.
A technique to test whether a particular sequence is not under selection is to use neutrality tests, which evaluate the distribution of genetic variations and can indicate whether a sequence has been subject to selective pressures.
You can also selectively examine mitochondrial DNA which is non-coding therefore not under selection.
What is the molecular clock? How are volcanic islands useful for setting the scale of the clock?
The molecular clock is a method used in molecular phylogenetics to estimate the time of evolutionary divergence between species based on the rate of genetic mutations. It assumes that mutations accumulate at a relatively constant rate over time, allowing researchers to infer when two species diverged from a common ancestor.
Volcanic islands are useful for setting the scale of the molecular clock because they provide a timeline of geological events. The ages of these islands can be dated, and scientists can study the evolutionary changes in species that inhabit them. By comparing genetic variation in these populations to the known ages of the islands, researchers can calibrate the molecular clock, giving them a more accurate estimate of divergence times.
How were researchers able to determine when HIV first invaded humans? How is this useful for Center for Disease Control scientists to track outbreaks?
Researchers determined when HIV first invaded humans by analyzing mitochondrial genetic sequences of the virus from different patients and identifying the most recent common ancestor through phylogenetic analysis. By estimating mutation rates and comparing the genetic diversity of HIV strains circulating in different populations, they were able to infer the timeline of the virus's emergence in human populations.
The time when it had the least amount of genetic diversity is when it first popped up.
This information is useful for the Center for Disease Control (CDC) scientists to track outbreaks by providing insights into how the virus spreads, its evolution over time, and informing public health strategies to control transmission.
What part of the genome is checked in determining evolutionary relationships?
Mitochondrial DNA
What is a paralogous gene?
Homologous genes that have arised through gene duplication
Explain sexual selection, give an example
Selection based on traits that maximize reproductive success. Ex: a female peacock choosing a male with the brightest feathers, a female mating with the strongest male.
What are pre-zygotic and post-zygotic barriers?
Pre-zygotic: Preventing the fetus form being conceived, Ex: Female eggs cannot be fertilized by fish sperm.
Post-zygotic: Issues with the offspring in it’s reproductive ability. Ex: Mules are sterile and cannot reproduce.
How do you determine the heritability of a trait?
Response/Strength of selection
Intersexual vs. Intrasexual selection
Intersexual Selection: Selection by females for which male traits she prefers. Females choose males based on traits that maximize their reproductive success (e.g., a female peacock choosing a male with the brightest feathers).
Intrasexual Selection: Selection within males for access to females. This occurs when males compete among themselves (e.g., fighting for territory or dominance) to attract females.
Founder’s effect vs Bottleneck effect
Both reduce genetic variability, and are mechanisms of drift.
Founder’s effect is when a group moves to an uninhabited region and starts reproducing there. Assuming there is no interbreeding with another group, that region’s gene pool will be limited to that of the o.g individuals that came there.
The bottleneck effect results from a catastrophe wiping out a large portion of teh population, and those who remain have to repopulate. The gene pool will be limited to the genes of that group that survived.
What does the biological species concept say?
The biological species concept states that a species is defined as a group of organisms that can mate and produce viable offspring that are also capable of reproduction. In other words, members of the same species can interbreed and create fertile young, distinguishing them from other species.
What is the downside to classifying based on shared traits?
Does not account for convergent evolution. Two organisms can share traits because they lives in the same ecological niche, not because they share a common ancestor.
Frequency-dependent selection is when a trait is only beneficial in certain frequencies relative to other traits
What determines rate of speciation?
Opportunity and innovation
Allopatric speciation is speciation due to the geographical separation of 2 groups
Stabilizing selection vs. Balancing selection
Stabilizing: elimination of extremes from an array of phenotype. The intermediate phenotype is favoured
Balancing: Maintenance of multiple alleles within a gene pool.
Species evolve at a constant rate, generation time varies because of reproduction time.
What is punctuated equilibrium?
Once a species appears in the fossil record, the population will undergo short evolutionary bursts and then remain stable for most of it’s geological history.
Mechanisms of natural selection
Flow
Drift
N.S
Mutation
Define adaptive radiation and give an example
Adaptive Radiation: Adaptive radiation is an evolutionary process in which a single ancestral species rapidly diversifies into a wide variety of forms to adapt to different environments or ecological niches. This process often occurs when a species colonizes an area with diverse habitats or following a mass extinction event that opens up new ecological opportunities. Caused by opportunity meeting innovation.
Example: A classic example of adaptive radiation is observed in the finches of the Galápagos Islands, often referred to as "Darwin's finches." These birds evolved from a common ancestor into various species, each adapted to utilize different food sources available on the islands, such as seeds, insects, and nectar.