Evolution Exam 2

Fossil Record patterns

-anagenesis

-adaptive radiation

-convergent evolution

-Dollo’s Law (of irreversibility)

Fossil Record rates

-phyletic gradualism

-punctuated equilibrium

Anagenesis

the gradual evolution of a single species within a single lineage over time, where the population changes so much that it becomes a new species while the ancestral form is replaced or considered extinct

Adaptive radiation

an evolutionary process in which organisms diversify rapidly from a single ancestral species into a multitude of new forms, particularly when an environmental change opens up new resources, niches, or ecological opportunities.

Dollo’s Law

once lost, a trait is not regained

Macroevolution

-evolution above the species level

-observed in the natural world and is recorded in the fossil record

Different macroevolutionary patterns

-convergent evolution

-adaptive radiations

-phenotypic plasticity

-morphological stasis

-Dollo’s Law (of irreversibility)

Phenotypic plasticity

a single genotype that may produce different phenotypes in different environments

Why are transitional forms so informative

-very rare

-these fossils have characteristics that are intermediate between 2 distinct taxonomic groups (fish and tetrapods)

Phyletic gradualism

-gradual change over a long period of time

-contains most transitional fossils (tiktaalik, dinos)

“saltation”

Punctuated equilibrium

-short periods of rapid change and macroevolutionary events during which new taxa arise (speciation)

-while morphology isnt changing, DNA still accumulates mutations over time

EX: stickleback fishes

“radualism”

What happens to stickleback fish when they change to salt to freshwater?

Freshwater: they lose their pelvic spines (increases fitness bc dragonfly larvae cant grab them)

Saltwater: gain pelvic spines (increases fitness bc they cant be swallowed by predator fish)

Neutrally evolving; molecular clocks

Neutrally evolving DNA sequences evolve in a clocklike manner

DNA substitutions is proportional to time

What is evolutionary developmental biology?

a field of biology that compares how different animals and plants grow from a single cell into an adult, helping scientists understand how new body shapes and traits evolve

What are typical model organisms used in Evo-Devo?

fruit flies

chicks

What is the genetic toolkit?

-genes in the genome that are used to form and pattern the body

-occurs typically during embryonic life

-deeply evolutionary conserved

-transcription and signaling factors

What are cis and trans acting components of the toolkit?

1. transcription factors (Hox) that regulate the expression of other genes

2. Signaling factors (sonic hedgehog) that mediate short and long-range interactions between cells

How does CRE variation in different organisms correlate to changes in gene expression and morphology?

alters gene expression in a modular, tissue-specific manner without disrupting the core pleiotropic functions of developmental proteins

What is a gene developmental gene network?

a complex biological blueprint made of interacting DNA segments, molecular regulators, and transcription factors that control how an organism develops from a single cell into a structured body plan

What is the main objective of evo-devo?

-to study the mechanisms that produce evolutionary changes in body plans

Fossil Record Pattern 1

Homology

correspondence or similarity of structures and function in different taxa due to shared common ancestory

Fossil Record Pattern 2

Homoplasy due to similar ecological/environmental pressures

ex: vetebrate and octopus eye, hyenas and dogs

Fossil Record Pattern 3

Dollo’s Law supported

-Due to natural selection and developmental constraints associated with a developmental toolkit expression

Dollo’s Law violated: common lizards and reproductive mode

Fossil Record Pattern 4

Anagenesis- “against growth”

-change in the trait (x-axis) as time (y-axis) proceeds from past towards the present

-there is no speciation event (no bifurcation

Fossil Record Pattern 5

Adaptive radiation

“bushy” and have polytomies

Rates of fossil record

Gradual vs punctuated

Von Baer’s developmental hourglass phylotypic stage conserved shows:

species specific changes occur later in development

The 3 Evo Devo principles

-deep homology of conserved toolkit loci (Hox)

-Pleiotropy (Pitx1 sticklbacks)

-Tinkering via modular CREs

What does Evo Devo investigate and compare?

Embryonic development in different organisms to better understand how these processes evolved and shaped the diversity of body plans

Evo Devo provides:

-a mechanistic understanding for the origin of traits (wings, lungs, feathers)

-insights into repeated patterns of evolution observed in different times and different lineages

-a mechanistic understanding of how traits are modified through time consistent with gradual vs punctuated models

Early ideas on embryonic development

Preformation-embryos are “preformed” and basically unroll and grow

-EPIGENESIS-embryo starts “from scratch” every generation (CORRECT HYPOTHESIS)

Who was the first to examine and describe embryos?

Aristotle

proposed epigenesis

Who was the first to describe homology in embryos?

Rathke

-studies how fish, salamanders, frogs, birds, mammals developed

-noticed striking similarities in the development of the different vetebrates

Darwin embraced:

That there is strong evidence of common ancestry and descent with modification in embryos

Model organism systems:

-must be able to get embryos

-rear in the lab

-genome resources

Camera eyes, independently evolved in cephalopds and vertebrates are an excellent example of:

Convergent evolution

The vertebrate camera eye, occurs _____ in phylogeny

Early, ~518 MYA

In all metazoans, there is a small and deeply conserved set of genomic loci that:

-act during embryonic life

-pattern the body plan

-can be “tinkered” with to produce diversity of body plans

They are referred to as “toolkit” genes because they “build body plans”

Von Baer’s Hourglass

add pic

Evo-Devo principle 1

Deep Homology

Experimental of drosophilia eyeless or the mouse orthology pax6 shows the function of eyeless/pax6 is conserved in developmental of analogous compound and single lens eyes

Evo Devo principle 2

Pleiotropy

Mouse pax6 is responsible for eye, brain, and pancreas patterning and development in embryonic life. pleiotropy is defined as a single genomic locus that is responsible for different traits

Evo devo 3

Modular CREs

Different CRE modules give specific and separate instructions to Pax6

They are bound by transcription factor proteins to control gene transcription/expression

Where, when, how quantity instructions for transcription and protein

Pax6 is a:

toolkit locus that acts in embryonic life to pattern the eyes of metazoans

Distalles (D11)

all species share deep homology of D11

Pleiotropy

genetic phenomenon where a single gene influences multiple, distinct, and seemingly unrelated phenotypic traits

Evo-devo helps us understand:

-difference between structural homology and deep homolgy

-Repeated evolution (convergent evolution) : pleiotropy, development bais/constraint

-rapid vs gradual evolution

-evolution of novel traits

Difference between structural homolgy and deep homolgy

-structures in adults of very distantly related species have NO structural homology

-all distantly related species share deep homology for the toolkit locus or loci (D11, Hox, pax6)

A mouse that doesnt have pax6 doesnt have eyes, but fruit fly protein can be used to give the mouse eyes. What evo-devo priniciple is this an example of?

DEEP HOMOLOGY

A genetic network that includes the Distalless (Dll) gene triggers outgrowths during

the development of starfish and insects. There is NO structural homology of the different outgrowths that serve as appendages. What evo-devo principle is this?

Deep homology

All species share deep homology of D11

Pleiotropy also _______ evolution

Constraints/limits

-range of variation of a single genomic locus is limited because it is responsible for many traits

Pitx1

Pleiotropic master regulator

Where is pitx1 found?

stickleback fishes

-it is expressed in several regions of the stickleback embryo, corresponding to different adult structures (pelvis, eye, jaw, pupitary)

What evo devo principle is pitx1?

Pleiotropy

In freshwater stickles, the CRE module that gives specific instructions to Pitx1 is _____

DISABLED

Pitx1 isnt expressed in these embryonic cells and adults dont have a pelvic spine

Can you lose the Pitx1 genomic locus?

NO because it is pleiotropic

it is lethal to the embryo

Von Baer’s developmental hourglass “variable” region is an example of what principle?

3

Von Baer’s “conserved” region is an example of what principles?

1, 2, 3

Deep homology and pleiotropy are extremely evolutionarily

conserved in metazoans. How did phenotypic diversity occur? How

do species-specific characteristics occur?

-modular CREs “permit” sequence variation that only affects one specific set of instructions but doesnt influence other instructions

-the flexibility of genetic variation WITHIN a CRE module explains diversity withing a species and between different species

Bmp4 is a pleiotropic toolkit locus that:

patterns different bone and cartilage structures

Heavy deep beaks: have high bmp4 expression in beak embryonic cells

Small, pointy beaks: almost undetectable bmp4 expression in beak embryonic cells

The CRE module of bmp4 that give instructions for HOW MUCH bmp4 expression in embryonic beak cells will show sequence variation in different finch species

Tbx4 and Tbx5 establish :

fore vs hindlimb

Shh (sonic hedgehog) establishes :

zone of polarizing activity

Fgfs establish:

apical ectoderm ridge

The timing and spatial pattern of gene activity differs in different species. Why?

Caused by species-specific differences in CRE modules

There are a few RARE examples of mutation in protein-coding DNA sequences of a toolkit genomic locus that cause phenotypic diversity

UBX is the gene

The sequences have changed leading to different embryonic patterning of the body plan

Example of a novel trait

Butterfly spots

How do evo devo principles explain evolution of novel traits?

-modular CREs can place a pleioptropic master regulator in a new spatial and/or temporal context in the embryo without interfering with the ancestral spatial and temporal contexts

-once a pleitropic master regulator toolkit locus in a cell, it will activate the GRN, composed of thousands of genomic loci\

-in closely related taxa that have acquired a new CRE module, further diversity can occur by sequence diversity in a given CRE

A fossil lineage shows a gradual change in body size through time, but the

lineage never splits into two branches. Which macroevolutionary pattern does

this best represent?

Anagenesis

A single ancestral lineage rapidly gives rise to many descendant lineages

occupying different environments. Which pattern is most consistent with the

diagram?

Adaptive radiation

Two distantly related lineages independently evolve similar saber-toothed

morphologies. What concept best explains this pattern?

Convergent evolution

Two structures look similar because their ancestors inherited the same

underlying feature from a common ancestor. Which term applies?

Homology

A lineage loses a complex anatomical trait. Based on Dollo’s Law, which

prediction would be most appropriate?

Regaining the same complex trait will NOT occur

A fossil sequence contains numerous transitional forms showing relatively

continuous morphological change through time. Which model does this

support?

Phyletic gradualism

A fossil lineage shows long periods with little morphological change followed by

relatively rapid change associated with speciation. Which model best fits?

Punctuated equilibrium

In a punctuated-equilibrium diagram, most morphological change is

concentrated around branching/speciation events. What does this pattern

indicate?

Substantial phenotypic change can occur during speciation events

A lineage appears to have a gap in the fossil record between two forms.

According to the presentation, what is an important interpretation of such a gap

under punctuated equilibrium?

The gap can mean rapid evolutionary change with speciation.

Researchers compare neutrally evolving DNA sequences between two lineages.

The number of substitutions is used to estimate how long ago they diverged.

Which concept is being applied?

Molecular clock

Embryos of different species show the greatest conservation during an

intermediate developmental stage, while species-specific differences become

more pronounced later. Which concept matches this pattern?

Developmental Hourglass

A single gene influences eye, brain, and pancreas development. A mutation

affecting that gene therefore produces effects in several traits. What term

describes this?

Pleiotropy

A mutation changes gene expression in the pelvic region of a fish while leaving

expression of the same gene in other tissues relatively unaffected. What feature

of gene regulation makes this possible?

Modular CREs

Freshwater sticklebacks have reduced pelvic structures because a

pelvic-specific regulatory element is disabled, while other Pitx1 functions

remain. Why is this mechanism useful evolutionarily?

It changes one developmental context without disrupting other functions

Embryonic beak cells in finches with deep, heavy beaks show higher Bmp4

expression than those with small, pointy beaks. What does this demonstrate?

Differences in gene expression for development

Fruit fly Pax6 can rescue eye development in a mouse lacking functional Pax6.

What concept is most directly illustrated?

Deep homology

A conserved developmental toolkit gene is brought into a new tissue or

developmental context through a new regulatory element, contributing to a

novel trait. What process is this?

Cooption

The python limb-bud diagram shows Fgf2 and msx expression in mesenchyme

but no AER, and Dlx is not detected in the limb bud. What does this evidence

most directly illustrate?

Protein-coding genes never change during evolution

Hox genes encode:

transcription factors