Evo. Exam 3

Phylogenetic trees that show congruence between organisms (e.g. lice and birds; bacteria and aphids) indicate

(1) cospeciation and (2) lack of host switching, i.e. specificity of a particular lice species to a particular bird species.

Toolkit genes mostly fall into two functional catergories

-transcription factors(like Hox genes) -signaling molecules(like sonic hedgehog, shh)

Three Developmental parameters:

1-rate of deve. 2-time of onset 3-time of offset

Architecture of CRE

100-2obps in length, with several transcription factor binding sites (6-8pairs), distinct in the genome.

Hox genes at the (blank) end of the cluster are expressed (blank) along the A-P axis and transcripts appear (blank) during embryonic life.

3'; anteriorly; earliest

Hox genes in paralog groups (blank) have been recruited into paired appendage development.

9-13

What paralog groups were recruited into paired appendages?

9-13

(blank) can give rise to several different protein products by alternative splicing

A single genomic locus

(blank) are traits that enhance fitness and are maintained and evolved by natural selection

Adaptations

Describes how the characteristics of living creatures change with size. It refers to the differential rate of growth of different parts or dimensions or an organism during its ontogeny.

Allometry

(blank) on a phylogenetic tree represent a lineage (extinct and living orgs)

Branches

Not promoter sequences, are enhancers (activation, expression) and silencers (silence,no expression) transcription. Highly conserved.

CRE (cis regulatory element)

1 Point mutation (SNPs) in existing TFBS and/or the creation of De novo TFBS in noncoding DNA 2 small insertions/deletions that alter TFBS within a CRE 3 duplications of entire CRE 4 Rearrangement and/or shuffling of CREs (could be transposon mediated)

CRE Evolution

(blank) is defined as a phenotype that is robust to changes in the genotype and the environment. As discussed in class, (blank) may be a consequence of complex developmental networks of interacting transcriptional regulators that constrains the genetic system to produce(blank), even without selection toward an optimum phenotype.

Canalization

(blank) can give a single gene many different functions

Cis-regulatory modules (CREs)

Why would co-opted gene networks help in the rapid evolution of complex structures?

Co-opted gene networks help rapid evolution because this allows genes in different areas to be turned on. When gene networks are co-opted, the same CREs can affect 2 phenotypes

(blank) posits that a gene has multiple functions and, following duplication, the functions are sub-divided in a noncomplementary way in the paralogs. Functional sequences can be protein coding and/or cis-regulatory.

DDC (Duplication, Degeneration, Complementation) model

(blank) have had a greater impact (2.7%) on changing the genomic landscape between human and chimpanzee more than base substitution alone (1.7%).

Duplications

T OR F-Genome complexity is directly related to the number of genes.

False

In mouse mutants, why do double knock-out mice have to be constructed in order to observe a limb phenotype (e.g. HoxA13 and HoxD13 both need to be knocked out in order to eliminate the autopod). Hint: think of functional redundancy of paralogs (HoxA13 and HoxD13).

For example, HoxA11 and HoxD11 are important for zeugopodium development. If you make a HoxA11/HoxD11 double knockout mouse, the zeugopodium is barely present yet the stylopodium and autopodium are almost normal. Hence the action of group 11 paralogs is restricted to the zeugopodium module

genotype by genotype

GxG

Protostomes today have at most a single (1)

Hox cluster

There were more tandem duplications, eventually resulting in a

Hox cluster (tandemly arrayed genes on the same chromosome).

Hox gene overalapping to non-overlapping, causing paired appendage budding in tetrapods

Hox gene role of tetrapod

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

It can lead to the recruitment of existing gene networks into different tissue types.

(blank) is above the species level. This is something we can observe in the natural world and is recorded in the fossil record. The pattern we see is descent (from a common ancestor) with modification.

Macroevolution

(blank) elements as drivers of genome evolution

Mobile DNA

(blank) is a characteristic that can help 'overcome' the robustness of phenotypes in canalization, and thus can help influence the evolution of a novelty. At the genetic level, (blank) can involve parcellation or integration.

Modularity

interactions between species that benefit individuals of both species. -can lead to extreme adaptations

Mutalism

The Ohno and DDC models of evolution following duplication differ in what respect?

NONE OF THIS -Resolution of functional redundancy. -Protein coding vs. CRE sequence evolution. -Maintenance of ancestral (important) function. -The time to the first fixed mutation.

The functional repertoire of noncoding DNA sequences, some which show striking degrees of evolutionary conservation, is much broader than imagined and not well understood

Noncoding DNA

(blank) posits one paralog retains the ancestral function while the other paralog is freed from selective constraints and can take on different fates including pseudogenenization (inactivation) or neofunctionalization (acquiring a new function).

Ohno's model

Heterochronic change in which the adult of a derived organism resembles a juvenile of the ancestor

Paedomorphosis

Two forms of heterohrony

Paedomorphosis and peramorphosis.

(blank) Describes sequences that are similar to one another as a result of gene or genome duplication.

Paralogs

Heterochronic change in which the juvenile of a derived organism resembles an adult of the ancestor. The adult has exaggerated features.

Peramorphosis

colinearity phenomenon is observed.

Phase I

(blank) is defined as a single genotype that may produce different phenotypes in different environments

Phenotypic plasticity

Why are CREs "flexible" in fixation of mutations as compared to protein coding sequences?

Proteins can be disrupted by a single-point mutation in TFBS. CREs contain multiple TFBS.

The amino acid sequence of developmental toolkit proteins is highly conserved in taxa as different as fruitfly and human. In fact, human proteins can rescue fruitflies that are mutant for the orthologous toolkit gene (e.g. pax6). What is critical for these rescue experiments to be successful?

The human protein must be placed in the fly in the appropriate biological context.*

Which of the following statements accurately describes CREs (cis regulatory elements)?

They are noncoding sequences composed of several transcription factor binding sites (TFBS) situated close to one another in the genome. And CREs can be identified as highly conserved noncoding sequence blocks by alignment of orthologous sequences in distantly related taxa, e.g. human and shark.

-Comparison of genes sets b/w phyla indicates that (blank) was assembled and expanded (by genome duplications) early in animal evo. -Has a very small set of genes. -Conserved amoung phyla.

Toolkit Genes

(blank) are being revisited in light of recent findings on their evolutionary conservation and functional effects.

Transposons

T OR F. The DDC pathway of evolution following duplication always leads to the retention of two paralogs.

True

T OR F. Toolkit genes typically fall into two broad categories: transcription factors and signaling molecules.

True

(blank) duplications occurred in the deuterostomes after divergence of Amphioxus. Humans and other jawed vertebrates have four (4) (blank). Each (blank) is on separate chromosome

Whole Hox cluster; Hox cluster; Hox cluster

CREs in comparative genomics

aligning non-coding sequences through various taxa in highly conserved sequences. If CNS is functional to gene expression, it is a conserved non-coding sequence.

The changes of proportion during development can lead to changes of form within and between species. This is based upon...

allometry

The position of each Hox gene in a cluster is critically important for its function in patterning the (blank) during embryonic life.

anterior-posterior axis

(small nodular bones and small long bones): wrist and hand (arm); ankle and foot (leg). Exhibits the highest degree of phenotypic variability across species, even amongst closely related taxa like primates. Innovation of the finlimb transition.

autopodium

out of the three limb modules, which is the most recent?

autopodium

Origin of new genes can occur...

by exon shuffling and by gene or genome duplication

The autopodium of modern tetrapods has five (5) digits, specified as 1,2,3,4,5. This phenotype is robust to perturbation, demonstrating (blank).

canalization

(blank) is reciprocal genetic change in interacting species, owing to natural selection imposed by each on the other

coevolution

The relationship between position of a Hox gene in a cluster and it's spatio-temporal expression along the A-P axis is called

collinearity

The gene toolkit...

is evolutionarily conserved across metazoan phylogeny. and it is emerged and diversified around the same time as the Cambrian explosion.

When the slope of the line is 1, this is called (blank) (not allometry); this means the size of the trait is growing proportionate to body size.

isometric growth

The tips or leaves on a tree represent...

living representation of a lineage.

Set of species derived fron any one common ancestor is...

monophyletic grp or a clade.

Variation in the toolkit accounts for...

morphological evo. and diversity

When the slope of the line is <1, this is called (blank) meaning the trait grows more slowly than the body as a whole.

negative allometry

KA/KS=1

neutral selection

A point where two branches separate from one another. It represents the most recent common ancestor or MRCA.

node

What are CREs?

non-coding sequence block (block of DNA non-coding)

HoxA13 in human, coelacanth, and shark are...

orthologs

Two homologous genes from different species are called

orthologs

HoxA13 in human, coelacanth, shark are

orthologs (sequences similar due to speciation events).

Two or more homologous genes in the same species are called

paralogs

HoxA13 and HoxD13 in human are

paralogs (sequences similar due to duplication events).

During phase (blank) of limb development, Hox genes in paralog groups 9-13 are expressed in a reverse-colinear manner.

phase II

When a gene influences several different phenotypic traits, this is called...

pleiotropy

When the slope of the line is >1, this is called (blank) meaning the trait grows faster than the body as a whole.

positive allometry

KA/KS>1

positive selection

KA/KS<1

purifying or negative selection

(blank) means that the fitnesses of two or more interacting species depend not only on their own genotypes (and associated traits), but also on each other's genotypes (and traits).

reciprocality of coevolutionary selection

Paedomorphosis...

results in an adult that has a more child-like appearance

(a single long bone of the upper limb): humerus (arm); femur (leg)

stylopodium

Fossil and living lobe-finned fishes (eg. coelacanth, lungfish) have paired appendage segments homologous to the (blank) and (blank). This means that genes and developmental processes that are responsible for development of these structures in paired appendages predate the fin-limb transition.

stylopodium; zeugopodium;

Members of a clade are untied by

synapomorphies (shared, derived chara.)

Mutations in cis-regulatory sequences (enhancers) have a high or higher probability of fixation because..

they have no effect on the amino acid sequence of a protein and are modular CREs can be easily duplicated or re-arranged in genomes.

What is a gene network?

they represent the regulatory interactions taking place over the course of development.

Transcription factors (proteins) act in (blank) by binding to enhancer sequences (CREs) which act in (blank). .

trans; cis

The genome of human contains several gene families where there are multiple members. This is a result of (blank) rounds of whole genome duplications in the evolutionary history of jawed vertebrates.

two rounds, 2R

What types of sequences can evolve?

wings and eyes AKA complex structures.

(two paired long bones of the lower limb): radius and ulna (arm); tibia and fibula (leg)

zeugopodium