Descent with modification: Application to the evolution of development

Homologous characters are derived (with modification) from a common ancestral character

Both structure and function of homologous traits are evolving away from the ancestral trait

The concept of homology can be applied to developmental mechanisms and the genes that control them

We need to identify homologous developmental pathways in divergent taxa, and to trace the evolution of their organization and function

Three levels of homology in developmentHomologous genes?

Homologous structures?Homologous developmental processes?

Homeotic mutants in Drosophila

Homeosis is a replacement of a body part with another, apparently normal body part (W. Bateson, 1894)

In Drosophila, homeotic mutants re-specify “segment identity”

HOX genes and axial patterning- Transcription factors with a highly conserved DNA-binding domain (the “homeobox”)

- Regulate expression of distinct sets (?) of target genes

- Expressed in distinct but usually overlapping domains along the anterior-posterior body axis in all Metazoans

- Organized in (usually) uninterrupted clusters

- The order of genes in the HOX cluster is (usually) the same as the order of their expression domains along the AP axis (collinearity)

The homeobox is a highly conserved DNA-binding domain

DrosophilaAmphioxusMouseHumanChickFrogFugu

Zebrafish

HOX4 homeodomain

HOX genes control axial patterning in all Metazoans

Axial patterning in the vertebrate brain

Evolution of HOX clusters in Bilateria

Evolution of tandem gene clusters

Gene duplication by unequal crossing-over

Divergence of coding and regulatory sequences

The complement of HOX genes continues to evolve

Evolution of HOX clusters in vertebrates

Mouse

Fugu

Zebrafish

- Vertebrates have multiple HOX clusters

- Paralogous HOX genes may have partly redundant functions

- Some genes and clusters become specialized for distinct functions

- Different lineages lose some genes and acquire new functions for others

New HOX genes for new segmental morphologies?

Ed Lewis'es model 1978

The entire HOX cluster pre-dates Arthropod radiation

HOX genes and the Proximo-Distal axis of the vertebrate limb

HOX genes acquire new functions

HOX gene expression boundary coincides with a morphological transition

HOX gene expression boundary coincides with a morphological transition

HOX gene expression boundary coincides with a morphological transition

HOX domain boundary coincides with a morphological transition

- Segment homology can be traced across all Crustaceans

- Segment and appendage morphology is highly variable in Crustacea

- HOX expression domain in different Crustaceans are NOT homologous

- The boundaries of HOX domains often coincide with morphological transitions

HOX domain boundaries and morphological transitions

Thorax/ Abdomen

Gnathal/ Thoracic

Poison claw/ walking legs

Stalk/ opisthosoma

?

Hindlimb

HoxC6 and the cervical/ thoracic boundary

The number of cervical metameres is different, but the Hoxc6 always marks the cervical/ thoracic boundary

Stellate ganglia - a novel structure

Combinatorial code?

HOX genes in a highly modified organism

Brachial crown

All Metazoans possess homologous HOX clusters

Individual HOX genes are highly conserved

HOX genes control A-P axial patterning in all Metazoans

The role of HOX genes in axial patterning is a Metazoan (or at least Bilaterian) synapomorphy

The complement of HOX genes is different in different taxa

Orthologous HOX genes are not always expressed in homologous domains

Orthologous HOX genes do not always specify homologous structures

HOX genes are not linked to specific morphologies or cell types; rather, they provide abstract spatial information

HOX genes may be recruited for new functions in structures that have no homologs in other taxa

Descent…

… with modification

What allows the HOX genes to retain their ancient strategic function, and yet have a different specific role in each context?

Hox genes act by regulating multiple target genes

Ubx- regulated

HOX genes specify abstract spatial information

Ubx provides the distinction between the forewing and the hindwing in all insects - but this distinction is different in each case

HOX genes regulate the expression of multiple target genes

Different HOX genes have distinct (but sometimes overlapping) sets of downstream targets

These sets of target genes change during evolution, leading to changes in HOX gene functions and to acquisition of new roles

The expression of HOX genes in distinct axial domains serves as the conserved backbone of a developmental mechanism, while the more peripheral aspects of that mechanism continuously evolve

We still know very little about the downstream targets of the HOX genes

The more things change, the more they stay the same

HOX genes and developmental homology

- HOX clusters are homologous across Metazoa

- The Anterior-Posterior body axis is also homologous in all Metazoa

- Specification of regional domains along the AP axis by HOX genes is a homologous developmental mechanism in all animals in which it is found

However, these three levels of homology are dissociable and to a large extent independent

Homologous genes

HOX genes Axial patterningey/ Pax6 Eye developmentDll/ Dlx Appendage developmentcd/ Cdx Hindgutotd/ Otx Anterior brain

dpp/ TGFhh/ Shhwg/ WntNotch

Transcription factors/ selectors

Signaling pathways

The functions of Notch signaling

Drosophila

Bristle developmentDorso-ventral patterning

in the wingOmmatidial cell fatesLeg joint formationA-P patterning of larval

epithelium

Vertebrates

Neuronal and glial cell development

Auditory hair cellsSomitogenesisT lymphocyte fatesLeft-right asymmetryChondroblast specificationPatterning feather primordia

There are many more signaling events that there are signaling pathways!

The functions of HOX genes

Drosophila Vertebrates

A-P patterning of:ectodermCNSmusclesvisceral mesoderm

A-P patterning of somitesand CNS

P-D axis of the limbsReproductive tractHair follicle development

Homologous genes often function in non-homologousstructures.

Engrailed functions in Drosophila segmentation

engrailed expression in Arthropods

Flea Cricket Crustacean

engrailed & Wnt expression in Annelids

Helobdella Platynereis

A common origin of segmentation in Protostomes?

Was the last common Bilaterian ancestor segmented?

Amphioxus neurula

A closer look at segmentation in the leech

- In early development, en is only expressed in a few clones in each segment-At later stages, segmental stripes form by cell rearrangement-The cells that express en in the segmental stripes are not always clonally related to the early en-expressing cells- This suggests that en is not required for segmentation, but acts after the segments are already established

Phylogenetic distribution of segmentation

Segmented ancestor is very unlikely…

Distal-less specifies distal appendage fates in Drosophila

Dll also specifies distal appendage fate in spiders

dac staining

RNAi

Lobopodia and parapodia

Onychophoran

Polychaete

Legs, tube feet and ampullae

Mouse

Ascidian

Sea urchin

Homologous developmental pathway for Proximo-Distal axis specification?

eyeless/ Pax6: a “master regulatory gene” for eye development

Photoreceptive neuronsFrontal eye precursor cellsPigment spot

Amphioxus

Pax6 expression in the presumptive eye field

Mouse

PhotoreceptorsLensIrisCorneaOlfactory epithelium

Pax6 in the Cephalopod eye

eyeless/ Pax6 expression in diverse Metazoans

Gene Drosophila Vertebrates Flatworms

Otd/ Otx Photoreceptor cells Neural retina Photoreceptor cells

ey/ Pax6 Eye imaginal disc Lens placode, Photoreceptor andoptic vesicle pigmented eye cells

toy Eye imaginal disc

So/ Six3 Eye imaginal disc, Eye precursor andphotoreceptor cells, photoreceptor cellsoptic lobes

Optix/ Six6 Eye imaginal disc Optic vesicle,neural retina,retinal epithelium

Rx Retinal cells

Opsin Photoreceptor cells Photoreceptors Photoreceptor cells

Conservation of the eye regulatory network

Eye evolution from a common ancestral organ?

Vertebrate Arthropod Cephalopod Arcoid

Differences in eye structure between animal phyla

Similar adult organs, but radically different development

Some differences between vertebrate and arthropod eyes

Vertebrates Arthropods

Optics Single front element Compound

Origin of CNS Epidermisphotoreceptors

Orientation of Inverse Eversephotoreceptors

Photoreceptor Ciliary Microvillarstructure

Secondary cGMP ITPmessenger

Mechanism of Membrane Membranelight detection hyperpolarization depolarization

Developmental homology and dissociation. Part I.

Homologous genes need not function in the development of homologous structures(HOX genes, Notch signaling)

Expression of a homologous gene does not imply that developmental pathways are also homologous(engrailed and metamerism)

Homologous developmental pathways may control the development of non-homologous structures(Dll in appendages, Pax6 in the eyes)

Segmentation of the Drosophila embryo

Genetic control of segmentation in Drosophila

Pair-rule gene expression in grasshopper

eve

ftz

Drosophila Tribolium

Developmental homology and dissociation. Part II.

Homologous genes need not function in the development of homologous structures

Expression of a homologous gene does not imply that developmental pathways are also homologous

Homologous developmental pathways may control the development of non-homologous structures

Homologous structures need not be specified by homologous genes (insect segmentation)