Evo-Devo Notes 3500

Evo-Devo (Evolution & Development)

• Neo-Darwinism focuses on genes, but evolution is about changing form, not just genes.
• Morphology (form) lies between genes and visible traits and is crucial.

Morphology & Development

• Morphology = result of gene interactions + environment, shaped during development (ontogeny).
• Evolution of form can't be fully explained by population genetics alone.

Evo-Devo Focus Areas

• Evolution of animal body plans, vertebrate/arthropod limbs, and flowers.

Homeotic Genes

• Control where and what cells become in embryos.
• Animals: Hox (homeobox) genes
• Plants: MADS-box genes
• Not homologous but perform similar functions.

Hox Genes in Animals

• Present in all major animal groups.
• Show spatial, temporal, and quantitative colinearity: gene order matches embryo pattern.
• Contain 180 bp homeobox coding for DNA-binding domain.
• Regulate other genes, not structures directly.

Hox in Drosophila

• Two clusters: Antennapedia (anterior) & Bithorax (posterior).
• Mutations lead to misplaced appendages.
• Hox genes define positions, not structures (e.g., “this is thorax”).

Hox Evolution

• Found even in non-segmented animals (not just segmentation genes).
• Likely evolved before multicellularity.
• More Hox loci = more complex body plans (e.g., vertebrates = 4 clusters).

Arthropod Segmentation

• All arthropods share 9 Hox genes.
• $Ubx$ gene variation may cause leg loss on insect abdomens.

Tetrapod Limb Evolution

• Tetrapod limbs evolved from lobe-finned fish (e.g., Eusthenopteron).
• Key regions:
  • AER: Secretes $Fgf2/Fgf8$ (proximal–distal axis)
  • ZPA: Secretes $Shh$ (anterior–posterior axis)
  • $Wnt7a$: Controls dorso–ventral axis
• Hox genes provide positional info in limbs.

Limb Development Implications

• Limb diversity arises from timing/location of gene expression changes ($Fgf$, $Shh$, $Wnt$, Hox).
• Hands/feet evolved from gene reactivation late in limb bud development.

Arthropod Limb Development

• $wg$ and $en$ define ant-post axis.
• $Dll$ (Distal-less) starts limb outgrowth.
• Hox genes decide limb type.
• Changes in $Dll$ affect limb branching.

Deep Homology

• $Dll$ used in limb formation across all bilaterians.

MADS-Box Genes in Plants

• Determine floral organ identity (ABC model).
• Analogous to Hox genes in animals.
• Mutations alter flower structure (e.g., APETALA, AGAMOUS).

Final Summary

• Evo-Devo bridges genetics and morphology.
• Shows how macro-evolution (body plans) stems from micro-evolutionary changes in conserved gene networks.
• Evolution = not just about gene presence, but when/where/how they’re used.

Recapitulation (Biogenetic Law)

• Ernst Haeckel (late 1800s): “Ontogeny recapitulates phylogeny” – embryo development mirrors evolutionary history.
• Inspired embryology
• Misused to support sexist/racist views
• Rejected in the 1920s (incompatible with genetics)
• Still misleadingly used to describe developmental similarity

Heterochrony

• Change in timing of developmental events due to ‘rate’ genes.
• Argued in 1930s–40s that macroevolution could result from timing shifts.
• Revived in 60s–70s via comparative embryology (esp. amphibians).
• Now seen as a subset of broader regulatory evolution.

Developmental Cascade & Bauplan

• Development = gene sequence activation → cell specialization (cleavage → gastrulation → morphogenesis → organogenesis)
• Early-acting genes = larger evolutionary impact
• Selection favors early gene stability → conserved body plans (Bauplans)

Raff’s Developmental Hourglass

• Hourglass Model:
  • Early development = flexible
  • Phylotypic stage = peak similarity across species (high constraint)
  • Later development = modular and more evolvable
• Modules (e.g., imaginal discs) can evolve independently

Regulatory Genes in Macroevolution

• Evolution of body plans driven by mutations in regulatory (transcription factor) genes
• Hox genes discovered via homeotic mutations (e.g., legs where antennae should be)
• Hox: Ordered on chromosomes like segments they pattern, all contain homeobox

Deep Homology

• Other regulatory genes (e.g., pax6) also show deep homology
• Shared gene toolkits control similar traits in distant species

The Homology Problem

Are traits similar because of:

• Homology (shared ancestry)?
• Homoplasy (convergent evolution)?

How to tell:

• Structure: Homoplasies often superficial
• Development: Homologies come from same embryonic tissue
• Genetics: Same regulatory/structural genes = likely homology
• Cladistics: More parsimonious trees may arise when homoplasies are properly identified (e.g., eye comparison)

Morphological Disparity

• Measures morphological variation across species/taxa.
• Assessed via morphometrics and descriptive traits.

Animal Diversity

• Multicellular, eukaryotic, heterotrophs.
• 1.5M+ described species (~1M are insects).
• Major phyla appear in the Cambrian (Burgess Shale, ~542 mya).
• Chordates: ~520–500 mya.

Descent with Modification

• Darwin: Diversity arises by modifying ancestral structures gradually.

Homology vs Novelty

• Homologous structures: Same structure, different forms/functions (Owen, 1843).
• Hierarchical homology: Based on structure, function, cell type, or genes.
• Analogous structures: Same function, evolved independently (e.g., wings in bats vs birds).

Deep Homology

• Coined by Shubin, Tabin & Carroll (1997).
• Refers to shared gene circuits in traits not structurally/developmentally homologous.
• Gene networks are older than the traits they control.

Hox Genes

• Found in all animals, plants, fungi.
• Contain 180 bp homeobox for DNA-binding.
• Exhibit spatial + quantitative colinearity.
• Regulate morphogenesis & differentiation.

Eye Development & Pax6

• Eyes use Pax6 gene across species.
• Raises questions:
  • Are all eyes homologous?
  • Or parallel/convergent evolution using shared tools?
• Photoreceptors:
  • Rhabdomeric (insects) → Phospholipase C
  • Ciliary (vertebrates) → Phosphodiesterase
  • Polychaetes have both types
  • Box jellyfish: Ciliary only (bilaterian innovation)

Limb Appendages

• Insects: epithelial limb buds
• Tetrapods: mesenchymal core + ectoderm
• Hedgehog genes, $Dpp/BMP-2/4$ = A/P patterning
• $Dll/Dlx5/6$ = P/D outgrowth (expressed across appendage types)

Deep Homology in Appendages

• $Dll$ knockout: limb/craniofacial defects in mice + beetles
• $Dll$ also found in neural folds (Amphioxus)
• Pharyngeal arches = another example of outgrowth theme

Co-option & CREs

• Co-option: re-use of gene pathways in new contexts
• Cis-Regulatory Elements (CREs):
  • Non-coding DNA for transcription factor binding
  • Include enhancers + promoters
  • Enhancers regulate where, when, and how much a gene is expressed
  • CREs act modularly

$Fgf$ Signaling & $Pitx1$

• $Fgf10$ co-opted in turtle shell ridge = new trait (rib attraction)
• $Pitx1$ enhancer loss in sticklebacks = loss of pelvic spines
• CRE mutations = deletions, insertions, SNPs, or mobile elements → drive phenotypic change

Confirming Deep Homology

• Use RNA-Seq to compare gene expression
• Examine which CREs are active
• Look for shared genetic pathways in different traits

Genital Development in Amniotes

• Example of organizer signal + cell competence
• Cell sources vary:
  • Chick: Lateral Plate Mesoderm (LPM) + Tail Bud
  • Mouse: Infraumbilical Mesenchyme + Tail Bud
  • Lizard: LPM as 2° bud from limb
  • Snake: Direct from LPM (no limb)
• Anolis: early genital bud resembles limb bud (transcriptome), later reprograms to genital identity
• Mouse: limb + genital buds are molecularly distinct from start

Overview

• All vertebrate limbs share the basic pattern:
  • Stylopod (e.g., humerus)
  • Zeugopod (e.g., ulna, radius)
  • Autopod (e.g., carpals, digits)
• Common models: Chickens, mice

Limb Development Stages

1. Initiation
2. Outgrowth & Patterning
3. Adult Form

Axes of Development:

• Proximal–Distal (P-D)
• Anterior–Posterior (A-P)
• Dorsal–Ventral (D-V)

Limb Origins

• Skeleton, tendons, dermis: from lateral plate mesoderm
• Muscle: from somites (myotome)
• Skin (epidermis): from ectoderm

Limb Bud Formation

• Skeletal condensation proceeds P→D
• Stylopod → Zeugopod → Autopod

Key genes in initiation:

• $Fgf10$, $Fgf8$, $Wnt-2b$, $Wnt-3a$, $Wnt-8c$, β-catenin
• $WNT3$ required for initiation
• $FGF10$ alone can induce limb buds

Limb Identity

• Identity is intrinsic to mesenchyme
• $Tbx5$ = forelimb
• $Tbx4$ = hindlimb
• $Pitx1$ works with $Tbx4$ (Ouimette 2010)

Apical Ectodermal Ridge (AER)

• Found at distal limb tip
• Interacts with underlying mesoderm
• Controls P–D growth
• Removal causes truncated limbs (Summerbell, 1973)

Limb Diversity: Chameleons

• Chameleons show cleft autopodia (digit splitting)
• AER remains intact during clefting
• Cell death occurs between all digits (shown with Nile blue)

Role of BMP & Gremlin

• BMP induces interdigital cell death (Weatherbee, 2006)
• Gremlin inhibits BMP → webbing
  • Chameleons: no abnormal Gremlin expression (unlike bats/ducks)
• Dorsomorphin (BMP inhibitor) prevents clefting in models

Origins of Novelty

Key Questions:

• How do novel traits emerge?
• Can small changes yield large effects?
• D’Arcy Thompson (1942):
  • Changes in growth rates → major phenotypic shifts
• Shell Morphogenesis Model:
  • $W$ = Expansion rate
  • $D$ = Distance from axis
  • $T$ = Translation

Developmental Drivers of Change

• Allometry: Relative growth of body parts (e.g., head vs torso)
  • $y = bx^a$
    • $a > 1$ → Positive allometry
    • $a < 1$ → Negative allometry
    • $a = 1$ → Isometry
• Heterochrony: Evolutionary change in timing/rate of development
  • Key in evolution of shape, size, and function

Allometry in Evolution

• Ants (Pheidole instabilis): Caste differentiation via allometric growth
• Ungulates: Horn/body scaling varies (Dik-dik vs. Irish Elk)
• Humans: Juvenile growth rates differ by region (e.g., head vs. legs)

Two Patterns of Heterochrony

I. Peramorphosis (Exaggeration of adult traits)

• Hypermorphosis: Prolonged growth period
• Acceleration: Increased growth rate
• Examples:
  • Titanothere skulls
  • Brain/body scaling in primates

II. Paedomorphosis (Retention of juvenile traits)

• Progenesis: Early sexual maturity
• Neoteny: Slower developmental rate
• Examples:
  • Axolotls (A. mexicanum) retain larval form
  • Humans vs. chimpanzees: juvenile features retained

Evolution via Reduction

• Loss of complexity is common
  • E.g., cave organisms lose eyes
  • Digit reduction in tetrapods (both natural and experimental)

Gradual Pathway to Novelty

• Most macroevolutionary changes come from:
  • Small modifications of existing structures
  • Changes in developmental timing (heterochrony)
  • Regulatory changes in gene networks
• Canalized traits may hide variation until revealed (latent potential)

Turtle Shell Formation

• Shell = Novel structure from endo- + exoskeleton
• Key element: Carapacial Ridge (CR)
  • Analogous to AER of limbs
  • Expresses FGF10, but not FGF8 (as in limb buds)
• Ribs expand dorsolaterally (unique patterning)
• FGF10 can redirect rib growth (chicken model)

Evolution of Venom Systems

• Venom delivery evolved independently ≥3 times in squamates
• Fang Morphology Varies:
  • Carnivores: slicing carnassials
  • Herbivores: grinding molars
  • Snakes: fang tips adapted to prey hardness
• Fang Types:
  • Solenoglyphous – folding front fangs (vipers)
  • Proteroglyphous – fixed front fangs (cobras)
  • Opisthoglyphous – rear fangs (grass snakes)

Snake Fang Development

• Fangs = modified teeth, linked to venom glands
• Study of 96 embryos from 8 snake species using Shh expression
• Findings:
  1. Front fangs develop posteriorly, like rear fangs
  2. They are homologous (same origin)
  3. In front-fanged snakes:
     • Anterior jaw lacks Shh
     • Fang moves forward during growth (ontogenetic allometry)
• Developmental steps:
  1. Ancestral dental lamina (continuous)
  2. Posterior lamina uncouples from anterior
  3. Venom gland genes integrate
  4. Anterior lamina lost → front fang derived from rear origin

Conclusion

• Small changes in growth, timing, or gene regulation can drive:
  • New organs (turtle shell)
  • New behaviors (venom delivery)
  • New morphologies (digit loss, fangs)
• Deep homology + modular gene use underpin many “novelties”