Chapter 10 Adaptation: from genes to traits


10.1 Cascades of Genes p. 304

  1. Evolution is not just something that happened in the distant past
    1. scientists are able to follow the relationship between mutations and adaptations in some model organisms
  2. Novel Traits
    1. Traits that arise de novo (i.e. not inherited from an ancestor) within a lineage and have no obvious counterparts (homologs) in related lineages.
    2. Regulatory networks
      1. Systems of interacting genes, transcription factors, promotors, RNA, and other molecules.

10.1 Innovation in Our Own Time p. 290

    1. Evolution of novel traits (Fig. 10.2)
      1. Bacteria make a major evolutionary shift in the lab (Lenski et al.)
      2. The ability to consume citrate is a complex adaptation
  • Evolution uses structures that are already present
    1. Preadaptation
    2. Exaption: taking on a new function 

    10.2 New Genes, New Uses p. 291

    • Some mutations can reprogram the conditions in which a gene is expressed, leading to new functions.
    • Novel phenotypic traits can arise when existing genes or processes are co-opted and expressed in new developmental contexts. 
    1. Regulatory networks are often involved in complex adaptation Fig. 10.3)
      1. Complex adaptations are novel traits that can require multiple mutations to achieve a fitness advantage.
      2. Regulatory networks are systems of interacting genes, transcription factors, promoters, RNA, and other molecules 
      3. Hox genes encode transcription factors that determine the identity of body parts along a head to tail axis
      4. Promiscuous proteins have more than one function.  They are often the starting point for novel traits
    2. Gene duplication can produce novel functions (Fig. 10.4)
      1. Paralogs
    3. Gene recruitment or co-option
      1. The reorganization of a preexisting regulatory network (cis regulation, Box 10.1) can be a major evolutionary event
    4. Horizontal gene transfer

    The Industrial (R)evolution p. 293

    1. Our activities have altered the natural environment, leading to natural experiments in evolutionary biology.
      1. Pesticides, Herbicides, Antibiotics, Pollution
    2. Sphingobium, a soil bacterium, has assembled a new metabolic pathway that can mineralize PCP by patching together promiscuous enzymes recruited from pre-existing pathways

    Venom Evolution: Borrowing Genes for Deadly New Jobs p. 294

    • Complex adaptations can evolve through the duplication and co-option of several proteins originally involved with other body functions
    1. Gene duplication and snake venoms (Fig. 10.5)
      1. Defensins evolved in the common ancestor of snakes and mammals
    2. Venom genes have been recruited from genes in other organs(Fig. 10.6)
    3. Venom evolved before snakes themselves (Fig. 10.7)
    4. Key Concepts
      1. Promiscuous proteins are often the starting point for novel traits –Duplication can lead to new functions
      2. Novel traits can arise when existing genes are expressed in new developmental contexts
        1. Recruitment or co-option
    5. Key Concepts
      1. Duplicated genes accumulate mutations rapidly because they are released from purifying selection
      2. Novel traits can evolve from duplication and co-option of proteins involved in other functions


    Gene Duplications

    1. Unequal crossing over [Fig. 5.6]  produces gene families (actins, myosins, histones, immunoglobulins, globins...)
      1. Duplicated genes can
        1. retain original function and provide an additional locus
        2. mutate differently, adding new functions, via selection 
        3. become functionless pseudogenes
    2. Gene Duplication by Retrotransposons
      1. Reverse transcription and insertion of a gene

    Unequal crossing over

    1. Normal crossing over
      1. Breaks up physical associations of genes on chromosomes
      2. Allows for recombination to produce new sets of alleles on chromosomes
    2. Unequal cross-over and the origin of gene duplications. (Fig. 5.6)

    Gene Duplication Events in the Globin Gene Family

    1. Time expression of different globin genes related to function [Fig. 5.7]
    2. structural similarity of transcription units [Fig. 5.8] 

     10.3 The Genetic Toolkit p. 298

    • The same underlying network of genes governs the development of all animals, no matter how different they look: a “genetic toolkit” that evolved over 570 million years ago.
    1. Evo-Devo
    2. Evolutionary Developmental Biology
    3. Hox genes are part of a conserved “genetic toolkit”  (Fig. 10.8)
      1. Flies and mice are separated by more than 570 million years
    4. Terminology (Fig. 10.9)
      1. Dorsal , venral, etc.
    5. Dorsal ventral-patterning is conserved (Fig. 10.10)
      1. Vertebrate and insect guts
    6. Fly legs and mouse legs patterned by same genetic cascade (Fig. 10.11)
      1. Orthologs

    Long Limbs, Missing Limbs p. 302

    • Traits can disappear when the expression of a patterning path- way is altered, blocked, or even just interrupted.
    • Subtle changes in the levels of expression of developmental genes can dramatically alter phenotypes.
    1. Expression differences in a single gene give rise to limb elongation (Fig. 10.12)
      1. These genes are orthologs
    2. Changes in limb patterning pathway result in limb loss (Fig. 10.14)
    3. Disruptions in Shh expression (Fig 10.13)

    Sculpting a beak p. 304

    1. Gene expression changes in adaptive radiation  (Fiure 10.15)
      1. Galapagos finches
    2. Key Concepts
      1. Ancient regulatory networks determine body patterning in bilaterans
      2. Blocking or interrupting a patterning pathway can result in complete loss of a structure
      3. Subtle expression changes can dramatically alter phenotypes

    Is the variation caused by environment or genetics?

    1. Fig 3.11 Genetic basis for beak development in Darwin's finches
      1. Left: Differences in beak size and shape among six species
      2. Middle and Right: cross sections of the upper beak bud in embryos at two stages of development. The cross sections have been treated with a probe that stains mRNA made from the gene for bone morphogenic protein 4, or BMP4.
      3. Ground finches with larger beaks make BMP4 mRNA earlier and in larger quantities

    10.4 Recycling Networks p. 307

    • Groups of genes are organized into relatively distinct modules that act independently of other genes, and this modularity makes it possible for evolution to recruit entire gene networks in the development of new adaptations.
    1. Mutations to gene networks can produce additional appendages (Figure 10.16)
    2. Table 10.1 Perturbing a patterning network
    3. Evolution of feathers (Fig. 10.17: 0-->1, 1-->2)
    4. Evolution of feathers (Fig. 10.17: 2-->3)
    5. Key Concepts
      1. Changes in the timing and location of expression of developmental genes can alter the shape or properties of a structure
    Evolution uses structures that are already present
    1. Preadaptation
    2. Exaption: taking on a new function 

    10.5 Evolving Eyes p. 311

    • The vertebrate eye is the result of a shared evolutionary history, a history that includes the co-option of genes and regulatory networks that can be found in organisms that lived 650 million years ago.
    1. Complex eyes have evolved in several lineages (Figure 10.18)
    2. Opsins evolved from serpentine proteins  (Figure 10.19)
    3. Opsins evolved at least ~650 million years ago  (Figure 10.20)
    4. Crystallins evolved through gene recruitment   (Figure 10.21)
    5. Hypothesis for evolution of the vertebrate eye  (Figure 10.22)
    6. Key Concepts
      1. Vertebrate eye the result of long history of gradual evolution
      2. Gene recruitment important


    1. History of the Controversy
    2. Perfection and Complexity in Nature
    3. natural theology versus the blind watchmaker
    4. evolution of the mollusk eye [Fig. 3.23]
    5. Exaption Fig. 3.25
      1. Gene co-option in the crystallins of animal eye lenses

    10.6 Constraining Evolution p. 316

    • Evolution is constrained by the paucity of genetic variation
    • genetic variation may be lacking because the resulting phenotypes are unsuccessful or because existing developmental mechanisms are incapable of generating particular phenotypes.
    1. Constraints on adaptation
      1. Laws of physics
      2. Pleiotropy : Single gene affects expression of many traits
    2. Antagonistic pleiotropy: number of cervical vertebrae (Fig. 10.23)
    3. Key Concepts
      1. Constraints on evolution arise when one evolutionary trajectory is more likely than any other
      2. Antagonistic pleiotropy can constrain evolution: Some phenotypes unsuccesful



    10.7 Building on History: Imperfections in Complex Adaptations p. 318

    • Adaptations are not perfect—they reflect the tinkering necessary to get the job done at the time.
    1. Complex adaptations are not perfect (Fig. 10.24)


    1. Organisms cannot simultaneously optimize all aspects of phenotype (or all aspects of fitness). 
    2. Organisms are not perfect.
    3. Factors limit adaptive evolution

     10.8 Convergent Evolution p. 319

    • Similar forms may result because of convergent evolution or because of deep and distant homologies
    1. Convergent evolution
      1. Independent evolution of similar traits in different lineages
      2. Result of similar selection pressures
    2. Convergent evolution in mammals (Fig. 10.25)
      1. similar features from different ancestors as a result of ecological equivalence
      2.   convergence in placental and marsupial mammals- Dr. George Johnson's Backgrounder
    3. Convergent evolution in mammals  (Fig. 10.25)
    4. Parallelism
      1. Convergent evolution that arises through mutation of the same genes
      2. Deep homology: traits in different lineages arise from same inherited regulatory networks
    5. Key Concepts
      1. Deep homology may help to explain cases of parallel evolution


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