Animal diversity II

Why might we study the genetic basis of traits in the wild?

It can help us understand how evolution works

• Genetic architecture = whether traits are controlled by a few genes with large effects or many genes with small effects

• Kinds of mutations = whether changes occur in coding or regulatory sequences

• Sources of variation

How can we identify the genes underlying a trait?

Genome Wide Association Studies (GWAS) scans across many individuals to find genetic variants that are associated with a particular trait or characteristic

E.g. we can use it for discrete traits by comparing allele frequencies between individuals in both groups

E.g. we can look at quantitative traits that vary continuously by looking for variation in the mean trait value between SNP categories

Multiple testing problem = this occurs when we perform a large number of statistical tests, by chance, some tests will appear significant (even if there’s no true effect)
Population structure = this occurs when genetic differences are due to ancestry or geographical background rather than the trait

GWAS generates candidate genes (which they believe influence a trait)

Instead we could use functional genetics (e.g. CRISPR-Cas9) which directly test causal relationships between genotypes and phenotypes
This is ideal to study developmental timing, patterning, and morphological changes

What is genetic architecture?

The number of genes affecting a trait, their distribution across the genome, how they interact (epistasis), and whether they affect multiple traits (pleiotropy)

Simple genetic architecture = a few genes with large effects

• Wall lizards = different ventral colours

• Heliconius butterflies = variation in wing pattern is shared across mimic species

Complex genetic architecture = many genes with small effects

• Human hair colour (blond and brown)

• Human height (polygenic)

How can genetic changes lead to new traits?

Change coding sequence

• We can alter the protein itself to impact all functions of the protein

• E.g. the pale coat of spirit bears is caused by a single mutation in the MC1R protein

Alteration of gene regulation (altering how much a gene is expressed rather than the protein itself) - the cis-regulatory hypothesis

• Cis-regulatory elements (CREs) switch genes on and off in different contexts (controlling expression in a particular tissue / particular time point)

• E.g. sticklebacks - a deletion near the Pitx1 gene stops spine development in the pelvis (but doesn’t affect expression of the same gene in the head) - the deletion is context-specific

• Regulatory evolution can repurpose existing genes for new functions
  E.g. prothoracic horns of a species of beetle might have evolved through redeployment of genes used in wing development (serial homologues)

What is the source of adaptive variation?

Novel mutations

• E.g. sticklebacks - Pitx1 CRE deletion has happened multiple times (because different populations have different lengths of deletion mutations)

Standing variation = the genetic variation already found in the population

Gene flow from other populations of the new species

• E.g. sticklebacks - EDA controls the loss of armour plates on the side of sticklebacks
  A phylogeny of this locus shows that the same allele has been shared among all freshwater populations

Introgression from different species through hybridisation

• E.g. wall lizards - colour alleles (SPR and BCO2) are ancient and are shared between species by introgression

• Heliconius butterflies - one version of the gene controlling for wing variation in one species is more closely related to a different species (rather than the same species)

What is phenotypic plasticity?

Variation in the phenotype of individuals without change in their genotype e.g. primates can learn different behaviours through learning (behavioural traits)

Not all plasticity is adaptive e.g. if a mother fails to find enough food for its offspring this will lead to them being small and weak (scarring)

What are reaction norms and how can we use them to depict plasticity?

Reaction norms show how a genotype’s phenotype changes across different environments (to illustrate phenotypic plasticity)

• Polyphenism = when there are two or more distinct forms

• Continuous = continuously varying traits

Plasticity can occur during development and be irreversible (developmental plasticity) or can occur in the adult and be reversible (acclimation)

Developmental polyphenism

• E.g. butterfly forms that change with the seasons

• E.g. the dry season form of an African butterfly species have fewer eyespots and are more cryptic (they are adapted to survive through the dry season)

Acclimation polyphenism

• E.g. arctic species moult into a white winter coat in response to environmental cues, which is better camouflaged in the snow

Developemental continuous plasticity

• E.g. guppy fish produce larger offspring in conditions of low food (because they are better competitors and more effective foragers)

Acclimation continuous plasticity

• E.g. muscle mass in humans which responds to weightlifting

When is the evolution of plasticity (one genotype producing different traits based on environmental context) favoured over polymorphism (the presence of multiple fixed forms in a population)?

The evolution of plasticity is favoured when there is a reliable cue that can predict future conditions
E.g. the African butterfly develops different season forms based on temperature (a trustworthy single of wet or dry seasons), but other butterfly species have multiple wing pattern forms controlled genetically because their environment is unpredictable and caterpillars don’t know which form will be the most advantageous

How can reaction norms (the way traits respond to the environment) evolve?

Genetic accomodation = the evolution of reaction norms

• E.g. phototactic behaviour in Daphnia depends on predator presence - populations with high predation will cause Daphnia to reduce their phototactic behaviour (to avoid being spot) - plasticity is more useful in the presence of predators

Genetic assimilarion = when plasticity is lose because one form becomes fixed
Plasticity could lead to populations colonising new environments, and then genetic assimilation could lead to adaptation to the new environment

• E.g. one species of spadefoot toads have plastic development times which help them survive in unpredictable wet environments, another species (which live in a more predictable, desert environment) have undergone genetic assimilation and fixed shorter developmental times

What is the genetic basis for plasticity?

Genes that sense environmental cues

Genes that control how the trait responds
E.g. a gene called Agouti controls whether snowshoe hares change their coat colour in winter, some hares have lost this plasticity (useful due to climate change - less snow) - the gene controls the trait

How can plasticity aid in adapting to a changing climate?

Plasticity can fail when environmental cues become unreliable (if the climate changes so much that previous reliable cues become poor predictors of the future)

E.g. Rockies yellow-bellied marmots are emerging earlier from hibernation because of warming temperatures, but increased snowfall in the winter means the date that snow melts has not changed - they are emerging when less food is available

The cue can also become disrupted by human activity e.g. European robins are confused by EM noise and cannot determine the direction for migration

Why is morphological evolution highly variable?

Punctuated equilibrium = long periods of stasis alternating with periods of rapid evolution
^This is supported by varying rates of evolution in the fossil record and by looking at phylogenies

Why does stasis occur

• Natural selection is too weak to keep changing direction (cannot generate rapid change) - this is unlikely due to estimates of strong selection in extant populations

• Evolution is fickle - even if rapid evolution occurs for a short amount of time, it often doesn’t maintain itself (it can sometimes appear that evolutionary changes haven’t occurred at all)

• Lack of genetic variation - there may be limited genetic variation for evolution

• Stable environments - some species may not need to change if their environment remains the same

• Limited spread of advantageous traits - even if some populations evolve, those changes might not spread across the whole species

What is adaptive radiation?

The rapid evolution of many species from a single common ancestor

• Common ancestry (the group should be monophyletic)

• Adaptive trait diversification - species should show trait differences that correlate with different environments (phenotype-environment correlation) and improve survival

• Rapid speciation

E.g. Anolis lizards - these lizards have evolved similar forms on different islands to suit different habitats and molecular evidence suggests that these similar forms evolved independently (convergent evolution)

What is ecological speciation (a key feature of adaptive radiation)?

Where adaptation to different environments leads to the formation of new species

This involves ecological divergence (adapting to different niches) and reproductive isolation

Ecological character displacement = competition for resources pushes species to evolve different traits
E.g. Darwin’s finches - an initial drought favoured larger-beaked birds, and a secondary drought favoured smaller-beaked birds (this demonstrates character displacement due to ecological competition, which supports the role of ecological divergence in speciation)
Finches sing to attract a mate and their songs are partly learnt and partly genetic - when species diverge in their beak size, this affects their song and contributes to reproductive isolation

Ecological speciation results when divergence in ecological traits allows two lineages to exploit different niches and also causes reproductive isolation