Evolution Exam 2 Flashcards
Relationship between gene flow and population difference
there is an inverse relationship where Fst = 1/(4Nem + 1), this model assumes an island model where there is an equal gene flow among all populations
Direct methods of studying gene flow
One direct method is to mark and recapture marker traits and alleles
Some disadvantages is that migration is not the same as gene flow, one observation may not always represent other populations, seasons, or environments, may miss key migration events
Indirect methods of studying gene flow
Gene flow can be inferred from the level of genetic differentiation calculated as Fst based on genetic data between populations
One assumption for this is that Fst reflects current gene flow but this may not be completely accurate since completely isolated populations may still have an Fst greater than 1 if they have been connected in the past and there hasn’t been enough time for genetic drift to completely fix different alleles
Another assumption is that an island model of gene flow is assumed, but Fst between populations generally suggests an isolation by distance model rather than an island model
Another assumption is that the genetic markers are selectively neutral and natural selection does not act on them, for most loci across the genome this assumption is okay
Selection favoring different alleles in different populations raises Fst (spatial environmental heterogeneity) and selection favoring the same allele in populations lowers Fst (overdominance, heterozygote advantage, when one high fitness allele spreads across population)
How can Fst be used as a tool for identifying genes evolving under natural selection?
Assume allelic variation in genes is not under selection for these genes and that Fst and inferred Nm reflect solely genetic drift and gene flow
Outlier genes reflect selection on that gene, outliers have a higher Fst when different alleles in different populations are favored and a lower Fst when same allele is favored in all populations, genes that are not outliers are generally used to track drift/gene flow
In genome studies high Fst outliers can be used to identify alleles where selection favors different alleles in different environments, low Fst outliers can be used to identify alleles with universal selective pressures acting to maintain the same alleles in all populations
How can gene flow be a constraint on evolution by natural selection?
One example is water snakes that are maladaptive to their environment because of juvenile dispersal
What are examples for how clines can evolve through the interaction of selection and gene flow?
One example could be if there is a threshold above which cyanogenesis is always favored and below which it is always disfavored a cline can develop
If isolation by distance gene flow occurs, then populations closest the boundary/an origin would be the most polymorphic and those further away would approach fixation for one phenotype vs another resulting in a cline
If the strength of selection gradually varies across a given space, a cline could be produced without requiring gene flow
Categories of non-random mating
Mating according to phenotype (assortative or disassortative), associated with sexual selection
Mating with relatives (inbreeding) or avoidance of mating with relatives (outbreeding)
Mechanisms of avoiding inbreeding
Species can distinguish relatives from non-relatives, these species generally show the evolution of mechanisms to avoid inbreeding (Self-incompatibility in plants at the S locus is one example)
Tiger salamander larvae are more likely to develop cannibalistic morphology if they are reared with non-relatives which demonstrates their ability to recognize kin, they also avoid inbreeding
Circumstances for inbreeding
Physical proximity of related individuals generally leads to inbreeding by default in species that can’t distinguish relatives (philopatry are organisms that do not disperse far from place of birth and exhibit high inbreeding)
Evolutionary consequences of inbreeding
Inbreeding alone does not change allele frequencies or cause evolution
But it reduces heterozygosity, since relatives share alleles inbreeding tends to bring together identical copies of an allele more often than would occur by chance
With a full sibling mating, there is a ¼ probability that an offspring will be a homozygote for one of the grandparents alleles and therefore a ¼ probability 2 alleles of a given gene are identical by descent assuming grandparents are heterozygotes
Inbreeding coefficient
measured by F, defined as the probability of identity by descent at the level of an individual based on their pedigree
How can expected heterozygosity be used to estimate inbreeding level?
F = [H(expected) - H(observed)]/H(expected) where H(expected) = 2pq, when there is a deficit of observed heterozygotes that is an indicator of inbreeding
Under the most extreme inbreeding conditions heterozygosity is reduced by half in each generation
What is inbreeding depression and why does it occur?
Inbreeding depression is the phenomenon of reduced fitness in a population due to inbreeding. This occurs since increased homozygosity as a result of inbreeding is more likely to lead to the expression of deleterious recessive alleles (diseases), additionally fitness advantages arising due to heterozygote advantage are lost
Consequences of inbreeding in real life populations
Inbreeding has been shown to exacerbate the expression of disease in populations that have gone through bottleneck and founder events (the Amish)
Inbreeding depression tends to be most evident in times of stress, selection against inbred song sparrows was more easily demonstrated during a natural population bottleneck
Individual heterozygosity rather than translocation distance predicted translocation success in Mojave desert tortoises since translocation is a stressor that can exacerbate inbreeding depression
Genetic rescue
When new individuals are introduced in a population with high inbreeding to increase genetic diversity and allow a population to recover from inbreeding depression
Mechanisms of preventing inbreeding
Behaviors such as the dispersal of juveniles and the recognition of relatives and avoidance of mating with them can prevent inbreeding, this can occur via several mechanisms (some species can recognize individuals with shared alleles at the MHC locus and avoid mating with them)
Inbreeding
violation of the HW assumption of random mating, alters genotype frequencies and increases homozygosity but not allele frequencies which means that it is technically not an evolutionary force
Quantifying inbreeding
At the level of the individual using pedigree info
At the level of the population by comparing observed vs expected frequencies of heterozygotes (Fis vs f)
Mechanisms that prevent inbreeding in plants
Self-incompatibility (S-locus alleles cannot be shared)
Dioecy (where male and female flowers are present on different plants)
Asynchronous flowering of male and female flowers on a single plant (where male flowers open first and spread pollen while female flowers bloom later)
Heterostyly where anthers and style are at different heights on a flower
Populations that do not avoid inbreeding
Fig wasps where siblings mate with one another after hatching within a fig
Some plant species are partially or entirely self-fertilizing such as Arabidopsis thaliana which has a model genetic system and Rice (Oryza sativa)
How can self-fertilization be evolutionarily favorable?
Reproductive assurance (a single seed can found a population and germinate via self-fertilization)
Low resource investment in attracting mates or pollinators
Inbreeding can also preserve coadapted gene complexes where linkage disequilibrium can occur much of the genome, this means that natural selection can favor these optimal combination of alleles across the genome, one downside is losing the possibility of phenotypic variation (may be evolutionary ‘dead ends’)
One unusual case was when inbreeding was shown to purge deleterious recessive alleles from a population and the complete homozygosity at 24 out of 25 loci were examined and there was no drop in viability or fecundity relative to other cattle
What are the consequences of severe inbreeding in normally outcrossing species and why? What are some examples?
This can lead to population extinction, Sewall Wright showed 35 guinea pig lines started from brother-sister matings and half went extinct within 9 years (W = 0.3 relative to control lines), When house mice lines were inbred only 1 line out of 20 persisted to 12 generations
Guppies
Bright coloration is favored for mating success which attracts females, but dull coloration is favored for protection from predators
Why is there competition for mates
sexes differ in energetic costs of reproduction (sperm are abundant and eggs are limited, more parenting investment by mother occurs)
Two consequences for this are there are fewer receptive females than males, females are a limited resource and reproduction is energetically limited for a female
Intrasexual selection
male-male dominance competition where the direct competition for mates occurs, often involves males competing for territories that females need to reproduce in, can happen right up until copulation
Sneaky males that mimic females will sneak and introduce sperm into female’s eggs which goes unnoticed (generally are able to dig)
A mix of male-male dominance and sneaky males leads to disruptive sexual selection on male morphology in Rhinoceros beetles
Sperm competition where males maximize the chance that their sperm will fertilize an egg, some strategies are removing competitors’ sperm, plugging female genitalia after mating, repeated matings, and producing more sperm (larger testes)
Infanticide, accounts for 25% of all lion cub deaths in the first year of life and 10% of lion mortality overall, but fitness benefit of infanticide seemed to allow this behavior to be favored overall since mating success is increased in males that engage in this behavior
Intersexual selection
Mate choice where females mate preferentially with showy males and also enlarged ornamental traits (coloration, vocalization, other behaviors), this commonly leads to the evolution of sexual dimorphism where males are showy and females have more drab, females also court the males when males differentially expend resources on reproduction
Evolutionary consequences of direct competition for mates
Selection for larger size occurs where traits that facilitate fighting successes, this leads to dimorphism between sexes
Species with sneaker males
Many fish species, dimorphism in Rhinoceros beetles where larger males battle for and guard females while smaller males sneak into females’ tunnels
Lizards and Negative FDS
In lizards there are three categories of males; ultra dominant males that aim to guard a large territory and take control, males that carefully guard a territory and mates with one female, males that sneak in on ultra dominants and do not guard a territory
Negative FDS occurs where sneaker males are favored if they are rare in the population so there is an oscillation of allele frequencies between sneaker and ultra dominant males
Effects of intersexual selection
Leads to trait divergence among isolated populations which can play a role in reproductive isolation which which can ultimately lead to speciation
How and why do female preferences arise?
Direct benefits where females choose males with traits that are favored by natural selection and there is a direct fitness advantage
Sensory biases where females have an intrinsic preference for a particular sensory stimulus
Indirect benefits where female preference develops based on indicators of genetic quality that indirectly benefit them or offspring
What are some examples where female mate choice provides direct benefits?
Female birds choose males that provide food, protection, female hangingflies prefer males that provide larger prey during mating, edible nuptial gift fits this
In Bittacus apicalis larger body size is correlated with a longer duration of copulation
What are some examples of how sensory bias can lead to the evolution of a particular male trait?
One example is lizard courtship movements, another example is that females of swordtail fishes prefer long tails even before males possessed them, long tails eventually evolved so the preference was shown to predate the species
What are some examples of the indirect benefits of female mate selection?
Good genes hypothesis posits that females may evolve preferences for male traits associated with high fitness or viability in offspring
Sexy-son hypothesis posits that an indirect fitness benefit is if females mate with males that have sexually preferable traits then their sons will inherit these traits and have a higher mating success indirectly benefiting females
Some examples are that female sticklebacks prefer males with red bellies since males with red-bellies tend to be well nourished and have good immune systems and offspring are resistant to parasites, this is also a possible explanation for energetic courtship displays since healthy males have more energy to allocate to courtship, cell duration in male gray tree frogs may also indicate genetic quality
Intrasexual selection
Male-male competition where females are passive players/limited resource and males compete for access to them
Intersexual selection
Mate choice competition where males compete for the attention of females who choose among them
How can sexual selection lead to reproductive isolation?
Since females seek out the trait that they prefer, if there is a polymorphism where different females prefer different traits, one set of females will have a preference for a set of males with that trait and a different set of females can have a preference with a different set of males. This can lead to reproductive isolation
Testing the sexy-son hypothesis
It was illustrated in sandflies that offspring of the most vs least attractive males did not differ in viability but tend to differ in fecundity/mating success
Sexually antagonistic coevolution
Since the fitness of a mate only matters to the extent that it ensures the fitness of the offspring, sexually antagonistic coevolution may emerge where selection favors traits in one sex that reduce the fitness of the other sex, one example of this is a peacock spider eating her mate after mating occurs since male spider is then eaten by female and offspring
Sexually antagonistic coevolution at the level of the gametes
Abalones can be present where selection on sperm occurs (increased speed at penetrating eggs due to increased lysin activity) along with selection on eggs (increased resistance to prevent polyspermy since this can lead to aborted embryo). As a result of this the evolution of the lysin gene occurred where there was a rapid change at nonsynonymous sites to alter protein to overcome egg barrier
In Drosophila sometimes proteins that make sperm resistant to dislodging by other males are toxic to females
Sexually antagonistic coevolution at the level of the individuals
Copulation can lead to injury or death due to traumatic insemination (bedbugs) or the drowning of female ducks
Because copulation can be aggressive, female traits/preferences that confer resistance to the males’ incentives to mate may be selected for, this phenomenon is known as chase away sexual selection.
In damselflies, males may have evolved flattened abdomens that can facilitate forced copulation and females may have evolved spines to prevent this, some evidence for this is that spines tend to be present in species with forced copulation
Praying mantis
In these species a female eats a male head down during copulation which generally results in successful fertilization. But studies showed that males tend to avoid being cannibalized since males tend to have multiple mating opportunities so there is not a fitness benefit to male cannibalism for males even though there is for females
Australian redneck spider
Males that were willingly cannibalized were much more likely to mate, mated 2x longer, produced 2x as many offspring, inserted a genital plug to prevent other males from fertilization, and male served as a feeding source for offspring. In this species, there are fitness benefits to cannibalism for males
Altruism
An act that benefits another individual without necessarily benefitting the actor, some examples are nest helpers in birds where birds stay with parents and raise their siblings rather than have offspring of their own and also warning calls in mammals/birds
Kin selection
Natural selection based on indirect fitness gains where an individual acts to benefit its relatives
Inclusive fitness
A fitness measure that is calculated from taking into account a combination of an individual’s fitness and the fitness gains to its relatives that result from its altruistic actions
Hamilton’s rule
Posits that altruism that benefits close relatives will evolve if Br > C where B is the benefit to the recipients of the altruistic act and C is the cost to the donor (both are measured in terms of fitness), and r is the coefficient measuring the proportion of shared alleles between the relatives (using identical by descent measures)
Parent to offspring and sibling to sibling is r = 1/2, sibling to half-sibling r = 1/4, individual to first cousin r = ⅛
Belding’s ground squirrel
Produces warning calls, individuals that issue warning cause have an 8% mortality risk and with no calls there is a 4% mortality risk. Frequency of warning calls is increased when relatives are present rather than when strangers are present which reinforces Hamilton’s rule
Cooperation in chasing off intruders is also present where squirrels are more likely to risk their lives and chase off intruders if relatives are present
White-fronted bee-eater
Exhibit nest helping behavior which tends to occur in harsh habitats where there are fewer opportunities to reproduce and a high mortality rate. Each helper is shown to double the number of surviving chicks and there is a differential care of relatives where daughter in laws help less
Discriminating cannibals
Tiger salamander cannibals that avoid eating siblings/kin. Kin selection should favor discriminating cannibals and researchers showed that survival rate doubled so B = 2 and there was no obvious cost so C = 0
Altruism at the level of the gametes
Sperm cooperation where sperm trains form with all the sperm from a given male, increases the locomotion speed of sperm
Eusociality
Phenomenon where groups of individuals in a colony rear individuals in a nest/hive and often forfeit their own reproduction. This is common in hymenoptera (wasps, bees, and ants) and commonly occurs with an individual’s siblings
What is haplodiploid sex determination and how does it come about?
This refers to a mating system that occurs when one parent, commonly a male, has a haploid genotype (generally develops from an unfertilized egg). Under this mating system sons inherit all of their diploid parent’s genes and daughters inherit half of the diploid parent’s genes and all of the haploid parent’s genes which results in females being more closely related to their sisters than their daughters
This is theorized to contribute to eusociality and the development of hive societies (which are common in hymenoptera) where individuals generally rear siblings and contribute to the survival of a hive or nest rather than reproduce individually
What are caveats for the haplodiploid explanations of eusociality?
Not all workers in a hive are full sisters since multiple fathers are commonly present and some species may have multiple queens
Not all haplodiploid species are eusocial and vice versa
This suggests that other factors besides haplodiploidy may also play a role in the development of eusociality
Complex colonies
Associated with eusociality which is characterized by complex nest building, extended larvae rearing, and the division of labor. Tends to be favored in harsh ecological conditions where natural selection may not favor individual reproduction
Naked mole rats
Tend to form subterranean colonies with 70-80 individuals but are not haplodiploid (XX and XY sex determination). One research group found the population was very inbred where 85% of matings are parent-offspring or sibling-sibling and F = 0.81, and this group hypothesized that high inbreeding led to the development of eusociality and colonies due to high kin selection within species. But other research groups found that inbreeding is not particularly high and eusociality likely developed due to harsh selective pressures that restricted the formation of new populations and individual reproduction
Parent-offspring conflicts
Offspring’s interest is to get as many resources as possible from parents and parent’s interest is to produce a maximum number of viable offspring. This means for many species there is an optimal number of offspring that a parent can successfully rear to maximize its own fitness
Ways parents may lower an offspring’s fitness
Infanticide with environmental stress and eating of offspring
Coerced nest helping where parents prevent offspring from leaving nest and reproduction, common in bee-eater males where parents may attack a male if male finds a mate and tries to leave nest
When parents withhold resources from an offspring, common in Dracula ants
Sibling-sibling conflicts
When siblings kill each other, sometimes in utero other times in a nest, generally occurs under stressful and resource limited conditions
Phylogenetics
Trees that infer relationships among groups of species or higher taxa. Nodes describe past speciation events
Monophyletic group
Group derived from one common ancestor that represents all descents of that common ancestor (clade)
Paraphyletic group
Group derived from one common ancestor that represents some but not all descendants of that common ancestor
Polyphyletic group
Group that does not share a single common ancestor in the time frame being considered
Homology
Trait similarity that reflects common ancestry
Synapomorphy
A shared and derived feature/trait that reflects common ancestry (how human/cat forelimbs have similar bone ratios)
Autapomorpy
Derived form of a trait that is unique to a taxon, does not talk about patterns of shared ancestry (long bat phalanges)
Cladogram
Phylogeny that is defined by nested synapomorphies. These can be determined by shared/derived traits or mutations in homologous genes
Polytomy
indicate unknown relationships between species, represented in a phylogenetic tree when more than two branches occur from one node
Homoplasy
When two traits are similar but similarity does not reflect common ancestry. This can arise via evolutionary convergence (analogous features can emerge), the independent evolution of a derived trait, or evolutionary reversal back to an ancestral form
How are synapomorphies defined for homologous genes?
Mutations can be used to define synapomorphies. Neutrally evolving gene regions such as the mtDNA Cytochrome C gene sequence are generally used. Phylogenies can be constructed by comparing ancestral and derived DNA sequences
How do we know which forms are derived for variable traits?
Outgroup comparisons can be used where species of interest are compared to a more distantly related species or outgroup. Outgroups have a similar trait or gene sequence to ingroup species, but we can assume the form of a trait or sequence found in the outgroup reflects a more distant common ancestor than among ingroups. The same approach can also be used for morphological traits
Examples of outgroup rooting
One example is a fish species where a female preference preceded the development of trait, long tails, that led to distinct species being formed.
How can DNA sequences be used to identify homoplasy?
When the number of mutational changes does not always correlate with the percent divergence, this indicates homoplasy has occurred via a reversal to ancestral sequence
This means that as time since the divergence from a common ancestor increases, the percentage of sequence divergence will approach 75% since chance alone generally accounts for genetic similarity between ancestral and individual sequence. Over time, multiple mutations at the same nucleotide site will obscure any phylogenetic signal
The molecular clock and divergence
Divergence tends to obey the molecular clock since there tends to be a linear relationship for divergence over time
A statistical correlation is needed for multiple mutational hits such as homoplasy. One example of this is to only look at exon regions or the 1st and 2nd codon positions
Long-branch attraction
Occurs when highly diverged lineages are incorrectly grouped together. This can occur if mutational rates differ among species lineages and faster DNA evolution occurs in some species or if some species reproduce at a faster rate than others. This means branches shown are not always in true proportion to the genetic distance rates of sequence evolution
What kinds of traits are more likely to show evolutionary convergence?
Traits that evolve under strong natural selection, such as root structures in an arid climate, are generally more likely to show evolutionary convergence
How can inferences from homoplasy be avoided?
Examining traits at multiple developmental stages (one example is that adult barnacles are similar but larval anatomy shows true phylogenetic relationships)
Look at many traits where a phylogenetic relationship can be uncovered so homologous traits can be distinguished from homoplasy
Distinguishing homology from homoplasy
The key is that one change on a phylogeny is required on synapomorphies that reflect homology while homoplasies require two or more changes since more distantly related organism have homoplasies
Maximum parsimony
criterion for generating phylogenetic trees that posits that the phylogeny that requires the fewest number of changes is the most probable true phylogeny, ocham’s razor
Consistency index
minimum number of possible steps/number of steps, CI = 1 indicates no homoplasy. Most parsimonious tree has the highest CI and least amount of homoplasy
What can synapomorphies be used to map?
They can map phylogenetic trees and distinguish between homoplasy and homology. Synapomorphies that reflect homology require one change while homoplasies require two or more changes
Maximum parsimony posits that the phylogeny that requires the fewest number of changes is the most probable true phylogeny
Limitations of using morphology to construct trees
Ankle bones were an imported to build phylogenetic trees of ungulate mammals, but whales lack ankle bones so there can be limitations with morphology
Problems with maximum parsimony analysis
Equally parsimonious trees
Ignores autapomorphies so information on the divergence that is specific to a taxon is not always represented by branch length, evolutionary divergence within taxa is not accounted for
Comparing branch lengths of species and their level of genetic divergence from ancestors is hard to generate and very computationally intensive
With maximum parsimony approaches there could be multiple equally parsimonious trees. What are some approaches that can be used to handle this?
One approach is bootstrapping which is when minor variations are changed in a dataset and a tree is resampledusing that different genetic data. This means that characters can be randomly sampled with replacement to create a simulated dataset with the same number of characters as the original dataset and this process can be repeated hundreds or even thousands of times to assess confidence in the branches of a tree. On a branch, the numbers indicate the percentage of bootstrap replicates that have that branch, >50% is considered good
Clades that are not strongly supported by genetic/morphological data can be collapsed into polytomies
Genetic distance trees
Constructed by converting information from different characteristics into a singular genetic distance value. This then involves calculating distance values between pairs of taxa and then grouping taxa by similarity (more sophisticated methods are correcting for multiple substitutions, weighing rare mutational changes more heavily)
Grouping by genetic distance (advantages and disadvantages)
Neighbor-joining approach is an unweighted pair-group method with arithmetic means (UPGMA), this is not a cladogram since individual characters are not looked at. This has the effect of creating a tree that best approximates pairwise differences and where branch lengths are an indication of genetic distances between species
Advantages of genetic distance methods are that they are computationally simple and often yield the same branching patterns as maximum parsimony. It also incorporates information on autapomorphies on a tree via branch lengths
Some disadvantages are that all information about different characteristics are condensed into a single number which causes you to lose information (this means homoplasy can introduce biases). Additionally specific synapomorphies cannot be mapped onto a tree since there is no time axis and taxonomic groups cannot be defined based on clades
Difficulties in all phylogenetic analyses
Scoring characters are tricky and measuring trait variation, this is because some related species can miss key characters and characters can also be correlated meaning assessments are not always independent
Homoplasy is also common, convergence due to natural selection or evolutionary reversal can occur
Hybridization can also violate the assumption of a bifurcating tree (plant species can originate through hybridization, at low levels such as graduations of traits from interspecific introgression)
Rapid species diversification can also occur, adaptive radiation includes Darwin’s finches, Hawaiian honeycreepers, etc. These are all closely related with few synapomorphies, phenotypic divergence through natural selection, lots of autapomorphies that include many homoplasies
Incomplete lineage sorting may also occur. This is because for recently diverged species, the rate at which new mutations arise and drift to fixation may not be fast enough to create haplotype groups within a species which means some haplotypes in one species may be more closely related to haplotypes in a different species than their own
Shared ancestral polymorphism
where the same haplotypes are present in two species, generally recently diverged species, even though no gene flow exists between those species
Incomplete lineage sorting
Since phylogenies inferred from DNA sequences may not always be congruent with species phylogeny, this results in incomplete lineage sorting
For recently diverged species, the rate at which new mutations arise and drift towards fixation may not be fast enough to create distinct haplotype groups for each species
Results in phylogenies that are inferred from DNA sequences not being completely congruent with species phylogeny since there is gene flow between separated populations
Divergence in the recent past may also cause haplotype trees to not be congruent with a species tree. Sometimes the same haplotypes in both species can reflect a shared ancestral polymorphism even though there is no gene flow between the two species, this means haplotype trees do not indicate a true species relationship
Ways to deal with incomplete lineage sorting
Sequencing multiple unlinked genes. Since genetic drift is random, patterns of incomplete lineage sorting will not be consistent across trees so the true phylogenetic signal should be apparent when relationships between multiple unlinked genes are averaged
Correlations with geography can also be used. If haplotype sharing coincides with the overlapping portions of a species genetic range and if haplotypes are shared at multiple loci, shared haplotypes are most likely to reflect hybridization and gene flow between species or introgression rather than shared phylogeny
Molecular evolution
Genetic/molecular differences between species that correspond with the length of time since species diverged from a common ancestor. Research on molecular evolution suggests that amino acid variation occurs at a steady rate of amino acid substitution
Molecular clock
Constant, steady rate of change at the molecular level (amino acids, DNA sequences, etc). Linear relationship between changes and time since divergence indicates a molecular clock
How were the observations from the molecular clock inconsistent with theories of natural selection?
There was an assumption that the primary evolutionary force behind changes in the molecular clock was natural selection but this was not shown to be the case. This is because researchers would have expected far fewer changes since overall protein functions generally did not change as a result of mutations and also since they would have expected to be episodic and associated with periods of natural selection rather than steady
The molecular clock instead suggests that most mutations that arise and go to fixation do so by genetic drift which is selectively neutral, this was revolutionary at the time
Neutral theory
posits that the majority of mutations that arise and eventually go to fixation are selectively neutral and persist to fixation via genetic drift. This, however, does not always mean that natural selection isn’t acting on these genes. Many mutations are quickly eliminated by natural selection and this theory is present for mutations that are selectively neutral. Very few mutations are fixed because they are favored by natural selection
Functional constraint
refers to the strength of purifying selection. Proteins that are under a lower functional constraint have a higher proportion of sites that can evolve neutrally and therefore more persisting mutations and a faster molecular clock. Different regions of a gene can have different levels of functional constraint (exons and nonsynonymous sites have a larger functional constraint than introns and synonymous sites)
