Evolution Exam 2

Question 1

Relationship between gene flow and population difference

Answer 1

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

Question 1

Direct methods of studying gene flow

Answer 1

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

Question 2

Indirect methods of studying gene flow

Answer 2

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)

Question 3

How can Fst be used as a tool for identifying genes evolving under natural selection?

Answer 3

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

Question 4

How can gene flow be a constraint on evolution by natural selection?

Answer 4

One example is water snakes that are maladaptive to their environment because of juvenile dispersal

Question 5

What are examples for how clines can evolve through the interaction of selection and gene flow?

Answer 5

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

Question 6

Categories of non-random mating

Answer 6

Mating according to phenotype (assortative or disassortative), associated with sexual selection

Mating with relatives (inbreeding) or avoidance of mating with relatives (outbreeding)

Question 7

Mechanisms of avoiding inbreeding

Answer 7

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

Question 8

Circumstances for inbreeding

Answer 8

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)

Question 9

Evolutionary consequences of inbreeding

Answer 9

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

Question 10

Inbreeding coefficient

Answer 10

measured by F, defined as the probability of identity by descent at the level of an individual based on their pedigree

Question 11

How can expected heterozygosity be used to estimate inbreeding level?

Answer 11

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

Question 12

What is inbreeding depression and why does it occur?

Answer 12

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

Question 13

Consequences of inbreeding in real life populations

Answer 13

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

Question 14

Genetic rescue

Answer 14

When new individuals are introduced in a population with high inbreeding to increase genetic diversity and allow a population to recover from inbreeding depression

Question 15

Mechanisms of preventing inbreeding

Answer 15

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)

Question 16

Inbreeding

Answer 16

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

Question 17

Quantifying inbreeding

Answer 17

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)

Question 18

Mechanisms that prevent inbreeding in plants

Answer 18

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

Question 19

Populations that do not avoid inbreeding

Answer 19

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)

Question 20

How can self-fertilization be evolutionarily favorable?

Answer 20

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

Question 21

What are the consequences of severe inbreeding in normally outcrossing species and why? What are some examples?

Answer 21

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

Question 22

Guppies

Answer 22

Bright coloration is favored for mating success which attracts females, but dull coloration is favored for protection from predators

Question 23

Why is there competition for mates

Answer 23

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

Question 24

Intrasexual selection

Answer 24

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

Question 25

Intersexual selection

Answer 25

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

Question 26

Evolutionary consequences of direct competition for mates

Answer 26

Selection for larger size occurs where traits that facilitate fighting successes, this leads to dimorphism between sexes

Question 27

Species with sneaker males

Answer 27

Many fish species, dimorphism in Rhinoceros beetles where larger males battle for and guard females while smaller males sneak into females’ tunnels

Question 28

Lizards and Negative FDS

Answer 28

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

Question 29

Effects of intersexual selection

Answer 29

Leads to trait divergence among isolated populations which can play a role in reproductive isolation which which can ultimately lead to speciation

Question 30

How and why do female preferences arise?

Answer 30

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

Question 31

What are some examples where female mate choice provides direct benefits?

Answer 31

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

Question 32

What are some examples of how sensory bias can lead to the evolution of a particular male trait?

Answer 32

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

Question 33

What are some examples of the indirect benefits of female mate selection?

Answer 33

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

Question 34

Intrasexual selection

Answer 34

Male-male competition where females are passive players/limited resource and males compete for access to them

Question 35

Intersexual selection

Answer 35

Mate choice competition where males compete for the attention of females who choose among them

Question 36

How can sexual selection lead to reproductive isolation?

Answer 36

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

Question 37

Testing the sexy-son hypothesis

Answer 37

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

Question 38

Sexually antagonistic coevolution

Answer 38

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

Question 39

Sexually antagonistic coevolution at the level of the gametes

Answer 39

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

Question 40

Sexually antagonistic coevolution at the level of the individuals

Answer 40

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

Question 41

Praying mantis

Answer 41

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

Question 42

Australian redneck spider

Answer 42

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

Question 43

Altruism

Answer 43

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

Question 44

Kin selection

Answer 44

Natural selection based on indirect fitness gains where an individual acts to benefit its relatives

Question 45

Inclusive fitness

Answer 45

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

Question 46

Hamilton’s rule

Answer 46

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

Question 47

Belding’s ground squirrel

Answer 47

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

Question 48

White-fronted bee-eater

Answer 48

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

Question 49

Discriminating cannibals

Answer 49

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

Question 50

Altruism at the level of the gametes

Answer 50

Sperm cooperation where sperm trains form with all the sperm from a given male, increases the locomotion speed of sperm

Question 51

Eusociality

Answer 51

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

Question 52

What is haplodiploid sex determination and how does it come about?

Answer 52

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

Question 53

What are caveats for the haplodiploid explanations of eusociality?

Answer 53

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

Question 54

Complex colonies

Answer 54

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

Question 55

Naked mole rats

Answer 55

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

Question 56

Parent-offspring conflicts

Answer 56

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

Question 57

Ways parents may lower an offspring’s fitness

Answer 57

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

Question 58

Sibling-sibling conflicts

Answer 58

When siblings kill each other, sometimes in utero other times in a nest, generally occurs under stressful and resource limited conditions

Question 59

Phylogenetics

Answer 59

Trees that infer relationships among groups of species or higher taxa. Nodes describe past speciation events

Question 60

Monophyletic group

Answer 60

Group derived from one common ancestor that represents all descents of that common ancestor (clade)

Question 61

Paraphyletic group

Answer 61

Group derived from one common ancestor that represents some but not all descendants of that common ancestor

Question 62

Polyphyletic group

Answer 62

Group that does not share a single common ancestor in the time frame being considered

Question 63

Homology

Answer 63

Trait similarity that reflects common ancestry

Question 64

Synapomorphy

Answer 64

A shared and derived feature/trait that reflects common ancestry (how human/cat forelimbs have similar bone ratios)

Question 65

Autapomorpy

Answer 65

Derived form of a trait that is unique to a taxon, does not talk about patterns of shared ancestry (long bat phalanges)

Question 66

Cladogram

Answer 66

Phylogeny that is defined by nested synapomorphies. These can be determined by shared/derived traits or mutations in homologous genes

Question 67

Polytomy

Answer 67

indicate unknown relationships between species, represented in a phylogenetic tree when more than two branches occur from one node

Question 68

Homoplasy

Answer 68

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

Question 69

How are synapomorphies defined for homologous genes?

Answer 69

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

Question 70

How do we know which forms are derived for variable traits?

Answer 70

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

Question 71

Examples of outgroup rooting

Answer 71

One example is a fish species where a female preference preceded the development of trait, long tails, that led to distinct species being formed.

Question 72

How can DNA sequences be used to identify homoplasy?

Answer 72

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

Question 73

The molecular clock and divergence

Answer 73

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

Question 74

Long-branch attraction

Answer 74

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

Question 75

What kinds of traits are more likely to show evolutionary convergence?

Answer 75

Traits that evolve under strong natural selection, such as root structures in an arid climate, are generally more likely to show evolutionary convergence

Question 76

How can inferences from homoplasy be avoided?

Answer 76

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

Question 77

Distinguishing homology from homoplasy

Answer 77

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

Question 78

Maximum parsimony

Answer 78

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

Question 79

Consistency index

Answer 79

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

Question 80

What can synapomorphies be used to map?

Answer 80

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

Question 81

Limitations of using morphology to construct trees

Answer 81

Ankle bones were an imported to build phylogenetic trees of ungulate mammals, but whales lack ankle bones so there can be limitations with morphology

Question 82

Problems with maximum parsimony analysis

Answer 82

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

Question 83

With maximum parsimony approaches there could be multiple equally parsimonious trees. What are some approaches that can be used to handle this?

Answer 83

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

Question 84

Genetic distance trees

Answer 84

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)

Question 85

Grouping by genetic distance (advantages and disadvantages)

Answer 85

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

Question 86

Difficulties in all phylogenetic analyses

Answer 86

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

Question 87

Shared ancestral polymorphism

Answer 87

where the same haplotypes are present in two species, generally recently diverged species, even though no gene flow exists between those species

Question 88

Incomplete lineage sorting

Answer 88

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

Question 89

Ways to deal with incomplete lineage sorting

Answer 89

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

Question 90

Molecular evolution

Answer 90

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

Question 91

Molecular clock

Answer 91

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

Question 92

How were the observations from the molecular clock inconsistent with theories of natural selection?

Answer 92

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

Question 93

Neutral theory

Answer 93

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

Question 94

Functional constraint

Answer 94

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)