BIOL 359 Midterm 2

Phylogenetic Characters

Characters are used to construct phylogenies. A character is an attribute of an org that can provide insights into history (shared ancestry).

In molecular phylogenies, characters are typically nucleotide positions in a gene sequence, and each position can possess 4-character states: A, C, G, T

Cladistict Character State Definitions

Plesiomorphy: refers to the ancestral character state

Apomorphy: a character state diff than the ancestral state, or derived state

• 2 types: synapomorphy and autapomorphy

Synapomorphy: a derived character state (apomorphy) that is SHARED by 2+ taxa due to inheritance from a common ancestor: these character states are phylogenetically informative using the parsimony or cladistics criterion

Autapomorphy: a uniquely derived character states

Phylogeny Definitions

Monophyletic: a group that includes ALL of the descendants of a common ancestor. Monophyletic groups are known as clades

Non-monophyletic: any case that does not satisfy the above, such as:

Paraphyletic: a group that includes some, but not all the descendants of a common ancestor

Polyphyletic: assemblages of taxa that have been erroneously grouped together based on homoplasious characters

Synapomorphies identify monophyletic groups

Homology vs Homoplasy

A character state that is shared b/w 2 DNA sequences or taxa may be so b/c they inherited it from a common ancestor, or it is homologous (a homology/ synapomorphy)

Alternatively, the shared character might occur b/c they were evolved independently, in which case they are called a homoplasy.

Why Can Homoplasy Occur?

Homoplasy Examples

Vultures are a polyphyletic group. New world and old world vultures provide an ex of homoplasy resulting from convergent evolution.

The 3 spines stickle back species pairs have evolved independently in coastal lakes of BC. Positive assortative mating and disruptive selection have been important in the divergence of these pairs.

Analogy

The fins of a whale and the fins of a shark are another ex of homoplasy due to a reversal, whales and dolphins are mammals that have reverted to the ancestral state.

Homoplasy often results in analogies

Parsimony (or cladistics)

The Principle of Parsimony: simple explanations are preferred over more complicated ones.

In terms of phylogenetic trees, less evolutionary steps are better than more steps to explain relationships and hypothesis. The tree (or hypothesis) w/ the least # of steps is the most parsimonious.

The parsimony method min the total # of evolutionary changes required to explain relationships

Constructing Phylogenetic Trees

We us homologous characters (synapomorphies) to construct phylogenetic tree and to identify groups that are monophyletic; synapomorphies are phylogenetically informative.

We want to avoid using homoplasious characters to construct phylogenies

Conducting Trees w/ Parsimony

Outgroup: When constructing a phylogeny for a group of orgs, we need to employ an outgroup, which is not part of the group of interest (the ingroup), but also not too distantly related to it

The character states possessed by the outgroup is defined a priori as ancestral (plesiomorphic). With this rule, we can then identify synapomorphies, which tell us about relationships (they identify monophyletic groups)

Whale Evolution

The artiodactyla are a group of hoofed mammals that possess an even # of toes. The perissodactyla are hoofed mammals that possess an odd # of toes.

Are whales really a member of the artiodactyla?

• but they do not have hooves/toes

The artiodactyls possess a distinctive astragalus. Are whales a group outside the artiodactyls, or are they actually artiodactyls? We have to use genetic sequencing.

Assuming Confidence in Phylogeny

Bootstrap Method: computational technique for estimating the confidence level of a phylogenetic hypothesis

• random generates new data sets from the og set (1000 replicates is most common)

• computes the # of times that a particular grouping (or branch) appeared in the tree

Phylogeny & Taxonomy

Taxonomic Groups can be:

• Monophyletic - contain all descendants of a common ancestor

• Paraphyletic - contain some but not all descendants of a common ancestor, or polyphyletic (erroneous homoplasious groupings - ex. vultures)

• The goal of cladistic taxonomy is to only recognize monophyletic groups as valid taxa, but traditional taxonomy has not always done this

Cladistics — use of parsimony to construct evolutionary relationships

Cladistic taxonomy = evolutionary taxonomy

Carl Woese

Carl Woese proposed that life is divided into 3 monophyletic domains (highest level) on the basis of DNA sequence data: the Bacteria, the Archaea, and the Eukarya.

Created the Tree of Life / Universal Tree

Before that, we used the Whittaker’s 5 Kingdom classification: Kingdom Monera, Kingdom Protista, Kingdom Plantae, Kingdom Fungi, Kingdom Animalia

• based on morphological characteristics and does not reflect actual phylogenetic relationship

Biogeography

Biogeography is the branch of science that seeks explanations for why orgs are found in some regions, but not others. This very often involves the use of phylogenies to test hypotheses concerning the geographic origins of diff species, or groups of species such as the Chameleons.

Using Phylogenies - Chameleons

Gandwana is a supercontinent. Seychelles (where the chameleons are from) are most closely related to India, then Madagascar, then Africa. And since we know when drift occurred

#1: They were always there

• If true, then the most recent ancestor to the Seychelles Chameleons would be Indian, than Madagascar

#2: they traveled

We see that in the phylogeny tree that the chameleons are more closely related the African species, so they like travelled and #2 is more correct

Coevolution

Using Phylogenies

Coevolution: the process where evolutionary changes in the traits of one species drive evolutionary changes in the traits of another species. Can involves predators and prey, hosts and parasites, and mutualisms, such as aphids and their endosymbiotic bacteria.

Coevolution can also result in co-speciation

Adaptation

A trait that increases the fitness of the individual relative to individuals that do not possess the trait - initially arise by mutation, and subsequent selection, but the process may be aided (or hindered) by drift and migration

• Must tests hypotheses concerning whether traits possessed by orgs are adaptive

• Adaptive significance of some traits are not always obvious

Testing Hypotheses - Oxpecker

Oxpecker + Tick Loads: no conclusive evidence to say that oxpeckers reduce the amount of tick loads on cattle, p >0.005

Oxpecker + Wounds: p < 0.05, the presence of oxpeckers increase the number of wounds

Oxpecker + Earwax: p < 0.05, the presence of oxpeckers reduce the amount of earwax in cattle, but no conclusion about whether this is beneficial or not

Key things of Adaptation

• Diff among pop are not always adaptations

• Not every trait an org possesses is adaptive

• Not every adaptation is perfect

3 methods to study adaptation: experimental studies, observational studies, comparative studies

The Tephritid Fly & The Jumping Spider

An experimental approach. When in the presence of jumping spider, the fly waves it’s marked wings What is the function of wing marking and waving?

H1 (null): flies do not mimic jumping spiders

H2: flies do mimic jumping spiders to deter other non-spider predators

H3: flies mimic jumping spider to deer predator by these spiders

Treatments: A - marking + waving, B - cut off and glued back on so marking + waving, C - waving only, D - marking only, E - neither

RESULT: marking + waving deters jumping spider but not other predators

Garter Snakes

Observational experiment. Are ectothermic (get heat from evn) or poikilothermic (body temp varies).

Do garter snakes made adaptive choices when looking for a nighttime retreat?

H1: snakes preferentially select rocks as nighttime retreats.

H0: snakes choose rock retreats at random

From the diff nighttime retreats, medium rocks are the only rocks that snakes can keep their temp in the stable range.

Result: contrasting # of rocks available and rocks chosen by snakes. More snakes proportionally choosing mediums rocks as 1/3 available rock and 2/3 of snakes choose those rocks.

Therefore, yes, garter snakes make adaptive choices in terms of nighttime retreats.

Comparative Approaches

The comparative in evolutionary bio evaluates the strength of hypotheses by testing for patterns across species or lineages. These can include correlations among traits, or among traits as they related to env factors.

Requires knowledge of the evolutionary relationships among the orgs being considered.

Bats

A comparative method of studying adaptations.

Why do some bats have larger testes than others>

Hypothesis: adaptation for sperm competition. It predicts that bat species in larger groups (greater sperm competition) will evolve larger tests for their body size b/c more males.

Gathered data for a variety of species to test this hypothesis/ Plotting group size vs testes size, there is a positive correlation.

But the small pop that have small testes come from the same ancestor and so do large pops w/ large testes grouping to the same ancestors.

Based on IPC, there is a positive correlation so yes, bats have testes size from adaptations of sperm competition

Phylogenetically Independent Contrasts

Phylogenetically Independent Contrasts: controlling for phylogenetic relationships and a method of evaluating cross species correlations among traits

Phenotypic Plasticity

Phenotypes arise b/c of genotypes and env interactions. Identical genotypes can result in diff phenotypes in diff env - referred to as phenotypic plasticity.

The Crustacean Genus Daphnia

Tradeoffs & Constraints

A trade-off is a compromise b/w one characters and another (or 2 aspects of a single character), which cannot be avoided. Tradeoffs prevent the simultaneous optimization of 2 diff characters, or aspect of a single character.

A factor that tends to retard rate of adaptive evolution or prevent a pop from optimizing a trait — constraint.

Begonia involucrata

trade-off: male (pollen) vs female (get fertilized) flowers.

H1: the more closely female flowers resemble males, the more often they are visited by bees (stabilizing selection hypothes)

H2: the more closely female flowers resemble the most rewarding (largest) males, the more often they will be visited by bees (directional selection hypothesis)

Result: bees approach the larger size (positive directional) so begonia should make female flower larger, but there is a negative correlation b/w size and # of flowers.

Tradeoff → the larger the flowers, the less # of flowers there are

Fuschia Excorticata

Type of physiological constraint.

A flower that has a window of fertilization period before turning red for multiple days w/ no possibility of being fertilized before falling off. But why d

Beetle Ophraella species

Type of genetical and ecological constraint.

Our Closest Relatives

Humans are more closely related to Bonobos and Chimps. Them + Gorilla are in the family Hominidae.

H1: independent evolution of trait in each lineage = 6 steps

H2: evolution of trait in a single common ancestor = 1 step

Parthenogenesis

Parthenogenesis — virgin birth / from unfertilized eggs which produce exact clones of the mother

Obligate Parthenogenesis: entire species consist of females only, which reproduce by making genetically identical clones of themselves.

• ex: mourning geckos on reproduce asexually and only females

Cyclical parthenogenesis: pop consist of females that reproduce clonally throughout most of the year, but at certain times males are produced, and sexual reproduction occurs

• ex: aphids, spring and summer produce female but fall produces males so when they sexually reproduce, the eggs will survive winter and are all females

Facultative Parthenogenesis: pop consist of males and females, but females can also reproduce via parthenogenesis in the absence of males

• ex. Komodo Dragos self-fertilize in the absence of males. ZW → Z and W eggs. chromosome within then duplicates to form ZZ and WW which means only males are produced

Hermaphrodites

• Orgs that have both male and female sex organs (gonads) and are (usually) capable of self-fertilization (or selfing).

• The strongest from of inbreeding but still a form of sexual reproduction b/c gametes are still formed via meiosis

• however, offspring of selfing hermaphrodites are genetically less diverse than the offspring of individuals that outcross (sex w/ unrelate individuals)

Maynard Smith’s Null Model

Maynard Smith proposed a null model to address the question of why sex exists. Assumptions:

• A female’s reproductive mode does not affect the # of offspring that she can male

  • Females can potentially produce more offspring if male provide more parental care

  • Only affects some species

• A female’s reproductive mode does not affect the probability that her offspring will survive

Pop w/ Asexual & Sexual Reproduction

In sexual reproduction, there is 4 total offspring in gen 2 and there is 8 offspring in gen 3.​

In asexual reproduction, also 4 offspring in gen 2, but each female can product their own 4 so 16 offspring in gen 3.

This means that asexual reproduces at a much faster rate = two-fold cost of sexual reproduction. This means that there must be benefits to sex

Purpose of Sexual Reproduction

1. Mating b/w diff individuals resulting in new combo of genes in the offspring

   • Outcrossing & restore HW eq

2. Recomb and crossing over in the process of meiosis (not possible in asexuals)

   • creates new allele combos for multilocus genotype & restores linkage eq

Together, these factors create genetically diverse offspring and allow the purging of deleterious mutations.

Effects of Recombo on Fav Gene Combos

Sexual recombo creates new combos of alleles and destroys existing combos. Recombo will always have at least some of the favorable genotypes (NS can act on) .

Sex creates new gene combos that may be more fit than then previously existing ones.

Linkage Diseq

If genes are located close together on the same chromosome, they are referred to as being linked. Linked genes do not segregate independently but can rather be inherited as a single unit — genotypes at 2 diff linked loci will not be randomly associated w/ each other.

When this is the case, the genes are in linkage diseq & there will be less genetic diveristy among offspring for genes (gene combo) in linkage diseq.

Recombo (during meiosis) breaks up linked genes and breaks down linkage diseq.

Muller’s Ratchet

Obligately asexual organisms accumulate deleterious mutations, which result in lowered fitness.

The total # of deleterious mutations and corresponding reduction in avg pop fitness is referred to as the genetic load, which will eventually become so high that the pop goes extinct.

Walking Stick Insets

An example of Muller’s Ratchet

Ancestral state is sexual reproducing but the lineage has split into some species being asexual while others are sexual.

Researchers sequenced highly conserved genes (important for cellular function) and the ratio of nonsynonymous to synonymous mutations for asexual is much higher than sexual. This means there is more deleterious mutations and so obligate asexual are likely to be short lived in nature.

The Red Queen Hypothesis + ex.

The central tenant of the Red Queen Hypothesis is that species must continuously evolve new adaptations in response to changes within other ogs.

If a species fails to evolve new adaptation in response to changes within other orgs its will go extinct.

Pathogen vs Host: An evolutionary advance by the pathogen results in an evolutionary​ advance in its host, and vice versa. Each species must continually​ evolve in a perpetual arms race to keep up with the other

C. elegan Evolutionary Arms Race

The control is roughly stable at 0.2 of the outcrossing rate b/c asexual reproduction is favorable as there is a stable env and no selective pressure.

The evolution has pathogens from a stock get introduce, this causes a peak in outcrossing to get the correct genotype to become resistant. But b/c the pathogen from the same stock is being introduced (w/ pathogen having no selective pressure), when the correct genotype is found, it is bad to recombo to disrupt the genotype so asexual is favored and outcrossing rate declines.

The coevolution has selective pressure on both C. elegans and the pathogens which result in the continuous sexual reproduction w/ a high outcrossing rate.

Advantages of Asexual Reproduction

1. Asexual orgs tend to have strong colonization abilities b/c an entire pop can be founded by a single individual.

2. They also propagate much faster when env are favorable. Remember, they can produce twice as many grandchildren as sexual.

Sexual Dimorphism

Sexual Dimorphism: refers to the phenotypic diff b/w males and females. In many cases, sexual dimorphisms cannot be explained by viability selection - if a trait results in an increased probability of survival, why wouldn’t both sexes possess it?

Sexual Selection: differential reproductive success resulting from differential abilities to find a mate

Parental Investment

Parental Investment refers to the energy, time and resources devoted to mating, gestating, and caring for offspring. The investment by parents increases the fitness of the offspring receiving it.

Parental investment is typically much greater for females. Eggs are expensive while sperm are cheap. Daily female egg production requires 3X the energy needed for daily basal metabolism.

Asymmetric Limits on Reproductive Potential

Usually (not always) females make a much greater investment than males, and as a result, their reproductive success is limited by the # of eggs that they can produce and rear (fecundity selection). In 90% of mammals, males provide no parental care for their offspring.

Reproductive success in males is potentially enormous as they can essentially produce an infinite quantity of sperm. As a result, male reproductive success is limited by the # of mates that they can obtain (sexual selection).

Intrasexual vs Intersexual Selection

Asymmetry in reproductive potential predicts the diff in mating behaviors will exist b/w the sexes:

• males: usually be competitive (combat, sperm competition, infanticide) - strong sexual selection

• females: will usually be selective, or choosy - weak sexual selection

Intrasexual selection: interactions b/w members of the same sex

Intersexual selection: interactions b/w members of the opposite sexes

Male-Male Competition: Combact

Intrasexual selection in male-male combat can favor morphological traits such as larger body size, amour, antlers and other offence/defense structures.

• e.g. in marine iguanas in the Galapagos there is considerable sexual dimorphism in size

SNEAKERS - alternative male mating strategies

Sneakers - Alternative Male-Mating Strategies

Jacks/ sneakers are really fast and quickly released their sperm on the females’ eggs while Hooknoses are the bigger stereotypical males. Phenotype diversity if maintained as hooknoses are father to hooknoses and jacks are fathers of jacks

3 Alternative Male Mating Strategies in Side-Blotched Lizards

• Orange males defend large territories w/ many females

• blue males defend small territories w/ few females

• Yellow males try to sneak into other male territories

Game of rock-paper-scissors game of evolution: orange beats blue, blue beats yellow, and yellow beats orange.

Male Sperm Competition

When a female mates w/ more than one male, the sperm from the diff males are in a race to fertilize the egg. one sperm competition strategy is to produce larger ejaculates. other include prolonging copulation, inserting a copulatory plug, and sperm removal (found in damsel fly).

Ex. Fruit flies in the present of other males perceive sperm competition and ejaculate more sperm than w/o no other males.

Male-Male competition: infanticide

Infanticide is the highest type of mortality among lion cubs. NS doesn’t try to act in the best interest of the species as then infanticide would not make sense.

Prides of lions usually consist of related females and 2 or 3 adult males that are unrelated to the females. Males go to a pride and attempt to evict its resident males and take over the pride.

Nursing females do not breed. By killing the previous male’s cubs, the male lions will gain more opportunities to mate.

In terms of fitness, male infanticide creates a conflict b/w new males who take over a lion pride, and its resident females. The females will defend their cubs against new males, and sometimes be killed in the process.

Baboons & the Bruce Effect

Gelada Baboons live in a social structure where one or a few males control a group of up to 12 females and their offspring. Males will often fight to take over groups of females, and if successful, infanticide of the previous male’s offspring typically follows. Pregnant females will frequently terminate (abort) their pregnancy, rather than continue to invest in doomed offspring.

The Bruce Effect: pregnancy termination in the presence of unfamiliar males

Female Choice

• Although initially controversial, female choice is now accepted as an extremely important factor in evolution

• In species where males are unable to monopolize females, or important resources for females, the males will typically advertise for mates, and the females choose the nest advertisements

• This can lead to elaborate courtship displays, and bizarre male morphological features

Red-Collared Widow Birds

Researchers conducted an experiment on female choice of mate based on their tail length. There was a control w/ avg tail length and a short where they cut the tail shorter.

Those w/ a longer tail (control) have a higher number of active nests than short tails. But the trade-off is that longer tails are more energetically expensive to maintain and thus they lose more body mass the longer their territory have been established. So, NS acts against it.

Gray Tree Frogs

Females can discriminate among “advertising” males, and this leads to evolution of courtship displays.

Male gray tree frogs produce many diff types of calls during breeding season - females prefer long male calls.

Model for the Evolution of Female Choice

4 explanations about how and why female preferences evolve.

1. The simplest hypothesis for female choice is that female preferences are arbitrary.

2. Consider the genetic variants our mated pairs will transmit to their offspring. Across gens, preference and display will become genetically correlated

3. As long as a pop’s average display and average preference place it on the line, the population will not evolve.

4. B/c display and preference are genetically correlated, selecting for female preference yields a correlated response in display. Likewise, selecting for male display yields a correlated response in preference.

When a pop moves off the eq line, it may never return, and this may mark the beginning of runaway selection which results in the evolution of male traits that are highly maladaptive w/ respect to viability selection.

Zebra Fish

A trait selected by females can initially be arbitrary and potentially neutral w respect to viability selection.

Experiments using mutant red male zebra fish shows that females have a statistically significant preference for the red mutant males over normal males.

Spotted Cucumber Bettles

In spotted cucumber beetles, females display a strong preference for fast stroking males as opposed to show stroking males, but the offspring of the 2 male types show no statistical diff in fitness parameters such as hatching success, development, fecundity, etc.

Neverless, the offspring of fast stroking males are also fast stroking, and fast stoking males get more mates

Why would females care or be so picky?

1. They may get better genes

   • ex. the offspring of long calling male gray tree frogs have higher fitness than the offspring of shorter calling males

2. A pre-existing sensory bias

   • a sensory bias may pre-dispose a female to be receptive to a male behavior or advertisement.

   • ex. In water mites, males increase a female’s propensity to receive a spermatophore by duplicating the vibrations created by the mite’s prey item-small copepod crustaceans

3. Resistance to Parasites

4. Choosy females might get better resources

   • Males can provide food, parental care or other resources, females can distinguish b/w good and bad providers

   • Hanging flies: Nuptial gifts - items from male to female to increase their reproductive success during, before, or after mating

     • The larger the gift the male presents = longer the pair copulates = more sperm the female allows the male to transfer.

Resistance to Parasites - Example

Barn Swallows and Tail Length

• Nests are infested w/ blood-sucking mites

• Nestling growth & adult tail size are reduced by parasites

• Females select males w/ longer tails

• Females then have offspring that are more resistant to mites

• Females also choose males w/ more symmetrical tails

Weird behaviors?

• Some species have taken nuptial fits to an extreme: widow spiders and mantises

  • Sexual Cannibalism

• Bed BUgs

• Marine flatworms

Consequences of Asymmetric Limits in Reproductive Potential Revisited

Consequences: the sex subject to strong sexual selection will be competitive and the sex subject to weaker sexual selection will be choosy.

In the majority of ex considered, it was males that were subject to strong sexual selection, and that is generally the case in nature — but not always.

Sexual selection in males often result in polygyny (male + 2+ females). But when males contribute significantly to parental care, sexual selection can act on females = polyandry (female + 2+ males)

Gunnison’s Prairie Dogs

An ex of female multiple matings

Female Gunnison’s prairie dogs increase their reproductive success by mating with multiple males. So, the more the # of sexual partners a mother has, the larger the litter size at first juvenile emergence.

Pipefish - sexual selection on female & male choice

Sexual selection is most likely to be stronger for females than males when males provide parental care.

In paired-choice tests, researchers place a male pipefish in an aquarium from which he can see two females. The researchers infer which female the male would prefer as a mate from where he spends more of his time. The result was that males often choose females that had a larger body size, large skin fold size, and fewer spots (which were tattooed on or not but represent parasites)

In paired-choice tests, females showed no tendency to discriminate between males of different sizes

Humans

Humans are sexually dimorphic as women and men differ in many characteristics like height.

The most basic knowledge of human reproductive biology suggests that the reproductive success of men is more likely to be associated with mating success than is the reproductive success of women.

Is Homicide a form of Male-Male Competition

Men who are more successful in male–male combat should have higher mating success and higher fitness, at least in premodern cultures w/o formal police and criminal justice systems.

Result: Killers (unokais) are more successful in fitness by having a higher avg # of wives and children. Whereas zealous warrior is less successful than other in terms of the cumulative # of wives and children surviving.