Last content (lectures 17-20) - BIEB150

Darwin didn’t discuss what?

origin of species (speciation)

what are species?

Species is Latin for ‘KIND’.

So, in many cases biologist used any

feature that reflected differences

what are dogs?

Dogs descend from a

domesticated population of the

grey wolf (Canis lupus)

Are dogs their own species?

No. They are a subspecies Canis lupus familiaris

reproductive isolation:

Horses and donkeys: Can produce

hybrids but they are sterile.

asexual species:

Many microbes, including some yeasts, reproduce largely asexually, making it difficult to assess reproductive isolation

species in the fossil record:

Impossible to assess behaviors

cryptic species:

Before 2001, African savanna and forest

elephants were considered the same

species. Now we know these are

independent species.

biological species concept:

“groups of actually or potentially interbreeding natural populations

which are reproductively isolated from other such groups”

Ernst Mayr 1942

• only relevant for sexually reproducing organisms

• difficult to assess in some geographic contexts

evolutionary species concept

“a single lineage of ancestor-descendant

populations of organisms which maintains its

identity from other such lineages [in space and

time] and which has its own evolutionary

tendencies and historical fate”

Wiley 1981

• developed by simpson in 1951 to include asexual organisms and extinct species

• does not work well with fossil data

• applying the evolutionary species record to extinct species requires a good fossil record

morphological species concept:

“a species is a community, or a number of related

communities, whose distinctive morphological

characters are, in the opinion of a competent

systematist, sufficiently definite to entitle it, or

them, to a specific name”

Regan 1926

• works with asexual organisms as well as fossils

• morphological characteristics can be subjective

• cryptic species and plasticity are massive problems

genetic species concept

Defines a species based on genetic similarity. Species are

considered distinct groups of organisms that are reproductively

isolated from each other, not through direct observation of

reproductive behaviors, but through evidence of significant

genetic divergence.

• very useful, expecially because of the availability of genetic data (now also from museum specimens, and very old samples)

• totally arbitrary thresholds (often 2-3% divergence in mtDNA)

species concepts: a comparison

see image

giraffes, one species or several?

• Giraffes were historically classified as one species with multiple populations.

• Researchers later found:

• 6 distinct genetic clusters

• Populations differ in coat patterns and morphology

• Populations are geographically separated

• They can still interbreed and produce fertile offspring

using gene flow to define species - biological species concept

Species are groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups

• gene flow (migration) is the movement of genes into or out of a population

• no or low gene flow = reproductive isolation

• therefore the study of speciation under this definition is really the study of evolution of reproductive isolation

what is reproductive isolation:

• mechanical = can’t (some sort of physical/size difference that prevents breeding)

• ecological = don’t (can physically interbreed but don’t due to geographic isolation due to habitat differences or due to breeding at different times of the year)

• behavioral = won’t (Taxa may be reproductively isolated even if they can interbreed AND they still come into contact … but they choose not to mate. There may be the evolution of a strong mating preference, and they don’t find individuals of opposite sex attractive from the other species)

reproductive isolating barriers - two flavors

prezygotic - occur before fertilization

postzygotic - occur after fertilization

prezygotic:

• premating barriers, prevent mating (habitat isolation, temporal isolation, behavioral isolation)

• postmating barriers, prevent zygote formation (mechanical isolation, gametic isolation)

temporal prezygotic isolation example:

Eastern Spotted skunk (Spilogale putorius)

- Eastern spotted skunks mate in late winter.

- Western spotted skunks mate in late summer.

- They come into contact but never have the

opportunity to breed due to timing.

ecological prezygotic isolation:

Example: Walking stick insects in California

(Timema cristinae)

• Live on different host plants Adenastoma or

Ceanothus.

• These bugs are adapted to the different plants

and if they wander onto the wrong plant they get

eaten by predators.

• Since they have to stick to their own plant they

don’t often mate.

• This is a vey common mechanism of isolation!

mechanical prezygotic isolation:

• Lock and key fit between male

and female genitals in many

species.

• Due to coevolution and often

sexual conflict!

• Example Ground

another example of prezygotic isolation:

Can also occur in plants although the morphologies were are talking about are often matched to pollinators

behavioral prezygotic isolation:

Example: “behavioral sterility” in hybrid hummingbird displays

• hybrids inherit a “weird” display pattern, that females of both species do not refer

Postzygotic barriers: Hybrid inviability

• Hybrids don’t completely develop, die before birth or die before reaching maturity.

• Example: goat-sheep hybrids are stillborn.

Postzygotic barriers: Hybrid sterility

• Hybrids are healthy (viable) and survive but aren’t fertile.

• Evolutionary dead end.

• can be due to differences in chromosome number

Postzygotic barriers: Hybrid breakdown

Hybrid breakdown is a type of post-zygotic reproductive failure where first-generation hybrid offspring are viable and fertile, but subsequent generations have low fitness.

• Caused by the separation of co-adapted gene complexes (epistatic interactions) from the parent species

• Example: Growth in stickleback hybrids

which evolves faster - prezygotic or postzygotic reproductive isolation? Why?

prezygotic, as it prevents mating from even taking place

Genetic basis of reproductive isolation: Intrinsic Postzygotic Isolation - DMIs

Dobzhansky-Muller Incompatibilities (DMIs)

• As populations diverge, different alleles may become fixed in each by natural selection or genetic drift (less likely to be important)

• DMIs can help explain how hybrid dysfunction evolves

• w DMIs evolution of reproductive isolation occurs as a byproduct of selection acting on other characteristics

Haldane’s Rule

• When in the offspring of two different animal (species) it is found that one sex is absent, rare, or sterile, that sex is usually the heterozygous [heterogametic, i.e. XY or ZW] sex J.B.S. Haldane (1922)

• Consistent across 95% of taxa surveyed (from birds to mammals to Drosophila!)

what could cause Haldane’s rule?

Dominance hypothesis (most widely accepted)

Many harmful genetic incompatibilities are recessive and located on the X (or Z) chromosome.

• The heterogametic sex has only one copy of the X (or Z) chromosome.

• Because there is no second copy to mask recessive harmful alleles, these incompatibilities are fully expressed.

• This can lead to hybrid sterility or death.

faster-male evolution hypothesis

faster-X hypothesis

genetic incompatibilities

geographic context of speciation, allopatric:

• The divergence and differentiation of populations that leads to a reduction of interbreeding can occur in several geographic contexts.

• allopatric speciation is considered the predominate mode of speciation

• can be a consequence of drift alone

• due to adaptation to contrasting conditions

Example: Allopatric speciation in Hawaiian fruit flies

• Limited gene flow between islands leads to speciation

Geographic Context of Speciation (sympatric)

Reproductive isolation in sympatry due to adaptation to contrasting conditions.

• Can occur if a trait simultaneously affects adaptation and mate preference

• These traits are called “magic traits”

sympatric speciation: Lord Howe Palms

• Lord Howe Island is exceptionally small: 15 km2! More than 1/3 of the plant species occur

nowhere else in the world.

• Lord Howe Palms are wind pollinated, so unlikely they were ever microgeographically isolated. But there are ecological differences.

Outcomes of hybridization:

Hybrids are often unfit.

• Can be sterile – if this is the case there is no gene flow

• Trouble attracting mates – low to no gene flow

• Reduced survival – low to no gene flow

categories of outcomes of hybridization:

• speciation by divergence (cladogenesis) may not be hybridization?

• stable hybrid zone (admixture and introgression)

• lineage fusion (or reversal speciation)

• unidirectional introgression

• speciation by hybridization

tension zone - hybridization

balance between dispersal into contact zone and selection against hybrids

introgression - hybridization

incorporation of alleles from one species into the gene pool of a divergent species via hybridization and backcrossing

Lake Victoria became so muddy that ongoing fish hybridization was reversed

• Females had species-specific mate preferences

• Due to human activity, water became so turbid that females could not use coloration as cue anymore

• Lineages started to interbreed

lineage fusion/reversal speciation

reinforcement

• You might be thinking that given the severe cost of hybridization, there might

be a tendency to try to avoid these heterospecific pairings.

• Well, this is in fact what is thought to be occurring, and this process has a

special name, it’s called reinforcement!

• Reinforcement occurs when there is natural selection for a decreased rate of maladaptive mating.

• natural selection AGAINST maladaptive hybridization

reproductive character displacement occurs when?

species differences become more exagerated in sympatry compared to allopatry

reinforcement bird example:

- One avian system where evidence suggests this type of post-mating isolation may be important is in the Ficedula flycatchers in Europe and Asia.

- Two populations on the islands of Oland and Gotland in the Baltic sea are areas where they hybridize extensively, and long-term pedigree’s have been studied

- If reinforcement is occurring, we would expect that traits that can be used to distinguish the taxa are more different where they occur together, in sympatry

- Indeed, pied and collared flycatchers look different where they occur together than where they occur apart – pied are slightly brown, whereas collared have a much broader collar.

reproductive character displacement in snail genitalia:

in those places where they coexist, they evolved differences in genital morphology, preventing costly matings

Macroevolutionary patterns

• Emergence of new species through speciation

• Disappearance of species through extinction

Contrasts to microevolutionary patterns which

involve shifts in traits and allele frequencies

within populations/species and can occur within

a few generations

Macroevolution: Diversification

An evolutionary increase in the number of species in a clade,

usually accompanied by divergence in phenotypic characters.

Macroevolution: Speciation

• Process of evolution that leads to the formation of new, distinct species,

reproductively isolated from one another.

• See this as the splitting of lineages

Speciation Rates

• Track origination of species over time.

• Not constant - change over time.

• Often, we see a trend of decreasing speciation rates over time as species saturate the available niche space.

• Also see variation in rates among different clades.

Macroevolution: Extinction

• The dying out or extermination of a species or clade

• can be a ‘mass’ extinction or loss of a single species/lineage

anthropocene:

• increased extinction rates

• humans have always had an impact on extinction in large mammals

extinction rates

• rates of species loss over time

• can vary over time and across clades

background extinction rate:

number of species expected to go extinct over a period of time - generally a steady rate

diversification rates

diversification rates are the combined effect of speciation and extinction and measure the accumulation of species over time

diversification equation

diversification = speciation - extinction

studying diversification - lineages through time (LTT)

• even rates through time

• early burst of speciation

• late burst of speciation

variation in diversity - in time

• tree includes nearly every single species of bird on Earth

• branches are colored by diversification rate

• blue clades tend to be early burst

• red clades are mostly late burst

why diversification? - Ecological Opportunity

• Defined as: the availability of ecologically accessible resources that may be evolutionarily exploited

• Generally impossible to measure in nature!

ecological opportunity - Geographic Colonization

The colonization of an isolated area (e.g., an island or lake) can provide a release from

competition and predation pressures, allowing a clade to diversify into a variety of

ecological niches from which they were previously blocked

ecology opportunity - extinction

Lineages able to survive extinction events may be presented with access to ecological space previously occupied by members of their own clade or by other competitors

ecological opportunity - New Resources

The appearance of new resources may provide ecological opportunities for species that can utilize them.

ecological opportunity - key innovations

The evolution of a feature that allows a lineage to interact with the environment in a novel way may provide the ability to utilize formerly unavailable resources.

Key adaptations facilitating diversity—Insects

Is a trait consistently associated with increased diversity in independent

groups? “

Non-herbivorous sister groups of 13 herbivorous clades. 11 of 13 the

herbivorous clades had more species!

Key adaptations facilitating diversity—Latex

Farrel et al. (1991) in another sister species comparison, looked at sister species of plant

where groups did or did not have latex. 13 of the 16 clades with latex had higher diversity

Lack of opportunity - Competitive Displacement

Competitive displacement occurs when one species (or population) is pushed out of part of its niche because another species is a better competitor there.

Adaptive Radiation

• When a single ancestor rapidly diversifies into a variety of types that occupy different niches.

• an evolutionary increase in the number of species in a clade, usually accompanied by divergence in phenotypic characters

Two components:

• ecological diversity (via natural selection)

• many species from a single ancestor

Adaptive radiation—cichlid fishes in east Africa

• In East African lakes, cichlid fish are immensely diverse, in both foraging ecology and coloration.

• In the three rift lakes, this diversity arose extremely rapidly.

• There is also phenotypic convergence between lakes.

The pharyngeal jaw: a key innovation

Cichlids evolved a second set of “throat” jaws that help with food processing

while the “regular” oral jaws can specialize on food capture

what drives diversification in African drift lakes?

• deeper the lake the more diversity there is

non-adaptive radiations

• Non-adaptive radiations: collections of related ecologically similar species that are allopatric replacements of one another

• Example: The Achatinella land snails of Hawaii.

• Diversification of these snails is suggested to be the result of persistence in nearly identical environments among the eroded valleys and ridges of the Hawaiian Islands.

• Species are distinguished based on color and shell shape, as well as by geographic

distribution.

• High species diversity, but low ecological differentiation

• in non-adaptive radiation, species diversify without ecological differentiation

non-adaptive radiation example:

• Island populations of monarch flycatchers from

northern Melanesia

• Evolved within 1 million year

• Ecologically very similar

• No strong differences in what they eat, or where they next, or when they reproduce

Macroevolutionary patterns – Evolutionary rates

Rate of evolution of body size.

• Evolutionary change appears much faster in living species than fossils.

• Actual changes in the trait don’t appear to accumulate until there are larger time scales. This is what we call the paradox of stasis.

How can evolution be very fast over short timescales, but only lead to phenotypic

differences between lineages over very long timescales?

Evolution can occur rapidly because allele frequencies can change within a few generations, but substantial phenotypic divergence between lineages usually requires the accumulation and persistence of many genetic changes over long periods, while stabilizing selection and changing environments often limit or reverse short-term evolutionary changes.

Does speciation affect the rate of evolution?

Two competing hypotheses:

• Punctuated equilibrium: Evolutionary change is marked by isolated episodes of rapid speciation between long periods of little or no change (stasis).

• Gradualism: Evolutionary change occurs sat a steady (continuous) speed, which results in the gradual transformation of whole lineages.

• ecidence of both in fossil record - ongoing debate which is more important/common

macroevolutionary patterns

• hypothetical data

• punctuated equilibria

• phyletic gradualism

phylo - genetic

phylo = tribe or race

genetic = origin/development of

phylogenetic terminology

see pic

rooted vs. unrooted trees

• root = comon ancestor of all taxa in the tree

• rooted trees incorporate relative time

example of unrooted tree

• tree of life

• classic unrooted tree, for a long time, it was hard to infer where to root the tree, because there is no known outgroup

example of a rooted tree:

• hominin tree

where does the root come from?

outgroup: a taxon outside of the group of interest. All the members of the group of interest are more closely related to each other than they are to the outgroup. Hence, the outgroup stems from the base of the tree. an outgroup can give you a sense of where on the bigger tree of life the main group of organisms falls

dated tree - where does the node age come from?

• fossils

• carbon dating

• geological time series

• molecular clocks (which are themselves calibrated)

using the molecular clock to date a phylogeny

If two species share a common ancestor, what happens to their

DNA over time?

• Mutations occur every generation

• Most mutations are neutral

• Neutral mutations accumulate approximately steadily

through time

→ The number of DNA differences between two species

reflects how long ago they diverged

Genetic distance ≈ mutation rate × time

different groupings:

• monophyletic - includes an ancestor and all of its descendants

• paraphyletic - includes ancestor and some, but not all of its descendents

• polyphyletic - includes two convergent descendants but not their common ancestor

monophyletic group":

consists of a node and all of its descendants, aka a “clade”. Clade is also used to describe the entire group (i.e. including those not on the tree in question, and including the common ancestor)

paraphyletic group:

contains a node and some, but not all, of its descendants. Either on the tree, or more generally

• the group reptiles does not include birds although they descended from the same common ancestor

polyphyletic group:

contains some, but not all, of a node’s descendants, and that also excludes that node

• warm blooded vertebrates

• endothermy evolved separately in mammals and birds

• birds and mammals are not close relatives, latest common ancestor is not the same

why do we care about monophyly?

Monophyletic groups represent true evolutionary lineages

• all members share a single common ancestor

• It’s a natural evolutionary unit.

In contrast:

• Paraphyletic groups leave out some descendants

• Polyphyletic groups group species that do not share a recent ancestor

identifying monophyletic clades:

“Synapomorphy”: a derived character shared by all members of the group

• e.g., All animals that have vertebrae form a single, monophyletic clade.

Vertebrae are a shared, derived character, not present in their ancestors

synapomorphy vs. homoplasy

Homoplasy: a character shared by a set of species but not present in their

common ancestor.

homology

Homologous traits are traits that are shared among species because they are

inherited from a common ancestor.

The arrangement of limb bones is a synapomorphy of tetrapods (four-legged

land vertebrates)

• synaptomorphy is a subcategory of homology

homology vs. homoplasy

Homology – wings are shared among penguins and falcons due to common descent

Homoplasy – independent evolution of wings in insects and birds

how do we build phylogenies?

• Parsimony is the idea that the best phylogenetic tree is the one that requires the fewest evolutionary changes.

• We use parsimony all the time in our daily life:

• If your friend doesn't answer your text, the simplest explanation is that they're busy, not that they were abducted by aliens.

• Likewise, when reconstructing evolutionary history, we prefer the scenario that requires the fewest DNA mutations unless there is evidence otherwise.

• least amount of genetic changes will always be assumed

some biological “difficulties” in generating phylogenies:

1. Horizontal Gene Transfer

2. Hybridization/ Introgression

3. Incomplete Lineage Sorting

4. Homoplasy

5. Saturation of DNA mutations

incomplete lineage sorting:

• Occurs when looking at several species recently diverged from a common ancestor.

• Due to the sorting of variation that was present in the ancestor.

• Causes gene trees to have a different topology than the species phylogeny.

rapid speciation:

• cichlids speciated very rapidly, adaptive radiation

solution: more characters

• consider lots of traits like

• wings

• mouth structure

• antennae

• leg number

• include genes!

some genes evolve too fast!

• DNA sites can undergo substitution multiple times.

• If there are too many or too little mutations, it becomes hard to reconstruct phylogenies

Solution: Different Data Types

• Because there are more codons than amino acids, the genetic code is redundant, and most redundancy occurs at the third codon position (the ‘wobble’ position)

• The third position experiences less intense selection and therefore accumulates mutations faster

what do we use trees for?

• To graphically represent how evolution has unrolled.

• To make our organization of biodiversity rational.

• To test hypotheses about evolutionary change

• To make inferences about evolution for practical reasons.

• To help guide conservation planning.

• To help explain patterns of biodiversity!

resolving classification - to make our organization of biodiversity rational

Linnaean approach: organisms grouped by shared characteristics

Darwinian approach: shared characteristics are (usually) due to common ancestry

common ancestry provides the basis for phylogeny and classification

why were phylogenies important during COVID?

By sequencing SARS-CoV-2 genomes from infected individuals, scientists could build phylogenetic trees and use them to:

• Trace how the virus spread between regions and countries

• Identify transmission clusters and superspreader events

• Distinguish local transmission from new introductions

• Estimate how quickly the virus was evolving

• Phylogenetic trees revealed the emergence of new SARS-CoV-2

variants

• As mutations accumulated, some lineages began to diversify rapidly:

• Alpha, Delta, Omicron

• Researchers could identify these expanding branches early and ask:

• Is this variant spreading faster?

• Is it better at evading immunity?

• Is it replacing other variants?

• Phylogenetics was critican in guiding public health responses, vaccine

updates, and global surveillance.