Week 12 Speciation, Taxonomy, Systematics

Allopatric Speciation

Allopatric speciation

Speciation by geographic isolation

• first proposed by a paleontologist studying fossil record of mammals

• gene flow between the soon-to-be species must be greatly reduced — but it doesn’t have to be reduced completely to zero.

Sympatric speciation

The evolution of a new species from a surviving ancestral species while both continue to inhabit the same geographic region. 

• occurs when members of a species that are within the same range diverge into two or more different species even though there are no physical barriers stopping them from breeding

  • there are no geographic barriers preventing gene flow 

• Can occur due to polyploidy, hybrid speciation, adaptation to local environments, and sexual selection.

Polyploidy

The heritable condition of possessing more than two complete sets of chromosome (more than two paired sets of (homologous) chromosomes) 

• Common in plants, as well as among certain groups of fish and amphibians.

• How does it occur: One mechanism is complete nondisjunction of chromosomes, which increases the number of chromosome sets in a given species (autopolyploidy).

Biogeography

The scientific study of the distribution of living organisms across different regions of the Earth and the factors influencing that distribution over time.

Biological species concept

If organisms can interbreed and produce viable, fertile offspring they are members of the same species

• Members of populations that actually or potentially interbreed in nature

Advantages: once lineages can’t interbreed, then species are independent

not arbitrary based on evolutionary processes

Disadvantages: doesn’t work for extinct species, doesn’t work for some groups

Morphological species concept

Classifies organisms into species based on their morphology

Advantages:

• No knowledge of genetics is necessary

• Equally applicable to sexual, asexual, and fossil species

Disadvantages:

• A single polymorphic species may be split into two species

• cannot identify cryptic species that differ in non-morphological traits 

subjective

Phylogenetic species concept

The smallest monophyletic group on the tree of life

A monophyletic group (clade, lineage) consists of an ancestral population plus all of its descendants.

Advantages:

• identifies entities with distinct evolutionary histories

Disadvantages:

• phylogenies not always available, hard to resolve

• probably lead to recognition of many more species than other major species concepts (advantage? disadvantage?)

Ex: Lineage C is a single species, according to the phylogenetic species concept. 

Monophyletic group

Sometimes called a clade, includes an ancestral taxon and all of its descendants. A monophyletic group can be separated from the root with a single cut,

Founder effect

The loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population.

• thought to lead to the speciation and subsequent evolution of new species.

Hox genes

The genetics of major morphological change

Ex: conserved functions from flies to mammals

Ancestral character state

The character state present in a lineage immediately before a character state change.

binomial nomenclature

the system of nomenclature in which two terms are used to denote a species of living organism, the first one indicating the genus and the second the specific epithet.

Character

A recognizable feature of an organism. Characters may be morphological, behavioral, physiological, or molecular. They are used to reconstruct phylogenies.

Character state

defined as discrete or discontinuous features used in phylogenetic analysis, representing distinct conditions of a character, such as variations in molecular or morphological traits.

Prezygotic

Barriers to mating

• Habitat

• Temporal

• Behavioral

• Mechanical

Reproductive Isolation

Reproductive Isolation: Gametic isolation

mating occurs, but fertilization does not

Reproductive Isolation: Postzygotic

Happens when hybrids of two species encounter issues in surviving or reproducing

Hybrid inviability

Hybrid sterility

Hybrid breakdown

Reproductive Isolation

The mechanisms of reproductive isolation are a collection of evolutionary mechanisms, behaviors and physiological processes critical for speciation. They prevent members of different species from producing offspring, or ensure that any offspring are sterile.

phylogenetic tree

(cladogram, tree of life, or evolutionary tree)

graphical representation resembling a tree that illustrates the evolutionary and phylogenetic relationships between biological taxa based on their physical or genetic characteristics

phylogeny

study of the evolutionary history of life using observable characteristics of organisms, which is known as phylogenetic inference.

Parsimony

The principle that the simplest explanation that can explain the data is to be preferred.

Ex: Hypothesis 1 is better due to having 6 evolutionary changes, compared to hypothesis 2 where there is 7 evolutionary changes

Systematics

Taxon (taxa-plural)

represents a level of grouping of organisms that is based on some easily observable characteristics

A phylogenetic tree is an illustration depicting the hypothesized degrees of evolutionary relationship amongst a selected set of taxa (singular = taxon)

taxonomy

the science of naming, describing and classifying organisms

Clade

A clade (also known as a monophyletic group) is a group of organisms that includes a single ancestor and all of its descendents.

Monophyly taxon

groups consisting of all the descendants of one (hypothetical) common ancestor

keeps descending from one common ancestor

outgroup

an outgroup is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup

homology

biological features including genes and their products that are descended from a feature present in a common ancestor.

1. Which of the following can cause postzygotic reproductive isolation (mark all that are correct)?

A) Temporal isolation

C. Behavioral isolation 

B) Gametic isolation

D. None, these are all prezygotic 

D) None, these are all prezygotic 

• Temporal isolation – prezygotic

• Behavioral isolation – prezygotic

• Gametic isolation – prezygotic

Sympatric speciation differs from allopatric speciation because in sympatric speciation

1. a population becomes geographically isolated

2. there are no geographic barriers preventing gene flow 

3. two populations of the same species merge to form a single population

4. hybrids are inviable

2. here are no geographic barriers preventing gene flow

For a sexually reproducing species to split into two species, which of the following is necessary:

1. two populations must live in very different habitats 

2. gene flow between two populations must be limited 

3. the populations must experience very strong selection that favors different phenotypes 

4. populations must start to diverge phenotypically 

2. gene flow between two populations must be limited 

Hybrid breakdown occurs when offspring produced by mating between species (interspecific hybrids) 

1. do not develop past the early embryonic stages

2. have shortened life spans

3. are infertile

4. are fertile but produce offspring with reduced viability and fertility

4) are fertile but produce offspring with reduced viability and fertility

“Hybrid breakdown occurs when the first-generation (F1) hybrids of two different species are viable and fertile, but subsequent generations (F2 and beyond) are inviable or sterile.”

Which best describes the concept of punctuated equilibrium:

1. the rate of evolution is constant, interspersed with short periods of no phenotypic evolution 

2. long periods of little phenotypic change are interrupted by short periods of major phenotypic change

3. evolution occurs gradually over time

4. small genetic changes accumulate, producing phenotypic change and speciation

long periods of little phenotypic change are interrupted by short periods of major phenotypic change

Which of the following would most directly  lead to ecological speciation in birds

1. Genetic drift that results in different alleles fixing in different populations 

2. Habitat fragmentation that prevents gene flow among populations 

3. Adaptation to seed characteristics affects characteristics of bird song 

4. Gene flow between partially isolated populations 

A clade is a:

1. paraphyletic group C.  monophyletic group 

2. polyphyletic group D.  none of the above 

 

C.  monophyletic group

Polyploidy can promote speciation because:

1. triploids are infertile (or at least have very very low fertility) 

2. triploids are not viable 

3. ploidy level affects cell size 

4. polyploids have higher mutation rates than diploids 

5. all of the above

 

Which statement represents the best explanation for the observation that nuclear DNA sequences from wolves and domestic dogs are highly similar? Dogs and wolves _____.

1. have very similar morphologies 

2. share a very recent common ancestor 

3. belong to the same Order 

4. have converged to have similar morphologies and behavior and therefore the genes responsible for these traits must be similar 

 

The ___________________ states that most of the genetic variation found in populations is not subject to natural selection:

1. principle of parsimony 

2. neutral theory 

3. maximum likelihood principle 

2. neutral theory of molecular evolution

that most of the genetic variation found in populations, particularly at the molecular level (DNA sequences), is selectively neutral, meaning it is not subject to natural selection. These neutral mutations are instead primarily governed by random genetic drift, with selection playing a minor role in their frequency changes within a population. 

Which of the following is true (mark all that are correct)?

1. animals and fungi are more closely related to one another than plants and fungi 

2. plants and fungi are more closely related to one another than plants and animals 

3. plants and animals are more closely related to one another than fungi and animals 

4. plants, fungi, and animals are all equally related to one another 

1. animals and fungi are more closely related to one another than plants and fungi 

   1. The last common ancestor of fungi and animals was a protist (a single-celled eukaryote) that lived about 1 to 1.5 billion years ago. This ancestor was the precursor to both the fungi and animal lineages. 

Hox genes (mark all that are correct)

1. are a direct cause of reproductive isolation 

2. are the genetic basis of color vision 

3. play an important role in animal development 

4. play an important role in plant development

3. play an important role in animal development 

Ultrametric tree:

Tips equidistant from the root

Not ultrametric:

More informative

Branch lengths proportional

to differences from root

Which of the following processes contribute to the evolutionary divergence of populations? 

A.  Allopatry B. Sympatry

C. Hybridization D. Selection

E. Gene flow F.  Genetic drift

G. Mutation H. Pleiotropy

A.  Allopatry: geographic isolation reduces gene flow → divergence

B. Sympatry: divergence can also occur without physical separation

C. Hybridization: can introduce new combinations of alleles → divergence

D. Selection: different selective pressures cause divergence

F.  Genetic drift: random changes cause populations to diverge

G. Mutation: provides new genetic variation leading to divergence

Paraphyly

True or False, these phenlogy trees are the same

True: Look at the species and then trace the nearest related species and see if it matches across all trees

4.  Suppose benthic (B) and limnetic (L) forms were sampled from each of four lakes 

• Benthic forms: B1, B2, B3, B4

• Limnetic forms: L1, L2, L3, L4

where 1, 2, 3 & 4 refer to the lakes.

Draw on your team's whiteboard what you think the phylogenetic tree for these 8 populations would look like if:

A. the benthic form had evolved only one time.

B. the benthic form had evolved in each lake independently

Neutral traits

DNA sequence data:  intergenic sites, introns, synonymous sites

4 states:  A   T   G   C

These are used for molecular DNA to trace species

Some challenges

same state due to independent mutations  (homoplasy)

reversals  A 🡪 T 🡪 A

mutations overwrite history

Build a tree from these data

Species

1: GGACTTCGGCGAATACT

2: AGACTCCGGAGCATACT

5: AGCGCCGACCGAAAACT

OUT: ATCGTCCATCTATTTTA

Speciation

Divergence of genetic composition of lineages

Ex: In the picture once the gene flow stops the populations diverge from one another

• (Aka once populations diverge gene flow ends)

Sympatric

• Genetic polymorphism leads to gene flow stopping, thus creating speciation as they can no longer mate with each other

Ex: Hawthorne vs Apple maggot fly

how does selection contribute to speciation?

• Its not able to pass on it’s genes to the next generation

Speciation → Hybridization

1. Large Cactus Finch got blown over to another island and mated with the only medium brown finches that lived on that island

2. Hybrids would only mate with each other

Happened very rapidly

Sympatric speciation by polyploidy

Polyploidy – results from an error in meiosis or mitosis 

that doubles chromosome number

• Triploids offspring lead to their offspring being sertile

• Quick way to lead to speciation