BIOS 317 - Evolution - Spring 2025 Lecture 28 question and answer

Flashcards for reviewing lecture notes on Systematics and Speciation.

What is long-branch attraction?

Long-branch taxa are grouped together due to independently derived shared characters.

What does phylogenetically uninformative mean?

Positions in a sequence alignment that do not provide useful phylogenetic information because all most parsimonious trees are equally parsimonious.

How can a time dimension be provided to calibrate a molecular clock?

Fossils or geological events.

Is there a reliable "molecular clock"?

Generally unlikely except over short time spans; mutation rates evolve and vary by site.

How can rates of molecular evolution be tested without fossils?

By comparing the amounts of change between an outgroup and two ingroup taxa with a common ancestor.

What is the difference between categories and taxa in systematics?

Categories are kingdom, phylum, class, order, family, genus, species; taxa are things like Metazoa, Chordata, Mammalia, Carnivora, Felidae.

Why are species the category that makes the most sense biologically?

Individuals of a species recognize themselves as such.

What is the biological species concept?

A population or group of populations whose members have the potential to interbreed with one another in nature to produce fertile offspring.

What are other species concepts besides the biological species concept?

Phylogenetic Species Concept and Morphological Species Concept.

How does speciation usually begin?

Some kind of physical isolation.

How do the patterns produced by vicariance and dispersal differ?

Dispersal: Gradient of species relatedness. Vicariance: Pairwise pattern of species relatedness.

How can genetic mechanisms initiate speciation?

Mutations can reduce fertility in hybrids and chromosomal rearrangements.

What is long-branch attraction in systematics?

Grouping long-branch taxa together because they have independently derived shared characters.

Which animal group is argued to be the sister group to all other animals, a question potentially affected by long-branch attraction?

Sponges or Ctenophores.

What methods have generally superseded parsimony as phylogenetic criteria?

Maximum likelihood and Bayesian methods.

In the example given, which base pair position provides the most useful phylogenetic information?

bp 2

How can time dimensions be provided in phylogenetic studies?

By fossils or geological events.

What does it mean to calibrate a "molecular clock"?

That mutation rate has an ordinal (in the same order) and interval (intervals on mutation scale same as on time scale) relationship to chronological time.

Is a molecular clock generally reliable?

Generally unlikely except over short time spans, and the clock at one bp position is not going to be the same as that of another bp position.

What are the two things that make the molecular clock unreliable?

Site variable and rate variable.

What is the formula for testing the molecular clock using the "relative rate test"?

D1:O - D2:O = A:D1 - A:D2

Name some traditional taxa that are paraphyletic.

Prokaryotes, protists, reptiles.

What typically results in paraphyly?

Defining a taxon on the basis of a shared primitive character.

With dichotomously branching phylogenies, what is the limitation on categories?

They can only meaningfully have two taxa in them.

What kind of analyses that should be used over category based analyses?

Evolutionary analyses should be tree-based, not category-based.

What is considered a fundamental problem in biology regarding speciation?

The formation of new species.

What "somethingness" applies to the biological unit of species?

Individuals of a species recognize themselves as such.

In what behavior in particular is the lion's species knowledge apparent?

Sex/reproduction.

What is the Biological Species Concept (BSC)?

Species is a population or group of populations whose members have the potential to interbreed with one another in nature to produce fertile offspring.

To what kind of organisms does the biological species concept apply?

The BSC only applies to eukaryotes.

How has the biological species concept been made easier to operationalize?

Molecular markers have made a huge difference.

How do we define a virus as the "same species"?

Assessment is based on genetic distance and conventions for naming viruses.

What is the Phylogenetic Species Concept?

Species are the smallest recognizable monophyletic group of populations.

What kind of data is used to identify species in the phylogenetic species concept?

Phylogenies are used to identify species.

What is the Morphological Species Concept or "Morphospecies Concept"?

A species is recognized on the basis of morphology.

What is a similarity between all species definitions?

Species are evolutionarily independent.

What does the biological species concept focus on, which might then lead to morphological and diagnosable phylogenetic differences?

Reproductive isolation.

What is the method used to analyze phyplankton Pseudonitzchia?

Analysis of morphological ultrastructure, phylogeny based on rbcL gene, and mating experiments yields similar picture of diversity.

What is a strength of the biological species concept?

Focuses on "somethingness" that organisms themselves recognize.

According to the the biological species concept, species formation is what?

The same as the formation of reproductive barriers.

What are the mechanisms of isolation/cohesion; these are the same thing?

Physical isolation, genetic isolation.

What are the two forms of physical speciation?

Dispersal and vicariance.

How does dispersal occur in Hawaiian Drosophila?

Volcanic hot spot makes chain of islands as the Pacific plate drifts over it.

What is the result of dispersal in Hawaiian Drosophila?

Gradient of species relatedness.

How is vicariance show in Panamanian shrimp?

Species from opposite sides of the Isthmus of Panama (Pacific vs Caribbean) are sister taxa.

What is the result of vicariance?

Pairwise pattern of species relatedness.

Which kind of mutations are primarily important in speciation?

Large-scale changes in chromosomes (polyploidization).

Why small chromosomal rearrangements may be important in yeast speciation?

They interfere with meiosis.

What kind of compatibility may also be important in speciation?

Compatibility between nuclear and mitochondrial genomes.

What is convergent evolution?

Independent evolution of similar traits in different lineages due to similar environmental pressures.

What is a homologous trait?

A shared trait inherited from a common ancestor.

What is phylogenetics?

The study of the evolutionary relationships among organisms.

What is a phylogenetic tree?

A branching diagram that represents the evolutionary relationships among a group of organisms.

What is speciation?

The process by which new species arise.

What is adaptive radiation?

The diversification of a group of organisms into new forms, often filling different ecological niches.

What is allopatric speciation?

The geographic separation of a population, which can lead to speciation.

What is sympatric speciation?

Speciation that occurs in the same geographic area.

What is a species?

A group of interbreeding populations that is reproductively isolated from other groups.

What is natural selection?

The process by which organisms better adapted to their environment tend to survive and reproduce more successfully.

What is evolution?

The change in the genetic makeup of a population over time.

What is a gene pool?

The sum total of alleles in a population.

What is genetic diversity?

A measure of the genetic variation in a population.

What is phylogeny?

The evolutionary history of a group of organisms.

What is a synapomorphy?

A character that is shared by two or more taxa because it originated in their common ancestor.

What is homoplasy?

A character that is similar in two or more taxa but that evolved independently in each lineage.

What is parsimony?

The principle that the simplest explanation is the most likely.

What is maximum likelihood?

A method of phylogenetic inference that uses statistical models to estimate the most likely tree given the data.

What is Bayesian inference?

A method of phylogenetic inference that uses Bayesian statistics to estimate the probability of a tree given the data.

What is a clade?

A group of organisms that includes an ancestor and all of its descendants.

What is a paraphyletic group?

A group of organisms that includes an ancestor but not all of its descendants.

What is a polyphyletic group?

A group of organisms that does not include their common ancestor.

What is a vestigial trait?

A character that is present in the ancestor of a group but has been lost or modified in some of its descendants.

What is convergent evolution?

The process by which different species evolve similar traits because they occupy similar ecological niches.

What is parallel evolution?

The evolution of similar traits in closely related species because they inherit the same developmental pathways.

What is divergent evolution?

The evolution of different traits in closely related species as they adapt to different ecological niches.

What is biogeography?

The study of the geographic distribution of organisms.

What is molecular phylogenetics?

The use of molecular data to infer evolutionary relationships.

What is a gene tree?

A diagram that shows the evolutionary relationships among a group of genes or proteins.

What is a species tree?

A diagram that shows the evolutionary relationships among a group of species.

What is horizontal gene transfer?

The transfer of genetic material between organisms that are not directly related.

What is fossil calibration?

The use of fossils to calibrate the rate of molecular evolution.

What is evolutionary developmental biology?

The study of the evolution of development.

What is a developmental gene?

A gene that plays a key role in development.

What is a mutation?

A change in the nucleotide sequence of DNA.

What is recombination?

The process by which new combinations of genes are created.

What is gene flow?

The movement of genes from one population to another.

What is genetic drift?

A change in the allele frequencies in a population due to chance events.

What is founder effect?

A type of genetic drift that occurs when a small number of individuals colonize a new area.

What is bottleneck effect?

A type of genetic drift that occurs when a population is drastically reduced in size.

What is sexual selection?

A form of natural selection in which individuals with certain inherited characteristics are more likely to obtain mates.

What is adaptation?

A form of natural selection in which individuals with certain inherited characteristics are more likely to survive and reproduce in a particular environment.

What is an adaptive trait?

A trait that increases an organism's fitness.

What is fitness?

The ability of an organism to survive and reproduce in its environment.

What is macroevolution?

The process by which new species arise.

What is microevolution?

Evolutionary change within a species or population.

What is punctuated equilibrium?

A pattern of evolution in which long periods of stasis are interrupted by brief periods of rapid change.

What is gradualism?

A pattern of evolution in which gradual change occurs over long periods of time.

What is ecology?

The study of the interactions between organisms and their environment.

What is a population?

A group of individuals of the same species that live in the same area.

What is a community?

A group of interacting populations of different species.