Theme 1: Topics 1-4

PHYLOGENY AND EVOLUTION

To-do:

• read

• notes/flashcards

• understand

• memorize

• quizzes

PRE CONCEPTS FOR THEME 1:

• Bio 30 Unit C - Classical Genetics

Important Concepts:

• Evolution

• The Linnaean System of Nomenclature

• Phylogenic trees

Topic 1: What is Biological Diversity? (Ch. 56. 1330-1336)

1. The three main components of biodiversity

The three main components of biodiversity are genetic diversity, species diversity, and ecosystem diversity. Biodiversity is the variety of all living things and their interactions. Genetic diversity is the variety of genes within a species. so the range of genetic material. Species diversity is the number and variety of species that live in a specific area, along with how many individuals of each species there are. A species is a population of organisms that can produce fertile offspring. A population is a group of individuals of the same species that live in the same area and interbreed, producing fertile offspring. Ecosystem diversity is the variety of ecosystems in a given area,, including the different habitats, communities, and processes that exist within them. An ecosystem is a community of organisms and their physical environment interacting together.

2. The ecosystem services that biodiversity provides

Biodiversity enables ecosystems that provide services such as provisioning services, regulating services, supporting services, and cultural services. Ecosystem services are the direct and indirect benefits that ecosystems provide humans. Provisioning services include any kind of benefit to people that can be extracted from nature such as fruits, vegetables, fish, livestock, water, fuel, gas, oil, and plants. Regulating services include benefits provided from ecosystem processes— such as pollination, water filtration done by plants, and more— that moderate natural phenomena and make life possible for people. Cultural services are non-material benefits that are provided by ecosystems that contribute to the development and cultural advancement of people such as the building of knowledge, the spreading of ideas, and the growth of creativity and recreation. Supporting services are processes that allow the Earth to sustain basic life forms, such as photosynthesis, nutrient cycling, and the water cycle.

3. The difference between extinction and extirpation

The difference between extinction and extirpation is that extinction is when a species no longer exists anywhere on the Earth and has no chance of returning. Extirpation is when a species no longer exists in a specific area but can still be found elsewhere.

4. The four major threats to biodiversity

Most species loss is traced to four major threats: habitat loss, invasive species, overexploitation, and global climate change.

Topic 2: The Scientific Method (Ch. 1 11-12, Ch. 26 586-597)

1. The difference between scientific theories and hypotheses

Evolution is the unifying theory that accounts for biodiversity, is is consistent beyond reasonable doubt. A hypothesis is an assumption made before any research has been done and is formed so that it can be tested to see if it might be true. A theory is a principle formed to explaining things already shown in data and is supported by evidence.

2. The steps in the scientific method

The steps in the scientific method are: 1. Making observations by collecting qualitative and quantitative data, 2. The use of inductive reasoning to make generalizations, 3. The forming of hypotheses, and 4. Testing hypotheses.

3. The difference between inductive reasoning and deductive reasoning

An example of inductive reasoning would be observing several instances of a phenomenon and generalizing a theory from them, whereas deductive reasoning involves starting with a theory and using it to make predictions or draw conclusions in specific cases. This is because inductive reasoning starts with what is specific and works to what is general while deductive reasoning starts with what is general and works to the specific. An example deductive argument that is both valid and sound is "All dogs are animals, Rover is a dog, therefore Rover is an animal." One example of an inductive argument would be reasoning that orange cats are friendly based on one's personal experience with orange cats.

Topic 3: Taxonomy (Ch. 1 11-12, Ch. 26 586-597)

1. Binomial nomenclature and hierarchical classification

The system that is used to classify organisms is the Linnaean System of Nomenclature, and it uses Latin as the universal language for scientific names. Hierarchical classification of species into increasingly broad categories or ranks is based on on the similarity of structures, functions, and other features. Hierarchical classification major taxonomic ranks, from broad to narrow, include: Domain, Kingdom, Phylum. Class, Order, Family, Genus, and Species. The broadest level f classification in which all organisms are classified into are three domains: Domain Bacteria, Domain Archaea, and Domain Eukarya. Domain Eukarya includes eukaryotes, protists, and the three kingdoms of multicellular organisms: Plantae, Fungi, and Animalia. Binomial nomenclature is the unique two-part scientific name for a species, which includes just the genus and species, like so: Genus species. It is not equivalent to the common name of the organism, common names can be confusing and misleading, so make sure to always use binomial nomenclature in it’s proper way.

2. The limitations of hierarchical classification

The limits of hierarchical classification are many. Higher-level taxa are not directly comparable across different lineages. Hierarchical classification also does not provide information about evolutionary relationships

Topic 4: Systematics and Phylogeny (Ch. 26 586-597)

1. Phylogenic trees

Systematics, is the theory and practice of classifying organisms based on evolutionary history (phylogeny). So phylogeny is evolutionary history of relationships. Phylogenies show hypotheses for evolutionary relationships between organisms (taxa). Phylogenies are inferred from morphological and molecular data.

Phylogenetic tree depict clades, a clade is a group of taxa that includes an ancestor and all its descendants. Clades form nested hierarchies hierarchies.

The branching pattern of a phylogenetic tree indicates relatedness, and they show evolutionary relationships, not evolutionary progress. A polytomy is a branch from which more than two groups emerge. which typically represent unresolved patterns of divergence.

2. The steps of building a phylogenetic tree

When it comes to building a phylogenetic tree one must remember that the characteristics/traits used to infer evolutionary relationships (phylogeny) must have evolved through shared ancestry. It is also important to remember the difference between homology and analogy. Homology is similarity between organisms due to shared ancestry (shared evolutionary origin). Homologous traits that are similar because they descended from a common ancestor. Analogy is the similarity between organisms due to convergent evolution. Analogous traits do not provide information about shared evolutionary history.

Using cladistic methods and derived characters you can build a phylogenetic tree in this manner:

• First, select taxa to be included in the analysis: compare ingroup and outgroup

• Then, identify the homologous traits (characters) that are shared among the taxa, and group taxa by shared derived characters

• Afterwards, using algorithmic methods to find the most likely evolutionary tree (maximum parsimony selects the tree with the fewest evolutionary changes (simplest explanation), minimizing the number of trait changes).

• Finally, construct the phylogenetic tree by grouping the taxa into nested clades based on shared derived characters

3. Linking classification and systematics

Hierarchical classifications are being continuously updated to align with phylogeny.

4. Cladistic concepts

Cladistics is a method used to infer evolutionary relationships using homologous characters that group taxa based on shared derived characters. Cladistic concepts include understanding the difference between Monophyletic, Paraphyletic, and Polyphyletic groups. It also includes understanding the difference between shared derived characters (synapomorphy) and shared ancestral characters (symplesiomorphy)

home:

• print phylogenic tree worksheet

• do topics 4 quizzes

Technical information needed to complete the assignment: 

• The attached image below is Castula strelkowi (originally published by first author William Bourland (last name: Bourland) in 2024 in the journal Protist, 

• The specimen measures 47 EPU under the 40X magnification lens,

• The image in the paper (when printed) is 75 mm when measured across the same axis as the ocular micrometer EPU.