Phylogeny and Classification

What are phylogenies? How are they constructed and read?

Phylogenies are diagrams that depict the evolutionary relationships among various biological species based on similarities and differences in their physical or genetic characteristics. They are constructed using data from morphological traits, genetic sequences, and other types of characters. Phylogenies are read by tracing the branches from the root to the tips, which represent the evolutionary pathways.

Which types of characters are used in constructing phylogenies and why?

Characters used include morphological traits, genetic sequences, and biochemical markers. These characters are used because they provide evidence of shared ancestry and evolutionary changes

What are monophyletic, paraphyletic, and polyphyletic groupings?

• Monophyletic groups include all descendants of a common ancestor.

• Paraphyletic groups include some but not all descendants of a common ancestor.

• Polyphyletic groups include species from different ancestors.

What is the Linnean classification scheme? How do we currently organize (or classify) organisms using this method?

The Linnean classification scheme organizes organisms into hierarchical categories: Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species. This method uses morphological and genetic data to classify organisms

What are the defining features of the prokaryotes?

Prokaryotes lack a nucleus and membrane-bound organelles. They have a single circular chromosome and reproduce by binary fission.

What characteristics unite the bacteria and archaea?

Both have similar cellular structures, lack a nucleus, and reproduce asexually. They have unique ribosomal RNA sequences and membrane lipid structures.

What characteristics allow you to differentiate between them?

Bacteria have peptidoglycan in their cell walls, while archaea have distinct membrane lipids and lack peptidoglycan.

What characteristics indicate that bacteria and archaea are distinctly different domains?

Differences in cell wall composition, membrane lipids, and genetic sequences.

What is an extremeophile?

• Extremophiles are organisms that thrive in extreme environments, such as high temperature, acidity, or salinity.

Know the phylogenetic relationships among the three domains of life (and, know what those three domains are).

The three domains are Bacteria, Archaea, and Eukarya. Bacteria and Archaea are prokaryotic, while Eukarya includes all eukaryotic organisms

What are the major cell-surface structures in prokaryotes and what are their functions?

Structures include the cell wall (provides shape and protection), capsule (protects against desiccation), pili (attachment), and flagella (movement).

What is the internal organization and DNA of prokaryotes like?

• Prokaryotes have a single circular chromosome located in the nucleoid region, plasmids, and ribosomes.

What leads to rapid evolution in prokaryotes? Explain the processes of transformation, transduction, conjugation. How can they lead to genetic variation?

• Rapid evolution is driven by high mutation rates and horizontal gene transfer.

  • Transformation: uptake of DNA from the environment.

  • Transduction: transfer of DNA by bacteriophages.

  • Conjugation: transfer of DNA through direct contact between cells.

Review the diverse mechanisms by which prokaryotes can obtain energy and carbon, undergo cellular respiration (metabolism), and metabolize nitrogen.

Prokaryotes can be photoautotrophs, chemoautotrophs, photoheterotrophs, or chemoheterotrophs. They use various pathways for cellular respiration and nitrogen fixation.

What are the defining features of eukaryotes?

Eukaryotes have a nucleus, membrane-bound organelles, and a cytoskeleton.

What traits are similar between archaea and eukarya

Similarities include certain genetic sequences and metabolic pathways.

What is endosymbiosis as it pertains to the eukaryotic cell?

Endosymbiosis is the process by which eukaryotic cells acquired organelles like mitochondria and chloroplasts through the engulfment of prokaryotic cells.

What groups have participated in this process/been formed as a result of this process?

Groups include plants, animals, fungi, and various protists

Distinguish between primary and secondary endosymbiosis. Be able to give examples

• Primary endosymbiosis: engulfment of a prokaryote by a eukaryote (e.g., mitochondria).

• Secondary endosymbiosis: engulfment of a eukaryotic cell by another eukaryote (e.g., chloroplasts in algae).

Where are plants, animals and fungi found within the proposed Eukaryotic supergroups?

• Plants are in the Archaeplastida, animals and fungi are in the Opisthokonta.

What are the origins of land plants?

Land plants originated from green algae.

How do plants differ from their algal ancestors (derived traits)?

Derived traits include multicellular embryos, apical meristems, and adaptations for terrestrial life

What benefits and problems did plants experience when they moved onto land?

• Benefits: access to sunlight and CO2. Problems: desiccation and structural support.

What characteristics allowed plants to be successful on land?

Characteristics include cuticles, stomata, vascular tissues, and reproductive adaptations

What is alternation of generations (details of stages and ploidy)?

• Alternation of generations involves a haploid gametophyte stage and a diploid sporophyte stage.

How does the relative importance of the two stages differ among the major groups of plants?

Nonvascular plants have dominant gametophytes, while seed plants have dominant sporophytes

How do nonvascular, seedless vascular, and seed plants differ from one another

• Nonvascular plants lack vascular tissues, seedless vascular plants have vascular tissues but no seeds, and seed plants have seeds.

What key characteristics allow you to differentiate between the groups?

Presence of vascular tissues, seeds, and reproductive structures.

What are the ecological and economic importance of the major groups of plants?

Plants provide oxygen, food, medicine, and materials.

What key characters unite the fungi?

• Fungi have chitin in their cell walls, hyphae, and reproduce via spores.

What are mycorrhizae? Why are they important?

• Mycorrhizae are symbiotic associations between fungi and plant roots, important for nutrient exchange.

Review the general life cycle of fungi.

• Fungi undergo plasmogamy (fusion of cytoplasm), karyogamy (fusion of nuclei), and produce spores.

What are plasmogamy and karyogamy? What is the heterokaryotic stage? Why are these processes important?

• Plasmogamy and karyogamy are stages in fungal reproduction. The heterokaryotic stage involves cells with two different nuclei, important for genetic diversity.

Why are fungi thought to be so important ecologically and economically?

Fungi decompose organic matter, form symbiotic relationships, and have medical and industrial applications

What characters suggest that fungi and animals are closely related taxa?

Similarities in genetic sequences and metabolic pathways.

What features unite the animals? Consider early development as well as nutrition.

Animals are multicellular, heterotrophic, and undergo specific developmental stages

Review the evolutionary history of animals

Animals evolved from single-celled ancestors, with major diversification during the Cambrian Explosion

What is the Cambrian Explosion, and why is it thought to be important for the evolution of animals

• The Cambrian Explosion was a period of rapid diversification of animal life, leading to the emergence of most major animal phyla.

What is the importance of body plan symmetry, tissues, and body cavities in animal development?

• Symmetry, tissues, and body cavities are important for organization and function in animals.

What features define protostomes and deuterostomes?

• Protostomes develop the mouth first, while deuterostomes develop the anus first.

What are the major trends in the evolution of animals?

• Trends include increased complexity, specialization, and diversification.

What are features and evolutionary history of invertebrates in general and representative phyla (e.g., Phylum Mollusca) and lower-level taxonomic groups (e.g., Crustaceans)?

• Invertebrates have diverse body plans and life histories. Mollusca includes snails and octopuses, while Crustaceans include crabs and lobsters.

Consider how sponges differ from eumetazoans, and how the three major groups (Deuterostomia, Ecdysozoa, and Lophotrochozoa) differ.

• Sponges: Lack true tissues and organs, have a simple body plan with pores and channels.

• Eumetazoans: Have true tissues and organs, more complex body plans.

• Deuterostomia: Includes echinoderms and chordates, characterized by deuterostome development (anus forms first).

• Ecdysozoa: Includes arthropods and nematodes, characterized by molting (ecdysis).

• Lophotrochozoa: Includes mollusks and annelids, characterized by lophophore feeding structures or trochophore larvae.

What are the key characteristics that define the chordates?

Chordates: Have a notochord, dorsal hollow nerve cord, pharyngeal slits, and post-anal tail at some stage of development

What are the key characteristics that define the vertebrates?

• Vertebrates: Have a backbone or spinal column, a more complex nervous system, and an endoskeleton.

What features allow you to differentiate between the major vertebrate groups?

• Fish: Aquatic, gills, fins.

• Amphibians: Dual life (aquatic larvae, terrestrial adults), moist skin.

• Reptiles: Dry, scaly skin, lay eggs on land.

• Birds: Feathers, beaks, lay eggs, endothermic.

• Mammals: Hair, mammary glands, endothermic

What are the major trends in vertebrate evolution?

Trends include the development of jaws, limbs, amniotic eggs, and adaptations to various environments.