Speciation and Species Concepts

• Speciation is a splitting event that creates two or more distinct species from an ancestral one.

Morphological Species Concept

• Species are identified by differences in morphological features like size and shape.
• It is widely applicable, including to asexual species.
• Problems include the fact that similar-looking organisms may not be closely related (cryptic species).
• It misidentifies polymorphic species that look different but are the same species.
• The process is subjective due to emphasis on similarity or differences (lumpers vs. splitters).

Biological Species Concept

• The concept is based on reproductive isolation and evolutionary independence.
• Two populations that don't breed in nature and produce viable, fertile offspring are considered two species.
• There are two types of isolation barriers: prezygotic and postzygotic.
• Prezygotic isolation prevents mating, and occurs before fertilization.
• Postzygotic isolation results in hybrid offspring that do not survive or reproduce, and occurs after fertilization.
• Temporal isolation occurs when breeding happens at different times.
• Habitat isolation occurs when breeding happens in different habitats.
• Behavioral isolation involves different courtship behaviors.
• Gametic isolation happens when egg and sperm are incompatible.
• Mechanical isolation affects when reproductive structures are incompatible.
• Hybrid viability issues involves offspring not developing normally, resulting in high mortality.
• Hybrid sterility involves offspring that can’t reproduce.
• Reproductive isolation cannot be evaluated in fossils.
• This concept can be hard to apply to populations that don't geographically overlap.

Phylogenetic Species Concept

• Monophyletic groups include an ancestral population and all of its descendants.
• Synapomorphy is a unique trait to a monophyletic group, shared and derived.
• Phylogenetic species are the smallest monophyletic groups.
• The concept is widely applicable and based on testable criteria.
• Limitations are that phylogenies are not well-estimated for all groups, and fossils.

Reproductive Isolation

• Prezygotic isolation prevents mating between species.
• Postzygotic isolation results in hybrid offspring that do not survive or reproduce.
• Reproductive isolation involves geographic isolation, divergence, and genetic isolation.
• Evolutionary history informs the sequence of speciation events and relatedness between species.
• Species sharing a recent common ancestor are more closely related in a phylogenetic tree.

Allopatric Speciation

• Speciation occurs through geographic separation.
• Gene flow is affected by barriers.

Sympatric Speciation

• Speciation occurs in the same geographic area.
• Gene flow is prevented via disruptive selection and polyploidization.

Reading Phylogenetic Trees

• Taxonomy is a formal system for naming and classifying species.
• Systematics is the classification and study of organisms with regard to their natural relationships.
• Cladograms include a root, a node, clades, and an outgroup.
• Monophyly includes complete groups.
• Paraphyly includes incomplete groups.
• Polyphyletic groups include organisms arising from multiple ancestral sources.

Building Phylogenetic Trees

• Important terms are homology, analogy/homoplasy, synapomorphy, and pleisomorphy.
• Synapomorphy is a trait unique to the group and its MRCA.
• Plesiomorphy is a trait possessed by taxa outside of the group, before MRCA.
• Homology and homoplasy are explanations for why two taxa have a similar trait.
• Common ancestry vs. convergent evolution are explanations for the above.
• Convergent evolution is the independent evolution of similar traits in distantly related organisms due to adaptation to similar environments and lifestyles.
• Parsimony says the simplest explanation is the most likely one.
• The simplest explanation involves the least number of changes.

Phylogenies Identifying Evolutionary Relationships

• Traits of species (morphological and/or molecular) are compared to infer relationships.
• Phylogenies are visualized as phylogenetic trees.
• They identify evolutionary relationships by depicting how species diverged from a common ancestor.
• Closer branches indicate more recent shared ancestry.
• Longer branches signify greater evolutionary distance between species.

History of Life

• Fossils form when an organism dies and is covered by sediment or volcanic ash.
• Water infiltrates the remains.
• Metal ions and minerals replace organic parts.
• Sediments accumulate and increase pressure, turning the remains to stone.
• The Punctuated Equilibrium hypothesis states that evolution primarily occurs in short bursts of rapid change, punctuated by long periods of relative stability.
• Adaptive radiation is a form of punctuated equilibrium after a mass extinction event.
• Mass extinction events allow remaining species to diversify rapidly due to niches being opened.
• Colonization events to new locations with new resources allow for rapid diversification.
• Evolutionary innovations that increase fitness also allow for rapid diversification.
• Major transitions happen during speciation.
• Fossils are physical evidence from organisms that lived in the past.
• Fossils help scientists track major changes over time, and allow for testing evolutionary hypotheses when paired with an understanding of geology and geography.
• There are patterns of speciation over time that are gradual, include punctuated equilibrium, and adaptive radiation.
• Major mass extinctions include the Permian extinction and cretaceous extinction.

General Characteristics of Prokaryotic Life

• Prokaryotes are unicellular organisms that don't have a nucleus.
• They are found almost everywhere: an average person is composed of more bacteria than human cells.

Prokaryotic Cell Structure

• The cytoplasm includes all the contents of a cell, excluding the nucleus (in eukaryotes).
• The cytosol is the fluid in the cytoplasm.
• Chromosomes are single and circular.
• Nucleoids are regions of cells where chromosomes are located.
• Plasmids are small DNA structures in addition to that found in the chromosome.
• Ribosomes are made of RNA and proteins, and are sites for manufacturing proteins.
• The small subunit reads RNA, and the large subunit joins amino acids.
• Other internal structures include photosynthetic membranes, cytoskeleton, and support proteins for shape.
• The cell membrane consists of a phospholipid bilayer and proteins + cholesterol.

Bacteria vs. Archaea

• Archaea contain isoprenoids in plasma.
• Bacteria contain phospholipids in plasma membrane.
• Archaea contain pseudomurein in the cell wall.
• Bacteria contain peptidoglycan (murein) in the cell wall.
• Archaea have larger ribosomes (68 proteins).
• Bacteria have smaller ribosomes (58 proteins).
• Archaea have RNA polymerase with 13 subunits.
• Bacteria have RNA polymerase with five subunits.
• Archaea have DNA with histone proteins associated like Eukaryotes.
• Bacteria do not have histones.
• Translation starts with methionine like Eukaryotes in archaea.
• Translation starts with formyl methionine membrane in bacteria.
• DNA replication and transcription are more like Eukaryotes in archaea.
• The evolutionary relationship among archaea, bacteria, and eukarya show they are the three main domains of life, sharing a common ancestor but diverging early in in Earth's history.
• DNA exchange in bacteria primarily occurs through transformation, conjugation, and transduction.

Microbial Life

• Microfossils of stromatolites are the earliest known fossils, dated at 3.45 billion years old, and come from Western Australia, providing evidence of microbial life 3 billion years ago.
• Functional diversity of prokaryotic life is largely based on metabolic diversity.
• Metabolism involves chemical reactions within the cell that convert molecules and transfer energy in living organisms.
• The two basic needs: Building blocks (Carbon) and Energy (Adenosine Triphosphate (ATP)).
• Early classification systems for prokaryotes relied on observable morphological and metabolic characteristics of bacteria.
• Molecular approaches involve the comparison of amino acid sequences, amino acids and DNA, and gene and rRNA sequencing.
• Prokaryotic life exhibits a wide range of morphologies, categorized by cell shape (cocci, bacilli, spirilla), arranged in groups or complex biofilm structures.

Extremophiles

• Extremophiles can thrive in temperatures from -20°C - 121°C, and a pH of 1.
• Hyperthermophiles thrive in extremely high temperatures.
• Psychrophiles thrive in extremely low temperatures.
• Halophiles thrive in high-salt conditions.
• Properties that facilitate rapid evolution are high rate of mutation, high rate of reproduction, and high rate of DNA exchange.
• Evolutionary concepts explain rapid drug resistance exhibited by prokaryotes Viruses.

Viruses

• The genome is made of DNA or RNA and includes a capsid (protein coat).
• An envelope may be present that is a lipid membrane derived from the host cell.
• All life is susceptible to viruses.
• Host range is narrow vs broad.
• Viruses reproduce in different ways once inside the host cell.
• Lysis involves highjacking the machinery to replicate, transcribe, and translate, which bursts the cell to release more virus.
• Lysogenic viruses integrate their genome with that of the host and release new virion's without destroying the cell.
• Relatively high mutation rates depend on mode of replication, and vary among viruses.
• Viruses are classified based on different shapes, the Baltimore system, and type of nucleic acids and modes of replication.