Descent with Modification

Descent with Modification

• Darwinian evolution comprises natural selection and descent with modification
• Natural selection results in organisms with advantageous traits surviving and reproducing more successfully
• Descent with modification leads to species changing over generations as traits are passed down and modified
• Five lines of evidence support descent from a common ancestor:
• Fossil record shows transitional forms and changes over time
• Comparative anatomy (homology) reveals similar structures in different species due to shared ancestry
• Embryology indicates early developmental similarities suggest a common origin
• Genetic evidence shows DNA similarities indicate evolutionary relationships
• Biogeography indicates geographic distribution of species supports common descent
• Homologous structures provide evidence supporting fossil records, embryological similarities, genetic evidence, and geographical distribution
• A fossil is a preserved remain, impression, or trace of ancient life typically found in sedimentary rocks
• Strata are layers of sedimentary rock
• Older fossils are found in deeper strata, aiding in the dating of evolutionary events
• Origination is the process by which a new species evolves
• Extinction is the complete disappearance of a species from Earth
• The shared genetic code (DNA, RNA, and protein synthesis mechanisms) of all life points to a common ancestral origin
• Life is organized in nested groups

Hierarchical Organization of Life

• Domain is the broadest category, followed by kingdom, phylum, class, order, family, genus, and species
• A hierarchical organization means species fit into nested groups, displaying a clear evolutionary pattern in trait distribution
• Organisms from a shared geographic area are closely related due to a recent common ancestor that has adapted to that region
• Vestigial structures are reduced or non-functional structures inherited from ancestors

Natural Selection

• Fitness is an organism's ability to survive and reproduce in its environment
• Genes code for traits
• Traits are characteristics shaped by genes that affect survival/reproduction
• Phenotype refers to observable traits influenced by genes and the environment
• Survival and reproduction are greater with higher fitness
• Adaptation is a heritable trait that enhances an organism's fitness in a specific environment and increases survival and reproductive success
• Natural selection requires:
• Variation, where individuals in a population differ in traits
• Heritability, where traits are genetically passed down
• Differential reproduction, where advantageous traits lead to increased reproduction
• Acclimation is a temporary physiological change in response to the environment, while adaptation is a permanent genetic change over generations in response to natural selection

Adaptations and Species

• Adaptations evolve due to environmental pressures, with traits beneficial in one environment becoming harmful in another
• Mutations introduce genetic variation, creating new traits acted on by natural selection
• The biological species concept defines a species as a group of organisms capable of interbreeding and producing viable, fertile offspring
• Allopatric speciation involves:
• Geographic isolation separating a population
• Different selection pressures pushing evolutionary changes
• Reproductive isolation eventually preventing interbreeding
• Pre-zygotic reproductive isolation happens before fertilization:
• Temporal isolation: mating at different times
• Behavioral isolation: different mating behaviors
• Mechanical isolation: incompatible reproductive structures
• Gametic isolation: sperm and egg fail to fuse
• Post-zygotic reproductive isolation happens after fertilization:
• Hybrid inviability: offspring won’t develop properly
• Hybrid sterility: offspring are sterile
• Hybrid breakdown: hybrid offspring are weak or infertile
• Adaptive radiation is the rapid diversification of a lineage into varied species adapted to different environments
• Traits that raise reproductive success, such as mate preference or competition, evolve through sexual selection
• Evolutionary trade-offs are traits enhancing fitness but also have downsides

Phylogeny and Tree Thinking

• A phylogenetic tree shows proposed relationships among species based on shared ancestry, revised with new data
• Phylogenetic trees depict common ancestry and divergence
• Linnaean hierarchy organizes species into nested taxonomic ranks and both methods classify by evolutionary relationships
• Yes, with phylogenetic trees, it can differ from a Linnean hierarchy because Linnaean classifications were originally based on morphology, which can be misleading
• Not all Linnean groupings are monophyletic, for example, reptiles including birds, are paraphyletic
• Nodes on a phylogeny show the most recent common ancestor of descendant species
• Branching points show speciation events as lineages split in two
• Speciation is linked to the biological species concept as it occurs when reproductive isolation evolves, preventing gene flow
• Homology indicates similar traits due to shared ancestry
• Analogy indicates similar traits due to convergent evolution, not common ancestry
• Homoplasy describes traits that appear similar but evolved independently, potentially through convergence
• Homologous traits infer evolutionary relationships
• Parsimony states the simplest explanation via the fewest evolutionary changes is more likely correct

Phylogenetic Tree Interpretation

• Find the most recent common ancestor (MRCA) at the node where taxa share a branch
• Taxa that share a more recent MRCA are more closely related
• The outgroup/basal taxon is the earliest diverging lineage on a tree
• Recognize monophyletic, paraphyletic, and polyphyletic groups:
• Monophyletic group: ancestor and all its descendants
• Paraphyletic group: ancestor but not all descendants
• Polyphyletic group: members from different ancestors
• Polytomies indicate unresolved branches or uncertain evolutionary relationships
• Evolutionary events shown by tick marks describe tip or node characteristics, such as feather, fur, or limb quantity
• Convergent evolution indicates different lineages that independently develop similar traits

Phylogenies and Data

• Determine which trees show the same evolutionary relationships
• Map evolutionary events (trait changes) using tick marks
• Find the most parsimonious tree by mapping evolutionary events
• The most parsimonious tree shows the fewest evolutionary changes
• Phylogenetic trees should use many characters to avoid misleading signals from convergent evolution and improve accuracy with independent data points
• Mutation rates provide a timeline and fossil ages which estimates absolute time to calibrate a molecular clock
• Molecular clocks assume mutation rates are constant and fossil records accurately reflect divergence times
• Varying mutation rates can skew divergence estimates, while missing fossils lead to branch length miscalculation

Bacteria and Bacterial Diversity

• Domain Archaea is more closely related to Domain Eukarya than to Domain Bacteria based on genetic and evolutionary evidence
• Domain Bacteria is the outgroup as it diverged first from the common ancestor of all life
• RNA was likely the genetic material in early organisms
• The RNA world hypothesis states RNA could store genetic information and catalyze reactions before DNA and proteins evolved
• Prokaryotes use energy and carbon from:
• Phototrophs use light energy
• Chemotrophs use chemical energy from inorganic or organic molecules
• Autotrophs use CO2 as carbon
• Heterotrophs obtain carbon from organic molecules
• Photosynthesis possibly evolved in bacteria ~2.5-3.5 billion years ago
• The evolution of photosynthesis changed atmospheric composition
• This led to the great oxygenation event (GOE)

Bacterial Genetic Transfer, Protists

• The great oxygenation event accumulated oxygen allowing the evolution of aerobic life
• The great oxygenation event also caused mass extinction of anaerobic organisms
• Conjugation is direct genetic transfer (plasmid) via pili for antibiotic resistance spread
• Transformation is uptake of naked DNA for genetic diversity. Genetic diversity is important for a species to survive and reproduce.
• Transduction is virus (bacteriophage) transfer of bacterial DNA for species gene transfer
• Domain Eukarya includes the eukaryotes

Protist Diversity

• Eukaryotes include protists, plants, fungi and animals
• They have cells with a nucleus and membrane-bound organelles
• Protists are eukaryotic
• Eukaryotic cells evolved from prokaryotic ancestors
• This is according to the endosymbiotic theory via complex, energy-efficient eukaryotic cells
• Mitochondria originated as engulfed ancestral aerobic bacterium
• Chloroplasts came from engulfed ancestral photosynthetic cyanobacterium
• Instead, they are nested within the eukaryotic tree
• No, plants, animals and fungi are not a sister taxon, but are paraphyletic and more closely related to various protists, plants, animals, and fungi
• Animals and fungi are closest relatives, plants are separate
• Multicellularity independently evolved multiple times in six eukaryote lines

Fungi Diversity

• Ascomycota is sac fungi for yeast, molds, and morels and spores in asci
• Basidiomycota is club fungi for mushrooms, puffballs, and shelf fungi and spores in basidia
• Fungi are animals than plants because all fungi and animals belong and share a opsithokonta clade
• A distinct common ancestor does exist
• Fungi is absorptive heterotrophic decomposers that secrete to digest and absorb nutrients
• Hyphae are fungal filaments that increase nutrient absorption surface
• Networks forms that infiltrates food
• Fungi reproduce asexually (spores, budding, fragmentation) and sexually with hyphae fusion from other individuals
• Plasmogamy is cytoplasm fusion into heterokaryotic/dikaryotic cells
• Karyogamy is nuclei fusion into diploid zygotes
• Fungi are important to ecosystems as decomposers, symbionts, and pathogens
• Fungi also aid in food production via fermentation
• Lichen is symbiosis between the ascomycota fungi, algae, or cyanobacteria
• Mycorrhizae is mutualism that aids plant roots for nutrient absorption

Animal Diversity

• Kingdom Animalia are multicellular and heterotrophic and lack cells walls. Metazoa include all animals including sponges. Eumetazoa are all animals besides sponges with true tissues
• Bilaterians have bilateralism, symmetry and three germ layers
• Deuterostomes have mouth derived from the blastopore. Includes chordates and echinoderms
• Chordates feature the nerve cord for pharyngeal slits and tail
• Vertebrates have backs for chordates
• Aminotes are verebrates and have a aminotic egg for reproduction from water (reptiles, birds, and mammals)
• Mammals have milk and hair
• Monotromes include egg laying platypus, echidna
• Marsupials are mammals and have early developed kangaroos, koalas
• Eutherians includes mammala that develop placenta with gestation that includes humans, dogs ,and whales
• Primates include placental with hands, eyes, and brains that includes monkeys, apes, and humans
• bony fish and lobe-finned fish are included
• Lobe finned fish is for the ancestor in the amphibiams and tetrapods
• Amphibians are vertebrates
• Notochord came first in chordates with vertebrae that appeared in vertebrates with the jaws in gnathostomes
• Lobe0finned fishes came first that had precursors for limbs
• Limbs with digits came in tetrapods amphibians, mammals and birds in amniotes that can reproduce on land
• Chordates have notochord and the dorsal hollow nerve cord
• Amphibians include moist skin and metamorphosis for cold blood in environments and eggs

Amniotes and Photosynthesis

• Amniotes are successful for eggs, less water loss
• Internal fertilization for survival
• Birds are theropod dinosaurs and closest relative for archosauria
• Diversity change over time and many animals
• Only homosapiens for evolution with support and transport that changed the carbon cycle
• Products of light reactions
• Sunlight, water, nadp, and adp
• Calvin Cycle has c02 as atmosphere
• G3p is sugar that is a part of reactions
• Tylakoid allows membrane

Cellular Respiration

• Photosystem I and etc facilitate movement.
• There is a separation between etc and stromna
• Glucose is photosynthesis
• There is cellular respiration because there are components that is the basis of the cycles for life
• Water splitting at the photosystem chain of h cycles
• H uses thylakoid ATP
• Carbon fixation is to inorganic, occurring in the stroma while fixing to rubp

Plant Anatomy

• Roots anchors and shoots transport with leaves that exchange nutrients
• Tissues aid what the function with 3 terms
• Dermis protects with vascular
• Parenchyma has photosynthesis
• Selctive Endoderma barriers regulated through the vascular
• Strip contains water regulation

Osmotic Pressure

• Water has a osmotic that allows the membrane
• Bulk flows the xylem
• Targid maintains
• Water transports pressure is the transpitation for plants
• cohesion transports it
• Pathways move that move cells
• Preforatiom allows movement
• Pholem has controled
• Pholiem transport in the cell with dead tissue
• Turgid swell gaurd open
• Meristems allow for stems