Spring 2025 Lecture 2: General Biology - Systematics & Origin of Life PDF

Systematics and Phylogeny 1 Basic class protocol 2 Students learning in an in-person setting 3 Needed General Biology Foundations (Dr. Ortega’s Section) 4...

Systematics and Phylogeny 1 Basic class protocol 2 Students learning in an in-person setting 3 Needed General Biology Foundations (Dr. Ortega’s Section) 4 Systematics  Branch of Biology that deals with classification of organisms Biologists group (= classify) organisms based on shared characteristics (morphology, DNA, ecology, behavior) Anthrax is an acute disease caused by the bacterium Bacillus anthracis. Most forms of the disease are lethal, and it affects both humans and animals A week after the September 11, 2001, letters with anthrax bacterium endospores (dormant bacteria) were sent to newspapers and politicians 5 Seven letters are believed to have been mailed in the U.S., resulting in 22 infections; five people died. 6  DNA from mailed dormant bacteria was isolated and particular genes had their nucleotides sequenced DNA sequences for particular genes were obtained from thousands of samples worldwide This is a typical study of systematics  Largest study of systematics ever conducted After comparisons using computer programs they concluded that the mailed strain.- – Belonged to a very lethal bacterium strain (“Ames Strain”) that was used for bio-defense research purposes Bruce E. Ivins, 62, who worked for the past eighteen years at the government's bio defense labs at Fort Detrick (Maryland) was the main suspect.- – FBI was about to lay charges on him but he committed suicide 7  Evolutionary trees or phylogenies to classify organisms  Systematics 8 9  Video: Discovering the Great Tree of Life https://www.youtube.com/watch?v=mD94D0KAn2U 10  Which of these branching trees for vascular plants is true? Sunflowers Sunflowers Ferns e e m Ancestor 2 e m Ancestor 2 Ancestor 2 Ti m Ancestor 1 is Ti Ti Ancestor 1 Ancestor 1 older than Ancestor 1 Pine trees Ferns Pine trees Ancestor 2 Ferns Pine trees Sunflowers Fossil record 11  Cladistics.- The study 1. Derived characteristic (in blue font) – Similarity that is inherited from the most recent common ancestor of an entire group. of Evolutionary trees – No vascular tissue  Vascular tissue – Spores  Seeds – Sporangia  Flowers or Cones 2. Ancestral characteristic (in red font) – Similarity that arose prior to the common ancestor of the group Angiosperms We will call this the outgroup (our evolutionary reference). In this case Time Flowers Algi Ancestor 2 » No vascular tissue  Vascular tissue Seeds » Spores  Seeds Cones Ancestor 1 » Sporangia  Flowers or Cones Gymnosperms 3. In cladistics, only shared derived characters are considered informative about evolutionary relationships Vascular – They are called synapomorphies (in red font, see 1 above)  tissue Ferns Character that originated in the common ancestor Sporangia Spores that are Algi produced in sporangia No vascular tissues, nutrients move through diffusion 12 OUTGROUP Sporophylls  Transitional forms to understand ancestors… Dream and nightmare of Darwin!!! Oldest cone fossil: 130,000,000 years ago Oldest cycad fossil: 250,000,000 years ago ~250,000,000 years ago ~370,000,000 years ago Sporophylls  Cladistics.- The study 1. Derived characteristic (in blue font) – Similarity that is inherited from the most recent common ancestor of an entire group. of Evolutionary trees – No vascular tissue  Vascular tissue – Spores  Seeds – Sporangia  Flowers or Cones 2. Ancestral characteristic (in red font) – Similarity that arose prior to the common ancestor of the group Angiosperms We will call this the outgroup (our evolutionary reference). In this case Time Flowers Algi Ancestor 2 » No vascular tissue  Vascular tissue Seeds » Spores  Seeds Cones Ancestor 1 » Sporangia  Flowers or Cones Gymnosperms 3. In cladistics, only shared derived characters are considered informative about evolutionary relationships Vascular – They are called synapomorphies (in red font, see 1 above)  tissue Ferns Character that originated in the common ancestor Sporangia Spores that are Algi produced in sporangia No vascular tissues, nutrients move through diffusion 16 OUTGROUP  The outgroup (in this case, the lamprey) does not possess any of the derived characters 17  18 In any cladistic analyses the first step is to “polarize” the characters.- Equal to determine if the characters are ancestral or derived in each ancestor. Using the outgroup as a reference For instance polarize “jaws” means to determine presence (derived) or absence of jaws in the most recent common ancestor.- In this tree.- Presence of jaws (derived state  synapomorphy) is in the common ancestor of fish, amphibians, and mammals  This branching tree is know as Cladogram. It depicts a hypothesis of evolutionary relationships 19  20 Gorilla and Human are called sister species as they: PAIR that Share the same direct common ancestor The “Gorilla-Human” clade (= Primates) is sister to the Carnivores (Tiger) because they: Share the same common ancestor Cladograms are compose of clades Clades.- Group of species that share a direct common ancestor as indicated by the possession of shared derived characters The Human – Gorilla clade (defined by the synapomorphy “Tail loss”) The Tiger – Gorilla – Human clade (defined by the synapomorphy presence of hair)  Cladogram – Depicts a hypothesis of evolutionary relationships Clade – Species that share a common ancestor as indicated by the possession of shared derived characters – Evolutionary units and refer to a common ancestor and all descendants – Defined by synapomorphies – derived characters shared by clade members 21  Homoplasy – a shared character state that has not been inherited from a the same direct common ancestor. There are two kinds of homoplasy 1) Convergent evolution Whales and Penguins share flippers as limbs But whales (mammals!!) and Penguins (birds!!!) do not share the same direct common ancestor They share this trait (synapomorphy for cetaceans and pinguins) because evolutionary convergence to be able to swim 22 Flippers: Synapomorphy of penguins (modified limb to swim) Flippers: Synapomorphy of whales (modified limb to swim)  Homoplasy – Two kinds of homoplasy 2) Evolutionary reversal Snakes and lampreys do not have limbs But lampreys (THE OUTGROUP  Only ancestral characters!!) Snakes and do not share the same direct common ancestor Absence of limbs is an evolutionary reversal in snakes that shows adaptation to crawl  – Still absence of limbs is a synapomorphy that defines snakes!!! 24 Lamprey No Limbs: Synapomorphy of (outgroup)  No snakes in the evolution of reptiles limbs: Ancestral Reptiles character Limbs 25  3 Tropical genera (36 species) – Rafflesia, Rhizanthes, Sapria Rafflesiaceae – SE Asia – Philippines – Indonesia – Malaysia All of them are holoparasites Unisexual flowers All of them parasite members of Tetrastigma (Vitaceae (grape family)  Tropical lianas) Rafflesia (28 species): Rhizanthes (4 species) & parasites on stems Sapria: parasites on roots  Euphorbia (3 mm) Synapomorphy = Synapomorphies Increase in vascular vessel size = Increase in flower size = Parasitism Synapomorphy = Large deletion of 50 nucleotides in Ribosomal Gene Euphorbiaceae Rafflesiaceae Peraceae = Outgroup: Outgroup Small flower size Pera (1 mm) Photosynthesis Davis, C. et al. (2007). Floral gigantism in Rafflesiaceae. Science, 315(5820), 1812-1812. http://www.people.fas.harvard.edu/~ccdavis/pdfs/Davis_et_al_Science_2007.pdf 29 Which is the real cladogram? Cladistics and Parsimony Principle The principle of parsimony, which favors the hypothesis that requires the fewest assumptions will this question What do we mean by the fewest assumptions? 30  Which is the real cladogram? You sail to a very remote and isolated island to rescue a person whose boat was wrecked When you arrive to the island you find the skeleton of a human and a tiger Which is the most obvious explanation? Fewest assumptions 1. The tiger attacked the person you tried to rescue explanations 2. Another person arrived to the island before you and killed the person you tried to rescue because he/she wanted to steal his money 3. This skeleton belongs to another person and somehow the person you tried to rescue was able to make a raft and to escape from the island 31  Salamander Frog Lizard Tiger Gorilla Human Salamander Lizard T iger Frog Gorilla Human Amphibians 32 Apes Hair loss Amniotic membrane loss Hair Tail loss Amniotic Hair membrane Amniotic Tail loss membrane a. b. Two possible cladograms for amphibians, reptiles, and mammals (terrestrial vertebrates) Based on the principle of parsimony, the cladogram that requires the fewest number of evolutionary changes or synapomorhies or steps is favored; in this case.- The cladogram in (a) requires four evolutionary changes or four steps The cladogram in (b) requires five evolutionary changes or five steps Therefore, fewer assumptions in cladogram (a) and we favor this one  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Salamander Frog Lizard Tiger Gorilla Human Salamander Lizard T iger Frog Gorilla Human Hair loss Amniotic membrane loss Hair Tail loss Amniotic Hair membrane Amniotic Tail loss membrane a. b. These cladograms have insights regarding.- Convergent evolution Evolutionary reversal 33  Which of these branching trees (cladograms) for apes is true? Fossil Record Homo sapiens 300,000 years ago from Morocco  Exam question e m Genus Homo Genus Homo Genus Homo Genus Pan e e Ti m m Ti Ti (chimps) 500,000 years ago – Kenya Genus Gorilla (gorillas) 8,000.000 years ago from Ethiopia 34 Which of these branching trees (cladograms) for apes is true? e m Genus Homo Genus Homo Genus Homo e e Ti m m Ti Ti Fossil record, DNA (Parsimony Principle) support this tree When Parsimony Analyses is based on morphology & anatomy Gorilla is sister to the clade Chimps + Homo  Systematics and Classification Classification – How we place species and higher groups into the taxonomic hierarchy – Genus, family, class, etc. Monophyletic group Paraphyletic group Polyphyletic group 36  Archosaurs Giraffe Bat Turtle Crocodile Stegosaurus Tyrannosaurus Velociraptor Hawk a. Monophyletic Group * Monophyletic group Includes direct ancestor of each of its members and the most recent common direct ancestor (*) of the group and all of its descendants Archosaurs form a monophyletic group 37  Dinosaurs Giraffe Bat Turtle Crocodile Stegosaurus Tyrannosaurus Velociraptor Hawk Paraphyletic Group * b. Paraphyletic group Includes the direct ancesror of all of its members and the most recent common direct ancestor of the group, but not all its descendants Dinosaurs as a group traditionally defined does not include one of the descendants (birds) of the common ancestor (*) 38  Flying Vertebrates 39 Giraffe Bat Turtle Crocodile Stegosaurus Tyrannosaurus Velociraptor Hawk * * Polyphyletic Group c. Polyphyletic group Does not include the most recent and direct common ancestor of all members of the group. When they are put together as a group, this group does not share a single direct ancestor. There are many other ancestor = between these two type of animals when they are treated as a single group The group of flying vertebrates does not include a single direct common ancestor fo  40 Synapomorphies and Classification of Organisms In the 1750s, Carolus Linnaeus instituted the use of two-part names, or binomials within a hierarchical system – Apis mellifera the European honeybee – Genus name capitalize and specific epithet name is not capitalized, all in italics Synapomorphies provide a new perspective to the Linnean classification system 41 The six species of the genus The six species of the Felis and its synapomorphies genus Felis: All share the same genus (Felis) Each species has a Felis chaus. From southern China different specific in the east through Southeast and Central Asia to the Nile Valley epithet – chaus Felis silvestris. Widespread in the Old World – margarita Felis margarita. Deserts of northern Africa and – sylvestris southwest and central Asia – nigripens – bieti – catus Each species has Felis nigripes. South synapomorphies that Africa, Namibia, and Felis bieti. Western China Felis catus. Domestic cat Botswana define them  Taxonomy is the science of classifying living things (example with genus Felis) – A classification level is called a taxon (plural taxa) – There is a category hierarchy with several levels. Each level has unique traits (synapomorphies!!! In red or purple below) to differentiate them… Example with “margarita” cat.- Class.- Mammalia (It has 26 orders). Mammary glands and hairs Order.- Carnivora (It has 8 families). Presence of carnassial teeth Family.- Felidae (It has 13 genera). Skull with short rostrum and facial area and short inflated braincase Genus.- Felis (It has six species). Small felines, cannot roar because unique structure of the throat https://www.yout Species.- margarita. Large ear pinnae and reduced weight and ube.com/watch? size v=XrRxPxzp0YQ 42 14: 43  Phylogenetics and Comparative Biology Basis for all comparative biology Homologous structures – Derived from the same ancestral source – Dolphin flipper and bird wings are modifications of limbs  Different function but same basic structure (source  bones of limbs that are modified for different fucntion) Homoplastic or analogous structures sources – Derive from different ancestral – Lungs of vertebrates vs lungs of land-snails Vertebrates: Modification of swim-bladder Land-snail: Modification of mantle tissue Two different sources swim-bladder vs mantle tissue 43 Origin of Life  Deep Time MYA = Million years ago 1) Geologic time is divided into four eons – Hadean (from Hades = Hell).- 4,500 MYA – 4,000 MYA – Archean (from Arkhē = Origin, ancient).- 4,000 MYA – 2,500 MYA – Proterozoic (from Proteros = Earlier + Zoōs = Life).- 2,500 MYA – 600 MYA – Phanerozoic (Phaneros = Visible, evident + Zoōs = Life).- 600 MYA – Present 2) The Earth formed as a hot mass of molten rock about 4.5 billion of years ago – As it cooled, chemically-rich oceans were formed from water condensation 3) Life originated approximately 3.5 billion of years ago in the Archean 45  Land snails do not form a monophyletic group There were at least10 independent Eons Eras Periods Present Appearance of humans Quaternary colonization events of land-snails from aquatic Cenozoic First primate Tertiary Bird radiation 50 MYA Mammal radiation Pollinating insects environments that included the independent development Cretaceous 100 MYA Diversification of flowering plants of “lungs” as a synapomorphy in land-snails First flowering plants, birds, Mesozoic 150 MYA after the marsupial Jurassic mammals First dinosaurs First terrestrial colonization happened 200 MYA Phanerozoic Triassic 250 MYA First gymnosperms Cambrian Explosion  Permian 4- Land snails. Invertebrates. Gastropoda Cambrian Explosion took place: ~500 million years ago 300 MYA First reptiles Carboniferous 350 MYA Cambrian Explosion was in aquatic environments. It has: Paleozoic First amphibians 3.- TERRESTRIAL Devonian vertebrates 400 MYA Bony fish, tetrapods, seed plants, and insects appear 2.- TERRESTRIAL First Chordates and primitive vertebrates Silurian 450 MYA Early vascular plants diversify by arthropoda All major invertebrate groups Ordovician Invertebrates dominate First land plants - 1.- TERRESTRIAL Cambrian 500 MYA Cambrian explosion; increase in diversity Appearance of animals and plants Late 0° First multicellular organisms Proterozoic 1000 MYA 30° Middle Oldest definite fossils of In aquatic 1500 MYA eukaryotes Early 2000 MYA Appearance of oxygen in atmosphere Cyanobacteria environments 2500 MYA Middle Late Archean 3000 MYA 3500 MYA Early Oldest fossils of prokaryotes Molten-hot surface of Earth becomes somewhat cooler 4000 MYA Oldest rocks Hadean 4500 MYA Formation of Earth 46 Cambrian fauna 47 Spiders. No Millipedes and known very Centipedes Arthropods are ancient There are invertebrates marine marine fossils fossils from Cambrian that possess an exoskeleton Land colonization, all at of all Arthropoda around the same time (invertebrates)  Aquatic 400,000,000 years ago  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 40 Atmospheric oxygen 30 Origin of level (%) Cyanobacteria First 20 (~3.7 BYA) multicellular organisms (0.6 BYA) 200 Oxygen mostly in the First land 10 MY lag oceans but also some in atmosphere plants (0.47 BYA) 3.0 2.0 1.0 0 Cambrian Time (BYA) Explosion (0.5 BYA) Atmospheric O2 levels over time 49  Biological origin for atmospheric oxygen 50 Oxygenic photosynthesis produced atmospheric O2 O2 is an atmospheric gas of organic origin (21%). Second most important gas O2 was not present in the very early atmosphere One big mystery is the 200-million-year lag between the origins of photosynthesis (cyanobacteria) and substantial levels of atmospheric O2. Explanation.- – O2 reacted with iron to form iron oxide in the oceans – Once O2 started to accumulate it paved the way for multicellularity (aerobic respirations produces much more ATPs.- 38 ATPs vs 2 ATPs per glucose molecule in anaerobic respiration) & Photosynthetic multicellular organisms also produced much more O2 per surface area where they live Extremely important development.- O2 in the atmosphere interacted with ultraviolet (UV) radiation from the Sun and formed O3 (ozone) – Critical to have life in the planet as it reduces the mutation rate caused UV light  Ever-Changing Life on Earth Life evolved into three monophyletic domains or clades 1) Eubacteria 2) Archaea 3) Eukaryotes Six supergroups identified within the eukaryotes 51  Prokaryotes Eukaryotes Chromalveolates Archaeplastida Amoebozoa Opisthokonta Eubacteria Excavata Archaea Rhizaria Six supergroups have been identified within the Eukaryote domain, one of three domains of life on Earth 52  Purple Rickettsia Gamma protobacteria sulfur Origin of Mitochondria type bacteria bacteria Prokaryotes Eukaryotes Alpha protobacteria Chromalveolates Archaeplastida Amoebozoa Opisthokonta Eubacteria Excavata Archaea Rhizaria Two critical Endosymbiosis and the origin of eukaryotes  Mitochondria and Chloroplasts A type of symbiosis in which one organism lives inside the other, the two typically behaving as a single organism 1.Mitochondria are the descendants of relatives of a “hybrid” microorganism involving 2 prokaryotes and one Eukaryote 1. PROKARYOTE: Purple sulfur bacteria (do not use water as electron donor (but hydrogen, sulfide, iron compounds) in photosynthesis, they release other compounds instead of O2)  Produce sugars through Calvin Cycle (see coming lecture on photosynthesis). Purple nonsulfur bacteria can be aerobic or anaerobic  PHOTOSYNTHESIS (Make sugar) 2. PROKARYOTE: The parasite bacteria Rickettsia (Gram-negative, Typhus and other human diseases) o Origin of mitochondria as a cell compartment. Rickettsia use Oxygen as the agent to oxidize sugars to produce ATP (AEROBIC RESPIRATION)  They have Krebs Cycle  They oxidize sugar o This Rickettsia bacteria becomes the mitochondria. Mitochondria have DNA inside and its nucleotide sequence is very similar to that of Rickettsia. But the vast majority involved in mitochondria respiration are found in the nucleus  Originally were in mitochondria  (1) was engulfed by (2) (MITOCHONDRIA HAVE TWO MEMBRANES)  (1) produced sugars that were oxidized by (2) through aerobic respiration  (1) + (2) later engulfed by a primitive EUKARYOTE cell (nucleus with membrane) 54  55 2. Chloroplasts & Endosymbiosis Algae acquired chloroplasts twice  Origin of the three known kinds of Algae Brown alga (1)Red Algae and Green Algae common ancestor.- an EUKARYOTIC cell that engulfed a cyanobacteria (PROKARYOTE) = Sugar factory  This cyanobacteria becomes the initial chloroplast Eukaryotic cell (1) Chloroplasts have DNA inside and their nucleotide sequences is engulfs red alga very similar to that of cyanobacteria. Most genes coding photosynthesis are inside the chloroplast genome (2) Chloroplasts have two membranes [outside Eukaryote, inside Prokaryote (cyanobacteria)] o Inner membrane from the cyanobacteria o Outer membrane from eukaryote when cyanobacteris was Red alga Green alga engulfed by the eukaryote (2)Brown algae  An Eukaryotic cell that engulfed a red alga Cyanobacteria (1) Chloroplasts have four membranes from outside to inside: Eukaryote  Eukaryote  Eukaryote  Prokaryote (cyanobacteria) Eukaryotic cell with mitochondria engulfs cyanobacteria  Primitive (Cyanobacteria) Eukaryote (Purple sulfur bacteria + bacteria belonging to Rickettsia group) The origin of mitochondria and chloroplasts Mitochondria and chloroplasts likely evolved from engulfed prokaryotes that once lived as independent organisms. At some point, a primitive eukaryotic cell engulfed the aerobic prokaryote, which then formed an endosymbiotic relationship with the host eukaryote, gradually developing into a mitochondrion. Eukaryotic cells containing mitochondria then engulfed photosynthetic prokaryotes, which evolved to become specialized chloroplast organelles Both mitochiondria and chloroplasts have inside DNA