BIO 140: Fossils, Biogeography, and Phylogeny (2024-2025) PDF

BIO 140: Fossils, Biogeography, and Phylogeny 1st Semester, 2024-2025 FOSSILS METHODS OF FOSSILIZATION Preserved remnants or impressions left by PRESERVATION WITHOUT ALTERATION organisms that lived in the past...

BIO 140: Fossils, Biogeography, and Phylogeny 1st Semester, 2024-2025 FOSSILS METHODS OF FOSSILIZATION Preserved remnants or impressions left by PRESERVATION WITHOUT ALTERATION organisms that lived in the past By dehydration E.g. Animal remains in extremely dry conditions (as in deserts) and Fossil Record in caves Ordered array in which fossils appear within By burial in Organic – bone, cartilage, chitin layers or strata of sedimentary rocks sediments ~ (exoskeleton) ~250.000 described fossil species - ~1% of species hard parts Inorganic – tricalcium phosphate, that lived in the past calcium carbonate (corals and mollusks), silica (sponges, TYPES OF FOSSILS diatoms, protozoans) Through Imprisonment in ice BODY FOSSILS mummification Preservation in amber Direct remains of the organism Preservation in acid bog Preservation in tar pit Bones and Teeth Common in vertebrates Shells and Common in invertebrates PRESERVATION WITH ALTERATION exoskeleton Leaves and wood Plant fossils including petrified Petrifaction Organic parts hardened to stone wood (organic material has Includes permineralization and been replaced with minerals) replacement Hair, skin, and Rare; delicate Carbonization Hard parts become carbonized or a feathers film of carbon is left as impression Preserved Amber fossils – e.g. insect in Formation of Mold – imprint of external or organisms tree resin replicas internal form of the skeleton or Fossil in glacial ice caps – e.g. body part (negative imprint) frozen mammoths Cast – replica of organism formed Exceptionally preserved fossils when skeletal or body parts are – have soft tissue present dissolved and the mold is filled with sediments (needs a mold; positive imprint kasi naka-emboss) TRACE FOSSILS Trace fossils – tracks, burrows, Indirect evidence of an organism’s presence and coprolites behavior FORMATION OF FOSSILS Footprints Impressions by animals (did they and tracks walk or crawl?) 1. Sand and silt are carried by rivers to seas and Burrows and Holes or tunnels in sediments or swamps borings wood (do they live in soil?) 2. Deposits pile up to compress other sediments Coprolites Fossilized feces below into rock Gastroliths Stones swallowed by animals, often 3. When organisms die, they settle along with the polished smooth inside the sediments; a tiny fraction preserved as fossils gastrointestinal system then 4. Over time, additional strata are added, containing fossilized fossils from each time period 5. As sea levels change and the seafloor is pushed upward, sedimentary rocks are exposed MJ KAGAOAN | 1 BIO 140: Fossils, Biogeography, and Phylogeny 1st Semester, 2024-2025 6. Erosion by rivers reveals strata; older strata Though incomplete, fossil records would still show: contain older fossils (madidiscover na ng 1. Gradual change paleontologists) - Over millions f years - Ex. Rib number in Trilobites Notes: 2. Rapid change Oldest fossils would be those at the bottom of the - Over thousands of years strata - Ex. Changes in dorsal spines of the stickleback Erosion reveals the strata fish (Gasterosteus sp.) Only forms on sedimentary rocks 3. Punctuated equilibria - A pattern in which a species exhibits a little or IMPORTANCE OF THE FOSSIL RECORD no detectable phenotypic change over long period of time but is interrupted by rapid 1. Provides evidence about the major outlines of shifts from one equilibrium state (stasis) to evolution another 2. Provides evidence about the appearance of - Ex. Evolution of a lineage of ectoprocts or extinct organisms moss animals 3. Provides means of making deductions about the - Based on morphology ancestors of living organisms - Only applicable within species 4. Provides an actual record of organisms that once lived, of where and when they lived, and the environment which they lived METHODS OF DATING FOSSILS 5. Enable one to trace lines of evolutionary RELATIVE DATING progression Uses fossils in each stratum of sedimentary rock Compare or correlate the strata at one location GAPS IN FOSSIL RECORDS and at another location by the presence of similar 1. Many kinds of organisms rarely become fossilized fossils called – “index fossils” because they are delicate, lack hard parts, or occupy environments where decay is rapid (e.g. ABSOLUTE DATING humid forests) Radiometric dating 2. Sediments generally form in a given locality very episodically, containing only a small fraction of Fossils contain isotopes of elements that species that inhabit a particular locality accumulated in the organisms when they were 3. Fossil formation and eventual discovery require alive several events to occur Unstable isotope – decays into a different - Sedimentation element exponentially - Solidification into rock Half-life of a radioactive isotope – the time taken - Persistence of the rock without being eroded, for half of its atoms to decay metamorphosed, or subducted - Exposure of the rock - Discovery by paleontologists 4. Evolutionary changes may not occur at a locality conducive for fossilization MJ KAGAOAN | 2 BIO 140: Fossils, Biogeography, and Phylogeny 1st Semester, 2024-2025 Measuring the rate of racemization Racemization – interconversion of levorotatory (L) and dextrorotatory (D) enantiomer amino acid forms Living organisms – have L-a.a. Dead organisms – mixture of L- and D- forms (in souls and sediments) One can determine based on the rate of racemization BIOGEOGRAPHY Study of the world (geographic) distributions of organisms Two components: 1. Historical biogeography - Certain distributions of organisms are the consequences of long-term evolutionary history - Continental drift, glacial advances, etc. 2. Ecological biogeography - Organisms’ distributions are the result of ecological factors operating at the present time - Abiotic aspects of the environment and biotic faotors BIOGEOGRAPHIC PIECES OF EVIDENCE 1. Diversity is not entirely accounted for by climate and environment 2. Geographical barriers can be factors in formation of various species (speciation). - E.g. frog subfamilies and Madagascar from India, aquatic rodents of South America 3. The plants and animals of each continent are distinctive; within each continent, organisms tend to be more related. 4. Island-continent relation: Species on oceanic islands show strong affinities to those on the nearest mainland. 5. Although oceanic islands have few species, those they have are often unique (endemic) and show relatedness to one another MJ KAGAOAN | 3 BIO 140: Fossils, Biogeography, and Phylogeny 1st Semester, 2024-2025 MAJOR PATTERS OF DISTRIBUTION BIOGEOGRAPHICAL OBSERVATIONS Endemic Restricted/limited to a certain ACROSS CONTINENTS region/area 1. Species that live in similar habitats will experience e.g. Varanus bitatawa (endemic to similar selection pressure from their environment, Philippines) so they may evolve similar adaptations or Cosmopolitan World-wide distribution; found on all continents (Orka) convergence, coming to look and behave very Disjunct When some taxa have gaps in much alike even though they are unrelated their distribution (Saxifagra - convergent evolution – organisms not closely cernua) related, independently evolve similar traits as a result of adaptation to similar environment Events/Factors Influencing Distribution or ecological order 1. Extinction - The distribution of a species may have been reduced by the death of some populations - Or the distribution of a higher taxon is reduced by the extinction of constituent species 2. Vicariance - Separation of populations of a widespread species by barriers arising from changes in geology, climate, or habitat - Separated by populations diverge, and often 2. Species living in one area should be the become different subspecies, species, or descendants of earlier species that lived in the higher taxa same place - Sometimes accounts for the presence of - E.g. Armadillo related taxa in disjunct areas - E.g. Isthmus of Panama BIOGEOGRAPHIC REALMS Inhabited by many characteristic higher taxa → 3. Dispersal taxonomic composition of the biota is more - When members of a species move and uniform within certain regions than between expand their range them - 2 kinds: Recognized by Wallace and other early o Range expansion – movement across biogeographers expanses of favorable habitat The results of the Earth’s history than of current o Jump dispersal – movement across an climate or landmass distribution already existing barrier o Wallace’s Line separates islands that despite - E.g. cattle egret (Bubulcus ibis) crossed major their close proximity and similar climate, barriers unassisted from Africa & Asia to differ greatly in their fauna South America (about 75 mya) - E.g. many plant species accidentally brought from Europe have expanded across most of North America - E.g. the European starling (Sturnus vulgaris) after its introduction in New York City in 1896 MJ KAGAOAN | 4 BIO 140: Fossils, Biogeography, and Phylogeny 1st Semester, 2024-2025 Phylogenetic analysis study of the genealogical relationships among species Darwin thought that species form a great “Tree of Life” or phylogenetic tree Biogeographic Realms Parts of a Phylogenetic Tree 1. Palearctic – temperate & tropical Eurasia and 1. Root – the common ancestor of all taxa Northern Africa 2. Node – represent a taxonomic unit 2. Nearctic – North America 3. Branch – defines the relationship of the taxa in 3. Ethiopian – sub-Saharan Africa terms of descent and ancestry 4. Oriental – India and Southeast Asia 4. Branch length – represent the number of changes 5. Australian – Australia, New Guinea, New Zealand, that have occurred in the branch & nearby islands 5. Clade – a group of two or more taxa that includes 6. Neotropical – Central and South America both their common ancestor and all their descendants THE TREE OF LIFE Biological classification Taxonomy – identification and classification of organisms; a component of systematics o Carolus Linnaeus – proposed a system of grouping species in a hierarchical classification of groups nested within larger groups Possible ways of drawing a phylogenetic tree: 1. Scaled Branches – different length or branches where you can readily see the number of changes that occurred to each 2. Unscaled Branches 3. Unrooted Tree with Scaled Branches 4. Unrooted Tree with Unscaled Branches Systematics Concerned with the diversity of life and reconstruction of phylogenetic histories Goal: to classify species based on evolutionary affinities Phylogeny a representation of the hypothetical evolutionary affinities MJ KAGAOAN | 5 BIO 140: Fossils, Biogeography, and Phylogeny 1st Semester, 2024-2025 What is the basis of groupings? 1. Homology - Likeness attributed to shared ancestry - Common ancestor, modified function 2. Analogy - Similarities due to convergent evolution not common ancestry - Different ancestors, same function Phylogenetic inference Process of developing an estimate of the evolutionary history of a group of organisms The unit of data used is the character o Plesiomorphic (ancestral) o Apomorphic (derived) Plesiomorphic Apomorphic Characters Characters Groupings Primitive Derived characteristics 1. Monophyletic characteristics shared Homologies that evolved - a group that includes all of the descendants of among all of the after a branch diverged a single common ancestor species of the from the phylogenetic tree 2. Paraphyletic cladogram and with Synapomorphies – shared - a group that includes some, but not all, of the the common ancestor derived stated (two taxa descendants of a single common ancestor are sharing these) 3. Polyphyletic - a group that is not based on common ancestry Homoplasious characters Shared by a set of species but not present in their common ancestor Resulting from convergent evolution or evolutionary reversal complicate phylogenies C – plesiomorphic character shared by sp. 1, 2, and 3 F1, G1 – apomorphic characters that came after divergence of sp. 2 and 3 from sp. 1 MJ KAGAOAN | 6 BIO 140: Fossils, Biogeography, and Phylogeny 1st Semester, 2024-2025 How are phylogenetic histories inferred? Maximum Parsimony Characteristic states are defined whether A method of reconstructing the phylogeny by plesiomorphic or apomorphic preferring the tree that produces the least Two species with the most number of shared number of evolutionary changes derived states (synapomorphies) are the most o Used when there is strong similarity among closely related taxa Each species in the cladogram is a mixture of plesiomorphic and apomorphic characters METHODS TO CREATE TREES Distance methods Based on genetic distance values o Neighbor-joining method – does not assume equal rates of evolution o UPGMA (Unweighted Pair Group Method Maximum likelihood with Arithmetic Mean) – assumes equal Calculates the probability of a data given a tree rates of evolution and model (probability of nucleotide substitutions and rates of these substitutions o Program produces trees o The tree which results to the highest probability is chosen Bayesian methods Propose that most likely evolutionary model given the data and known phylogenetic relationships o Program proposes models o Probability of the evolutionary model is calculated based on the data and tree Testing Significance of Distance Measures o Bootstrap – generates confidence intervals of parameter estimates *shows how confident you are of the relationship MJ KAGAOAN | 7