Chapter 23 This phylogenetic tree depicts the evolutionary relationships of about 3,000 species (less than 1 % of known species). How do we organize the diversity of life? • 1.8 million identified species – many more we have not yet discovered • At least 1 million species of insects • Estimated that there are actually between 10 and 100 million species Naming species • In the 18th century, Carolus Linnaeus published a system of taxonomy for naming and organizing species • Species are identified by a two-name system (binomial nomenclature) • Scientific name is universal – used worldwide – standardized among all scientists – In Latin, so no confusion between different languages – No two species can have the same scientific name • The first name is the genus name and the second is the species name (must have both parts of the name) – Styloctenium wallacei (Wallace's stripe-faced fruit bat) – Semioptera wallacei (Wallace’s standard-wing bird of paradise) • The first letter of the genus is capitalized but the species name is lowercase • Both the genus and species names are italicized • Ex. Homo sapiens (humans) Ursus americanus (American black bear) • Taxonomy is the branch of biology that names and classifies species according to a system of broader and broader groups • Each smaller taxon is nested within a larger group • Ex. Carnivores are one Order of mammals within the Class Mammalia Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia Bacteria Domain: Eukarya Archaea Taxonomic Categories Species Domain Kingdom Phylum Class Order Family Genius Species Genus Family Order Class Phylum Ursus Ursidae Carnivora Ursus americanus Mammalia (American black bear) Chordata Animalia Eukarya Kingdom Domain Dumb Kids Playing Carelessly On Freeways Get Squashed Species Genus Family Order Class Phylum Ursus Ursidae Carnivora Ursus americanusMammalia (American Chordata black bear) Animalia Eukarya Kingdom Domain • By placing species into taxonomic groups based on relatedness, we are assuming that evolution occurred • If different species don’t have a common ancestor, how can they be related? (ex. cousins are related because they have a common ancestor - their grandparents) • Scientists create phylogenetic trees to illustrate taxonomic relationships between species • Phylogenetic trees are hypotheses about the relationships among different species • Phylogenetic trees can be made using many different types of data: –Morphological –Fossil –Molecular –Genetic Example of a very simple phylogenetic tree for the Animal, Plant, and Fungi Kingdoms Which group is Fungi’s closest relative? Fungi are more closely related to animals than they are to plants The last time plants and fungi had a common ancestor was longer ago than the last common ancestor between fungi and animals Last common ancestor between animals and fungi Last common ancestor between plants and fungi Phylogenetic trees • Each branch point or node represents the divergence of two species (a speciation event) • The node represents the last common ancestor between 2 groups • Sister taxa are groups that share an immediate common ancestor • The outgroup is the most distantly related species outgroup on the tree Sister taxa Phylogenetic tree of living groups of tetrapods Branch point (common ancestor) Lungfishes Amphibians 1 Mammals 2 Tetrapod limbs Lizards and snakes 3 Amnion 4 5 Ostriches 6 Feathers Hawks and other birds Birds Homologous characteristic Crocodiles What is C’s sister taxa in each of the sample trees? (a) A B D B D C C C B D A A (b) (c) What is C’s sister taxa in each of the sample trees? (a) A B D B D C C C B D A A (b) (c) What is the last common ancestor of B & C in each tree? (a) A B D B D C C C B D A A (b) (c) What is the last common ancestor of B & C in each tree? (a) A B D B D C C C B D A A (b) (c) What is the outgroup in each sample tree? (a) A B D B D C C C B D A A (b) (c) What is the outgroup in each sample tree? (a) A B D B D C C C B D A A (b) (c) In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage Drosophila Lancelet Zebrafish Frog Chicken Human Mouse In other trees, branch length can represent chronological time Drosophila Lancelet Zebrafish Frog Chicken Human Mouse PALEOZOIC 542 MESOZOIC 251 Millions of years ago CENOZOIC 65.5 Present Similarity may not accurately predict evolutionary relationships Early systematists relied on the expectation that the greater the time since two species diverged from a common ancestor, the more different they would be But they found that is not always the case bc: • • • 1) Convergent Evolution – 2 different species evolve to look/function more similarly 2) Evolutionary reversals – species can re-evolve a trait that was lost but can be found in an older ancestor 3) Rates of evolution vary (some traits/genes/species may experience faster rates of evolution) © 2020 McGraw-Hill Education. 23-23 How convergent evolution can affect phylogeny • When constructing a phylogeny, scientists need to distinguish whether a similarity is the result of common ancestry or not • Homology is similarity due to shared ancestry • Scientists use homologous traits to help construct phylogenetic trees • You should not use analogous traits when constructing phylogenetic trees Homologous traits • Amphibians, reptiles, birds, and mammals all have 4 limbs because their common ancestor had 4 limbs Secretary bird • Plotting homologous character traits can help you place species on a phylogenetic tree Iguana Outgroup (reptile) Duck-billed platypus Hair, mammary glands Kangaroo Gestation Beaver Long gestation Ingroup (mammals) Homoplasies/Analogous traits • Analogous trait – similar due to adaptation to a similar environmental condition, not due to common ancestry • The 2 species evolved the similar trait separately • Cannot use analogous traits to determine relatedness/make phylogenetic trees • Ex. eyes of vertebrates and some mollusks • They look very similar, but they evolved separately and are structurally different • You would not group mammals and squid together based on both having a complex eye How homoplasies/analogous traits affect phylogenetic trees shark lion dolphin This is the correct phylogeny Dolphins are more closely related to lions than sharks Dolphins and lions are both mammals Dolphins have a more recent common ancestor with lions than they do with sharks How homoplasies/analogous traits affect phylogenetic trees lion shark dolphin If you used analogous traits such as overall morphology, you may group sharks and dolphins together and come up with this inaccurate tree • When creating phylogenetic trees, it can be useful to make the data for each trait more quantifiable and less subjective • Scientists will often characterize each trait as present(1) or absent (0) • You can see on this table how they categorized the presence or absence of each trait for each species that they will be placing on the phylogenetic tree • Then they used that data to construct the tree • You can see how they created the tree and placed each trait on the tree where they believed it evolved • The derived character traits are shared by all organisms above the branch points and are not present in any below them • See how tigers, gorillas, and humans all have hair (a derived trait for mammals), but the species that branched off earlier in the tree do not have hair • Ideally all species that have the derived trait will be grouped together on the tree after the evolution of the trait, but it is not always that simple • Humans, gorillas, and frogs all lack tails • Does that mean that they should be grouped together and considered close relatives as is shown in this tree? • No, obviously humans and frogs are not closely related simply because neither has a tail • Some traits evolve more than once in separate lineages • Tails were lost in frogs and apes • So you see how the trait tail loss is shown on the tree twice Evolutionary Reversals can confuse phylogenetic trees • Sometimes a species will evolve a trait and then later it will revert to the old trait • These are called evolutionary reversals • They can be confusing when creating trees because the species looks like it has the ancestral trait and therefore should not be part of the group with derived traits, but in reality that species had the derived trait and then later lost it Evolutionary reversal - leglessness • Tetrapods (amphibians, reptiles, birds, and mammals) all originally had 4 limbs • Some groups later lost their legs (caecillians, legless lizards, snakes) • If you were making a tree, would it make sense to put caecillians, legless lizards, and snakes with fish (because they are also legless)? lizards snakes legless lizards caecillians fish frogs & mammals salamanders with legs • No, they have many other derived traits that tetrapods have (lungs, 3 chambered hearts) birds Data from DNA • Comparing nucleic acid sequences or other molecules (usually proteins) to infer relatedness is a valuable tool for tracing an organism’s evolutionary history • Molecular systematics uses DNA and other molecular data to determine evolutionary relationships • You can compare the same gene in 2 different species and treat each nucleotide base as a character • Then create a tree using this data, just like you would for morphological traits • You can compare genes in two species to see how much change has occurred and infer how much time has passed since they diverged • The genes can diverge only after speciation occurs (have separate gene pools) Ancestral gene Ancestral species Speciation with divergence of gene Species A Species B Phylogenetic tree for canid species • The phylogenetic tree is based on 15 kb of exon and intron sequence • What is the outgroup? Phylogenetic tree for canid species • The phylogenetic tree is based on 15 kb of exon and intron sequence • What is the outgroup? Phylogenetic tree for canid species • The phylogenetic tree is based on 15 kb of exon and intron sequence • Who is the closest relative of the wolf? Phylogenetic tree for canid species • The phylogenetic tree is based on 15 kb of exon and intron sequence • Who is the closest relative of the wolf? Rate of evolution within “junk dna” • Stretches of DNA with no function have higher rates of evolution because there is no selection to maintain a functional copy of the gene • As a result, they evolve new character states more quickly because mutations and genetic drift are not selected against • If a gene gets duplicated, it is no longer necessary because the original gene is already performing the necessary function • It may evolve more quickly like “junk DNA” • The duplicated gene may end up developing a new function Species A Gene duplication and divergence Duplicated genes may evolve and acquire new functions Species A after many generations Example of Gene Duplication • Evolution of vertebrates from invertebrate animals was associated with alterations in Hox genes (a set of master control genes found in all animals) • Two duplications of Hox genes have occurred in the vertebrate lineage • These duplications may have been important in the evolution of new vertebrate characteristics Hypothetical vertebrate ancestor (invertebrate) with a single Hox cluster First Hox duplication Hypothetical early vertebrates (jawless) with two Hox clusters Vertebrates (with jaws) with four Hox clusters Second Hox duplication Complex Traits • Most complex traits do not evolve in one step • Many steps along the way where each step improves the function – Eyes • Sometimes traits evolve for one purpose and later come to be used for different purpose – Feathers • Scientists can still explain how these traits evolved via natural processes • Dinosaurs originally used feathers for insulation and/or display (earliest feathers developed ~190 mya) • Feathers changed over time • Later they began to use them to glide • Eventually they were used for true flight (~150 mya) • Live Science talked to the paleontologist (Jack Horner) who advised Steven Spielberg on Jurassic Park, he said "Even when 'Jurassic Park' came out [in 1993], we knew that Velociraptors should have feathers, but at that time, it would have been technically difficult to do it, just from a CG [computer-generated] point of view. And Steven wasn't really too excited about it, anyway. When I told him they should be colorful and they should be feathered, and he said, 'Feathered Technicolor dinosaurs aren't scary enough.’" Velociraptors in “Jurassic Park” Velociraptors in reality (feathered & much smaller) Parsimony • Principal that the simplest explanation is most likely correct • Can be used in phylogeny • If create two trees and do not have enough data to know which is correct, scientists will use parsimony to make an educated guess until more data becomes available • According to the principal of parsimony, the tree that requires the fewest number of changes is most likely the correct one Parsimony • The first tree requires four changes, whereas the second tree would require 5 evolutionary changes to have occurred • Based on the principle of parsimony, the first tree is more likely to be correct Reversals are common in nucleotides so parsimony doesn’t always work with molecular data • Only 4 character states are possible (A, T, G,C) so there is a high probability that two species will independently evolve the same derived character state at any particular base position – Any given mutation could easily create the same “trait” – (A T could easily happen more than once in separate species) • DNA data is very useful for phylogenetic analysis, but some sections of DNA evolve very rapidly and using parsimony can be misleading • Scientists use a lot of data to increase accuracy, luckily most species have millions or billions of base pairs of DNA New information continues to revise our understanding of the tree of life • Early taxonomists classified all species as either plants or animals • Later, five kingdoms were recognized: – Monera (prokaryotes) – Protista (single celled eukaryotes) – Plantae – Fungi – Animalia • We have gained better insight into the very deepest branches of the tree of life through molecular systematics • More recently, the three-domain system has been adopted: – Bacteria – Archaea – Eukarya • The three-domain system is supported by data from many sequenced genomes 3 Domains of Life Bacteria -prokaryotic -true bacteria -blue-green algae Archaea Eukarya -prokaryotic -live in harsh environments -salt ponds -hot springs -hydrothermal vents -eukaryotic -protists, fungi, plants, and animals Note that Eukarya and Archaea had a common ancestor after they split off from the Bacteria. Therefore Archaea and Eukarya are more closely related to each other than either is to the Bacteria even though Archaea and Bacteria are both prokaryotes Bacteria Earliest organisms Prokaryotes Archaea Eukarya Eukaryotes Archaea and Eukarya have a more recent common ancestor than either does with the Bacteria EUKARYA Dinoflagellates Land plants Green algae Forams Ciliates Red algae Cellular slime molds Diatoms Amoebas Euglena Trypanosomes Leishmania Animals Fungi Sulfolobus Green nonsulfur bacteria Thermophiles Halophiles (Mitochondrion) COMMON ANCESTOR OF ALL LIFE Spirochetes Chlamydia Green sulfur bacteria BACTERIA Methanobacterium ARCHAEA Cyanobacteria (Plastids, including chloroplasts) EUKARYA Dinoflagellates Land plants Green algae Forams Ciliates Red algae Cellular slime molds Diatoms Amoebas Euglena Trypanosomes Leishmania Animals Fungi Sulfolobus Green nonsulfur bacteria Thermophiles Halophiles (Mitochondrion) COMMON ANCESTOR OF ALL LIFE Spirochetes Chlamydia Green sulfur bacteria BACTERIA Methanobacterium ARCHAEA Under the old system, all of this was considered Kingdom Monera Cyanobacteria (Plastids, including chloroplasts) Kingdom Plantae Classifications may still need to be updated EUKARYA Dinoflagellates Land plants Green algae Forams Ciliates Red algae Under the old and the new system, everything in the blue circle except the red lines are considered Kingdom Protista Diatoms Kingdom Animalia Amoebas Cellular slime molds Euglena Trypanosomes Leishmania Animals Protista is paraphyletic Fungi Kingdom Fungi Sulfolobus Green nonsulfur bacteria Thermophiles Halophiles (Mitochondrion) COMMON ANCESTOR OF ALL LIFE Spirochetes Chlamydia Green sulfur bacteria BACTERIA Methanobacterium ARCHAEA Cyanobacteria (Plastids, including chloroplasts) Clade – organisms grouped together on a phylogenetic tree • Monophyletic group - signifying that it consists of the ancestor species and all its descendants • Paraphyletic group - consists of an ancestral species and some, but not all, of the descendants • Polyphyletic group - consists of various species that lack a common ancestor Taxonomic groups are described as being monophyletic, paraphyletic, or polyphyletic When creating taxonomic groups scientists strive for all groups to be monophyletic • Monophyletic group - signifying that it consists of the ancestor species and all its descendants This is not ideal, but many taxonomic groups are actually paraphyletic • Paraphyletic group - consists of an ancestral species and some, but not all, of the descendants This is never an acceptable grouping • Polyphyletic group - consists of various species that lack a common ancestor Are each of these groups monophyletic, paraphyletic, or polyphyletic? A A A B B C C C D D D E E F F F G G G B Group I Group II E Group III A A A B B C C C D D D E E F F F G G G (b) Paraphyletic group (c) Polyphyletic group B Group I (a) Monophyletic group (clade) Group II E Group III ray finned fish lobe finned fish amphibians anapsids therapsids synapsids lizards & snakes crocodilians archosaurs amniotes Are mammals a monophyletic, paraphyletic, or polyphyletic grouping? diapsids turtles Ornithischian dinosaurs Saurischian dinosaurs Theropod dinosaurs birds mammals cynodonts dimetrodon ray finned fish lobe finned fish amphibians anapsids therapsids synapsids lizards & snakes crocodilians archosaurs amniotes Mammals are a monophyletic grouping diapsids turtles Ornithischian dinosaurs Saurischian dinosaurs Theropod dinosaurs birds mammals cynodonts dimetrodon ray finned fish lobe finned fish amphibians anapsids therapsids synapsids lizards & snakes crocodilians archosaurs amniotes Are bony fish a monophyletic, paraphyletic, or polyphyletic grouping? diapsids turtles Ornithischian dinosaurs Saurischian dinosaurs Theropod dinosaurs birds mammals cynodonts dimetrodon ray finned fish lobe finned fish amphibians anapsids therapsids synapsids lizards & snakes crocodilians archosaurs amniotes Bony fish are technically a paraphyletic grouping because they exclude tetrapods diapsids turtles Ornithischian dinosaurs Saurischian dinosaurs Theropod dinosaurs birds mammals cynodonts dimetrodon ray finned fish lobe finned fish amphibians anapsids therapsids synapsids lizards & snakes crocodilians archosaurs amniotes Are birds a monophyletic, paraphyletic, or polyphyletic grouping? diapsids turtles Ornithischian dinosaurs Saurischian dinosaurs Theropod dinosaurs birds mammals cynodonts dimetrodon ray finned fish lobe finned fish amphibians anapsids therapsids synapsids lizards & snakes crocodilians archosaurs amniotes Birds are a monophyletic grouping diapsids turtles Ornithischian dinosaurs Saurischian dinosaurs Theropod dinosaurs birds mammals cynodonts dimetrodon ray finned fish lobe finned fish amphibians anapsids therapsids synapsids lizards & snakes crocodilians archosaurs amniotes Are reptiles a monophyletic, paraphyletic, or polyphyletic grouping? diapsids turtles Ornithischian dinosaurs Saurischian dinosaurs Theropod dinosaurs birds mammals cynodonts dimetrodon ray finned fish lobe finned fish amphibians anapsids therapsids synapsids lizards & snakes crocodilians archosaurs amniotes Reptiles are a paraphyletic grouping because they exclude birds diapsids turtles Ornithischian dinosaurs Saurischian dinosaurs Theropod dinosaurs birds mammals cynodonts dimetrodon • As you can see, traditional taxonomic groupings do not always fit well with the phylogenetic trees that have been created with more recent scientific data • Ex. Birds’ ancestor is a dinosaur (a reptile), but birds are not included within the reptiles • A more accurate phylogeny should include birds within the reptiles OR • We could create a Class Archosaur that would include crocs, dinosaurs, and birds (Reptiles would still be paraphyletic bc it excludes the archosaurs) Remember that phylogenetic trees represent hypotheses about evolutionary relationships These trees show two possible hypotheses: 1) whales evolved from a common ancestor of all arteriodactyls OR 2) they evolved from a more recent common ancestor with hippos You should now understand: • Be able to identify the correct form for a species’ scientific name. • List the taxonomic categories in order. • Be able to read a phylogenetic tree. • Be able to create a phylogenetic tree based on character traits or DNA sequences. • What is the difference between homologous and analogous traits? Which type of traits can be used to create phylogenetic trees? You should now understand: • Understand the idea of parsimony and how it relates to phylogenetic trees. • Be able to identify monophyletic, paraphyletic, and polyphyletic clades. • Recall that phylogenetic trees represent a hypothesis about how species are related. • Be able to draw and label a phylogenetic tree for the 3 domains of life.
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