Lecture 4 (Fall 2024) - Phylogeny and Cladograms PDF

ECTURE 4: Evolution & Phylogenetic Systematics From Chapter 3 of Dinosaurs (4th Ed.) ECTURE 4: Evolution & Phylogenetic Systematics From Chapter 3 of Dinosaurs (4th Ed.) Lecture Outline Evolution and Phylogenetic Systematics Watch the 12 min PBS video “How E...

ECTURE 4: Evolution & Phylogenetic Systematics From Chapter 3 of Dinosaurs (4th Ed.) ECTURE 4: Evolution & Phylogenetic Systematics From Chapter 3 of Dinosaurs (4th Ed.) Lecture Outline Evolution and Phylogenetic Systematics Watch the 12 min PBS video “How Evolution Works” ECTURE 4: Evolution & Phylogenetic Systematics From Chapter 3 of Dinosaurs (4th Ed.) Objectives Understand the concept of Evolution Understand phylogeny - the mechanism behind the fundamental genealogical connections among organisms Understand the concept of Phylogenetic Systematics – how to reconstruct patterns of evolution Understand what a cladogram is and how to read it Part 1. Evolution (review)  A Short Glossary of Important Evolutionary Terms EVOLUTION - The process by which living things can gradually change over time. ADAPTATION - How living things are specialized to suit their environment. INHERITENCE - The process of passing on features from parents to offspring. VARIATION - The differences between living things in a species.  What is evolution? Biological evolution refers to the cumulative changes that occur in a population over time (‘descent with modification’). These changes are produced at the genetic level as organisms' genes mutate and/or recombine in different ways during reproduction and are passed on to future generations. Morphology is what we see being modified, but evolution is actually happen at the level of the gene (genotypic evolution) and we see it expressed in a organism’s morphology (phenotypic evolution)  What is evolution? continued Sometimes individuals inherit new characteristics that give them a survival and reproductive advantage in their local environments; these characteristics tend to increase in frequency in the population, while those that are disadvantageous decrease in frequency. This process of differential survival and reproduction is known as natural selection. Non-genetic changes that occur during an organism's life span, such as increases in muscle mass due to exercise and diet, cannot be passed on to the next generation and are not examples of evolution.  What is a Species? SPECIES (biological) - A group of living things with very similar characteristics. They can breed together to make more living things of the same type. SPECIES (phylogenetic) - the smallest set (clade) of organisms that share an ancestor and can be distinguished from other such sets by possessing a combination of certain defining, or derived, traits.  What is a Species? SPECIES (biological) - A group of living things with very similar characteristics. They can breed together to make more living things of the same type. SPECIES (phylogenetic) - the smallest set (clade) of organisms that share an ancestor and can be distinguished from other such sets by possessing a combination of certain defining, or derived, traits. 99.9999% of all species that have ever existed are extinct. If we are lucky, we know about them through their fossils.  Part 2. Phylogenetic Systematics PHYLOGENETIC Phylum (group of related organisms) + Genesis (origin) SYSTEMATICS The organized arrangement of components  People have attempted to classify life since before evolution was understood. In the mid-1700s, Carolus Linnaeus introduced what has come to be known as the Linnaean system. It is based upon “overall similarity” organisms grouped together based upon whether they generally look like each other. The Linnaean system features a nested hierarchy of taxa (singular  Linnean Classification Hominidae Primates Mammalia Chordata Animalia https://byjus.com/cbse/taxonomy-nomenclature Relationship and Linnaean Classification This classification was not originally evolutionary, but with the evolutionary formulation of Charles Darwin (1859), it was co-opted to represent the result of evolution. This means that members of groups within the classification are purported more closely related to each other than to anything else. That makes the classification important, because dentify (Infer) Evolutionary Relationships Scientifically gh Phylogenetic Systematics (aka Cladistics) Cladogram –a hierarchical diagram of shared diagnostic characters (dependent on the characters used). Identify characters – features possessed by organisms; we look for diagnostic characters, which are characters that are unique for a particular taxon Recognize the hierarchy – A simple cladogram showing characters in all the organisms characters shared by two taxa are arranged hierarchically - an (bear and human). Note that order of the taxa makes no plicating the cladogram: 3 taxa Establishing the hierarchy: with three taxa, two must be more closely related to each other than either is to the third. The cladogram is a hypothesis of relationship. Here, the gorilla (added) is shown to be more closely related to the human than to the bear. Intuitively correct, but Characters used in phylogenetic analyses must be homologous HOMOLOGY is similarity due to shared ancestry between a pair of structures or genes in different taxa and is NOT related to function. E.g., humerus (blue), radius (orange) & ulna (red) are homologous for Fig all these University © Cambridge taxa Press 2016  The Opposite of Homologous: Analogous Cambridge Press, 2015 ANALOGOUS structures are examples of convergent evolution, where two organisms separately evolved similar structural features (e.g., legs). ANALOGY is similarity in function, but not  Let’s Review Cladograms are branching diagrams that show hierarchies of diagnostic shared characters Diagnostic characters (in this example): warm-blooded; fur (or hair) Diagnostic Taxa (clades)characters linked byare shared shared by all taxa characters (clades/groups) at nodes above can be named the hatch (e.g., mark Mammalia) Node is athe Rotating branch point (a branches onand a cladogram that b) does not separates change two taxa (or the cladograms  Cladograms are not evolutionary trees, but they can be used to infer evolutionary relationships (ancestor-descendent) relationships based on the shared characters (synapomorphies) used in the analysis that generated the cladogram = phylogenetic tree. A phylogram is a phylogenetic tree where the branch lengths are proportional to the amount of character change. A chronogram is a phylogenetic tree that explicitly represents time Images: Creative Common through its branch lengths. Many cladograms incorporate both time and amount of character change. Images: Creative Commons See Box 3.1/Table B3.1 for Phylogram more info on Chronogram phylogenetic Parsimony: Distinguishing between hypotheses of relationship Parsimony is a concept that has guided scientific explanations since the 15th century. It states that the explanation with the least number of steps is likely the correct. Applied to the two hypotheses ofand (a) The bat relationship below: the human are (b) The bat and the bird are more more closely related to each other closely related to each other than than either is to the bird. either is to the human. Cladogram (b) requires birds to have once had, and then lost, fur and mammary glands. These and many other characters suggest that (b) requires more evolutionary steps than (a); because cladogram (b) is less parsimonious than cladogram (a), the preferred hypothesis of relationship is (a), even though (a) Here is a hypothesis of relationship read from the cladogram: The human and gorilla are more closely related to each other than either is to the bear (based upon diagnostic characters not shown); They, their most recent common ancestor, and all its descendants are therefore a monophyletic group (or clade) (because they uniquely share diagnostic characters); The bear, human, and gorilla, their most recent common ancestor, and all its descendants are also a  Important (and sometimes confusing) Phylogenetic Terms What is a character? For the purposes of this course, a character is a morphological feature of an organism that can be explicitly defined qualitatively or quantitatively. Types of characters (depends on the context of the phylogenetic analysis) Primitive (ancestral) – a character state expressed in an ancestral taxon relative to a descendent. Advanced (derived) – a character expressed in a descendent taxon relative to an ancestor.  What Characters to Use? Systematists choose the characters in any analysis In choosing characters, it is essential to realize that evolutionary relationships are only revealed by traits that are similar because they were derived from a common ancestor...the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical. (Darwin, 1872: 346) Photos: D. Evans There are computer programs that can run an algorithm to determine which tree is the best fit (most parsimonious) for the data Typical phylogenetic datasets are too large for this to have been practical before the advent of computers A monophyletic group (clade) of taxa shares a single common ancestor and also includes all of the descendants of that common ancestor. On a phylogenetic tree, a monophyletic clade includes a node and all of the descendants of that node, represented by both nodes and terminal taxa. Thus, a monophyletic group is also a clade Nested monophyletic clades of vertebrates showing how each clade corresponds to a taxon at a different taxonomic rank.  A paraphyletic group (not a clade)(blue & yellow) includes a single ancestor and some, but not all, of its descendants It is similar to a monophyletic group, but some A polyphyletic group (not a clade) is a group that is not defined by a single common ancestor. Taxa A, B, E, and H collectively represent a polyphyletic group. Image by Jonathan R. Hendricks is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. A crown group (clade) (green) is a clade defined by extant (living) taxa. It consists of the most recent shared common ancestor of all extant members of a clade, as well as all of the descendants of that common ancestor, whether they are A stem group (not a clade) (yellow) consists of a paraphyletic grouping of extinct species that are positioned basal to a given crown group (in other words, on its "stem"). A stem group is more closely related to its corresponding crown group than to the extant sister clade of the crown group. Because stem groups are always Cladograms are scientific hypotheses– they can be revised or overturned by new data You do not need to know the contents of this Ezcurra et al. 2020 Phylogenetic Systematics vs. Linnaean Classification Linnaean Classification Based on untested inferences of morphological similarity between taxa to generate ‘trees of live’. The historical Linnaean terms given to groups (e.g., Order, Family, Genus, Species) are still in common use today and can overlap with clade names in phylogenetic systematics. Phylogenetic Systematics Based on the analysis of shared, derived characters to determine the most parsimonious explanation for the distribution of these characters within the taxa studied. The resulting evolutionary hypothesis of ancestral-descendent relationship is dependent on the characters chosen, how they are defined, and the taxa examined. The nodes within the phylogenetic trees generated are DEFINITIONS OF SOME PHYLOGENETIC TERMS CHARACTER – a specialized trait or character that is unique to a group or species. It is also called an APOMORPHY. AUTOAPOMORPHY – is a distinctive feature, known as a DERIVED TRAIT, that is unique to a given taxon. SYNAPOMORPHY – a characteristic present in an ancestral species and shared exclusively (in more or less modified form) by its evolutionary descendants. PLESIOMORPHY (“near form”) is an ancestral character state. SYMPLESIOMORPHY – (from syn- “together”) is a plesiomorphy shared by two or more taxa (including taxa earlier in the clade). DEFINITIONS OF SOME PHYLOGENETIC TERMS STEM GROUP: A paraphyletic group consisting of an ancestor and all its descendants, excluding the living representatives of a collection of species. CROWN GROUP: The living representatives of a collection of species, together with their ancestors back to their most recent common ancestor as well as all of that ancestor's descendants. EXTANT – Alive EXTINCT – No living members DEFINITIONS OF SOME PHYLOGENETIC TERMS HOMOLOGOUS structures share a common evolutionary origin. ANALOGOUS structures have a similar function, but do NOT share a common evolutionary origin. COMMON ANCESTOR – A common ancestor is not a single individual or a link in a chain, but instead represents a population of individuals from which the fossil animal of interest descended with modification. PARSIMONY - a hypothesis of relationships that requires the smallest number of character changes is most likely to be correct. cientific Classification ade: Dinosauria ‘dinosaur(s)’ er: Ornithischia ‘ornithischian(s)’ de: Ceratopsia ‘ceratopsian(s)’ mily: Ceratopsidae ‘ceratopsid(s)’ Genus: Triceratops Species: horridus cientific Classification ade: Dinosauria ‘dinosaur(s)’ der: Saurischia ‘saurischian(s)’ ade: Theropoda ‘theropod(s)’ y: Tyrannosauridae ‘tyrannosaurid(s)’ or ‘tyrannosaurs’ Genus: Tyrannosaurus Species: rex Then Now