Evolutionary Trees Lecture 3 PDF

Announcements HW1 (15 MC questions) will be opened after today’s lecture and is due this weekend (9/8 Sun 23:59). Check your participation points on Canvas and sort out iClicker issues as necessary! (grade dispute policy: within two weeks of posting) No pending exit poll questions, so...

Announcements HW1 (15 MC questions) will be opened after today’s lecture and is due this weekend (9/8 Sun 23:59). Check your participation points on Canvas and sort out iClicker issues as necessary! (grade dispute policy: within two weeks of posting) No pending exit poll questions, so we’ll get right onto lecture!  Clicker Question Which of these people shared the credit for the theory of evolution by natural selection with Darwin? A) Jean-Baptiste Lamarck B) Alfred Wallace C) Thomas Malthus D) Charles Lyell  Clicker Question Organisms adapt to their environment. Adaptation ______. A) introduces new variation into the population B) leads to more complex life forms C) leads to higher fitness in a specific environment D) creates the perfect phenotype for an environment  Lecture 3 Evolutionary Trees I © 2014 Pearson Education, Inc.  Learning Objectives Interpret species relationships represented within phylogenetic trees. Recognize equivalent phylogenetic relationships drawn in different styles of trees. Construct the most parsimonious phylogenetic tree in simple cases. Describe the problems associated with defining modern species as “primitive/advanced” or “lower/higher” based on the structure of a phylogenetic tree.  Outline Darwin’s insight: common ancestry How to read a phylogenetic tree How to build a phylogenetic tree Key Tree concepts  Outline Darwin’s insight: common ancestry How to read a phylogenetic tree How to build a phylogenetic tree Key Tree concepts  Darwin’s insight: common ancestry In 1837, Charles Darwin drew the first phylogenetic tree. “Case must be that one generation then should be as many living as now. To do this & to have many species in same genus (as is) requires extinction. Thus between A & B immense gap of relation. C & B the finest gradation, B & D rather greater distinction. Thus genera would be formed. - bearing relation to Charles Darwin, “B” notebook, 1837 ancient types with several extinct forms...” Darwin’s insight: common ancestry Charles Darwin, The Origin of Species, 1859 Modern Phylogenetic Tree  Clicker Question What information is represented on the vertical axis of this phylogenetic tree? A. Trait differences B. Complexity C. Environmental change ? D. Time E. No particular information Tree documents evolving populations  Outline Darwin’s insight: common ancestry How to read a phylogenetic tree How to build a phylogenetic tree Key Tree concepts Reading a Phylogenetic Tree Reading a Phylogenetic Tree Describes the relatedness of species Reading a Phylogenetic Tree Describes the relatedness of species Species that shared a more recent most recent common ancestor are more related  Reading a Phylogenetic Tree 6 is the most recent common ancestor of Canada lynx and bobcat Describes the relatedness of species Species that shared a more recent most recent common ancestor are more related  Reading a Phylogenetic Tree 1 is the most recent common ancestor of Canada lynx and snow leopard Describes the relatedness of species Species that shared a more recent most recent common ancestor are more related Reading a Phylogenetic Tree Describes the relatedness of species Species that shared a more recent most recent common ancestor are more related Clicker Question Which species is the LEAST related to the Lion? A) Jaguar B) Tiger C) Snow leopard D) Equally related to all three Clicker Question Which species is LESS related to the Snow leopard? A) Jaguarundi B) Tiger C) Equally related to both  Reading a Phylogenetic Tree Describes the relatedness of species Bobbed tail Species that shared a more recent most recent common ancestor are more related Transitions marks the evolutionary emergence of a derived trait Clicker Question What transition does the red arrow mark? A) Bobbed tail to long tail B) Long tail to bobbed tail C) Flecked coat to plain coat D) Plain coat to flecked coat  Trees can be drawn in different styles As long as the relationships are preserved, the trees are considered identical.  Trees can be rotated at internal nodes Branches can be rotated at internal nodes without changing the relationships between species Flensted Mobiles Baum et al. 2005 Science  Clicker Question Which phylogenetic tree is different from the other three? B D C A C B D A A B C D  Clicker Question According to this tree, which clade is the Ranitomeya most closely related to? A) Minyobates B) Andinobates C) Allobates D) Dendrobates  Trees can be pruned and extended These two trees convey the same info about evolutionary history for the five species in black. Gregory 2008. https://link.springer.com/article/10.1007/s12052 008 0035 x  Outline Darwin’s insight: common ancestry How to read a phylogenetic tree How to build a phylogenetic tree Key Tree concepts  Building a phylogenetic tree How can we construct a phylogenetic tree that infers the relatedness between these five species? https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree  Building a phylogenetic tree Step 1: Select traits to base the relationships on Common homology evidence for building a tree: Morphological traits Developmental evidence Genetics Vertebrae + + + + + https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree  Building a phylogenetic tree Step 2: Establish polarity determine which traits are ancestral and which are derived Did animals start without lungs and evolve them? Or start with lungs and lose them? Fossil records or outgroup can often help us determine polarity (we’ll talk more about this next week) https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree  Building a phylogenetic tree Step 3: Find the most parsimonious tree (i.e. one that requires fewest character state change) https://evolution.berkeley.edu/evolibrary/article/0_0_0/evotrees_build_07  Building a phylogenetic tree Step 3: Find the most parsimonious tree (i.e. one that requires fewest character state change) https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree  Building a phylogenetic tree Step 3: Find the most parsimonious tree (i.e. one that requires fewest character state change) https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree  Building a phylogenetic tree Step 3: Find the most parsimonious tree (i.e. one that requires fewest character state change) https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree  Building a phylogenetic tree Step 3: Find the most parsimonious tree (i.e. one that requires fewest character state change) https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree  Building a phylogenetic tree Step 3: Find the most parsimonious tree (i.e. one that requires fewest character state change) https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree  Building a phylogenetic tree Step 3: Find the most parsimonious tree (i.e. one that requires fewest character state change) https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree Clicker Question We mapped 6 traits, but only some of them actually gave us information about species relationships. Which of these 6 traits are useful for resolving species relationships? A) Vertebrae B) Jaws & Lungs C) Jaws, Lungs, and Gizzard D) Everything except Vertebrae E) All of them are useful Ancestral vs Derived Traits Plesiomorphy: ancestral trait (vertebrae) Apomorphy: derived trait Synapomorphy: shared derived trait among at least 2 species; useful for phylogenetic inference (jaws, lungs, gizzard) Autapomorphy: unique derived trait of one species (feathers, fur)  Clicker Question According to this tree, is the sea bass more closely related to the lamprey or the antelope? A. Lamprey B. Antelope C. Equally related to both  Clicker Question For tetrapods (animals with four limbs), the trait “amniotic egg” is a(n) ________. A) Apomorphy B) Plesiomorphy  Clicker Question For the group consisting crocodiles, dinosaurs, and birds, the trait “amniotic egg” is a(n) ________. A) Apomorphy B) Plesiomorphy  Ancestral vs Derived Traits A trait can be plesiomorphic (i.e. ancestral) in one context and apomorphic (i.e. derived) in another The mask is a synapomorphy for the 3 mask species within the set of all four species  Outline Darwin’s insight: common ancestry How to read a phylogenetic tree How to build a phylogenetic tree Key Tree concepts  Clicker Question According to this tree, which animal is most closely related to the ancestor of all mammals? A) Platypus (Monotremata) B) Elephant (Proboscidea) C) Panther (Carnivora) D) Equally related to all three  All living species have the same evolutionary age all lineages have existed for the same time since they diverged from their common ancestor Fishes are not “lower”, “more ancient”, “more primitive”, or “closer to an ancestor” compared to human. Gregory 2008 Understanding Evolutionary Trees  Think-Pair-Share “Science shows that us human evolved from chimpanzees.” Is there anything problematic with this statement?  Living Species are not our ancestors A common but inaccurate depiction of “Evolution” O “human and common chimps shared a recent primate X “human evolved from chimps” ancestor” Gregory 2008 Understanding Evolutionary Trees O “human evolved from an earlier ape”  Monophyletic Group Monophyletic group: or “Clade”; an ancestor and all of its descendants Considered a “good evolutionary unit” in the study of taxonomy https://en.wikipedia.org/wiki/Monophyly#/media/File:Phylogenetic-Groups.svg Clicker Question Consider the phylogeny of Tetrapods. Are the traditionally considered “reptiles” (lizard, snake, turtle, crocodiles) a clade? A) Yes B) No  Clicker Question In this tree, do the old world and new world monkeys form a monophyletic group? A) Yes B) No  Think-Pair-Share Scientists often debate about phylogenetic trees. For example, whether comb jellies or ? ? sponges were the first to branch off in the animal phylogeny. Why is that? Why are there uncertainties in a phylogeny? https://www.nature.com/articles/s41586-023-05936-6  Learning Objectives Interpret species relationships represented within phylogenetic trees. Recognize equivalent phylogenetic relationships drawn in different styles of trees. Construct the most parsimonious phylogenetic tree in simple cases. Describe the problems associated with defining modern species as “primitive/advanced” or “lower/higher” based on the structure of a phylogenetic tree. Questions, Comments, Concerns, etc? Exit Poll