Lecture 10: Phylogenetics & Macroevolution PDF

Lecture/Slide Deck 10 ; Phylogenetics & Macroevolution - Taxonomy & Systematics;  - How to think about phylogines?  - Taxonomy is theory and practice of classification and naming things;  - Giving things names and keeping them organised -...

Lecture/Slide Deck 10 ; Phylogenetics & Macroevolution - Taxonomy & Systematics;  - How to think about phylogines?  - Taxonomy is theory and practice of classification and naming things;  - Giving things names and keeping them organised - Nomenclature basically  - Systematics is the study of biodiversity and evolutionary relationships *among* organisms;  - We bring evolution into the mix and look at evolutionary history and relationships among species  - "To understand the evolutionary connections and how different species are related through common ancestry."  - Taxonomy is organising your music library by genre, systematics is understanding the history behind each genre and how theyre related to eachother - Taxonomic names are assigned based on our current understanding of evolutionary relationships  - So similar species have similar names (liek *panthera le and Panther tigris* lion an tiger) because they share common ancestors compared to other species  - "In modern taxonomy, scientists try to name organisms in a way that reflects their evolutionary relationships. This means they look at how species are related to each other through evolution and try to group them based on common ancestors." - "For example, if two species share a recent common ancestor, they might be placed in the same genus or family. This approach helps scientists understand and communicate about the diversity of life on Earth in a way that reflects how species have evolved over time. It\'s like organizing a family tree, but for all living things!" - Carolus Linnaeus (oh silvia, you didnt know how i'd see this again...) (this man...)  - Father of western taxonomy  - Sought out to organism worlds biodiversity into a common framework - Created binomial nomenclature system;  - Each species has two names, a genus name and a species name - Its hierarchical system of nomenclature which is nice cuz evolution creates heiecarl patterns as well - We got the 7 step system to remember (any one of these 7 categories/unit is a taxon)  - King Philip Came Over For Great Soda  - Kingdom  - Phylum  - Class - Order  - Family  - Genus  - Species  - May have spurred thoughts of evolution by encouraging people to think about how things are related - Purpise of biological classification;  - Taxonomy is really important because facilitates communication  - It allows us to share key information about an organism in just its name because all the informatin related to it, is tied to its name like articles and stuff - Has predictive power because you can just know something about the organism from its naem without having to do extra work - Allows us to encode evolutionary history into the name (like the panthera) and show these relationships *in* just the name  - SO LONG AS THE NAME IS STABLE  - Sometimes taxonimists liek to switch things up and change names which is no bueno because then all literature of the past has a different name than the literature of the future and that makes thins muy hard to find info on!  - Systematics!  - NEEDS A ROBUST AND STABLE SYSTEMS OF ORGANISING ORGANISMS - Understanding Phylogenies;  - Phylogenetic Tree Basics - The image shows how evolution builds up from individuals to populations then species and then the broad relationships between different species  - We start with A the first step which shows individuals within a population (like similar butterflies)  - Then B which shows that within this population these butterflies will produce offspring  - After is C which indicates that the parent-child links create "lines of descent" that connect generations to previous generations  - For D we see individual family lines mix with other family lines within the population and form the population\'s gene pool by mixing the genes of its members A screenshot of a computer Description automatically generated - With E we see that species are made up of many populations that are linked by gene flow, the populations can be spread out and not in the same place but still be the same species (like humans!)  - Now almost done, with F we see that as populations f the same species bceom RI or evolve separately and develop RI or become isolated or adapt to different environments, they can evelo into different species and that is shown y the splitting of branches, the little one means the species evolved then went extinct, it ended without further divergence  - Lastly with G we see a phylogeny which maps out how different species are related through time and how different species diverged, their common ancestors, the whole shebang  - Components of a phylogenetic tree;  - Nodes;  - Historical linage splitting event, one species speciated and split into two  - Whenever we have a phylogeny where each node splits into exactly two branches, we will always have N-1 nodes (N=number of species)  - Branches (sometimes called edges); A diagram of a diagram of a diagram Description automatically generated - Correspond to single ancestor-descentdant linages - Connected to each other by nodes - Length can sometimes indicate evolutionary time/change passed - Tips! Leave! Terminals! OTUS! - Dont have descendants  - Can represent different things like;  - Individuals;  - If the individuals is being used as a representative of a whole species, liek a rare bird you only have one of and is a meuasme artifiact - Species;  - Most common - Species name at every tip - Clades;  - Each tip corresponds to like cats or dogs, whole caldes of stuffA diagram of a diagram of a branch Description automatically generated with medium confidence - Internal and external branches;  - Internal branches connect node to node  - External branches connect tip to node (terminal branches)  - Root  -  Earlliest point in time of phylogeny  - Often represents THE bad boy big guy one and only most common ancestor but is often also unlabelled  - Can hav eunroote phylogenies :( but noot common cuz we always wanna know about the species originsA diagram of a family tree Description automatically generated - Sister taxa - Immidetate descendants of any given ancestor - Branch off the same node - Parents and daughters;  - Ancestors and descendants relationships - Branch (parent) that gives rise to other branches (daughters) - Ingroups and outgroups; - Ingroups are the species you are interested in studying, like a bunch of frogs A diagram of a tree Description automatically generated - Outgroups are a related species, but not the same species that you use as a reference point to see what traits are derived.new (within the ingroup) and what are ancestral/old (common with outgroup)  - Provides a reference point to place root, ne node between ingroup and outgroup tells you where to put root - MCRA;  - Most recent common ancestor  - Youngest node ancestral to all lineages being looked at - You know this, don\'t really have to explain it - Clade; A diagram of taxon and taxon Description automatically generated - Any piece of the phylogenetic tree that includes an MRCA/node and its all of descendants - Natural evolutionary group because the are related bia a common ancestor - N-1 clades  - Monophyly is the act of separating things into clades, basically it is a clade - A phylogenetic tree can contain many clades - Grouping concepts  - Monophyly; A pair of scissors with a diagram Description automatically generated - A clade is a monophyletic group  - Important because they are natural evolutionary groups  - Clade test is that if you can separate them from the rest of the phylogeny with a single snip of the scissors its a clade  - Paraphyly - Not a natural evolutionary grouping concept because it leaves someone out :(  - Like reptiles, we tradionatlly dont include birds in with reptiles through they did evolve from.with reptiles adn so they are a part of the clade, so repltiesl are not a "real"evoletionary group because you gotta make two cuts, one to split it with the MCRA and anothe rto get rid of the birds!  - Just because you make two cuts doesnt mean paralhyly, theres another option 😮 - Polyphyly; A pair of scissors and a diagram Description automatically generated - A group of organisms classified together, but they dont share an immediate ancestor  - Eg, flying animals, includes bats (mammals), birds (repltiles...or not), insects (insects...)  - You got a group of organsims but no ancestor :(  - Trait evolution;  - Ancestral traits;  - A trait inherited from the MCRA  - Derived traits;  - Traits arisen within the given clade - A traits can be ancestral for once clade then derived for another A diagram of a person\'s evolution Description automatically generated - Synapomorphy;  - Trait shared by two or more groups of organism inherited from their MCRA - That branch is a synapomorphy  - Homology;  - Shared traits in different taxa due to a common ancestor! - Helps us understand evolutionary realtionships - Homoplasy;  - Shared traits in different taxa not due to a common ancestor!  - Convergent evolution be at work here :)  - A red herring and blight on our understand, meant to confused us and lead us astray (will mislead us basically) - Reconstructing Phylogenies;  - Why conduct phylogenetic analysis; A diagram of a dna molecule Description automatically generated - Understand the history of life  - Understand how things work.where they came from  - Understand large-scale patterns of evolution - Understand what traits evolved, when, where, how (what conditions) how fast etc.  - Understanding spread of disease sliek covid etc. - We can have a commone ancestor giving rise to descendants which have their own descendants etc and they will all have traits that are either shared or unique due to evolution  - Some traits may even go away with time  - Wehn reconstruction a phylogeny given the triats/variation of different species its really fun and cool and interesting A diagram of a tree Description automatically generated - You look at only the common traits amon the species - You then look at which species share more traits with another  - And from this you can infer the phylogenetic tree - I\'m not explaining it well here but look at the photos and you'll understand  - This is a very simplistic model and will only work for homologous traits not ones with homoplasy  - Notes on phylogeny reconstruction;  - Professional physlogenetic recoenstriction uses statistical models and data sets to make inferences  - Uses observed trati data, either phenotypic or genetic (often genetic because there so much genetic data)  - The relatedness is inferred from homologus traits which is going to be sytmeid by homoplasty mislead us  - Reconstructing the Tree of Life;  - Adanves in molecular sequencing technology has helped us to reconstruct more of the tree of life - Macroevolution: Understanding Large‐scale Evolutionary Patterns & Processes;  - Macroevolutinary insights often come from one of two disciplines;  - Palentology;  - Insights into macroevolution from fossil record - Direct evidence of evolutionary change  - Not everything fossilises well so lots of groups are not represented in the fossil record - Phylogentics;  - Insights into evolution from branching relations between organisims - Indiect eveidence of evolutionary changes because we have to construct phylogenies ourselves to learn about the past  - Works great for organisms with living relative because we can use their DNA ot make robust phylogenies - Fossil record;  - Helps us gain mega insight into mass extinction events (which there have been 5 of, we may be in the 6th with the way our extinction rates are going) A dinosaur and graph of graph Description automatically generated with medium confidence - We would have no idea about extinct species if not for fossils  - We would not know much about mass extinction events if not for fossils  - Fossils provide the only evidence we have for clades that have gone extinct - Only way of documenting long term global biodiversity (can document millions of years worth of change for example)  - Phylogenetics;  - Can help us study mass extinct event by documenting explosive diversification events that follow mass extinction - Liek after the asteroid wiped out the dinosaurs, birds and mammals diversified a lot and specieated A LOT - Other features associated with increased diversification; A diagram of insects and bugs Description automatically generated - Many traits are associated with diversification liek sexual seletion (makes them more lielky to diversify)  - We can make phylogenetic trees of sister taxa and see if the group that has the trait is more diverse than the other (if the one that has it is more diverse, then that trait is likely good for divesification Keywords for this section;  - ***[Taxon/Taxa:]***  any unit from the 7 stuff of classification  - ***[Phylogeny:]*** phylogenetic tree - ***[Bionmial nomenclature:]***  genus and species which make up the scientific name of stuffs - ***[Clade:]***  any group on a phylogeny including the MCRA and its descendants  - ***[Linnean hierarchy:]***  KPCOFGS