Biology 1108: Chapters 20, 23, 24 & 25

(Chapter 20)

(Chapter 20)

(Chapter 23)

(Chapter 23)

This is why it's true to say that humans are apes

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History - Calendar:

- 14 Bya - January 1: Origin of the universe (Big Bang) - 11 Bya - March 16: Formation of Milky Way galaxy - 4.5 Bya - September 2: Formation of Earth - 4.1 Bya - September 21: First life appears on Earth - 3.4 Bya - September 30: Photosynthesis - 2.4 Bya - October 29: Oxygenated atmosphere - 2.0 Bya - November 9: MRCA of all eukaryotes - 800 Mya - December 5: Multicellular life - 450 Mya - December 20: the first plants colonize land - 400 Mya - December 21: MRCA of all tetrapods - 200 Mya - December 26: MRCA of all mammals - 65 Mya- December 30: (most) dinosaurs go extinct DECEMBER: - 10 Mya - 6:00 PM: MRCA of humans and chimps - 200,000 ya - 11:52 PM: Anatomically modern humans - 12,000 ya - 11:59:32 PM: argiuclture - 200 ya - 11:59:59.5 PM: Industrial revolution NOTE: - Know that billion years (Bya - Billion years ago)

This is why it's true to say that birds are dinosaurs

- Bird's are literally dinosaurs - Bird's are more related to a brontosaurus than a t-rex - The only species of dinosaurs that aren't extinct are birds

Real-world applications of phylogenetics:

- Classifying species is a way to structure our human view of the world. - Example: We lump together various species of trees to which we give the common name of pines and distinguish them from other trees that we call first. - Higher classification levels are usually defined by particular characters chosen by taxonomists. - Characters that are useful for classifying one group of organisms may not be appropriate for other organisms. - The larger categories often are not comparable between lineages - Example: An order of snails does not exhibit the same degree of morphological or genetic diversity as an order of mammals.

Cladistics

- Common ancestry is the primary criterion used to classify organisms - Biologist place species into groups called clades NOTE: - An approach to systematic

Phylogenetic tree

Branching diagram of the evolutionary history of a group of organisms NOTE: - Describes the evolutionary relationship from one species to another - Names are assigned only to groups that include a common ancestor and all of its descendants - Example: because birds evolved from a group of reptiles, Aves is considered a subgroup of Reptilia

Orders ➝

Classes

Paraphyletic ("beside the tribe") Group

Consists of an ancestral species and some, but not all, of its descendants

Domain Archea

Consists of diverse group of prokaryotic organisms that inhabit a wide variety of environments

Domain Bacteria

Contains most of the currently known prokaryotes

Branch point

Represents a common ancestor of the two evolutionary lineages diverging from it. NOTE: - Example: Each tree has a branch point that represents the common ancestor of chimpanzees and humans. Chimps and humans are considered sister taxa.

Monophyletic ("single tribe") Group

Signifying that it consists of an ancestral species and all of its descendants

Of course, humans can be classified the same way:

Species: Homo sapiens Genus: Homo Family: Hominidae Order: Primates Class: Mammalia Phylum: Chordata Kingdom: Animalia Domain: Eukarya NOTE: - The more of these we share with another organism, the more closely related we are - Example: We have the same domain, kingdom, phylum, and class as elephants but only the same domain as bananas

Phylogenies

Teach us about the complex history of life on Earth NOTE: - Within every one of your cells is mitochondria. It branches off and never intersects again. But it might connect somewhere else - It is important to note that they are constantly being revised

Root

The most recent common ancestor of all taxa on the tree

Binomial

The name of the genus combined with the name of the specific epithet. NOTE: - Genus to which the species belongs - Epithet is unique for each species within the genus - Example: Panthera pardus, the scientific name for the leopard. Notice that the first letter of the genus is capitalized and the entire binomial is italicized.

Phylogeny (or phylogenetic tree): Nodes or branch points

The points at the ends of branches represent sequences or hypothetical sequences at various points in evolutionary history. NOTE: - They show an speciation event - Think about it going from the ancient time to the present - This occurs any time the branch splits from one to two

Taxonomy

The scientific study of how living things are organisms are named and classified NOTE: - Taxonomists employ comprehensive categories of classification - The taxonomic system is known as the Linnaean system

Systematics:

The study of the diversification of living forms and the relationships among these organisms through time

Systematic

The study of the diversification of living forms and the relationships among these organisms through time.

Taxon

The taxonomic unit at any level of the hierarchy NOTE: - Example: Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level that includes all the many orders of mammals. - Taxa broader than the genus are not italicized, though they are capitalized.

Phylogeny (or phylogenetic tree): Tips or taxa

The tips of the tree represent groups of descendent taxa (often species)

Phylogeny (or phylogenetic tree): Sister taxa

Two taxa that are each other's closest extant (living) relatives NOTE: - Closest living/extant relative - Among all the other ones represented on the tree, they are each other's relatives

Each species receives a ______—a two-part scientific name consisting of the genus and species

binomial

Phylogeny (or phylogenetic tree):

branching diagram showing a hypothesis about the evolutionary relationships among species NOTE: - Farther to the left is further back in time - Closer to the right is closer to the present time

Question: Birds, bats, and insects all separately evolved wings. Thus, the most recent common ancestor of birds, bats, and insects did not have wings. If you were to draw a phylogenetic group of all organisms with wings, it would be __________: a) monophyletic b) paraphyletic c) polyphyletic

c) polyphyletic NOTE: - The common ancestor isn't included! - Only the tips were included

The genus is always

capitalized NOTE: - Example:

This particular node is at the ____-showing the most recent common ancestor of all taxa on the tree.

root NOTE: - The first life on earth connects at some point - The most recent point in time where we share the most recent ancestor

Each of these levels can be referred to as a _____ (plural = taxa)-A named taxonomic unit at any given level of classification

taxon NOTE: - Example: The family Felidae and class Mammalia are both taxa

Phylogeny (or phylogenetic tree): How can we read a phylogeny and interpret evolutionary relationships?

the key is to look for where two taxa share a most recent common ancestor (MRCA) NOTE: - We don't want to focus on the order of the tips on the tree, but where two taxa share the most recent common ancestor - MRCA = Most Recent Common Ancestor - Example:

Closely related genera belong to

the same family NOTE: - Example: The genera Panthera and Puma (including mountain lions) both belong to the family Felidae

Closely related species belong to

the same genus NOTE: - Example: The leopard (Panthera pardus) and the lion (Panthera leo) a erboth in the same genus (Panthera)

All the different lineages that descend from a common ancestor have survived for

the same number of years. NOTE: - Example: Humans and bacteria had a common ancestor that lived over 3 billion years ago

Real-world applications of phylogenetics:

- Consider maize (corn), which originated in the Americas and is now an important food crop worldwide. From a phylogeny of maize based on DNA data, researchers have identified two species of wild grasses that may be maize's closest living relatives. These two close relatives may be useful as "reservoirs" of beneficial alleles that can be transferred to cultivated maize by cross-breeding or genetic engineering. - Phylogenetic trees can be used to infer species identities by analyzing the relatedness of DNA sequences from different organisms. - Example: Researchers have used this approach to investigate whether "whale meat" had been harvested illegally from whale species protected under international law rather than from species that can be harvested legally, such as minke whales caught in the Southern Hemisphere

Phylogenies can be rotated on any node:

- Each of the above phylogenies shows the exact same relationships - (We've simply roated them on the nodes shown in blue!) - important implication: The order of the tips on the phylogeny does not tell you relationships among taxa! NOTE: - Imagine that each branch has a swivel - This changes the order of the tips, but has not changed the relationships at all - The branching pattern has not changed at all - The relationships has not changed (look at where all the taxa share a common ancestor) - THIS IS WHY YOU CAN'T LOOK AT JUST THE TIPS - (ON EXAM) -

History:

- It can be hard for our little primate brains to comprehend huge amounts of time - One way to do this is to map these amounts of time onto an annual calendar--a metaphor we sometimes call a comic Callender - Beginning of universe: 12:01 AM on January 1st - Present day = 11:59 PM

Different Phylogenies Shapes:

- Phylogenies can be drawn in many different ways - Each of the example phylogenies show the exact same relationships - Despite their different shapes, each of these phylogenies shows the exact same relationships

Linnaean system: Categorization

- Places related genera into the same family - Families into orders - Orders into classes - Classes into phyla (singular, phylum) - Phyla into kingdoms, - Kingdoms into domains NOTE: - Example: This is like a postal address identifying a person in a particular apartment, in a building with many apartments, on a street with many apartment buildings, in a city with many streets, and so on.

Shared derived characters: - Part 2

- We look for these shared derived traits to help classify and understand the relationships between organisms - These are also the traits most useful for inferring phylogenies - Example: Milk in mammals - We share ancestry with turtles, but they do not produce milk

Key points of Phylogenetic Trees

1 . First, they are intended to show patterns of descent, not phenotypic similarity - Although closely related organisms often resemble one another due to their common ancestry, they may not if their lineages have evolved at different rates or faced very different environmental conditions - Example: Even though crocodiles are more closely related to birds than to lizards, they look more like lizards because morphology has changed dramatically in the bird lineage. 2. We cannot necessarily infer the ages of the taxa or branch points shown in a tree - Example: Just because humans and chimps are in a sister taxa does not indicate that chimpanzees evolved before humans. Rather, the tree shows only that chimpanzees and humans share a recent common ancestor, but we cannot tell when that ancestor lived or when the first chimpanzees or humans arose. - Unless we are given specific information about what the branch lengths in a tree mean we should interpret the diagram solely in terms of patterns of decent 3. We should not assume that a taxon on a phylogenetic tree evolved from the taxon next to it - Example: Just because humans and chimps are in a sister taxa does not indicate that humans evolved from chimpanzees or vice versa. We can infer only that the lineage leading to humans and the lineage leading to chimpanzees both evolved from a recent common ancestor. That ancestor, which is now extinct, was neither a human nor a chimpanzee.

Three Domains of Life:

1. Bacteria 2. Archaea 3. Eukarya NOTE: - They are a taxonomic level higher than the kingdom level - Much of the history of life has been about single-celled organisms

Three terms of phylogenetic:

1. Monophyletic 2. Paraphyletic 3. Polyphyletic

Two distinct components of systematics:

1. Taxonomy 2. Phylogenetics NOTE: - You have to have a representative

We want to create taxonomic classifications that

reflect evolutionary history and name only monophyletic groups (a.k.a. clades)

Rooted

A branch point within the tree that represents the most recent common ancestor of all taxa in the tree.

Shared ancestral characters:

A character that is shared by members of a particular clade but that originated in an ancestor that is not a member of that clade NOTE: - It is a shared one, but not unique to just itself

Shared ancestral character

A character that originated in an ancestor of the taxon NOTE: - Organisms have characters they share with their ancestors, and they also have characters that differ from those of their ancestors. - Example: All mammals have backbones, but a backbone does not distinguish mammals from other vertebrates because all vertebrates have backbones. - Example: For mammals, the backbone is an example

Clade

A group of species that includes an ancestral species and all its descendants.

Monophyletic

A group of taxa that includes a common ancestor and all of its descendants; a clade NOTE: - Common ancestor of a particular node - Common ancestor of A and B; Common ancestor of A and B; also C

Paraphyletic

A group of taxa that includes a common ancestor and some, but not all of its descendants NOTE: - It is missing A - It's missing one of the common decedents of an ancestor

Polyphyletic

A group of taxa that includes distantly related organisms but does not include their most recent common ancestor. NOTE: - (ON THE TEST) - Focuses on distant species

Basal taxon

A lineage that diverges from all other members of its group early in the history of the group NOTE: - Lies on one of the two branches diverging from the branch point that represents the common ancestor of the group. - The lineages represented by these two branches originated at the same point in time; hence, they have been evolving for the same length of time.

Taxon

A named taxonomic unit at any given level of classification. NOTE: - The taxonomic unit at any level of the hierarchy - Example: The family Felidae and class Mammalia are both taxa - Example: Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level that includes all the many orders of mammals. - Taxa broader than the genus is not italicized, though they are capitalized.

Phylogenetics

A scientific discipline concerned with inferring the evolutionary relationships among organisms

Taxonomy

A scientific discipline concerned with naming and classifying organisms NOTE: - Example: Bufo Bufo - Example: Plenthodon pauleyi - Should reflect evolutionary history

Outgroups

A species or group of species from an evolutionary lineage that is closely related to but not part of the group of species we are studying NOTE: - Example: The lancelet, a small animal that lives in mudflats and (like vertebrates) is a member of the more inclusive group called the chordates. Unlike the vertebrates, however, the lancelet does not have a backbone.

Ingroups

A suitable outgroup can be determined based on evidence from morphology, paleontology, embryonic development, and gene sequences.

Question 2#: Which is the closest relative of Taxon D?

A, B, and C equally NOTE: - Trace back each individual tip - D share's the most common ancestor with C, A, and C - DON'T JUST FOCUS ON THE TIPS, focus on tracing back to the most common ancestor (do it once at a time)

Domain Eukarya

All the organisms that have cells containing true nuclei. NOTE: - Includes many groups of single-celled organisms as well as multicellular plants, fungi, and animals.

Shared derived character

An evolutionary novelty unique to a clade NOTE: - Example: Hair is a character shared by all mammals but not found in their ancestors - This can refer to the loss of a feature - Example: The loss of limbs in snakes or whales. - It is a relative matter whether a character is considered ancestral or derived. - A backbone can qualify as a shared derived character, but only at a deeper branch point that distinguishes all vertebrates from other animals. - Unique to particular clades - All features of organisms arose at some point in the history of life

Monophyletic groups (clades)

Are important because they can teach us about the evolution of shared traits NOTE: - We care about the origin of species

Kingdom ➝

Domains

Shared derived characters:

Evolutionary novelties that are unique to a particular clade NOTE: - These are also the traits most useful for inferring phylogenies - Feathers are absent from D - These feathers have a different shape, but it is still a feather - It is an evolutionary novelty - We can say that the only ones that have these feathers are birds

Genera ➝

Family

Order of Hierarchical Classification:

Genera ➝ Family ➝ Order ➝ Class ➝ Phyla ➝ Kingdom ➝ Domains

Is Taxon B more closely related to Taxon A or to Taxon C?

Here the Most Recent Common Ancestor (MRCA) of Taxon A and Taxon B Here the Most Recent Common Ancestor (MRCA) of Taxon C and Taxon B is here. Because Taxon B shares a more recent common ancestor with Taxon A than it does with Taxon C, it is more closely related to Taxon A

Clades

Includes an ancestral species and all of its descendants NOTE - Clades are nested within a larger clades - Example: The cat group (Felidae) represents a clade within a larger clade (Carnivora) that also includes the dog group (Canidae).

Polyphyletic ("many tribes") Group

Includes distantly related species but does not include their most recent common ancestor NOTE: - Most recent common ancestor is not part of the group - Example: A group consisting of even-toed ungulates (hippopotamuses, deer, and their relatives) and their common ancestor is paraphyletic because it does not include cetaceans (whales, dolphins, and porpoises), which descended from that ancestor. - In contrast, a group consisting of seals and cetaceans (based on their similar body forms) is polyphyletic because it does not include the common ancestor of seals and cetaceans

Phyla ➝

Kingdom

Question 1# Which of the following taxonomic groups in the most inclusive?

Kingdom NOTE: - A kingdom includes the most phyla as it is the one closest to the bottom

Families ➝

Orders

Phylogenetic Trees as Hypotheses

Organisms in the tree are related to one another. The best hypothesis is the one that fits all the viable data NOTE: - A phylogenetic hypothesis may be modified when new evidence compels systematists to revise their trees. - While many older phylogenetic hypotheses have been supported by new morphological and molecular data, others have been changed or rejected. - We can make and test predictions based on the assumption that a particular phylogeny

Classes ➝

Phyla

Phylogenies Real World Examples:

Phylogenies have direct utility in epidemiology and public health. NOTE: - We can build phylogenies that are building rapidly in modern time - Example: We can sequence information from the SARS-CoV-2 virus to figure out where they come from and how other forms of the virus connect back to it

Phylogenetic bracketing,

We can predict (by parsimony) that features shared by two groups of closely related organisms are present in their common ancestor and all of its descendants unless independent data indicate otherwise. NOTE: - Example: There is evidence that birds descended from the theropods, a group of bipedal saurischian dinosaurs. As seen in, the closest living relatives of birds are crocodiles. Birds and crocodiles share numerous features: They have four-chambered hearts, they "sing" to defend territories and attract mates (although a crocodile's "song" is more like a bellow), and they build nests. Both birds and crocodiles also care for their eggs by brooding, a behavior in which a parent warms the eggs with its body. Birds brood by sitting on their eggs, whereas crocodiles cover their eggs with their neck. Reasoning that any feature shared by birds and crocodiles is likely to have been present in their common ancestor and all of its descendants, biologists predicted that dinosaurs had four-chambered hearts, sang, built nests, and exhibited brooding.

Maximum parsimony.

We should first investigate the simplest explanation that is consistent with the facts. NOTE: - Systematists can never be sure of finding the most accurate tree in large data sets - But, they can narrow the possibilities by applying the principle of Maximum Parsimony - Example: In the case of trees based on morphology, the most parsimonious tree requires the fewest evolutionary events, as measured by the origin of shared derived morphological characters. - Example: For phylogenies based on DNA, the most parsimonious tree requires the fewest base changes.

Horizontal Gene Transfer

a process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infections, and fusions of organisms. NOTE: - Phylogenetic trees are based on the assumption that genes are passed vertically from one generation to the next - Horizontal gene transfer is very important - Example: 80% of the genes in 181 prokaryotic genomes had moved between species at some point during the course of evolution. - It was common in the early history of life - It can occur between eukaryotes - Example: Over 200 cases of the horizontal transfer of transposons have been reported in eukaryotes, including humans and other primates, plants, birds, and reptiles. Nuclear genes have also been transferred horizontally from one eukaryote to another. -Eukaryotes can acquire nuclear genes from bacteria and archaea - Example: An 2013 genomic analysis showed that the alga Galdieria sulphuraria acquired about 5% of its genes from various bacterial and archaeal species. Unlike most eukaryotes, this alga can survive in environments that are highly acidic or extremely hot, as well as those with high concentrations of heavy metals. - Horizontal gene transfer has played a key role throughout the evolutionary history of life

Evolutionary lineage

a sequence of ancestral organisms leading to a particular descendant taxon.

binomial

a two-part, scientific name consisting of the genus and species NOTE: - All species have their own unique binomial name - The genus is always capitalized, and both the genus and species are italicized - Example: The leopard has the binomial Panthera pardus

A key step in reconstructing phylogenies is to distinguish homologous features from

analogous ones

A character found in both the outgroup and the ingroup is assumed to be

ancestral

The lengths of the tree's branches do not indicate the ______ __ ____________ ______ in each lineage

degree of evolutionary change NOTE: - The chronology represented by the branching pattern of the tree is relative (earlier versus later) rather than absolute (how many millions of years ago). - In some tree diagrams, branch lengths are proportional to the amount of evolutionary change or to the length of time since particular events occurred. - Example: Each branch length of the phylogenetic tree reflects the number of changes that have taken place in a particular DNA sequence in that lineage.

The order of the tips on the phylogeny ____ ___ tell you about relationships among taxa!

does not

Question: Of those listed, which of the following is the least inclusive and comprehensive taxonomic rank? 1. Genus 2. Family 3. Class 4. Order

genus NOTE: - Class is the most inclusive

Hierarchical Classification of Linnaeus: Species that appear to be closely related are

grouped into the same genus NOTE: - Example: The leopard (Panthera pardus) belongs to a genus that also includes the African lion (Panthera leo), the tiger (Panthera tigris), and the jaguar (Panthera onca).

Sister taxa

groups of organisms that share an immediate common ancestor that is not shared by any other group. NOTE: - The members of a sister group are each other's closest relatives - Useful way to describe the evolutionary relationships shown in a tree - Example: The evolutionary lineage leading to lizards shares an immediate common ancestor with the lineage leading to chimpanzees and humans. Thus, we can describe this portion of the tree by saying that of the groups shown here, lizards are the sister taxon to a group consisting of chimpanzees and humans.

Taxonomic classifications are __________. meaning that they're increasingly inclusive and comprehensive (i/e/. have more taxa)

hierarchical NOTE: - Each of these levels can be referred to as a taxon (plural = taxa)-A named taxonomic unit at any given level of classification - Example: The family Felidae and class Mammalia are both taxa - Each species receives a binomial—a two-part scientific name consisting of the genus and species - The genus is always capitalized, and both the genus and species are italicized - Example: The leopard has the binomial Panthera pardus - Closely related species belong to the same genus - Example: The leopard (Panthera pardus) and the lion (Panthera leo) are both in the same genus (Panthera) - To be a species, you have to be able to produce viable offspring. - Closely related genera belong to the same family - Example: The genera Panthera and Puma (including mountain lions) both belong to the family Felidae - Each of these taxa is increasingly more inclusive and comprehensive - Example: There are only one species that is Panthera pardus, but there are many more species in the genus Panthera, even more in the family Felidae, and even more in the order Carnivora, etc.

A phylogenetic tree represents a

hypothesis about evolutionary relationships

Each of these taxa is increasingly more ________ and _____________.

inclusive; comprehensive NOTE: - Example: There are only one species that is Panthera pardus, but there are many more species in the genus Panthera, even more in the family Felidae, and even more in the order Carnivora, etc.

Both the genus and species are

italicized NOTE: - Example:

Question 3# Which of the following is a shared derived trait in mammals? presence of hair presence of wings presence of a backbone presence of a heart

presence of hair