Chapter 23

phylogeny

"production of phyla", the evolutionary history of any group of organisms from a common ancestor. To do this scientists need evidence from shared traits (homologous traits), geographic distributions like fossils. Classifications are based on the patterns of shared ancestry. once established they help us understand evolutionary patters that might provide clues to the origins and spread of HIV and other pathogens. Phylogenies also help identify new species and predict their characteristics, biodiversity, and ecological mechanisms. Phylogenies are testable hypotheses. They are either supported or falsified by the available data. Systematics proceeds by constantly re-evaluating data, hypotheses, and theoretical constructs. Evolutionary history of group of organisms: who evolved from what, in what order, and (possibly) when Represents TESTABLE HYPOTHESIS

diapsids

(traditional reptiles and birds) and the mammals. Within the diapsid group, the archosaurs include the crocodiles, flying reptiles (the extinct pterosaurs), the extinct dinosaurs, and the birds. The diapsids and the archosaurus are two large monophyletic groups within the amniota.

systematics

-study of the diversity of organisms and their evolutionary relationships -Goal of systematics is to reconstruct phylogenies -Phylogenies help answer other biological questions -Aid in identifying/ describing new species -Helps understand biodiversity To build phylogenies systematists use Morphology, Physiology, Molecules (molecular systematics) DNA RNA Proteins, Fossils, Behavior, Development, Geographic Distributions

carolus Linnaeus

Father of modern taxonomy 1) Binomial nomenclature 2) Hierarchical classification Wrote systema Natural and Species plantarum Linnaeus classification of all know living organisms: Classified all life as either plant or animal Classifications based on structural similarities, not explicitly evolutionary relationships.

Important concepts guide interpretation of cladograms

First, the relationships among taxa are determined only by tracing along the branches back to the most recent common ancestor and not by the relative placement of the branches along the horizontal axis. A second important concept is that the cladogram tells us which taxa shared a common ancestor and how recently they shared a common ancestor. The ancestor itself remains unspecified. The cladogram does not estab- lish direct ancestor-descendant relationships among taxa. In other words, a cladogram does not suggest thata taxon gave rise to any other taxon. Note that any particular cladogram, depicts only SOME of the nodes and branches in the tree of life.

some organisms do not fit into the current classification...

For example beetles have 400,000 species so there are... subclasses in a class, each subclass has infraorders, each infraorder has multiple superfamilies, and each superfamily has numerous families.

a two kingdom system

Linnaeus Plantae and Animalia

Population

Made up of all the individuals of the same species that live in a particular area. A population has a dimension in space-its geographic range-and also a dimension in time. Each population extends backward in time. Somewhat like branches of a tree, a population may diverge from other populations enough to become a new species. There are various degrees of evolutionary relationships, depending on the degree of genetic divergence since their populations branched from a common ancestor.

Archaea

Prokaryotes, unicellular, microscopic, NO peptidoglycan, they differ biochemically from bacteria Decomposers, recycle carbon, nitrogen, and other nutrients, methanogens are anaerobes that inhabit sewage, swamps, and animal digestive tracts, extreme halophiles inhabit salty environments, extreme thermophiles inhabit hot, sometimes acidic environments.

Bacteria

Prokaryotes, unicellular, microscopic, cell walls include peptidoglycan. Most are decomposers, parasitic, pathogenic, chemosynthetic autotrophs, important in recycling nitrogen and other elements, some used in industrial processes.

Synapomorphies

Shared DERIVED characters are homologous characters unique to particular taxa These characters were inherited from more RECENT common ancestor These are used to construct phylogenies Example: is hair is synapomorphy of mammals This character is useful in vertebrate phylogeny reconstruction because only mammals possess this trait Distinguishes mammals from all other vertebrates More synapomorphies= More recent common ancestor -synapomorphies can be lost No longer possessed by certain members of clade

convergent evolution

Similar structures sometimes evolve when unrelated or distantly related species become adapted to similar environmental conditions. Thus, wings may occur in two or more species not derived from a recent common ancestor. Sharks and dolphins have similar, but independently derived, body forms because they have become adapted to similar environments (aquatic) and lifestyles (predatory).

maximum likelihood

Systematists also use maximum likelihood to make deci- sions, especially when analyzing molecular data. Maximum likelihood is a statistical method that depends on probability (e.g., the probability that nucleotide sequences in DNA change at a constant rate over time). Complex computer programs analyze large data sets and report the probability of a particular tree. -often used with MOLECULAR DATA -statistical method based on probabilities of certain events such as G mutating to A.

species

basic unit of classification Group of organisms that can interbreed and produce fertile offspring

CBOL's DNA barcode effort

scientists will find a particular region of DNA (1) that is present in all species, (2) that is relatively short and easy to sequence, and (3) for which each species has a unique sequence of nitrogenous bases. This DNA region would be a global tool for species identification.

sister taxa

sister groups, share a more recent common ancestor with one another than either taxon does with any other group shown on a cladogram.

steps in constructing a cladogram

1. Select the taxa, which may consist of individuals, species, genera, or other taxonomic levels 2. Select the homologous characters to be analyzed. In our example we use seven characters. For each character, we must define all the different conditions, or states, as they exist in our taxa. For simplicity, we consider our characters to have only two different states: present or absent. Keep in mind that many characters used in cladistics have more than two states. For example, black, brown, yellow, and red may be only a few of the many possible states for the character of hair color. 3. organize the character states into their correct evolutionary order. For this step, we use outgroup analysis

amnion

A membrane that forms a fluid filled sac around the embryo. Reptiles, birds, and males all have this. The fluid within the amnion prevents them from drying out. Thus, the amnion allows development in terrestrial environments. Animals with an amnion make up a monophyletic group, the amniotes, or Amniota

monophyletic group

A monophyletic group includes an ancestral species and all its descendants (FIG. 23-7a). It is defined by shared derived characters. Mammals, for example, have mammary glands that produce milk for the young, three small bones in the middle ear, and a muscular diaphragm. All mammals are thought to have evolved from a common ancestral mammal that had these shared derived characters, and all descendants of this ancestor are mammals. Monophyletic taxa are clades. They are referred to as "natural" groupings because they represent true evolutionary relationships and include all close relatives -Systematist attempt to recognize/ form monophyletic groups (clades) of organisms -monophyletic group: includes ancestral species and all of its descendants. defined by many synapomorphies -example: mammals are monophyletic group/clade and the synapomorphies include hair, ammary glands, three middle ear bones, muscular diaphragm, etc. -notice that phylogenies containsn MULTIPLE NESTED monophyletic groups

paraphyletic group

A paraphyletic group is a group that contains a common ancestor and some of, but not all, its descendants. Members of the group share ancestral characters. As discussed the traditional class Reptilia is paraphyletic because it does not include all descendants of the most recent common ancestor of reptiles. Birds share a recent common ancestor with reptiles. -systematists try to re-classify old paraphyletic groupings. paraphyletic group: contain common ancestor and some, but not all, of its descendants Example: old 'Class Reptillia' excludes birds -Paraphyletic groups share ancestral characters (symplesiomorphies)

polyphyletic group

A polyphyletic group consists of several evolutionary lines that do not share the same recent common ancestor. Biologists might have mistakenly classified the members of such a group together because these organisms share similar (homoplastic) features arising from convergent evolution. Systematists try to avoid constructing polyphyletic taxa because they are unnatural and misrepresent evolutionary relationships. Polyphyletic taxa are sometimes accepted temporarily until research proved additional data.

ways molecular systematics has helped...

According to rRNA analysis, fungi are more closely related to animals than to plants. Animals and fungi share a more recent common ancestor, perhaps a flagellate, a one-celled protist that has one or more long, whiplike flagella (used for locomotion). These gene sequences for rRNA are useful because the number of base pairs is manageable, the DNA has shown little change over long evolutionary periods, and the genes show some species-specific variability among bacteria and archaea. Researchers now typically compare nitrogenous base sequences from many different genes of the organisms under study. Molecular sequence data have been sampled from the majority of all known species. Analysis of the comparisons of exon and intron nucleotide sequences allowed these researchers to build a cladogram of Canidae species. The data indicated that the dog is most closely related to the gray wolf.

outgroup

An outgroup is a taxon that is considered to have branched off earlier than the taxa under investigation -An ideal outgroup is the closest relative of the group being studied, its sister taxon, and has not been highly modified since its origin. Recall that sister taxa evolved from the same recent common ancestor. Systematists argue that an outgroup is likely to retain the ancestral state for characters being used in the analysis, allowing the researchers to identify the evolutionary changes leading to derived characters. -used to determine of homologous characters are ancestral (symplesiomorphies) or derived (synapomorphies) -taxon that diverged earlier than taxa being studied (in group) -Best outgrip is closest relative (sister taxa) of in-group -represent approximation of ancestral condition of in-group

Reversal

Another challenge in deciding homology, in which a trait reverts to its ancestral state. A reversal removes a similarity that had evolved. A characteristic that superficially appears homologous but is actually independently acquired by convergent evolution or reversal is described as exhibiting homoplasy.

Shared ancestral characters

Are features that were present in an ancestral species and remain present in all groups descended from that ancestor. For example, the vertebrae, present in all vertebrates (with the exception of the hagfishes), is an ancestral character for study of classes within the subphylum Vertebrata. -Studying the presence or absence of the vertebrae does not help us discriminate among various classes of vertebrates (e.g., between amphibians and mammals) because all indi- viduals in these classes (except the hagfishes) have vertebrae.

2 different groups of prokaryotes

Bacteria and Archaea. They're different from one another but archaea are genealogically more closely related to the eukaryotes than they are to the bacteria. Archaea have a combination of bacteria-like and eukaryote-like genes. Bacteria are characterized by the presence of a compound called peptidoglycan in their cell walls, whereas this compound is not present in archaea.

Binomial system of nomenclature

Carolus Linnaeus developed this system to name organisms. Organisms are named using a binomial system. Each species is assigned a unique two-part name. Genus is the first part: Noun and capitalized Specific epithet is second part: Adjective and lowercase Full name is italicized Derived from Latin or Greek

systematist base taxonomic decisions on recent shared ancestry

Dolphins share important homologous derived characters (synapomorphies) with mam- mals: mammary glands, which produce milk for the young; three small bones in the middle ear; and a muscular diaphragm that helps move air into and out of the lungs, to name just a few traits. Thus, our evidence suggests that dolphins and mammals share a common ancestor, and we classify dolphins as mammals. Dolphins are included within the Mammalia because all the available evidence suggests that they evolved from the same recent ancestor as the rest of the mammals. Even if dolphins evolved to completely lose all body hair, they would still be classified within the Mammalia because of their ancestry.

branch points

Each branch points represents a major evolutionary step. Note that shared derived characters are nested. As you trace the tree from its root to its tips, each branch reflects the addition of one or more shared derived characters. When we compare the nodes, the order of divergence (branching) is indicated by relative distance from the base of the diagram. The farther a node is located from the base of the cladogram, the more recently the group diverged.

kingdom Protista...

Euglena was placed in this group. Other unicellular organisms like protozoa. Algae is assigned here too (including multicellular forms), water molds, and slime molds. It is mainly unicellular, aquatic eukaryotic organisms.

Tetrapods

Had 4 limbs instead of the pectoral and pelvic fins of their fish ancestors. All the modern amphibians, reptiles, birds, and mammals evolved from that group of early tetrapods, members of the modern taxa share many traits. For example, the wings of bats, the front legs and paws of tigers, the front flippers of whales, and the front limbs of frogs all share similar bone structures because the genes for these bones were inherited from the same earliest tetrapods. We say that the bones are homologous among these animals. Because of shared ancestry they are known as the group Tetrapoda. The taxonomic group Tetrapoda is not defined by the presence of four legs; in fact, many groups of animals that are classified as tetrapods have either no limbs (e.g., snakes and limbless lizards) or greatly modified limbs (e.g., whales and birds).

remote common ancestry

Homologous characteristics in the largest group (such as phylum or class) of organisms being studied and interprets them as indicating the most remote common ancestry.

The three MAIN domains

Include Archaea, Bacteria, and Eukarya. Many suggest that genes of eukaryotes came from archaea. An archaean was the host cell in the endosymbiosis that led to the evolution of eukaryotes. These three domains have a common ancestor of all living organisms.

Eukarya

Include... PROTIST- Eukaryotes, unicellular or simple multicelular. Protozoa are important part of zooplankton. Algae are producers in marine and freshwater ecosystems. Oxygen source. some protist cause diseases like Malaria. PLANTAE- Eukaryotes, multicellular, photosynthetic, has multicellular reproductive organs, cell walls of cellulose. Terrestrial biosphere as primary producers important source of oxygen in earths atmosphere. FUNGI- Eukaryotes, heterotrophic, absorb nutrients, no photosynthesis, body is composed of hyphae that are threadlike which infiltrate food or habitats, cell walls of chitin. Decomposers, some parasitic and pathogenic, symbiotic relationships like plant roots and mycorrhizae or algae and lichens, yeast used in bread, alcohol, chemicals, or antibiotics ANIMALIA- Eukaryotes, multicellular heterotrophs, exhibit tissue differentiation and complex organ systems, most able to move by muscular contraction, nervous tissue coordinates response to stimuli. Consumers, some are herbivores, predators or detritus feeders.

Symplesiomorphies

Not all homologous characters are equally useful symplesiomorphies, shared ancestral characters possessed by most or all taxa being studies, aren't very useful These characters were inherited by more distant common ancestor Example: Vertebrae are shared ancestral character of all members of subphylum vertebrata: this character is NOT useful in understanding how vertebrates are related to one another because they all possess it

homoplasy

Organisms can also be similar due to homoplasy Homoplasy: when organisms share a similar characteristic die to convergent evolution Convergent evolution: occurs when natural selection INDEPENDENTLY produces similar adaptations in organisms under similar environmental pressures Similar characteristics DID NOT come from their common ancestor Homoplasius characters should NOT be used in constructing phylogenies

HIV

Phylogenetic information has proven important in medical research and often has public health implications. Human immunodeficiency virus (HIV), the virus that causes acquired immunodeficiency syndrome (AIDS) in humans, has had a devastating effect on humans since it first became prevalent in the 1980s. A major medical question concerned theorigin of this virus. HIV is a lentivirus, a group of retroviruses (viruses that use RNA as their genetic material). Scientists have been able to determine the sequences of nucleotides in the RNA of many strains of HIV that have infected humans around the world. Researchers have sequenced somewhat similar viruses, called SIV viruses, that infect other primate species. Systematists have used these nucleotide sequences to generate phylogenetic trees for the viruses. -When researchers mapped the primate host species onto the phylogeny for the viruses, they found that HIV-2, the somewhat less virulent virus, is most closely related to an SIV virus in a species of monkey (sooty mangabey) -The more virulent HIV-1 strains have evolved from a virus that infected chimpanzees. -Many primate species are hosts for human pathogens that have spread into human populations, causing epidemics. Understanding the source and spread of these infections may lead to prevention measures that mitigate or prevent future epidemics.

kingdoms include...

Plantae, Animalia, Protista, Fungi (which include the mushrooms, molds, and yeasts), Prokaryotae (established to accommodate the bacteria, they do not have nuclei and other membranous organelles and do not undergo mitotic division) There are 5 kingdoms

Genus

The first part of a binomial scientific name is a noun that designates the genus. Always capitalized. Underlined or italicized. The genus or generic name can be used alone to designate all species in the genus.

parsimony

The most common criterion is the principle of parsimony: they choose the simplest explanation to interpret the data. Parsimony, a guiding principle in many areas of research, is based on the experience that the simplest explanation is probably the correct one. Applied to choice of cladograms, parsimony requires that the cladogram with the fewest changes in characters (the one with the fewest homoplasies) be accepted as most probable it is often possible to generate several cladograms that are equally parsimonious. The cladograms that are selected are the ones with more shared derived char- acters. The cladograms with more homoplasies are excluded because homoplasies are less likely to evolve than shared derived characters. -common criterion fro constructing phylogenies -MOST SIMPLE explanation is most likely: phylogeny with fewest character changes (fewest homoplasies) most probable

shared derived characters/ synapomorphies

The novel traits that evolve and remain present in the descendant taxa. Shared derived characters originate in a recent common ancestor and are present in its descendants. Species that share derived characters form a clade. These are recently evolved homologies, and they are used to identify points where groups diverged from one another. A trait viewed as a derived character in a more inclusive (broader) taxon may also be con- sidered an ancestral character in a less inclusive (narrower) taxon. For example, vertebrae are a shared derived character among vertebrates, but an ancestral character among mammals. -The presence of a blowhole in dolphins is a derived character within mammals. When we compare dogs, dolphins, and whales, we find that dolphins and whales share this derived character, providing evidence that these animals evolved from a common ancestor not shared by dogs.

molecular clocks

The num- ber of differences in certain DNA nucleotide sequences in two groups of organisms may approximately reflect how much time has passed since the groups branched from a common ances- tor. (This can be true only when the mutations in DNA occur at a steady rate.) Thus, specific DNA sequences may be useful as molecular clocks.

Hierarchy

The range of taxonomic categories. Carolus Linnaeus devised a system for assigning species to a hierarchy of increase broader groups. From most broad or general to most specific is... Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species. Dear King Phillip Came Over From Great Spain Domain is the most inclusive while Species is the least inclusive

Specific epithet

The second part is an adjective modifying the genus-noun, is called the specific epithet. Usually not capitalized. Underlined or italicized. A specific epithet alone is not the name of the species, some can be used as a second name of species in different genera. Never used alone, it always needs to follow the full or abbreviated genus name.

Biological diversity/ biodiversity

The variety of living organisms and the ecosystems they are part of are referred to as biological diversity, or biodiversity. The totality of life on Earth represents our biological heritage, and the quality of life for all organisms depends on the health and balance of this worldwide web of life-forms. For example, we depend on organisms to maintain the life-sustaining composition of gases in the atmosphere, form soil, break down wastes, recycle nutrients, and provide food for one another.

Difference between Prokaryote and Eukaryote...

procariotique ("before nucleus"), to describe bacteria eucariotique ("true nucleus"), to describe all other cells

molecular homologies

These ell clarify phylogeny. Variations in the structure of specific macromolecules among species, just like differences in anatomical structure, result from mutations. Advances in molecular biology have provided the tools for biologists to compare the macromolecules of various organ- isms. In fact, organisms can now be identified by their molecular structure.

Why do some organisms share many features?

They share features because they have all inherited those traits from the same ancestor. They are "related" via shared ancestors and the traits they share are homologous traits.

a five kingdom system

Whittaker 1969 Monera, Protista, Fungi, Plantae, Animalia

A six kingdom system

Woese Eu-bacteria, Archae-bacteria, Protista, Fungi, Plantae, Animalia

A three domain system

Woese 1990 Bacteria, Archaea, Eukarya Ancient archaean was likely host cell in the endosymbiosis that ed to eukaryotes archaeans more closely related to eukaryotes than to bacteria. -Two domains consist of unicellular prokaryotes: microorganisms with no internal membrane-bound organelles or nucleus. Domain Bacteria and Archaea -Domain Eukarya comprised of unicellular and multicellular organisms with membrane-bound organelles and a nucleus in their cells: subdivided into kingdoms Plantae, Fungi, Animalia, and many 'protist' supergroups Based on current knowledge these are the 3 main branches of the tree of life

how a cladogram is constructed...

a cladogram is constructed by considering shared derived characters. Our objective is to construct a cladogram that requires the fewest number of evolutionary changes in the characters. Taxa are grouped by the presence of shared derived characters. To form a valid monophyletic group, all members must share at least one derived character. Membership in a clade cannot be established by shared ancestral characters. -Recall that the root, or base, of the cladogram represents the common ancestor for all taxa being analyzed. -cladorgrams are hypothetical evolutionary relationships; they are constructed by analyzing shared DERIVED characters.

endosymbiosis

a process in which one organism lives inside the cell of another organism and the two become dependent on each other. Eukaryotic cells most likely evolved from prokaryotic cells that lived symbiotically, one within another. Mitochondria and chloroplast originated from prokaryotes.

phylogenetic systematics

also know and cladistics. There are many different approaches to name and make relationships between different organisms. Three major schools emerged were... Phenetics (numerical taxonomy), evolutionary taxonomy, and phylogenetic systematics. The consensus has come to borrow from the three different approaches but largely adopts from the phylogenetic systematics. The goal is to reconstruct the genealogical relationships among species and that the best evidence for such relationships can be found in the patterns of traits shared by organisms (homologous traits). When scientist cant separate ancestor and derived states for certain traits; there the more statistical approaches from phonetics are employed to construct phylogenies. -Systematists find that some traditional group names do not reflect monophyletic groups and previously this is what they wanted to use to name a lot of species. -to reconstruct phylogenies they use common ancestry inferred from shared characters, including structural, developmental, behavioral, and molecular similarities, as well as from fossil evidence.

molecular systematics

focuses on molecular structure to clarify evolutionary relationships. DNA, RNA, and amino acid sequencing are used to compare the macromolecules of organisms being studied. Macromolecules that are functionally similar in two different types of organisms are con- sidered homologous if their subunit sequence is similar. Such comparisons provide systematists with valuable information about the degree of relatedness among organisms. The more similar the sequences are the more closely related they are to one another. Systematists look to ribosomal RNA (rRNA) structure and the DNA sequences that code for the RNA in ribosomes (ribosomal DNA) to help determine phylogenies. The division of organisms into 3 domains was based on the comparison of rRNA. rRNA have been highly conserved during evolution.

horizontal gene transfer

gene swapping takes place between one genome and another within one taxon or between genomes in different taxa. Genes move from one individual to another or from one species to another species in the same generation. Can occur by exchange of DNA among different populations or species of bacteria or arches or by interbreeding between closely related groups. Another way is through endosymbiosis in eukaryotes. Horizontal gene transfer occurs between free-living organisms classified in different domains. The common ancestor of all living things may have been a community of species that traded their genes. Common ancestor of all life may have been community of species that frequently engaged in HGT -exchange of genetic information between 2 individuals (of same or different species) that are NOT parent and offspring -HGT between bacteria and archaea may have given rise to eukaryotes

vertical gene transfer

genes are transmitted from parent to offspring within the same species. similarities among species in their heritable traits to be the result of shared ancestry, or homology. For example, if two species share the same sequence of nitrogenous bases in their DNA for a particular gene, we hypothesize that this sharing is due to the two species having inherited that particular gene from the same ancestor.

phylogenetic trees

graphically represent hypothesized evolutionary relationships among organisms that have a common ancestor. The type of tree we use is a cladogram and each branch is a clade, a group of organisms with a common ancestor. Each branching point know as the node represent divergence or splitting from a common ancestor. A phylogram can be constructed to indicate time or rate of evolution as well as relationships among taxa. in a phylogram the length of the branch is proportional to the amount of inferred change in characteristics. Branches represent clades: and clades are groups of organisms with a common ancestor -External/ terminal branches usually have EXTANT ( Living( taxa at their tips -Internal branches represent ancestors (usually EXTINCT) of taxa on external branches -Nodes (branching points) represent taxa diverging from their common ancestor. Represent LAST common ancestor from that node. Further node is from root= more recently taxa diverged -Root represents most recent common ancestor of all taxa depicted in tree -Root= node at base of tree -branches of trees represent entire lineage of organisms -splitting (divergence) of a branch represents separation of two lineages that no longer interbreed with each other

Taxon or taxa

is a formal grouping of organisms at any given level. Organisms are placed into their particular taxa because they share particular ancestry.

Classification

means arranging organisms into groups based on similarities that reflect evolutionary relationships among lineages.

Outgroup analysis

outgroup analysis is used in constructing and interpreting cladograms. -a research method for estimating which attributes are shared derived characters in a given group of organisms.

homology

systematist use homologous characters when constructing phylogenies Homology: is when two or more species share a similar characteristic because they inherited it from their common ancestor

Taxonomy

the science of naming, describing, and classifying organisms, is an important aspect of systematics. -systematic classification:arranging into groups based on similarities that reflect evolutionary relationships

ingroup

the taxa under investigation are the ingroup.