Phylogenies

parisomy

the logical principle that the most likely explanation of a phenomenon is the most economical or simplest. When applied to comparison of alternative phylogenetic trees, it suggests that the one requiring the fewest evolutionary changes is most likely to be correct.

root

the most ancestral branch in the tree

cladistic approach

the most commonly used method of inferring phylogenetic trees. is based on the principle that relationships among species can be reconstructed by identifying shared derived characters - synapomorphies

Several complications to resolve when inferring a tree

- traits can be similar in two species not because those traits were preset in a common ancestor, but because similar traits evolved independently in two different lineages - sometimes a reversal in a change occurs, such as an A->C transition in a nucleotide in one branch followed by a C->A change in the same nucleotide in a subsequent branch, thus creating the appearance that no change has occurred - sometimes the species forms a monophyletic group one way according to one trait in the matrix and a different way according to a different trait in the matrix

What is the difference between a branch and a node on a phylogenetic tree?

A branch is a population through time; a node is where a population splits into two independent populations.

Which of the following would be useful in creating a phylogenetic tree of a taxon? I) morphological data from fossil species II) genetic sequences from living species III) behavioral data from living species

All three

Which of the following statements most accurately explains why analogous traits are NOT informative for constructing phylogenetic trees?

Analogous traits represent convergent evolution, and do not represent synapomorphies defining a monophyletic group.

How do lizard species on mainland California compare in diversity to those found on islands?

Due to more open ecological opportunities on a given island, greater differences occur between island species.

Why is bipedalism (walk on two feet) considered a synapomorphy for hominins (the group that includes humans)?

Hominins are the only mammal group to walk on two legs. No other group in mammals has this trait

Are streamlined bodies in dolphins and ichthyosaurs homologous or convergent

In a phylogenentic analysis, the tree shows that dolphins occur within the mammal clade, whereas ichthyosaurs are more closely related to lizards. The sister groups to dolphins and ichthyosaurs (the most closely related branches on the tree) do not posses streamlined bodies, flippers, and fins like dolphins and ichthyosaurs do. Based on this data, it is logical to argue that the similarities between ichthyosaurs and dlphins result from convergent evolution. The convergent traits do not occur in the common ancestor of the similar species. Streamlines bodies, flippers, and dorsal fins are adaptations that help any aquatic species - whether it is a reptile or mammal - chase down fish in open water

Which of the following statements is true about a phylogeny, as represented by a phylogenetic tree? I) Descendant groups (branches) from the same node do not necessarily share any derived characters. II) A monophyletic group can be properly based on convergent features. III) The ancestral group often has all the synapomorphies of the descendant species.

None. Not I, II, or III.

A "one-snip test" is recommended to identify monophyletic groups - meaning that if you cut any branch on a tree, everything that "falls off" is a monophyletic group. Why is this valid?

One snip gets an ancestor and all of its descendants.

Are Hox Genes in fruit flies and human homologous or convergent?

Scientists believe that the Hox genes in fruit flies and humans are homologous. Evidence to support the hypothesis - Group of Hox genes are organized on chromosomes in a similar way. They are found in gene clusters, and similar gene are often found in the same order on the chromosome. Genes with these characteristics are called gene families. The organization of the gene families is nearly identical among insect and vertebrate species -All Hox genes share a 180-base-pair sequence called the homeobox. The portion of a protein encoded by the homeobox is almost identical in insects and vertebrates and has similar function. It binds to DNA and regulates the expression of other genes. - The products of the Hox genes have similar functions: identifying the locations of cells in embryos. They are also expressed in similar patterns in time and space. Further, if traits found in distantly related lineages are similar due top common ancestry, then similar traits should be found in many intervening lineages on the tree of life - because all of the species in question inherited the trait from the same common ancestor. Indeed, all other lineages of animals that branched off between insects and mammals have similar Hox genes. The internal consistency of the genetic, developmental, and phylogenetic data provide strong evidence that Hox genes in fruit flies and humans are homologous.

Why is the principle of parsimony important in constructing phylogenies?

The principle of parsimony reduces the effect homoplasy will have on the phylogenetic tree. Employing the principle of parsimony reduces the effect homoplasy will have on the phylogenetic tree. Using parsimony, the most likely tree is the one with the least number of changes.

Members of two different species possess a similar-looking structure that they use in a similar way to perform about the same function. Which of the following would suggest that the relationship more likely represents homology instead of convergent evolution?

The two species share many proteins in common, and the nucleotide sequences that code for these proteins are almost identical.

Why are gene duplications, such as those in the Hox loci, often associated with evolutionary divergence?

When there is only one copy of a gene, natural selection may purge a mutation, preventing it from performing a new function. Selection on the second copy may be relaxed because the first copy is producing all necessary gene products. Mutations conferring new properties may accumulate in the second copy. Having an extra copy of a gene allows an organism to retain the existing function with one copy, but to "experiment" through mutations with the second copy.

paraphyletic group

a group that includes an ancestral population and some but not all of its descendants

polytomy

a node that depicts an ancestral branch dividing into three or more (rather than two) descendant branches; usually indicates that insufficient data were available to resolve which taxa are more closely related.

outgroup

a taxon that diverged prior to the taxa that are the focus of the study; helps to root the tree used to establish the polarity of each trait - that is, whether a character state is ancestral or derived

synapomorphy

a trait found in two or more taxa that is present in their most recent common ancestor but is missing in more distant ancestors Synapomorphies allow biologists to recognize monophyletic groups, also called clades or lineages

Which of the following statements best describes the rationale for applying the principle of parsimony in constructing phylogenetic trees? a. Similarity due to common ancestry should be more common than similarity due to convergent evolution. b. The outgroup roots the tree, allowing the principle of parsimony to be applied. c. The molecular clock validates the principle of parsimony. d. Parsimony allows the researcher to "root" the tree.

a. Similarity due to common ancestry should be more common than similarity due to convergent evolution.

nodes

aka a fork - a point within the tree where a branch splits into two or more branches

monophyletic group

an evolutionary unit that includes an ancestral population and all of its descendants, but no others. Synapomorphies identify monophyletic groups.

character

any genetic, morphological, physiological, or behavioral characteristic to be studied.

taxon (taxa plural)

any named group of organisms at any level of classification system

Trees created using cladistic analysis focuses on branching patterns - the branching lengths are

arbitrary. some analyses produce trees who branch lengths represent genetic distances or time since divergence (but its obvious)

ancestral trait

characteristic that existed in an ancestor

Some beetles and flies have antler-like structures on their heads, much like male deer do. The existence of antlers in beetle, fly, and deer species with strong male-male competition is an example of _____.

convergent evolution

Which is strong evidence that similar traits in different evolutionary lineages are the result of homology and not homoplasy? a. The traits are analogous. b. The traits are genetic, not morphological. c. The traits are not also found in many intervening lineages on the tree of life. d. The traits are also found in many intervening lineages on the tree of life.

d. The traits are also found in many intervening lineages on the tree of life. If intervening lineages also share the trait, it was most likely inherited from the same common ancestor. c. The traits are not also found in many intervening lineages on the tree of life. - homolapsy

Which of the following is an example of homoplasy? a. Hox genes in humans and snails b. astragalus ankle bones in cow and peccary c. hair in humans and fur in deer d. streamlined bodies in dolphins and ichthyosaurs

d. streamlined bodies in dolphins and ichthyosaurs

The first step in inferring evolutionary relationships is to...

decide which populations, species, or higher taxa to compare and which characteristics to use - usually morphological or genetic characteristics, or both. ex. scientists may use fossils to reconstruct relationships

tips

endpoint of a branch; represents a living or extinct group of genes, species, families, phyla, or other taxa

the relationships depicted in phylogenetic trees must be ____ from the best available data

estimated

phylogenetic tree

graphical summary of a history of a group of organisms, showing the ancestor-descendant relationships among populations, species, or higher taxa. - can be used in taxonomy to define species - provide evidence for the endosymbiosis theory - that mitochondria and chloroplasts orginated as free-living bacteria. - can be used to examine how the HIV virus jumped from other primates to humans - can aid in identifying species that are priority for conversation extremely effective at summarizing data and testing hypotheses.

Cladistic methods of phylogenetics depend on _____.

identifying monophyletic groups based on shared, derived characters Using synapomorphies-shared, derived traits-in phylogenetic reconstruction is the key feature of cladistics.

tree of life

most universal of all phylogenetic trees, depicting the evolutionary relationships among all living organisms on earth.

genome

n organism's complete set of DNA, including all of its genes.

convergent evolution

occurs when natural selection favors similar solutions to the problems posed by a similar way of making a living in different species. Since species have many characteristics, some may be homologous with characteristics in other species, while others may be convergent.

homology

occurs when traits are similar due to shared ancestry. similar genes

homolapsy

occurs when traits are similar for other reasons other than common ancestry (comes from convergent evolution)

derived trait

one that is a modified form of the ancestral trait, found in a descendant. They originate via mutation, selection, and genetic drift.

SINEs

parasitic DNA sequences (short interspersed nuclear elements) occasionally insert themselves into the genomes of mammals. they are transposable elements. they provide convincing evidence of relationships because the chance of the same SINE inserting itself in exactly the same place in the same genome of two species is astronomically small. transposable elements that do not increase the fitness of the host genome that transcribes to a particular trait. they just gradually appear due to the new DNA sequence. the presence of a particular SINE represents a derived character SINEs aren't considered homolapsy because they are not inserted due to convergent evolution. They only enter the genome of specific species, because they decide that they are a worthy host for insertion, replication, expression, and amplification.

analogous

performing a similar function but having a different evolutionary origin, such as the wings of insects and birds. - homolapsy

Charles Darwin raised ____________, which inspired some of his ideas regarding natural selection.

pigeons

Some molecular data place the giant panda in the bear family (Ursidae) but place the lesser panda in the raccoon family (Procyonidae). If the molecular data best reflect the evolutionary history of these two groups, then the morphological similarities of these two species is most likely due to _____

possession of analogous (convergent) traits

branches

represents a population through time

As your textbook describes, morphological data supports a close relationship between whales and hippos, but DNA evidence contradicts this reconstruction. However, the distribution of SINEs helped researchers reconcile this apparent conflict. This is an example of _____.

resolving scientific discrepancies with additional data

divergent evolutions

the accumulation of differences between groups which can lead to the formation of new species, usually a result of diffusion of the same species to different and isolated environments which blocks the gene flow among the distinct populations allowing differentiated fixation of characteristics through genetic drift and natural selection.

taxonomy

the branch of biology concerned with the classification and naming of organisms.

phylogeny

the evolutionary history of a group of organisms

since independent evolution of traits should be rare compared with similarity due to shared descent...

the tree that implies the fewest overall evolutionary changes is hypothesized to be the one that most accurately reflects what really happened during evolution.