Phylogeny II & the Species Concept (9)

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1
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When allele frequencies change because of genetic drift, you expect _____. A. the average fitness of the population to increase

B. the average fitness of the population to decrease

C. the average fitness of the population to remain the same

D. the effect of drift on average fitness is not predictable

D: Genetic drift --> decrease in genetic variation --> can't predict what effect it will have on average fitness 

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Which of the following evolutionary mechanisms increases the amount of genetic variation in a population?

A. Genetic drift

B. Mutation

C. Sexual selection

D. Directional natural selection

E. Stabilizing natural selection

B: mutation adds alleles to population --> increases genetic variation 

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How do biologist classify life on Earth?

  • hierarchical classificaiton system

  • Domain, Kingdom, Phylum, Class, Order, Family, Genus,

    Species

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What is the principle of Parsimony (Occam’s razor)?

  • used to construct PT

  • The simplest explanation is most likely to be correct (Unless other data suggest more complicated explanation)

  • Evolution of trait evolving twice is unlikely (emerging multiple times in a tree) 

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What is the simplest possible explanation?

  • tree with the fewest amount of evolutionary changes

  • fewest amount of traits appearing independently

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What is Parsimony used to construct PTs?

  • Evolution of character twice is extremely unlikely

  • Evolutionary trees with derived characters appearing once are most parsimonious

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What does parsimony minimize in PTs?

  • Minimize the number of evolutionary changes that must be assumed

    • fewest homoplasis

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What are characters?

morphological, physiological, or molecular features that make up an organism

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What are character states?

  • several observed conditions in characters

  • Simple: character is absent or present

    • wings in tetrapods, but not other vertebrates

  • More common: multiple character states

    • Petals on flower: character

    • State: arrangement of petals (helical, whorl, fused, etc.)

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What are identified when constructing phylogenies?

derived traits

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What kinds of traits are used to construct phylogenies?

  • • Morphological

  • Developmental

  • Paleontological

  • Behavioural

  • Molecular

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what are the limitations of morphology in PT construction?

  • Comparing Distantly related things: very different looking things  

  • Some morphological variation caused by environment: find source of variation 

  • Some species show few morphological Differences:

    • wide spread butterfly in Brazil --> molecular work finds its 17 species that look identical 

    • Sometimes always impossible  

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What are examples of morphological traits?

  • Features of the skeletal system in vertebrates

  • Floral structures in plants

  • External features of exoskeleton in insects

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What can developmental traits reveal?

Similarities in development patterns may reveal evolutionary relationships

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How do sea squirts and frogs show evolutionary relation?

  • Different morphology in adult form 

  • In developmental stage: identify characteristic of Chordata 

  • Two organisms are related because they share the notochord 

<ul><li><p><span style="background-color: inherit; line-height: 19.55px; color: windowtext;">Different morphology in adult form</span><span style="line-height: 19.55px; color: windowtext;">&nbsp;</span></p></li><li><p class="Paragraph SCXO79361055 BCX0" style="text-align: left;"><span style="background-color: inherit; line-height: 19.55px; color: windowtext;">In developmental stage: identify characteristic of Chordata</span><span style="line-height: 19.55px; color: windowtext;">&nbsp;</span></p></li><li><p class="Paragraph SCXO79361055 BCX0" style="text-align: left;"><span style="background-color: inherit; line-height: 19.55px; color: windowtext;">Two organisms are related because they share the notochord</span><span style="line-height: 19.55px; color: windowtext;">&nbsp;</span></p></li></ul><p></p>
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What are the limitations to developmental traits?

complicated to quantify

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What does paleontological traits show in PTs?

Fossils provide information about morphology of past organisms, and where and when they lived.

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Why are paleontological traits important?

Important in determining derived and ancestral traits, and when lineages diverged.

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What are the limitations of paleontological traits? 

  • incomplete fossil record and rare to find 

    • Morphology: live in present 

    • Paleontological: mostly extinct organisms 

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Where do behavioral traits originate from?

Can be inherited but some are culturally transmitted.

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Why are frog calls able to be used in phylogenic trees?

  • Frog calls are genetically determined

  • Genes responsible for call length

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What is an example of a behavioral limitation for PTs?

  • Bird songs are often learned and may not be a useful trait for phylogenies.

  • Ex: European Starlings

    • Population in cities call louder than outside 

    • Can mimic car sounds etc. 

    • Environmental dependence on behavior --> be able to choose what are valuable  

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What are considered molecular characters?

DNA, RNA and amino acid changes reflect evolution

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What are the advantages of molecular characters?

  • Abundant data

  • Easier comparison of distant or very close relations

  • No direct environmental effect

  • Effective at comparing very different species 

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What is the disadvantages of molecular characters?

  • Only four states in nucleotides, 20 in amino acids

  • Not very useful for comparing very closely related species

  • Base changes may have evolved independently

    • because there are so few bases

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How do scientists use molecular data for PTs?

  • Can isolate region of DNA that we know is unique to clade in group and compare and contrast base pair sequence 

  • Environment affects phenotype, but not accumulation of data in genotype 

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What is the molecular clock?

The number of changes, or mutations, which accumulate in the gene sequences of different species over time is relatively constant

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What is mosiac evolution?

  • Each DNA sequence has a different clock tick

  • different parts of an organism, or different traits within a lineage, evolve at different rates.

  • "patchwork" of primitive and derived features rather than a uniform transformation of the entire body at once

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What part of the molecular clock is used often?

Noncoding regions

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Why are noncoding regions important for building PTs?

  • Coding regions creates proteins —> expressed

  • change less frequently but have a more constant ‘tick’

  • In DNA we accumulate mutations and all species collect mutations at constant rate in the noncoding region 

  • Can measure time before species became two (index for divergence) 

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Why do noncoding regions change less frequently and are more stable?

  • In DNA there is redundancy --> not under as much selection 

    • Coding for things that are redundant/repetitive/ basic recipes for material important in physiological process

      • if one altered, the others could produce something that could also work) 

      • less important = mutations more likely to linger

    • Not under strong selection --> mutations collected there are more constant and variable  

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Noncoding DNA vs Important Coding DNA

  • Important coding DNA extremely important (could lead to death or major changes) and under strong selection --> resistant to change

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How is the molecular clock used in PTs?

Molecular differences between pairs of species are proportional to the time of their separation and we can index the time of divergence between species

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What part of molecular characters reflect evolutionary relationships?

  • DNA/RNA sequence of amino acids 

  • nucleotide bases

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How are DNA sequences used to find evolutionary relationships?

  • Different specific regions in DNA are relevent for different groups of organisms 

  • Sequence of DNA must be lined up in the same positions of base pairs 

    • Look for differences in ACGT 

    • Find positions that have changed to different nucleotide state, deleted, or inserted 

    • The more differences --> the more distantly related 

<ul><li><p><span style="background-color: inherit; line-height: 19.55px; color: windowtext;">Different specific regions in DNA are relevent for different groups of organisms</span><span style="line-height: 19.55px; color: windowtext;">&nbsp;</span></p></li><li><p><span style="background-color: inherit; line-height: 19.55px; color: windowtext;">Sequence of DNA must be lined up in the same positions of base pairs</span><span style="line-height: 19.55px; color: windowtext;">&nbsp;</span></p><ul><li><p class="Paragraph SCXO3123178 BCX0" style="text-align: left;"><span style="background-color: inherit; line-height: 19.55px; color: windowtext;">Look for differences in ACGT</span><span style="line-height: 19.55px; color: windowtext;">&nbsp;</span></p></li><li><p class="Paragraph SCXO3123178 BCX0" style="text-align: left;"><span style="background-color: inherit; line-height: 19.55px; color: windowtext;">Find positions that have changed to different nucleotide state, deleted, or inserted</span><span style="line-height: 19.55px; color: windowtext;">&nbsp;</span></p></li><li><p class="Paragraph SCXO3123178 BCX0" style="text-align: left;"><span style="background-color: inherit; line-height: 19.55px; color: windowtext;">The more differences --&gt; the more distantly related</span><span style="line-height: 19.55px; color: windowtext;">&nbsp;</span></p></li></ul></li></ul><p></p>
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Why must sequences be aligned to the same position?

mutations can change length of DNA (computer programs, e.g., Clustal)

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What has become the most widely used data for constructing PT trees?

DNA sequences

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What kind of DNA is used?

Mitochondrial and chloroplast DNA is used as well as nuclear DNA, compared against reference database

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What is Genomic Data?

All of the DNA

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Unrooted vs. Rooted trees

  • Unrooted: tree doesn’t illustrate relatedness

    • too many different combinations possible to show relatedness

  • Rooted: shows related closeness 

<ul><li><p>Unrooted: tree doesn’t illustrate relatedness</p><ul><li><p>too many different combinations possible to show relatedness</p></li></ul></li><li><p>Rooted: shows related closeness&nbsp;</p></li></ul><p></p>
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What is combinatorial explosion?

  • the more taxa that are compared —> the more unrooted tree possibilities

<ul><li><p>the more taxa that are compared —&gt; the more unrooted tree possibilities </p></li></ul><p></p>
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How are the # of PTs reduced?

  • computer software that uses principles of parsimony

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What do we do when parsimony is not possible with the quality or quantity of data?

  • uses maximum liklehood and Bayesian-based tree (didn’t explain more)

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<p>What is the most parsimonious tree?&nbsp;</p>

What is the most parsimonious tree? 

Hypothesis 2 less parsimonious because same trait evolved two times 

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What does 0 represent in table of traits (characteristics)

traits that are the same as the outgroup

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What does 1 represent in table of traits (characteristics)

a derived trait

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How to construct tree based on graph?

  • Look for groups with the highest amount of derived traits

  • taxa that don’t have that derived trait most likely occur before the other taxa

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What is a species?

  • Smallest independently evolving unit

  • Species follow independent evolutionary trajectories

  • definition is contentious

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What does Pelage show us?

  •  5 to 10 different subspecies of giraffes.

    • Distinctions partly based on geographic range and pelage pattern

  • There are abrupt transitions between pelage types in some areas not obviously associated with geographic barriers to the movement of giraffes

  • By analyzing DNA sequences, it has been established that giraffes show six genealogically distinct lineages

<ul><li><p>&nbsp;5 to 10 different subspecies of giraffes.</p><ul><li><p> Distinctions partly based on geographic range and pelage pattern </p></li></ul></li><li><p>There are abrupt transitions between pelage types in some areas not obviously associated with geographic barriers to the movement of giraffes </p></li><li><p>By analyzing DNA sequences, it has been established that giraffes show six genealogically distinct lineages</p></li></ul><p></p>
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How does mating work with different pelage patterns?

can all interbreed, but Giraffes prefer to mate with those with the same pelage pattern

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What is the morphological species concept?

  • Linnaeus

  • described/grouped species based on their appearance

  • Originated the binomial system of nomenclature (genus + species name)

  • morphospecies concept holds that members of the same species usually look alike

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What is the basic thought behind morphological species concept?

Members of species look alike because they share many alleles.

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What does the morphological species concept also extend to outside of phentype?

  • members of the same species usually have similar DNA sequences that are distinct from those of other species.

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What is a barcode?

  • Under morphological species concept

  • every species has a unique signature in a certain region of DNA 

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What are the limitations of the morphological species concept

  • • But males and females may not look alike. 

    • Ex: sexual dimorphism

  • Immature individuals may not look like their parents. 

  • Other types of information must be used to determine species

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What is the biological species concept?

  • A species is a group of organisms that can interbreed and produce fertile offspring

    • members of same species capable of producing offspring together

    • members of diff species incapable of producing offspring together

  • One we traditionally use

  • members of different species are reproductively isolated from one another.

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Why is the Asian and Sri Lankan elephant the same species?

  • They can potentially interbreed

  • never have to because of geographical separation

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What kind of gene bool is a species according to BSC?

  • closed gene pool

  • alleles shared among members of species but not with members of others

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What are the issues with biological species?

  • Closely related species hybridize and may produce offspring

  • Plant cultivars

  • Excludes Asexual organisms

    • do not interbreed, instead asexual reproduction

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Why can testing BSC be difficult?

  • unnatural circumstances could impact animal behavior/mating

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What are plant cultivars?

  • plants cultivated to suit human use

  • can breed and are the same species, but look very different

<ul><li><p>plants cultivated to suit human use</p></li><li><p>can breed and are the same species, but look very different</p></li></ul><p></p>
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What are hybrid offspring under BSC?

  • first pair of populations represents two species, whereas the second pair represents just one

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What is hybridization often caused by?

  • incomplete reproductive isolation

  • In one location, the two groups may be reproductively isolated from each other, while in another location, they interbreed

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What kind of organisms is reproductive isolation common?

  • plants

  • Ex: different species of willow, oak, and dandelion than exchange genes and produce hybrids

  • But, species maintain distinct appearance rather than a single merged population —> NS discriminates against hybrid offspring

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What can become an issue with hybridization?

  • Example: western and Eastern meadowlark have differentient themselves by calls

    • In Areas they overlap and interact with each other —> they mate

    • Why they mate--> produces hybridization--> different call --> no one wants to mate with him

      • often don't survive and don't become a new species) 

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What does a horse and donkey mating create?

  • creates infertile mule (hybridization)

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Why is a mule infertile?

  • has uneven set of chromosomes

    • may reproduce but creates errors in zygote formation that can lead to death

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What is an Androdioecous species?

  • Reproductive system characterized by the coexistence of males and hermaphrodites

  • asexual species

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What is a Gynogenetic species?

  • Embryo contains only maternal chromosomes due to activation of an egg by sperm that degenerates without fusing with the egg nucleus

  • asexual species

  • decreases genetic diversity more than androdioecious species

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How do killfish show limitations of biological species?

  • Androdioecous species

  • Killfish live in Low oxygen areas  and dries out quickly  and sporadic (temporal habitats) --> only has males and hermaphrodites 

  • Can produce generation by itself because of crazy conditions 

  • Individual can lay eggs and produce their own sperm to create clone of itself  

  • Males also persist --> can provide sperm --> increases genetic variation --> recombination can occur 

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How does the amazonian molly  show limitations of biological species?

  • All female population

  • Produce eggs (clones of themselves)--> mate with closely related species that enacts that process  

    • Will go extinct some day 

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What is the ecological species concept?

  • A species is a group of organisms that share a distinct ecological niche

  • Different species use ecological resources differently, to become divergent in behaviour and location, leading to isolation from one another as a species.

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Why. is the ecological species concept not used

  • states that niches are unique own species —> a one-to-one correspondence between a species and its niche

  • But niches can have variation

    • ex: fundamental niche

      • full range of environmental conditions and resources within which a species could survive and reproduce in the absence of limiting factors

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What is the phylogenetic species concept?

  • A species is a group of organisms bound by a unique ancestry (single common ancestor)

  • emphasizes that members of a species all share a common ancestry and a common fate  

<ul><li><p>A species is a group of organisms bound by a unique ancestry (single common ancestor)</p></li><li><p><span>emphasizes that members of a species all share a common ancestry and a common fate</span><span style="background-color: inherit; line-height: 19.55px; color: windowtext;"> </span><span style="line-height: 19.55px; color: windowtext;">&nbsp;</span></p></li></ul><p></p>
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Limitations of phylogenetic species concept

  • Does not specify scale that should be used

    • Ex: thousands of mammals that evolved since long-ago common ancestor

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What is the phylogenetic species concept more useful for?

  • asexual species 

    • Don’t breed with different individual

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What is introgression? 

  • on path of diff species has collapsed back into each other

  • Ex: Ravin in Artic Vs. California

    • Artic: separate in space and have not bred with the one in California —>on path to become new species

    • But, there is a bridge between them 

    • DNA tested and genetic details —> of Olarghic (Artic) population stronger —> traits of weaker species may be lost during introgression

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Why is there controversy around species? 

  • Species are dynamic, evolving individuals, but we attempt to force them into rigid classes 

    • Nature does not conform to our boundaries or classification

  • Species are real evolutionary groups and not categories which are created as a direct function of perceived distinction

  • Taxa may be at various stages of divergence

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